Soil & Water Res., 2019, 14(1):22-31 | DOI: 10.17221/10/2018-SWR
Genetic diversity and community structure of soil bacteria in Chinese fir plantationsOriginal Paper
- 1 Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Zhuang Autonomous Region Forestry Research Institute, Nanning, P.R. China
- 2 Central South University of Forest and Technology, Changsha, P.R. China
- 3 Hubei Institute of Photogrammetry and Remote Sensing, Wuhan, P.R. China
To explore the diversity of soil bacteria and changes in the bacterial community structure of Chinese fir plantations of different generations and developmental stages, the genetic diversity of soil bacteria was studied using the 454 sequencing technology. The results showed that the bacterial genetic diversity and community structure of Chinese fir plantation plots under monoculture planting and rotation planting practices were as follows: the Shannon diversity indices of first-generation young plantation of Chinese fir plantations (FYC), second-generation young plantation (SYC), and third-generation young plantation (TYC) initially decreased and then increased to 8.45, 8.1, and 8.43, respectively. Due to different management and tending measures, the phyla showing considerable differences in relative abundance were Cyanobacteria, Nitrospirae, Fibrobacteres, Thermotogae, and Planctomycetes. The bacterial genetic diversity and community structure of Chinese fir plantations at different developmental stages were as follows: the bacterial diversity and the number of operational taxonomic units (OTUs) decreased with increasing forest age; with the increasing forest age of Chinese fir, the bacteria with considerable differences in the relative abundance were Burkholderiales, Xanthomonadales, Ktedonobacteria, Nitrosomonadales, Anaerolineae, and Holophagae. The predominant bacteria of the Chinese fir plantations were Acidothermus, Bradyrhizobium, Lactococcus, Planctomyces, Sorangium, and Bryobacter.
Keywords: Cunninghamia lanceolata; soil bacteria diversity; 454 pyrosequencing
Published: March 31, 2019 Show citation
References
- Blum U. (1998): Effects of microbial utilization of phenolic acids and their phenolic acid breakdown products on allelopathic interactions. Journal of Chemical Ecology, 24: 685-708.
Go to original source...
- Buckley D.H., Huangyutitham V., Nelson T.A., Rumberger A., Thies J.E. (2006): Diversity of Planctomycetes in soil in relation to soil history and environmental heterogeneity. Applied and Environmental Microbiology, 72: 4522-4531.
Go to original source...
Go to PubMed...
- Bush A.M., Markey M.J., Marshall C.R. (2004): Removing bias from diversity curves: the effects of spatially organized biodiversity on sampling-standardization. Paleobiology, 30: 666-686.
Go to original source...
- Chao A. (1984):Nonparametric estimation of the number of classes in a population. Scandinavian Journal of Statistics, 11: 265-270.
- Chao A., Lee S. (1992): Estimating the number of classes via sample coverage. Publications of the American Statistical Association, 87: 210-217.
Go to original source...
- Doran J.W., Sarrantonio M., Liebig M.A. (1996): Soil health and sustainability. Advances in Agronomy, 56: 51-54.
Go to original source...
- Edgar R.C., Haas B.J., Clemente J.C., Quince C., Knight R. (2011): UCHIME improves sensitivity and speed of chimera detection. Bioinformatics, 27: 2194-2200.
Go to original source...
Go to PubMed...
- Esty W.W. (1986): The efficiency of good's nonparametric coverage estimator. Annals of Statistics, 14: 1257-1260.
Go to original source...
- Fiere N., Jackson R.B. (2006): The diversity and biogeography of soil bacterial communities. Proceedings of the National Academy of Sciences of the United States of America, 103: 626.
Go to original source...
Go to PubMed...
- Gans J., Wolinsky M., Dunbar J. (2005): Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science, 309: 1387-1390.
Go to original source...
Go to PubMed...
- Hill M.O. (1973): Diversity and evenness: a unifying notation and its consequences. Ecology, 54: 427-432.
Go to original source...
- Hollister E.B., Engledow A.S., Hammett A.J.M., Provin T.L., Wilkinson H.H., Gentry T.J. (2010): Shifts in microbial community structure along an ecological gradient of hypersaline soils and sediments. The ISME Journal, 4: 829.
Go to original source...
Go to PubMed...
- Jeddi K., Cortina J., Chaieb M. (2009): Acacia salicina, Pinus halepensis and Eucalyptus occidentalis improve soil surface conditions in arid southern Tunisia. Journal of Arid Environments, 73: 1005-1013.
Go to original source...
- Jiang C.Y., Sheng X.F., Qian M., Wang Q.Y. (2008) Isolation and characterization of a heavy metal-resistant Burkholderia sp. from heavy metal-contaminated paddy field soil and its potential in promoting plant growth and heavy metal accumulation in metal-polluted soil. Chemosphere, 72: 157-164.
Go to original source...
Go to PubMed...
- Kaschuk G., Alberton O., Hungria M. (2011): Quantifying effects of different agricultural land uses on soil microbial biomass and activity in Brazilian biomes: inferences to improve soil quality. Plant and Soil, 338: 467-481.
Go to original source...
- Kanazawa S., Miyashita K. (1986): A method for the determination of cellulase activity in forest soil. Soil Science and Plant Nutrition, 32: 71-79.
Go to original source...
- Liang C., Zhen W., Zhang C., Yin B. (2009): Determination of phenolic acids in decomposing products of maize straw and their allelopathy on pathogens of wheat soilborne disease. Chinese Agricultural Science Bulletin, 25: 210-213.
- Liu C., Ma K., Lu Y., Hang Y. (1998): Measurement of biotic community diversity. VI. The statistical aspects of diversity measures. Chinese Biodiversity, 6: 229-239.
Go to original source...
- Moorthi S.D., Dennett M.R., Moran D.M., Jones A.C. (2009): Defining DNA-based operational taxonomic units for microbial-eukaryote ecology. Applied and Environmental Microbiology, 75: 5797-5808.
Go to original source...
Go to PubMed...
- Moulin L., Munive A., Dreyfus B., Boivinmasson C. (2001): Nodulation of legumes by members of the beta-subclass of Proteobacteria. Nature, 411: 948-950.
Go to original source...
Go to PubMed...
- Newton A. (2007): Forest Ecology and Conservation. Techniques in Ecology & Conservation Series. Oxford, Oxford University Press: 128-131.
Go to original source...
- O'Donnell A.G., Seasman M., Macrae A., Waite I., Davies J.T. (2001): Plants and fertilisers as drivers of change in microbial community structure and function in soils. Plant and Soil, 232: 135-145.
Go to original source...
- Samuel A.D., Blidar C.F., Domuța C., Șandor M., Vușcan A., Borza I., Brejea R. (2015): Influence of Heavy Metal Contamination on Soil Enzyme Activities. Social Science Electronic Publishing: 111-120.
- Schloss P.D., Westcott S.L., Ryabin T., Hall J.R., Hartmann M., Hollister E.B., Lesniewski R.A., Oakley B.B., Parks D.H., Robinson C.J. (2009): Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology, 75: 7537.
Go to original source...
Go to PubMed...
- Simpson E.H. (1949): The measurement of diversity. Nature, 163: 688.
Go to original source...
- Smith K.P., Goodman R.M. (1999): Host variation for interactions with benificial plant- associated microbes. Annual Review of Phytopathology, 37: 473-491.
Go to original source...
Go to PubMed...
- Tabatabai M.A., Bremner J.M. (1972): Assay of urease activity in soils. Soil Biology and Biochemistry, 4: 479-487.
Go to original source...
- Van Der Heijden M.G.A., Bardgett R.D., Van Straalen N.M. (2008): The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecology Letters, 11: 296-310.
Go to original source...
Go to PubMed...
- Van'kova A.A., Ivanov P.I., Emtsev V.T. (2013): Filtrating forms of soil bacteria. Eurasian Soil Science, 46: 303-309.
Go to original source...
- Ward N.L., Challacombe J.F., Janssen P.H., Henrissat B., Coutinho P.M., Wu M., Xie G., Haft D.H., Sait M., Badger J., Barabote R.D., Bradley B., Brettin T.S., Brinkac L.M., Bruce D., Creasy T., Daugherty S.C., Davidsen T.M., DeBoy R.T., Detter J.C., Dodson R.J., Durkin A.S., Ganapathy A., Gwinn-Giglio M., Han C.S., Khouri H., Kiss H., Kothari S.P., Madupu R., Nelson K.E., Nelson W.C., Paulsen I., Penn K., Ren Q., Rosovitz M.J., Selengut J.D., Shrivastava S., Sullivan S.A., Tapia R., Thompson L.S., Watkins K.L., Yang Q., Yu C., Zafar N., Zhou L., Kuske C.R. (2009): Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils. Applied and Environmental Microbiology, 75: 2046-2056.
Go to original source...
Go to PubMed...
- Wilson D.B. (2008): Three microbial strategies for plant cell wall degradation. Annals of the New York Academy of Sciences, 1125: 289-297.
Go to original source...
Go to PubMed...
- Wu Y.L., Wang B., Zhao C., Dai W., Li P. (2011): Comprehensive evaluation of soil fertility in different developing stages of Chinese Fir Plantations. Journal of Northwest A&F University, 39: 69-75.
- Yao H., He Z., Wilson M.J., Campbell C.D. (2000): Microbial biomass and community structure in a sequence of soils with increasing fertility and changing land use. Microbial Ecology, 40: 223.
Go to original source...
Go to PubMed...
- Yin C., Kennethl J., Dallase P., Karena G., Scoth H., Timothyc P. (2010): Members of soil bacterial communities sensitive to tillage and crop rotation. Soil Biology Biochemistry, 42: 2111-2118.
Go to original source...
- Yu Y., Wang H., Liu J., Wang Q., Shen T., Guo W., Wang R. (2012): Shifts in microbial community function and structure along the successional gradient of coastal wetlands in Yellow River estuary. European Journal of Soil Biology, 49: 12-21.
Go to original source...
- Zhou J., Xia B., Treves D.S., Wu L.Y., Marsh T.L., O'Neill R.V., Palumbo A.V., Tiedje J.M. (2002): Spatial and resource factors influencing high microbial diversity in soil. Applied and Environmental Microbiology, 68: 326-334.
Go to original source...
Go to PubMed...
- Zhou L.K. (1988): Soil Enzymology. Beijing, Science Press: 21-23.
This is an open access article distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International (CC BY NC 4.0), which permits non-comercial use, distribution, and reproduction in any medium, provided the original publication is properly cited. No use, distribution or reproduction is permitted which does not comply with these terms.