Members of the bacterial phylum Gemmatimonadota are ubiquitous in most natural environments and represent one of the top 10 most abundant bacterial phyla in soil. Sequences affiliated with Gemmatimonadota were also reported from diverse aquatic habitats; however, it remains unknown whether they are native organisms or represent bacteria passively transported from sediment or soil. To address this question, we analyzed metagenomes constructed from five freshwater lakes in central Europe. Based on the 16S rRNA gene frequency, Gemmatimonadota represented from 0.02 to 0.6% of all bacteria in the epilimnion and between 0.1 and 1% in the hypolimnion. These proportions were independently confirmed using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Some cells in the epilimnion were attached to diatoms (Fragilaria sp.) or cyanobacteria (Microcystis sp.), which suggests a close association with phytoplankton. In addition, we reconstructed 45 metagenome-assembled genomes (MAGs) related to Gemmatimonadota They represent several novel lineages, which persist in the studied lakes during the seasons. Three lineages contained photosynthesis gene clusters. One of these lineages was related to Gemmatimonas phototrophica and represented the majority of Gemmatimonadota retrieved from the lakes' epilimnion. The other two lineages came from hypolimnion and probably represented novel photoheterotrophic genera. None of these phototrophic MAGs contained genes for carbon fixation. Since most of the identified MAGs were present during the whole year and cells associated with phytoplankton were observed, we conclude that they represent truly limnic Gemmatimonadota distinct from the previously described species isolated from soils or sediments.IMPORTANCE Photoheterotrophic bacterial phyla such as Gemmatimonadota are key components of many natural environments. Its first photoheterotrophic cultured member, Gemmatimonas phototrophica, was isolated in 2014 from a shallow lake in the Gobi Desert. It contains a unique type of photosynthetic complex encoded by a set of genes which were likely received via horizontal transfer from Proteobacteria We were intrigued to discover how widespread this group is in the natural environment. In the presented study, we analyzed 45 metagenome-assembled genomes (MAGs) that were obtained from five freshwater lakes in Switzerland and Czechia. Interestingly, it was found that phototrophic Gemmatimonadota are relatively common in euphotic zones of the studied lakes, whereas heterotrophic Gemmatimonadota prevail in deeper waters. Moreover, our analysis of the MAGs documented that these freshwater species contain almost the same set of photosynthesis genes identified before in Gemmatimonas phototrophica originating from the Gobi Desert.

Department of Aquatic Microbial Ecology Institute of Hydrobiology Biology Centre of the Czech Academy of Sciences České Budějovice Czechia

Department of Ecosystem Biology Faculty of Science University of South Bohemia České Budějovice Czechia

Laboratory of Anoxygenic Phototrophs Centre Algatech Institute of Microbiology of the Czech Academy of Sciences Třeboň Czechia

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Giovannoni SJ, Britschgi TB, Moyer CL, Field KG. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60–63. doi:10.1038/345060a0. PubMed DOI

Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil PA, 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

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. doi:10.1038/nmicrobiol.2016.48. PubMed DOI

Whitman WB, Oren A, Chuvochina M, da Costa MS, Garrity GM, Rainey FA, Rossello-Mora R, Schink B, Sutcliffe I, Trujillo ME, Ventura S. 2018. Proposal of the suffix –ota to denote phyla. Addendum to ‘Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes.’ Int J Syst Evol Microbiol 68:967–969. doi:10.1099/ijsem.0.002593. PubMed DOI

Hugenholtz P, Tyson GW, Webb RI, Wagner AM, Blackall LL. 2001. Investigation of candidate division TM7, a recently recognized major lineage of the domain Bacteria, with no known pure-culture representatives. Appl Environ Microbiol 67:411–419. doi:10.1128/AEM.67.1.411-419.2001. PubMed DOI PMC

Mummey DL, Stahl PD. 2003. Candidate division BD: phylogeny, distribution and abundance in soil ecosystems. Syst Appl Microbiol 26:228–235. doi:10.1078/072320203322346074. PubMed DOI

Madrid VM, Aller JY, Aller RC, Chistoserdov AY. 2001. High prokaryote diversity and analysis of community structure in mobile mud deposits off French Guiana: identification of two new bacterial candidate divisions. FEMS Microbiol Ecol 37:197–209. doi:10.1111/j.1574-6941.2001.tb00867.x. DOI

Zhang H, Sekiguchi Y, Hanada S, Hugenholtz P, Kim H, Kamagata Y, Nakamura K. 2003. Gemmatimonas aurantiaca gen. nov., sp. nov., a Gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov. Int J Syst Evol Microbiol 53:1155–1163. doi:10.1099/ijs.0.02520-0. PubMed DOI

DeBruyn JM, Fawaz MN, Peacock AD, Dunlap JR, Nixon LT, Cooper KE, Radosevich M. 2013. Gemmatirosa kalamazoonesis gen. nov., sp. nov., a member of the rarely-cultivated bacterial phylum Gemmatimonadetes. J Gen Appl Microbiol 59:305–312. doi:10.2323/jgam.59.305. PubMed DOI

Pascual J, García-López M, Bills GF, Genilloud O. 2016. Longimicrobium terrae gen. nov., sp. nov., an oligotrophic bacterium of the under-represented phylum Gemmatimonadetes isolated through a system of miniaturized diffusion chambers. Int J Syst Evol Microbiol 66:1976–1985. doi:10.1099/ijsem.0.000974. PubMed DOI

Pascual J, Foesel BU, Geppert A, Huber KJ, Boedeker C, Luckner M, Wanner G, Overmann J. 2018. Roseisolibacter agri gen. nov., sp. nov., a novel slow-growing member of the under-represented phylum Gemmatimonadetes. Int J Syst Evol Microbiol 68:1028–1036. doi:10.1099/ijsem.0.002619. PubMed DOI

Hanada S, Sekiguchi Y. 2014. The phylum Gemmatimonadetes, p 677–681. In Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (ed), The prokaryotes, 4th ed, vol 11. Springer, Berlin, Germany.

Park D, Kim H, Yoon S. 2017. Nitrous oxide reduction by an obligate aerobic bacterium, Gemmatimonas aurantiaca strain T-27. Appl Environ Microbiol 83:e00502-17. doi:10.1128/AEM.00502-17. PubMed DOI PMC

Zeng Y, Feng F, Medová H, Dean J, Koblížek M. 2014. Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes. Proc Natl Acad Sci U S A 111:7795–7800. doi:10.1073/pnas.1400295111. PubMed DOI PMC

Dachev M, Bína D, Sobotka R, Moravcová L, Gardian Z, Kaftan D, Šlouf V, Fuciman M, Polívka T, Koblížek M. 2017. Unique double concentric ring organization of light harvesting complexes in Gemmatimonas phototrophica. PLoS Biol 15:e2003943. doi:10.1371/journal.pbio.2003943. PubMed DOI PMC

Ward LM, Cardona T, Holland-Moritz H. 2019. Evolutionary implications of anoxygenic phototrophy in the bacterial phylum Candidatus Eremiobacterota (WPS-2). Front Microbiol 10:1658. doi:10.3389/fmicb.2019.01658. PubMed DOI PMC

Cardona T. 2019. Thinking twice about the evolution of photosynthesis. Open Biol 9:180246. doi:10.1098/rsob.180246. PubMed DOI PMC

Zeng Y, Selyanin V, Lukeš M, Dean J, Kaftan D, Feng F, Koblížek M. 2015. Characterization of the microaerophilic, bacteriochlorophyll a-containing bacterium Gemmatimonas phototrophica sp. nov., and emended descriptions of the genus Gemmatimonas and Gemmatimonas aurantiaca. Int J Syst Evol Microbiol 65:2410–2419. doi:10.1099/ijs.0.000272. PubMed DOI

Cardona T. 2016. Origin of bacteriochlorophyll a and the early diversification of photosynthesis. PLoS One 11:e0151250. doi:10.1371/journal.pone.0151250. PubMed DOI PMC

DeBruyn JM, Nixon LT, Fawaz MN, Johnson AM, Radosevich M. 2011. Global biogeography and quantitative seasonal dynamics of Gemmatimonadetes in soil. Appl Environ Microbiol 77:6295–6300. doi:10.1128/AEM.05005-11. PubMed DOI PMC

Zeng Y, Baumbach J, Barbosa EGV, Azevedo V, Zhang C, Koblížek M. 2016. Metagenomic evidence for the presence of phototrophic Gemmatimonadetes bacteria in diverse environments. Environ Microbiol Rep 8:139–149. doi:10.1111/1758-2229.12363. PubMed DOI

Huang Y, Zeng Y, Lu H, Feng H, Zeng Y, Koblížek M. 2016. Novel acsF gene primers revealed a diverse phototrophic bacterial population, including Gemmatimonadetes, in Lake Taihu (China). Appl Environ Microbiol 82:5587–5594. doi:10.1128/AEM.01063-16. PubMed DOI PMC

Delgado-Baquerizo M, Oliverio AM, Brewer TE, Benavent-González A, Eldridge DJ, Bardgett RD, Maestre FT, Singh BK, Fierer N. 2018. A global atlas of the dominant bacteria found in soil. Science 359:320–325. doi:10.1126/science.aap9516. PubMed DOI

Cary SC, McDonald IR, Barrett JE, Cowan DA. 2010. On the rocks: the microbiology of Antarctic Dry Valley soils. Nat Rev Microbiol 8:129–138. doi:10.1038/nrmicro2281. PubMed DOI

Bakermans C, Skidmore ML, Douglas S, McKay CP. 2014. Molecular characterization of bacteria from permafrost of the Taylor Valley, Antarctica. FEMS Microbiol Ecol 89:331–346. doi:10.1111/1574-6941.12310. PubMed DOI

Ren C, Chen J, Lu X, Doughty R, Zhao F, Zhong Z, Han X, Yang G, Feng Y, Ren G. 2018. Responses of soil total microbial biomass and community compositions to rainfall reductions. Soil Biol Biochem 116:4–10. doi:10.1016/j.soilbio.2017.09.028. 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

Song H, Li Z, Du B, Wang G, Ding Y. 2012. Bacterial communities in sediments of the shallow Lake Dongping in China. J Appl Microbiol 112:79–89. doi:10.1111/j.1365-2672.2011.05187.x. PubMed DOI

Zhang J, Yang Y, Zhao L, Li Y, Xie S, Liu Y. 2015. Distribution of sediment bacterial and archaeal communities in plateau freshwater lakes. Appl Microbiol Biotechnol 99:3291–3302. doi:10.1007/s00253-014-6262-x. PubMed DOI

Gugliandolo C, Michaud L, Lo Giudice A, Lentini V, Rochera C, Camacho A, Maugeri TL. 2016. Prokaryotic community in lacustrine sediments of Byers Peninsula (Livingston Island, Maritime Antarctica). Microb Ecol 71:387–400. doi:10.1007/s00248-015-0666-8. PubMed DOI

Gołębiewski M, Całkiewicz J, Creer S, Piwosz K. 2017. Tideless estuaries in brackish seas as possible freshwater-marine transition zones for bacteria: the case study of the Vistula river estuary. Environ Microbiol Rep 9:129–143. doi:10.1111/1758-2229.12509. PubMed DOI

Traving SJ, Rowe O, Jakobsen NM, Sørensen H, Dinasquet J, Stedmon CA, Andersson A, Riemann L. 2017. The effect of increased loads of dissolved organic matter on estuarine microbial community composition and function. Front Microbiol 8:351. doi:10.3389/fmicb.2017.00351. PubMed DOI PMC

Parks DH, Rinke C, Chuvochina M, Chaumeil PA, Woodcroft BJ, Evans PN, Hugenholtz P, Tyson GW. 2017. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat Microbiol 2:1533–1542. doi:10.1038/s41564-017-0012-7. PubMed DOI

Holland-Moritz H, Stuart J, Lewis LR, Miller S, Mack MC, McDaniel SF, Fierer N. 2018. Novel bacterial lineages associated with boreal moss species. Environ Microbiol 20:2625–2638. doi:10.1111/1462-2920.14288. PubMed DOI

Cabello-Yeves PJ, Zemskaya TI, Rosselli R, Coutinho FH, Zakharenko AS, Blinov VV, Rodriguez-Valera F. 2017. Genomes of novel microbial lineages assembled from the sub-ice waters of Lake Baikal. Appl Environ Microbiol 84:e02132-17. doi:10.1128/AEM.02132-17. PubMed DOI PMC

Zeng Y, Nupur, Wu N, Madsen AM, Chen X, Gardiner AT, Koblížek M. 2021. Gemmatimonas groenlandica sp. nov. is an aerobic anoxygenic phototroph in the phylum Gemmatimonadetes. Front Microbiol 11:606612. doi:10.3389/fmicb.2020.606612. PubMed DOI PMC

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

Konstantinidis KT, Rosselló-Móra R, Amann R. 2017. Uncultivated microbes in need of their own taxonomy. ISME J 11:2399–2406. doi:10.1038/ismej.2017.113. PubMed DOI PMC

Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. 2019. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 36:1925–1927. doi:10.1093/bioinformatics/btz848. PubMed DOI PMC

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

Kavagutti VS, Andrei AŞ, Mehrshad M, Salcher MM, Ghai R. 2019. Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics. Microbiome 7:135. doi:10.1186/s40168-019-0752-0. PubMed DOI PMC

Ameryk A, Kownacka J, Zalewski M, Piwosz K. 2021. Typical freshwater and marine bacterial lineages dynamics at salinity between 0 and 4 in the Vistula Lagoon. Estuar Coast Shelf Sci 250:107100. doi:10.1016/j.ecss.2020.107100. DOI

Morrison JM, Baker KD, Zamor RM, Nikolai S, Elshahed MS, Youssef NH. 2017. Spatiotemporal analysis of microbial community dynamics during seasonal stratification events in a freshwater lake (Grand Lake, OK, USA). PLoS One 12:e0177488. doi:10.1371/journal.pone.0177488. PubMed DOI PMC

Cai H, Jiang H, Krumholz LR, Yang Z. 2014. Bacterial community composition of size-fractioned aggregates within the phycosphere of cyanobacterial blooms in a eutrophic freshwater lake. PLoS One 9:e102879. doi:10.1371/journal.pone.0102879. PubMed DOI PMC

Shia L, Cai Y, Wang X, Li P, Yu Y, Kong F. 2010. Community structure of bacteria associated with Microcystis colonies from cyanobacterial blooms. J Freshw Ecol 25:193–203. doi:10.1080/02705060.2010.9665068. DOI

Fauteux L, Cottrell MT, Kirchman DL, Borrego CM, Garcia-Chaves MC, Del Giorgio PA. 2015. Patterns in abundance, cell size and pigment content of aerobic anoxygenic phototrophic bacteria along environmental gradients in northern lakes. PLoS One 10:e0124035. doi:10.1371/journal.pone.0124035. PubMed DOI PMC

Hauruseu D, Koblízek 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

Xing P, Kong F, Cao H, Zhang M, Tan X. 2007. Variations of bacterioplankton community composition during Microcystis spp. blooms in a shallow eutrophic lake. J Freshw Ecol 22:61–67. doi:10.1080/02705060.2007.9664146. DOI

Šimek K, Horňák K, Jezbera J, Mašín M, Nedoma J, Gasol JM, Schauer M. 2005. Influence of top-down and bottom-up manipulations on the R-BT065 subcluster of β-proteobacteria, an abundant group in bacterioplankton of a freshwater reservoir. Appl Environ Microbiol 71:2381–2390. doi:10.1128/AEM.71.5.2381-2390.2005. PubMed DOI PMC

Salcher MM, Pernthaler J, Posch T. 2011. Seasonal bloom dynamics and ecophysiology of the freshwater sister clade of SAR11 bacteria that rule the waves (LD12). ISME J 5:1242–1252. doi:10.1038/ismej.2011.8. PubMed DOI PMC

Simek K, Hornák 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

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

Goecke F, Thiel V, Wiese J, Labes A, Imhoff JF. 2013. Algae as an important environment for bacteria – phylogenetic relationships among new bacterial species isolated from algae. Phycologia 52:14–24. doi:10.2216/12-24.1. DOI

Piwosz K, Vrdoljak A, Frenken T, González-Olalla JM, Šantić D, McKay RM, Spilling K, Guttman L, Znachor P, Mujakić I, Fecskeová LK, Zoccarato L, Hanusová M, Pessina A, Reich T, Grossart H-P, Koblížek M. 2020. Light and primary production shape bacterial activity and community composition of aerobic anoxygenic phototrophic bacteria in a microcosm experiment. mSphere 5:e00673-20. doi:10.1128/mSphere.00673-20. PubMed DOI PMC

Zheng Q, Zhang R, Koblížek M, Boldareva EN, Yurkov V, Yan S, Jiao N. 2011. Diverse arrangement of photosynthetic gene clusters in aerobic anoxygenic phototrophic bacteria. PLoS One 6:e25050. doi:10.1371/journal.pone.0025050. PubMed DOI PMC

Hendrickson EL, Leigh JA. 2008. Roles of coenzyme F420-reducing hydrogenases and hydrogen- and F420-dependent methylenetetrahydromethanopterin dehydrogenases in reduction of F420 and production of hydrogen during methanogenesis. J Bacteriol 190:4818–4821. doi:10.1128/JB.00255-08. PubMed DOI PMC

Vavourakis CD, Mehrshad M, Balkema C, Van Hall R, Andrei AŞ, Ghai R, Sorokin DY, Muyzer G. 2019. Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake. BMC Biol 17:69. doi:10.1186/s12915-019-0688-7. PubMed DOI PMC

Zorz JK, Sharp C, Kleiner M, Gordon PMK, Pon RT, Dong X, Strous M. 2019. A shared core microbiome in soda lakes separated by large distances. Nat Commun 10:4230. doi:10.1038/s41467-019-12195-5. PubMed DOI PMC

Hanson TE, Tabita FR. 2001. A ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO)-like protein from Chlorobium tepidum that is involved with sulfur metabolism and the response to oxidative stress. Proc Natl Acad Sci U S A 98:4397–4402. doi:10.1073/pnas.081610398. PubMed DOI PMC

Tabita FR, Hanson TE, Satagopan S, Witte BH, Kreel NE. 2008. Phylogenetic and evolutionary relationships of RubisCO and the RubisCO-like proteins and the functional lessons provided by diverse molecular forms. Philos Trans R Soc Lond B Biol Sci 363:2629–2640. doi:10.1098/rstb.2008.0023. PubMed DOI PMC

Ashida H, Danchin A, Yokota A. 2005. Was photosynthetic RuBisCO recruited by acquisitive evolution from RuBisCO-like proteins involved in sulfur metabolism? Res Microbiol 156:611–618. doi:10.1016/j.resmic.2005.01.014. PubMed DOI

Ashida H, Saito Y, Kojima C, Kobayashi K, Ogasawara N, Yokota A. 2003. A functional link between RuBisCO-like protein of Bacillus and photosynthetic RuBisCO. Science 302:286–290. doi:10.1126/science.1086997. PubMed DOI

Yurkov V, Hughes E. 2017. Aerobic anoxygenic phototrophs: four decades of mystery, p 193–214. In Modern topics in the phototrophic prokaryotes: environmental and applied aspects. Springer International Publishing, Cham, Switzerland.

Piwosz K, Kaftan D, Dean J, Šetlík J, Koblížek M. 2018. Nonlinear 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

Znachor P, Hejzlar J, Vrba J, Nedoma J, Seda J, Simek K, Komarkova J, Kopacek J, Sorf M, Kubecka J, Matena J, Riha M, Peterka J, Cech M, Vasek M. 2016. Brief history of long-term ecological research into aquatic ecosystems and their catchments in the Czech Republic. Part I: manmade reservoirs. Biology Centre CAS, v.v.i., Institute of Hydrobiology, České Budějovice, Czechia.

Bushnell B. 2015. BBMap (version 35.14). https://sourceforge.net/projects/bbmap/.

Bushnell B, Rood J, Singer E. 2017. BBMerge – accurate paired shotgun read merging via overlap. PLoS One 12:e0185056. doi:10.1371/journal.pone.0185056. PubMed DOI PMC

Bushnell B. 2016. Reformat. https://github.com/BioInfoTools/BBMap/blob/master/sh/reformat.sh.

Li D, Luo R, Liu C-M, Leung C-M, Ting H-F, Sadakane K, Yamashita H, Lam T-W. 2016. MEGAHIT v1.0: a fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods 102:3–11. doi:10.1016/j.ymeth.2016.02.020. PubMed DOI

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

Steinegger M, Söding J. 2017. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat Biotechnol 35:1026–1028. doi:10.1038/nbt.3988. PubMed DOI

Nawrocki EP. 2009. Structural RNA homology search and alignment using covariance models. PhD thesis. Washington University in St. Louis, St. Louis, MO.

Anderson MJ, Legendre P. 1999. An empirical comparison of permutation methods for tests of partial regression coefficients in a linear model. J Stat Comput Simul 62:271–303. doi:10.1080/00949659908811936. DOI

Legendre P, Anderson MJ. 1999. Distance-based redundancy analysis: testing multispecies responses in multifactorial ecological experiments. Ecol Monogr 69:1–24. doi:10.1890/0012-9615(1999)069[0001:DBRATM]2.0.CO;2. DOI

Bushnell B. 2016. BBMap short-read aligner, and other bioinformatic tools. https://sourceforge.net/projects/bbmap.

Kang DD, Froula J, Egan R, Wang Z. 2015. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ 3:e1165. doi:10.7717/peerj.1165. PubMed DOI PMC

Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055. doi:10.1101/gr.186072.114. PubMed DOI PMC

Haft DH, Selengut JD, White O. 2003. The TIGRFAMs database of protein families. Nucleic Acids Res 31:371–373. doi:10.1093/nar/gkg128. PubMed DOI PMC

Löytynoja A. 2014. Phylogeny-aware alignment with PRANK. Methods Mol Biol 1079:155–170. doi:10.1007/978-1-62703-646-7_10. PubMed DOI

Criscuolo A, Gribaldo S. 2010. BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol Biol 10:210. doi:10.1186/1471-2148-10-210. PubMed DOI PMC

Nguyen LT, Schmidt HA, Von Haeseler A, Minh BQ. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 32:268–274. doi:10.1093/molbev/msu300. PubMed DOI PMC

Kalyaanamoorthy S, Minh BQ, Wong TKF, Von Haeseler A, Jermiin LS. 2017. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods 14:587–589. doi:10.1038/nmeth.4285. PubMed DOI PMC

Konstantinidis KT, Tiedje JM. 2005. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci U S A 102:2567–2572. doi:10.1073/pnas.0409727102. PubMed DOI PMC

Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948. doi:10.1093/bioinformatics/btm404. PubMed DOI

Mirarab S, Nguyen N, Guo S, Wang LS, Kim J, Warnow T. 2015. PASTA: ultra-large multiple sequence alignment for nucleotide and amino-acid sequences. J Comput Biol 22:377–386. doi:10.1089/cmb.2014.0156. PubMed DOI PMC

Bulzu PA, Andrei AŞ, Salcher MM, Mehrshad M, Inoue K, Kandori H, Beja O, Ghai R, Banciu HL. 2019. Casting light on Asgardarchaeota metabolism in a sunlit microoxic niche. Nat Microbiol 4:1129–1137. doi:10.1038/s41564-019-0404-y. PubMed DOI

Whelan S, Irisarri I, Burki F. 2018. PREQUAL: detecting non-homologous characters in sets of unaligned homologous sequences. Bioinformatics 34:3929–3930. doi:10.1093/bioinformatics/bty448. PubMed DOI

Weese D, Holtgrewe M, Reinert K. 2012. RazerS 3: faster, fully sensitive read mapping. Bioinformatics 28:2592–2599. doi:10.1093/bioinformatics/bts505. PubMed DOI

Huang Y, Gilna P, Li W. 2009. Identification of ribosomal RNA genes in metagenomic fragments. Bioinformatics 25:1338–1340. doi:10.1093/bioinformatics/btp161. PubMed DOI PMC

Kumar S, Stecher G, Tamura K. 2016. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874. doi:10.1093/molbev/msw054. PubMed DOI PMC

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

Behrens S, Rühland C, Inácio J, Huber H, Fonseca A, Spencer-Martins I, Fuchs BM, Amann R. 2003. In situ accessibility of small-subunit rRNA of members of the domains Bacteria, Archaea, and Eucarya to Cy3-labeled oligonucleotide probes. Appl Environ Microbiol 69:1748–1758. doi:10.1128/aem.69.3.1748-1758.2003. PubMed DOI PMC

Fuchs BM, Glockner FO, Wulf J, Amann R. 2000. Unlabeled helper oligonucleotides increase the in situ accessibility to 16S rRNA of fluorescently labeled oligonucleotide probes. Appl Environ Microbiol 66:3603–3607. doi:10.1128/aem.66.8.3603-3607.2000. PubMed DOI PMC

Rychtecký P, Znachor P. 2011. Spatial heterogeneity and seasonal succession of phytoplankton along the longitudinal gradient in a eutrophic reservoir. Hydrobiologia 663:175–186. doi:10.1007/s10750-010-0571-6. DOI

Porter KG, Feig YS. 1980. The use of DAPI for identifying and counting aquatic microflora. Limnol Oceanogr 25:943–948. doi:10.4319/lo.1980.25.5.0943. DOI

Sekar R, Pernthaler A, Pernthaler J, Warnecke F, Posch T, Amann R. 2003. An improved protocol for quantification of freshwater Actinobacteria by fluorescence in situ hybridization. Appl Environ Microbiol 69:2928–2935. doi:10.1128/aem.69.5.2928-2935.2003. PubMed DOI PMC

Predicting climate-change impacts on the global glacier-fed stream microbiome

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