Regional factors as major drivers for microbial community turnover in tropical cascading reservoirs

. 2022 ; 13 () : 831716. [epub] 20220818

Status PubMed-not-MEDLINE Jazyk angličtina Země Švýcarsko Médium electronic-ecollection

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/pmid36060758

The turnover of microbial communities across space is dictated by local and regional factors. Locally, selection shapes community assembly through biological interactions between organisms and the environment, while regional factors influence microbial dispersion patterns. Methods used to disentangle the effects of local and regional factors typically do not aim to identify ecological processes underlying the turnover. In this paper, we identified and quantified these processes for three operational microbial subcommunities (cyanobacteria, particle-attached, and free-living bacteria) from a tropical cascade of freshwater reservoirs with decreasing productivity, over two markedly different dry and rainy seasons. We hypothesized that during the dry season communities would mainly be controlled by selection shaped by the higher environmental heterogeneity that results from low hydrological flow and connectivity between reservoirs. We expected highly similar communities shaped by dispersal and a more homogenized environment during the rainy season, enhanced by increased flow rates. Even if metacommunities were largely controlled by regional events in both periods, the selection had more influence on free-living communities during the dry period, possibly related to elevated dissolved organic carbon concentration, while drift as a purely stochastic factor, had more influence on cyanobacterial communities. Each subcommunity had distinct patterns of turnover along the cascade related to diversity (Cyanobacteria), lifestyle and size (Free-living), and spatial dynamics (particle-attached).

Zobrazit více v PubMed

Bahram M., Kohout P., Anslan S., Harend H., Abarenkov K., Tedersoo L. (2016). Stochastic distribution of small soil eukaryotes resulting from high dispersal and drift in a local environment. ISME J. 10, 885–896. doi: 10.1038/ismej.2015.164, PMID: PubMed DOI PMC

Berger B., Hoch B., Kavka G., Herndl G. (1996). Bacterial colonization of suspended solids in the river Danube. Aquat. Microb. Ecol. 10, 37–44. doi: 10.3354/ame010037 DOI

Bie T., Meester L., Brendonck L., Martens K., Goddeeris B., Ercken D., et al. . (2012). Body size and dispersal mode as key traits determining metacommunity structure of aquatic organisms. Ecol. Lett. 15, 740–747. doi: 10.1111/j.1461-0248.2012.01794.x, PMID: PubMed DOI

Chase J. M. (2010a). Stochastic community assembly causes higher biodiversity in more productive environments. Science 328, 1388–1391. doi: 10.1126/science.1187820, PMID: PubMed DOI

Chase J. M. (2010b). Stochastic community assembly causes higher biodiversity in more productive environments. Science 328, 1388–1391. doi: 10.1126/science.1187820, PMID: PubMed DOI

Chase J. M., Myers J. A. (2011). Disentangling the importance of ecological niches from stochastic processes across scales. Philos. Trans. Royal Soc. B: Biol. Sci. 366, 2351–2363. doi: 10.1098/rstb.2011.0063, PMID: PubMed DOI PMC

Declerck S. A. J., Winter C., Shurin J. B., Suttle C. A., Matthews B. (2013). Effects of patch connectivity and heterogeneity on metacommunity structure of planktonic bacteria and viruses. ISME J. 7, 533–542. doi: 10.1038/ismej.2012.138, PMID: PubMed DOI PMC

Dziallas C., Grossart H.-P. (2011). Temperature and biotic factors influence bacterial communities associated with the cyanobacterium Microcystis sp.: bacteria associated with Microcystis sp. Environ. Microbiol. 13, 1632–1641. doi: 10.1111/j.1462-2920.2011.02479.x, PMID: PubMed DOI

Edgar R. C. (2013). UPARSE: Highly accurate OTU sequences from microbial amplicon reads. Nat. Methods 10, 996–998. doi: 10.1038/nmeth.2604, PMID: PubMed DOI

Emily Graham and James Stegen (2017). Dispersal-based microbial community assembly decreases biogeochemical function. PRO 5:65. doi: 10.3390/pr5040065 DOI

Farjalla V. F., Srivastava D. S., Marino N. A. C., Azevedo F. D., Dib V., Lopes P. M., et al. . (2012). Ecological determinism increases with organism size. Ecology 93, 1752–1759. doi: 10.1890/11-1144.1, PMID: PubMed DOI

Fenchel T., Finlay B. J. (2004). The ubiquity of small species: Patterns of local and global diversity. Bioscience 54:777. doi: 10.1641/0006-3568(2004)054[0777:TUOSSP]2.0.CO;2 DOI

Fine P. V. A., Kembel S. W. (2011). Phylogenetic community structure and phylogenetic turnover across space and edaphic gradients in western Amazonian tree communities. Ecography 34, 552–565. doi: 10.1111/j.1600-0587.2010.06548.x DOI

Finlay B. J. (2002). Global dispersal of free-living microbial eukaryote species. Science 296, 1061–1063. doi: 10.1126/science.1070710, PMID: PubMed DOI

Freitas R., Vieira H. H., de Moraes G. P., de Melo M. L., Vieira A. A. H., Sarmento H. (2018). Productivity and rainfall drive bacterial metabolism in tropical cascading reservoirs. Hydrobiologia 809, 233–246. doi: 10.1007/s10750-017-3472-0 DOI

Herlemann D. P., Labrenz M., Jürgens K., Bertilsson S., Waniek J. J., Andersson A. F. (2011). Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea. ISME J. 5, 1571–1579. doi: 10.1038/ismej.2011.41, PMID: PubMed DOI PMC

Hubbell S. P. (2001). The Unified neutral Theory of Biodiversity and Biogeography. Princeton: Princeton University Press. PubMed

Izabel-Shen D., Höger A.-L., Jürgens K. (2021). Abundance-occupancy relationships along taxonomic ranks reveal a consistency of niche differentiation in marine Bacterioplankton With distinct lifestyles. Front. Microbiol. 12:690712. doi: 10.3389/fmicb.2021.690712, PMID: PubMed DOI PMC

Jones S. E., Lennon J. T. (2010). Dormancy contributes to the maintenance of microbial diversity. Proc. Natl. Acad. Sci. 107, 5881–5886. doi: 10.1073/pnas.0912765107, PMID: PubMed DOI PMC

Kembel S. W., Cowan P. D., Helmus M. R., Cornwell W. K., Morlon H., Ackerly D. D., et al. . (2010). Picante: R tools for integrating phylogenies and ecology. Bioinformatics 26, 1463–1464. doi: 10.1093/bioinformatics/btq166, PMID: PubMed DOI

Kent A. D., Yannarell A. C., Rusak J. A., Triplett E. W., McMahon K. D. (2007). Synchrony in aquatic microbial community dynamics. ISME J. 1, 38–47. doi: 10.1038/ismej.2007.6, PMID: PubMed DOI

Kirchman D., Mitchell R. (1982). Contribution of particle-bound bacteria to total microheterotrophic activity in five ponds and two marshes. Appl. Environ. Microbiol. 43, 200–209. doi: 10.1128/aem.43.1.200-209.1982, PMID: PubMed DOI PMC

Langenheder S., Székely A. J. (2011). Species sorting and neutral processes are both important during the initial assembly of bacterial communities. ISME J. 5, 1086–1094. doi: 10.1038/ismej.2010.207, PMID: PubMed DOI PMC

Legendre P., Mi X., Ren H., Ma K., Yu M., Sun I.-F., et al. . (2009). Partitioning beta diversity in a subtropical broad-leaved forest of China. Ecology 90, 663–674. doi: 10.1890/07-1880.1, PMID: PubMed DOI

Leibold M. A., Holyoak M., Mouquet N., Amarasekare P., Chase J. M., Hoopes M. F., et al. . (2004). The metacommunity concept: A framework for multi-scale community ecology: The metacommunity concept. Ecol. Lett. 7, 601–613. doi: 10.1111/j.1461-0248.2004.00608.x DOI

Lindström E. S., Bergström A.-K. (2005). Community composition of bacterioplankton and cell transport in lakes in two different drainage areas. Aquat. Sci. 67, 210–219. doi: 10.1007/s00027-005-0769-2 DOI

Lindstrom E. S., Kamst-Van Agterveld M. P., Zwart G. (2005). Distribution of typical freshwater bacterial groups is associated with pH, temperature, and Lake water retention time. Appl. Environ. Microbiol. 71, 8201–8206. doi: 10.1128/AEM.71.12.8201-8206.2005, PMID: PubMed DOI PMC

Logares R. (2017). Ramalok/Amplicon_Processing: Workflow For Analysing Miseq Amplicons Based On Uparse.

Logares R., Sunagawa S., Salazar G., Cornejo-Castillo F. M., Ferrera I., Sarmento H., et al. . (2014). Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities: using mi tag s to explore microbial communities. Environ. Microbiol. 16, 2659–2671. doi: 10.1111/1462-2920.12250, PMID: PubMed DOI

Logue J. B., Mouquet N., Peter H., Hillebrand H. (2011). Empirical approaches to metacommunities: A review and comparison with theory. Trends Ecol. Evol. 26, 482–491. doi: 10.1016/j.tree.2011.04.009, PMID: PubMed DOI

Lorenzen C. J. (1967). Determination of chlorophyll and pheo-pigments: Spectrophotometric equations. Limnol. Oceanogr. 12, 343–346. doi: 10.4319/lo.1967.12.2.0343 DOI

Losos J. B. (2008). Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species. Ecol. Lett. 11, 995–1003. doi: 10.1111/j.1461-0248.2008.01229.x, PMID: PubMed DOI

Mahé F., Rognes T., Quince C., de Vargas C., Dunthorn M. (2014). Swarm: Robust and fast clustering method for amplicon-based studies. Peer J 2:e593. doi: 10.7717/peerj.593, PMID: PubMed DOI PMC

Marker A. F., Nush E. A., Rai H., Riemann B. (1980). The measurement of photosynthetic Pigments in freshwaters and standardization of methods: conclusions and recommendations. Archives fur Hydrobiologie 14, 91–106.

Minillo A. (2005). Análise da distribuição, densidade e toxicidade de florações de cianobactérias em reservatórios do médio e baixo rio Tietê (SP) e relação com as características limnológicas do sistema.

Nemergut D. R., Schmidt S. K., Fukami T., O’Neill S. P., Bilinski T. M., Stanish L. F., et al. . (2013). Patterns and processes of microbial community assembly. Microbiol. Mol. Biol. Rev. 77, 342–356. doi: 10.1128/MMBR.00051-12, PMID: PubMed DOI PMC

Newton R. J., Jones S. E., Eiler A., McMahon K. D., Bertilsson S. (2011). A guide to the natural history of freshwater Lake bacteria. Microbiol. Mol. Biol. Rev. 75, 14–49. doi: 10.1128/MMBR.00028-10, PMID: PubMed DOI PMC

Nusch E. A. (1980). Comparison of different methods for Chlorophyll and Phaeopigments Determination. Arch. Hydrobiol. 14, 4–36.

Ofiteru I. D., Lunn M., Curtis T. P., Wells G. F., Criddle C. S., Francis C. A., et al. . (2010). Combined niche and neutral effects in a microbial wastewater treatment community. Proc. Natl. Acad. Sci. 107, 15345–15350. doi: 10.1073/pnas.1000604107, PMID: PubMed DOI PMC

Pedrós-Alió C., Brock T. D. (1982). Assessing biomass and production of bacteria in eutrophic Lake Mendota, Wisconsin. Appl. Environ. Microbiol. 44, 203–218. doi: 10.1128/aem.44.1.203-218.1982, PMID: PubMed DOI PMC

Rappé M. S., Giovannoni S. J. (2003). The uncultured microbial majority. Annu. Rev. Microbiol. 57, 369–394. doi: 10.1146/annurev.micro.57.030502.090759 PubMed DOI

R Core Team (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. Available at: https://www.R-project.org/

Ricklefs R. E., Miller G. (1990). Ecology 1999. WH Fr. and C. New York, 898.

Rodgher S. (2001). Estudos ecotoxicológicos e limnológicos nos reservatórios em cascata do médio e baixo rio Tietê: uma análise espacial e temporal.

Rodgher S., Espíndola E. L. G., Rocha O., Fracácio R., Pereira R. H. G., Rodrigues M. H. S. (2005). Limnological and ecotoxicological studies in the cascade of reservoirs in the Tietê river (São Paulo, Brazil). Braz. J. Biol. 65, 697–710. doi: 10.1590/S1519-69842005000400017 PubMed DOI

Smith M. W., Zeigler Allen L., Allen A. E., Herfort L., Simon H. M. (2013). Contrasting genomic properties of free-living and particle-attached microbial assemblages within a coastal ecosystem. Front. Microbiol. 4:120. doi: 10.3389/fmicb.2013.00120, PMID: PubMed DOI PMC

Smith W. S., Espíndola E. L. G., Rocha O. (2014). Environmental gradient in reservoirs of the medium and low Tietê River: Limnological differences through the habitat sequence. Acta Limnol. Bras. 26, 73–88. doi: 10.1590/S2179-975X2014000100009 DOI

Sotero-Santos R. B., Silva C. R. D. S. E., Verani N. F., Nonaka K. O., Rocha O. (2006). Toxicity of a cyanobacteria bloom in Barra Bonita reservoir (middle Tietê River, São Paulo, Brazil). Ecotoxicol. Environ. Saf. 64, 163–170. doi: 10.1016/j.ecoenv.2005.03.011, PMID: PubMed DOI

Stegen J. C., Lin X., Fredrickson J. K., Chen X., Kennedy D. W., Murray C. J., et al. . (2013). Quantifying community assembly processes and identifying features that impose them. ISME J. 7, 2069–2079. doi: 10.1038/ismej.2013.93, PMID: PubMed DOI PMC

Stewart E. J. (2012). Growing unculturable bacteria. J. Bacteriol. 194, 4151–4160. doi: 10.1128/JB.00345-12, PMID: PubMed DOI PMC

Tuomisto H., Ruokolainen L., Ruokolainen K. (2012). Modelling niche and neutral dynamics: On the ecological interpretation of variation partitioning results. Ecography 35, 961–971. doi: 10.1111/j.1600-0587.2012.07339.x DOI

Vellend M. (2016). The Theory of Ecological Communities (MPB-57). Available at: 10.1515/9781400883790, [Accessed January 30 2019]. DOI

Verreydt D., De Meester L., Decaestecker E., Villena M.-J., Van Der Gucht K., Vannormelingen P., et al. . (2012). Dispersal-mediated trophic interactions can generate apparent patterns of dispersal limitation in aquatic metacommunities: Dispersal-mediated metacommunity responses. Ecol. Lett. 15, 218–226. doi: 10.1111/j.1461-0248.2011.01728.x, PMID: PubMed DOI

Webb C. O., Ackerly D. D., Kembel S. W. (2008). Phylocom: Software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics 24, 2098–2100. doi: 10.1093/bioinformatics/btn358, PMID: PubMed DOI

Zhang Z., Schwartz S., Wagner L., Miller W. (2000). A greedy algorithm for aligning DNA sequences. J. Comput. Biol. 7, 203–214. doi: 10.1089/10665270050081478, PMID: PubMed DOI

Zhou J., Liu W., Deng Y., Jiang Y.-H., Xue K., He Z., et al. . (2013). Stochastic assembly leads to alternative communities with distinct functions in a bioreactor microbial community. mBio 4 4:e00584-12-e00584-12. doi: 10.1128/mBio.00584-12, PMID: PubMed DOI PMC

Najít záznam

Citační ukazatele

Nahrávání dat ...

Možnosti archivace

Nahrávání dat ...