Knowledge about the biogeography of organisms has long been a focus in ecological research, including the mechanisms that generate and maintain diversity. In this study, we targeted a microbial group relatively underrepresented in the microbial biogeographic literature, the soil Archaea. We surveyed the archaeal abundance and community composition using real-time quantitative PCR and T-RFLP approaches for 105 soil samples from 2 habitat types to identify the archaeal distribution patterns and factors driving these patterns. Results showed that the soil archaeal community was affected by spatial and environmental variables, and 79% and 51% of the community variation was explained in the non-flooded soil (NS) and flooded soil (FS) habitat, respectively, showing its possible biogeographic distribution. The diversity patterns of soil Archaea across the landscape were influenced by a combination of stochastic and deterministic processes. The contribution from neutral processes was higher than that from deterministic processes associated with environmental variables. The variables pH, sample depth and longitude played key roles in determining the archaeal distribution in the NS habitat, while sampling depth, longitude and NH4+-N were most important in the FS habitat. Overall, there might be similar ecological drivers in the soil archaeal community as in macroorganism communities.
References
[1]
Martiny JBH, Bohannan BJM, Brown JH, Colwell RK, Fuhrman JA, et al. (2006) Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol 4: 102–112.
Hawkins BA, Field R, Cornell HV, Currie DJ, Guegan JF, et al. (2003) Energy, water, and broad-scale geographic patterns of species richness. Ecology 84: 3105–3117.
[4]
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. Journal of Biogeography 37: 1341–1351.
[5]
Finlay BJ (2002) Global dispersal of free-living microbial eukaryote species. Science 296: 1061–1063.
[6]
Griffiths RI, Thomson BC, James P, Bell T, Bailey M, et al. (2011) The bacterial biogeography of British soils. Environ Microbiol 13: 1642–1654.
[7]
Caruso T, Chan Y, Lacap DC, Lau MC, McKay CP, et al. (2011) Stochastic and deterministic processes interact in the assembly of desert microbial communities on a global scale. ISME J 5: 1406–1413.
[8]
Fierer N, McCain CM, Meir P, Zimmermann M, Rapp JM, et al. (2011) Microbial elevational diversity does not follow the biogeographical trends of plants and animals. Ecology 92: 797–804.
[9]
Langenheder S, Székely AJ (2011) Species sorting and neutral processes are both important during the initial assembly of bacterial communities. ISME J 5: 1086–1094.
[10]
Auguet JC, Barberan A, Casamayor EO (2010) Global ecological patterns in uncultured Archaea. ISME J 4: 182–190.
[11]
Angel R, Soares MIM, Ungar E, D, Gillor O (2010) Biogeography of soil archaea and bacteria along a steep precipitation gradient. ISME J 4: 553–563.
[12]
Delong EF (1992) Archaea in coastal marine environments. Proc Natl Acad Sci USA 89: 5685–5689.
[13]
Leininger S, Urich T, Schloter M, Schwark L, Qi J, et al. (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442 806–809.
[14]
Lipp JS, Morono Y, Inagaki F, Hi K-U (2008) Significant contribution of Archaea to extant biomass in marine subsurface sediments. Nature 454: 991–994.
[15]
Bates ST, Berg-Lyons D, Caporaso JG, Walters WA, Knight R (2011) Examining the global distribution of dominant archaeal populations in soil. ISME J 5: 908–917.
[16]
Law R, Morton RD (1996) Permanence and the assembly of ecological communities. Ecology 77: 762–775.
[17]
Chase JM, Leibold MA (2003) Ecological Niche. Chicago: The University of Chicago Press.
[18]
Bell G (2001) Neutral macroecology. Science 293: 2413–2418.
[19]
Hubbell SP (2001) The Unified Neutral Theory of Biodiversity and Biogeography. Princeton: Princeton University Press.
[20]
Chesson PL, Case TJ (1986) Overview: non-equilibrium community theories: chance, variability, history and co-exis-tence. In: Diamond, J. and Case, T.J. Community Ecology. Harper and Row, NewYork. 229–239 p.
[21]
Chesson P (2000) Mechanisms of maintenance of species diversity. Annu Rev Ecol Evol Syst 31: 343–366.
[22]
Condit R, Ashton P, Bunyavejchewin S, Dattarja HS, Davies S, et al. (2006) The importance of demographic niches to tree diversity. Science 313: 98–101.
[23]
Wilson JB (1991) Methods for fitting dominance/diversity curves. J Veg Sci 2: 35–46.
Samuels CL, Drake JA (1997) Divergent perspectives on community convergence. TREE 12: 427–432.
[30]
Clark JS, McLachlan JS (2003) Stability of forest biodiversity. Nature 423: 635–638.
[31]
Tuomisto H, Ruokolainen K, Yli-Halla M (2003) Dispersal, environment, and ？oristic variation of western Amazonian forests. Science 299: 241–244.
[32]
Volkov I, Banavar JR, Hubbell SP, Maritan A (2007) Patterns of relative species abundance in rain forest and coral reefs. Nature 450: 45–49.
[33]
Kraft NJB, Valencia R, Ackerly DD (2008) Functional traits and niche-based tree community assembly in an amazonian forest. Science 322: 580–582.
[34]
Chytry M, Lososová Z, Horsák M, Uher B, ？ejka T, et al. (2012) Dispersal limitation is stronger in communities of microorganisms than macroorganisms across Central European cities. Journal of Biogeography 39: 1101–1111.
[35]
Locey KJ (2010) Synthesizing traditional biogeography with microbial ecology: the importance of dormancy. Journal of Biogeography 37: 1835–1841.
[36]
Horner-Devine MC, Silver JM, Leibold MA, Bohannan BJM, Colwell RK, et al. (2007) A comparison of taxon co-occurrence patterns for macro- and microorganisms. Ecology 88: 1345–1353.
[37]
Bryant JA, Lamanna C, Morlon H, Kerkhoff AJ, Enquist BJ, et al. (2008) Microbes on mountainsides: Contrasting elevational patterns of bacterial and plant diversity. Proc Natl Acad Sci USA 105: 11505–11511.
[38]
Wang JJ, Soininen J, Zhang Y, Wang BX, Yang XD, et al. (2012) Patterns of elevational beta diversity in micro- and macroorganisms. Global Ecol Biogeogr 21: 743–750.
[39]
The Earth Microbiom Project. Available: http://www.earthmicrobiome.org/. Accessed 2013 April 9.
[40]
Lauber CL, Hamady M, Knight R, Fierer N (2012) Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale. Appl Environ Microbiol 75: 5111–5120.
[41]
Fierer N, Jackson RB (2006) The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA 103: 626–631.
[42]
Bates ST, Clemente JC, Flores GE, Walters WA, Parfrey LW, et al. (2013) Global biogeography of highly diverse protistan communities in soil. ISME J 7: 652–659.
[43]
Martiny JBH, Eisen JA, Penn K, Allison SD, Horner-Devine MC (2011) Drivers of bacterial ？-diversity depend on spatial scale. Proc Natl Acad Sci USA 108: 7850–7854.
[44]
Ge Y, He JZ, Zhu YG, Zhang JB, Xu ZH, et al. (2008) Differences in soil bacterial diversity: driven by contemporary disturbances or historical contingencies? ISME J 2: 254–264.
[45]
Papke RT, Ramsing NB, Bateson MM, Ward DM (2003) Geographical isolation in hot spring cyanobacteria. Environ Microbiol 5: 650–659.
[46]
Cao P, Zhang LM, Shen JP, Zheng YM, Di HJ, et al. (2012) Distribution and diversity of archaeal communities in selected Chinese soils. FEMS Microbiology Ecology 80: 146–158.
[47]
Bremner JM (1996) Nitrogen-total. Methods of Soil Analysis: Part 3-Chemical Methods, Vol. 37 (Sparks DL et al., eds), 1085–1121. Soil Science Society of America, American Society of Agronomy, Madison, WI.
[48]
Dumas JBA (1831) Procedes de ？analyse organic, Ann Chim Phys. 247: 198–213.
[49]
Hershberger KL, Barns SM, Reysenbach AL, Dawson SC, Pace NR (1996) Wide diversity of Crenarchaeota. Nature 384: 420.
[50]
Kemnitz D, Kolb S, Conrad R (2005) Phenotypic characterization of Rice Cluster III archaea without prior isolation by applying quantitative polymerase chain reaction to an enrichment culture. Environ Microbiol 7: 553–565.
[51]
Klappenbach JA, Saxman PR, Cole JR, Schmidt TM (2001) Rrndb: the ribosomal RNA operon copy number database. Nucleic Acids Res 29: 181–184.
[52]
Lee ZM, Bussema C, Schmidt TM (2009) RrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea. Nucleic Acids Res 37, Database issue D489–D493.
[53]
Dumbrell AJ, Nelson M, Helgason T, Dytham C, Fitter AH (2010) Relative roles of niche and neutral processes in structuring a soil microbial community. ISME J 4: 1078–1078.
[54]
Borcard D, Legendre P, Avois-Jacquet C, Tuomisto H (2004) Dissecting the spatial structure of ecological data at multiple scales. Ecology 85: 1826–1832.
[55]
Dray S, Legendre P, Peres-Neto PR (2006) Spatial modelling: a comprehensive framework for principal coordinate analysis of neighbour matrices (PCNM). Ecol Model 196: 483–493.
[56]
Legendre P, Borcard D, Peres-Neto PR (2005) Analyzing beta diversity: Partitioning the spatial variation of community composition data. Ecol Monogr 75: 435–450.
[57]
Legendre P, Mi X, Ren H, Ma K, Yu M, et al. (2009) Partitioning beta diversity in a subtropical broad-leaved forest of China. Ecology 90: 663–674.
[58]
Kemnitz D, Kolb S, Conrad R (2007) High abundance of Crenarchaeota in a temperate acidic forest soil. FEMS Microbiol Ecol 60: 442–448.
[59]
Legendre P, Borcard D, Peres-Neto P (2008) Analyzing or explaining beta diversity? Comment. Ecology 89: 3238–3244.
[60]
Borcard D (1992) Partialling out the spatial component of ecological variation. Ecology 73: 1045–1055.
[61]
van der Gast CJ, Ager D, Lilley AK (2008) Temporal scaling of bacterial taxa is influenced by both stochastic and deterministic ecological factors. Environ Microbiol 10: 1411–1418.
[62]
Tian H, Wang S, Liu J, Pan S, Chen H, et al. (2006) Patterns of soil nitrogen storage in China. Global Biogeochem Cycles 20: GB1001 doi:10.1029/2005GB002464.
[63]
He JZ, Shen JP, Zhang LM, Zhu YG, Zheng YM, et al. (2007) Quantitative analyses of the abundance and compositions of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices. Environ Microbiol 9: 2364–2374.
