Spatiotemporal dynamics and determinants of planktonic bacterial and microeukaryotic communities in a Chinese subtropical river

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• 作者：Yongming Wang ; Lemian Liu ; Huihuang Chen…
• 关键词：River ecology ; Plankton ; Microbial community ; Distance ; decay ; Variation partitioning ; Path analysis ; Structural equation modeling
• 刊名：Applied Microbiology and Biotechnology
• 出版年：2015
• 出版时间：November 2015
• 年：2015
• 卷：99
• 期：21
• 页码：9255-9266
• 全文大小：856 KB
• 参考文献：Amin SA, Hmelo LR, van Tol HM, Durham BP, Carlson LT, Heal KR, Morales RL, Berthiaume CT, Parker MS, Djunaedi B, Ingalls AE, Parsek MR, Moran MA, Armbrust EV (2015) Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria. Nature 522:98–101CrossRef PubMed
  Arndt H (1993) Rotifers as predators on components of the microbial web (bacteria, heterotrophic flagellates, ciliates)—a review. Hydrobiologia 255:231–246CrossRef
  Astorga A, Oksanen J, Luoto M, Soininen J, Virtanen R, Muotka T (2012) Distance decay of similarity in freshwater communities: do macro- and microorganisms follow the same rules? Glob Ecol Biogeogr 21:365–375CrossRef
  Azovsky AI (2002) Size-dependent species-area relationships in benthos: is the world more diverse for microbes? Ecography 25:273–282CrossRef
  Barcina I, Ayo B, Muela A, Egea L, Iriberri J (1991) Predation rates of flagellate and ciliated protozoa on bacterioplankton in a river. FEMS Microbiol Lett 85:141–149CrossRef
  Beier S, Witzel KP, Marxsen J (2008) Bacterial community composition in Central European running waters examined by temperature gradient gel electrophoresis and sequence analysis of 16S rRNA genes. Appl Environ Microbiol 74:188–199PubMedCentral CrossRef PubMed
  Bianchi F, Acri F, Aubry FB, Berton A, Boldrin A, Camatti E, Cassin D, Comaschi A (2003) Can plankton communities be considered as bio-indicators of water quality in the lagoon of Venice? Mar Pollut Bull 46:964–971CrossRef PubMed
  Bienhold C, Boetius A, Ramette A (2011) The energy–diversity relationship of complex bacterial communities in Arctic deep-sea sediments. ISME J 6:724–732PubMedCentral CrossRef PubMed
  Borcard D, Legendre P (2002) All-scale spatial analysis of ecological data by means of principal coordinates of neighbour matrices. Ecol Model 153:51–68CrossRef
  Chen NW, Hong HS (2012) Integrated management of nutrients from the watershed to coast in the subtropical region. Curr Opin Environ Sustain 4:233–242CrossRef
  Chen NW, Hong HS, Zhang LP, Cao WZ (2008) Nitrogen sources and exports in an agricultural watershed in Southeast China. Biogeochemistry 87:169–179CrossRef
  Chen ZB, Zhou ZY, Peng X, Xiang H, Xiang SN, Jiang ZX (2013) Effects of wet and dry seasons on the aquatic bacterial community structure of the three Gorges Reservoir. World J Microbiol Biotechnol 29:841–853CrossRef PubMed
  Chrost RH, Faust MA (1983) Organic carbon release by phytoplankton: its composition and utilization by bacterioplankton. J Plankton Res 5:477–493CrossRef
  Clarke KR, Gorley RN (2001) PRIMER v5: user manual/tutorial. PRIMER-E, Plymouth
  Crump BC, Hobbie JE (2005) Synchrony and seasonality in bacterioplankton communities of two temperate rivers. Limnol Oceanogr 50:1718–1729CrossRef
  Crump BC, Adams HE, Hobbie JE, Kling GW (2007) Biogeography of bacterioplankton in lakes and streams of an arctic tundra catchment. Ecology 88:1365–1378CrossRef PubMed
  de Bie T, De Meester L, Brendonck L, Martens K, Goddeeris B, Ercken D, Hampel H, Denys L, Vanhecke L, Van der Gucht K, Van Wichelen J, Vyverman W, Declerck SAJ (2012) Body size and dispersal mode as key traits determining metacommunity structure of aquatic organisms. Ecol Lett 15:740–747CrossRef PubMed
  Díez B, Pedrós-Alió C, Marsh TL, Massana R (2001) Application of denaturing gradient gel electrophoresis (DGGE) to study the diversity of marine picoeukaryotic assemblages and comparison of DGGE with other molecular techniques. Appl Environ Microbiol 67:2942–2951PubMedCentral CrossRef PubMed
  Fierer N, Morse JL, Berthrong ST, Bernhardt ES, Jackson RB (2007) Environmental controls on the landscape-scale biogeography of stream bacterial communities. Ecology 88:2162–2173CrossRef PubMed
  Freimann R, Bürgmann H, Findlay SE, Robinson CT (2013) Bacterial structures and ecosystem functions in glaciated floodplains: contemporary states and potential future shifts. ISME J 7:2361–2373PubMedCentral CrossRef PubMed
  Fuhrman JA (2009) Microbial community structure and its functional implications. Nature 459:193–199CrossRef PubMed
  Fuhrman JA, Steele JA, Hewson I, Schwalbach MS, Brown MV, Green JL, Brown JH (2008) A latitudinal diversity gradient in planktonic marine bacteria. Proc Natl Acad Sci U S A 105:7774–7778PubMedCentral CrossRef PubMed
  Goebes MD, Strader R, Davidson C (2003) An ammonia emission inventory for fertilizer application in the United States. Atmos Environ 37:2539–2550CrossRef
  Goldenberg A, Dam H, Loon EE, Vonk JA, Der HG, Admiraal W (2014) Eutrophication decreases distance decay of similarity in diatom communities. Freshw Biol 59:1522–1531CrossRef
  Green J, Bohannan BJ (2006) Spatial scaling of microbial biodiversity. Trends Ecol Evol 21:501–507CrossRef PubMed
  Hall T (1999) Biological sequence alignment editor for Win95/98/NT/2K/XP. IBIS Biosciences, Carlsbad
  Hanson CA, Fuhrman JA, Horner-Devine MC, Martiny JBH (2012) Beyond biogeographic patterns: processes shaping the microbial landscape. Nat Rev Microbiol 10:497–506PubMed
  Hu AY, Yang XY, Chen NW, Hou LY, Ma Y, Yu CP (2014) Response of bacterial communities to environmental changes in a mesoscale subtropical watershed, Southeast China. Sci Total Environ 472:746–756CrossRef PubMed
  Hullar MA, Kaplan LA, Stahl DA (2006) Recurring seasonal dynamics of microbial communities in stream habitats. Appl Environ Microbiol 72:713–722PubMedCentral CrossRef PubMed
  Ip YK, Chew SF, Randall DJ (2001) Ammonia toxicity, tolerance, and excretion. In: Wright PA, Anderson PM (eds) Fish physiology, vol. 19 nitrogen excretion. Academic Press, New York, pp. 109–148CrossRef
  Ju LH, Yang J, Liu LM, Wilkinson DM (2014) Diversity and distribution of freshwater testate amoebae (Protozoa) along latitudinal and trophic gradients in China. Microb Ecol 68:657–670PubMedCentral CrossRef PubMed
  Kent AD, Yannarell AC, Rusak JA, Triplett EW, McMahon KD (2007) Synchrony in aquatic microbial community dynamics. ISME J 1:38–47CrossRef PubMed
  Langenheder S, Ragnarsson H (2007) The role of environmental and spatial factors for the composition of aquatic bacterial communities. Ecology 88:2154–2161CrossRef PubMed
  Lear G, Washington V, Neale M, Case B, Buckley H, Lewis G (2013) The biogeography of stream bacteria. Glob Ecol Biogeogr 22:544–554CrossRef
  Legendre P, Legendre L (1998) Numerical ecology. Elsevier Science BV, Amsterdam
  Lepš J, Šmilauer P (2003) Multivariate analysis of ecological data using CANOCO. Cambridge University Press, CambridgeCrossRef
  Li YY, Jiao JX, Wang Y, Yang W, Meng C, Li BZ, Li Y, Wu JS (2015) Characteristics of nitrogen loading and its influencing factors in several typical agricultural watersheds of subtropical China. Environ Sci Pollut Res 22:1831–1840CrossRef
  Liu LM, Yang J, Zhang YY (2011) Genetic diversity patterns of microbial communities in a subtropical riverine ecosystem (Jiulong River, southeast China). Hydrobiologia 678:113–125CrossRef
  Liu LM, Yang J, Yu XQ, Chen GJ, Yu Z (2013) Patterns in the composition of microbial communities from a subtropical river: effects of environmental, spatial and temporal factors. PLoS One 8:e81232PubMedCentral CrossRef PubMed
  Liu LM, Yang J, Lv H, Yu Z (2014) Synchronous dynamics and correlations between bacteria and phytoplankton in a subtropical drinking water reservoir. FEMS Microbiol Ecol 90:126–138CrossRef PubMed
  Liu LM, Yang J, Yu Z, Wilkinson DM (2015) The biogeography of abundant and rare bacterioplankton in the lakes and reservoirs of China. ISME J. doi:10.​1038/​ismej.​2015.​29
  Mazaris AD, Moustaka-Gouni M, Michaloudi E, Bobori DC (2010) Biogeographical patterns of freshwater micro- and macroorganisms: a comparison between phytoplankton, zooplankton and fish in the eastern Mediterranean. J Biogeogr 37:1341–1351CrossRef
  Miller SR, Strong AL, Jones KL, Ungerer MC (2009) Bar-coded pyrosequencing reveals shared bacterial community properties along the temperature gradients of two alkaline hot springs in Yellowstone National Park. Appl Environ Microbiol 75:4565–4572PubMedCentral CrossRef PubMed
  Mostajir B, Amblard C, Buffan-Dubau E, De Wit R, Lensi R, Sime-Ngando T (2015) Microbial food webs in aquatic and terrestrial ecosystems. In: Bertrand JC, Caumette P, Lebaron P, Matheron R, Normand P, Sime-Ngando T (eds) Environmental microbiology: fundamentals and applications. Springer, The Netherlands, pp. 485–509
  Muscarella ME, Bird KC, Larsen ML, Placella SA, Lennon JT (2014) Phosphorus resource heterogeneity in microbial food webs. Aquat Microb Ecol 73:259–272CrossRef
  Muyzer G, De Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695–700PubMedCentral PubMed
  Nekola JC, White PS (1999) The distance decay of similarity in biogeography and ecology. J Biogeogr 26:867–878CrossRef
  Newton RJ, McMahon KD (2011) Seasonal differences in bacterial community composition following nutrient additions in a eutrophic lake. Environ Microbiol 13:887–899CrossRef PubMed
  Obernosterer I, Herndl GJ (1995) Phytoplankton extracellular release and bacterial growth: dependence on the inorganic N: P ratio. Mar Ecol Prog Ser 116:247–257CrossRef
  Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O’Hara RB, Simpson GL, Solymos P, Stevens MHH, Wagner H (2013) Vegan: community ecology package. R package version 2.0-6
  Pantelić D, Svirčev Z, Simeunović J, Vidović M, Trajković I (2013) Cyanotoxins: characteristics, production and degradation routes in drinking water treatment with reference to the situation in Serbia. Chemosphere 91:421–441CrossRef PubMed
  Pernthaler J (2005) Predation on prokaryotes in the water column and its ecological implications. Nat Rev Microbiol 3:537–546CrossRef PubMed
  Pinhassi J, Sala MM, Havskum H, Peters F, Guadayol O, Malits A, Marrasé C (2004) Changes in bacterioplankton composition under different phytoplankton regimens. Appl Environ Microbiol 70:6753–6766PubMedCentral CrossRef PubMed
  Pomeroy LR, Wiebe WJ (2001) Temperature and substrates as interactive limiting factors for marine heterotrophic bacteria. Aquat Microb Ecol 23:187–204CrossRef
  Portillo MC, Anderson SP, Fierer N (2012) Temporal variability in the diversity and composition of stream bacterioplankton communities. Environ Microbiol 14:2417–2428CrossRef PubMed
  Read DS, Gweon HS, Bowes MJ, Newbold LK, Field D, Bailey MJ, Griffiths RI (2015) Catchment-scale biogeography of riverine bacterioplankton. ISME J 9:516–526PubMedCentral CrossRef PubMed
  Robert P, Escoufier Y (1976) A unifying tool for linear multivariate statistical methods: the RV-coefficient. Appl Stat 25:257–265CrossRef
  Schäfer H, Muyzer G (2001) Denaturing gradient gel electrophoresis in marine microbial ecology. Method Microbiol 30:425–468CrossRef
  Schermelleh-Engel K, Moosbrugger H, Müller H (2003) Evaluating the fit of structural equation models: tests of significance and descriptive goodness-of-fit measures. Method Psychol Res 8:23–74
  Sherr EB, Sherr BF (1987) High rates of consumption of bacteria by pelagic ciliates. Nature 325:710–711CrossRef
  Soininen J, Luoto M (2014) Predictability in species distributions: a global analysis across organisms and ecosystems. Glob Ecol Biogeogr 23:1264–1274CrossRef
  Soininen J, Korhonen JJ, Karhu J, Vetterli A (2011) Disentangling the spatial patterns in community composition of prokaryotic and eukaryotic lake plankton. Limnol Oceanogr 56:508–520CrossRef
  Soininen J, Korhonen JJ, Luoto M (2013) Stochastic species distributions are driven by organism size. Ecology 94:660–670CrossRef PubMed
  Staley C, Gould TJ, Wang P, Phillips J, Cotner JB, Sadowsky MJ (2014) Bacterial community structure is indicative of chemical inputs in the Upper Mississippi River. Front Microbiol 5:524PubMedCentral PubMed
  Stomp M, Huisman J, Mittelbach GG, Litchman E, Klausmeier CA (2011) Large-scale biodiversity patterns in freshwater phytoplankton. Ecology 92:2096–2107CrossRef PubMed
  van Hannen EJ, Mooij W, van Agterveld MP, Gons HJ, Laanbroek HJ (1999) Detritus-dependent development of the microbial community in an experimental system: qualitative analysis by denaturing gradient gel electrophoresis. Appl Environ Microbiol 65:2478–2484PubMedCentral PubMed
  Wang YM, Yang J, Liu LM, Yu Z (2015) Quantifying the effects of geographical and environmental factors on distribution of stream bacterioplankton within nature reserves of Fujian, China. Environ Sci Pollut Res 22:11010–11021CrossRef
  Weitere M, Arndt H (2003) Structure of the heterotrophic flagellate community in the water column of the River Rhine (Germany). Eur J Protistol 39:287–300CrossRef
  Yang J, Smith HG, Sherratt TN, Wilkinson DM (2010) Is there a size limit for cosmopolitan distribution in free-living microorganisms? A biogeographical analysis of testate amoebae from polar areas. Microb Ecol 59:635–645CrossRef PubMed
  Yang J, Yu XQ, Liu LM, Zhang WJ, Guo PY (2012) Algae community and trophic state of subtropical reservoirs in southeast Fujian, China. Environ Sci Pollut Res 19:1432–1442CrossRef
  Yu LY, Zhang WJ, Liu LM, Yang J (2015) Determining microeukaryotic plankton community around Xiamen Island, southeast China, using Illumina MiSeq and PCR-DGGE techniques. PLoS One 10:e0127721PubMedCentral CrossRef PubMed
  Zhang X, Zhang DD, Zhang H, Lou ZX, Yan CZ (2012) Occurrence, distribution, and seasonal variation of estrogenic compounds and antibiotic residues in Jiulongjiang River, South China. Environ Sci Pollut Res 19:1392–1404CrossRef
  
• 作者单位：Yongming Wang (1) (2)
  Lemian Liu (1)
  Huihuang Chen (1)
  Jun Yang (1)
  
  1. Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
  2. University of Chinese Academy of Sciences, Beijing, 100049, China
  
• 刊物类别：Chemistry and Materials Science
• 刊物主题：Chemistry
  Biotechnology
  Microbiology
  Microbial Genetics and Genomics
  
• 出版者：Springer Berlin / Heidelberg
• ISSN：1432-0614

文摘

The spatiotemporal distribution of microbial diversity, community composition, and their major drivers are fundamental issues in microbial ecology. In this study, the planktonic bacterial and microeukaryotic communities of the Jiulong River were investigated across both wet and dry seasons by using denaturing gradient gel electrophoresis (DGGE). We found evidence of temporal change between wet and dry seasons and distinct spatial patterns of bacterial and microeukaryotic communities. Both bacterial and microeukaryotic communities were strongly correlated with temperature, NH₄-N, PO₄-P, and chlorophyll a, and these environmental factors were significant but incomplete predictors of microbial community composition. Local environmental factors combined with spatial and temporal factors strongly controlled both bacterial and microeukaryotic communities in complex ways, whereas the direct influence of spatial and temporal factors appeared to be relatively small. Path analysis revealed that the microeukaryotic community played key roles in shaping bacterial community composition, perhaps through grazing effects and multiple interactions. Both Betaproteobacteria and Actinobacteria were the most dominant and diverse taxa in bacterial communities, while the microeukaryotic communities were dominated by Ciliophora (zooplankton) and Chlorophyta (phytoplankton). Our results demonstrated that both bacterial and microeukaryotic communities along the Jiulong River displayed a distinct spatiotemporal pattern; however, microeukaryotic communities exhibited a stronger distance-decay relationship than bacterial communities and their spatial patterns were mostly driven by local environmental variables rather than season or spatial processes of the river. Therefore, we have provided baseline data to support further research on river microbial food webs and integrating different microbial groups into river models.