Abstract
Marine sediments are the largest carbon sink on earth. Nearly half of dark carbon fixation in the oceans occurs in coastal sediments, but the microorganisms responsible are largely unknown. By integrating the 16S rRNA approach, single-cell genomics, metagenomics and transcriptomics with 14C-carbon assimilation experiments, we show that uncultured Gammaproteobacteria account for 70–86% of dark carbon fixation in coastal sediments. First, we surveyed the bacterial 16S rRNA gene diversity of 13 tidal and sublittoral sediments across Europe and Australia to identify ubiquitous core groups of Gammaproteobacteria mainly affiliating with sulfur-oxidizing bacteria. These also accounted for a substantial fraction of the microbial community in anoxic, 490-cm-deep subsurface sediments. We then quantified dark carbon fixation by scintillography of specific microbial populations extracted and flow-sorted from sediments that were short-term incubated with 14C-bicarbonate. We identified three distinct gammaproteobacterial clades covering diversity ranges on family to order level (the Acidiferrobacter, JTB255 and SSr clades) that made up >50% of dark carbon fixation in a tidal sediment. Consistent with these activity measurements, environmental transcripts of sulfur oxidation and carbon fixation genes mainly affiliated with those of sulfur-oxidizing Gammaproteobacteria. The co-localization of key genes of sulfur and hydrogen oxidation pathways and their expression in genomes of uncultured Gammaproteobacteria illustrates an unknown metabolic plasticity for sulfur oxidizers in marine sediments. Given their global distribution and high abundance, we propose that a stable assemblage of metabolically flexible Gammaproteobacteria drives important parts of marine carbon and sulfur cycles.
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Alonso C, Pernthaler J . (2005). Incorporation of glucose under anoxic conditions by bacterioplankton from coastal North Sea surface waters. Appl Environ Microbiol 71: 1709–1716.
Anantharaman K, Breier JA, Sheik CS, Dick GJ . (2013). Evidence for hydrogen oxidation and metabolic plasticity in widespread deep-sea sulfur-oxidizing bacteria. Proc Natl Acad Sci USA 110: 330–335.
Baker BJ, Lazar CS, Teske AP, Dick GJ . (2015). Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria. Microbiome 3: 14.
de Beer D, Wenzhöfer F, Ferdelman TG, Boehme SE, Huettel M, van Beusekom JEE et al. (2005). Transport and mineralization rates in North Sea sandy intertidal sediments, Sylt-Rømø Basin, Wadden Sea. Limnol Oceanogr 50: 113–127.
Billerbeck M, Werner U, Polerecky L, Walpersdorf E, deBeer D, Huettel M . (2006). Surficial and deep pore water circulation governs spatial and temporal scales of nutrient recycling in intertidal sand flat sediment. Mar Ecol Prog Ser 326: 61–76.
Boschker HTS, Nold SC, Wellsbury P, Bos D, de Graaf W, Pel R et al. (1998). Direct linking of microbial populations to specific biogeochemical processes by 13C-labelling of biomarkers. Nature 392: 801–805.
Boschker HTS, Vasquez-Cardenas D, Bolhuis H, Moerdijk-Poortvliet TWC, Moodley L . (2014). Chemoautotrophic carbon fixation rates and active bacterial communities in intertidal marine sediments. PLoS ONE 9: e101443.
Bowman JP, McCammon SA, Dann AL . (2005). Biogeographic and quantitative analyses of abundant uncultivated γ-proteobacterial clades from marine sediment. Microb Ecol 49: 451–460.
Bowman JP, McCuaig RD . (2003). Biodiversity, community structural shifts, and biogeography of prokaryotes within Antarctic continental shelf sediment. Appl Environ Microbiol 69: 2463–2483.
Burdige DJ . (2007). Preservation of organic matter in marine sediments: controls, mechanisms, and an imbalance in sediment organic carbon budgets? Chem Rev 107: 467–485.
Canfield DE, Stewart FJ, Thamdrup B, Brabandere LD, Dalsgaard T, Delong EF et al. (2010). A cryptic sulfur cycle in oxygen-minimum-zone waters off the Chilean coast. Science 330: 1375–1378.
Cleland D, Krader P, McCree C, Tang J, Emerson D . (2004). Glycine betaine as a cryoprotectant for prokaryotes. J Microbiol Methods 58: 31–38.
Cline JD . (1969). Spectrophotometric determination of hydrogen sulfide in natural waters. Limnol Oceanogr 14: 454–458.
Duarte CM, Middelburg JJ, Caraco N . (2005). Major role of marine vegetation on the oceanic carbon cycle. Biogeosciences 2: 1–8.
Emil Ruff S, Probandt D, Zinkann A-C, Iversen MH, Klaas C, Würzberg L et al. (2014). Indications for algae-degrading benthic microbial communities in deep-sea sediments along the Antarctic Polar Front. Deep Sea Res Part II Top Stud Oceanogr 108: 6–16.
Gittel A, Mußmann M, Sass H, Cypionka H, Könneke M . (2008). Identity and abundance of active sulfate-reducing bacteria in deep tidal flat sediments determined by directed cultivation and CARD-FISH analysis. Environ Microbiol 10: 2645–2658.
Glaubitz S, Kießlich K, Meeske C, Labrenz M, Jürgens K . (2013). SUP05 dominates the gammaproteobacterial sulfur oxidizer assemblages in pelagic redoxclines of the central Baltic and Black Seas. Appl Environ Microbiol 79: 2767–2776.
Gobet A, Böer SI, Huse SM, van Beusekom JEE, Quince C, Sogin ML et al. (2012). Diversity and dynamics of rare and of resident bacterial populations in coastal sands. ISME J 6: 542–553.
Grote J, Schott T, Bruckner CG, Glöckner FO, Jost G, Teeling H et al. (2012). Genome and physiology of a model Epsilonproteobacterium responsible for sulfide detoxification in marine oxygen depletion zones. Proc Natl Acad Sci USA 109: 506–510.
Hallberg KB, Hedrich S, Johnson DB . (2011). Acidiferrobacter thiooxydans, gen. nov. sp. nov.; an acidophilic, thermo-tolerant, facultatively anaerobic iron- and sulfur-oxidizer of the family Ectothiorhodospiraceae. Extremophiles 15: 271–279.
Han Y, Perner M . (2014). The role of hydrogen for Sulfurimonas denitrificans’ metabolism. PLoS One 9: e106218.
Hansen M, Perner M . (2015). A novel hydrogen oxidizer amidst the sulfur-oxidizing Thiomicrospira lineage. ISME J 9: 696–707.
Hawley AK, Brewer HM, Norbeck AD, Paša-Tolić L, Hallam SJ . (2014). Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes. Proc Natl Acad Sci USA 111: 11395–11400.
Hedges JI, Keil RG . (1995). Sedimentary organic matter preservation: an assessment and speculative synthesis. Mar Chem 49: 81–115.
Herlemann DP, Labrenz M, Jürgens K, Bertilsson S, Waniek JJ, Andersson AF . (2011). Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea. ISME J 5: 1571–1579.
Holkenbrink C, Barbas SO, Mellerup A, Otaki H, Frigaard N-U . (2011). Sulfur globule oxidation in green sulfur bacteria is dependent on the dissimilatory sulfite reductase system. Microbiology 157: 1229–1239.
Hügler M, Sievert SM . (2011). Beyond the Calvin cycle: autotrophic carbon fixation in the ocean. Annu Rev Mar Sci 3: 261–289.
Hunter EM, Mills HJ, Kostka JE . (2006). Microbial community diversity associated with carbon and nitrogen cycling in permeable shelf sediments. Appl Environ Microbiol 72: 5689–5701.
Jansen S, Walpersdorf E, Werner U, Billerbeck M, Böttcher ME, de Beer D . (2009). Functioning of intertidal flats inferred from temporal and spatial dynamics of O2, H2S and pH in their surface sediment. Ocean Dyn 59: 317–332.
Jørgensen BB . (1990). A thiosulfate shunt in the sulfur cycle of marine sediments. Science 249: 152–154.
Jørgensen BB . (2011). Deep subseafloor microbial cells on physiological standby. Proc Natl Acad Sci USA 108: 18193–18194.
Jost G, Zubkov MV, Yakushev E, Labrenz M, Jürgens K . (2008). High abundance and dark CO2 fixation of chemolithoautotrophic prokaryotes in anoxic waters of the Baltic Sea. Limnol Oceanogr 53: 14–22.
Kelly DP, Shergill JK, Lu W-P, Wood AP . (1997). Oxidative metabolism of inorganic sulfur compounds by bacteria. Antonie Van Leeuwenhoek 71: 95–107.
Kim B-S, Kim BK, Lee J-H, Kim M, Lim YW, Chun J . (2008). Rapid phylogenetic dissection of prokaryotic community structure in tidal flat using pyrosequencing. J Microbiol 46: 357–363.
Klatt JM, Polerecky L . (2015). Assessment of the stoichiometry and efficiency of CO2 fixation coupled to reduced sulfur oxidation. Aquat Microbiol 6: 484.
Kleiner M, Wentrup C, Lott C, Teeling H, Wetzel S, Young J et al. (2012). Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use. Proc Natl Acad Sci USA 109: E1173–E1182.
Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M et al. (2012). Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 41: e1.
Langmead B, Salzberg SL . (2012). Fast gapped-read alignment with Bowtie 2. Nat Methods 9: 357–359.
Laurinavichene TV, Rákhely G, Kovács KL, Tsygankov AA . (2007). The effect of sulfur compounds on H2 evolution/consumption reactions, mediated by various hydrogenases, in the purple sulfur bacterium Thiocapsa roseopersicina. Arch Microbiol 188: 403–410.
Lavik G, Stührmann T, Brüchert V, Van der Plas A, Mohrholz V, Lam P et al. (2009). Detoxification of sulphidic African shelf waters by blooming chemolithotrophs. Nature 457: 581–584.
Lee N, Nielsen PH, Andreasen KH, Juretschko S, Nielsen JL, Schleifer KH et al. (1999). Combination of fluorescent in situ hybridization and microautoradiography - a new tool for structure-function analyses in microbial ecology. Appl Environ Microbiol 65: 1289–1297.
Lenk S, Arnds J, Zerjatke K, Musat N, Amann R, Mußmann M . (2011). Novel groups of Gammaproteobacteria catalyse sulfur oxidation and carbon fixation in a coastal, intertidal sediment. Environ Microbiol 13: 758–774.
Lenk S, Moraru C, Hahnke S, Arnds J, Richter M, Kube M et al. (2012). Roseobacter clade bacteria are abundant in coastal sediments and encode a novel combination of sulfur oxidation genes. ISME J 6: 2178–2187.
Li W . (1982). Estimating heterotrophic bacterial productivity by inorganic radiocarbon uptake - importance of establishing time courses of uptake. Mar Ecol Prog Ser 8: 167–172.
Liu J, Liu X, Wang M, Qiao Y, Zheng Y, Zhang X-H . (2014). Bacterial and archaeal communities in sediments of the north Chinese marginal seas. Microb Ecol 70: 105–117.
Lösekann T, Robador A, Niemann H, Knittel K, Boetius A, Dubilier N . (2008). Endosymbioses between bacteria and deep-sea siboglinid tubeworms from an Arctic Cold Seep (Haakon Mosby Mud Volcano, Barents Sea). Environ Microbiol 10: 3237–3254.
Manefield M, Whiteley AS, Griffiths RI, Bailey MJ . (2002). RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl Environ Microbiol 68: 5367–5373.
Marchant HK, Lavik G, Holtappels M, Kuypers MMM . (2014). The fate of nitrate in intertidal permeable sediments. PLoS ONE 9: e104517.
Markowitz VM, Chen I-MA, Palaniappan K, Chu K, Szeto E, Grechkin Y et al. (2012). IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res 40: D115–D122.
Mattes TE, Nunn BL, Marshall KT, Proskurowski G, Kelley DS, Kawka OE et al. (2013). Sulfur oxidizers dominate carbon fixation at a biogeochemical hot spot in the dark ocean. ISME J 7: 2349–2360.
Meyer B, Kuever J . (2007). Molecular analysis of the diversity of sulfate-reducing and sulfur-oxidizing prokaryotes in the environment, using aprA as functional marker gene. Appl Environ Microbiol 73: 7664–7679.
Middelburg JJ . (2011). Chemoautotrophy in the ocean. Geophys Res Lett 38: 94–97.
Molari M, Manini E, Dell’Anno A . (2013). Dark inorganic carbon fixation sustains the functioning of benthic deep-sea ecosystems. Glob Biogeochem Cycles 27: 212–221.
Musat N, Halm H, Winterholler B, Hoppe P, Peduzzi S, Hillion F et al. (2008). A single-cell view on the ecophysiology of anaerobic phototrophic bacteria. Proc Natl Acad Sci USA 105: 17861–17866.
Muyzer G, Brinkhoff T, Nuebel U, Santegoeds C, Schaefer H, Waver C . (1998). Denaturing gradient gel electrophoresis (DGGE) in microbial ecology. In: Akkermans ADL, van Elsas JD, de Bruijn FJ (ed). Molecular Microbial Ecology Manual. Kluwer Academic Publishers: Dordrecht, The Netherlands, pp 1–27.
Orcutt BN, Sylvan JB, Knab NJ, Edwards KJ . (2011). Microbial ecology of the dark ocean above, at, and below the seafloor. Microbiol Mol Biol Rev 75: 361–422.
Parkes RJ, Cragg BA, Getliff JM, Harvey SM, Fry JC, Lewis CA et al. (1993). A quantitative study of microbial decomposition of biopolymers in Recent sediments from the Peru Margin. Mar Geol 113: 55–66.
Pernthaler A, Pernthaler J, Amann R . (2002). Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl Environ Microbiol 68: 3094–3101.
Petersen JM, Zielinski FU, Pape T, Seifert R, Moraru C, Amann R et al. (2011). Hydrogen is an energy source for hydrothermal vent symbioses. Nature 476: 176–180.
Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J et al. (2007). SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35: 7188–7196.
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P et al. (2013). The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41: D590–D596.
Radajewski S, Ineson P, Parekh NR, Murrell JC . (2000). Stable-isotope probing as a tool in microbial ecology. Nature 403: 646–649.
Reinthaler T, van Aken HM, Herndl GJ . (2010). Major contribution of autotrophy to microbial carbon cycling in the deep North Atlantic’s interior. Deep Sea Res Part II Top Stud Oceanogr 57: 1572–1580.
Rinke C, Schmitz-Esser S, Stoecker K, Nussbaumer AD, Molnár DA, Vanura K et al. (2006). ‘Candidatus Thiobios zoothamnicoli,’ an ectosymbiotic bacterium covering the giant marine ciliate Zoothamnium niveum. Appl Environ Microbiol 72: 2014–2021.
Roslev P, Larsen MB, Jorgensen D, Hesselsoe M . (2004). Use of heterotrophic CO2 assimilation as a measure of metabolic activity in planktonic and sessile bacteria. J Microbiol Methods 59: 381–393.
Røy H, Lee JS, Jansen S, de Beer D . (2008). Tide-driven deep pore-water flow in intertidal sand flats. Limnol Oceanogr 53: 1521–1530.
Ruff SE, Biddle JF, Teske AP, Knittel K, Boetius A, Ramette A . (2015). Global dispersion and local diversification of the methane seep microbiome. Proc Natl Acad Sci USA 112: 4015–4020.
Salman V, Bailey JV, Teske A . (2013). Phylogenetic and morphologic complexity of giant sulphur bacteria. Antonie Van Leeuwenhoek 104: 169–186.
Schauer R, Bienhold C, Ramette A, Harder J . (2009). Bacterial diversity and biogeography in deep-sea surface sediments of the South Atlantic Ocean. ISME J 4: 159–170.
Schippers A, Neretin LN, Kallmeyer J, Ferdelman TG, Cragg BA, John Parkes R et al. (2005). Prokaryotic cells of the deep sub-seafloor biosphere identified as living bacteria. Nature 433: 861–864.
Seidel M, Graue J, Engelen B, Köster J, Sass H, Rullkötter J . (2012). Advection and diffusion determine vertical distribution of microbial communities in intertidal sediments as revealed by combined biogeochemical and molecular biological analysis. Org Geochem 52: 114–129.
Sekar R, Fuchs BM, Amann R, Pernthaler J . (2004). Flow sorting of marine bacterioplankton after fluorescence in situ hybridization. Appl Environ Microbiol 70: 6210–6219.
Siyambalapitiya N, Blackall LL . (2005). Discrepancies in the widely applied GAM42a fluorescence in situ hybridisation probe for Gammaproteobacteria. FEMS Microbiol Lett 242: 367–373.
Swan BK, Martinez-Garcia M, Preston CM, Sczyrba A, Woyke T, Lamy D et al. (2011). Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean. Science 333: 1296–1300.
Thomas F, Giblin AE, Cardon ZG, Sievert SM . (2014). Rhizosphere heterogeneity shapes abundance and activity of sulfur-oxidizing bacteria in vegetated salt marsh sediments. Front Microbiol 5: 1–14.
Vasquez-Cardenas D, van de Vossenberg J, Polerecky L, Malkin SY, Schauer R, Hidalgo-Martinez S et al. (2015). Microbial carbon metabolism associated with electrogenic sulphur oxidation in coastal sediments. ISME J 9: 1966–1978.
Wang L, Liu L, Zheng B, Zhu Y, Wang X . (2013). Analysis of the bacterial community in the two typical intertidal sediments of Bohai Bay, China by pyrosequencing. Mar Pollut Bull 72: 181–187.
Wood HG, Werkman CH . (1936). The utilisation of CO2 in the dissimilation of glycerol by the propionic acid bacteria. Biochem J 30: 48–53.
Woyke T, Teeling H, Ivanova NN, Huntemann M, Richter M, Gloeckner FO et al. (2006). Symbiosis insights through metagenomic analysis of a microbial consortium. Nature 443: 950–955.
Wright JJ, Konwar KM, Hallam SJ . (2012). Microbial ecology of expanding oxygen minimum zones. Nat Rev Microbiol 10: 381–394.
Zerjatke K . (2009). Mikroautoradiographie und Genexpression von Bakterien im Oberflächensediment der Gezeitenzone des Wattenmeeres. Diploma thesis. University of Bremen: Bremen, Germany.
Zheng B, Wang L, Liu L . (2014). Bacterial community structure and its regulating factors in the intertidal sediment along the Liaodong Bay of Bohai Sea, China. Microbiol Res 169: 585–592.
Zhou J, Bruns MA, Tiedje JM . (1996). DNA recovery from soils of diverse composition. Appl Environ Microbiol 62: 316–322.
Ziehe D . (2009) Aminosäure-D/L-Verhältnisse in biogenen Carbonaten als Schlüssel zur Datierung holozäner Sedimentationsvorgänge im norddeutschen Küstenraum PhD thesis. University of Oldenburg: Oldenburg, Germany.
Zubkov MV, Fuchs BM, Tarran GA, Burkill PH, Amann R . (2003). High rate of uptake of organic nitrogen compounds by Prochlorococcus cyanobacteria as a key to their dominance in oligotrophic oceanic waters. Appl Environ Microbiol 69: 1299–1304.
Acknowledgements
We greatly acknowledge the crew of R/V Navicula from the ICBM Oldenburg for ship time and assistance. We thank the crew of the R/V Meteor and R/V Sonne and the ROV team of the MARUM Quest 4000 m. We greatly acknowledge the chief scientist Wolfgang Bach for his excellent support during cruise SO216 with R/V Sonne, which was an integral part of the Cluster of Excellence of the MARUM ‘The Ocean in the Earth System, Research Area GB: Geosphere-Biosphere Interactions’ funded by the German Research Foundation (DFG). The cruise SO216 was funded by a grant (03G0216) from the Bundesministerium für Bildung und Forschung (BMBF) awarded to Wolfgang Bach and co-PIs. RS was supported by the US National Science Foundation grant OCE-1232982. We thank Falk Warnecke for support in sediment sampling and for sequencing of the subsurface samples. Special thanks go to Rudolf Amann for helpful discussions and continuous support. This study contributes to the project ABYSS funded by the European Research Council Advanced Investigator Grant 294757 to Antje Boetius. Further funding was provided by the Max Planck Society.
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Dyksma, S., Bischof, K., Fuchs, B. et al. Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments. ISME J 10, 1939–1953 (2016). https://doi.org/10.1038/ismej.2015.257
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DOI: https://doi.org/10.1038/ismej.2015.257
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