Function prediction and network analysis to investigate the response of microbial communities to a single environmental factor

References

• Antwis RE, Griffiths SM, Harrison XA, Aranega-Bou P, Arce A, Bettridge AS, et al. 2017. Fifty important research questions in microbial ecology. FEMS Microbiol Ecol. 93.
   PubMed Web of Science ®Google Scholar
• Archer S, Scifres C, Bassham CR, Maggio R. 1988. Autogenic succession in a subtropical savanna: conversion of grassland to thorn woodland. Ecol. Monogr. 58(2):111–127.
   Web of Science ®Google Scholar
• Arias CR, Lafrentz S, Cai W, Olivares-Fuster O. 2012. Adaptive response to starvation in the fish pathogen Flavobacterium columnare: cell viability and ultrastructural changes. BMC Microbiol. 12:266
   PubMed Web of Science ®Google Scholar
• Bai J, Chen X, Li J, Yang L, Fang H. 2011. Changes in the area of inland lakes in arid regions of central Asia during the past 30 years. Environ Monit Assess. 178(1-4):247–256.
   PubMed Web of Science ®Google Scholar
• Bai Y, Shi Q, Wen D, Li Z, Jefferson WA, Feng C, Tang X. 2012. Bacterial communities in the sediments of Dianchi Lake, a partitioned eutrophic waterbody in China. PloS One. 7(5):e37796.
   PubMed Web of Science ®Google Scholar
• Bajerski F, Wagner D, Mangelsdorf K. 2017. Cell membrane fatty acid composition of Chryseobacterium frigidisoli PB4T, isolated from Antarctic glacier forefield soils, in response to changing temperature and pH conditions. Front Microbiol. 8:677
   PubMed Web of Science ®Google Scholar
• Bayer-Santos E, Lima LDP, Ceseti L. d M, Ratagami CY, de Santana ES, da Silva AM, Farah CS, Alvarez-Martinez CE. 2018. Xanthomonas citri T6SS mediates resistance to Dictyostelium predation and is regulated by an ECF σ factor and cognate Ser/Thr kinase. Environ Microbiol. 20(4):1562–1575.
   PubMed Web of Science ®Google Scholar
• Campbell BJ, Kirchman DL. 2013. Bacterial diversity, community structure and potential growth rates along an estuarine salinity gradient. ISME J. 7(1):210–220.
   PubMed Web of Science ®Google Scholar
• Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, et al. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 7(5):335–336.
   PubMed Web of Science ®Google Scholar
• Crump BC, Hopkinson CS, Sogin ML, Hobbie JE. 2004. Microbial biogeography along an estuarine salinity gradient: combined influences of bacterial growth and residence time. Appl Environ Microbiol. 70(3):1494–1505.
   PubMed Web of Science ®Google Scholar
• Dafre AL, Schmitz AE, Maher P. 2017. Methylglyoxal-induced AMPK activation leads to autophagic degradation of thioredoxin 1 and glyoxalase 2 in HT22 nerve cells. Free Radic Biol Med. 108:270–279.
   PubMed Web of Science ®Google Scholar
• Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 26(19):2460–2461.
   PubMed Web of Science ®Google Scholar
• Edmonds JW, Weston NB, Joye SB, Mou X, Moran MA. 2009. Microbial community response to seawater amendment in low-salinity tidal sediments. Microb Ecol. 58(3):558–568.
   PubMed Web of Science ®Google Scholar
• Evans TG, Hofmann GE. 2012. Defining the limits of physiological plasticity: how gene expression can assess and predict the consequences of ocean change. Philos Trans R Soc Lond, B: Biol Sci. 367(1596):1733–1745.
   PubMed Web of Science ®Google Scholar
• Faust K, Sathirapongsasuti JF, Izard J, Segata N, Gevers D, Raes J, Huttenhower C. 2012. Microbial co-occurrence relationships in the human microbiome. PLoS Comput Biol. 8(7):e1002606.
   PubMed Web of Science ®Google Scholar
• Fierer N, Leff JW, Adams BJ, Nielsen UN, Bates ST, Lauber CL, Owens S, Gilbert JA, Wall DH, Caporaso JG, et al. 2012. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc Natl Acad Sci USA. 109(52):21390–21395.
   PubMed Web of Science ®Google Scholar
• García-Giménez JL, Seco-Cervera M, Aguado C, Romá-Mateo C, Dasí F, Priego S, Markovic J, Knecht E, Sanz P, Pallardó FV, et al. 2013. Lafora disease fibroblasts exemplify the molecular interdependence between thioredoxin 1 and the proteasome in mammalian cells. Free Radic Biol Med. 65:347–359.
   PubMed Web of Science ®Google Scholar
• Guimera R, Amaral LAN. 2005. Functional cartography of complex metabolic networks. Nature. 433:895–900.
   PubMed Web of Science ®Google Scholar
• Herlemann DPR, Labrenz M, Jurgens K, Bertilsson S, Waniek JJ, Andersson AF. 2011. Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea. ISME J. 5(10):1571–1579.
   PubMed Web of Science ®Google Scholar
• Herlemann DP, Lundin D, Andersson AF, Labrenz M, Jürgens K. 2016. Phylogenetic signals of salinity and season in bacterial community composition across the salinity gradient of the Baltic Sea. Front Microbiol. 7:1883
   PubMed Web of Science ®Google Scholar
• Hollister EB, Engledow AS, Hammett AJM, Provin TL, Wilkinson HH, Gentry TJ. 2010. Shifts in microbial community structure along an ecological gradient of hypersaline soils and sediments. ISME J. 4(6):829–838.
   PubMed Web of Science ®Google Scholar
• Jiao S, Liu Z, Lin Y, Yang J, Chen W, Wei G. 2016. Bacterial communities in oil contaminated soils: Biogeography and co-occurrence patterns. Soil Biol Biochem. 98:64–73.
   Web of Science ®Google Scholar
• Kan J, Evans SE, Chen F, Suzuki MT. 2008. Novel estuarine bacterioplankton in rRNA operon libraries from the Chesapeake Bay. Aquat Microb Ecol. 51:55–66.
   Web of Science ®Google Scholar
• Kim KK, Lee KC, Oh HM, Lee JS. 2008. Chryseobacterium aquaticum sp. nov., isolated from a water reservoir. Int J Syst Evol Microbiol. 58(Pt 3):533–537.
   PubMed Web of Science ®Google Scholar
• Kirchman DL, Dittel AI, Malmstrom RR, Cottrell MT. 2005. Biogeography of major bacterial groups in the Delaware Estuary. Limnol Oceanogr. 50(5):1697–1706.
   Web of Science ®Google Scholar
• Kowalchuk GA, Buma DS, de Boer W, Klinkhamer PG, van Veen JA. 2002. Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms. Antonie Van Leeuwenhoek. 81(1–4):509–520.
   PubMed Web of Science ®Google Scholar
• Krause AE, Frank KA, Mason DM, Ulanowicz RE, Taylor WW. 2003. Compartments revealed in food-web structure. Nature. 426(6964):282–285.
   PubMed Web of Science ®Google Scholar
• León-Lorenzana D, Arit S, Delgado-Balbuena L, Domínguez-Mendoza CA, Navarro-Noya YE, Luna-Guido M, et al. 2018. Soil salinity controls relative abundance of specific bacterial groups involved in the decomposition of maize plant residues. Front Ecol Evol. 6:51.
   Web of Science ®Google Scholar
• Levy R, Borenstein E. 2013. Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules. Proc Natl Acad Sci USA. 110(31):12804–12809.
   PubMed Web of Science ®Google Scholar
• Liang J, Liu J, Wang X, Lin H, Liu J, Zhou S, Sun H, Zhang X-H. 2019. Spatiotemporal dynamics of free-living and particle-associated Vibrio communities in the northern Chinese marginal seas. Appl Environ Microbiol. 85(9):19. e00217
   Web of Science ®Google Scholar
• LindströM ES, Kamst-Van Agterveld MP, Zwart G. 2005. Distribution of typical freshwater bacterial groups is associated with pH, temperature, and lake water retention time. AEM. 71(12):8201–8206.
   Web of Science ®Google Scholar
• Liu Y, Yao T, Jiao N, Zhu L, Hu A, Liu X, Gao J, Chen Z-Q. 2013. Salinity impact on bacterial community composition in five high-altitude lakes from the Tibetan Plateau, Western China. Geomicrobiol J. 30(5):462–469.
   Web of Science ®Google Scholar
• Lozupone CA, Knight R. 2007. Global patterns in bacterial diversity. Proc Natl Acad Sci Usa. 104(27):11436–11440.
   PubMed Web of Science ®Google Scholar
• Lu J, Holmgren A. 2012. Thioredoxin system in cell death progression. Antioxid Redox Signal. 17(12):1738–1747.
   PubMed Web of Science ®Google Scholar
• Mitter EK, de Freitas JR, Germida JJ. 2017. Bacterial root microbiome of plants growing in oil sands reclamation covers. Front Microbiol. 8:849.
   PubMed Web of Science ®Google Scholar
• Moody J. 2001. Race, school integration, and friendship segregation in America. Am J Sociol. 107(3):679–716.
   Web of Science ®Google Scholar
• Newman MEJ. 2003. The structure and function of complex networks. SIAM Rev. 45(2):167–256.
   Web of Science ®Google Scholar
• Newton RJ, Jones SE, Eiler A, McMahon KD, Bertilsson S. 2011. A guide to the natural history of freshwater lake bacteria. Microbiol Mol Biol Rev. 75(1):14–49.
   PubMed Web of Science ®Google Scholar
• Oren A. 2001. The bioenergetic basis for the decrease in metabolic diversity at increasing salt concentrations: implications for the functioning of salt lake ecosystems. Dordrecht: Springer; p. 61–72.
   Google Scholar
• Pastor-Satorras R, Vespignani A. 2001. Epidemic spreading in scale-free networks. Phys Rev Lett. 86(14):3200–3203.
   PubMed Web of Science ®Google Scholar
• Proulx SR, Promislow DEL, Phillips PC. 2005. Network thinking in ecology and evolution. Trends Ecol Evol (Amst). 20(6):345–353.
   PubMed Web of Science ®Google Scholar
• R Core Team, 2013. R: A language and environment for statistical computing. Computing. 1:12–21.
   Google Scholar
• Rivas R, Velázquez E, Willems A, Vizcaíno N, Subba-Rao NS, Mateos PF, Gillis M, Dazzo FB, Martínez-Molina E. 2002. A new species of Devosia that forms a unique nitrogen-fixing root-nodule symbiosis with the aquatic legume Neptunia natans (Lf) Druce. Appl Environ Microbiol. 68(11):5217–5222.
   PubMed Web of Science ®Google Scholar
• Rizzatti G, Lopetuso LR, Gibiino G, Binda C, Gasbarrini A. 2017. Proteobacteria: a common factor in human diseases. Biomed Res Int. 2017:9351507.
   PubMed Web of Science ®Google Scholar
• Schütte UME, Abdo Z, Bent SJ, Williams CJ, Schneider GM, Solheim B, Forney LJ. 2009. Bacterial succession in a glacier foreland of the high Arctic. ISME J. 3(11):1258–1268.
   PubMed Web of Science ®Google Scholar
• Steiner PA, Sintes E, Simó R, De Corte D, Pfannkuchen DM, Ivančić I, Najdek M, Herndl GJ. 2019. Seasonal dynamics of marine snow-associated and free-living demethylating bacterial communities in the coastal northern Adriatic Sea. Environ Microbiol Rep. 11(5):699–707.
   PubMed Web of Science ®Google Scholar
• Tagnon MD, Simeon KO. 2017. Aldehyde dehydrogenases may modulate signaling by lipid peroxidation-derived bioactive aldehydes. Plant Signal Behav. 12(11):e1387707
   PubMed Web of Science ®Google Scholar
• Tang X, Xie G, Shao K, Chen Y, Gao G. 2012. Influence of salinity on the bacterial community composition in Lake Bosten, a large oligosaline lake in arid northwestern China. Appl Environ Microbiol. 78:4748–4751.
   PubMed Web of Science ®Google Scholar
• Tang X, Xie G, Shao K, Dai J, Chen Y, Xu Q, Gao G. 2015. Bacterial community composition in oligosaline lake Bosten: Low overlap of betaproteobacteria and bacteroidetes with freshwater ecosystems. Microbes Environ. 30(2):180–188.
   Google Scholar
• Tiao G, Lee CK, McDonald IR, Cowan DA, Cary SC. 2012. Rapid microbial response to the presence of an ancient relic in the Antarctic Dry Valleys. Nat Commun. 3(1):18.
   Web of Science ®Google Scholar
• Van Der Heijden MGA, Bardgett RD, Van Straalen NM. 2008. The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol Lett. 11(3):296–310.
   PubMed Web of Science ®Google Scholar
• Van Horn DJ, Okie JG, Buelow HN, Gooseff MN, Barrett JE, Takacs-Vesbach CD. 2014. Soil microbial responses to increased moisture and organic resources along a salinity gradient in a polar desert. Appl Environ Microbiol. 80(10):3034–3043.
   PubMed Web of Science ®Google Scholar
• Walker LR, Del Moral R. 2003. Primary succession and ecosystem rehabilitation. Cambridge: Cambridge University Press.
   Google Scholar
• Wang Y, Pan J, Yang J, Zhou Z, Pan Y, Li M. 2020. Patterns and processes of free‐living and particle‐associated bacterioplankton and archaeaplankton communities in a subtropical river‐bay system in South China. Limnol Oceanogr. 65(S1).
   Web of Science ®Google Scholar
• Wang H, Wu P, Liu J, Yang S, Ruan B, Rehman S, Liu L, Zhu N. 2020. The regulatory mechanism of Chryseobacterium sp. resistance mediated by montmorillonite upon cadmium stress. Chemosphere. 240:124851
   PubMed Web of Science ®Google Scholar
• Wei FS, Qi WQ, Bi T, Sun ZG, Huang YR, Sheng YW. 2002. Discharge standard of pollutants for municipal wastewater treatment plant. 291–2981. Beijing: China Environmental Science Press (in Chinese). 
   Google Scholar
• Weiher E, Clarke GDP, Keddy PA. 1998. Community assembly rules, morphological dispersion, and the coexistence of plant species. Oikos. 81(2):309–322.
   Web of Science ®Google Scholar
• Wu QL, Zwart G, Schauer M, Kamst-van Agterveld MP, Hahn MW. 2006. Bacterioplankton community composition along a salinity gradient of sixteen high-mountain lakes located on the Tibetan Plateau, China. Appl Environ Microbiol. 72(8):5478–5485.
   PubMed Web of Science ®Google Scholar
• Xiao M, Wu F, Liao H, Li W, Lee X, Huang R. 2010. Characteristics and distribution of low molecular weight organic acids in the sediment porewaters in Bosten Lake. China J Environ Sci. 22(3):328–337.
   PubMed Web of Science ®Google Scholar
• Xue L, Ren H, Li S, Leng X, Yao X. 2017. Soil bacterial community structure and co-occurrence pattern during vegetation restoration in karst rocky desertification area. Front Microbiol. 8:2377
   PubMed Web of Science ®Google Scholar
• Yan N, Marschner P. 2012. Response of microbial activity and biomass to increasing salinity depends on the final salinity, not the original salinity. Soil Biol Biochem. 53:50–55.
   Web of Science ®Google Scholar
• Zahran HH. 1997. Diversity, adaptation and activity of the bacterial flora in saline environments. Biol Fertil Soils. 25(3):211–223.
   Web of Science ®Google Scholar
• Zak DR, Holmes WE, White DC, Peacock AD, Tilman D. 2003. Plant diversity, soil microbial communities, and ecosystem function: are there any links?. Ecology. 84(8):2042–2050.
   Web of Science ®Google Scholar
• Zhang L, Gao G, Tang X, Shao K. 2014. Can the freshwater bacterial communities shift to the “‘marine-like’taxa?”J Basic Microbiol. 54(11):1264–1272.
   PubMed Web of Science ®Google Scholar
• Zhang L, Gao G, Tang X, Shao K, Bayartu S, Dai J. 2013. Bacterial community changes along a salinity gradient in a Chinese wetland. Can J Microbiol. 59(9):611–619.
   PubMed Web of Science ®Google Scholar
• Zwart G, Crump BC, Kamst-van Agterveld MP, Hagen F, Han SK. 2002. Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers. Aquat Microb Ecol. 28:141–155.
   Web of Science ®Google Scholar