Key publications
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".
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.
Abstract.
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.
Publications by category
Journal articles
Giovannoni SJ, Halsey KH, Saw J, Muslin O, Suffridge CP, Sun J, Lee C-P, Moore ER, Temperton B, Noell SE, et al (In Press). 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.
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.
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".
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.
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.
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.
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.
Full text.
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
Giovannoni SJ, Halsey KH, Saw J, Muslin O, Suffridge CP, Sun J, Lee C-P, Moore ER, Temperton B, Noell SE, et al (In Press). 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.
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.
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".
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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2019
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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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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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.
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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). 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.
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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.
