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- P-ISSN2287-8327
- E-ISSN2288-1220
- SCOPUS, KCI
ISSN : 2287-8327
Bacterial and fungal community composition across the soil depth profiles in a fallow field
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Abstract
Background: Soil microorganisms play key roles in nutrient cycling and are distributed throughout the soil profile. Currently, there is little information about the characteristics of the microbial communities along the soil depth because most studies focus on microorganisms inhabiting the soil surface. To better understand the functions and composition of microbial communities and the biogeochemical factors that shape them at different soil depths, we analyzed microbial activities and bacterial and fungal community composition in soils up to a 120 cm depth at a fallow field located in central Korea. To examine the vertical difference of microbial activities and community composition, β-1,4-glucosidase, cellobiohydrolase, β-1,4-xylosidase, β-1,4-N-acetylglucosaminidase, and acid phosphatase activities were analyzed and barcoded pyrosequencing of 16S rRNA genes (bacteria) and internal transcribed spacer region (fungi) was conducted. Results: The activity of all the soil enzymes analyzed, along with soil C concentration, declined with soil depth. For example, acid phosphatase activity was 125.9 (± 5.7 (± 1 SE)), 30.9 (± 0.9), 15.7 (± 0.6), 6.7 (± 0.9), and 3.3 (± 0.3) nmol g−1 h−1 at 0–15, 15–30, 30–60, 60–90, and 90–120 cm soil depths, respectively. Among the bacterial groups, the abundance of Proteobacteria (38.5, 23.2, 23.3, 26.1, and 17.5% at 0–15, 15–30, 30–60, 60–90, and 90–120 cm soil depths, respectively) and Firmicutes (12.8, 11.3, 8.6, 4.3, and 0.4% at 0–15, 15–30, 30–60, 60–90, and 90–120 cm soil depths, respectively) decreased with soil depth. On the other hand, the abundance of Ascomycota (51.2, 48.6, 65.7, 46.1, and 45.7% at 15, 30, 60, 90, and 120 cm depths, respectively), a dominant fungal group at this site, showed no clear trend along the soil profile. Conclusions: Our results show that soil C availability can determine soil enzyme activity at different soil depths and that bacterial communities have a clear trend along the soil depth at this study site. These metagenomics studies, along with other studies on microbial functions, are expected to enhance our understanding on the complexity of soil microbial communities and their relationship with biogeochemical factors.
- keywords
- Soil enzymes, Pyrosequencing, Microbial community composition, Diversity
Reference
Agnelli, A., Ascher, J., Corti, G., Ceccherini, M. T., 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 Biology and Biochemistry, 36, 859–868.
Aislabie, J., & Deslippe, J. R. (2013). Soil microbes and their contribution to soil services. In J. R. Dymond (Ed.), Ecosystem services in New Zealand: Conditions and trends (pp. 143–161). Lincoln: Manaaki Whenua Press.
Axelrood, P. E., Chow, M. L., Radomski, C. C., McDermott, J. M., & Davies, J. (2002). Molecular characterization of bacterial diversity from British Columbia forest soils subjected to disturbance. Canadian Journal of Microbiology, 48, 655–674.
Baldrian, P., Kolarik, M., Stursova, M., Kopecky, J., Valaskova, V., Vetrovsky, T.,Zifcakova, L., Snajdr, J., Ridl, J., Vlcek, C., & Voriskova, J. (2012). Active and total microbial communities in forest soil are largely different and highly stratified during decomposition. ISME Journal, 6, 248–258.
Blume, E., Bischoff, M., Reichert, J. M., Moorman, T., Konopka, A., & Turco, R. F.(2002). Surface and subsurface microbial biomass, community structure and metabolic activity as a function of soil depth and season. Applied Soil Ecology, 20, 171–181.
Buss, H. L., Bruns, M. A., Schultz, M. J., Moore, J., Mathur, C. F., & Brantley, S. L.(2005). The coupling of biological iron cycling and mineral weathering during saprolite formation, Luquillo Mountains, Puerto Rico. Geobiology, 3, 247–260.
Chun, J., Kim, K. Y., Lee, J. H., & Choi, Y. (2010). The analysis of oral microbial communities of wild-type and toll-like receptor 2-deficient mice using a 454GS FLX titanium pyrosequencer. BMC Microbiology, 10, 101.
Eilers, K. G., 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 Biology and Biochemistry, 50, 58–65.
Fierer, N., Schimel, J. P., & Holden, P. A. (2003). Variations in microbial community composition through two soil depth profiles. Soil Biology and Biochemistry, 35, 167–176.
Fierer, N., Jackson, J. A., Vilgalys, R., & Jackson, R. B. (2005). Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays. Applied and Environmental Microbiology, 71, 4117–4120.
Fierer, N., Bradford, M. A., & Jackson, R. B. (2007). Toward an ecological classification of soil bacteria. Ecology, 88, 1354–1364.
Goberna, M., Insam, H., Klammer, S., Pascual, J. A., & Sanchez, J. (2005). Microbial community structure at different depths in disturbed and undisturbed semiarid mediterranean forest soils. Microbial Ecology, 50, 315–326.
Hamady, M., Lozupone, C., & Knight, R. (2010). Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME Journal, 4, 17–27.
Hansel, C., Fendorf, S., Jardine, P., & Francis, C. (2008). Changes in bacterial and archaeal community structure and functional diversity along a geochemically variable soil profile. Applied and Environmental Microbiology, 74, 1620–1633.
Huber, T., Faulkner, G., & Hugenholtz, P. (2004). Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics, 20, 2317–2319.
Hur, M., Kim, Y., Song, H. R., Kim, J. M., Choi, Y. I., & Yi, H. (2011). Effect of genetically modified poplars on soil microbial communities during the phytoremediation of waste mine tailings. Applied and Environmental Microbiology, 77, 7611–7619.
Kim, B. S., Kim, J. N., Yoon, S. H., Chun, J., & Cerniglia, C. E. (2012a). Impact of enrofloxacin on the human intestinal microbiota revealed by comparative molecular analysis. Anaerobe, 18, 310–320.
Kim, O. S., Cho, Y. J., Lee, K., Yoon, S. H., Kim, M., Na, H., Park, S. C., Jeon, Y. S.,Lee, J. H., Yi, H., Won, S., & Chun, J. (2012b). Introducing Eztaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. International Journal of Systematic and Evolutionary Microbiology, 62, 716–721.
LaMontagne, M., Schimel, J., & Holden, P. (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. Microbial Ecology, 46, 216–227.
McCaig, A. E., Glover, L. A., & Prosser, J. I. (1999). Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures. Applied and Environmental Microbiology, 65, 1721–1730.
Nannipieri, P., Ascher, J., Ceccherini, M. T., Landi, L., Pietramellara, G., & Renella, G.(2003). Microbial diversity and soil functions. European Journal of Soil Science, 54, 655–670.
Rumpel, C., & Kogel-Knabner, I. (2011). Deep soil organic matter-a key but poorly understood component of terrestrial C cycle. Plant and Soil, 338, 143–158.
Saiya-Cork, K. R., Sinsabaugh, R. L., & Zak, D. R. (2002). The effects of long term nitrogen deposition on extracellular enzyme activity in an Acer saccharum forest soil. Soil Biology and Biochemistry, 34, 1309–1315.
Sengupta, A., & Dick, W. A. (2015). Bacterial community diversity in soil under two tillage practices as determined by pyrosequencing. Microbial Ecology, 70, 853–859.
Stursova, M., & Baldrian, P. (2011). Effects of soil properties and management on the activity of soil organic matter transforming enzymes and the quantification of soil-bound and free activity. Plant and Soil, 338, 99–110.
Trumbore, S. (2000). Age of soil organic matter and soil respiration: Radiocarbon constraints on belowground C dynamics. Ecological Applications, 10, 399–411.
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 pyrosequencingbased analysis of 16S rRNA genes. Applied and Environmental Microbiology, 76, 6751–6759.
Xu, X., Thornton, P. E., & Post, W. M. (2013). A global analysis of soil microbial biomass carbon, nitrogen and phosphorus in terrestrial ecosystems. Global Ecology and Biogeography, 22, 737–749.
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