While mechanisms of different carbon dioxide (CO2 ) assimilation pathways in chemolithoautotrohic prokaryotes are well understood for many isolates under laboratory conditions, the ecological significance of diverse CO2 fixation strategies in the environment is mostly unexplored. Six stratified freshwater lakes were chosen to study the distribution and diversity of the Calvin-Benson-Bassham (CBB) cycle, the reductive tricarboxylic acid (rTCA) cycle, and the recently discovered archaeal 3-hydroxypropionate/4-hydroxybutyrate (HP/HB) pathway. Eleven primer sets were used to amplify and sequence genes coding for selected key enzymes in the three pathways. Whereas the CBB pathway with different forms of RubisCO (IA, IC and II) was ubiquitous and related to diverse bacterial taxa, encompassing a wide range of potential physiologies, the rTCA cycle in Epsilonproteobacteria and Chloribi was exclusively detected in anoxic water layers. Nitrifiying Nitrosospira and Thaumarchaeota, using the rTCA and HP/HB cycle respectively, are important residents in the aphotic and (micro-)oxic zone of deep lakes. Both taxa were of minor importance in surface waters and in smaller lakes characterized by an anoxic hypolimnion. Overall, this study provides a first insight on how different CO2 fixation strategies and chemical gradients in lakes are associated to the distribution of chemoautotrophic prokaryotes with different functional traits.

Institute for Ecology University of Innsbruck Innsbruck Austria

Institute of Hydrobiology Biology Centre CAS České Budějovice Czech Republic

Limnological Station Department of Plant and Microbial Biology University of Zurich Kilchberg Switzerland

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Alfreider A, Schirmer M, Vogt C. Diversity and expression of different forms of RubisCO genes in polluted groundwater under different redox conditions. FEMS Microbiol Ecol. 2012;79:649–660. PubMed

Alfreider A, Vogt C, Kaiser M, Psenner R. Distribution and diversity of autotrophic bacteria in groundwater systems based on the analysis of RubisCO genotypes. System Appl Microbiol. 2009;32:140–150. PubMed

Auguet JC, Borrego CM, Bañeras L, Casamayor EO. Fingerprinting the genetic diversity of the biotin carboxylase gene (accC) in aquatic ecosystems as a potential marker for studies of carbon dioxide assimilation in the dark. Environ Microbiol. 2008;10:2527–2536. PubMed

Auguet J-C, Triado-Margarit X, Nomokonova N, Camamero L, Casamayor EO. Vertical segregation and phylogenetic characterization of ammonia-oxidizing archaea in a deep oligotrophic lake. ISME J. 2012;6:1786–1797. PubMed PMC

Badger MR, Bek EJ. Multiple Rubisco forms in proteobacteria: their functional significance in relation to CO2 acquisition by the CBB cycle. J Exp Bot. 2008;59:1525–1541. PubMed

Baptista JDC, Lunn M, Davenport RJ, Swan DL, Read LF, Brown MR, et al. Agreement between amoA gene-specific quantitative PCR and fluorescence in situ hybridization in the measurement of ammonia-oxidizing bacteria in activated sludge. Appl Environ Microbiol. 2014;80:5901–5910. PubMed PMC

Baxter NJ, Hirt RP, Bodrossy L, Kovacs KL, Embley TM, Prosser JI, Murrell JC. The ribulose-1,5-bisphosphate carboxylase/oxygenase gene cluster of Methylococcus capsulatus (Bath) Arch Microbiol. 2002;177:279–289. PubMed

Berdjeb L, Pollet T, Chardon C, Jacquet S. Spatiotemporal changes in the structure of archaeal communities in two deep freshwater lakes. FEMS Microbiol Ecol. 2013;86:215–230. PubMed

Berg IA. Ecological aspects of the distribution of different autotrophic CO2 fixation pathways. Appl Environ Microbiol. 2011;77:1925–1936. PubMed PMC

Bergauer K, Sintes E, Bleijswijk JV, Witte H, Reinthaler T, Herndl GJ. Abundance and distribution of archaeal acetyl-CoA/propionyl-CaA carboxylase genes indicative for putatively chemoautotrophic Archaea in the tropical Atlantic’s interior. FEMS Microb Ecol. 2013;84:461–473. PubMed PMC

Bollmann A, Sedlacek CJ, Norton J, Laanbroek HJ, Suwa Y, Stein LY, et al. Complete genome sequence of Nitrosomonas sp. Is79, an ammonia oxidizing bacterium adapted to low ammonium concentrations. Stand Genomic Sci. 2013;7:469–482. PubMed PMC

Bouskill NJ, Eveillard D, Chien D, Jayakumar A, Ward BB. Environmental factors determining ammonia-oxidizing organism distribution and diversity in marine environments. Environ Microbiol. 2012;14:714–729. PubMed

Callieri C. Micro-players for macro-roles: aquatic microbes in deep lakes. J Limnol. 2016;75:191–200.

Callieri C, Coci M, Eckert EM, Salcher MM, Bertoni R. Archaea and bacteria in deep lake hypolimnion: in situ dark inorganic carbon uptake. J Limnol. 2014;73:31–38.

Casamayor EO. Vertical distribution of planktonic auto-trophic thiobacilli and dark CO2 fixation rates in lakes with oxygen-sulfide interfaces. Aquat Microb Ecol. 2010;59:217–228.

Coci M, Odermatt N, Salcher M, Pernthaler J, Corno G. Ecology and distribution of Thaumarchaea in the deep hypolimnion of Lake Maggiore. Archaea. 2015;2015:590434. PubMed PMC

Daims H, Lebedeva EV, Pjevac P, Han P, Herbold C, Albertsen M, et al. Complete nitrification by Nitrospira bacteria. Nature. 2015;528:504–509. PubMed PMC

Daims H, Lücker S, Wagner M. A new perspective on microbes formerly known as nitrite-oxidizing bacteria. Trends Microbiol. 2016;24:699–712. PubMed PMC

Dedysh SN, Smirnova KV, Khmelenina VN, Suzina NE, Liesack W, Trotsenko YA. Methylotrophic autotrophy in Beijerinckia mobilis. J Bacteriol. 2005;187:3884–3888. PubMed PMC

Ferguson SJ, Jackson JB, McEwan AG. Anaerobic respiration in the Rhodospirillaceae: characterization of pathways and evaluation of roles in redox balancing during photosynthesis. FEMS Microbiol Rev. 1987;46:117–143.

Field CB, Behrenfeld MJ, Randerson JT, Falkowski P. Primary production in the biosphere: Integrating terrestrial and oceanic components. Science. 1998;281:237–240. PubMed

Fixen KR, Starkenburg SR, Hovde BT, Johnson SL, Deodato CR, Daligault HE, et al. Genome sequences of eight bacterial species found in coculture with the haptophyte Chrysochromulina tobin. Genome Announc. 2016;4:e01162–16. PubMed PMC

French E, Kozlowski JA, Mukherjee M, Bullerjahn G, Bollmann A. Ecophysiological characterization of ammonia-oxidizing archaea and bacteria from freshwater. Appl Environ Microbiol. 2012;78:5773–5780. PubMed PMC

Giri BJ, Bano N, Hollibaugh J. Distribution of RuBisCO genotypes along a redox gradient in Mono Lake California. Appl Environ Microbiol. 2004;70:3443–3448. PubMed PMC

Herndl GJ, Reinthaler T. Microbial control of the dark end of the biological pump. Nature Geosci. 2013;6:718–724. PubMed PMC

Hu A, Yang Z, Yu C-P, Jiao N. Dynamics of autotrophic marine planktonic Thaumarchaeota in the East China Sea. PLoS One. 2013;8:e61087. PubMed PMC

Hugerth LW, Larsson J, Alneberg J, Lindh MV, Legrand C, Pinhassi J, et al. Metagenome-assembled genomes uncover a global brackish microbiome. Genome Biol. 2015;16:18. PubMed PMC

Hügler M, Sievert SM. Beyond the Calvin Cycle: autotrophic carbon fixation in the ocean. Ann Rev Mar Sci. 2011;3:261–289. PubMed

Hügler M, Wirsen CO, Fuchs G, Taylor CD, Sievert SM. Evidence for autotrophic CO2 fixation via the reductive tricarboxylic acid cycle by members of the ∈ subdivision of proteobacteria. J Bacteriol. 2005;187:3020–3027. PubMed PMC

Hugoni M, Domaizon I, Taib N, Biderre-Petit C, Agogué H, Galand PE, Debroas D, Mary I. Temporal dynamics of active Archaea in oxygen-depleted zones of two deep lakes. Environ Microbiol Rep. 2015;7:321–329. PubMed

Hugoni M, Etien S, Bourges A, Lepère C, Domaizon I, Mallet C, et al. Dynamics of ammonia-oxidizing archaea and bacteria in contrasted freshwater ecosystems. Res Microbiol. 2013;164:360–370. PubMed

Kojima H, Fukui M. Sulfuricella denitrificans gen. nov., sp. nov., a sulfur-oxidizing autotroph isolated from a freshwater lake. Int J Syst Evol Microbiol. 2010;60:2862–2866. PubMed

Kong W, Chuchiolo A, Priscu JC, Morgan-Kiss RM. Evidence of form II RubisCO (cbbM) in a perennially ice-covered Antarctic lake. FEMS Microbiol Ecol. 2012a;82:491–500. PubMed

Kong W, Ream DC, Priscu JC, Morgan-Kiss RM. Diversity and expression of RubisCO genes in a perennially ice-covered Antarctic lake during the polar night transition. Appl Environ Microbiol. 2012b;78:4358–4366. PubMed PMC

Könneke M, Schubert DM, Brown PC, Hügler M, Standfest S, Schwander T, et al. Ammonia-oxidizing archaea use the most energy efficient aerobic pathway for CO2 fixation. Proc Natl Acad Sci USA. 2014;111:8239–8244. PubMed PMC

Kovaleva OL, Tourova TP, Muyzer G, Kolganova TV, Sorokin DY. Diversity of RuBisCO and ATP citrate lyase genes in soda lake sediments. FEMS Microbiol Ecol. 2011;75:37–47. PubMed

La Cono V, La Spada G, Arcadi E, Placenti F, Smedile F, Ruggeri G, et al. Partaking of Archaea to bio-geochemical cycling in oxygen-deficient zones of meromictic saline Lake Faro (Messina, Italy) Environ Microbiol. 2013;15:1717–1733. PubMed

Lücker S, Wagner M, Maixner F, Pelletier E, Koch H, Vacherie B. A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria. Proc Natl Acad Sci USA. 2010;107:13479–13484. PubMed PMC

Lücker S, Nowka B, Rattei T, Spieck E, Daims H. The genome of Nitrospina gracilis illuminates the metabolism and evolution of the major marine nitrite oxidizer. Front Microbiol. 2013;4:27. PubMed PMC

Luo H, Tolar BB, Swan BK, Zhang CL, Stepanauskas R, Moran MA, Hollibaugh JT. Single-cell genomics shedding light on marine Thaumarchaeota diversification. ISME J. 2014;8:732–736. PubMed PMC

Mangiapia M, Scott K. From CO2 to cell: energetic expense of creating biomass using the Calvin-Benson-Bassham and reductive citric acid cycles based on genome data. FEMS Microbiol Lett 2016. 2016;363:7. PubMed

Martinez-Garcia M, Swan BK, Poulton NJ, Gomez ML, Masland D, Sieracki ME, Stepanauskas R. High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton. ISME J. 2012;6:113–123. PubMed PMC

McKinlay JB, Harwood CS. Carbon dioxide fixation as a central redox cofactor recycling mechanism in bacteria. Proc Natl Acad Sci USA. 2010;107:11669–11675. PubMed PMC

Merbt S, Stahl DA, Casamayor EO, Eugenia M, Nicol GW, Prosser JI. Differential photoinhibition of bacterial and archaeal ammonia oxidation. FEMS Microbiol Lett. 2012;327:41–46. PubMed

Middelburg J. Chemoautotrophy in the ocean. Geophys Res Lett. 2011;38:L24604.

Molari M, Manini E, Dell’Anno A. Dark inorganic carbon fixation sustains the functioning of benthic deep-sea ecosystems. Global Biogeochem Cycles. 2013;27:212–221.

Noguerola I, Picazo A, Lliros M, Camacho A, Borrego CM. Diversity of freshwater Epsilonproteo-bacteria and dark inorganic carbon fixation in the sulphidic redoxcline of a meromictic karstic lake. FEMS Microbiol Ecol. 2015;91:fiv086. PubMed

Penton CR, Johnson T, Quensen J, Tiedje J. Functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter. Front Microbiol. 2013;4:279. PubMed PMC

Pinto AJ, Marcus DN, Ijaz UZ, Bautista-de Lose Santos QM, Dick GJ, Raskin L. Metagenomic evidence for the presence of comammox Nitrospira-like bacteria in a drinking water system. mSphere. 2016;1:e00054–e00015. PubMed PMC

Pjevac P, Schauberger C, Poghosyan L, Herbold CW, van Kessel MAHJ, Daebeler A, et al. AmoA-targeted polymerase chain reaction primers for the specific detection and quantification of comammox Nitrospira in the environment. bioRxiv. 2016 doi: 10.1101/096891. PubMed DOI PMC

Raven JA. Contributions of anoxygenic and oxygenic phototrophy and chemolithotrophy to carbon and oxygen fluxes in aquatic environments. Aquat Microb Ecol. 2009;56:177–192.

Seong HS, Soon DL. Actinoplanes subtropicus sp. nov., isolated from rhizosphere soil. International Meeting of the Microbiological Society of Korea. 2009:181.

Shiba H, Kawasumi T, Igarashi Y, Kodama T, Minoda Y. The CO2 assimilation via the reductive tricarboxylic-acid cycle in an obligately autotrophic, aerobic hydrogen-oxidizing bacterium, Hydrogenobacter thermophilus. Arch Microbiol. 1985;141:198–203.

Small GE, Bullerjahn GS, Sterner RW, Beall BFN, Brovold S, Finlay JC, et al. Rates and controls of nitrification in a large oligotrophic lake. Limnol Oceangr. 2013;58:276–286.

Šmilauer P, Lepš J. Multivariate Analysis of Ecological Data Using CANOCO5. Cambridge: UK Cambridge University Press; 2014.

Suwa Y, Norton JM, Bollmann A, Klotz MG, Stein LY, Laanbroek HJ, et al. Genome sequence of Nitrosomonas sp. strain AL212, an ammonia-oxidizing bacterium sensitive to high levels of ammonia. J Bacteriol. 2011;193:5047–5048. PubMed PMC

Swan BK, Martinez-Garcia M, Preston CM, Sczyrba A, Woyke T, Lamy D, et al. Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean. Science. 2011;333:1296–1300. PubMed

Tabita FR, Satagopan S, Hanson TE, Kreel NE, Scott SS. Distinct form I, II, III, and IV Rubisco proteins from the three kingdoms of life provide clues about Rubisco evolution and structure/function relationships. J Exp Bot. 2008;59:1515–1524. PubMed

Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Mol Biol Evol. 2013;30:2725–2729. PubMed PMC

Tolar B, King GM, Hollibaugh JT. An analysis of Thaumarchaeota populations from the Northern Gulf of Mexico. Front Microbiol. 2013;4:72. PubMed PMC

Tourova TP, Kovaleva OL, Sorokin DY, Muyzer G. Ribulose-1,5-bisphosphate carboxylase/oxygenase genes as a functional marker for chemolithoautotrophic halophilic sulfur-oxidizing bacteria in hypersaline habitats. Microbiol-UK. 2010;156:2016–2025. PubMed

van Kessel MA, Speth DR, Albertsen M, Nielsen PH, Op den Camp HJ, Kartal B, et al. Complete nitrification by a single microorganism. Nature. 2015;528:555–559. PubMed PMC

Vissers EW, Anselmetti FS, Bodelier PL, Muyzer G, Schleper C, Tourna M, Laanbroek HJ. Temporal and spatial coexistence of archaeal and bacterial amoA genes and gene transcripts in Lake Lucerne. Archaea. 2013;2013:289478. PubMed PMC

Watanabe T, Kojima H, Fukui M. Draft genome sequence of a psychrotolerant sulfur-oxidizing bacterium, Sulfuricella denitrificans skB26, and proteomic insights into cold adaptation. Appl Environ Microbiol. 2012;78:6545–6549. PubMed PMC

Wendeberg A. Fluorescence in situ hybridization for the identification of environmental microbes. Cold Spring Harb Protoc. 2010 doi: 10.1101/pdb.prot5366. PubMed DOI

Wilhelm SW, Bullerjahn GS, Eldridge ML, Rinta-Kanto JM, Poorvin L, Bourbonniere RA. Seasonal hypoxia and the genetic diversity of prokaryote populations in the central basin hypolimnion of Lake Erie: evidence for abundant cyanobacteria and photosynthesis. J Great Lakes Res. 2006;32:657–671.

Xu Q, Tabita FR. Ribulose-1,5-bisphosphate carboxylase/oxygenase gene expression and diversity of Lake Erie planktonic microorganisms. Appl Environ Microbiol. 1996;62:1913–1920. PubMed PMC

Yakimov MM, La Cono V, Denaro R. A first insight into the occurrence and expression of functional amoA and accA genes of autotrophic and ammonia oxidizing bathypelagic Crenarchaeota of Tyrrhenian Sea. Deep Sea Res. 2009;56:748–754.

Yakimov MM, La Cono V, Smedile F, Deluca TH, Juárez S, Ciordia S, et al. Contribution of crenarchaeal autotrophic ammonia oxidizers to the dark primary production in Tyrrhenian deep waters (Central Mediterranean Sea) ISME J. 2011;5:945–961. PubMed PMC

Yamamoto M, Arai H, Ishii M, Igarashi Y. Role of two 2-oxoglutarate:ferredoxin oxidoreductases in Hydrogenobacter thermophilus under aerobic and anaerobic conditions. FEMS Microbiol Lett. 2006;263:189–193. PubMed

Yoshizawa Y, Toyoda K, Arai H, Ishii M, Igarashi Y. CO2-responsive expression and gene organization of three ribulose-1,5-bisphosphate carboxylase/oxygenase enzymes and carboxysomes in Hydrogenovibrio marinus strain MH-110. J Bacteriol. 2004;186:5685–5691. PubMed PMC

Autotrophic carbon fixation strategies used by nitrifying prokaryotes in freshwater lakes