Publications by year
In Press
Buchholz H, Michelsen M, Parsons R, Bates N, Temperton B (In Press). Draft genomes of Pelagimyophage Mosig EXVC030M and Pelagipodophage Lederberg EXVC029P isolated from Devil’s Hole in Bermuda. Microbiology Resource Announcements
Buchholz H, Michelsen M, Temperton B, Bolanos L, Allen M (In Press). Efficient Dilution-to-Extinction isolation of novel virus-host model systems for fastidious heterotrophic bacteria. The ISME Journal: multidisciplinary journal of microbial ecology
Witherall L, Wagley S, Butler C, Tyler C, Temperton B (In Press). Genome sequences of four Vibrio parahaemolyticus strains isolated from the English Channel and the River Thames. Microbiology Resource Announcements
Warwick-Dugdale J, Buchholz H, Allen M, Temperton B (In Press). Host-hijacking and Planktonic Piracy: How Phages Command the Microbial High Seas. Virology
Warwick-Dugdale J, Moore K, Allen M, Temperton B (In Press). Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands. PeerJ
Temperton B (In Press). Marine viral macro- and micro-diversity from pole to pole.
CellAbstract:
Marine viral macro- and micro-diversity from pole to pole
Microbes drive most ecosystems and are modulated by viruses that impact their lifespan, gene flow and metabolic outputs. However, the influence of viral community diversity
at the ecosystem level remains difficult to assess due to classification issues and few reference genomes. Here we establish a ~12-fold expanded global ocean virome dataset of 195,728 viral populations, now including the Arctic Ocean, and validate that these populations form discrete genotypic clusters. Meta-community analyses revealed just five ecological zones throughout the global ocean, and established local and global patterns and drivers in viral community diversity at levels of both macrodiversity (inter-population diversity) and microdiversity (intra-population genetic variation). These patterns sometimes, but not always, paralleled those from macro- organisms and revealed temperate and tropical surface waters and the Arctic as biodiversity hotspots and mechanistic hypotheses to explain them. With this further understanding of viral
populations and ecology in the ocean, viruses can be more broadly included in ecosystem models.
Abstract.
2024
Eigemann F, Tait K, Temperton B, Hellweger FL (2024). Heterotrophic prokaryotes internal carbon recycling compensates mismatches between phytoplankton production and heterotrophic prokaryotic consumption.
Bell AG, McMurtrie J, Bolaños LM, Cable J, Temperton B, Tyler CR (2024). Influence of host phylogeny and water physicochemistry on microbial assemblages of the fish skin microbiome.
FEMS Microbiology Ecology,
100(3).
Abstract:
Influence of host phylogeny and water physicochemistry on microbial assemblages of the fish skin microbiome
Abstract
. The skin of fish contains a diverse microbiota that has symbiotic functions with the host, facilitating pathogen exclusion, immune system priming, and nutrient degradation. The composition of fish skin microbiomes varies across species and in response to a variety of stressors, however, there has been no systematic analysis across these studies to evaluate how these factors shape fish skin microbiomes. Here, we examined 1922 fish skin microbiomes from 36 studies that included 98 species and nine rearing conditions to investigate associations between fish skin microbiome, fish species, and water physiochemical factors. Proteobacteria, particularly the class Gammaproteobacteria, were present in all marine and freshwater fish skin microbiomes. Acinetobacter, Aeromonas, Ralstonia, Sphingomonas and Flavobacterium were the most abundant genera within freshwater fish skin microbiomes, and Alteromonas, Photobacterium, Pseudoalteromonas, Psychrobacter and Vibrio were the most abundant in saltwater fish. Our results show that different culturing (rearing) environments have a small but significant effect on the skin bacterial community compositions. Water temperature, pH, dissolved oxygen concentration, and salinity significantly correlated with differences in beta-diversity but not necessarily alpha-diversity. To improve study comparability on fish skin microbiomes, we provide recommendations for approaches to the analyses of sequencing data and improve study reproducibility.
Abstract.
McParland EL, Wittmers F, Bolanos LM, Carlson CA, Giovannoni SJ, Michelsen M, Parsons R, Kido Soule MC, Swarr GJ, Temperton B, et al (2024). Seasonal exometabolites are regulated by essential microbial metabolisms in the oligotrophic ocean.
Abstract:
Seasonal exometabolites are regulated by essential microbial metabolisms in the oligotrophic ocean
Predictions of how the biogeochemical reservoir of marine dissolved organic matter (DOM) will respond to future ocean changes are limited by bulk characterizations that mask a complex network of thousands of individual microbe-molecule interactions. The marine microbial community regulates the transformation and fate of organic carbon by utilizing DOM molecules as the products and reactants of their diverse enzymatic functions. Linking these molecules with the microbial taxa responsible for their utilization requires characterization of both microbial activity and the resulting metabolic footprint. Here we present a time series of the seasonal dynamics of both the exometabolome and the bacterioplankton community at the Bermuda Atlantic Time series Study (BATS) site and show that metabolic functions are greater predictors of DOM composition than microbial taxonomy. Putative exometabolite identifications (gonyol, glucose 6-sulfate, succinate, and trehalose) indicate that at least a portion of the exometabolome contains rapidly remineralized, labile molecules. We hypothesize that observations of seasonal accumulation of these labile molecules result from decoupled enrichments of microbial production and consumption enzymes. Critically, we found the composition of seasonal DOM features was more stable inter-annually than the microbial community structure. By estimating redundancy in the BATS metagenomes of metabolisms responsible for cycling these molecules, we propose a paradigm whereby microbial metabolisms that are essential, either to all or to a subset of marine microbes, determine DOM composition. The molecular-level characterization of DOM achieved herein greatly enhances possibilities for connecting the mechanisms behind the DOM-microbe network that cycle Earth's largest reservoir of organic carbon.
Abstract.
Fletcher J, Manley R, Fitch C, Bugert C, Moore K, Farbos A, Michelsen M, Alathari S, Senior N, Mills A, et al (2024). The Citizen Phage Library: Rapid Isolation of Phages for the Treatment of Antibiotic Resistant Infections in the UK.
Microorganisms,
12(2), 253-253.
Abstract:
The Citizen Phage Library: Rapid Isolation of Phages for the Treatment of Antibiotic Resistant Infections in the UK
Antimicrobial resistance poses one of the greatest threats to global health and there is an urgent need for new therapeutic options. Phages are viruses that infect and kill bacteria and phage therapy could provide a valuable tool for the treatment of multidrug-resistant infections. In this study, water samples collected by citizen scientists as part of the Citizen Phage Library (CPL) project, and wastewater samples from the Environment Agency yielded phages with activity against clinical strains Klebsiella pneumoniae BPRG1484 and Enterobacter cloacae BPRG1482. A total of 169 and 163 phages were found for K. pneumoniae and E. cloacae, respectively, within four days of receiving the strains. A third strain (Escherichia coli BPRG1486) demonstrated cross-reactivity with 42 E. coli phages already held in the CPL collection. Seed lots were prepared for four K. pneumoniae phages and a cocktail combining these phages was found to reduce melanisation in a Galleria mellonella infection model. The resources and protocols utilised by the Citizen Phage Library enabled the rapid isolation and characterisation of phages targeted against multiple strains. In the future, within a clearly defined regulatory framework, phage therapy could be made available on a named-patient basis within the UK.
Abstract.
2023
Alathari S, Chaput DL, Bolaños LM, Joseph A, Jackson VLN, Verner-Jeffreys D, Paley R, Tyler CR, Temperton B (2023). A Multiplexed, Tiled PCR Method for Rapid Whole-Genome Sequencing of Infectious Spleen and Kidney Necrosis Virus (ISKNV) in Tilapia.
Viruses,
15(4), 965-965.
Abstract:
A Multiplexed, Tiled PCR Method for Rapid Whole-Genome Sequencing of Infectious Spleen and Kidney Necrosis Virus (ISKNV) in Tilapia
Tilapia farming is one of the most important sectors in aquaculture worldwide and of major importance to global food security. Infectious spleen and kidney necrosis virus (ISKNV) has been identified as an agent of high morbidity and mortality, threatening tilapia aquaculture. ISKNV was detected in Lake Volta, Ghana, in September 2018 and spread rapidly, with mortality rates between 60 and 90% and losses of more than 10 tonnes of fish per day. Understanding the spread and evolution of viral pathogens is important for control strategies. Here, we developed a tiled-PCR sequencing approach for the whole-genome sequencing of ISKNV, using long read sequencing to enable field-based, real-time genomic surveillance. This work represents the first use of tiled-PCR for whole genome recovery of viruses in aquaculture, with the longest genome target (>110 kb dsDNA) to date. Our protocol was applied to field samples collected from the ISKNV outbreaks from four intensive tilapia cage culture systems across Lake Volta, between October 2018 and May 2022. Despite the low mutation rate of dsDNA viruses, 20 single nucleotide polymorphisms accumulated during the sampling period. Droplet digital PCR identified a minimum requirement of template in a sample to recover 50% of an ISKNV genome at 275 femtograms (2410 viral templates per 5 µL sequencing reaction). Overall, tiled-PCR sequencing of ISKNV provides an informative tool to assist in disease control in aquaculture.
Abstract.
Noell SE, Hellweger FL, Temperton B, Giovannoni SJ (2023). A Reduction of Transcriptional Regulation in Aquatic Oligotrophic Microorganisms Enhances Fitness in Nutrient-Poor Environments.
Microbiology and Molecular Biology Reviews,
87(2).
Abstract:
A Reduction of Transcriptional Regulation in Aquatic Oligotrophic Microorganisms Enhances Fitness in Nutrient-Poor Environments
In this review, we consider the regulatory strategies of aquatic oligotrophs, microbial cells that are adapted to thrive under low-nutrient concentrations in oceans, lakes, and other aquatic ecosystems. Many reports have concluded that oligotrophs use less transcriptional regulation than copiotrophic cells, which are adapted to high nutrient concentrations and are far more common subjects for laboratory investigations of regulation.
Abstract.
Mitchelmore P, Michell S, Fletcher J, Manley R, Chait R, Graham J, Fitch C, Zheng J, Sacher J, Mills A, et al (2023). A citizen phage library for respiratory infection. Respiratory infections and bronchiectasis.
Alathari S, Chaput DL, Bolaños LM, Joseph A, Jackson VLN, Verner-Jeffreys D, Paley R, Tyler CR, Temperton B (2023). Correction: Alathari et al. A Multiplexed, Tiled PCR Method for Rapid Whole-Genome Sequencing of Infectious Spleen and Kidney Necrosis Virus (ISKNV) in Tilapia. Viruses 2023, 15, 965.
Viruses,
15(7), 1476-1476.
Abstract:
Correction: Alathari et al. A Multiplexed, Tiled PCR Method for Rapid Whole-Genome Sequencing of Infectious Spleen and Kidney Necrosis Virus (ISKNV) in Tilapia. Viruses 2023, 15, 965
In the original publication [. ]
Abstract.
Alathari S, Joseph A, Bolaños LM, Studholme D, Jeffries A, Appenteng P, Duodu K, Sawyerr E, Paley R, Tyler CR, et al (2023). In field use of water samples for genomic surveillance of ISKNV infecting tilapia fish in Lake Volta, Ghana.
Abstract:
In field use of water samples for genomic surveillance of ISKNV infecting tilapia fish in Lake Volta, Ghana
AbstractViral outbreaks are a constant threat to aquaculture, limiting production for better global food security. A lack of diagnostic testing and monitoring in resource-limited areas hinders the capacity to respond rapidly to disease outbreaks and to prevent viral pathogens becoming endemic in fisheries productive waters. Recent developments in diagnostic testing for emerging viruses, however, offers a solution for rapidin situmonitoring of viral outbreaks. Genomic epidemiology has furthermore proven highly effective in detecting viral mutations involved in pathogenesis and assisting in resolving chains of transmission.Here, we demonstrate the application of an in-field epidemiological tool kit to track viral outbreaks in aquaculture on farms with reduced access to diagnostic labs, and with non-destructive sampling. Inspired by the “lab in a suitcase” approach used for genomic surveillance of human viral pathogens and wastewater monitoring of COVID19, we evaluated the feasibility of real-time genome sequencing surveillance of the fish pathogen, Infectious spleen and kidney necrosis virus (ISKNV) in Lake Volta. Viral fractions from water samples collected from cages holding Nile tilapia (Oreochromis niloticus) with suspected ongoing ISKNV infections were concentrated and used as a template for whole genome sequencing, using a previously developed tiled PCR method for ISKNV. Mutations in ISKNV in samples collected from the water surrounding the cages matched those collected from infected caged fish, illustrating that water samples can be used for detecting predominant ISKNV variants in an ongoing outbreak. This approach allows for the detection of ISKNV and tracking of the dynamics of variant frequencies, and may thus assist in guiding control measures for the rapid isolation and quarantine of infected farms and facilities.
Abstract.
Cotton S, McHugh MP, Dewar R, Haas JG, Templeton K, Consortium TCGU, Robson SC, Connor TR, Loman NJ, Golubchik T, et al (2023). Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes. Journal of Hospital Infection, 135, 28-36.
Zhong Z-P, Vik D, Rapp J, Zablocki O, Maughan H, Temperton B, Deming J, Sullivan M (2023). Lower viral evolutionary pressure under stable versus fluctuating conditions in subzero Arctic brines.
Zhong Z-P, Vik D, Rapp JZ, Zablocki O, Maughan H, Temperton B, Deming JW, Sullivan MB (2023). Lower viral evolutionary pressure under stable versus fluctuating conditions in subzero Arctic brines.
Microbiome,
11(1).
Abstract:
Lower viral evolutionary pressure under stable versus fluctuating conditions in subzero Arctic brines.
BACKGROUND: Climate change threatens Earth's ice-based ecosystems which currently offer archives and eco-evolutionary experiments in the extreme. Arctic cryopeg brine (marine-derived, within permafrost) and sea ice brine, similar in subzero temperature and high salinity but different in temporal stability, are inhabited by microbes adapted to these extreme conditions. However, little is known about their viruses (community composition, diversity, interaction with hosts, or evolution) or how they might respond to geologically stable cryopeg versus fluctuating sea ice conditions. RESULTS: We used long- and short-read viromics and metatranscriptomics to study viruses in Arctic cryopeg brine, sea ice brine, and underlying seawater, recovering 11,088 vOTUs (~species-level taxonomic unit), a 4.4-fold increase of known viruses in these brines. More specifically, the long-read-powered viromes doubled the number of longer (≥25 kb) vOTUs generated and recovered more hypervariable regions by >5-fold compared to short-read viromes. Distribution assessment, by comparing to known viruses in public databases, supported that cryopeg brine viruses were of marine origin yet distinct from either sea ice brine or seawater viruses, while 94% of sea ice brine viruses were also present in seawater. A virus-encoded, ecologically important exopolysaccharide biosynthesis gene was identified, and many viruses (~half of metatranscriptome-inferred "active" vOTUs) were predicted as actively infecting the dominant microbial genera Marinobacter and Polaribacter in cryopeg and sea ice brines, respectively. Evolutionarily, microdiversity (intra-species genetic variations) analyses suggested that viruses within the stable cryopeg brine were under significantly lower evolutionary pressures than those in the fluctuating sea ice environment, while many sea ice brine virus-tail genes were under positive selection, indicating virus-host co-evolutionary arms races. CONCLUSIONS: Our results confirmed the benefits of long-read-powered viromics in understanding the environmental virosphere through significantly improved genomic recovery, expanding viral discovery and the potential for biological inference. Evidence of viruses actively infecting the dominant microbes in subzero brines and modulating host metabolism underscored the potential impact of viruses on these remote and underexplored extreme ecosystems. Microdiversity results shed light on different strategies viruses use to evolve and adapt when extreme conditions are stable versus fluctuating. Together, these findings verify the value of long-read-powered viromics and provide foundational data on viral evolution and virus-microbe interactions in Earth's destabilized and rapidly disappearing cryosphere. Video Abstract.
Abstract.
Author URL.
Bell AG, Thornber K, Chaput DL, Hasan NA, Mehedi Alam M, Haque MM, Cable J, Temperton B, Tyler CR (2023). Metagenomic assessment of the diversity and ubiquity of antimicrobial resistance genes in Bangladeshi aquaculture ponds. Aquaculture Reports, 29, 101462-101462.
Buchholz HH, Bolaños LM, Bell AG, Michelsen ML, Allen MJ, Temperton B (2023). Novel pelagiphage isolate Polarivirus skadi is a polar specialist that dominates SAR11-associated bacteriophage communities at high latitudes.
ISME J,
17(10), 1660-1670.
Abstract:
Novel pelagiphage isolate Polarivirus skadi is a polar specialist that dominates SAR11-associated bacteriophage communities at high latitudes.
The SAR11 clade are the most abundant members of surface marine bacterioplankton and a critical component of global biogeochemical cycles. Similarly, pelagiphages that infect SAR11 are ubiquitous and highly abundant in the oceans. Pelagiphages are predicted to shape SAR11 community structures and increase carbon turnover throughout the oceans. Yet, ecological drivers of host and niche specificity of pelagiphage populations are poorly understood. Here we report the global distribution of a novel pelagiphage called "Polarivirus skadi", which is the sole representative of a novel genus. P. skadi was isolated from the Western English Channel using a cold-water ecotype of SAR11 as bait. P. skadi is closely related to the globally dominant pelagiphage HTVC010P. Along with other HTVC010P-type viruses, P. skadi belongs to a distinct viral family within the order Caudovirales, for which we propose the name Ubiqueviridae. Metagenomic read recruitment identified P. skadi as one of the most abundant pelagiphages on Earth. P. skadi is a polar specialist, replacing HTVC010P at high latitudes. Experimental evaluation of P. skadi host range against cold- and warm-water SAR11 ecotypes supported cold-water specialism. Relative abundance of P. skadi in marine metagenomes correlated negatively with temperature, and positively with nutrients, available oxygen, and chlorophyll concentrations. In contrast, relative abundance of HTVC010P correlated negatively with oxygen and positively with salinity, with no significant correlation to temperature. The majority of other pelagiphages were scarce in most marine provinces, with a few representatives constrained to discrete ecological niches. Our results suggest that pelagiphage populations persist within a global viral seed bank, with environmental parameters and host availability selecting for a few ecotypes that dominate ocean viromes.
Abstract.
Author URL.
Williams J, Severin J, Temperton B, Mitchelmore PJ (2023). Phage Therapy Administration Route, Regimen, and Need for Supplementary Antibiotics in Patients with Chronic Suppurative Lung Disease. PHAGE, 4(1), 4-10.
Parsons RJ, Liu S, Longnecker K, Yongblah K, Johnson C, Bolaños LM, Comstock J, Opalk K, Kido Soule MC, Garley R, et al (2023). Suboxic DOM is bioavailable to surface prokaryotes in a simulated overturn of an oxygen minimum zone, Devil's Hole, Bermuda.
Front Microbiol,
14Abstract:
Suboxic DOM is bioavailable to surface prokaryotes in a simulated overturn of an oxygen minimum zone, Devil's Hole, Bermuda.
Oxygen minimum zones (OMZs) are expanding due to increased sea surface temperatures, subsequent increased oxygen demand through respiration, reduced oxygen solubility, and thermal stratification driven in part by anthropogenic climate change. Devil's Hole, Bermuda is a model ecosystem to study OMZ microbial biogeochemistry because the formation and subsequent overturn of the suboxic zone occur annually. During thermally driven stratification, suboxic conditions develop, with organic matter and nutrients accumulating at depth. In this study, the bioavailability of the accumulated dissolved organic carbon (DOC) and the microbial community response to reoxygenation of suboxic waters was assessed using a simulated overturn experiment. The surface inoculated prokaryotic community responded to the deep (formerly suboxic) 0.2 μm filtrate with cell densities increasing 2.5-fold over 6 days while removing 5 μmol L-1 of DOC. After 12 days, the surface community began to shift, and DOC quality became less diagenetically altered along with an increase in SAR202, a Chloroflexi that can degrade recalcitrant dissolved organic matter (DOM). Labile DOC production after 12 days coincided with an increase of Nitrosopumilales, a chemoautotrophic ammonia oxidizing archaea (AOA) that converts ammonia to nitrite based on the ammonia monooxygenase (amoA) gene copy number and nutrient data. In comparison, the inoculation of the deep anaerobic prokaryotic community into surface 0.2 μm filtrate demonstrated a die-off of 25.5% of the initial inoculum community followed by a 1.5-fold increase in cell densities over 6 days. Within 2 days, the prokaryotic community shifted from a Chlorobiales dominated assemblage to a surface-like heterotrophic community devoid of Chlorobiales. The DOM quality changed to less diagenetically altered material and coincided with an increase in the ribulose-1,5-bisphosphate carboxylase/oxygenase form I (cbbL) gene number followed by an influx of labile DOM. Upon reoxygenation, the deep DOM that accumulated under suboxic conditions is bioavailable to surface prokaryotes that utilize the accumulated DOC initially before switching to a community that can both produce labile DOM via chemoautotrophy and degrade the more recalcitrant DOM.
Abstract.
Author URL.
Debnath SC, McMurtrie J, Temperton B, Delamare-Deboutteville J, Mohan CV, Tyler CR (2023). Tilapia aquaculture, emerging diseases, and the roles of the skin microbiomes in health and disease.
Aquaculture International,
31(5), 2945-2976.
Abstract:
Tilapia aquaculture, emerging diseases, and the roles of the skin microbiomes in health and disease
AbstractAquaculture is playing an increasingly important role in global food security, especially for low-income and food-deficit countries. The majority of aquaculture production occurs in freshwater earthen ponds and tilapia has quickly become one of the most widely adopted culture species in these systems. Tilapia are now farmed in over 140 countries facilitated by their ease of production, adaptability to a wide range of environmental conditions, fast growth, and high nutritional value. Typically, tilapia have been considered a hardy, disease resilient species; however, the disease is increasing with subsequent threats to the industry as their production is intensified. In this review, we discuss tilapia production, with a focus on Bangladesh as one of the top producing countries, and highlight the problems associated with disease and treatment approaches for them, including the misuse of antimicrobials. We address a key missing component in understanding health and disease processes for sustainable production in aquaculture, specifically the role played by the microbiome. Here we examine the importance of the microbiome in supporting health, focused on the symbiotic microbial community of the fish skin mucosal surface, the abiotic and biotic factors that influence the microbiome, and the shifts that are associated with diseased states. We also identify conserved taxa of skin microbiomes that may be used as indicators of health status for tilapia offering new opportunities to mitigate and manage the disease and optimize environmental growing conditions and farming practices.
Abstract.
2022
Buchholz HH, Bolaños LM, Bell AG, Michelsen ML, Allen MJ, Temperton B (2022). A Novel and Ubiquitous Marine Methylophage Provides Insights into Viral-Host Coevolution and Possible Host-Range Expansion in Streamlined Marine Heterotrophic Bacteria.
Appl Environ Microbiol,
88(7).
Abstract:
A Novel and Ubiquitous Marine Methylophage Provides Insights into Viral-Host Coevolution and Possible Host-Range Expansion in Streamlined Marine Heterotrophic Bacteria.
The methylotrophic OM43 clade are Gammaproteobacteria that comprise some of the smallest free-living cells known and have highly streamlined genomes. OM43 represents an important microbial link between marine primary production and remineralization of carbon back to the atmosphere. Bacteriophages shape microbial communities and are major drivers of mortality and global marine biogeochemistry. Recent cultivation efforts have brought the first viruses infecting members of the OM43 clade into culture. Here, we characterize a novel myophage infecting OM43 called Melnitz. Melnitz was isolated independently from water samples from a subtropical ocean gyre (Sargasso Sea) and temperate coastal (Western English Channel) systems. Metagenomic recruitment from global ocean viromes confirmed that Melnitz is globally ubiquitous, congruent with patterns of host abundance. Bacteria with streamlined genomes such as OM43 and the globally dominant SAR11 clade use riboswitches as an efficient method to regulate metabolism. Melnitz encodes a two-piece tmRNA (ssrA), controlled by a glutamine riboswitch, providing evidence that riboswitch use also occurs for regulation during phage infection of streamlined heterotrophs. Virally encoded tRNAs and ssrA found in Melnitz were phylogenetically more closely related to those found within the alphaproteobacterial SAR11 clade and their associated myophages than those within their gammaproteobacterial hosts. This suggests the possibility of an ancestral host transition event between SAR11 and OM43. Melnitz and a related myophage that infects SAR11 were unable to infect hosts of the SAR11 and OM43, respectively, suggesting host transition rather than a broadening of host range. IMPORTANCE Isolation and cultivation of viruses are the foundations on which the mechanistic understanding of virus-host interactions and parameterization of bioinformatic tools for viral ecology are based. This study isolated and characterized the first myophage known to infect the OM43 clade, expanding our knowledge of this understudied group of microbes. The nearly identical genomes of four strains of Melnitz isolated from different marine provinces and the global abundance estimations from metagenomic data suggest that this viral population is globally ubiquitous. Genome analysis revealed several unusual features in Melnitz and related genomes recovered from viromes, such as a curli operon and virally encoded tmRNA controlled by a glutamine riboswitch, neither of which are found in the host. Further phylogenetic analysis of shared genes indicates that this group of viruses infecting the gammaproteobacterial OM43 shares a recent common ancestor with viruses infecting the abundant alphaproteobacterial SAR11 clade. Host ranges are affected by compatible cell surface receptors, successful circumvention of superinfection exclusion systems, and the presence of required accessory proteins, which typically limits phages to singular narrow groups of closely related bacterial hosts. This study provides intriguing evidence that for streamlined heterotrophic bacteria, virus-host transitioning may not be necessarily restricted to phylogenetically related hosts but is a function of shared physical and biochemical properties of the cell.
Abstract.
Author URL.
Baker S, Dougan G, Hess C, Kingston N, Lehner PJ, Lyons PA, Matheson NJ, Owehand WH, Saunders C, Summers C, et al (2022). Author Correction: SARS-CoV-2 evolution during treatment of chronic infection. Nature, 608(7922), e23-e23.
Baker S, Dougan G, Hess C, Kingston N, Lehner PJ, Lyons PA, Matheson NJ, Owehand WH, Saunders C, Summers C, et al (2022). Author Correction: Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies. Nature, 608(7922), e24-e24.
Aggarwal D, Page AJ, Schaefer U, Savva GM, Myers R, Volz E, Ellaby N, Platt S, Groves N, Gallagher E, et al (2022). Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission. Nature Communications, 13(1).
Aggarwal D, Warne B, Jahun AS, Hamilton WL, Fieldman T, du Plessis L, Hill V, Blane B, Watkins E, Wright E, et al (2022). Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission.
Nature Communications,
13(1).
Abstract:
Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission
AbstractUnderstanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and following a national lockdown. Transmission clusters were largely segregated within the university or the community. Our study highlights key determinants of SARS-CoV-2 transmission and effective interventions in a higher education setting that will inform public health policy during pandemics.
Abstract.
Bolaños LM, Tait K, Somerfield PJ, Parsons RJ, Giovannoni SJ, Smyth T, Temperton B (2022). Influence of short and long term processes on SAR11 communities in open ocean and coastal systems.
Abstract:
Influence of short and long term processes on SAR11 communities in open ocean and coastal systems
AbstractSAR11 bacteria dominate the surface ocean and are major players in converting fixed carbon back to atmospheric carbon dioxide. The SAR11 clade is comprised of niche-specialized ecotypes that display distinctive spatiotemporal transitions. We analysed SAR11 ecotype seasonality in two long-term 16S rRNA amplicon time series representing different North Atlantic regimes: the Sargasso Sea (subtropical ocean-gyre; BATS) and the temperate coastal Western English Channel (WEC). Using phylogenetically resolved amplicon sequence variants (ASVs), we evaluated seasonal environmental constraints on SAR11 ecotype periodicity. Despite large differences in temperature and nutrient availability between the two sites, at both SAR11 succession was defined by summer and winter clusters of ASVs. Summer cluster was dominated by ecotype Ia.3 in both sites. Winter clusters were dominated by ecotypes Ib and IIa.A at BATS and Ia.1 and IIa.B at WEC. A two-year weekly analysis within the WEC time series showed that the response of SAR11 communities to short-term environmental fluctuations was variable. In 2016, community shifts were abrupt and synchronised to environmental shifts. However, in 2015, changes were gradual and decoupled from environmental fluctuations, likely due to increased mixing from strong winds. We demonstrate that interannual weather variability disturb the pace of SAR11 seasonal progression.
Abstract.
Bolaños LM, Tait K, Somerfield PJ, Parsons RJ, Giovannoni SJ, Smyth T, Temperton B (2022). Influence of short and long term processes on SAR11 communities in open ocean and coastal systems.
ISME Communications,
2(1).
Abstract:
Influence of short and long term processes on SAR11 communities in open ocean and coastal systems
Abstract
. SAR11 bacteria dominate the surface ocean and are major players in converting fixed carbon back to atmospheric carbon dioxide. The SAR11 clade is comprised of niche-specialized ecotypes that display distinctive spatiotemporal transitions. We analyzed SAR11 ecotype seasonality in two long-term 16S rRNA amplicon time series representing different North Atlantic regimes: the Sargasso Sea (subtropical ocean-gyre; BATS) and the temperate coastal Western English Channel (WEC). Using phylogenetically resolved amplicon sequence variants (ASVs), we evaluated seasonal environmental constraints on SAR11 ecotype periodicity. Despite large differences in temperature and nutrient availability between the two sites, at both SAR11 succession was defined by summer and winter clusters of ASVs. The summer cluster was dominated by ecotype Ia.3 in both sites. Winter clusters were dominated by ecotypes Ib and IIa.A at BATS and Ia.1 and IIa.B at WEC. A 2-year weekly analysis within the WEC time series showed that the response of SAR11 communities to short-term environmental fluctuations was variable. In 2016, community shifts were abrupt and synchronized to environmental shifts. However, in 2015, changes were gradual and decoupled from environmental fluctuations, likely due to increased mixing from strong winds. We demonstrate that interannual weather variability disturb the pace of SAR11 seasonal progression.
Abstract.
Warwick-Dugdale J, Tian F, Michelsen M, Cronin DR, Moore K, Farbos A, Chittick L, Bell A, Buchholz HH, Parsons RJ, et al (2022). Long-read powered viral metagenomics in the Oligotrophic Sargasso Sea.
Abstract:
Long-read powered viral metagenomics in the Oligotrophic Sargasso Sea
ABSTRACTIn the summer months, the waters of the Sargasso Sea are nutrient-limited and strongly stratified, serving as a model system for the predicted warmer and nutrient-limited oceans of the Anthropocene. The dominant microorganisms of surface waters are key drivers of the global carbon cycle. However, the viruses of the Sargasso Sea that shape these host communities and influence host biogeochemical function are not well understood. Here, we apply a hybrid sequencing approach that combines short- and long reads to survey Sargasso Sea phage communities via metagenomics at the viral maximum (80m) and mesopelagic (200m) depths. Taxonomically, we identified 2,301 Sargasso Sea phage populations (~species-level taxonomy) across 186 genera. Over half of the phage populations lacked representation in other global ocean viral metagenomes, whilst 177 phage genera lacked representation in phage isolate databases. Viral fraction and cell-associated viral communities captured in short-read data were distinct and decoupled at both depths, possibly indicating low active lytic viral replication in the Sargasso Sea, with viral turnover occurring across periods longer than the sampling period of three days. Inclusion of long read data was critical for (1) the identification of 79 ecologically important and common viral genomes; (2) capturing the extent of viral genome microdiversity; and (3) enabling the recovery of hypervariable regions in viral genomes predicted to encode proteins involved in host recognition, DNA synthesis and DNA packaging. Host prediction was only possible for ~4% of viral populations. Genomes of phages known to infect Prochlorococcus and Pelagibacter were poorly represented in our data, supporting recent evidence of low infection levels in the dominant bacterial taxa of oligotrophic regions.SubjectsBioinformatics, Genomics, Marine Biology, Microbiology, VirologySequence data accession numbersPRJNA767318
Abstract.
Gregory AC, Gerhardt K, Zhong Z-P, Bolduc B, Temperton B, Konstantinidis KT, Sullivan MB (2022). MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations.
Microbiome,
10(1).
Abstract:
MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations.
BACKGROUND: Microbes and their viruses are hidden engines driving Earth's ecosystems from the oceans and soils to humans and bioreactors. Though gene marker approaches can now be complemented by genome-resolved studies of inter-(macrodiversity) and intra-(microdiversity) population variation, analytical tools to do so remain scattered or under-developed. RESULTS: Here, we introduce MetaPop, an open-source bioinformatic pipeline that provides a single interface to analyze and visualize microbial and viral community metagenomes at both the macro- and microdiversity levels. Macrodiversity estimates include population abundances and α- and β-diversity. Microdiversity calculations include identification of single nucleotide polymorphisms, novel codon-constrained linkage of SNPs, nucleotide diversity (π and θ), and selective pressures (pN/pS and Tajima's D) within and fixation indices (FST) between populations. MetaPop will also identify genes with distinct codon usage. Following rigorous validation, we applied MetaPop to the gut viromes of autistic children that underwent fecal microbiota transfers and their neurotypical peers. The macrodiversity results confirmed our prior findings for viral populations (microbial shotgun metagenomes were not available) that diversity did not significantly differ between autistic and neurotypical children. However, by also quantifying microdiversity, MetaPop revealed lower average viral nucleotide diversity (π) in autistic children. Analysis of the percentage of genomes detected under positive selection was also lower among autistic children, suggesting that higher viral π in neurotypical children may be beneficial because it allows populations to better "bet hedge" in changing environments. Further, comparisons of microdiversity pre- and post-FMT in autistic children revealed that the delivery FMT method (oral versus rectal) may influence viral activity and engraftment of microdiverse viral populations, with children who received their FMT rectally having higher microdiversity post-FMT. Overall, these results show that analyses at the macro level alone can miss important biological differences. CONCLUSIONS: These findings suggest that standardized population and genetic variation analyses will be invaluable for maximizing biological inference, and MetaPop provides a convenient tool package to explore the dual impact of macro- and microdiversity across microbial communities. Video abstract.
Abstract.
Author URL.
Buchholz HH, Bolaños LM, Bell AG, Michelsen ML, Allen MJ, Temperton B (2022). Pelagibacter phage Skadi - an abundant polar specialist that exemplifies ecotypic niche specificity among the most abundant viruses on Earth.
Robson SC, Connor TR, Loman NJ, Golubchik T, Martinez Nunez RT, Bonsall D, Rambaut A, Snell LB, Ludden C, Corden S, et al (2022). Publisher Correction: Genomic reconstruction of the SARS CoV-2 epidemic in England. Nature, 606(7915), e18-e18.
McMurtrie J, Alathari S, Chaput DL, Bass D, Ghambi C, Nagoli J, Delamare-Deboutteville J, Mohan CV, Cable J, Temperton B, et al (2022). Relationships between pond water and tilapia skin microbiomes in aquaculture ponds in Malawi. Aquaculture, 558, 738367-738367.
Ashford F, Best A, Dunn SJ, Ahmed Z, Siddiqui H, Melville J, Wilkinson S, Mirza J, Cumley N, Stockton J, et al (2022). SARS-CoV-2 Testing in the Community: Testing Positive Samples with the TaqMan SARS-CoV-2 Mutation Panel to Find Variants in Real Time. Journal of Clinical Microbiology, 60(4), e02408-e02421.
Bell AG, Thornber K, Chaput DL, Hasan NA, Alam MM, Haque MM, Cable J, Temperton B, Tyler CR (2022). The Diversity and Ubiquity of Antibiotic Resistance Genes in Finfish Culture Ponds in Bangladesh.
Abstract:
The Diversity and Ubiquity of Antibiotic Resistance Genes in Finfish Culture Ponds in Bangladesh
AbstractIn Bangladesh, fish provide over 60% of animal-source food with 56.2% of this coming from aquaculture produced predominantly in rural freshwater ponds. Increasing demand for fish products is driving intensification and resulting in higher disease prevalence, posing a risk to food security. Biosecurity is often absent in rural aquaculture practices in Bangladesh and antibiotics are commonly used to treat and prevent disease outbreaks. Antibiotics are often administered incorrectly - a key factor associated with the development of antimicrobial resistance (AMR). AMR can be disseminated rapidly within microbial ecosystems via mobile genetic elements, posing a risk for humans and animals infected with AMR pathogens as treatments with antibiotics become ineffective. Early AMR detection and understanding of the spread of antimicrobial resistant genes (ARGs) in rural aquaculture practices is critical for both food security and human health protection. Here, we apply a metagenomic approach to assess the ARG composition in pond water from six finfish (tilapia and pangasius) farms in the Mymensingh division of North-central Bangladesh. We found microbial communities within the ponds had similar alpha and beta diversities, with multiple ARGs predicted to confer resistance to eighteen different classes of antimicrobials. The most common ARGs conferred resistance to aminoglycosides and sulphonamides and were present in taxa associated with both fish and human pathogens. This ARG diversity potentially confers resistance to a wide variety of antibiotic classes and questions the effectiveness of current and future treatment of diseases with antibiotics in earthen aquaculture ponds. The microbial and ARG compositions between fish ponds within each farm were similar, which may relate to parallels in farming practices creating similar microbial selection pressures and thus comparable microbial populations. Without a more controlled approach towards antibiotic usage, will inevitably further exacerbate the challenges in treating and preventing disease outbreaks as aquaculture production intensifies in Bangladesh.HighlightsARGs in Bangladesh rural fishponds indicate resistance to 18 different antibioticsThe most common AMR were to aminoglycosides and sulphonamidesARGs were present in plasmids and taxa-associated pathogensFarming practices strongly influence microbial and ARG compositionsIdentified ARGs question antibiotic treatment of disease in rural aquaculture
Abstract.
2021
Bell A (2021). Analysis of viral signatures from Marine Microorganisms by Single-cell Amplified Genomes and Metagenomic Assembled Genomes.
Abstract:
Analysis of viral signatures from Marine Microorganisms by Single-cell Amplified Genomes and Metagenomic Assembled Genomes
70% of the world’s surface is covered by oceans; its impact on the global carbon cycle, climate change, and acid-base biochemistry remain crucial to our understanding of the natural world. The oceans act as important buffers against climate change, absorbing 25% of anthropogenic carbon and over 90% of rising temperatures. 90% of the ocean’s biomass is composed of marine microorganisms and their impact on global systems, particularly in the face of anthropogenic climate change, remains an active area of research. Marine microorganisms are critical in the energy cycle and are the foundation for marine life. Warmer waters have led to increasingly stratified and nutrient-depleted water masses at the ocean surface, favouring low-nutrient microbial specialists. One group of these, known as the SAR11 clade, comprise up to 40% of the microbial community and are estimated to convert up to 20% of all global primary production back to atmospheric CO2 as well as being an important biological source of methane. Increasing SAR11 abundance in warming oceans and concomitant increases in remineralisation of CO 2 and methane may create a positive feedback loop for global warming.
A potential brake on the influence of SAR11 carbon remineralisation is their associated viruses, which are predicted to lyse up to 20% of cellular biomass daily. These viruses also encode an enormous array of genetic diversity and its relationship with both physical and biological factors is key to understanding the marine biome’s population dynamics. Predation of cells by viruses is a major driver of carbon export to the deep ocean, but our knowledge of these interactions in the SAR11 clade is limited, in part due to the paucity of host-virus model systems for this clade.
However, studying these microorganisms remains challenging since only a few SAR11 strains have been isolated and cultured for in vitro experimentation. Alternative study methods include obtaining genomes via metagenomics studies and Single-cell Amplified Genomes (SAGs). Therefore, the goal of this project is to extract and explore SAR11 host and associated phage genomes from metagenomic and SAG data. Here, I present a study of 451 SAGs collected from the Tara Ocean expeditions and twelve prokaryotic metagenomic samples from the Bermuda Atlantic Time Series (BATS).
Overall, I summarise the difficulty of obtaining contiguous and high-quality SAR11 genomes from metagenomic data. I conclude possible reasons why existing bioinformatics tools are ineffective at recovering such sequences and suggest improvements through long-read technology. Through SAG data, I identified and evaluated genomic regions associated with phage defence to improve our understanding of SAR11-associated viral dynamics in the oceans. Additionally, I characterised two previously undescribed clades of SAR11, both phylogenetically and ecologically. Our 451 SAGS contained fewer phage sequences than SAGs from other taxa, indicating the SAR11 clade does not conform to the expected statement that 20% of all marine microorganisms are infected at any given time. Lastly, I confirmed that a hypervariable region identified as a putative site for host-virus Red Queen dynamics is present within all clades of SAR11, and concluded these regions are enriched in genes related to cell wall biosynthesis. I hypothesise that these genes are related to phage defence, altering the cell wall receptors and preventing recognition of a host by SAR11 phages, therefore resisting infection. These findings together increase our understanding of additional host-phage interactions SAR11 has and impact current models when calculating SAR11 phage carbon-sequestering via the viral shunt.
Abstract.
du Plessis L, McCrone JT, Zarebski AE, Hill V, Ruis C, Gutierrez B, Raghwani J, Ashworth J, Colquhoun R, Connor TR, et al (2021). Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK.
Science,
371(6530), 708-712.
Abstract:
Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK
Lineage dynamics
.
. The scale of genome-sequencing efforts for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is unprecedented. The United Kingdom has contributed more than 26,000 sequences to this effort. This volume of data allowed du Plessis
. et al.
. to develop a detailed picture of the influxes of virus reaching U.K. shores as the pandemic developed during the first months of 2020 (see the Perspective by Nelson). Before lockdown, high travel volumes and few restrictions on international travel allowed more than 1000 lineages to become established. This accelerated local epidemic growth and exceeded contact tracing capacity. The authors were able to quantify the abundance, size distribution, and spatial range of the lineages that were transmitted. Transmission was highly heterogeneous, favoring some lineages that became widespread and subsequently harder to eliminate. This dire history indicates that rapid or even preemptive responses should have been used as they were elsewhere where containment was successful.
.
.
. Science
. this issue p.
. 708
. ; see also p.
. 680
.
Abstract.
Volz E, Hill V, McCrone JT, Price A, Jorgensen D, O’Toole Á, Southgate J, Johnson R, Jackson B, Nascimento FF, et al (2021). Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. Cell, 184(1), 64-75.e11.
Buchholz HH, Bolaños LM, Bell AG, Michelsen ML, Allen MJ, Temperton B (2021). Genomic evidence for inter-class host transition between abundant streamlined heterotrophs by a novel and ubiquitous marine Methylophage.
Abstract:
Genomic evidence for inter-class host transition between abundant streamlined heterotrophs by a novel and ubiquitous marine Methylophage
ABSTRACTThe methylotrophic OM43 clade are Gammaproteobacteria that comprise some of the smallest free-living cells known and have highly streamlined genomes. OM43 represents an important microbial link 0between marine primary production and remineralisation of carbon back to the atmosphere. Bacteriophages shape microbial communities and are major drivers of microbial mortality and global marine biogeochemistry. Recent cultivation efforts have brought the first viruses infecting members of the OM43 clade into culture. Here we characterize a novel myophage infecting OM43 called Melnitz. Melnitz was isolated independently on three separate occasions (with isolates sharing >99.95% average nucleotide identity) from water samples from a subtropical ocean gyre (Sargasso Sea) and temperate coastal (Western English Channel) systems. Metagenomic recruitment from global ocean viromes confirmed that Melnitz is globally ubiquitous, congruent with patterns of host abundance. Bacteria with streamlined genomes such as OM43 and the globally dominant SAR11 clade use riboswitches as an efficient method to regulate metabolism. Melnitz encodes a two-piece tmRNA (ssrA), controlled by a glutamine riboswitch, providing evidence that riboswitch use also occurs for regulation during phage infection of streamlined heterotrophs. Virally encoded tRNAs and ssrA found in Melnitz were phylogenetically more closely related to those found within the alphaproteobacterial SAR11 clade and their associated myophages than those within their gammaproteobacterial hosts. This suggests the possibility of an ancestral inter-class host transition event between SAR11 and OM43. Melnitz and a related myophage that infects SAR11 were unable to infect hosts of the SAR11 and OM43, respectively, suggesting host transition rather than a broadening of host range.IMPORTANCEIsolation and cultivation of viruses is the foundation on which the mechanistic understanding of virus-host interactions and ground-truthing is based. This study isolated and characterised the first myophage known to infect the OM43 clade, expanding our knowledge of this understudied group of microbes. The near-identical genomes of four strains of Melnitz isolated from different marine provinces and global abundance estimations from metagenomic data suggest that this viral population is globally ubiquitous. Genome analysis revealed several unusual features in Melnitz and related genomes recovered from viromes, such as a curli operon and virally encoded tmRNA controlled by a glutamine riboswitch, neither of which are found in the host. Further phylogenetic analysis of shared genes indicates that this group of viruses infecting the gammaproteobacterial OM43 shares a recent common ancestor with viruses infecting the abundant alphaproteobacterial SAR11 clade. Host ranges are affected by compatible cell surface receptors, successful circumvention of superinfection exclusion systems and the presence of required accessory proteins, which typically limits phages to singular narrow groups of closely related bacterial hosts. This study provides intriguing evidence that for streamlined heterotrophic bacteria, virus-host transitioning is not necessarily restricted to phylogenetically related hosts, but is a function of shared physical and biochemical properties of the cell.
Abstract.
Vöhringer HS, Sanderson T, Sinnott M, De Maio N, Nguyen T, Goater R, Schwach F, Harrison I, Hellewell J, Ariani CV, et al (2021). Genomic reconstruction of the SARS-CoV-2 epidemic in England.
Nature,
600(7889), 506-511.
Abstract:
Genomic reconstruction of the SARS-CoV-2 epidemic in England
AbstractThe evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus leads to new variants that warrant timely epidemiological characterization. Here we use the dense genomic surveillance data generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 71 different lineages in each of 315 English local authorities between September 2020 and June 2021. This analysis reveals a series of subepidemics that peaked in early autumn 2020, followed by a jump in transmissibility of the B.1.1.7/Alpha lineage. The Alpha variant grew when other lineages declined during the second national lockdown and regionally tiered restrictions between November and December 2020. A third more stringent national lockdown suppressed the Alpha variant and eliminated nearly all other lineages in early 2021. Yet a series of variants (most of which contained the spike E484K mutation) defied these trends and persisted at moderately increasing proportions. However, by accounting for sustained introductions, we found that the transmissibility of these variants is unlikely to have exceeded the transmissibility of the Alpha variant. Finally, B.1.617.2/Delta was repeatedly introduced in England and grew rapidly in early summer 2021, constituting approximately 98% of sampled SARS-CoV-2 genomes on 26 June 2021.
Abstract.
Knipe H, Temperton B, Lange A, Bass D, Tyler CR (2021). Probiotics and competitive exclusion of pathogens in shrimp aquaculture.
REVIEWS IN AQUACULTURE,
13(1), 324-352.
Author URL.
McMurtrie J, Alathari S, Chaput DL, Bass D, Ghambi C, Nagoli J, Delamare-Deboutteville J, Mohan CV, Cable J, Temperton B, et al (2021). Relationships between pond water and tilapia skin microbiomes in aquaculture ponds in Malawi.
Kemp SA, Collier DA, Datir RP, Ferreira IATM, Gayed S, Jahun A, Hosmillo M, Rees-Spear C, Mlcochova P, Lumb IU, et al (2021). SARS-CoV-2 evolution during treatment of chronic infection.
Nature,
592(7853), 277-282.
Abstract:
SARS-CoV-2 evolution during treatment of chronic infection
The spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for virus infection through the engagement of the human ACE2 protein1 and is a major antibody target. Here we show that chronic infection with SARS-CoV-2 leads to viral evolution and reduced sensitivity to neutralizing antibodies in an immunosuppressed individual treated with convalescent plasma, by generating whole-genome ultra-deep sequences for 23 time points that span 101 days and using in vitro techniques to characterize the mutations revealed by sequencing. There was little change in the overall structure of the viral population after two courses of remdesivir during the first 57 days. However, after convalescent plasma therapy, we observed large, dynamic shifts in the viral population, with the emergence of a dominant viral strain that contained a substitution (D796H) in the S2 subunit and a deletion (ΔH69/ΔV70) in the S1 N-terminal domain of the spike protein. As passively transferred serum antibodies diminished, viruses with the escape genotype were reduced in frequency, before returning during a final, unsuccessful course of convalescent plasma treatment. In vitro, the spike double mutant bearing both ΔH69/ΔV70 and D796H conferred modestly decreased sensitivity to convalescent plasma, while maintaining infectivity levels that were similar to the wild-type virus.The spike substitution mutant D796H appeared to be the main contributor to the decreased susceptibility to neutralizing antibodies, but this mutation resulted in an infectivity defect. The spike deletion mutant ΔH69/ΔV70 had a twofold higher level of infectivity than wild-type SARS-CoV-2, possibly compensating for the reduced infectivity of the D796H mutation. These data reveal strong selection on SARS-CoV-2 during convalescent plasma therapy, which is associated with the emergence of viral variants that show evidence of reduced susceptibility to neutralizing antibodies in immunosuppressed individuals.
Abstract.
Collier DA, De Marco A, Ferreira IATM, Meng B, Datir RP, Walls AC, Kemp SA, Bassi J, Pinto D, Silacci-Fregni C, et al (2021). Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies.
NATURE,
593(7857), 136-+.
Author URL.
Zablocki O, Michelsen M, Burris M, Solonenko N, Warwick-Dugdale J, Ghosh R, Pett-Ridge J, Sullivan MB, Temperton B (2021). VirION2: a shortand long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature.
PeerJ,
9Abstract:
VirION2: a shortand long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature
Microbes play fundamental roles in shaping natural ecosystem properties and functions, but do so under constraints imposed by their viral predators. However, studying viruses in nature can be challenging due to low biomass and the lack of universal gene markers. Though metagenomic short-read sequencing has greatly improved our virus ecology toolkit—and revealed many critical ecosystem roles for viruses—microdiverse populations and fine-scale genomic traits are missed. Some of these microdiverse populations are abundant and the missed regions may be of interest for identifying selection pressures that underpin evolutionary constraints associated with hosts and environments. Though long-read sequencing promises complete virus genomes on single reads, it currently suffers from high DNA requirements and sequencing errors that limit accurate gene prediction. Here we introduce VirION2, an integrated shortand long-read metagenomic wet-lab and informatics pipeline that updates our previous method (VirION) to further enhance the utility of long-read viral metagenomics. Using a viral mock community, we first optimized laboratory protocols (polymerase choice, DNA shearing size, PCR cycling) to enable 76% longer reads (now median length of 6,965 bp) from 100-fold less input DNA (now 1 nanogram). Using a virome from a natural seawater sample, we compared viromes generated with VirION2 against other library preparation options (unamplified, original VirION, and short-read), and optimized downstream informatics for improved long-read error correction and assembly. VirION2 assemblies combined with short-read based data (‘enhanced’ viromes), provided significant improvements over VirION libraries in the recovery of longer and more complete viral genomes, and our optimized error-correction strategy using longand short-read data achieved 99.97% accuracy. In the seawater virome, VirION2 assemblies captured 5,161 viral populations (including all of the virus populations observed in the other assemblies), 30% of which were uniquely assembled through inclusion of long-reads, and 22% of the top 10% most abundant virus populations derived from assembly of long-reads. Viral populations unique to VirION2 assemblies had significantly higher microdiversity means, which may explain why short-read virome approaches failed to capture them. These findings suggest the VirION2 sample prep and workflow can help researchers better investigate the virosphere, even from challenging low-biomass samples. Our new protocols are available to the research community on protocols.io as a ‘living document’ to facilitate dissemination of updates to keep pace with the rapid evolution of long-read sequencing technology.
Abstract.
Masoli JAH, Jeffries A, Temperton B, Auckland C, Michelsen M, Warwick-Dugdale J, Manley R, Farbos A, Ellard S, Knight B, et al (2021). Viral genetic sequencing identifies staff transmission of COVID-19 is important in a community hospital outbreak.
Abstract:
Viral genetic sequencing identifies staff transmission of COVID-19 is important in a community hospital outbreak
AbstractBackgroundWe have successfully used whole-genome sequencing to provide additional information for transmission pathways in infectious spread. We report and interpret genomic sequencing results in clinical context from a large outbreak of COVID-19 with 46 cases across staff and patients in a community hospital in the UK.MethodsFollowing multiple symptomatic cases within a two-week period, all staff and patients were screened by RT-PCR and staff subsequently had serology tests.ResultsThirty staff (25%) and 16 patients (62%) tested positive for COVID-19. Genomic sequencing data showed significant overlap of viral haplotypes in staff who had overlapping shift patterns. Patient haplotypes were more distinct from each other but had overlap with staff haplotypes.ConclusionsThis study includes clinical and genomic epidemiological detail that demonstrates the value of a combined approach. Viral genetic sequencing has identified that staff transmission of COVID-19 was important in this community hospital outbreak.Key pointsDetailed analysis of a large community hospital outbreak in older adults and staff with concurrent clinical and genomic data, including working patterns.Staff transmission was important in this community hospital outbreak.We found plausible associations between staff and patient cases.
Abstract.
2020
Alathari S (2020). AlathariS.
Abstract:
AlathariS
Aquaculture is of major and increasing importance to global food security, particularly in Low Income, Food Deficit Countries (LIFDCs), where it also serves as a significant contribution to poverty alleviation. Disease is widely acknowledged as the prominent bottleneck to achieving global food security and poverty alleviation targets relating to aquaculture, with annual losses exceeding >$6bn (Food and Agriculture Organization 2014). Outbreaks of disease caused by endemic and emerging pathogens impact directly on farmer income and their nutritional security. Avoidance of yield-limiting disease outbreaks is a fundamental requirement for future growth and resilience of aquaculture in LIFDCs. Advances in molecular techniques coupled with next-generation sequencing have provided a step-change in understanding the role of host-associated bacteria, archaea, protists and viruses (the microbiome) in host homeostasis. Shifts in microbiome communities under stressful conditions can contribute to disease states. However, the role of microbiomes in the emergence of diseases in aquaculture, where stressors include feeding, antibiotic and disinfectant use and over-stocking, is poorly studied.
Here our study presents an evaluation of the microbiomes (bacteria and viruses) associated with tilapia and their pond environments in aquaculture, using 16S rRNA community profiling techniques and viral amplicon sequencing. Samples investigated in this project were collected from Malawi tilapia fish farms; their skin community composition and diversity were examined across geographical scales. The high variability observed of the microbial communities in small geographic regions, showed that future sampling to detect shifts due to dysbiosis will require time-resolved sampling of ponds under study. Nanopore sequencing of full length 16S rRNA genes, using MinION, allowed us to examine the microbial communities at higher taxonomic resolution than short read sequencing techniques. Its success lays the foundation for in-situ microbial profiling of aquaculture ponds for disease, and offers independence to farmers to monitor their own ponds. Successful amplification of the T4-like Myoviridae phylogenetic markers from one rearing water sample was achieved, although the required degeneracy of the primers inhibited multiplexing. Therefore, our findings suggest that inclusion of bacteriophages in microbiome studies is better served using shotgun metagenomic methods, rather than amplicon sequencing.
Finally, we investigated the use of skin swabbing as an alternative to bucket incubations to minimise animal stress when categorising the fish skin microbiome. Skin swabbing successfully captured similar microbial communities in comparison to bucket incubations, with greater diversity and variance between fish.
Abstract.
Lucchesi AM, Henson MW, Temperton B, Thrash JC (2020). Complete Genome Sequence of. <i>Marinobacterium</i>. sp. Strain LSUCC0821, Isolated from the Coastal Gulf of Mexico.
Microbiology Resource Announcements,
9(49).
Abstract:
Complete Genome Sequence of. Marinobacterium. sp. Strain LSUCC0821, Isolated from the Coastal Gulf of Mexico
. Here, we present the complete genome sequence of
. Marinobacterium
. sp. strain LSUCC0821, isolated from the coastal Gulf of Mexico with artificial seawater using high-throughput dilution-to-extinction (DTE) cultivation. The 2.36-Mbp circularized genome sequence has 2,231 predicted genes, a 91.5% coding density, and a GC content of 47.8%.
.
Abstract.
Manley R, Temperton B, Boots M, Wilfert L (2020). Contrasting impacts of a novel specialist vector on multihost viral pathogen epidemiology in wild and managed bees.
Mol Ecol,
29(2), 380-393.
Abstract:
Contrasting impacts of a novel specialist vector on multihost viral pathogen epidemiology in wild and managed bees.
Typically, pathogens infect multiple host species. Such multihost pathogens can show considerable variation in their degree of infection and transmission specificity, which has important implications for potential disease emergence. Transmission of multihost pathogens can be driven by key host species and changes in such transmission networks can lead to disease emergence. We study two viruses that show contrasting patterns of prevalence and specificity in managed honeybees and wild bumblebees, black queen cell virus (BQCV) and slow bee paralysis virus (SBPV), in the context of the novel transmission route provided by the virus-vectoring Varroa destructor. Our key result is that viral communities and RNA virus genetic variation are structured by location, not host species or V. destructor presence. Interspecific transmission is pervasive with the same viral variants circulating between pollinator hosts in each location; yet, we found virus-specific host differences in prevalence and viral load. Importantly, V. destructor presence increases the prevalence in honeybees and, indirectly, in wild bumblebees, but in contrast to its impact on deformed wing virus (DWV), BQCV and SBPV viral loads are not increased by Varroa presence, and do not show genetic evidence of recent emergence. Effective control of Varroa in managed honeybee colonies is necessary to mitigate further disease emergence, and alleviate disease pressure on our vital wild bee populations. More generally, our results highlight the over-riding importance of geographical location to the epidemiological outcome despite the complexity of multihost-parasite interactions.
Abstract.
Author URL.
Buchholz HH, Michelsen M, Bolaños LM, Browne E, Allen MJ, Temperton B (2020). Efficient Dilution-to-Extinction isolation of novel virus-host model systems for fastidious heterotrophic bacteria.
Abstract:
Efficient Dilution-to-Extinction isolation of novel virus-host model systems for fastidious heterotrophic bacteria
AbstractMicrobes and their associated viruses are key drivers of biogeochemical processes in marine and soil biomes. While viruses of phototrophic cyanobacteria are well-represented in model systems, challenges of isolating marine microbial heterotrophs and their viruses have hampered experimental approaches to quantify the importance of viruses in nutrient recycling. A resurgence in cultivation efforts has improved the availability of fastidious bacteria for hypothesis testing, but this has not been matched by similar efforts to cultivate their associated bacteriophages. Here, we describe a high-throughput method for isolating important virus-host systems for fastidious heterotrophic bacteria that couples advances in culturing of hosts with sequential enrichment and isolation of associated phages. Applied to six monthly samples from the Western English Channel, we first isolated one new member of the globally dominant bacterial SAR11 clade and three new members of the methylotrophic bacterial clade OM43. We used these as bait to isolate 117 new phages including the first known siphophage infecting SAR11, and the first isolated phage for OM43. Genomic analyses of 13 novel viruses revealed representatives of three new viral genera, and infection assays showed that the viruses infecting SAR11 have ecotype-specific host-ranges. Similar to the abundant human-associated phage ΦCrAss001, infection dynamics within the majority of isolates suggested either prevalent lysogeny or chronic infection, despite a lack of associated genes; or host phenotypic bistability with lysis putatively maintained within a susceptible subpopulation. Broader representation of important virus-host systems in culture collections and genomic databases will improve both our understanding of virus-host interactions, and accuracy of computational approaches to evaluate ecological patterns from metagenomic data.
Abstract.
Henson MW, Lanclos VC, Pitre DM, Weckhorst JL, Lucchesi AM, Cheng C, Temperton B, Thrash JC (2020). Expanding the Diversity of Bacterioplankton Isolates and Modeling Isolation Efficacy with Large-Scale Dilution-to-Extinction Cultivation.
Applied and Environmental Microbiology,
86(17).
Abstract:
Expanding the Diversity of Bacterioplankton Isolates and Modeling Isolation Efficacy with Large-Scale Dilution-to-Extinction Cultivation
Even before the coining of the term “great plate count anomaly” in the 1980s, scientists had noted the discrepancy between the number of microorganisms observed under the microscope and the number of colonies that grew on traditional agar media. New cultivation approaches have reduced this disparity, resulting in the isolation of some of the “most wanted” bacterial lineages. Nevertheless, the vast majority of microorganisms remain uncultured, hampering progress toward answering fundamental biological questions about many important microorganisms. Furthermore, few studies have evaluated the underlying factors influencing cultivation success, limiting our ability to improve cultivation efficacy. Our work details the use of dilution-to-extinction (DTE) cultivation to expand the phylogenetic and geographic diversity of available axenic cultures. We also provide a new model of the DTE approach that uses cultivation results and natural abundance information to predict taxon-specific viability and iteratively constrain DTE experimental design to improve cultivation success.
Abstract.
Henson MW, Lanclos VC, Pitre DM, Weckhorst JL, Lucchesi AM, Cheng C, Temperton B, Thrash JC (2020). Expanding the diversity of bacterioplankton isolates and modeling isolation efficacy with large scale dilution-to-extinction cultivation.
Gregory AC, Gerhardt K, Zhong Z-P, Bolduc B, Temperton B, Konstantinidis KT, Sullivan MB (2020). MetaPop: a pipeline for macro- and micro-diversity analyses and visualization of microbial and viral metagenome-derived populations.
Henson M, Temperton B, Thrash C (2020). Modified 1D Native Barcoding genomic DNA protocol. from the Temperton Lab (University of Exeter) v1.
Abstract:
Modified 1D Native Barcoding genomic DNA protocol. from the Temperton Lab (University of Exeter) v1
Modified 1D Native Barcoding genomic DNA protocol (v. NBE_9006_v103_revO_21Dec2016for SQK-LSK108) from the Temperton Lab (University of Exeter).
Abstract.
Witherall L (2020). Phage Encapsulation as a Treatment for Vibriosis in Oyster Aquaculture.
Abstract:
Phage Encapsulation as a Treatment for Vibriosis in Oyster Aquaculture
With our global population expected to increase to as much as 9.8 billion by 2050, strategies for obtaining worldwide food security become increasingly important. The oceans act as a generous resource for reaching our global nutrition targets, yet overfishing in recent decades has caused great harm, including localised population extinction, to fish and shellfish stocks. Aquaculture, the act of maintaining and farming marine or freshwater animal organisms, has become a popular alternative to wild fisheries. However, with a high demand for food sources, comes a move towards more intensive farming practices, whereby denser communities of farmed animals are kept in waters with high nutrient input. Such farming practices can favour pathogenic bacterial communities, which can cause disease in farmed animals and consequently lead to reduced stock numbers. Not only does this affect yield, but there can be further economic impacts to the detriment of those whose livelihoods depend on the aquaculture sector.
Traditionally, antibiotics have been used with abundance to treat disease in aquaculture, however overuse and misuse has led to a global rise in antibiotic resistance. This is particularly apparent in aquaculture, where antibiotics can be directly applied to organisms and also, easily accumulate within the water column. Therefore, as the global antibiotic crisis worsens, it has become ever more important to develop novel therapeutic alternatives. One such promising alternative is the use of bacteriophages (phages) – viruses which kill bacteria. However, application of phages requires more research to become commercially viable. Encapsulation of such phages may improve their therapeutic use through increased concentrations during application, improved stability and increased protection. Long term storage of encapsulated phages, e.g. after lyophilisation (freeze drying), would facilitate development of a robust phage library and enable rapid construction of bespoke phage cocktails, whereby distinct phages are combined to combat bacterial resistance. Droplet microfluidics is an emerging field, which can be used for the high-throughput encapsulation of bacteriophages, for use against bacterial infections, not only in aquaculture, but also in clinical settings.
Vibrio parahaemolyticus is a highly pathogenic bacterium, capable of infecting shellfish and subsequently cause gastroenteritis in humans. V. parahaemolyticus is commonly isolated from oysters, for example Crassostrea gigas, which is the most commonly farmed species of oyster in the UK. and there is increasing evidence of antibiotic resistance in V. parahaemolyticus.
This project aimed to evaluate the use of droplet microfluidics and subsequent freeze-drying in order to encapsulate bacteriophages specific for V. parahaemolyticus, a highly pathogenic bacterium, capable of infecting shellfish and subsequently cause gastroenteritis in humans. V. parahaemolyticus is commonly isolated from oysters, for example Crassostrea gigas, which is the most commonly farmed species of oyster in the UK and furthermore, there is increasing evidence of antibiotic resistance in V. parahaemolyticus. In order to develop of an encapsulated viral library for phage therapy of V. parahaemolyticus, the following four challenges needed to be addressed: (1) isolate novel vibriophages specific for V. parahaemolyticus, (2) develop a novel protocol for the synthesis of monodisperse sodium alginate microcapsules, using microfluidics, (3) encapsulate vibriophages in alginate droplets and (4) use such encapsulated phages to treat V. parahaemolyticus infection of C. gigas.
The genomes of four strains of V. parahaemolyticus (EXE V18/004, V12/024, V05/313 and V05/027) were sequenced. In total, 10 dsDNA high quality (category 5) prophage and 5 Inoviruses were detected and manually curated across the four genomes. Furthermore, in this instance the isolation of novel vibriophages was unsuccessful. Despite this, a novel protocol was developed for the synthesis of monodisperse alginate droplets, using a glass microfluidic device. Droplets were synthesised with an alginate concentration of 1 % (w/w) and collected in calcium chloride (CaCl2) solution with a concentration of 2 % (w/w). Bacteriophage T4, vibriophage sm030 and vibriophage sm031 were successfully encapsulated within alginate microcapsules and later lyophilised. Lyophilised droplets containing bacteriophage T4, vibriophage sm030 or vibriophage sm031 were able to cause infection and reduce cell growth in broth cultures of Escherichia coli and V. parahaemolyticus, respectively. More research is needed into phage encapsulation in bacteriophage therapy before its widespread use.
Abstract.
Zablocki O, Michelsen M, Burris M, Solonenko N, Warwick-Dugdale J, Ghosh R, Pett-Ridge J, Sullivan MB, Temperton B (2020). VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature.
Abstract:
VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature
ABSTRACTMicrobes play fundamental roles in shaping natural ecosystem properties and functions, but do so under constraints imposed by their viral predators. However, studying viruses in nature can be challenging due to low biomass and the lack of universal gene markers. Though metagenomic short-read sequencing has greatly improved our virus ecology toolkit— and revealed many critical ecosystem roles for viruses — microdiverse populations and fine-scale genomic traits are missed. Some of these microdiverse populations are abundant and the missed regions may be of interest for identifying selection pressures that underpin evolutionary constraints associated with hosts and environments. Though long-read sequencing promises complete virus genomes on single reads, it currently suffers from high DNA requirements and sequencing errors that limit accurate gene prediction. Here we introduce VirION2, an integrated short- and long-read metagenomic wet-lab and informatics pipeline that updates our previous method (VirION) to further enhance the utility of long-read viral metagenomics. Using a viral mock community, we first optimized laboratory protocols (polymerase choice, DNA shearing size, PCR cycling) to enable 76% longer reads (now median length of 6,965 bp) from 100-fold less input DNA (now 1 nanogram). Using a virome from a natural seawater sample, we compared viromes generated with VirION2 against other library preparation options (unamplified, original VirION, and short-read), and optimized downstream informatics for improved long-read error correction and assembly. VirION2 assemblies combined with short-read based data (‘enhanced’viromes), provided significant improvements over VirION libraries in the recovery of longer and more complete viral genomes, and our optimized error-correction strategy using long- and short-read data achieved 99.97% accuracy. In the seawater virome, VirION2 assemblies captured 5,161 viral populations (including all of the virus populations observed in the other assemblies), 30% of which were uniquely assembled through inclusion of long-reads, and 22% of the top 10% most abundant virus populations derived from assembly of long-reads. Viral populations unique to VirION2 assemblies had significantly higher microdiversity, which may explain why short-read virome approaches failed to capture them. These findings suggest the VirION2 sample prep and workflow (updated at protocols.io) can help researchers better investigate the virosphere, even from challenging low-biomass samples. Our new protocols are available to the research community on protocols.io as a ‘living document’ to facilitate dissemination of updates to keep pace with the rapid evolution of long read sequencing technology. Taken together, the addition of long-reads uniquely enabled the recovery of 22% of the most abundant viruses—that would have been missed in short-read only assemblies.
Abstract.
Buchholz H, Michelsen M, Allen M, Temperton B (2020). Viral isolation for SAR11 and OM43 hosts v1.
Abstract:
Viral isolation for SAR11 and OM43 hosts v1
Working protocol
Abstract.
2019
Giovannoni SJ, Halsey KH, Saw J, Muslin O, Suffridge CP, Sun J, Lee C-P, Moore ER, Temperton B, Noell SE, et al (2019). A Parasitic Arsenic Cycle That Shuttles Energy from Phytoplankton to Heterotrophic Bacterioplankton.
mBio,
10(2).
Abstract:
A Parasitic Arsenic Cycle That Shuttles Energy from Phytoplankton to Heterotrophic Bacterioplankton.
In many regions of the world oceans, phytoplankton face the problem of discriminating between phosphate, an essential nutrient, and arsenate, a toxic analogue. Many phytoplankton, including the most abundant phytoplankton group known, Prochlorococcus, detoxify arsenate (AsV) by reduction to arsenite (AsIII), followed by methylation and excretion of the methylated arsenic products. We synthesized [14C]dimethyl arsenate (DMA) and used it to show that cultured Pelagibacter strain HTCC7211 (SAR11) cells oxidize the methyl group carbons of DMA, producing 14CO2 and ATP. We measured [14C]DMA oxidation rates in the P-depleted surface waters of the Sargasso Sea, a subtropical ocean gyre. [14C]DMA was oxidized to 14CO2 by Sargasso Sea plankton communities at a rate that would cause turnover of the estimated DMA standing stock every 8.1 days. SAR11 strain HTCC7211, which was isolated from the Sargasso Sea, has a pair of arsenate resistance genes and was resistant to arsenate, showing no growth inhibition at As/P ratios of >65:1. Across the global oceans, there was a strong inverse relationship between the frequency of the arsenate reductase (LMWPc_ArsC) in Pelagibacter genomes and phosphate concentrations. We propose that the demethylation of methylated arsenic compounds by Pelagibacter and possibly other bacterioplankton, coupled with arsenate resistance, results in the transfer of energy from phytoplankton to bacteria. We dub this a parasitic cycle because the release of arsenate by Pelagibacter in principle creates a positive-feedback loop that forces phytoplankton to continually regenerate arsenate detoxification products, producing a flow of energy to P-limited ocean regions.IMPORTANCE in vast, warm regions of the oceans, phytoplankton face the problem of arsenic poisoning. Arsenate is toxic because it is chemically similar to phosphate, a scarce nutrient that phytoplankton cells need for growth. Many phytoplankton, including the commonest phytoplankton type in warm oceans, Prochlorococcus, detoxify arsenate by adding methyl groups. Here we show that the most abundant non-photosynthetic plankton in the oceans, SAR11 bacteria, remove the methyl groups, releasing poisonous forms of arsenic back into the water. We postulate that the methylation and demethylation of arsenic compounds creates a cycle in which the phytoplankton can never get ahead and must continually transfer energy to the SAR11 bacteria. We dub this a parasitic process and suggest that it might help explain why SAR11 bacteria are so successful, surpassing all other plankton in their numbers. Field experiments were done in the Sargasso Sea, a subtropical ocean gyre that is sometimes called an ocean desert because, throughout much of the year, there is not enough phosphorous in the water to support large blooms of phytoplankton. Ocean deserts are expanding as the oceans absorb heat and grow warmer.
Abstract.
Author URL.
Martinez MA, Woodcroft BJ, Ignacio Espinoza JC, Zayed AA, Singleton CM, Boyd JA, Li YF, Purvine S, Maughan H, Hodgkins SB, et al (2019). Discovery and ecogenomic context of a global Caldiserica-related phylum active in thawing permafrost, Candidatus Cryosericota phylum nov. Ca. Cryosericia class nov. Ca. Cryosericales ord. nov. Ca. Cryosericaceae fam. nov. comprising the four species Cryosericum septentrionale gen. nov. sp. nov. Ca. C. hinesii sp. nov. Ca. C. odellii sp. nov. Ca. C. terrychapinii sp. nov.
Systematic and Applied Microbiology,
42(1), 54-66.
Abstract:
Discovery and ecogenomic context of a global Caldiserica-related phylum active in thawing permafrost, Candidatus Cryosericota phylum nov. Ca. Cryosericia class nov. Ca. Cryosericales ord. nov. Ca. Cryosericaceae fam. nov. comprising the four species Cryosericum septentrionale gen. nov. sp. nov. Ca. C. hinesii sp. nov. Ca. C. odellii sp. nov. Ca. C. terrychapinii sp. nov.
The phylum Caldiserica was identified from the hot spring 16S rRNA gene lineage ‘OP5’ and named for the sole isolate Caldisericum exile, a hot spring sulfur-reducing chemoheterotroph. Here we characterize 7 Caldiserica metagenome-assembled genomes (MAGs) from a thawing permafrost site in Stordalen Mire, Arctic Sweden. By 16S rRNA and marker gene phylogenies, and average nucleotide and amino acid identities, these Stordalen Mire Caldiserica (SMC) MAGs form part of a divergent clade from C. exile. Genome and meta-transcriptome and proteome analyses suggest that unlike Caldisericum, the SMCs (i) are carbohydrate- and possibly amino acid fermenters that can use labile plant compounds and peptides, and (ii) encode adaptations to low temperature. The SMC clade rose to community dominance within permafrost, with a peak metagenome-based relative abundance of ∼60%. It was also physiologically active in the upper seasonally-thawed soil. Beyond Stordalen Mire, analysis of 16S rRNA gene surveys indicated a global distribution of this clade, predominantly in anaerobic, carbon-rich and cold environments. These findings establish the SMCs as four novel phenotypically and ecologically distinct species within a single novel genus, distinct from C. exile clade at the phylum level. The SMCs are thus part of a novel cold-habitat phylum for an understudied, globally-distributed superphylum encompassing the Caldiserica. We propose the names Candidatus Cryosericota phylum nov. Ca. Cryosericia class nov. Ca. Cryosericales ord. nov. Ca. Cryosericaceae fam. nov. Ca. Cryosericum gen. nov. Ca. Cryosericum septentrionale sp. nov. Ca. C. hinesii sp. nov. Ca. C. odellii sp. nov. and Ca. C. terrychapinii sp. nov.
Abstract.
Manley R, Temperton B, Doyle T, Gates D, Hedges S, Boots M, Wilfert L (2019). Knock-on community impacts of a novel vector: spillover of emerging DWV-B from Varroa-infested honeybees to wild bumblebees.
Ecol Lett,
22(8), 1306-1315.
Abstract:
Knock-on community impacts of a novel vector: spillover of emerging DWV-B from Varroa-infested honeybees to wild bumblebees.
Novel transmission routes can directly impact the evolutionary ecology of infectious diseases, with potentially dramatic effect on host populations and knock-on effects on the wider host community. The invasion of Varroa destructor, an ectoparasitic viral vector in Western honeybees, provides a unique opportunity to examine how a novel vector affects disease epidemiology in a host community. This specialist honeybee mite vectors deformed wing virus (DWV), an important re-emerging honeybee pathogen that also infects wild bumblebees. Comparing island honeybee and wild bumblebee populations with and without V. destructor, we show that V. destructor drives DWV prevalence and titre in honeybees and sympatric bumblebees. Viral genotypes are shared across hosts, with the potentially more virulent DWV-B overtaking DWV-A in prevalence in a current epidemic. This demonstrates disease emergence across a host community driven by the acquisition of a specialist novel transmission route in one host, with dramatic community level knock-on effects.
Abstract.
Author URL.
Burris M, Solonenko N, Zablocki O, Temperton B (2019). Long Read Viromics Amplification Library Preparation (VirION 2) v1.
Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, Kuhn JH, Lavigne R, Brister JR, Varsani A, et al (2019). Minimum Information about an Uncultivated Virus Genome (MIUViG).
Nat Biotechnol,
37(1), 29-37.
Abstract:
Minimum Information about an Uncultivated Virus Genome (MIUViG).
We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere.
Abstract.
Author URL.
Messer A (2019). The evaluation of metagenomic analysis software, using in-silico and in-vitro mock community datasets, for the accurate study of bio-aerosol samples.
Abstract:
The evaluation of metagenomic analysis software, using in-silico and in-vitro mock community datasets, for the accurate study of bio-aerosol samples.
The bio-aerosol is an important medium for the potential dispersal of biological warfare agents within the battlefield space. In order to better protect the military personnel who work within this environment it is imperative that we increase our understanding of this matrix, especially the naturally occurring variation and its causes. Understanding the naturally occurring variation within the bio-aerosol will enable future and current biological detection platforms to be put through better test and evaluation processes, thus reducing the potential for false alarms and false negatives. Analysing bio-aerosol samples collected across a temporal gradient through a metagenomics approach will enable the natural variation to be better understood. However, metagenomic analysis tools have been shown to have contradictory reviews within the literature, it is therefore essential to identify the most suitable analysis approach.
Here I developed a metagenomic analysis pipeline which delivers high confidence taxonomic identification to species level, as well as accurate measures of diversity and homogeneity. The analysis pipeline that was developed takes the output from multiple tools thus reducing the number of false positives, delivering high confidence taxonomic identification. The analysis pipeline also gives a more accurate measure of diversity and homogeneity compared to any of the tools being used individually. This improved accuracy will deliver superior results when measuring the change in abundance of species identified within the bio-aerosol in sampling regimes carried out at Dstl. These improvements will lead to more accurate test bio-aerosols being developed for biological detection platform evaluation. Fundamentally this will improve the UK military’s capability to detect biological warfare releases within the battlespace.
Abstract.
2018
JWD Warwick-Dugdale J, Temperton B (2018). 'VirION': Long-read, low-input, viral metagenomic sequencing; Library Preparation and MinION (Oxford Nanopore Technologies) Sequencing (lib. prep. kit SQK-LSK108; flow cell: R9.4)&nbsp;v4 v1.
Abstract:
'VirION': Long-read, low-input, viral metagenomic sequencing; Library Preparation and MinION (Oxford Nanopore Technologies) Sequencing (lib. prep. kit SQK-LSK108; flow cell: R9.4) v4 v1
This protocol describes a generalizable, long-read, low-input metagenomic sequencing approach ('VirION') for the survey of viral communities. A significant obstacle in adopting long-read technology for viral metagenomics lies in obtaining the amount of DNA required; e.g. viral DNA extraction from 20 L of seawater yields far less than the micrograms of DNA recommended for efficient long-read sequencing. To overcome this limitation, we developed a Long-Read Linker-Amplified Shotgun Library approach for long-read viral metagenomics. The VirION method has been demonstrated to be as relatively quantitative as short-read methods, and analyses that combined VirION long-read data with Illumina, short-read data, captured many abundant and ubiquitous viral genomes that were missed by short-read assemblies. This approach was also shown to have overcome issues of microdiversity, and to have captured more genomic islands than short-read assemblies. Thus, VirION provides a high throughput and cost-effective alternative to fosmid and single-virus genomic approaches.
Abstract.
Warwick-Dugdale J, Solonenko N, Moore K, Chittick L, Gregory AC, Allen MJ, Sullivan MB, Temperton B (2018). Long-read viral metagenomics enables capture of abundant and microdiverse viral populations and their niche-defining genomic islands.
Abstract:
Long-read viral metagenomics enables capture of abundant and microdiverse viral populations and their niche-defining genomic islands
AbstractMarine viruses impact global biogeochemical cycles via their influence on host community structure and function, yet our understanding of viral ecology is constrained by limitations in culturing of important hosts and the lack of a ‘universal’ gene to facilitate community surveys. Short-read viral metagenomic studies have provided clues to viral function and first estimates of global viral gene abundance and distribution. However, short-read assemblies are confounded by populations with high levels of strain evenness and nucleotide diversity (microdiversity), limiting assembly of some of the most abundant viruses on Earth. Assembly across genomic islands which likely contain niche-defining genes that drive ecological speciation is also challenging. While such populations and features are successfully captured by single-virus genomics and fosmid-based approaches, both techniques require considerable cost and technical expertise. Here we established a low-cost, low-input, high throughput alternative method for improving assembly of viral metagenomics using long read technology. Named ‘VirION’ (Viral, long-read metagenomics via MinION sequencing), our sequencing approach and complementary bioinformatics pipeline (i) increased number and completeness of assembled viral genomes compared to short-read sequencing methods; (ii) captured populations of abundant viruses with high microdiversity missed by short-read methods and (iii) captured more and longer genomic islands than short-read methods. Thus, VirION provides a high throughput and cost-effective alternative to fosmid and single-virus genomic approaches to more comprehensively explore viral communities in nature.
Abstract.
Thrash JC, Baker BJ, Seitz KW, Temperton B, Campbell LG, Rabalais NN, Henrissat B, Masond OU (2018). Metagenomic assembly and prokaryotic metagenome-assembled genome sequences from the Northern Gulf of Mexico "dead Zone".
Microbiology Resource Announcements,
7(9).
Abstract:
Metagenomic assembly and prokaryotic metagenome-assembled genome sequences from the Northern Gulf of Mexico "dead Zone"
Coastal regions experiencing declining dissolved oxygen are increasing in number and severity around the world. However, despite the importance of microbial metabolism in coastal hypoxia, few metagenomic surveys exist. Our data set from within the second largest human-caused hypoxic region provides opportunities to more deeply explore the microbiology of these systems.
Abstract.
2017
Thrash JC, Seitz KW, Baker BJ, Temperton B, Gillies LE, Rabalais NN, Henrissat B, Mason OU (2017). Metabolic Roles of Uncultivated Bacterioplankton Lineages in the Northern Gulf of Mexico "Dead Zone".
mBio,
8(5).
Abstract:
Metabolic Roles of Uncultivated Bacterioplankton Lineages in the Northern Gulf of Mexico "Dead Zone".
Marine regions that have seasonal to long-term low dissolved oxygen (DO) concentrations, sometimes called "dead zones," are increasing in number and severity around the globe with deleterious effects on ecology and economics. One of the largest of these coastal dead zones occurs on the continental shelf of the northern Gulf of Mexico (nGOM), which results from eutrophication-enhanced bacterioplankton respiration and strong seasonal stratification. Previous research in this dead zone revealed the presence of multiple cosmopolitan bacterioplankton lineages that have eluded cultivation, and thus their metabolic roles in this ecosystem remain unknown. We used a coupled shotgun metagenomic and metatranscriptomic approach to determine the metabolic potential of Marine Group II Euryarchaeota, SAR406, and SAR202. We recovered multiple high-quality, nearly complete genomes from all three groups as well as candidate phyla usually associated with anoxic environments-Parcubacteria (OD1) and Peregrinibacteria Two additional groups with putative assignments to ACD39 and PAUC34f supplement the metabolic contributions by uncultivated taxa. Our results indicate active metabolism in all groups, including prevalent aerobic respiration, with concurrent expression of genes for nitrate reduction in SAR406 and SAR202, and dissimilatory nitrite reduction to ammonia and sulfur reduction by SAR406. We also report a variety of active heterotrophic carbon processing mechanisms, including degradation of complex carbohydrate compounds by SAR406, SAR202, ACD39, and PAUC34f. Together, these data help constrain the metabolic contributions from uncultivated groups in the nGOM during periods of low DO and suggest roles for these organisms in the breakdown of complex organic matter.IMPORTANCE Dead zones receive their name primarily from the reduction of eukaryotic macrobiota (demersal fish, shrimp, etc.) that are also key coastal fisheries. Excess nutrients contributed from anthropogenic activity such as fertilizer runoff result in algal blooms and therefore ample new carbon for aerobic microbial metabolism. Combined with strong stratification, microbial respiration reduces oxygen in shelf bottom waters to levels unfit for many animals (termed hypoxia). The nGOM shelf remains one of the largest eutrophication-driven hypoxic zones in the world, yet despite its potential as a model study system, the microbial metabolisms underlying and resulting from this phenomenon-many of which occur in bacterioplankton from poorly understood lineages-have received only preliminary study. Our work details the metabolic potential and gene expression activity for uncultivated lineages across several low DO sites in the nGOM, improving our understanding of the active biogeochemical cycling mediated by these "microbial dark matter" taxa during hypoxia.
Abstract.
Author URL.
2016
Learman DR, Henson MW, Thrash JC, Temperton B, Brannock PM, Santos SR, Mahon AR, Halanych KM (2016). Biogeochemical and microbial variation across 5500 km of Antarctic surface sediment implicates organic matter as a driver of benthic community structure.
Frontiers in Microbiology,
7Abstract:
Biogeochemical and microbial variation across 5500 km of Antarctic surface sediment implicates organic matter as a driver of benthic community structure
Western Antarctica, one of the fastest warming locations on Earth, is a unique environment that is underexplored with regards to biodiversity. Although pelagic microbial communities in the Southern Ocean and coastal Antarctic waters have been well studied, there are fewer investigations of benthic communities and most have a focused geographic range. We sampled surface sediment from 24 sites across a 5,500 km region of Western Antarctica (covering the Ross Sea to the Weddell Sea) to examine relationships between microbial communities and sediment geochemistry. Sequencing of the 16S and 18S rRNA genes showed microbial communities in sediments from the Antarctic Peninsula (AP) and Western Antarctica (WA), including the Ross, Amundsen, and Bellingshausen Seas, could be distinguished by correlations with organic matter concentrations and stable isotope fractionation (total organic carbon; TOC, nitrogen, and δ13C). Overall, samples from the AP were higher in nutrient content (TOC, nitrogen, and NH4+) and communities in these samples had higher relative abundances of operational taxonomic units (OTUs) classified as the diatom, Chaetoceros, a marine cercozoan and four OTUs classified as Cytophaga or Flavobacteria. As these OTUs were strongly correlated with TOC, the data suggests the diatoms could be a source of organic matter and the Bacteroidetes and cercozoan are grazers that consume the organic matter. Additionally, samples from WA have lower nutrients and were dominated by Thaumarchaeota, which could be related to their known ability to thrive as lithotrophs. This study documents the largest analysis of benthic microbial communities to date in the Southern Ocean, representing almost half the continental shoreline of Antarctica, and documents trophic interactions and coupling of pelagic and benthic communities. Our results indicate potential modifications in carbon sequestration processes related to change in community composition, identifying a prospective mechanism that links climate change to carbon availability.
Abstract.
Thrash JC, Seitz KW, Baker BJ, Temperton B, Gillies LE, Rabalais NN, Henrissat B, Mason OU (2016). Metabolic roles of uncultivated bacterioplankton lineages in the northern Gulf of Mexico “Dead Zone”.
Abstract:
Metabolic roles of uncultivated bacterioplankton lineages in the northern Gulf of Mexico “Dead Zone”
AbstractMarine regions that have seasonal to long-term low dissolved oxygen (DO) concentrations, sometimes called ‘dead zones,’ are increasing in number and severity around the globe with deleterious effects on ecology and economics. One of the largest of these coastal dead zones occurs on the continental shelf of the northern Gulf of Mexico (nGOM), which results from eutrophication-enhanced bacterioplankton respiration and strong seasonal stratification. Previous research in this dead zone revealed the presence of multiple cosmopolitan bacterioplankton lineages that have eluded cultivation, and thus their metabolic roles in this ecosystem remain unknown. We used a coupled shotgun metagenomic and metatranscriptomic approach to determine the metabolic potential of Marine Group II Euryarchaeota, SAR406, and SAR202. We recovered multiple high-quality, nearly complete genomes from all three groups as well as those belonging to Candidate Phyla usually associated with anoxic environments-Parcubacteria (OD1) and Peregrinibacteria. Two additional groups with putative assignments to ACD39 and PAUC34f supplement the metabolic contributions by uncultivated taxa. Our results indicate active metabolism in all groups, including prevalent aerobic respiration, with concurrent expression of genes for nitrate reduction in SAR406 and SAR202, and dissimilatory nitrite reduction to ammonia and sulfur reduction by SAR406. We also report a variety of active heterotrophic carbon processing mechanisms, including degradation of complex carbohydrate compounds by SAR406, SAR202, ACD39, and PAUC34f. Together, these data help constrain the metabolic contributions from uncultivated groups in the nGOM during periods of low DO and suggest roles for these organisms in the breakdown of complex organic matter.ImportanceDead zones receive their name primarily from the reduction of eukaryotic macrobiota (demersal fish, shrimp, etc.) that are also key coastal fisheries. Excess nutrients contributed from anthropogenic activity such as fertilizer runoff result in algal blooms and therefore ample new carbon for aerobic microbial metabolism. Combined with strong stratification, microbial respiration reduces oxygen in shelf bottom waters to levels unfit for many animals (termed hypoxia). The nGOM shelf remains one of the largest eutrophication-driven hypoxic zones in the world, yet despite its potential as a model study system, the microbial metabolisms underlying and resulting from this phenomenon—many of which occur in bacterioplankton from poorly understood lineages—have received only preliminary study. Our work details the metabolic potential and gene expression activity for uncultivated lineages across several low DO sites in the nGOM, improving our understanding of the active biogeochemical cycling mediated by these “microbial dark matter” taxa during hypoxia.
Abstract.
Sun J, Todd JD, Thrash JC, Qian Y, Qian MC, Temperton B, Guo J, Fowler EK, Aldrich JT, Nicora CD, et al (2016). The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol. Nature Microbiology, 1(8).
Sun J, Todd JD, Thrash JC, Qian Y, Qian MC, Temperton B, Guo J, Fowler EK, Aldrich JT, Nicora CD, et al (2016). The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol. Corrigendum. Nature Microbiology, 1(11).
2014
Airs RL, Temperton B, Sambles C, Farnham G, Skill SC, Llewellyn CA (2014). Chlorophyll f and chlorophyll d are produced in the cyanobacterium Chlorogloeopsis fritschii when cultured under natural light and near-infrared radiation.
FEBS Letters, ---.
Abstract:
Chlorophyll f and chlorophyll d are produced in the cyanobacterium Chlorogloeopsis fritschii when cultured under natural light and near-infrared radiation
Abstract We report production of chlorophyll f and chlorophyll d in the cyanobacterium Chlorogloeopsis fritschii cultured under near-infrared and natural light conditions. C. fritschii produced chlorophyll f and chlorophyll d when cultured under natural light to a high culture density in a 20 L bubble column photobioreactor. In the laboratory, the ratio of chlorophyll f to chlorophyll a changed from 1:15 under near-infrared, to an undetectable level of chlorophyll f under artificial white light. The results provide support that chlorophylls f and d are both red-light inducible chlorophylls in C. fritschii.
Abstract.
Carini P, Campbell EO, Morré J, Sañudo-Wilhelmy SA, Cameron Thrash J, Bennett SE, Temperton B, Begley T, Giovannoni SJ (2014). Discovery of a SAR11 growth requirement for thiamin’s pyrimidine precursor and its distribution in the Sargasso Sea.
The ISME Journal,
8(8), 1727-1738.
Abstract:
Discovery of a SAR11 growth requirement for thiamin’s pyrimidine precursor and its distribution in the Sargasso Sea
Abstract
. Vitamin traffic, the production of organic growth factors by some microbial community members and their use by other taxa, is being scrutinized as a potential explanation for the variation and highly connected behavior observed in ocean plankton by community network analysis. Thiamin (vitamin B1), a cofactor in many essential biochemical reactions that modify carbon–carbon bonds of organic compounds, is distributed in complex patterns at subpicomolar concentrations in the marine surface layer (0–300 m). Sequenced genomes from organisms belonging to the abundant and ubiquitous SAR11 clade of marine chemoheterotrophic bacteria contain genes coding for a complete thiamin biosynthetic pathway, except for thiC, encoding the 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) synthase, which is required for de novo synthesis of thiamin’s pyrimidine moiety. Here we demonstrate that the SAR11 isolate ‘Candidatus Pelagibacter ubique’, strain HTCC1062, is auxotrophic for the thiamin precursor HMP, and cannot use exogenous thiamin for growth. In culture, strain HTCC1062 required 0.7 zeptomoles per cell (ca. 400 HMP molecules per cell). Measurements of dissolved HMP in the Sargasso Sea surface layer showed that HMP ranged from undetectable (detection limit: 2.4 pm) to 35.7 pm, with maximum concentrations coincident with the deep chlorophyll maximum. In culture, some marine cyanobacteria, microalgae and bacteria exuded HMP, and in the Western Sargasso Sea, HMP profiles changed between the morning and evening, suggesting a dynamic biological flux from producers to consumers.
Abstract.
Giovannoni SJ, Cameron Thrash J, Temperton B (2014). Implications of streamlining theory for microbial ecology.
The ISME Journal,
8(8), 1553-1565.
Abstract:
Implications of streamlining theory for microbial ecology
Abstract
. Whether a small cell, a small genome or a minimal set of chemical reactions with self-replicating properties, simplicity is beguiling. As Leonardo da Vinci reportedly said, ‘simplicity is the ultimate sophistication’. Two diverging views of simplicity have emerged in accounts of symbiotic and commensal bacteria and cosmopolitan free-living bacteria with small genomes. The small genomes of obligate insect endosymbionts have been attributed to genetic drift caused by small effective population sizes (Ne). In contrast, streamlining theory attributes small cells and genomes to selection for efficient use of nutrients in populations where Ne is large and nutrients limit growth. Regardless of the cause of genome reduction, lost coding potential eventually dictates loss of function. Consequences of reductive evolution in streamlined organisms include atypical patterns of prototrophy and the absence of common regulatory systems, which have been linked to difficulty in culturing these cells. Recent evidence from metagenomics suggests that streamlining is commonplace, may broadly explain the phenomenon of the uncultured microbial majority, and might also explain the highly interdependent (connected) behavior of many microbial ecosystems. Streamlining theory is belied by the observation that many successful bacteria are large cells with complex genomes. To fully appreciate streamlining, we must look to the life histories and adaptive strategies of cells, which impose minimum requirements for complexity that vary with niche.
Abstract.
Thrash JC, Temperton B, Swan BK, Landry ZC, Woyke T, DeLong EF, Stepanauskas R, Giovannoni SJ (2014). Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype.
The ISME Journal,
8(7), 1440-1451.
Abstract:
Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype
Abstract
. Bacterioplankton of the SAR11 clade are the most abundant microorganisms in marine systems, usually representing 25% or more of the total bacterial cells in seawater worldwide. SAR11 is divided into subclades with distinct spatiotemporal distributions (ecotypes), some of which appear to be specific to deep water. Here we examine the genomic basis for deep ocean distribution of one SAR11 bathytype (depth-specific ecotype), subclade Ic. Four single-cell Ic genomes, with estimated completeness of 55%–86%, were isolated from 770 m at station ALOHA and compared with eight SAR11 surface genomes and metagenomic datasets. Subclade Ic genomes dominated metagenomic fragment recruitment below the euphotic zone. They had similar COG distributions, high local synteny and shared a large number (69%) of orthologous clusters with SAR11 surface genomes, yet were distinct at the 16S rRNA gene and amino-acid level, and formed a separate, monophyletic group in phylogenetic trees. Subclade Ic genomes were enriched in genes associated with membrane/cell wall/envelope biosynthesis and showed evidence of unique phage defenses. The majority of subclade Ic-specfic genes were hypothetical, and some were highly abundant in deep ocean metagenomic data, potentially masking mechanisms for niche differentiation. However, the evidence suggests these organisms have a similar metabolism to their surface counterparts, and that subclade Ic adaptations to the deep ocean do not involve large variations in gene content, but rather more subtle differences previously observed deep ocean genomic data, like preferential amino-acid substitutions, larger coding regions among SAR11 clade orthologs, larger intergenic regions and larger estimated average genome size.
Abstract.
2013
Zhao Y, Temperton B, Thrash JC, Schwalbach MS, Vergin KL, Landry ZC, Ellisman M, Deerinck T, Sullivan MB, Giovannoni SJ, et al (2013). Abundant SAR11 viruses in the ocean. Nature, 494(7437), 357-360.
Giovannoni S, Temperton B, Zhao Y (2013). Giovannoni et al. reply. Nature, 499(7459), E4-E5.
Vergin KL, Beszteri B, Monier A, Thrash JC, Temperton B, Treusch AH, Kilpert F, Worden AZ, Giovannoni SJ (2013). High-resolution SAR11 ecotype dynamics at the Bermuda Atlantic Time-series Study site by phylogenetic placement of pyrosequences.
The ISME Journal,
7(7), 1322-1332.
Abstract:
High-resolution SAR11 ecotype dynamics at the Bermuda Atlantic Time-series Study site by phylogenetic placement of pyrosequences
Abstract
. Advances in next-generation sequencing technologies are providing longer nucleotide sequence reads that contain more information about phylogenetic relationships. We sought to use this information to understand the evolution and ecology of bacterioplankton at our long-term study site in the Western Sargasso Sea. A bioinformatics pipeline called PhyloAssigner was developed to align pyrosequencing reads to a reference multiple sequence alignment of 16S ribosomal RNA (rRNA) genes and assign them phylogenetic positions in a reference tree using a maximum likelihood algorithm. Here, we used this pipeline to investigate the ecologically important SAR11 clade of Alphaproteobacteria. A combined set of 2.7 million pyrosequencing reads from the 16S rRNA V1–V2 regions, representing 9 years at the Bermuda Atlantic Time-series Study (BATS) site, was quality checked and parsed into a comprehensive bacterial tree, yielding 929 036 Alphaproteobacteria reads. Phylogenetic structure within the SAR11 clade was linked to seasonally recurring spatiotemporal patterns. This analysis resolved four new SAR11 ecotypes in addition to five others that had been described previously at BATS. The data support a conclusion reached previously that the SAR11 clade diversified by subdivision of niche space in the ocean water column, but the new data reveal a more complex pattern in which deep branches of the clade diversified repeatedly across depth strata and seasonal regimes. The new data also revealed the presence of an unrecognized clade of Alphaproteobacteria, here named SMA-1 (Sargasso Mesopelagic Alphaproteobacteria, group 1), in the upper mesopelagic zone. The high-resolution phylogenetic analyses performed herein highlight significant, previously unknown, patterns of evolutionary diversification, within perhaps the most widely distributed heterotrophic marine bacterial clade, and strongly links to ecosystem regimes.
Abstract.
2012
Temperton B, Giovannoni SJ (2012). Metagenomics: microbial diversity through a scratched lens. Current Opinion in Microbiology, 15(5), 605-612.
2011
Gilbert JA, Steele JA, Caporaso JG, Steinbrück L, Reeder J, Temperton B, Huse S, McHardy AC, Knight R, Joint I, et al (2011). Defining seasonal marine microbial community dynamics.
The ISME Journal,
6(2), 298-308.
Abstract:
Defining seasonal marine microbial community dynamics
Abstract
. Here we describe, the longest microbial time-series analyzed to date using high-resolution 16S rRNA tag pyrosequencing of samples taken monthly over 6 years at a temperate marine coastal site off Plymouth, UK. Data treatment effected the estimation of community richness over a 6-year period, whereby 8794 operational taxonomic units (OTUs) were identified using single-linkage preclustering and 21 130 OTUs were identified by denoising the data. The Alphaproteobacteria were the most abundant Class, and the most frequently recorded OTUs were members of the Rickettsiales (SAR 11) and Rhodobacteriales. This near-surface ocean bacterial community showed strong repeatable seasonal patterns, which were defined by winter peaks in diversity across all years. Environmental variables explained far more variation in seasonally predictable bacteria than did data on protists or metazoan biomass. Change in day length alone explains &gt;65% of the variance in community diversity. The results suggested that seasonal changes in environmental variables are more important than trophic interactions. Interestingly, microbial association network analysis showed that correlations in abundance were stronger within bacterial taxa rather than between bacteria and eukaryotes, or between bacteria and environmental variables.
Abstract.
Gilbert JA, Laverock B, Temperton B, Thomas S, Muhling M, Hughes M (2011). Metagenomics.
,
733, 173-183.
Abstract:
Metagenomics
Metagenomics has evolved over the last 3 decades from the analysis of single genes and their apparent diversity in an ecosystem to the provision of complex genetic information relating to whole ecosystems. Metagenomics is a vast subject area in terms of methodology, which encompasses a suite of molecular technologies employed to investigate genomic information from all members of a microbial community. However, the relatively recent developments in high-throughput sequencing platforms have meant that metagenomic can be performed simply by extracting DNA and sequencing it. Here, we outline explicit methodologies for the extraction of metagenomic DNA from marine and sediments/soil environmental samples, the subsequent production and sequencing of large-insert metagenomic libraries, and also shotgun pyrosequencing considerations. We also provide relevant advice on bioinformatic analyses of the complex metagenomic datasets. We hope that the information provided here will be useful to establish the techniques in most reasonably equipped molecular biology laboratories.
Abstract.
Temperton B, Gilbert JA, Quinn JP, McGrath JW (2011). Novel Analysis of Oceanic Surface Water Metagenomes Suggests Importance of Polyphosphate Metabolism in Oligotrophic Environments. PLoS ONE, 6(1), e16499-e16499.
Temperton B, Thomas S, Tait K, Parry H, Emery M, Allen M, Quinn J, Macgrath J, Gilbert J (2011). Permanent draft genome sequence of Vibrio tubiashii strain NCIMB 1337 (ATCC19106).
Standards in Genomic Sciences,
4(2), 183-190.
Abstract:
Permanent draft genome sequence of Vibrio tubiashii strain NCIMB 1337 (ATCC19106)
Vibrio tubiashii NCIMB 1337 is a major and increasingly prevalent pathogen of bivalve mol-lusks, and shares a close phylogenetic relationship with both V. orientalis and V. coralliilyti-cus. It is a Gram-negative, curved rod-shaped bacterium, originally isolated from a moribund juvenile oyster, and is both oxidase and catalase positive. It is capable of growth under both aerobic and anaerobic conditions. Here we describe the features of this organism, together with the draft genome and annotation. The genome is 5,353,266 bp long, consisting of two chromosomes, and contains 4,864 protein-coding and 86 RNA genes.
Abstract.
2010
Beszteri B, Temperton B, Frickenhaus S, Giovannoni SJ (2010). Average genome size: a potential source of bias in comparative metagenomics.
The ISME Journal,
4(8), 1075-1077.
Abstract:
Average genome size: a potential source of bias in comparative metagenomics
Abstract
. In gene-centric comparative metagenomics, differences in observed relative gene abundances among samples are often assumed to reflect the biological importance of individual genes in different habitats. Statistical tests and data mining for genes that represent habitat-specific adaptations are frequently based on this measure. We demonstrate that this measure is biased by the average genome size of the communities sampled. Average genome sizes can be estimated from the metagenomic data themselves, and taken into account in comparative analyses. We suggest that this would enable ecologically more meaningful comparisons, especially when the average genome sizes of compared communities differ substantially. We illustrate the influence of average genome-size differences on comparative analyses, with an example to highlight the need for further exploration of this bias.
Abstract.
Gilbert J, Somerfield P, Temperton B, Huse S, Joint I, Field D (2010). Day-length is central to maintaining consistent seasonal diversity in marine bacterioplankton. , 1-1.
Craft JA, Gilbert JA, Temperton B, Dempsey KE, Ashelford K, Tiwari B, Hutchinson TH, Chipman JK (2010). Pyrosequencing of Mytilus galloprovincialis cDNAs: Tissue-Specific Expression Patterns. PLoS ONE, 5(1), e8875-e8875.
Gilbert JA, Field D, Swift P, Thomas S, Cummings D, Temperton B, Weynberg K, Huse S, Hughes M, Joint I, et al (2010). The Taxonomic and Functional Diversity of Microbes at a Temperate Coastal Site: a ‘Multi-Omic’ Study of Seasonal and Diel Temporal Variation. PLoS ONE, 5(11), e15545-e15545.
2009
Temperton B, Field D, Oliver A, Tiwari B, Mühling M, Joint I, Gilbert JA (2009). Bias in assessments of marine microbial biodiversity in fosmid libraries as evaluated by pyrosequencing.
The ISME Journal,
3(7), 792-796.
Abstract:
Bias in assessments of marine microbial biodiversity in fosmid libraries as evaluated by pyrosequencing
Abstract
. On the basis of 16S rRNA gene sequencing, the SAR11 clade of marine bacteria has an almost universal distribution, being detected as abundant sequences in all marine provinces. Yet, SAR11 sequences are rarely detected in fosmid libraries, suggesting that the widespread abundance may be an artefact of PCR cloning and that SAR11 has a relatively low abundance. Here the relative abundance of SAR11 is explored in both a fosmid library and a metagenomic sequence data set from the same biological community taken from fjord surface water from Bergen, Norway. Pyrosequenced data and 16S clone data confirmed an 11–15% relative abundance of SAR11 within the community. In contrast, not a single SAR11 fosmid was identified in a pooled shotgun sequence data set of 100 fosmid clones. This underrepresentation was evidenced by comparative abundances of SAR11 sequences assessed by taxonomic annotation and fragment recruitment. Analysis revealed a similar underrepresentation of low-GC Flavobacteriaceae. We speculate that a contributing factor towards the fosmid bias may be DNA fragmentation during preparation because of the low GC content of SAR11 sequences and other underrepresented taxa. This study suggests that, although fosmid libraries can be extremely useful, caution must be taken when directly inferring community composition from metagenomic fosmid libraries.
Abstract.
Temperton B, Oliver A, Field D, Tiwari B, Muhling M, Joint I, Gilbert J (2009). Bias in culture-independent assessments of microbial biodiversity in the global ocean. , 1-1.
Thomas S, Burdett H, Temperton B, Wick R, Snelling D, McGrath JW, Quinn JP, Munn C, Gilbert JA (2009). Evidence for phosphonate usage in the coral holobiont.
The ISME Journal,
4(3), 459-461.
Abstract:
Evidence for phosphonate usage in the coral holobiont
Abstract
. Phosphonates are characterized by a stable carbon–phosphorus bond and commonly occur as lipid conjugates in invertebrate cell membranes. Phosphonoacetate hydrolase encoded by the phnA gene, catalyses the cleavage of phosphonoacetate to acetate and phosphate. In this study, we demonstrate the unusually high phnA diversity in coral-associated bacteria. The holobiont of eight coral species tested positive when screened for phnA using degenerate primers. In two soft coral species, Sinularia and Discosoma, sequencing of the phnA gene showed 13 distinct groups on the basis of 90% sequence identity across 100% of the sequence. A total of 16 bacterial taxa capable of using phosphonoacetate as the sole carbon and phosphorus source were isolated; 8 of which had a phnA+ genotype. This study enhances our understanding of the wide taxonomic and environmental distribution of phnA, and highlights the importance of phosphonates in marine ecosystems.
Abstract.