Phytoplankton is a key component of aquatic microbial communities, and metabolic coupling between phytoplankton and bacteria determines the fate of dissolved organic carbon (DOC). Yet, the impact of primary production on bacterial activity and community composition remains largely unknown, as, for example, in the case of aerobic anoxygenic phototrophic (AAP) bacteria that utilize both phytoplankton-derived DOC and light as energy sources. Here, we studied how reduction of primary production in a natural freshwater community affects the bacterial community composition and its activity, focusing primarily on AAP bacteria. The bacterial respiration rate was the lowest when photosynthesis was reduced by direct inhibition of photosystem II and the highest in ambient light condition with no photosynthesis inhibition, suggesting that it was limited by carbon availability. However, bacterial assimilation rates of leucine and glucose were unaffected, indicating that increased bacterial growth efficiency (e.g., due to photoheterotrophy) can help to maintain overall bacterial production when low primary production limits DOC availability. Bacterial community composition was tightly linked to light intensity, mainly due to the increased relative abundance of light-dependent AAP bacteria. This notion shows that changes in bacterial community composition are not necessarily reflected by changes in bacterial production or growth and vice versa. Moreover, we demonstrated for the first time that light can directly affect bacterial community composition, a topic which has been neglected in studies of phytoplankton-bacteria interactions.IMPORTANCE Metabolic coupling between phytoplankton and bacteria determines the fate of dissolved organic carbon in aquatic environments, and yet how changes in the rate of primary production affect the bacterial activity and community composition remains understudied. Here, we experimentally limited the rate of primary production either by lowering light intensity or by adding a photosynthesis inhibitor. The induced decrease had a greater influence on bacterial respiration than on bacterial production and growth rate, especially at an optimal light intensity. This suggests that changes in primary production drive bacterial activity, but the effect on carbon flow may be mitigated by increased bacterial growth efficiencies, especially of light-dependent AAP bacteria. Bacterial activities were independent of changes in bacterial community composition, which were driven by light availability and AAP bacteria. This direct effect of light on composition of bacterial communities has not been documented previously.

Center Algatech Institute of Microbiology Czech Academy of Sciences Třeboň Czechia

Department Experimental Limnology Leibniz Institute of Freshwater Ecology and Inland Fisheries Stechlin Germany

Department of Aquatic Ecology Netherlands Institute of Ecology Wageningen The Netherlands

Department of Life and Environmental Sciences Università Politecnica delle Marche Ancona Italy

Department of Natural Sciences University of Agder Kristiansand Norway

Great Lakes Institute for Environmental Research University of Windsor Windsor Ontario Canada

Haifa University Haifa Israel

Institute of Biochemistry and Biology Potsdam University Potsdam Germany

Institute of Hydrobiology Biology Centre Czech Academy of Sciences České Budějovice Czechia

Institute of Oceanography and Fisheries Split Croatia

Israel Oceanographic and Limnological Research National Center for Mariculture Eilat Israel

Marine Research Centre Finnish Environment Institute Helsinki Finland

University Institute of Water Research University of Granada Granada Spain

Erratum v

mSphere. 2020 Jul 15;5(4):e00673-20. doi: 10.1128/mSphere.00673-20 PubMed

Zobrazit více v PubMed

Brett MT, Bunn SE, Chandra S, Galloway AWE, Guo F, Kainz MJ, Kankaala P, Lau DCP, Moulton TP, Power ME, Rasmussen JB, Taipale SJ, Thorp JH, Wehr JD. 2017. How important are terrestrial organic carbon inputs for secondary production in freshwater ecosystems? Freshw Biol 62:833–853. doi:10.1111/fwb.12909. DOI

Guillemette F, McCallister SL, del Giorgio PA. 2016. Selective consumption and metabolic allocation of terrestrial and algal carbon determine allochthony in lake bacteria. ISME J 10:1373–1382. doi:10.1038/ismej.2015.215. PubMed DOI PMC

Hawkes J, Patriarca C, Sjöberg P, Tranvik L, Bergquist J. 2018. Extreme isomeric complexity of dissolved organic matter found across aquatic environments: extreme isomeric complexity of DOM. Limnol Oceanogr 3:21–30. doi:10.1002/lol2.10064. DOI

Koehler B, Wachenfeldt E, Kothawala D, Tranvik L. 2012. Reactivity continuum of dissolved organic carbon decomposition in lake water. J Geophysical Res (Biogeosciences) 117:1024.

Maki K, Kim C, Yoshimizu C, Tayasu I, Miyajima T, Nagata T. 2010. Autochthonous origin of semi-labile dissolved organic carbon in a large monomictic lake (Lake Biwa): carbon stable isotopic evidence. Limnology 11:143–153. doi:10.1007/s10201-009-0299-z. DOI

Toming K, Tuvikene L, Vilbaste S, Agasild H, Viik M, Kisand A, Feldmann T, Martma T, Jones R, Noges T. 2013. Contributions of autochthonous and allochthonous sources to dissolved organic matter in a large, shallow, eutrophic lake with a highly calcareous catchment. Limnol Oceanogr 58:1259–1270. doi:10.4319/lo.2013.58.4.1259. DOI

Fouilland E, Mostajir B. 2010. Revisited phytoplanktonic carbon dependency of heterotrophic bacteria in freshwaters, transitional, coastal and oceanic waters. FEMS Microbiol Ecol 73:419–429. doi:10.1111/j.1574-6941.2010.00896.x. PubMed DOI

Šimek K, Horňák K, Jezbera J, Nedoma J, Znachor P, Hejzlar J, Sed’a J. 2008. Spatio-temporal patterns of bacterioplankton production and community composition related to phytoplankton composition and protistan bacterivory in a dam reservoir. Aquat Microb Ecol 51:249–262. doi:10.3354/ame01193. DOI

Kritzberg ES, Cole JJ, Pace ML, Graneli W, Bade DL. 2004. Autochthonous versus allochthonous carbon sources of bacteria: results from whole-lake C-13 addition experiments. Limnol Oceanogr 49:588–596. doi:10.4319/lo.2004.49.2.0588. DOI

Kritzberg ES, Cole JJ, Pace MM, Graneli W. 2005. Does autochthonous primary production drive variability in bacterial metabolism and growth efficiency in lakes dominated by terrestrial C inputs? Aquat Microb Ecol 38:103–111. doi:10.3354/ame038103. DOI

Bertilsson S, Jones JB. 2003. Supply of dissolved organic matter to aquatic ecosystems: autochthonous sources, p 3–24. In Findlay SEG, Sinsabaugh RL (ed), Aquatic ecosystems. Academic Press, Burlington, VT.

Eiler A, Heinrich F, Bertilsson S. 2012. Coherent dynamics and association networks among lake bacterioplankton taxa. ISME J 6:330–342. doi:10.1038/ismej.2011.113. PubMed DOI PMC

Camarena-Gómez MT, Lipsewers T, Piiparinen J, Eronen-Rasimus E, Perez-Quemaliños D, Hoikkala L, Sobrino C, Spilling K. 2018. Shifts in phytoplankton community structure modify bacterial production, abundance and community composition. Aquat Microb Ecol 81:149–170. doi:10.3354/ame01868. DOI

Šimek K, Nedoma J, Znachor P, Kasalický V, Jezbera J, Horňák K, Sed’a J. 2014. A finely tuned symphony of factors modulates the microbial food web of a freshwater reservoir in spring. Limnol Oceanogr 59:1477–1492. doi:10.4319/lo.2014.59.5.1477. DOI

Eckert EM, Salcher MM, Posch T, Eugster B, Pernthaler J. 2012. Rapid successions affect microbial N-acetyl-glucosamine uptake patterns during a lacustrine spring phytoplankton bloom. Environ Microbiol 14:794–806. doi:10.1111/j.1462-2920.2011.02639.x. PubMed DOI

Horňák K, Kasalický V, Šimek K, Grossart HP. 2017. Strain-specific consumption and transformation of alga-derived dissolved organic matter by members of the Limnohabitans-C and Polynucleobacter-B clusters of Betaproteobacteria. Environ Microbiol 19:4519–4535. doi:10.1111/1462-2920.13900. PubMed DOI

Wang H, Zhu R, Zhang X, Li Y, Ni L, Xie P, Shen H. 2019. Abiotic environmental factors override phytoplankton succession in shaping both free-living and attached bacterial communities in a highland lake. AMB Express 9:170. doi:10.1186/s13568-019-0889-z. PubMed DOI PMC

Danger M, Leflaive J, Oumarou C, Ten-Hage L, Lacroix G. 2007. Control of phytoplankton-bacterium interactions by stoichiometric constraints. Oikos 116:1079–1086. doi:10.1111/j.2007.0030-1299.15424.x. DOI

Gurung TB, Urabe J, Nakanishi M. 1999. Regulation of the relationship between phytoplankton Scenedesmus acutus and heterotrophic bacteria by the balance of light and nutrients. Aquat Microb Ecol 17:27–35. doi:10.3354/ame017027. DOI

Mindl B, Sonntag B, Pernthaler J, Vrba J, Psenner R, Posch T. 2005. Effects of phosphorus loading on interactions of algae and bacteria: reinvestigation of the “phytoplankton-bacterium paradox” in a continuous cultivation system. Aquat Microb Ecol 38:203–213. doi:10.3354/ame038203. DOI

Paver SF, Kent AD. 2017. Direct and context-dependent effects of light, temperature, and phytoplankton shape bacterial community composition. Ecosphere 8:e01948. doi:10.1002/ecs2.1948. DOI

Pope CA, Halvorson HM, Findlay RH, Francoeur SN, Kuehn KA. 2020. Light and temperature mediate algal stimulation of heterotrophic activity on decomposing leaf litter. Freshw Biol doi:10.1111/fwb.13465. DOI

Durán-Romero C, Medina-Sánchez JM, Carrillo P. 2020. Uncoupled phytoplankton-bacterioplankton relationship by multiple drivers interacting at different temporal scales in a high-mountain Mediterranean lake. Sci Rep 10:350. doi:10.1038/s41598-020-62863-6. PubMed DOI PMC

Garcia SL, Szekely AJ, Bergvall C, Schattenhofer M, Peura S. 2019. Decreased snow cover stimulates under-ice primary producers but impairs methanotrophic capacity. mSphere 4:e00626-18. doi:10.1128/mSphere.00626-18. PubMed DOI PMC

Yurkov VV, Beatty JT. 1998. Aerobic anoxygenic phototrophic bacteria. Microbiol Mol Biol Rev 62:695–724. doi:10.1128/MMBR.62.3.695-724.1998. PubMed DOI PMC

Hauruseu D, Koblížek M. 2012. Influence of light on carbon utilization in aerobic anoxygenic phototrophs. Appl Environ Microbiol 78:7414–7419. doi:10.1128/AEM.01747-12. PubMed DOI PMC

Piwosz K, Kaftan D, Dean J, Šetlík J, Koblížek M. 2018. Non-linear effect of irradiance on photoheterotrophic activity and growth of the aerobic anoxygenic phototrophic bacterium Dinoroseobacter shibae. Environ Microbiol 20:724–733. doi:10.1111/1462-2920.14003. PubMed DOI

Garcia-Chaves MC, Cottrell MT, Kirchman DL, Ruiz-González C, Del Giorgio PA. 2016. Single-cell activity of freshwater aerobic anoxygenic phototrophic bacteria and their contribution to biomass production. ISME J 10:1579–1588. doi:10.1038/ismej.2015.242. PubMed DOI PMC

Ferrera I, Gasol JM, Sebastian M, Hojerová E, Koblížek M. 2011. Comparison of growth rates of aerobic anoxygenic phototrophic bacteria and other bacterioplankton groups in coastal Mediterranean waters. Appl Environ Microbiol 77:7451–7458. doi:10.1128/AEM.00208-11. PubMed DOI PMC

Martinez-Garcia M, Swan BK, Poulton NJ, Gomez ML, Masland D, Sieracki ME, Stepanauskas R. 2012. High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton. ISME J 6:113–123. doi:10.1038/ismej.2011.84. PubMed DOI PMC

Kasalický V, Zeng Y, Piwosz K, Šimek K, Kratochvilová H, Koblížek M. 2017. Common presence of aerobic anoxygenic photosynthesis within the genus Limnohabitans. Appl Environ Microbiol 84:e02116-17. doi:10.1128/AEM.02116-17. PubMed DOI PMC

Kolářová E, Medová H, Piwosz K, Koblížek M. 2019. Seasonal dynamics of aerobic anoxygenic phototrophs in freshwater lake Vlkov. Folia Microbiol 64:705–710. doi:10.1007/s12223-019-00735-x. PubMed DOI

Cepáková Z, Hrouzek P, Žišková E, Nuyanzina-Boldareva E, Šorf M, Kozlíková-Zapomělová E, Salka I, Grossart H-P, Koblížek M. 2016. High turnover rates of aerobic anoxygenic phototrophs in European freshwater lakes. Environ Microbiol 18:5063–5071. doi:10.1111/1462-2920.13475. PubMed DOI

González-Olalla JM, Medina-Sánchez JM, Lozano IL, Villar-Argaiz M, Carrillo P. 2018. Climate-driven shifts in algal-bacterial interaction of high-mountain lakes in two years spanning a decade. Sci Rep 8:10278. doi:10.1038/s41598-018-28543-2. PubMed DOI PMC

Grossart H-P, Czub G, Simon M. 2006. Algae-bacteria interactions and their effects on aggregation and organic matter flux in the sea. Environ Microbiol 8:1074–1084. doi:10.1111/j.1462-2920.2006.00999.x. PubMed DOI

Grossart H-P. 1999. Interactions between marine bacteria and axenic diatoms (Cylindrotheca fusiformis, Nitzschia laevis, and Thalassiosira weissflogii) incubated under various conditions in the lab. Aquat Microb Ecol 19:1–11. doi:10.3354/ame019001. DOI

Hosler JP, Yocum CF. 1987. Regulation of cyclic photophosphorylation during ferredoxin-mediated electron transport. Plant Physiol 83:965–969. doi:10.1104/pp.83.4.965. PubMed DOI PMC

Nedoma J, Porcalová P, Komárková J, Vyhnálek V. 1993. A seasonal study of phosphorus deficiency in a eutrophic reservoir. Freshwater Biol 30:369–376. doi:10.1111/j.1365-2427.1993.tb00821.x. DOI

Znachor P, Zapomělová E, Řeháková K, Nedoma J, Šimek K. 2008. The effect of extreme rainfall on summer succession and vertical distribution of phytoplankton in a lacustrine part of a eutrophic reservoir. Aquat Sci 70:77–86. doi:10.1007/s00027-007-7033-x. DOI

Thingstad TF, Bellerby RGJ, Bratbak G, Børsheim KY, Egge JK, Heldal M, Larsen A, Neill C, Nejstgaard J, Norland S, Sandaa RA, Skjoldal EF, Tanaka T, Thyrhaug R, Töpper B. 2008. Counterintuitive carbon-to-nutrient coupling in an Arctic pelagic ecosystem. Nature 455:387–390. doi:10.1038/nature07235. PubMed DOI

Ferrera I, Sánchez O, Kolářová E, Koblížek M, Gasol JM. 2017. Light enhances the growth rates of natural populations of aerobic anoxygenic phototrophic bacteria. ISME J 11:2391–2393. doi:10.1038/ismej.2017.79. PubMed DOI PMC

Šimek K, Weinbauer MG, Horňák K, Jezbera J, Nedoma J, Dolan JR. 2007. Grazer and virus-induced mortality of bacterioplankton accelerates development of Flectobacillus populations in a freshwater community. Environ Microbiol 9:789–800. doi:10.1111/j.1462-2920.2006.01201.x. PubMed DOI

Horňák K, Jezbera J, Nedoma J, Gasol JM, Šimek K. 2006. Effects of resource availability and bacterivory on leucine incorporation in different groups of freshwater bacterioplankton, assessed using microautoradiography. Aquat Microb Ecol 45:277–289. doi:10.3354/ame045277. DOI

Fecskeová LK, Piwosz K, Hanusová M, Nedoma J, Znachor P, Koblížek M. 2019. Diel changes and diversity of pufM expression in freshwater communities of anoxygenic phototrophic bacteria. Sci Rep 9:18766. doi:10.1038/s41598-019-55210-x. PubMed DOI PMC

Shabarova T, Kasalický V, Šimek K, Nedoma J, Znachor P, Posch T, Pernthaler J, Salcher MM. 2017. Distribution and ecological preferences of the freshwater lineage LimA (genus Limnohabitans) revealed by a new double hybridization approach. Environ Microbiol 19:1296–1309. doi:10.1111/1462-2920.13663. PubMed DOI

Ruiz-González C, Simo R, Sommaruga R, Gasol JM. 2013. Away from darkness: a review on the effects of solar radiation on heterotrophic bacterioplankton activity. Front Microbiol 4:131. doi:10.3389/fmicb.2013.00131. PubMed DOI PMC

Znachor P, Nedoma J, Hejzlar J, Seďa J, Kopáček J, Boukal D, Mrkvička T. 2018. Multiple long-term trends and trend reversals dominate environmental conditions in a man-made freshwater reservoir. Sci Total Environ 624:24–33. doi:10.1016/j.scitotenv.2017.12.061. PubMed DOI

Sinning I. 1992. Herbicide binding in the bacterial photosynthetic reaction center. Trends Biochem Sci 17:150–154. doi:10.1016/0968-0004(92)90324-3. PubMed DOI

Lund JWG, Kipling C, Le Cren ED. 1958. The inverted microscope method of estimating algal numbers and the statistical basis of estimations by counting. Hydrobiologia 11:143–170. doi:10.1007/BF00007865. DOI

Peterson BJ. 1980. Aquatic primary productivity and the 14C-CO2 method: a history of the productivity problem. Annu Rev Ecol Syst 11:359–385. doi:10.1146/annurev.es.11.110180.002043. DOI

Hoppe H-G. 1993. Use of fluorogenic model substrates for extracellular enzyme activity (EEA) measurement of bacteria. Lewis Publishers, Boca Raton, FL.

Eaton AD, Franson M. 2005. Standard methods for the examination of water and wastewater. American Public Health Association/American Water Works Association/Water Environment Federation, Washington, DC.

Armstrong FAJ, Stearns CR, Strickland J. 1967. The measurement of upwelling and subsequent biological process by means of the Technicon Autoanalyzer and associated equipment. Deep Sea Res Oceanographic Abstr 14:381–389. doi:10.1016/0011-7471(67)90082-4. DOI

Coleman AW. 1980. Enhanced detection of bacteria in natural environments by fluorochrome staining of DNA. Limnol Oceanogr 25:948–951. doi:10.4319/lo.1980.25.5.0948. DOI

Jochem F. 2001. Morphology and DNA content of bacterioplankton in the northern Gulf of Mexico: analysis by epifluorescence microscopy and flow cytometry. Aquat Microb Ecol 25:179–194. doi:10.3354/ame025179. DOI

Marie D, Partensky F, Jacquet S, 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 Environ Microbiol 63:186–193. doi:10.1128/AEM.63.1.186-193.1997. PubMed DOI PMC

Medina-Sánchez JM, Herrera G, Durán C, Villar-Argaiz M, Carrillo P. 2017. Optode use to evaluate microbial planktonic respiration in oligotrophic ecosystems as an indicator of environmental stress. Aquat Sci 79:529–541. doi:10.1007/s00027-016-0515-y. DOI

Kirchman D, K’nees E, Hodson R. 1985. Leucine incorporation and its potential as a measure of protein-synthesis by bacteria in natural aquatic system. Appl Environ Microbiol 49:599–607. doi:10.1128/AEM.49.3.599-607.1985. PubMed DOI PMC

Simon M, Azam F. 1989. Protein content and protein synthesis rates of planktonic marine bacteria. Mar Ecol Prog Ser 51:201–213. doi:10.3354/meps051201. DOI

Fukuda R, Ogawa H, Nagata T, Koike I. 1998. Direct determination of carbon and nitrogen contents of natural bacterial assemblages in marine environments. Appl Environ Microbiol 64:3352–3358. doi:10.1128/AEM.64.9.3352-3358.1998. PubMed DOI PMC

Nercessian O, Noyes E, Kalyuzhnaya MG, Lidstrom ME, Chistoserdova L. 2005. Bacterial populations active in metabolism of C-1 compounds in the sediment of Lake Washington, a freshwater lake. Appl Environ Microbiol 71:6885–6899. doi:10.1128/AEM.71.11.6885-6899.2005. PubMed DOI PMC

Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glöckner FO. 2013. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 41:e1. doi:10.1093/nar/gks808. PubMed DOI PMC

Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17:10–12. doi:10.14806/ej.17.1.200. DOI

Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. 2016. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods 13:581–583. doi:10.1038/nmeth.3869. PubMed DOI PMC

Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glöckner FO. 2007. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35:7188–7196. doi:10.1093/nar/gkm864. PubMed DOI PMC

Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil P-A, Hugenholtz P. 2018. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 36:996–1004. doi:10.1038/nbt.4229. PubMed DOI

Koblížek M. 2015. Ecology of aerobic anoxygenic phototrophs in aquatic environments. FEMS Microbiol Rev 39:854–870. doi:10.1093/femsre/fuv032. PubMed DOI

Yutin N, Suzuki MT, Béjà O. 2005. Novel primers reveal wider diversity among marine aerobic anoxygenic phototrophs. Appl Environ Microbiol 71:8958–8962. doi:10.1128/AEM.71.12.8958-8962.2005. PubMed DOI PMC

Fish J, Chai B, Wang Q, Sun Y, Brown CT, Tiedje J, Cole J. 2013. FunGene: the functional gene pipeline and repository. Front Microbiol 4:291. doi:10.3389/fmicb.2013.00291. PubMed DOI PMC

Andrei A-Ş, Salcher MM, Mehrshad M, Rychtecký P, Znachor P, Ghai R. 2019. Niche-directed evolution modulates genome architecture in freshwater Planctomycetes. ISME J 13:1056–1071. doi:10.1038/s41396-018-0332-5. PubMed DOI PMC

Mehrshad M, Salcher MM, Okazaki Y, Nakano S-I, Šimek K, Andrei A-S, Ghai R. 2018. Hidden in plain sight: highly abundant and diverse planktonic freshwater Chloroflexi. Microbiome 6:176. doi:10.1186/s40168-018-0563-8. PubMed DOI PMC

Piwosz K, Shabarova T, Pernthaler J, Posch T, Šimek K, Porcal P, Salcher MM. 2020. Bacterial and eukaryotic small-subunit amplicon data do not provide a quantitative picture of microbial communities, but they are reliable in the context of ecological interpretations. mSphere 5:e00052-20. doi:10.1128/mSphere.00052-20. PubMed DOI PMC

Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:550. doi:10.1186/s13059-014-0550-8. PubMed DOI PMC

Ter Braak CJ, Šmilauer P. 2012. Canoco reference manual and user’s guide: software for ordination, version 5.0. Microcomputer Power, Ithaca, NY.

Diversity dynamics of aerobic anoxygenic phototrophic bacteria in a freshwater lake

Photoheterotrophy by aerobic anoxygenic bacteria modulates carbon fluxes in a freshwater lake

Lineage-Specific Growth Curves Document Large Differences in Response of Individual Groups of Marine Bacteria to the Top-Down and Bottom-Up Controls