Publications by category
Journal articles
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 Full text.
Warwick-Dugdale J, Buchholz H, Allen M, Temperton B (In Press). Host-hijacking and Planktonic Piracy: How Phages Command the Microbial High Seas.
Virology Full text.
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 Full text.
Warwick-Dugdale J, Solonenko N, Moore K, Chittick L, Gregory AC, Allen MJ, Sullivan MB, Temperton B (In Press). 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.
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.
Full text.
Thrash JC, Seitz KW, Baker BJ, Temperton B, Gillies LE, Rabalais NN, Henrissat B, Mason OU (In Press). 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.
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.
Manley R, Temperton B, Boots M, Wilfert L (2019). Contrasting impacts of a novel specialist vector on multihost viral pathogen epidemiology in wild and managed bees.
Mol EcolAbstract:
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.
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.
© 2018 the Authors 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.
Full text.
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.
Full text.
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.
Full text.
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"
© 2018 Thrash et al. 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.
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.
Full text.
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.
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Sun J, Todd JD, Thrash JC, Qian Y, Qian MC, Temperton B, Guo J, Fowler EK, Aldrich JT, Nicora CD, et al (2016). Corrigendum: the abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol.
Nat Microbiol,
1(11).
Author URL.
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).
Full text.
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.
Full text.
Giovannoni SJ, Cameron Thrash J, Temperton B (2014). Implications of streamlining theory for microbial ecology.
The ISME Journal,
8(8), 1553-1565.
Full text.
Cameron Thrash J, 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.
Full text.
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, Cameron Thrash J, 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.
Temperton B, Giovannoni SJ (2012). Metagenomics: microbial diversity through a scratched lens. Current Opinion in Microbiology, 15(5), 605-612.
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.
Gilbert JA, Laverock B, Temperton B, Thomas S, Muhling M, Hughes M (2011). Metagenomics.
Methods in molecular biology (Clifton, N.J.),
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.
Full text.
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.
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.
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.
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.
Publications by year
In Press
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 Full text.
Warwick-Dugdale J, Buchholz H, Allen M, Temperton B (In Press). Host-hijacking and Planktonic Piracy: How Phages Command the Microbial High Seas.
Virology Full text.
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 Full text.
Warwick-Dugdale J, Solonenko N, Moore K, Chittick L, Gregory AC, Allen MJ, Sullivan MB, Temperton B (In Press). 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.
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.
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Thrash JC, Seitz KW, Baker BJ, Temperton B, Gillies LE, Rabalais NN, Henrissat B, Mason OU (In Press). 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.
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.
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Author URL.
Manley R, Temperton B, Boots M, Wilfert L (2019). Contrasting impacts of a novel specialist vector on multihost viral pathogen epidemiology in wild and managed bees.
Mol EcolAbstract:
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.
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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.
© 2018 the Authors 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.
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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.
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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.
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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.
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2018
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"
© 2018 Thrash et al. 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.
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Author URL.
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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.
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Sun J, Todd JD, Thrash JC, Qian Y, Qian MC, Temperton B, Guo J, Fowler EK, Aldrich JT, Nicora CD, et al (2016). Corrigendum: the abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol.
Nat Microbiol,
1(11).
Author URL.
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).
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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.
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Giovannoni SJ, Cameron Thrash J, Temperton B (2014). Implications of streamlining theory for microbial ecology.
The ISME Journal,
8(8), 1553-1565.
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Cameron Thrash J, 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.
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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, Cameron Thrash J, 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.
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.
Gilbert JA, Laverock B, Temperton B, Thomas S, Muhling M, Hughes M (2011). Metagenomics.
Methods in molecular biology (Clifton, N.J.),
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.
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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.
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.
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.
