Sulphide-driven anoxygenic photosynthesis is an ancient microbial metabolism that contributes significantly to inorganic carbon fixation in stratified, sulphidic water bodies. Methods commonly applied to quantify inorganic carbon fixation by anoxygenic phototrophs, however, cannot resolve the contributions of distinct microbial populations to the overall process. We implemented a straightforward workflow, consisting of radioisotope labelling and flow cytometric cell sorting based on the distinct autofluorescence of bacterial photopigments, to discriminate and quantify contributions of co-occurring anoxygenic phototrophic populations to in situ inorganic carbon fixation in environmental samples. This allowed us to assign 89.3% ± 7.6% of daytime inorganic carbon fixation by anoxygenic phototrophs in Lake Rogoznica (Croatia) to an abundant chemocline-dwelling population of green sulphur bacteria (dominated by Chlorobium phaeobacteroides), whereas the co-occurring purple sulphur bacteria (Halochromatium sp.) contributed only 1.8% ± 1.4%. Furthermore, we obtained two metagenome assembled genomes of green sulphur bacteria and one of a purple sulphur bacterium which provides the first genomic insights into the genus Halochromatium, confirming its high metabolic flexibility and physiological potential for mixo- and heterotrophic growth.

Center of Excellence for Science and Technology Integrating Mediterranean Region Microbial Ecology Zagreb Croatia

Department of Chemical Analytics and Biogeochemistry Leibniz Institute for Freshwater Ecology and Inland Fisheries Berlin Germany

Department of Molecular Ecology Max Planck Institute for Marine Microbiology Bremen Germany

Institute of Microbiology CAS Center Algatech Třeboň Czech Republic

MARUM Center for Marine Environmental Sciences Bremen Germany

Ruđer Bošković Institute Zagreb Croatia

University of Vienna Center for Microbiology and Environmental Systems Science Division of Microbial Ecology Vienna Austria

Zobrazit více v PubMed

Abella, C., Montesinos, E., and Guerrero, R. (1980) Field studies on the competition between purple and green sulfur bacteria for available light (Lake Siso, Spain). In Shallow Lakes Contributions to their Limnology, Dokulil, H., Metz, H., and Jewson, D. (eds). Netherlands: Springer, pp. 173-181.

Aziz, R.K., Bartels, D., Best, A.A., DeJongh, M., Disz, T., Edwards, R.A., et al. (2008) The RAST server: rapid annotations using subsystems technology. BMC Genomics 9: 75.

Barešić, J., Horvatinčić, N., and Roller-Lutz, Z. (2011) Spatial and seasonal variations in the stable C isotope composition of dissolved inorganic carbon and in physico-chemical water parameters in the Plitvice Lakes system. Isot Environ Healt S 47: 316-329.

Bankevich, A., Nurk, S., Antipov, D., Gurevich, A.A., Dvorkin, M., Kulikov, A.S., et al. (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19: 455-477.

Berg, J.S., Pjevac, P., Sommer, T., Buckner, C.R., Philippi, M., Hach, P.F., et al. (2018) Dark aerobic sulfide oxidation by anoxygenic phototrophs in anoxic waters. Environ Microbiol 21: 1611-1626. https://doi.org/10.1111/1462-2920.14543.

Bossard, P., Gammeter, S., Lehmann, C., Schanz, F., Bachofen, R., Bürgi, H.R., et al. (2001) Limnological description of the lakes Zürich, Lucerne, and Cadagno. Aquat Sci 63: 225-249.

Brocks, J.J., Love, G.D., Summons, R.E., Knoll, A.H., Logan, G.A., and Bowden, S.A. (2005) Biomarker evidence for green and purple sulphur bacteria in a stratified Palaeoproterozoic Sea. Nature 437: 866-870.

Bura-Nakić, E., Helz, G.R., Ciglenečki, I., and Ćosović, B. (2009) Reduced sulfur species in a stratified seawater Lake (Rogoznica lake, Croatia); seasonal variations and argument for organic carriers of reactive sulfur. Geochim Cosmochim Acta 73: 3738-3751.

Camacho, A., and Vicente, E. (1998) Carbon photoassimilation by sharply stratified phototrophic communities at the chemocline of Lake Arcas (Spain). FEMS Microbiol Ecol 25: 11-22.

Camacho, A., Erez, J., Chicote, A., Florín, M., Squires, M.M., Lehmann, C., and Backofen, R. (2001) Microbial microstratification, inorganic carbon photoassimilation and dark carbon fixation at the chemocline of the meromictic Lake Cadagno (Switzerland) and its relevance to the food web. Aquat Sci 63: 91-106.

Casamayor, E.O., García-Cantizano, J., Mas, J., and Pedrós-Alió, C. (2001) Microbial primary production in marine oxic/anoxic interfaces: main role of dark fixation in the Ebro River salt wedge estuary. Mar Ecol Prog Ser 215: 49-56.

Casamayor, E.O., Ferrera, I., Cristina, X., Borrego, C.M., and Gasol, J.M. (2007) Flow cytometric identification and enumeration of photosynthetic sulfur bacteria and potential for ecophysiological studies at the single-cell level. Environ Microbiol 9: 1969-1985.

Caumette, P., Baulaigue, R., and Matheron, R. (1988) Characterization of Chromatium salexigens sp. nov., a halophilic Chromatiaceae isolated from Mediterranean Salinas. Syst Appl Microbiol 10: 284-292.

Caumette, P., Imhoff, J.F., Süling, J., and Matheron, R. (1997) Chromatium glycolicum sp. nov., a moderately halophilic purple sulfur bacterium that uses glycolate as substrate. Arch Microbiol 167: 11-18.

Chew, A.G., and Bryant, D.A. (2007) Chlorophyll biosynthesis in bacteria: the origins of structural and functional diversity. Annu Rev Microbiol 61: 113-129.

Cline, J.D. (1969) Spectrophotometric determination of hydrogen sulfide in natural waters. Anal Chem 21: 1005-1009.

Cohen, Y., Krumbein, W.E., and Shilo, M. (1977) Solar Lake (Sinai). 2. Distribution of photosynthetic microorganisms and primary production. Limnol Oceanogr 22: 609-620.

Cossarini, G., Lazzari, P., and Solidoro, C. (2015) Spatiotemporal variability of alkalinity in the Mediterranean Sea. Biogeosciences 12: 1647-1658.

Culver, D.A., and Brunskill, G.J. (1969) Fayetteville green Lake, New York. V. Studies of primary production and zooplankton in a Meromictic marl LAKE1. Limnol Oceanogr 14: 862-873.

Dyksma, S., Bischof, K., Fuchs, B.M., Hoffmann, K., Meier, D.V., Meyerdierks, A., et al. (2016) Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments. ISME J 10: 1939-1953.

Eisen, J.A., Nelson, K.E., Paulsen, I.T., Heidelberg, J.F., Wu, M., Dodson, R.J., et al. (2002) The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium. Proc Nat Acad S USA 99: 9509-9514.

Ferdelman, T.G., Church, T.M., and Luther, G.W. (1991) Sulfur enrichment of humic substances in a Delaware salt marsh sediment core. Geochim Cosmochim Acta 55: 979-988.

Florea, L.J., Dugan, C.R., and McKinney, C. (2016) Geochemistry of cave pools connected to an alpine epikarst-Timpanogos cave National Monument, Utah. Geol Soc Am Spec Paper 516: 165-179.

Fontes, M.L.S., Suzuki, M.T., Cottrell, M.T., and Abreu, P.C. (2011) Primary production in a subtropical stratified coastal lagoon - contribution of anoxygenic phototrophic bacteria. Microb Ecol 61: 223-237.

Frigaard, N.U., and Bryant, D.A. (2008) Genomic insights into the sulfur metabolism of phototrophic green sulfur bacteria. In Sulfur Metabolism in Phototrophic Organisms, Hell, R., et al. (eds). Netherlands: Springer, pp. 337-355.

García-Cantizano, J., Casamayor, E.O., Gasol, J.M., Guerrero, R., and Pedrós-Alió, C. (2005) Partitioning of CO2 incorporation among planktonic microbial guilds and estimation of in situ specific growth rates. Microb Ecol 50: 230-241.

Gemayel, E., Hassoun, A.E.R., Benallal, M.A., Goyet, C., Rivaro, P., Abboud-Abi Saab, M., et al. (2015) Climatological variations of total alkalinity and total dissolved inorganic carbon in the Mediterranean Sea surface waters. Earth Syst Dynam 6: 789-800.

Gorlenko, V.M. (1970) A new phototrophic green sulfur bacterium-- Prosthecochloris aestuarii nov. gen. nov. sp. Z Allg Mikrobiol 10: 147-149.

Gruber-Vodicka, H.R., Seah, B.K., and Pruesse, E. (2019) phyloFlash - rapid SSU rRNA profiling and targeted assembly from metagenomes. bioRxiv 521922.

Guerrero, R., Montesinos, E., Pedrós-Alió, C., Esteve, I., Mas, J., Van Gemerden, H., et al. (1985) Phototrophic sulfur bacteria in two Spanish lakes: vertical distribution and limiting factors. Limnol Oceanogr 30: 919-931.

Harada, J., Mizoguchi, T., Satoh, S., Tsukatani, Y., Yokono, M., Noguchi, M., et al. (2013) Specific gene bciD for C7-methyl oxidation in bacteriochlorophyll e biosynthesis of brown-colored green sulfur bacteria. PLoS One 8: e60026.

Imhoff, J.F. (2006a) The Chromatiaceae. In Prokaryotes 6, Dworkin, M., Falkow, S., Rosenberg, E., Schleifer, K.-H., and Stackebrandt, E. (eds). Berlin, Heidelberg: Springer-Verlag, pp. 846-873.

Imhoff, J.F. (2006b) The family Ectothiorhodospiraceae. In Prokaryotes 6, Dworkin, M., Falkow, S., Rosenberg, E., Schleifer, K.-H., and Stackebrandt, E. (eds). Berlin, Heidelberg: Springer-Verlag, pp. 874-886.

Jørgensen, B.B., Kuenen, J.G., and Cohen, Y. (1979) Microbial transformations of sulfur compounds in a stratified Lake (solar lake, Sinai). Limnol Oceanogr 24: 799-822.

Kamyshny, A., Jr., Zerkle, A.L., Mansaray, Z.F., Ciglenečki, I., Bura-Nakić, E., Farquhar, J., and Ferdelman, T.G. (2011) Biogeochemical sulfur cycling in the water column of a shallow stratified sea-water lake: speciation and quadruple sulfur isotope composition. Mar Chem 127: 144-154.

Kumar, P.A., Srinivas, T.N.R., Sasikala, C., and Ramana, C.V. (2007) Halochromatium roseum sp. nov., a non-motile phototrophic gammaproteobacterium with gas vesicles, and emended description of the genus Halochromatium. Int J Syst Evol Micr 57: 2110-2113.

Letunic, I., and Bork, P. (2016) Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nuc Acid Res 44: W242-W245.

Lipizer, M., Partescano, E., Rabitti, A., Giorgetti, A., and Crise, A. (2014) Qualified temperature, salinity and dissolved oxygen climatologies in a changing Adriatic Sea. Ocean Science 10: 771-797.

Llorens-Marès, T., Yooseph, S., Goll, J., Hoffman, J., Vila-Costa, M., Borrego, C.M., et al. (2015) Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics. ISME J 9: 1648-1661.

Luedin, S.M., Storelli, N., Danza, F., Roman, S., Wittwer, M., Pothier, J.F., and Tonolla, M. (2019) Mixotrophic growth under micro-oxic conditions in the purple Sulfur bacterium “Thiodictyon syntrophicum”. Front Microbiol 10: 384.

Malešević, N., Ciglenečki, I., Bura-Nakić, E., Carić, M., Dupčić, I., Hrustić, E., et al. (2015) Diatoms in an extreme euxinic environment (Rogoznica Lake, eastern Adriatic coast). Acta Bot Croat 74: 333-343.

Marie, D., Partensky, F., Jacquet, S., and Vaulot, D. (1997) Enumeration and cell cycle analysis of natural populations of marine picoplankton by flow cytometry using the nucleic acid stain. SYBR Green I Appl Eviron Microbiol 63: 186-193.

Marschall, E., Jogler, M., Hessge, U., and Overmann, J. (2010) Large-scale distribution and activity patterns of an extremely low-light-adapted population of green sulfur bacteria in the Black Sea. Environ Microbiol 12: 1348-1362.

Mas, J., and van Gemerden, H. (1995) Storage products in purple and green sulfur bacteria. In Anoxygenic Photosynthetic Bacteria, Blankenship, R.E., Madigan, M.T., and Bauer, C.E. (eds). Dordrecht: Springer, pp. 973-990.

Massana, R., Murray, A.E., Preston, C.M., and DeLong, E.F. (1997) Vertical distribution and phylogenetic characterization of marine planktonic archaea in the Santa Barbara Channel. Appl Environ Microbiol 63: 50-56.

Morana, C., Roland, F.A., Crowe, S.A., Llirós, M., Borges, A.V., Darchambeau, F., and Bouillon, S. (2016) Chemoautotrophy and anoxygenic photosynthesis within the water column of a large meromictic tropical Lake (lake Kivu, East Africa). Limnol Oceanogr 61: 1424-1437.

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 U S A 105: 17861-17866.

Mußmann, M., Pjevac, P., Krüger, K., and Dyksma, S. (2017) Genomic repertoire of the Woeseiaceae/JTB255, cosmopolitan and abundant core members of microbial communities in marine sediments. ISME J 11: 1276-1281.

Overmann, J., Cypionka, H., and Pfennig, N. (1992) An extremely low-light-adapted phototrophic sulfur bacterium from the Black Sea. Limnol Oceanogr 37: 150-155.

Overmann, J. (2006) The family Chlorobiaceae. In Prokaryotes 6, Dworkin, M., Falkow, S., Rosenberg, E., Schleifer, K.-H., and Stackebrandt, E. (eds). Berlin, Heidelberg: Springer-Verlag, pp. 359-378.

Overmann, J., and Garcia-Pichel, F. (2013) The phototrophic way of life. In Prokaryotes, Rosenberg, E., DeLong, E.F., Lory, S., Stackebrandt, E., and Thompson, F. (eds). Berlin, Heidelberg: Springer-Verlag, pp. 203-257.

Parks, D.H., Imelfort, M., Skennerton, C.T., Hugenholtz, P., and Tyson, G.W. (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2: 1043-1055. https://10.1101/gr.186072.11425/7/1043.

Pjevac, P., Korlević, M., Berg, J.S., Bura-Nakić, E., Ciglenečki, I., Amann, R., and Orlić, S. (2015) Community shift from phototrophic to chemotrophic sulfide oxidation following anoxic holomixis in a stratified seawater lake. Appl Environ Microbiol 81: 298-308.

Pruesse, E., Peplies, J., and Glöckner, F.O. (2012) SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28: 1823-1829.

Rodriguez-R, L.M., Gunturu, S., Harvey, W.T., Rosselló-Mora, R., Tiedje, J.M., Cole, J.R., and Konstantinidis, K.T. (2018) The microbial genomes atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and bacteria at the whole genome level. Nuc Acid Res 46: W282-W288.

Scheer, H. (2006) An overview of chlorophylls and bacteriochlorophylls: biochemistry, biophysics, functions and applications. In Chlorophylls and Bacteriochlorophylls, Grimm, B., Porra, R.J., Rüdiger, W., and Scheer, H. (eds). Dordrecht: Springer, pp. 1-26.

Stomp, M., Huisman, J., Stal, L.J., and Matthijs, H.C. (2007) Colorful niches of phototrophic microorganisms shaped by vibrations of the water molecule. ISME J 1: 271-282.

Storelli, N., Peduzzi, S., Saad, M.M., Frigaard, N.U., Perret, X., and Tonolla, M. (2013) CO2 assimilation in the chemocline of Lake Cadagno is dominated by a few types of phototrophic purple sulfur bacteria. FEMS Microbiol Ecol 84: 421-432.

Strous, M., Kraft, B., Bisdorf, R., and Tegetmeyer, H. (2012) The binning of metagenomic contigs for microbial physiology of mixed cultures. Front Microbiol 3: 410.

Trifinopoulos, J., Nguyen, L.T., von Haeseler, A., and Minh, B.Q. (2016) W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nuc Acid Res 44: W232-W235.

Vila-Costa, M., Simó, R., Harada, H., Gasol, J.M., Slezak, D., and Kiene, R.P. (2006) Dimethylsulfoniopropionate uptake by marine phytoplankton. Science 314: 652-654.

Zimmermann, M., Escrig, S., Hübschmann, T., Kirf, M.K., Brand, A., Inglis, R.F., et al. (2015) Phenotypic heterogeneity in metabolic traits among single cells of a rare bacterial species in its natural environment quantified with a combination of flow cell sorting and NanoSIMS. Front Microbiol 6: 243.

Zopfi, J., Ferdelman, T.G., and Fossing, H. (2004) Distribution and fate of sulfur intermediates - sulfite, tetrathionate, thiosulfate, and elemental sulfur - in marine sediments. Geol Soc Am Spec P 379: 97-116.

Zubkov, M.V., Fuchs, B.M., Tarran, G.A., Burkill, P.H., and 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.

Žic, V., Carić, M., and Ciglenečki, I. (2013) The impact of natural water column mixing on iodine and nutrient speciation in a eutrophic anchialine pond (Rogoznica Lake, Croatia). Estuar Coast Shelf Sci 133: 260-272.