Biogeographic patterns of abundant and rare bacterial and microeukaryotic subcommunities in connected freshwater lake zones subjected to different levels of nutrient loading.

Szczegóły
Abstrakt

Tytuł:: Biogeographic patterns of abundant and rare bacterial and microeukaryotic subcommunities in connected freshwater lake zones subjected to different levels of nutrient loading.
Autorzy:: Cao X; State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Joint International Research Laboratory of Global Change and Water Cycle, Hohai University, Nanjing, China.; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China.
Zhao D; State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Joint International Research Laboratory of Global Change and Water Cycle, Hohai University, Nanjing, China.
Zeng J; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China.
Huang R; State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Joint International Research Laboratory of Global Change and Water Cycle, Hohai University, Nanjing, China.; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China.
He F; Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of the People's Republic of China, Nanjing, China.
Źródło:: Journal of applied microbiology [J Appl Microbiol] 2021 Jan; Vol. 130 (1), pp. 123-132. Date of Electronic Publication: 2020 Jul 23.
Typ publikacji:: Journal Article
Język:: English
Imprint Name(s):: Publication: 2022- : Oxford : Oxford University Press
Original Publication: Oxford : Published for the Society for Applied Bacteriology by Blackwell Science, c1997-
MeSH Terms:: Microbiota*
Bacteria/*isolation & purification
Eukaryota/*isolation & purification
Lakes/*microbiology
Nutrients/*analysis
Bacteria/classification ; Bacteria/genetics ; Biodiversity ; China ; Ecosystem ; Eukaryota/classification ; Eukaryota/genetics ; Lakes/chemistry ; Phylogeography ; RNA, Ribosomal/genetics
References:: Alexander, E., Stock, A., Breiner, H.W., Behnke, A., Bunge, J., Yakimov, M.M. and Stoeck, T. (2009) Microbial eukaryotes in the hypersaline anoxic L'Atalante deep-sea basin. Environ Microbiol 11, 360-381.
Andrei, A.-Ş., Robeson Ii, M.S., Baricz, A., Coman, C., Muntean, V., Ionescu, A., Etiope, G., Alexe, M. et al. (2015) Contrasting taxonomic stratification of microbial communities in two hypersaline meromictic lakes. ISME J 9, 2642-2656.
Baas-Becking, L.G.M. (1934) Geobiologie of inleiding tot de milieukunde. Den Haag: W.P. Van Stockum & Zoon.
Bachy, C. and Worden, A.Z. (2014) Microbial ecology: finding structure in the rare biosphere. Curr Biol 24, R315-R317.
Bokulich, N.A., Subramanian, S., Faith, J.J., Gevers, D., Gordon, J.I., Knight, R., Mills, D.A. and Caporaso, J.G. (2013) Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods 10, 57-59.
Bolger, A.M., Lohse, M. and Usadel, B. (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114-2120.
Bowman, J.P., Mccammon, S.A., Rea, S.M. and Mcmeekin, T.A. (2000) The microbial composition of three limnologically disparate hypersaline Antarctic lakes. FEMS Microbiol Lett 183, 81-88.
Campbell, B.J., Yu, L., Heidelberg, J.F. and Kirchman, D.L. (2011) Activity of abundant and rare bacteria in a coastal ocean. Proc Natl Acad Sci 108, 12776-12781.
Cao, X., Zhao, D., Xu, H., Huang, R., Zeng, J. and Yu, Z. (2018) Heterogeneity of interactions of microbial communities in regions of Taihu Lake with different nutrient loadings: a network analysis. Sci Rep 8, 1-11.
Caporaso, J.G., Bittinger, K., Bushman, F.D., Desantis, T.Z., Andersen, G.L. and Knight, R. (2010a) PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26, 266-267.
Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., Fierer, N., Pena, A.G. et al. (2010b) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7, 335-336.
Caron, D.A., Countway, P.D., Savai, P., Gast, R.J., Schnetzer, A., Moorthi, S.D., Dennett, M.R., Moran, D.M. et al. (2009) Defining DNA-based operational taxonomic units for microbial-eukaryote ecology. Appl Environ Microbiol 75, 5797-5808.
Cavicchioli, R. (2015) Microbial ecology of Antarctic aquatic systems. Nat Rev Microbiol 13, 691-706.
Creer, S. and Sinniger, F. (2012) Cosmopolitanism of microbial eukaryotes in the global deep seas. Mol Ecol 21, 1033-1035.
Crisp, M.D., Arroyo, M.T., Cook, L.G., Gandolfo, M.A., Jordan, G.J., Mcglone, M.S., Weston, P.H., Westoby, M. et al. (2009) Phylogenetic biome conservatism on a global scale. Nature 458, 754-756.
Dasgupta, A., Saikia, R. and Handique, P.J. (2018) Mapping the bacterial community in Digboi Oil Refinery, India by high-throughput sequencing approach. Curr Microbiol 75, 1441-1446.
Dawson, S.C. and Hagen, K.D. (2009) Mapping the protistan 'rare biosphere'. J Biol 8, 105.
Deng, W., Wang, Y., Liu, Z., Cheng, H. and Xue, Y. (2014) HemI: a toolkit for illustrating heatmaps. PLoS One 9, e111988.
Edgar, R.C. (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460-2461.
Edgar, R.C. (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10, 996-998.
Edgar, R.C., Haas, B.J., Clemente, J.C., Quince, C. and Knight, R. (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194-2200.
Faith, D.P. (1992) Conservation evaluation and phylogenetic diversity. Biol Conserv 61, 1-10.
Foissner, W. (2006) Biogeography and dispersal of micro-organisms: a review emphasizing protists. Acta Protozool 45, 111-136.
Fuhrman, J.A. (2009) Microbial community structure and its functional implications. Nature 459, 193-199.
Galand, P.E., Casamayor, E.O., Kirchman, D.L. and Lovejoy, C. (2009) Ecology of the rare microbial biosphere of the Arctic Ocean. Proc Natl Acad Sci 106, 22427-22432.
Gobet, A., Böer, S.I., Huse, S.M., Van Beusekom, J.E., Quince, C., Sogin, M.L., Boetius, A. and Ramette, A. (2012) Diversity and dynamics of rare and of resident bacterial populations in coastal sands. ISME J 6, 542-553.
Green, J. and Bohannan, B.J. (2006) Spatial scaling of microbial biodiversity. Trends Ecol Evol 21, 501-507.
Grossart, H.-P. and Ploug, H. (2001) Microbial degradation of organic carbon and nitrogen on diatom aggregates. Limnol Oceanogr 46, 267-277.
Haukka, K., Kolmonen, E., Hyder, R., Hietala, J., Vakkilainen, K., Kairesalo, T., Haario, H. and Sivonen, K. (2006) Effect of nutrient loading on bacterioplankton community composition in lake mesocosms. Microb Ecol 51, 137-146.
Hugoni, M., Taib, N., Debroas, D., Domaizon, I., Dufournel, I.J., Bronner, G., Salter, I., Agogué, H. et al. (2013) Structure of the rare archaeal biosphere and seasonal dynamics of active ecotypes in surface coastal waters. Proc Natl Acad Sci 110, 6004-6009.
Jiao, C., Zhao, D., Huang, R., Cao, X., Zeng, J., Lin, Y. and Zhao, W. (2018) Abundant and rare bacterioplankton in freshwater lakes subjected to different levels of tourism disturbances. Water 10, 1075.
Kim, T.S., Jeong, J.Y., Wells, G.F. and Park, H.D. (2013) General and rare bacterial taxa demonstrating different temporal dynamic patterns in an activated sludge bioreactor. Appl Microbiol Biotechnol 97, 1755-1765.
Legendre, P. and Legendre, L.F. (2012) Numerical Ecology. Amsterdam: Elsevier.
Lennon, J.T. and Jones, S.E. (2011) Microbial seed banks: the ecological and evolutionary implications of dormancy. Nat Rev Microbiol 9, 119-130.
Li, H., Zeng, J., Ren, L., Wang, J., Xing, P. and Wu, Q.L. (2017) Contrasting patterns of diversity of abundant and rare bacterioplankton in freshwater lakes along an elevation gradient. Limnol Oceanogr 62, 1570-1585.
Liu, L., Yang, J., Yu, Z. and Wilkinson, D.M. (2015) The biogeography of abundant and rare bacterioplankton in the lakes and reservoirs of China. ISME J 9, 2068-2077.
Logares, R., Audic, S., Bass, D., Bittner, L., Boutte, C., Christen, R., Claverie, J.-M., Decelle, J. et al. (2014) Patterns of rare and abundant marine microbial eukaryotes. Curr Biol 24, 813-821.
Lozupone, C. and Knight, R. (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71, 8228-8235.
Magoč, T. and Salzberg, S.L. (2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957-2963.
Martiny, J.B.H., Bohannan, B.J., Brown, J.H., Colwell, R.K., Fuhrman, J.A., Green, J.L., Horner-Devine, M.C., Kane, M. et al. (2006) Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol 4, 102-112.
Pedrós-Alió, C. (2006) Marine microbial diversity: can it be determined? Trends Microbiol 14, 257-263.
Pedrós-Alió, C. (2012) The rare bacterial biosphere. Ann Rev Mar Sci 4, 449-466.
Price, M.N., Dehal, P.S. and Arkin, A.P. (2010) FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One 5, e9490.
Qin, B., Liu, Z. and Havens, K. (2007) Eutrophication of Shallow Lakes with Special Reference to Lake Taihu, China. Dordrecht: Springer Science & Business Media.
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J. and Glöckner, F.O. (2012) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41, D590-D596.
Raes, J., Letunic, I., Yamada, T., Jensen, L.J. and Bork, P. (2011) Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data. Mol Syst Biol 7, 473.
Ramette, A. and Tiedje, J.M. (2007) Biogeography: an emerging cornerstone for understanding prokaryotic diversity, ecology, and evolution. Microb Ecol 53, 197-207.
Ren, L., He, D., Chen, Z., Jeppesen, E., Lauridsen, T.L., Søndergaard, M., Liu, Z. and Wu, Q.L. (2017) Warming and nutrient enrichment in combination increase stochasticity and beta diversity of bacterioplankton assemblages across freshwater mesocosms. ISME J 11, 613-625.
Rognes, T., Flouri, T., Nichols, B., Quince, C. and Mahé, F. (2016) VSEARCH: a versatile open source tool for metagenomics. PeerJ 4, e2584.
Scheckenbach, F., Hausmann, K., Wylezich, C., Weitere, M. and Arndt, H. (2010) Large-scale patterns in biodiversity of microbial eukaryotes from the abyssal sea floor. Proc Natl Acad Sci 107, 115-120.
Sison-Mangus, M.P., Jiang, S., Kudela, R.M. and Mehic, S. (2016) Phytoplankton-associated bacterial community composition and succession during toxic diatom bloom and non-bloom events. Front Microbiol 7, 1433.
Smith, V.H., Tilman, G.D. and Nekola, J.C. (1999) Eutrophication: impacts of excess nutrient inputs on freshwater, marine, and terrestrial ecosystems. Environ Pollut 100, 179-196.
Staley, C., Unno, T., Gould, T.J., Jarvis, B., Phillips, J., Cotner, J.B. and Sadowsky, M.J. (2013) Application of Illumina next-generation sequencing to characterize the bacterial community of the Upper Mississippi River. J Appl Microbiol 115, 1147-1158.
Stegen, J.C., Lin, X., Fredrickson, J.K., Chen, X., Kennedy, D.W., Murray, C.J., Rockhold, M.L. and Konopka, A. (2013) Quantifying community assembly processes and identifying features that impose them. ISME J 7, 2069-2079.
Stegen, J.C., Lin, X., Fredrickson, J.K. and Konopka, A.E. (2015) Estimating and mapping ecological processes influencing microbial community assembly. Front Microbiol 6, 370.
Stock, A., Edgcomb, V., Orsi, W., Filker, S., Breiner, H.-W., Yakimov, M.M. and Stoeck, T. (2013) Evidence for isolated evolution of deep-sea ciliate communities through geological separation and environmental selection. BMC Microbiol 13, 150.
Wang, J., Pan, F., Soininen, J., Heino, J. and Shen, J. (2016) Nutrient enrichment modifies temperature-biodiversity relationships in large-scale field experiments. Nat Commun 7, 1-9.
Wang, J., Shen, J., Wu, Y., Tu, C., Soininen, J., Stegen, J.C., He, J., Liu, X. et al. (2013) Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes. ISME J 7, 1310-1321.
Wang, Q., Garrity, G.M., Tiedje, J.M. and Cole, J.R. (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73, 5261-5267.
Wemheuer, B., Güllert, S., Billerbeck, S., Giebel, H.-A., Voget, S., Simon, M. and Daniel, R. (2014) Impact of a phytoplankton bloom on the diversity of the active bacterial community in the southern North Sea as revealed by metatranscriptomic approaches. FEMS Microbiol Ecol 87, 378-389.
Wu, Q.L., Zwart, G., Wu, J., Kamst-Van Agterveld, M.P., Liu, S. and Hahn, M.W. (2007) Submersed macrophytes play a key role in structuring bacterioplankton community composition in the large, shallow, subtropical Taihu Lake, China. Environ Microbiol 9, 2765-2774.
Wu, Q.-L., Xing, P., Li, H.-B. and Zeng, J. (2013) Impacts of regime shift between phytoplankton and macrophyte on the microbial community structure and its carbon cycling in lakes. Microbiology/Weishengwuxue Tongbao 40, 87-97.
Xing, P., Guo, L., Tian, W. and Wu, Q.L. (2011) Novel Clostridium populations involved in the anaerobic degradation of Microcystis blooms. ISME J 5, 792-800.
Zeng, J., Bian, Y., Xing, P. and Wu, Q.L. (2012) Macrophyte species drive the variation of bacterioplankton community composition in a shallow freshwater lake. Appl Environ Microbiol 78, 177-184.
Zeng, J., Jiao, C., Zhao, D., Xu, H., Huang, R., Cao, X., Yu, Z. and Wu, Q.L. (2019) Patterns and assembly processes of planktonic and sedimentary bacterial community differ along a trophic gradient in freshwater lakes. Ecol Indic 106, 105491.
Zhao, D., Cao, X., Huang, R., Zeng, J., Shen, F., Xu, H., Wang, S., He, X. et al. (2017a) The heterogeneity of composition and assembly processes of the microbial community between different nutrient loading lake zones in Taihu Lake. Appl Microbiol Biotechnol 101, 5913-5923.
Zhao, D., Xu, H., Zeng, J., Cao, X., Huang, R., Shen, F. and Yu, Z. (2017b) Community composition and assembly processes of the free-living and particle-attached bacteria in Taihu Lake. FEMS Microbiol Ecol 93, fix062.
Zhou, J., Liu, W., Deng, Y., Jiang, Y.-H., Xue, K., He, Z., Van Nostrand, J.D., Wu, L. et al. (2013) Stochastic assembly leads to alternative communities with distinct functions in a bioreactor microbial community. MBio 4, https://doi.org/10.1128/mBio.00584-12.
Zhou, J. and Ning, D. (2017) Stochastic community assembly: does it matter in microbial ecology? Microbiol Mol Biol Rev 81, https://doi.org/10.1128/MMBR.00002-17.
Grant Information:: 2018490211 Belt and Road Special Foundation of the State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering; 201906710009 China Scholarship Council; D2017-2-2 Fisheries Technology Foundation of Jiangsu Province; BK20181311 Natural Science Foundation of Jiangsu Province; 2018B43414 Fundamental Research Funds for the Central Universities; 2017ZX07301006 Major Science and Technology Program for Water Pollution Control and Treatment; Hohai University; KU Leuven
Contributed Indexing:: Keywords: bacterioplankton; diversity; freshwater lake; microbial community; microeukaryotes; nutrient loading; rare and abundant
Substance Nomenclature:: 0 (RNA, Ribosomal)
Entry Date(s):: Date Created: 20200520 Date Completed: 20210108 Latest Revision: 20210108
Update Code:: 20240105
DOI:: 10.1111/jam.14720
PMID:: 32427406
: Czasopismo naukowe

Full Text Finder

Aims: To reveal whether the patterns of abundant and rare subcommunity composition of both bacteria and microeukaryotes vary between connected regions with different levels of nutrient loading in freshwater lakes.
Methods and Results: We investigated the abundant and rare subcommunity composition of both bacteria and microeukaryotes in two connected zones (Meiliang Bay (MLB) and Xukou Bay (XKB)) of a large shallow freshwater Lake Taihu via the high-throughput sequencing of bacterial 16S rRNA and microeukaryotic 18S rRNA genes. Even though these two lake zones are connected and share a species bank, they diverge in community composition. Significantly higher alpha diversity was observed for the abundant bacterial subcommunity in the MLB. However, no significant difference in alpha diversity between the rare bacterial subcommunities, as well as both rare and abundant microeukaryotic subcommunities were observed between MLB and XKB. It is demonstrated that both environmental factors and geographic distance play central roles in controlling the rare and abundant microbial subcommunities in the two connected lake zones.
Conclusions: The abundant subcommunity composition of bacteria and microeukaryotes vary between connected regions with different levels of nutrient loading. Dispersal limitation plays a vital role in shaping microbial communities even in connected zones of freshwater lakes.
Significance and Impact of the Study: Leading to a comprehensive understanding of the characteristics of microbial community in connected lake regions with different levels of nutrient loading.
(© 2020 The Society for Applied Microbiology.)

Informacja