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Soil Bacterial Diversity and its Determinants in the Riparian Zone of the Lijiang River, China
This study was designed to analyse the soil bacterial community composition and diversity, as well as their relationships with various environmental factors in a riparian ecosystem. The 16S rRNA sequencing technology was applied to profile the bacterial composition of 120 samples from four different transects (long, moderate, less and rare inundation) in ten different study sites along the Lijiang riparian zone; the corresponding soil properties were also measured. The results indicated that, diversity was lowest in the rare inundation transect and there were high yet not significantly different bacterial community diversities in the long, moderate, and less inundation transects. The dominant bacterial groups of the four transects were similar, but there were great differences in the abundances of specific groups. Proteobacteria (29.28%), with the dominant classes of Beta- (15.65%), Delta- (5.75%), Gamma- (4.46%) and Alpha-proteobacteria (3.32%), was the most abundant phylum in the studied riparian soils. The genus Candidatus Nitrososphaera including ammonia-oxidizing archaea (AOA) and the genus Nitrospira including nitrite-oxidizing bacteria were both sensitive to inundation gradient changes. Redundancy analysis revealed that soil properties such as soil pH, inundation frequency, sand content, soil water content, total N and available N were significantly correlated with the bacterial community diversity and structure. The study suggests that the flood disturbance gradient and the spatial heterogeneity of soil properties affect the composition and diversity of bacterial communities in the Lijiang riparian zone.
Bacterial Diversity, Inundation, River Zone, 16s rRNA Sequencing, Soil Physicochemical Properties.
- Fierer, N., Schimel, J. P. and Holden, P. A., Variations in microbial community composition through two soil depth profiles. Soil Biol. Biochem., 2003, 35, 167–176.
- Douterelo, I., Goulder, R. and Lillie, M., Soil microbial community response to land management and depth, related to the degradation of organic matter in English wetlands: implications for the in situ preservation of archaeological remains. Appl. Soil Ecol., 2010, 44, 219–227.
- Hansel, C. M., Fendorf, S., Jardine, P. M. and Francis, C. A., Changes in bacteria and archaeal community structure and functional diversity along a geochemically variable soil profile. Appl. Environ. Microb., 2008, 74, 1620–1633.
- Peralta, A. L., Matthews, J. W. and Kent, A. D., Microbial community structure and denitrification in a wetland mitigation bank. Appl. Environ. Microb., 2010, 76, 4207–4215.
- Borcard, D., Gillet, F. and Legendre, P., Numerical Ecology with R. Matisse, 2011, 77, 332–334.
- Marschner, P., Yang, C. H., Lieberei, R. and Crowley, D. E., Soil and plant specific effects on bacterial community composition in the rhizosphere. Soil Biol. Biochem., 2001, 33, 1437–1445.
- Kuang, J. L., Huang, L. N., Chen, L. X., Hua, Z. S., Li, S. J. and Hu, M., Contemporary environmental variation determines microbial diversity patterns in acid mine drainage. ISME J., 2013, 7, 1038–1050.
- Ludemann, H., Arth, I. and Liesack, W., Spatial changes in the bacterial community structure along a vertical oxygen gradient in flooded paddy soil cores. Appl. Environ. Microb., 2000, 66, 754– 762.
- Zhou, J. Z., Xia, B. C., Huang, H., Palumbo, A. V. and Tiedje, J. M., Microbial diversity and heterogeneity in sandy subsurface soils. Appl. Environ. Microb., 2004, 70, 1723–1734.
- Yu, Y., Wang, H., Liu, J., Wang, Q., Shen, T., Guo, W. and Wang, R., Shifts in microbial community function and structure along the successional gradient of coastal wetlands in Yellow River Estuary. Eur. J. Soil Biol., 2011, 49, 12–21.
- Wang, J. T., Zheng, Y. M., Hu, H. W., Zhang, L. M., Li, J. and He, J. Z., Soil pH determines the alpha diversity but not beta diversity of soil fungal community along altitude in a typical Tibetan forest ecosystem. J. Soil Sediment, 2015, 15, 1224–1232.
- Fierer, N. and Jackson, R. B., The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. USA, 2006, 103, 626–631.
- Rinklebe, J. and Langer, U., Microbial diversity in three floodplain soils at the Elbe River (Germany). Soil Biol. Biochem., 2006, 38, 2144–2151.
- Moche, M., Gutknecht, J., Schulz, E., Langer, U. and Rinklebe, J., Monthly dynamics of microbial community structure and their controlling factors in three floodplain soils. Soil Biol. Biochem., 2015, 90, 169–178.
- Wilson, J. S., Baldwin, D. S., Rees, G. N. and Wilson, B. P., The effects of short-term inundation on carbon dynamics, microbial community structure and microbial activity in floodplain soil. J. Microbiol. Meth., 2011, 27, 213–225.
- Naiman, R. J. and Décamps, H., The ecology of interface: Riparian zones. Annu. Rev. Ecol. Syst., 1997, 28, 621–658.
- Gregory, S. V., Swanson, F. J., McKee, W. A. and Cummins, K. W., An ecosystem perspective of riparian zones focus on links between land and water. BioScience, 1991, 41, 540–551.
- Malanson, G. P., Riparian Landscapes, Cambridge University Press, New York, 1993.
- Naiman, R. J., Bechtold, J. S., Drake, D. C., Latterell, J. J., O’Keefe, T. C. and Balian, E. V., Origins, patterns, and importance of heterogeneity in riparian systems. In Ecosystem Function in Heterogeneous Landscape (eds Lovett, G. M. et al.), Springer, New York, 2005, pp. 279–309.
- Samaritani, E. et al., Heterogeneity of soil carbon pools and fuxes in a channelized and a restored floodplain section (Thur River, Switzerland). Hydrol. Earth Syst. Sci., 2011, 15, 1757–1769.
- Thorp, J. H., Thoms, M. C. and Delong, M. D., The riverine ecosystem synthesis: Biocomplexity in river networks across space and time. River Res. Appl., 2006, 22, 123–147.
- Huang, W. J., Liu, X. Z. and Cai, D. S., Researches on Lijiang River Ecosystem. Ecol. Environ., 2007, 3, 130–135.
- Liu, J. R., Feng, H., Yu, X. L., Song, G. J. and Ye, Q., A preliminary discussion on the historic change of the name for the Lijiang river system. Carsologica Sin., 2003, 22, 77–83.
- Huang, Z. W., Chen, Y. D., Jiang, Y. P. and Cheng, Y. P., Analysis on water resources of Lijiang River Basin. J. Guangxi Acad. Sci., 2005, 21, 56–60.
- Li, Y., Wang, D. M. and Xin, Z. B., Spatial distribution of vegetation and soil in aquatic-terrestrial ecotone, Li River. Trans. CSAE, 2013, 29, 121–128.
- Lu, R. K., Method of Analysis in Soil and Agrochemistry, China Agricultural Science and Technology Press, Beijing, 2000.
- Bates, S., Berg, L. D., Caporaso, J., Walters, W., Knight, R. and Fierer, N., Examining the global distribution of dominant archaeal populations in soil. ISME J., 2010, 5, 908–917.
- Fierer, N., Hamady, M., Lauber, C. L. and Knight, R., The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc. Natl. Acad. Sci. USA, 2008, 105, 17994–17999.
- Schloss, P. D. et al., Introducing mothur: open-source, platformindependent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microb., 2009, 75, 7537–7541.
- Caporaso, J. G. et al., QIIME allows analysis of high-throughput community sequencing data. Nat. Methods, 2010, 7, 335–336.
- Quince, C. et al., Noise and the accurate determination of microbial diversity from 454 pyrosequencing data. Nat. Methods, 2009, 6, 639–641.
- Huse, S. M., Welch, D. M., Morrison, H. G. and Sogin, M. L., Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ. Microbiol., 2010, 12, 1889–1898.
- Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. and Knight, R., UCHIME improves sensitivity and speed of chimera detection. Bioinformatics, 2011, 27, 2194–2200.
- Edgar, R. C., Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 2010, 26, 2460–2461.
- Wang, Q., Garrity, G. M., Tiedje, J. M. and Cole, J. R., Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microb., 2007, 73, 5261–5267.
- Oksanen, J. et al., Vegan: Community Ecology Package. R Package Version 2.3-0.2. 2015; http://CRAN.R-project.org/package=vegan 37. Junk, W. J., Bayley, P. B. and Sparks, R. E., The flood pulse concept in river-floodplain systems. Can. J. Fish. Aquat. Sci., 1989, 106, 110–127.
- Lal, R., Agricultural activities and the global carbon cycle. Nutr. Cycling Agroecosyst., 2004, 70, 103–106.
- Zhalnina, K. et al., Soil pH determines microbial diversity and composition in the park grass experiment. Microbial Ecol., 2015, 69, 395–406.
- Röske, K., Sachse, R., Scheerer, C. and Röske, I., Microbial diversity and composition of the sediment in the drinking water reservoir Saidenbach (Saxonia, Germany). Syst. Appl. Microbiol., 2012, 35, 35–44.
- Ligi, T., Oopkaup, K., Truu, M., Preem, J. K., Nölvak, H. and Mitsch, W. J., Characterization of bacterial communities in soil and sediment of a created riverine wetland complex using highthroughput 16S rRNA amplicon sequencing. Ecol. Eng., 2014, 72, 56–66.
- Peralta, R. M., Ahn, C. and Gillevet, P. M., Characterization of soil bacterial community structure and physicochemical properties in created and natural wetlands. Sci. Total Environ., 2013, 443, 725–732.
- Wang, Y., Sheng, H. F., He, Y., Wu, J. Y., Jiang, Y. X., Tam, N. F. Y. and Zhou, H. W., Comparison of the levels of bacterial diversity in freshwater, intertidal wetland, and marine sediments by using millions of Illumina tags. Appl. Environ. Microb., 2012, 78, 8264–8271.
- Spang, A. et al., Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota. Trends Microbiol., 2010, 18, 331–340.
- Brochier-Armanet, C., Boussau, B., Gribaldo, S. and Forteere, P., Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat. Rev. Microbiol., 2008, 6, 245–252.
- Hatzenpichler, R. et al., A moderately thermophilic ammoniaoxidizing crenarchaeote from a hot spring. Proc. Natl. Acad. Sci. USA, 2008, 105, 2134–2139.
- Könneke, M., Bernhard, A. E., de la Torre, J. R., Walker, C. B., Waterbury, J. B. and Stahl, D. A., Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature, 2005, 437, 543–546.
- Treusch, A. H., Leininger, S., Kletzin, A., Schuster, S. C., Klenk, H. P. and Schleper, C., Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environ. Microbiology, 2005, 7, 1985–1995.
- Jones, R. T., Robeson, M. S., Lauber, C. L., Hamady, M., Knight, R. and Fierer, N., A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J., 2009, 3, 442–453.
- Newton, R. J., Jones, S. E., Eiler, A., Mcmahon, K. and Bertilsson, S., A guide to the natural history of freshwater lake bacteria. Microbiol. Mol. Biol. R., 2011, 75, 14–49.
- Ahn, C. and Peralta, R. M., Soil bacterial community structure and physicochemical properties in mitigation wetlands created in the Piedmont region of Virginia (USA). Ecol. Eng., 2009, 35, 1036– 1042.
- Nacke, H. et al., Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils. PLoS ONE, 2011, 6, 1–12.
- Preem, J. K. et al., Bacterial community structure and its relationship to soil physico-chemical characteristics in alder stands with different management histories. Ecol. Eng., 2012, 49, 10–17.
- Hartman, W. H., Richardson, C. J., Vilgalys, R. and Bruland, G. L., Environmental and anthropogenic controls over bacterial communities in wetland soils. Proc. Natl. Acad. Sci. USA, 2008, 105, 17842–17847.
- Tisdall, J. M. and Oades, J. M., Organic matter and water stable aggregates in soils. Soil Sci., 1982, 33, 141–163.
- Ladd, J. N., Foster, R. C., Nannipieri, P. and Oades, J. M., Soil structure and biological activity. Soil Biochem., 1996, 9, 23–78.
- Gestel, M. V., Merckx, R. and Vlasse, K., Spatial distribution of microbial biomass in microaggregates of a silty-loam soil and the relation with the resistance of microorganisms to soil drying. Soil Biol. Biochem., 1996, 28, 503–510.
- Aber, J. D., Nitrogen cycling and nitrogen saturation in temperate forest ecosystems. Trends Ecol. Evol., 1992, 7, 220–223.
- Vanotti, M. B., Leclerc, S. A. and Bundy, L. G., Short-term effects of nitrogen fertilization on soil organic nitrogen availability. Soil Sci. Soc. Am. J., 1995, 59, 1350–1359.
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