Faculty & Staff

  • Image of Karthik Anantharaman

    Karthik Anantharaman

    Assistant Professor of Bacteriology

    4550 Microbial Sciences Building
    Office: (608) 265-4537
    Lab: (608) 265-4307
    karthik@bact.wisc.edu

Start and Promotion Dates

  • Assistant Professor: 2018

Education

B.Tech., Civil Engineering, National Institute of Technology, Karnataka, India. 2007
M.S.E., Civil and Environmental Engineering, University of Michigan. 2008
Ph.D., Earth and Environmental Sciences, University of Michigan. 2014
Postdoctoral Research: University of California-Berkeley

Areas of Study

Microbial sulfur metabolism
Microbial community interactions
Biogeochemistry
Coevolution of viruses and their hosts

Research Overview

Microbial metabolism has the potential to impact the evolutionary ecology of a system across various spatial and temporal scales ranging from the scope of a single cell, ecosystem, to the earth as a whole. Understanding how microbial communities function is critical to unraveling how they underpin human health, and predicting global ecosystem dynamics, especially in the context of environmental perturbations like anthropogenic global change. The broad goal of our research is to unravel how (i) fine-scale genomic diversity impacts microbial community structure and function across various environments, (ii) individual microbes function in a community context, and (iii) microbes impact biogeochemical cycling at various spatial and temporal scales.

Evolutionary ecology of microbial sulfur metabolism. Microorganisms control and modulate transformations associated with the element sulfur in natural and engineered systems. Sulfur plays a central role in biochemistry, impacts carbon and nitrogen turnover in various environments, and is critical to maintaining the health of oceans in the future. We use biotic sulfur transformations as a model to study the evolution and ecology of microbial energy metabolism. These processes are abundant across both aerobic (sulfur oxidation) and anaerobic environments (sulfate reduction). We utilize a combination of fieldwork, laboratory experiments, and multi-omics based approaches to investigate the microbiology of sulfureous environments such as deep-sea hydrothermal vents, freshwater ecosystems, and the human gut.

Microbial community interactions. Recent advances in DNA sequencing and bioinformatics approaches have enabled the recovery of thousands of strain-resolved microbial genomes from a single ecosystem thereby providing a window into fine scale microbial interactions and metabolic networks in complex communities. Broadly, we are interested in studying three types of interactions in microbial communities using sulfur transformations as a model – virus-microbe, microbe-microbe, and microbial “metabolic handoffs”. We focus on virus-microbe interactions involving “auxiliary metabolic genes”, which are host-derived genes utilized by viruses in selfishly altering microbial metabolism. We also study microbe-microbe interactions, and “metabolic handoffs” primarily focused on dissimilatory sulfur metabolism. We seek to quantify and predict the impact of such interactions on biogeochemical cycling at cellular, ecosystem, and global scales.

Lab Personnel

Picture of Adams
Alyssa Adams
Postdoc
amadams4@wisc.edu
Picture of Bachand
Samantha Bachand
Research Intern
sbachand@wisc.edu
Picture of Breister
Adam Breister
Research Technician
breister2@wisc.edu
Picture of Cowley
Elise Cowley
Grad Student
ecowley@wisc.edu
Picture of Dieppa
Etan Dieppa
Grad Student
edieppa@wisc.edu
Picture of Klier
Katherine Klier
Grad Student
kklier@wisc.edu
Picture of Langwig
Marguerite Langwig
Grad Student
langwig@wisc.edu
Picture of Martin
Cody Martin
Grad Student
ccmartin6@wisc.edu
Picture of Tran
Patricia Tran
Grad Student
ptran5@wisc.edu
Picture of Zhou
Chao (Zhichao) Zhou
Postdoc
zzhou388@wisc.edu

Research Papers

  • Chelluboina B, Kieft K, Breister A, Anantharaman K, Vemuganti R (2022) Gut virome dysbiosis following focal cerebral ischemia in mice. Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism 42((9)):1597-1602 PMC9441728 · Pubmed · DOI

    No abstract available.

  • Kieft K, Adams A, Salamzade R, Kalan L, Anantharaman K (2022) vRhyme enables binning of viral genomes from metagenomes. Nucleic acids research 50((14)):e83 PMC9371927 · Pubmed · DOI

    No abstract available.

  • Wolf PG, Cowley ES, Breister A, Matatov S, Lucio L, Polak P, Ridlon JM, Gaskins HR, Anantharaman K (2022) Diversity and distribution of sulfur metabolic genes in the human gut microbiome and their association with colorectal cancer. Microbiome 10((1)):64 PMC9016944 · Pubmed · DOI

    No abstract available.

  • Kieft K, Anantharaman K (2022) Deciphering Active Prophages from Metagenomes. mSystems 7((2)):e0008422 PMC9040807 · Pubmed · DOI

    No abstract available.

  • Zhou Z, Tran PQ, Breister AM, Liu Y, Kieft K, Cowley ES, Karaoz U, Anantharaman K (2022) METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks. Microbiome 10((1)):33 PMC8851854 · Pubmed · DOI

    No abstract available.

  • Kieft K, Anantharaman K (2022) Virus genomics: what is being overlooked? Current opinion in virology 53:101200 · Pubmed · DOI

    No abstract available.

  • Feng J, Qian Y, Zhou Z, Ertmer S, Vivas EI, Lan F, Hamilton JJ, Rey FE, Anantharaman K, Venturelli OS (2022) Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions. Cell host & microbe 30((2)):200-215.e12 PMC9060796 · Pubmed · DOI

    No abstract available.

  • Xie BB, Li M, Anantharaman K, Ravin NV (2021) Editorial: The Uncultured Microorganisms: Novel Technologies and Applications. Frontiers in microbiology 12:756287 PMC8652222 · Pubmed · DOI

    No abstract available.

  • Tran PQ, Anantharaman K (2021) Biogeochemistry Goes Viral: towards a Multifaceted Approach To Study Viruses and Biogeochemical Cycling. mSystems 6((5)):e0113821 PMC8510517 · Pubmed · DOI

    No abstract available.

  • Kieft K, Breister AM, Huss P, Linz AM, Zanetakos E, Zhou Z, Rahlff J, Esser SP, Probst AJ, Raman S, Roux S, Anantharaman K (2021) Virus-associated organosulfur metabolism in human and environmental systems. Cell reports 36((5)):109471 · Pubmed · DOI

    No abstract available.

  • Kieft K, Zhou Z, Anderson RE, Buchan A, Campbell BJ, Hallam SJ, Hess M, Sullivan MB, Walsh DA, Roux S, Anantharaman K (2021) Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages. Nature communications 12((1)):3503 PMC8190135 · Pubmed · DOI

    No abstract available.

  • Mangalea MR, Paez-Espino D, Kieft K, Chatterjee A, Chriswell ME, Seifert JA, Feser ML, Demoruelle MK, Sakatos A, Anantharaman K, Deane KD, Kuhn KA, Holers VM, Duerkop BA (2021) Individuals at risk for rheumatoid arthritis harbor differential intestinal bacteriophage communities with distinct metabolic potential. Cell host & microbe 29((5)):726-739.e5 PMC8186507 · Pubmed · DOI

    No abstract available.

  • Doden HL, Wolf PG, Gaskins HR, Anantharaman K, Alves JMP, Ridlon JM (2021) Completion of the gut microbial epi-bile acid pathway. Gut microbes 13((1)):1-20 PMC8096331 · Pubmed · DOI

    No abstract available.

  • Tran PQ, Bachand SC, McIntyre PB, Kraemer BM, Vadeboncoeur Y, Kimirei IA, Tamatamah R, McMahon KD, Anantharaman K (2021) Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika. The ISME journal 15((7)):1971-1986 PMC8245535 · Pubmed · DOI

    No abstract available.

  • Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P, Kämpfer P, Konstantinidis KT, Lane CE, Papke RT, Parks DH, Rossello-Mora R, Stott MB, Sutcliffe IC, Thrash JC, Venter SN, Whitman WB, Acinas SG, Amann RI, Anantharaman K, Armengaud J, Baker BJ, Barco RA, Bode HB, Boyd ES, Brady CL, Carini P, Chain PSG, Colman DR, DeAngelis KM, de Los Rios MA, Estrada-de Los Santos P, Dunlap CA, Eisen JA, Emerson D, Ettema TJG, Eveillard D, Girguis PR, Hentschel U, Hollibaugh JT, Hug LA, Inskeep WP, Ivanova EP, Klenk HP, Li WJ, Lloyd KG, Löffler FE, Makhalanyane TP, Moser DP, Nunoura T, Palmer M, Parro V, Pedrós-Alió C, Probst AJ, Smits THM, Steen AD, Steenkamp ET, Spang A, Stewart FJ, Tiedje JM, Vandamme P, Wagner M, Wang FP, Yarza P, Hedlund BP, Reysenbach AL (2020) Author Correction: Roadmap for naming uncultivated Archaea and Bacteria. Nature microbiology 6((1)):136 PMC7752755 · Pubmed · DOI

    No abstract available.

  • Zhou Z, Liu Y, Pan J, Cron BR, Toner BM, Anantharaman K, Breier JA, Dick GJ, Li M (2020) Gammaproteobacteria mediating utilization of methyl-, sulfur- and petroleum organic compounds in deep ocean hydrothermal plumes. The ISME journal 14((12)):3136-3148 PMC7784996 · Pubmed · DOI

    No abstract available.

  • McDaniel EA, Peterson BD, Stevens SLR, Tran PQ, Anantharaman K, McMahon KD (2020) Expanded Phylogenetic Diversity and Metabolic Flexibility of Mercury-Methylating Microorganisms. mSystems 5((4)): PMC7438021 · Pubmed · DOI

    No abstract available.

  • Kieft K, Zhou Z, Anantharaman K (2020) VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences. Microbiome 8((1)):90 PMC7288430 · Pubmed · DOI

    No abstract available.

  • Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P, Kämpfer P, Konstantinidis KT, Lane CE, Papke RT, Parks DH, Rossello-Mora R, Stott MB, Sutcliffe IC, Thrash JC, Venter SN, Whitman WB, Acinas SG, Amann RI, Anantharaman K, Armengaud J, Baker BJ, Barco RA, Bode HB, Boyd ES, Brady CL, Carini P, Chain PSG, Colman DR, DeAngelis KM, de Los Rios MA, Estrada-de Los Santos P, Dunlap CA, Eisen JA, Emerson D, Ettema TJG, Eveillard D, Girguis PR, Hentschel U, Hollibaugh JT, Hug LA, Inskeep WP, Ivanova EP, Klenk HP, Li WJ, Lloyd KG, Löffler FE, Makhalanyane TP, Moser DP, Nunoura T, Palmer M, Parro V, Pedrós-Alió C, Probst AJ, Smits THM, Steen AD, Steenkamp ET, Spang A, Stewart FJ, Tiedje JM, Vandamme P, Wagner M, Wang FP, Yarza P, Hedlund BP, Reysenbach AL (2020) Roadmap for naming uncultivated Archaea and Bacteria. Nature microbiology 5((8)):987-994 PMC7381421 · Pubmed · DOI

    No abstract available.

  • Zhou Z, Tran PQ, Kieft K, Anantharaman K (2020) Genome diversification in globally distributed novel marine Proteobacteria is linked to environmental adaptation. The ISME journal 14((8)):2060-2077 PMC7367891 · Pubmed · DOI

    No abstract available.

  • Chen LX, Anantharaman K, Shaiber A, Eren AM, Banfield JF (2020) Accurate and complete genomes from metagenomes. Genome research 30((3)):315-333 PMC7111523 · Pubmed · DOI

    No abstract available.

  • Al-Shayeb B, Sachdeva R, Chen LX, Ward F, Munk P, Devoto A, Castelle CJ, Olm MR, Bouma-Gregson K, Amano Y, He C, Méheust R, Brooks B, Thomas A, Lavy A, Matheus-Carnevali P, Sun C, Goltsman DSA, Borton MA, Sharrar A, Jaffe AL, Nelson TC, Kantor R, Keren R, Lane KR, Farag IF, Lei S, Finstad K, Amundson R, Anantharaman K, Zhou J, Probst AJ, Power ME, Tringe SG, Li WJ, Wrighton K, Harrison S, Morowitz M, Relman DA, Doudna JA, Lehours AC, Warren L, Cate JHD, Santini JM, Banfield JF (2020) Clades of huge phages from across Earth's ecosystems. Nature 578((7795)):425-431 PMC7162821 · Pubmed · DOI

    No abstract available.

  • Diamond S, Andeer PF, Li Z, Crits-Christoph A, Burstein D, Anantharaman K, Lane KR, Thomas BC, Pan C, Northen TR, Banfield JF (2019) Mediterranean grassland soil C-N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms. Nature microbiology 4((8)):1356-1367 PMC6784897 · Pubmed · DOI

    No abstract available.

  • Matheus Carnevali PB, Schulz F, Castelle CJ, Kantor RS, Shih PM, Sharon I, Santini JM, Olm MR, Amano Y, Thomas BC, Anantharaman K, Burstein D, Becraft ED, Stepanauskas R, Woyke T, Banfield JF (2019) Author Correction: Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria. Nature communications 10((1)):1451 PMC6435703 · Pubmed · DOI

    No abstract available.

  • Bouma-Gregson K, Olm MR, Probst AJ, Anantharaman K, Power ME, Banfield JF (2019) Impacts of microbial assemblage and environmental conditions on the distribution of anatoxin-a producing cyanobacteria within a river network. The ISME journal 13((6)):1618-1634 PMC6776057 · Pubmed · DOI

    No abstract available.

  • Devoto AE, Santini JM, Olm MR, Anantharaman K, Munk P, Tung J, Archie EA, Turnbaugh PJ, Seed KD, Blekhman R, Aarestrup FM, Thomas BC, Banfield JF (2019) Megaphages infect Prevotella and variants are widespread in gut microbiomes. Nature microbiology 4((4)):693-700 PMC6784885 · Pubmed · DOI

    No abstract available.

  • Matheus Carnevali PB, Schulz F, Castelle CJ, Kantor RS, Shih PM, Sharon I, Santini JM, Olm MR, Amano Y, Thomas BC, Anantharaman K, Burstein D, Becraft ED, Stepanauskas R, Woyke T, Banfield JF (2019) Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria. Nature communications 10((1)):463 PMC6349859 · Pubmed · DOI

    No abstract available.

  • Linz AM, He S, Stevens SLR, Anantharaman K, Rohwer RR, Malmstrom RR, Bertilsson S, McMahon KD (2018) Freshwater carbon and nutrient cycles revealed through reconstructed population genomes. PeerJ 6:e6075 PMC6292386 · Pubmed · DOI

    No abstract available.

  • Castelle CJ, Brown CT, Anantharaman K, Probst AJ, Huang RH, Banfield JF (2018) Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations. Nature reviews. Microbiology 16((10)):629-645 · Pubmed · DOI

    No abstract available.

  • Anantharaman K, Hausmann B, Jungbluth SP, Kantor RS, Lavy A, Warren LA, Rappé MS, Pester M, Loy A, Thomas BC, Banfield JF (2018) Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle. The ISME journal 12((7)):1715-1728 PMC6018805 · Pubmed · DOI

    No abstract available.

  • Probst AJ, Ladd B, Jarett JK, Geller-McGrath DE, Sieber CMK, Emerson JB, Anantharaman K, Thomas BC, Malmstrom RR, Stieglmeier M, Klingl A, Woyke T, Ryan MC, Banfield JF (2018) Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface. Nature microbiology 3((3)):328-336 PMC6792436 · Pubmed · DOI

    No abstract available.

  • Zecchin S, Mueller RC, Seifert J, Stingl U, Anantharaman K, von Bergen M, Cavalca L, Pester M (2017) Rice Paddy Nitrospirae Carry and Express Genes Related to Sulfate Respiration: Proposal of the New Genus "Candidatus Sulfobium". Applied and environmental microbiology 84((5)): PMC5812927 · Pubmed · DOI

    No abstract available.

  • Banfield JF, Anantharaman K, Williams KH, Thomas BC (2017) Complete 4.55-Megabase-Pair Genome of " Candidatus Fluviicola riflensis," Curated from Short-Read Metagenomic Sequences. Genome announcements 5((47)): PMC5701471 · Pubmed · DOI

    No abstract available.

  • Hernsdorf AW, Amano Y, Miyakawa K, Ise K, Suzuki Y, Anantharaman K, Probst A, Burstein D, Thomas BC, Banfield JF (2017) Potential for microbial H and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments. The ISME journal 11((8)):1915-1929 PMC5520028 · Pubmed · DOI

    No abstract available.

  • Kantor RS, Huddy RJ, Iyer R, Thomas BC, Brown CT, Anantharaman K, Tringe S, Hettich RL, Harrison ST, Banfield JF (2017) Genome-Resolved Meta-Omics Ties Microbial Dynamics to Process Performance in Biotechnology for Thiocyanate Degradation. Environmental science & technology 51((5)):2944-2953 · Pubmed · DOI

    No abstract available.

  • Zaremba-Niedzwiedzka K, Caceres EF, Saw JH, Bäckström D, Juzokaite L, Vancaester E, Seitz KW, Anantharaman K, Starnawski P, Kjeldsen KU, Stott MB, Nunoura T, Banfield JF, Schramm A, Baker BJ, Spang A, Ettema TJ (2017) Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541((7637)):353-358 · Pubmed · DOI

    No abstract available.

  • Burstein D, Harrington LB, Strutt SC, Probst AJ, Anantharaman K, Thomas BC, Doudna JA, Banfield JF (2016) New CRISPR-Cas systems from uncultivated microbes. Nature 542((7640)):237-241 PMC5300952 · Pubmed · DOI

    No abstract available.

  • Marcus DN, Pinto A, Anantharaman K, Ruberg SA, Kramer EL, Raskin L, Dick GJ (2016) Diverse manganese(II)-oxidizing bacteria are prevalent in drinking water systems. Environmental microbiology reports 9((2)):120-128 · Pubmed · DOI

    No abstract available.

  • Anantharaman K, Brown CT, Hug LA, Sharon I, Castelle CJ, Probst AJ, Thomas BC, Singh A, Wilkins MJ, Karaoz U, Brodie EL, Williams KH, Hubbard SS, Banfield JF (2016) Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat Commun 7:13219 (PMC5079060) · Pubmed

    The subterranean world hosts up to one-fifth of all biomass, including microbial communities that drive transformations central to Earth's biogeochemical cycles. However, little is known about how complex microbial communities in such environments are structured, and how inter-organism interactions shape ecosystem function. Here we apply terabase-scale cultivation-independent metagenomics to aquifer sediments and groundwater, and reconstruct 2,540 draft-quality, near-complete and complete strain-resolved genomes that represent the majority of known bacterial phyla as well as 47 newly discovered phylum-level lineages. Metabolic analyses spanning this vast phylogenetic diversity and representing up to 36% of organisms detected in the system are used to document the distribution of pathways in coexisting organisms. Consistent with prior findings indicating metabolic handoffs in simple consortia, we find that few organisms within the community can conduct multiple sequential redox transformations. As environmental conditions change, different assemblages of organisms are selected for, altering linkages among the major biogeochemical cycles.

  • Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, Butterfield CN, Hernsdorf AW, Amano Y, Ise K, Suzuki Y, Dudek N, Relman DA, Finstad KM, Amundson R, Thomas BC, Banfield JF (2016) A new view of the tree of life. Nat Microbiol 1:16048 · Pubmed

    The tree of life is one of the most important organizing principles in biology(1). Gene surveys suggest the existence of an enormous number of branches(2), but even an approximation of the full scale of the tree has remained elusive. Recent depictions of the tree of life have focused either on the nature of deep evolutionary relationships(3-5) or on the known, well-classified diversity of life with an emphasis on eukaryotes(6). These approaches overlook the dramatic change in our understanding of life's diversity resulting from genomic sampling of previously unexamined environments. New methods to generate genome sequences illuminate the identity of organisms and their metabolic capacities, placing them in community and ecosystem contexts(7,8). Here, we use new genomic data from over 1,000 uncultivated and little known organisms, together with published sequences, to infer a dramatically expanded version of the tree of life, with Bacteria, Archaea and Eukarya included. The depiction is both a global overview and a snapshot of the diversity within each major lineage. The results reveal the dominance of bacterial diversification and underline the importance of organisms lacking isolated representatives, with substantial evolution concentrated in a major radiation of such organisms. This tree highlights major lineages currently underrepresented in biogeochemical models and identifies radiations that are probably important for future evolutionary analyses.

  • Probst AJ, Castelle CJ, Singh A, Brown CT, Anantharaman K, Sharon I, Hug LA, Burstein D, Emerson JB, Thomas BC, Banfield JF (2016) Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO concentrations. Environmental microbiology 19((2)):459-474 · Pubmed · DOI

    No abstract available.

  • Anantharaman K, Brown CT, Burstein D, Castelle CJ, Probst AJ, Thomas BC, Williams KH, Banfield JF (2016) Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum. PeerJ 4:e1607 (PMC4736985) · Pubmed

    Five closely related populations of bacteria from the Candidate Phylum (CP) Peregrinibacteria, part of the bacterial Candidate Phyla Radiation (CPR), were sampled from filtered groundwater obtained from an aquifer adjacent to the Colorado River near the town of Rifle, CO, USA. Here, we present the first complete genome sequences for organisms from this phylum. These bacteria have small genomes and, unlike most organisms from other lineages in the CPR, have the capacity for nucleotide synthesis. They invest significantly in biosynthesis of cell wall and cell envelope components, including peptidoglycan, isoprenoids via the mevalonate pathway, and a variety of amino sugars including perosamine and rhamnose. The genomes encode an intriguing set of large extracellular proteins, some of which are very cysteine-rich and may function in attachment, possibly to other cells. Strain variation in these proteins is an important source of genotypic variety. Overall, the cell envelope features, combined with the lack of biosynthesis capacities for many required cofactors, fatty acids, and most amino acids point to a symbiotic lifestyle. Phylogenetic analyses indicate that these bacteria likely represent a new class within the Peregrinibacteria phylum, although they ultimately may be recognized as members of a separate phylum. We propose the provisional taxonomic assignment as 'Candidatus Peribacter riflensis', Genus Peribacter, Family Peribacteraceae, Order Peribacterales, Class Peribacteria in the phylum Peregrinibacteria.

  • Burstein D, Sun CL, Brown CT, Sharon I, Anantharaman K, Probst AJ, Thomas BC, Banfield JF (2016) Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems. Nat Commun 7:10613 (PMC4742961) · Pubmed

    Current understanding of microorganism-virus interactions, which shape the evolution and functioning of Earth's ecosystems, is based primarily on cultivated organisms. Here we investigate thousands of viral and microbial genomes recovered using a cultivation-independent approach to study the frequency, variety and taxonomic distribution of viral defence mechanisms. CRISPR-Cas systems that confer microorganisms with immunity to viruses are present in only 10% of 1,724 sampled microorganisms, compared with previous reports of 40% occurrence in bacteria and 81% in archaea. We attribute this large difference to the lack of CRISPR-Cas systems across major bacterial lineages that have no cultivated representatives. We correlate absence of CRISPR-Cas with lack of nucleotide biosynthesis capacity and a symbiotic lifestyle. Restriction systems are well represented in these lineages and might provide both non-specific viral defence and access to nucleotides.

  • Varaljay VA, Satagopan S, North JA, Witte B, Dourado MN, Anantharaman K, Arbing MA, Hoeft McCann S, Oremland RS, Banfield JF, Wrighton KC, Tabita FR (2015) Functional metagenomic selection of ribulose 1, 5-bisphosphate carboxylase/oxygenase from uncultivated bacteria. Environ. Microbiol. 18(4):1187-99 · Pubmed

    Ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) is a critical yet severely inefficient enzyme that catalyses the fixation of virtually all of the carbon found on Earth. Here, we report a functional metagenomic selection that recovers physiologically active RubisCO molecules directly from uncultivated and largely unknown members of natural microbial communities. Selection is based on CO2 -dependent growth in a host strain capable of expressing environmental deoxyribonucleic acid (DNA), precluding the need for pure cultures or screening of recombinant clones for enzymatic activity. Seventeen functional RubisCO-encoded sequences were selected using DNA extracted from soil and river autotrophic enrichments, a photosynthetic biofilm and a subsurface groundwater aquifer. Notably, three related form II RubisCOs were recovered which share high sequence similarity with metagenomic scaffolds from uncultivated members of the Gallionellaceae family. One of the Gallionellaceae RubisCOs was purified and shown to possess CO2 /O2 specificity typical of form II enzymes. X-ray crystallography determined that this enzyme is a hexamer, only the second form II multimer ever solved and the first RubisCO structure obtained from an uncultivated bacterium. Functional metagenomic selection leverages natural biological diversity and billions of years of evolution inherent in environmental communities, providing a new window into the discovery of CO2 -fixing enzymes not previously characterized.

  • Anantharaman K, Breier JA, Dick GJ (2015) Metagenomic resolution of microbial functions in deep-sea hydrothermal plumes across the Eastern Lau Spreading Center. ISME J 10(1):225-39 (PMC4681857) · Pubmed

    Microbial processes within deep-sea hydrothermal plumes affect ocean biogeochemistry on global scales. In rising hydrothermal plumes, a combination of microbial metabolism and particle formation processes initiate the transformation of reduced chemicals like hydrogen sulfide, hydrogen, methane, iron, manganese and ammonia that are abundant in hydrothermal vent fluids. Despite the biogeochemical importance of this rising portion of plumes, it is understudied in comparison to neutrally buoyant plumes. Here we use metagenomics and bioenergetic modeling to describe the abundance and genetic potential of microorganisms in relation to available electron donors in five different hydrothermal plumes and three associated background deep-sea waters from the Eastern Lau Spreading Center located in the Western Pacific Ocean. Three hundred and thirty one distinct genomic 'bins' were identified, comprising an estimated 951 genomes of archaea, bacteria, eukarya and viruses. A significant proportion of these genomes is from novel microorganisms and thus reveals insights into the energy metabolism of heretofore unknown microbial groups. Community-wide analyses of genes encoding enzymes that oxidize inorganic energy sources showed that sulfur oxidation was the most abundant and diverse chemolithotrophic microbial metabolism in the community. Genes for sulfur oxidation were commonly present in genomic bins that also contained genes for oxidation of hydrogen and methane, suggesting metabolic versatility in these microbial groups. The relative diversity and abundance of genes encoding hydrogen oxidation was moderate, whereas that of genes for methane and ammonia oxidation was low in comparison to sulfur oxidation. Bioenergetic-thermodynamic modeling supports the metagenomic analyses, showing that oxidation of elemental sulfur with oxygen is the most dominant catabolic reaction in the hydrothermal plumes. We conclude that the energy metabolism of microbial communities inhabiting rising hydrothermal plumes is dictated by the underlying plume chemistry, with a dominant role for sulfur-based chemolithoautotrophy.

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