Effect of pH on soil bacterial diversity
1
조회
0
다운로드
2
인용
0
참고문헌
키워드
초록
Background: In order to evaluate the effect of pH, known as a critical factor for shaping the biogeographical microbial patterns in the studies by others, on the bacterial diversity, we selected two sites in a similar geographical location (site 1; north latitude 35.3, longitude 127.8, site 2; north latitude 35.2, longitude 129.2) and compared their soil bacterial diversity between them. The mountain soil at site 1 (Jiri National Park) represented naturally acidic but almost pollution free (pH 5.2) and that at site 2 was neutral but exposed to the pollutants due to the suburban location of a big city (pH 7.7). Methods: Metagenomic DNAs from soil bacteria were extracted and amplified by PCR with 27F/518R primers and pyrosequenced using Roche 454 GS FLX Titanium. Results: Bacterial phyla retrieved from the soil at site 1 were more diverse than those at site 2, and their bacterial compositions were quite different: Almost half of the phyla at site 1 were Proteobacteria (49 %), and the remaining phyla were attributed to 10 other phyla. By contrast, in the soil at site 2, four main phyla (Actinobacteria, Bacteroidetes, Proteobacteria, and Cyanobacteria) composed 94 %; the remainder was attributed to two other phyla. Furthermore, when bacterial composition was examined on the order level, only two Burkholderiales and Rhizobiales were found at both sites. So depending on pH, the bacterial community in soil at site 1 differed from that at site 2, and although the acidic soil of site 1 represented a non-optimal pH for bacterial growth, the bacterial diversity, evenness, and richness at this site were higher than those found in the neutral pH soil at site 2. Conclusions: These results and the indices regarding diversity, richness, and evenness examined in this study indicate that pH alone might not play a main role for bacterial diversity in soil.
Abstract
Background: In order to evaluate the effect of pH, known as a critical factor for shaping the biogeographical microbial patterns in the studies by others, on the bacterial diversity, we selected two sites in a similar geographical location (site 1; north latitude 35.3, longitude 127.8, site 2; north latitude 35.2, longitude 129.2) and compared their soil bacterial diversity between them. The mountain soil at site 1 (Jiri National Park) represented naturally acidic but almost pollution free (pH 5.2) and that at site 2 was neutral but exposed to the pollutants due to the suburban location of a big city (pH 7.7). Methods: Metagenomic DNAs from soil bacteria were extracted and amplified by PCR with 27F/518R primers and pyrosequenced using Roche 454 GS FLX Titanium. Results: Bacterial phyla retrieved from the soil at site 1 were more diverse than those at site 2, and their bacterial compositions were quite different: Almost half of the phyla at site 1 were Proteobacteria (49 %), and the remaining phyla were attributed to 10 other phyla. By contrast, in the soil at site 2, four main phyla (Actinobacteria, Bacteroidetes, Proteobacteria, and Cyanobacteria) composed 94 %; the remainder was attributed to two other phyla. Furthermore, when bacterial composition was examined on the order level, only two Burkholderiales and Rhizobiales were found at both sites. So depending on pH, the bacterial community in soil at site 1 differed from that at site 2, and although the acidic soil of site 1 represented a non-optimal pH for bacterial growth, the bacterial diversity, evenness, and richness at this site were higher than those found in the neutral pH soil at site 2. Conclusions: These results and the indices regarding diversity, richness, and evenness examined in this study indicate that pH alone might not play a main role for bacterial diversity in soil.
참고문헌 (37)
- 안병구, "시설수박 연작지 토양특성에 대한 후작물 재배의 영향", 한국토양비료학회지(Korean Journal of Soil Science and Fertilizer), 40(1), pp.98~107 (2007), 한국토양비료학회
- Alexander, M, "Introduction to soil microbiology (Vol. 142)", pp.12~13 (1977), John Wiley & Sons
- Amann, R, "Bergey’s Manual of Systematic Bacteriology (Vol. I)", pp.67~82 (2001), Springer
- Brons, JK, "Analysis of bacterial communities in soil by use of denaturing gradient gel electrophoresis and clone libraries, as influenced by different reverse primers", Applied and Environmental Microbiology, 74, pp.2717~2727 (2008)
- Cookson, WR, "Controls on soil nitrogen cycling and microbial community composition across land use and incubation temperature", Soil Biology and Biochemistry, 39, pp.744~756 (2007)
- DeLong, EF, "Phylogenetic strains; ribosomal RNA-based probes for the identification of single microbial cells", Science, 243, pp.1360~1363 (1989)
- Environment standard methods, "2009-255, ES07400. 2. Metals by inductively coupled plasma-atomic emission spectrometry", Ministry of Environment standard, ~ (2009)
- Fierer, N, "The diversity and biogeography of soil bacterial communities", PNAS, 103, pp.626~631 (2006)
- Green, JL, "Microbial biogeography : from taxonomy to traits", Science, 320, pp.1039~1043 (2008)
- Haas, BJ, "Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyro-sequenced PCR amplicons", Genome Research, 21, pp.494~504 (2011)
- 한송이, "활엽수림과 침엽수림 부식토 내 세균군집의 계통학적 특성 비교", 미생물학회지, 44(3), pp.237~243 (2008), 한국미생물학회
- Hartman, WH, "Environmental and anthropogenic controls over bacterial communities in wetland soils", PNAS, 105, pp.17842~17847 (2008)
- Herlemann, DPR, "The termite group I Phylum is highly diverse and wide-spread in the environment", Applied and Environmental Microbiology, 73, pp.6682~6685 (2007)
- Horner-Devine, MC, "An ecological perspective on bacterial diversity", Proceedings of the Biological Sciences, 271(1535), pp.113~122 (2004)
- 황옥화, "Deodorization of Pig Slurry and Characterization of Bacterial Diversity Using 16S rDNA Sequence Analysis", The Journal of Microbiology, 52(11), pp.918~929 (2014), 한국미생물학회[DOI]
- Kelly, JJ, "Changes in soil microbial communities over time resulting from one time application of zinc : a laboratory microcosm study", Soil Biology and Biochemistry, 31, pp.1455~1465 (1999)
- Kennedy, AC, "Soil microbial diversity and the sustainability of agricultural soils", Plant and Soil, 170, pp.75~86 (1995)
- "Korea Forest Service"[URL]
- Lauber, CL, "Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale", Applied and Environmental Microbiology, 75, pp.5111~5120 (2009)
- 이은영, "Removal of Heavy Metals by an Enriched Consortium", The Journal of Microbiology, 46(1), pp.23~28 (2008), 한국미생물학회[DOI]
- Yuanyuan Li, "454 Pyrosequencing Analysis of Bacterial Diversity Revealed by a Comparative Study of Soils from Mining Subsidence and Reclamation Areas", Journal of Microbiology and Biotechnology, 24(3), pp.313~323 (2014), 한국미생물·생명공학회[DOI]
- Liang, Y, "Functional gene diversity of soil microbial communities from five oilcontaminatedfields in China", ISME Journal, 5, pp.403~413 (2011)
- Liu, Z, "Short pyrosequencing reads suffice for accurate microbial community analysis", Nucleic Acids Research, 35, pp.e120~ (2007)
- Ludwig, W, "Bergey’s Manual of Systematic Bacteriology (Vol. I)", pp.49~65 (2001), Springer
- Madigan, MT, "Global", pp.670~711 (2010), Benjamin Cummings
- Maier, RM, "Environmental microbiology", pp.57~82 (2009), Academic
- Marilley, L, "Phylogenetic diversity of bacterial communities differing in degree of proximity of Lolium perenne and Trifolium repens roots", Applied Soil Ecology, 13, pp.127~136 (1999)
- "OTU clustering; mothur (version 1.27.0)"[URL]
- Roane, TM, "Microbial responses to environmentally toxic cadmium", Microbial Ecology, 38, pp.358~364 (2000)
- Sandaa, RA, "Influence of long term heavy metal contamination on microbial communities in soil", Soil Biology and Biochemistry, 33, pp.287~295 (2001)
- Schramm, A, "1998. Identification and activities in situ of Nitrosospira and Nitrospira spp. as dominant populations in a nitrifying fluidized bed reactor", Applied and Environmental Microbiology, 64, pp.3480~3485 (1998)
- Sessitsch, A, "Microbial population structures in soil particle size fractions of long-term fertilizer field experiment", Applied and Environmental Microbiology, 67, pp.4215~4224 (2001)
- "Silva rRNA database"[URL]
- Smit, E, "Diversity and seasonal fluctuations of the dominant members of the bacterial soil community in a wheat field as determined by cultivation and molecular methods", Applied and Environmental Microbiology, 67, pp.2284~2291 (2001)
- Torsvik, V, "Microbial diversity and function in soil : from genes to ecosystems", Current Opinion in Microbiology, 5, pp.240~245 (2002)
- Torsvik, V, "Comparison of phenotypic diversity and DNA heterogeneity in a population of soil bacteria", Applied and Environmental Microbiology, 56, pp.776~781 (1990)
- Will, C, "Horizon-specific bacterial community composition of German grassland soils, as revealed by pyrosequencingbased analysis of 16S rRNA genes", Applied and Environmental Microbiology, 76, pp.6751~6759 (2001)