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Articles

Depth-Dependent Patterns of Bacterial Communities and Assembly Processes in a Typical Red Soil Critical Zone

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Pages 201-212 | Received 22 Dec 2018, Accepted 30 Oct 2019, Published online: 12 Nov 2019

References

  • Agnelli A, Ascher J, Corti G, Ceccherini MT, Nannipieri P, Pietramellara G. 2004. Distribution of microbial communities in a forest soil profile investigated by microbial biomass, soil respiration and DGGE of total and extracellular DNA. Soil Biol Biochem 36(5):859–868.
  • Akob DM, Küsel K. 2011. Where microorganisms meet rocks in the earth’s Critical Zone. Biogeosciences 8(12):3531–3543.
  • Andam CP, Doroghazi JR, Campbell AN, Kelly PJ, Choudoir MJ, Buckley DH. 2016. A latitudinal diversity gradient in terrestrial bacteria of the genus Streptomyces. mBio 7(2):e02200–15.
  • Anderson MJ. 2003. DISTLM Forward: A FORTRAN computer program to calculate a distance-based multivariate analysis for a linear model using forward selection. New Zealand: Department of Statistics, University of Auckland.
  • Blume E, Bischoff M, Reichert JM, Moorman T, Konopka A, Turco RF. 2002. Surface and subsurface microbial biomass, community structure and metabolic activity as a function of soil depth and season. Appl Soil Ecol 20(3):171–181.
  • Buss HL, Bruns MA, Schultz MJ, Moore J, Mathur CF, Brantley SL. 2005. The coupling of biological iron cycling and mineral weathering during saprolite formation, Luquillo Mountains, Puerto Rico. Geobiology 3(4):247–260.
  • 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.
  • Chase JM, Myers JA. 2011. Disentangling the importance of ecological niches from stochastic processes across scales. Phil Trans R Soc B 366(1576):2351–2363.
  • Chen S, Wang F, Zhang Y, Qin S, Wei S, Wang S, Hu C, Liu B. 2018. Organic carbon availability limiting microbial denitrification in the deep vadose zone. Environ Microbiol 20(3):980–992.
  • Chu H, Sun H, Tripathi BM, Adams JM, Huang R, Zhang Y, Shi Y. 2016. Bacterial community dissimilarity between the surface and subsurface soils equals horizontal differences over several kilometers in the western Tibetan Plateau. Environ Microbiol 18(5):1523–1533.
  • Delgado-Baquerizo M, Bissett A, Eldridge DJ, Maestre FT, He J-Z, Wang J-T, Hamonts K, Liu Y-R, Singh BK, Fierer N. 2017. Palaeoclimate explains a unique proportion of the global variation in soil bacterial communities. Nat Ecol Evol 1(9):1339–1347.
  • Dini-Andreote F, Stegen JC, van Elsas JD, Salles JF. 2015. Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession. Proc Natl Acad Sci USA 112(11):E1326–E1332.
  • Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26(19):2460–2461.
  • Eilers K, Debenport S, Anderson S, Fierer N. 2012. Digging deeper to find unique microbial communities: the strong effect of depth on the structure of bacterial and archaeal communities in soil. Soil Biol Biochem 50:58–65.
  • Ekelund F, Rønn R, Christensen S. 2001. Distribution with depth of protozoa, bacteria and fungi in soil profiles from three Danish forest sites. Soil Biol Biochem 33(4–5):475–481.
  • Faith DP. 1992. Conservation evaluation and phylogenetic diversity. Biol Conserv 61(1):1–10.
  • Fan K, Weisenhorn P, Gilbert JA, Shi Y, Bai Y, Chu H. 2018. Soil pH correlates with the co-occurrence and assemblage process of diazotrophic communities in rhizosphere and bulk soils of wheat fields. Soil Biol Biochem 121:185–192.
  • Fierer N. 2017. Embracing the unknown: disentangling the complexities of the soil microbiome. Nat Rev Microbiol 15(10):579–590.
  • Fierer N, Jackson RB. 2006. The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA 130:626–631.
  • Fierer N, Schimel JP, Holden PA. 2003. Variations in microbial community composition through two soil depth profiles. Soil Biol Biochem 35(1):167–176.
  • Fine PVA, Kembel SW. 2011. Phylogenetic community structure and phylogenetic turnover across space and edaphic gradients in western Amazonian tree communities. Ecography 34(4):552–565.
  • Gao L, Lv Y, Wang D, Muhammad T, Biswas A, Peng X. 2016. Soil water storage prediction at high space-time resolution along an agricultural hillslope. Agr Water Manage 165:122–130.
  • Geen JL, Bohannan BJM, Whitaker RJ. 2008. Microbial biogeography: from taxonomy to traits. Science 320:1039–1043.
  • Gittel A, Bárta J, Kohoutová I, Mikutta R, Owens S, Gilbert J, Schnecker J, Wild B, Hannisdal B, Maerz J, et al. 2014. Distinct microbial communities associated with buried soils in the Siberian tundra. ISME J 8(4):841–853.
  • Gittel A, Bárta J, Kohoutová I, Schnecker J, Wild B, Čapek P, Kaiser C, Torsvik VL, Richter A, Schleper C, et al. 2014. Site- and horizon-specific patterns of microbial community structure and enzyme activities in permafrost-affected soils of Greenland. Front Microbiol 5:541.
  • Griffiths RI, Thomson BC, James P, Bell T, Bailey M, Whiteley AS. 2011. The bacterial biogeography of British soils. Environ Microbiol 13(6):1642–1654.
  • Hansel CM, Fendorf S, Jardine PM, Francis C. 2008. Changes in bacterial and archaeal community structure and functional diversity along a geochemically variable soil profile. Appl Environ Microbiol 74(5):1620–1633.
  • Hartmann M, Lee S, Hallam SJ, Mohn WW. 2009. Bacterial, archaeal and eukaryal community structures throughout soil horizons of harvested and naturally disturbed forest stands. Environ Microbiol 11(12):3045–3062.
  • He X, Xie W, Deng S, Lu S. 1983. The problems and achievements about improving use red-yellow soil in China [in Chinese]. Chin J Soil Sci (2):1–4.
  • Helgason BL, Konschuh HJ, Bedard-Haughn A, VandenBygaart AJ. 2014. Microbial distribution in an eroded landscape: buried A horizons support abundant and unique communities. Agr Ecosyst Environ 196:94–102.
  • Hu X, Wei J, Du Y, Xu L-F, Wang H-B, Zhang G-L, Ye W, Zhu L-D. 2010. Regional distribution of the Quaternary red clay with aeolian dust characteristics in subtropical China and its paleoclimatic implications. Geoderma 159(3-4):317–334.
  • Hu X-F, Du Y, Liu X-J, Zhang G-L, Jiang Y, Xue Y. 2015. Polypedogenic case of loess overlying red clay as a response to the last glacial-interglacial cycle in mid-subtropical Southeast China. Aeolian Res 16:125–142.
  • Hue SM, Huber JA, Morrison HG, Sogin ML, Welch DM. 2007. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 8:R143.
  • IUSS Working Group WRB. 2015. World Reference Base for Soil Resources 2014, update 2015, International soil classification system for naming soils and creating legends for soil maps. World Soil Resources Reports No. 106. Rome, Italy: Food and Agriculture Organization of the United Nations.
  • Jones DL, Magthab EA, Gleeson DB, Hill PW, Sanchez-Rodriguez AR, Roberts P, Ge T, Murphy DV. 2018. Microbial competition for nitrogen and carbon is as intense in the subsoil as in the topsoil. Soil Biol Biochem 117:72–82.
  • Kembel SW. 2009. Disentangling niche and neutral influences on community assembly: assessing the performance of community phylogenetic structure tests. Ecol Lett 12(9):949–960.
  • LaMontagne MG, Schimel JP, Holden PA. 2003. Comparison of subsurface and surface soil bacterial communities in California grassland as assessed by terminal restriction fragment length polymorphisms of PCR-amplified 16S rRNA genes. Microb Ecol 46(2):216–227.
  • Lauber CL, Hamady M, Knight R, Fierer N. 2009. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75(15):5111–5120.
  • Li B, Wen X, David D, Qiu S, Dong Y, Li Z, Du S, Ou X, Li H, Niu D, et al. 2008. Paleoclimate change recorded in the red earth and brown-yellow sediment of late Quaternary for northeastern part of Guangdong Province, south to the Nanling Mountains, China. Sci Bull 53:3866–3875.
  • Li C, Yan K, Tang L, Jia Z, Li Y. 2014. Change in deep soil microbial communities due to long-term fertilization. Soil Biol Biochem 75:264–272.
  • Liermann LJ, Albert I, Buss HL, Minyard M, Brantley SL. 2015. Relating microbial community structure and geochemistry in deep regolith developed on volcaniclastic rock in the Luquillo Mountains, Puerto Rico. Geomicrobiol J 32(6):494–510.
  • Lozupone C, Hamady M, Knight R. 2006. UniFrac-an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics 7(1):371.
  • Lozupone CA, Knight R. 2007. Global patterns in bacterial diversity. Proc Natl Acad Sci USA 104(27):11436–11440.
  • Madsen E. 1995. Impacts of agricultural practices on subsurface microbial ecology. Adv Agron 54:1–67.
  • Maestre FT, Delgado-Baquerizo M, Jeffries TC, Eldridge DJ, Ochoa V, Gozalo B, Quero JL, García-Gómez M, Gallardo A, Ulrich W, et al. 2015. Increasing aridity reduces soil microbial diversity and abundance in global drylands. Proc Natl Acad Sci USA 112(51):15684–15689.
  • Martiny J. 2016. History leaves its mark on soil bacterial diversity. Mbio 7(3):e00784–16.
  • Martiny JBH, Bohannan BJM, Brown JH, Colwell RK, Fuhrman JA, Green JL, Horner-Devine MC, Kane M, Krumins JA, Kuske CR, et al. 2006. Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol 4(2):102–112.
  • Meyer KM, Memiaghe H, Korte L, Kenfack D, Alonso A, Bohannan B. 2018. Why do microbes exhibit weak biogeographic patterns? ISME J 12(6):1404–1413.
  • Minyard ML, Bruns MA, Liermann LJ, Buss HL, Brantley SL. 2012. Bacterial associations with weathering minerals at the regolith-bedrock interface, Luquillo experimental forest, Puerto Rico. Geomicrobiol J 29(9):792–803.
  • Minyard ML, Bruns MA, Martínez CE, Liermann LJ, Buss HL, Brantley SL. 2011. Halloysite nanotubes and bacteria at the saprolite–bedrock interface, Rio Icacos watershed, Puerto Rico. Soil Sci Soc Am J 75(2):348–356.
  • National Research Council (NRC) 2001. Basic Research Opportunities in Earth Science. Washington DC: National Academy Press.
  • Ofiţeru ID, Lunn M, Curtis TP, Wells GF, Criddle CS, Francis CA, Sloan WT. 2010. Combined niche and neutral effects in a microbial wastewater treatment community. Proc Natl Acad Sci USA 107:15345–15350.
  • Orgiazzi A, Bardgett RD, Barrios E, Behan-Pelletier V, Briones MJI, Chotte J-L, De Deyn GB, Eggleton P, Fierer N, Fraser T, et al. 2016. Global Soil Biodiversity Atlas. Luxembourg: European Commission, Publications Office of the European Union.
  • R Development Core Team. 2016. R: a language and environment for statistical computing. Vienna: R Foundation for Statistical Computing.
  • Richter DD, Billings SA, Groffman PM, Kelly EF, Lohse KA, McDowell WH, White TS, Anderson SA, Baldocchi DD, Banwart S, et al. 2018. Ideas and perspectives: strengthening the biogeosciences in environmental research networks. Biogeosciences 15(15):4815–4832.
  • Richter DD, Markewitz D. 1995. How deep is soil?: soil, the zone of the earth's crust that is biologically active, is much deeper than has been thought by many ecologists. BioScience 45(9):600–609.
  • Sagova-Mareckova M, Zadorova T, Penizek V, Omelka M, Tejnecky V, Pruchova P, Chuman T, Drabek O, Buresova A, Vanek A, et al. 2016. The structure of bacterial communities along two vertical profiles of a deep colluvial soil. Soil Biol Biochem 101:65–73.
  • Schütz K, Kandeler E, Nagel P, Scheu S, Ruess L. 2010. Functional microbial community response to nutrient pulses by artificial groundwater recharge particle in surface soils and subsoils. FEMS Microbiol Ecol 72(3):445–455.
  • Seuradge BJ, Oelbermann M, Neufeld JD. 2017. Depth-dependent influence of different land-use systems on bacterial biogeography. FEMS Microbiol Ecol 93(2):fiw239.
  • Shen C, Ni Y, Liang W, Wang J, Chu H. 2015. Distant soil bacterial communities along a small-scale elevational gradient in alpine tundra. Front Microbiol 6:582.
  • Shen C, Xiong J, Zhang H, Feng Y, Lin X, Li X, Liang W, Chu H. 2013. Soil pH drives the spatial distribution of bacterial communities along elevation on Changbai Mountain. Soil Biol Biochem 57:204–211.
  • Shi Y, Grogan P, Sun H, Xiong J, Yang Y, Zhou J, Chu H. 2015. Multi-scale variability analysis reveals the importance of spatial distance in shaping Arctic soil microbial functional communities. Soil Biol Biochem 86:126–134.
  • Shi Y, Li Y, Xiang X, Sun R, Yang T, He D, Zhang K, Ni Y, Zhu Y-G, Adams JM, et al. 2018. Spatial scale affects the relative role of stochasticity versus determinism in soil bacterial communities in wheat fields across the North China Plain. Microbiome 6(1):27.
  • Soil Survey Staff. 2014. Keys to Soil Taxonomy. 12th ed. Washington DC: USDA-Natural Resources Conservation Service.
  • Stegen JC, Lin X, Konopka AE, Fredrickson JK. 2012. Stochastic and deterministic assembly processes in subsurface microbial communities. ISME J 6(9):1653–1664.
  • Stone MM, DeForest JL, Plante AF. 2014. Changes in extracellular enzyme activity and microbial community structure with soil depth at the Luquillo Critical Zone Observatory. Soil Biol Biochem 75:237–247.
  • Sul WJ, Asuming-Brempong S, Wang Q, Tourlousse DM, Penton CR, Deng Y, Rodrigues JLM, Adiku SGK, Jones JW, Zhou J, et al. 2013. Tropical agricultural land management influences on soil microbial communities through its effect on soil organic carbon. Soil Biol Biochem 65:33–38.
  • USDA. 2006. USDA Natural Resources Conservation Service Website. Accessed June 10, 2018. Available at https://nrcspad.sc.egov.usda.gov/DistributionCenter/pdf.aspx?productID=587.
  • Vellend M. 2010. Conceptual synthesis in community ecology. Quart Rev Biol 85(2):183–206.
  • Webb CO, Ackerly DD, McPeek MA, Donoghue MJ. 2002. Phylogenies and community ecology. Annu Rev Ecol Syst 33(1):475–505.
  • Will C, Thurmer A, Wollherr A, Nacke H, Herold N, Schrumpf M, Gutknecht J, Wubet T, Buscot F, Daniel R. 2010. Horizon-specific bacterial community composition of German grassland soils, as revealed by pyrosequencing-based analysis of 16S rRNA gene. Appl Environ Microbiol 76(20):6751–6759.
  • Wilson MJ, He Z, Yang X. 2004. The red soils of China: their nature, management and utilization. New York: Springer Science + Business Media.
  • Wu H, Song X, Zhao X, Peng X, Zhou H, Hallett PD, Hodson ME, Zhang G-L. 2019. Accumulation of nitrate and dissolved organic nitrogen at depth in a red soil Critical Zone. Geoderma 337:1175–1185.
  • Xiong J, Liu Y, Lin X, Zhang H, Zeng J, Hou J, Yang Y, Yao T, Knight R, Chu H. 2012. Geographic distance and pH drive bacterial distribution in alkaline lake sediments across Tibetan Plateau. Environ Microbiol 14(9):2457–2466.
  • Zhao Q, Huang G, Ma Y. 2013. The problems in red soil ecosystem in southern of China and its countermeasures [in Chinese]. Acta Ecol Sin 33:7615–7622.

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