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Dr Ben Temperton

Dr Ben Temperton

Lecturer in Bioinformatics

 5434

 01392 725434

 Geoffrey Pope 323

 

Geoffrey Pope Building, University of Exeter , Stocker Road, Exeter, EX4 4QD, UK

Overview

I am a microbial ecologist, specializing in bioinformatic analyses of ‘big data’ (metagenomics, metatranscriptomics, metaproteomics) to better understand how interactions within microbial communities enable functional diversity and efficiency that is greater than the sum of its parts. As a former professional software developer, I am interested in combining high-performance computing with multivariate statistical analyses to identify putative drivers of function and diversity in complex communities. Importantly, these hypotheses are then tested in the laboratory using model systems. During my postdoc with Prof. Steve Giovannoni at Oregon State University, I was involved in the discovery of (probably) the most abundant virus on Earth, and my current research continues to explore the fascinating biology of this system.

Broad research specialisms:

Marine microbial ecology, bioinformatics, host-phage interaction, community dynamics, single-cell genomics.

Qualifications

PhD. Microbiology, Queens University Belfast, 2009-2011
MSc Information Technology (Software Engineering), University of Nottingham, 1998-1999
BSc Chemistry (2:i), University Of Birmingham, 1995-1998

Research group links

Research

Research interests

My research focuses on the systems biology of marine microbial communities, particularly members like the ubiquitous SAR11 clade which take advantage of communal resources to streamline their genomes to maximize efficiency in oligotrophic environments. This streamlining has an impact on ecotypic specialisation, viral infectivity and defence and community connectedness. Ultimately, co-evolution of streamlined organisms and their communities (particularly their associated viruses) underpins the efficacy of biogeochemical cycling. My research combines bioinformatic analysis of meta 'omics and single-cell genomics with experimental validation of emergent hypotheses in cultured model organisms. I am a strong proponent of open science and founder of the

Bioinformatics Testing Consortium

to improve the quality of bioinformatics via codebase peer-review.

Research projects

Development of sequencing technology for field-based long-read sequencing of marine viruses (NERC)

Microbial Mechanisms of marine carbon flux in the Sargasso Sea (BIOS-SCOPE)

Development of an algal crop protection program through vaccination by novel viruses. (Phyconet)

Using flow cytometry and genomics to characterise and optimise microalgal-bacterial consortia cultivated on Wastewater to produce biomass for Biofuel (BBSRC)

Current Grants:

  • 2018: A War of Tiny Giants - Do viruses impact Pelagibacterales genotype dynamics in the Western English Channel (£798k, NERC)
  • 2016: Developing methods for long-read marine viral metagenomics (£39k, NERC)
  • 2016: Developing Nanopore MinION as a platform for long read viral metagenomics and in-situ screening of viral threats (£10k, Royal Society)
  • 2015: BIOS-SCOPE Fellowship to investigate carbon biogeochemistry in the Sargasso Sea (£90k, Simons Foundation International)
  • 2015: Sea-DNA Development and application of eDNA tools to assess the structure and function of coastal sea ecosystems (£369k, NERC)
  • 2015: Development of an algal crop protection program through vaccination by novel viruses (£70k, Phyconet, BBSRC)
  • 2014: Environmental Single Cell Genomics Instrumentation
    (£495,954, NERC Strategic Environmental Science Capital Call)
  • 2014: AVaRICE: Algal Valorisation & Remediation of metal Ion Contaminated Effluents
    (£70k, GW4+ Funding Panel)
  • 2015: UK Centre of Excellence for Environmental Single Cell Genomics (eSCG)
    (£500,000, Wolfson Foundation

Publications

Key publications | Publications by category | Publications by year

Key publications


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.  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, 7 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.
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.

Publications by category


Journal articles

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.  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, 7 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.
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.
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.  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

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.  Author URL.  Full text.

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, 7 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.

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.
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.

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.
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.  Full text.

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.

Ben_Temperton Details from cache as at 2018-12-10 04:27:52

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External Engagment and Impact

Committee/panel activities

Member of the International Organizing Committee for the Aquatic Virus Workshop (AVG)


Editorial responsibilities

Editor for the journal Biomolecular Detection and Quantification


Invited lectures

2014: NERC workshop on ‘Omics Miniaturisation, Oxford

2012: Panel discussion on Openness of Standards and Standards of Openness at the 13th Annual Bioinformatics Open Source Conference (BOSC), Long Beach, CA.

2012: Metabolic reconstruction in marine bacterial communities: from parts list to pathways. Bioinformatics Special Interest Group, Gordon and Betty More Foundation Investigator Symposium.

Teaching

I teach both bioinformatics and marine microbial ecology to second and third year students. I combine lecture material with online courses via DataCamp.

 

BIO1333 - Fundamental Principles for Bioscientists

BIO2092 - Genomics and Introductory Bioinformatics

BIO3092 - Bioinformatics

BIO3097 - Living in a Microbial World

Supervision / Group

Postgraduate researchers

  • Holger Buchholz
  • Anthony Messer Anthony's MRes is focused on evaluating currently available metagenomic bioinformatic pipelines against a known microbial community to determine biases in taxonomic and functional annotation. He is based at DSTL.
  • Joanna Warwick-Dugdale Jo's PhD is aimed at investigating the role of the benthic-pelagic boundary layer (sometimes called the 'fluff' layer) in the remineralization of dissolved organic carbon from phytoplankton blooms by microbial communities in the Western English Channel

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