in

Terrestrial connectivity, upstream aquatic history and seasonality shape bacterial community assembly within a large boreal aquatic network

[adace-ad id="91168"]
  • 1.

    McGill BJ, Etienne RS, Gray JS, Alonso D, Anderson MJ, Benecha HK, et al. Species abundance distributions: moving beyond single prediction theories to integration within an ecological framework. Ecol Lett. 2007;10:995–1015.

    PubMed 

    Google Scholar 

  • 2.

    Magurran AE, Henderson PA. Explaining the excess of rare species in natural species abundance distributions. Nature. 2003;422:714–6.

    CAS 
    PubMed 

    Google Scholar 

  • 3.

    Nakadai R, Okazaki Y, Matsuoka S. Describing macroecological patterns in microbes: Approaches for comparative analyses of operational taxonomic unit read number distribution with a case study of global oceanic bacteria. Environ DNA. 2020;2:535–43.

    Google Scholar 

  • 4.

    Vellend M. Conceptual synthesis in community ecology. Q Rev Biol. 2010;85:183–206.

    PubMed 

    Google Scholar 

  • 5.

    Zhou J, Ning D. Stochastic community assembly: Does it matter in microbial ecology? Micro Mol Biol Rev. 2017;81:1–32.

    Google Scholar 

  • 6.

    Fukami T. Assembly history interacts with ecosystem size to influence species diversity. Ecology. 2004;85:3234–42.

    Google Scholar 

  • 7.

    Shade A, Gilbert JA. Temporal patterns of rarity provide a more complete view of microbial diversity. Trends Microbiol. 2015;23:335–40.

    CAS 
    PubMed 

    Google Scholar 

  • 8.

    Comte J, Berga M, Severin I, Logue JB, Lindström ES. Contribution of different bacterial dispersal sources to lakes: Population and community effects in different seasons. Environ Microbiol. 2017;19:2391–404.

    CAS 
    PubMed 

    Google Scholar 

  • 9.

    Fukami T. Historical contingency in community assembly: Integrating niches, species pools, and priority effects. Annu Rev Ecol Evol Syst. 2015;46:1–23.

    Google Scholar 

  • 10.

    Niño-García JP, Ruiz-González C, del Giorgio PA. Interactions between hydrology and water chemistry shape bacterioplankton biogeography across boreal freshwater networks. ISME J. 2016;10:1755–66.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 11.

    Ruiz-González C, Niño-García JP, Berggren M, del Giorgio PA. Contrasting dynamics and environmental controls of dispersed bacteria along a hydrologic gradient. Adv Ocean Limnol. 2017;8:222–34.

    Google Scholar 

  • 12.

    Ruiz-González C, Niño-García JP, del Giorgio PA. Terrestrial origin of bacterial communities in complex boreal freshwater networks. Ecol Lett. 2015;18:1198–206.

    PubMed 

    Google Scholar 

  • 13.

    Crump BC, Amaral-Zettler LA, Kling GW. Microbial diversity in arctic freshwaters is structured by inoculation of microbes from soils. ISME J. 2012;6:1629–39.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 14.

    Besemer K, Singer G, Quince C, Bertuzzo E, Sloan W, Battin TJ. Headwaters are critical reservoirs of microbial diversity for fluvial networks. Proc R Soc B. 2013;280:20131760.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 15.

    Wisnoski NI, Muscarella ME, Larsen ML, Peralta AL, Lennon JT. Metabolic insight into bacterial community assembly across ecosystem boundaries. Ecology. 2020;101:e02968.

    PubMed 

    Google Scholar 

  • 16.

    Nelson CE, Sadro S, Melack JM. Contrasting the influences of stream inputs and landscape position on bacterioplankton community structure and dissolved organic matter composition in high-elevation lake chains. Limnol Oceanogr. 2009;54:1292–305.

    CAS 
    Article 

    Google Scholar 

  • 17.

    de Melo ML, Bertilsson S, Amaral JHF, Barbosa PM, Forsberg BR, Sarmento H. Flood pulse regulation of bacterioplankton community composition in an Amazonian floodplain lake. Freshw Biol. 2019;64:108–20.

    Google Scholar 

  • 18.

    Caillon F, Besemer K, Peduzzi P, Schelker J. Soil microbial inoculation during flood events shapes headwater stream microbial communities and diversity. Microb Ecol. 2021;82:591–601.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 19.

    Vass M, Langenheder S. The legacy of the past: effects of historical processes on microbial metacommunities. Aquat Micro Ecol. 2017;79:13–19.

    Google Scholar 

  • 20.

    Stegen JC, Lin X, Fredrickson JK, Chen X, Kennedy DW, Murray CJ, et al. Quantifying community assembly processes and identifying features that impose them. ISME J. 2013;7:2069–79.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 21.

    Niño-García JP, Ruiz-González C, del Giorgio PA. Landscape-scale spatial abundance distributions discriminate core from random components of boreal lake bacterioplankton. Ecol Lett. 2016;19:1506–15.

    PubMed 

    Google Scholar 

  • 22.

    Mansour I, Heppell CM, Ryo M, Rillig MC. Application of the microbial community coalescence concept to riverine networks. Biol Rev. 2018;93:1832–45.

    PubMed 

    Google Scholar 

  • 23.

    Nemergut DR, Costello EK, Hamady M, Lozupone C, Jiang L, Schmidt SK, et al. Global patterns in the biogeography of bacterial taxa. Environ Microbiol. 2011;13:135–44.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 24.

    Shade A, Gregory Caporaso J, Handelsman J, Knight R, Fierer N. A meta-analysis of changes in bacterial and archaeal communities with time. ISME J. 2013;7:1493–506.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 25.

    Logue JB, Lindström ES. Species sorting affects bacterioplankton community composition as determined by 16S rDNA and 16S rRNA fingerprints. ISME J. 2010;4:729–38.

    CAS 
    PubMed 

    Google Scholar 

  • 26.

    Adams HE, Crump BC, Kling GW. Metacommunity dynamics of bacteria in an arctic lake: The impact of species sorting and mass effects on bacterial production and biogeography. Front Microbiol. 2014;5:82.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 27.

    Langenheder S, Wang J, Karjalainen SM, Laamanen TM, Tolonen KT, Vilmi A, et al. Bacterial metacommunity organization in a highly connected aquatic system. FEMS Microbiol Ecol. 2017;93:1–9.

    Google Scholar 

  • 28.

    Winter C, Hein T, Kavka G, Mach RL, Farnleitner AH. Longitudinal changes in the bacterial community composition of the Danube River: a whole-river approach. Appl Environ Microbiol. 2007;73:421–31.

    CAS 
    PubMed 

    Google Scholar 

  • 29.

    Savio D, Sinclair L, Ijaz UZ, Parajka J, Reischer GH, Stadler P, et al. Bacterial diversity along a 2600 km river continuum. Environ Microbiol. 2015;17:4994–5007.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 30.

    Hauptmann AL, Markussen TN, Stibal M, Olsen NS, Elberling B, Bælum J, et al. Upstream freshwater and terrestrial sources are differentially reflected in the bacterial community structure along a small Arctic river and its estuary. Front Microbiol. 2016;7:1–16.

    Google Scholar 

  • 31.

    Doherty M, Yager PL, Moran MA, Coles VJ, Fortunato CS, Krusche AV, et al. Bacterial biogeography across the Amazon river-ocean continuum. Front Microbiol. 2017;8:882.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 32.

    Gweon HS, Bowes MJ, Moorhouse HL, Oliver AE, Bailey MJ, Acreman MC, et al. Contrasting community assembly processes structure lotic bacteria metacommunities along the river continuum. Environ Microbiol. 2021;23:484–98.

    CAS 
    PubMed 

    Google Scholar 

  • 33.

    Widder S, Besemer K, Singer GA, Ceola S, Bertuzzo E, Quince C, et al. Fluvial network organization imprints on microbial co-occurrence networks. Proc Natl Acad Sci. 2014;111:12799–804.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 34.

    Read DS, Gweon HS, Bowes MJ, Newbold LK, Field D, Bailey MJ, et al. Catchment-scale biogeography of riverine bacterioplankton. ISME J. 2015;9:516–26.

    CAS 
    PubMed 

    Google Scholar 

  • 35.

    Hassell N, Tinker KA, Moore T, Ottesen EA. Temporal and spatial dynamics in microbial community composition within a temperate stream network. Environ Microbiol. 2018;20:3560–72.

    PubMed 

    Google Scholar 

  • 36.

    Wisnoski NI, Lennon JT. Microbial community assembly in a multi-layer dendritic metacommunity. Oecologia. 2021;195:13–24.

    PubMed 

    Google Scholar 

  • 37.

    Cole JJ. Aquatic microbiology for ecosystem scientists: New and recycled paradigms in ecological microbiology. Ecosystems. 1999;2:215–25.

    Google Scholar 

  • 38.

    Jones SE, Lennon JT. Dormancy contributes to the maintenance of microbial diversity. Proc Natl Acad Sci. 2010;107:5881–6.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 39.

    Bowsher AW, Kearns PJ, Shade A. 16S rRNA/rRNA gene ratios and cell activity staining reveal consistent patterns of microbial activity in plant-associated soil. mSystems. 2019;4:e00003–19.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 40.

    Székely AJ, Berga M, Langenheder S. Mechanisms determining the fate of dispersed bacterial communities in new environments. ISME J. 2013;7:61–71.

    PubMed 

    Google Scholar 

  • 41.

    Aanderud ZT, Vert JC, Lennon JT, Magnusson TW, Breakwell DP, Harker AR. Bacterial dormancy is more prevalent in freshwater than hypersaline lakes. Front Microbiol. 2016;7:853.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 42.

    Denef VJ, Fujimoto M, Berry MA, Schmidt ML. Seasonal succession leads to habitat-dependent differentiation in ribosomal RNA:DNA ratios among freshwater lake bacteria. Front Microbiol. 2016;7:1–13.

    Google Scholar 

  • 43.

    Muscarella ME, Jones SE, Lennon JT. Species sorting along a subsidy gradient alters bacterial community stability. Ecology. 2016;97:2034–43.

    PubMed 

    Google Scholar 

  • 44.

    Peter H, Jeppesen E, De Meester L, Sommaruga R. Changes in bacterioplankton community structure during early lake ontogeny resulting from the retreat of the Greenland Ice Sheet. ISME J. 2018;12:544–55.

    Google Scholar 

  • 45.

    Blazewicz SJ, Barnard RL, Daly RA, Firestone MK. Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses. ISME J. 2013;7:2061–8.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 46.

    Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2013;17:10–12.

    Google Scholar 

  • 47.

    Callahan BJ, McMurdie PJ, Holmes SP. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. ISME J. 2017;11:2639–43.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 48.

    Wright ES. Using DECIPHER v2.0 to analyze big biological sequence data in R. R J. 2016;8:352–9.

    Google Scholar 

  • 49.

    Murali A, Bhargava A, Wright ES. IDTAXA: A novel approach for accurate taxonomic classification of microbiome sequences. Microbiome. 2018;6:1–14.

    Google Scholar 

  • 50.

    Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil PA, et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol. 2018;36:996.

    CAS 
    PubMed 

    Google Scholar 

  • 51.

    Větrovský T, Baldrian P. The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses. PLoS One. 2013;8:1–10.

    Google Scholar 

  • 52.

    Paulson JN, Colin Stine O, Bravo HC, Pop M. Differential abundance analysis for microbial marker-gene surveys. Nat Methods. 2013;10:1200–2.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 53.

    Bray JR, Curtis JT. An ordination of the upland forest communities of Southern Wisconsin. Ecol Monogr. 1957;27:325–49.

    Google Scholar 

  • 54.

    Legendre P, Legendre L Numerical ecology, 2nd ed. 1998. Elsevier, Amsterdam.

  • 55.

    Paradis E, Schliep K. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 2019;35:526–8.

    CAS 
    PubMed 

    Google Scholar 

  • 56.

    Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, et al. vegan: Community Ecology Package. 2019.

  • 57.

    Tabak J Differential Geometry. Geometry: The language of Space and Form. 2004. Facts on File, Inc, New York, p 150.

  • 58.

    Brown BL. Spatial heterogeneity reduces temporal variability in stream insect communities. Ecol Lett. 2003;6:316–25.

    Google Scholar 

  • 59.

    Osterholz H, Singer G, Wemheuer B, Daniel R, Simon M, Niggemann J, et al. Deciphering associations between dissolved organic molecules and bacterial communities in a pelagic marine system. ISME J. 2016;10:1717–30.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 60.

    Sørensen T. A method of establishing groups of equal amplitude in plant sociology based on similarity of species content, and its application to analysis of the vegetation on Danish commons. Biol Skr K Dan Vidensk Selsk. 1948;5:1–34.

    Google Scholar 

  • 61.

    R Core Team. R: A language and environment for statistical computing. 2020. Vienna.

  • 62.

    RStudio Team. RStudio: Integrated development for R. 2020. RStudio, Inc., Boston, MA.

  • 63.

    Anderson MJ, Walsh DCI. Anderson and Walsh (2013) PERMANOVA, ANOSIM, and the Mantel test in the face of heterogeneous dispersions- What null hypothesis are you.pdf. Ecol Monogr. 2013;83:557–74.

    Google Scholar 

  • 64.

    Wilhelm L, Besemer K, Fasching C, Urich T, Singer GA, Quince C, et al. Rare but active taxa contribute to community dynamics of benthic biofilms in glacier-fed streams. Environ Microbiol. 2014;16:2514–24.

    CAS 
    PubMed 

    Google Scholar 

  • 65.

    Campbell BJ, Yu L, Heidelberg JF, Kirchman DL. Activity of abundant and rare bacteria in a coastal ocean. Proc Natl Acad Sci. 2011;108:12776–81.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 66.

    Carrara F, Rinaldo A, Giometto A, Altermatt F. Complex interaction of dendritic connectivity and hierarchical patch size on biodiversity in river-like landscapes. Am Nat. 2013;183:13–25.

    PubMed 

    Google Scholar 

  • 67.

    Lindström ES, Forslund M, Algesten G, Bergström A-K. External control of bacterial community structure in lakes. Limnol Oceanogr. 2006;51:339–42.

    Google Scholar 

  • 68.

    Hausmann B, Pelikan C, Rattei T, Loy A, Pester M. Long-term transcriptional activity at zero growth of a cosmopolitan rare biosphere member. MBio. 2019;10:e02189–18.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 69.

    Luo X, Xiang X, Yang Y, Huang G, Fu K, Che R, et al. Seasonal effects of river flow on microbial community coalescence and diversity in a riverine network. FEMS Microbiol Ecol. 2020;96:1–13.

    Google Scholar 

  • 70.

    Paruch L, Paruch AM, Eiken HG, Skogen M, Sørheim R. Seasonal dynamics of lotic bacterial communities assessed by 16S rRNA gene amplicon deep sequencing. Sci Rep. 2020;10:16399.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 71.

    Ruiz-González C, Niño-García JP, Kembel SW, del Giorgio PA. Identifying the core seed bank of a complex boreal bacterial metacommunity. ISME J. 2017;11:2012–21.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 72.

    Stadler M, Ejarque E, Kainz MJ. In-lake transformations of dissolved organic matter composition in a subalpine lake do not change its biodegradability. Limnol Oceanogr. 2020;65:1554–72.

    CAS 

    Google Scholar 

  • 73.

    Hutchins RHS, Aukes P, Schiff SL, Dittmar T, Prairie YT, del Giorgio PA. The optical, chemical, and molecular dissolved organic matter succession along a boreal soil-stream-river continuum. J Geophys Res Biogeosciences. 2017;122:2892–908.

    CAS 

    Google Scholar 

  • 74.

    Besemer K, Singer G, Limberger R, Chlup A-K, Hochedlinger G, Hödl I, et al. Biophysical controls on community succession in stream biofilms. Appl Environ Microbiol. 2007;73:4966–74.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 75.

    Battin TJ, Kaplan LA, Denis Newbold J, Hansen CME. Contributions of microbial biofilms to ecosystem processes in stream mesocosms. Nature. 2003;426:439–42.

    CAS 
    PubMed 

    Google Scholar 

  • 76.

    McDougald D, Rice SA, Barraud N, Steinberg PD, Kjelleberg S. Should we stay or should we go: mechanisms and ecological consequences for biofilm dispersal. Nat Publ Gr. 2011;10:39–50.

    Google Scholar 

  • 77.

    Besemer K, Peter H, Logue JB, Langenheder S, Lindström ES, Tranvik LJ, et al. Unraveling assembly of stream biofilm communities. ISME J. 2012;6:1459–68.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 78.

    Hall EK, Bernhardt ES, Bier RL, Bradford MA, Boot CM, Cotner JB, et al. Understanding how microbiomes influence the systems they inhabit. Nat Microbiol. 2018;3:977–82.

    CAS 
    PubMed 

    Google Scholar 

  • 79.

    Stadler M CarBBAS/Paper_Stadler-delGiorgio_ISMEJ_2021. 2021. Zenodo.

  • 80.

    Stadler M, Ruiz-González C, Vick-Majors TJ, del Giorgio PA Microbial 16S rRNA gene (DNA) and transcripts (cDNA) along a boreal soil-freshwater-estuary continuum. 2021. Zenodo.


  • Source: Ecology - nature.com

    Local adaptations of Mediterranean sheep and goats through an integrative approach

    Predicting spring migration of two European amphibian species with plant phenology using citizen science data