Effects of Cattle Manure and Green Manure on the Microbial Community Structure in Upland Soil Determined by Denaturing Gradient Gel Electrophoresis

Sekiguchi, Hiroyuki; Kushida, Atsuhiko; Takenaka, Shigehito

doi:10.1264/jsme2.22.327

Cited by 18 publications

(8 citation statements)

References 51 publications

(52 reference statements)

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“…The community composition of soil microbes based on functional genes detected by GeoChip (functional gene composition) in the CT treatment was significantly different from those in the LI or ORG treatment by both DCA and nonparametric tests, while the communities in the LI and ORG treatments did not differ from one another, as measured by nonparametric tests, but were readily distinguishable in the DCA profile. The impacts of different management systems on soil microbial community composition, but not functional gene composition as measured by GeoChip, were also observed previously in other studies (4,5,56,57). At the same experiment site, KBS LTER, by using T-RFLP, the compositions of microbial communities in various soil fractions were previously reported to be significantly different among different agricultural systems with conventionally and organically managed corn and continuous alfalfa (16,17).…”

Section: Discussionsupporting

confidence: 78%

Functional Gene Differences in Soil Microbial Communities from Conventional, Low-Input, and Organic Farmlands

Xue

Deng

et al. 2013

Appl Environ Microbiol

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dVarious agriculture management practices may have distinct influences on soil microbial communities and their ecological functions. In this study, we utilized GeoChip, a high-throughput microarray-based technique containing approximately 28,000 probes for genes involved in nitrogen (N)/carbon (C)/sulfur (S)/phosphorus (P) cycles and other processes, to evaluate the potential functions of soil microbial communities under conventional (CT), low-input (LI), and organic (ORG) management systems at an agricultural research site in Michigan. Compared to CT, a high diversity of functional genes was observed in LI. The functional gene diversity in ORG did not differ significantly from that of either CT or LI. Abundances of genes encoding enzymes involved in C/N/P/S cycles were generally lower in CT than in LI or ORG, with the exceptions of genes in pathways for lignin degradation, methane generation/oxidation, and assimilatory N reduction, which all remained unchanged. Canonical correlation analysis showed that selected soil (bulk density, pH, cation exchange capacity, total C, C/N ratio, NO 3 ؊ , NH 4 ؉ , available phosphorus content, and available potassium content) and crop (seed and whole biomass) variables could explain 69.5% of the variation of soil microbial community composition. Also, significant correlations were observed between NO 3 ؊ concentration and denitrification genes, NH 4 ؉ concentration and ammonification genes, and N 2 O flux and denitrification genes, indicating a close linkage between soil N availability or process and associated functional genes.

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Section: Discussionsupporting

confidence: 78%

Functional Gene Differences in Soil Microbial Communities from Conventional, Low-Input, and Organic Farmlands

Xue

Deng

et al. 2013

Appl Environ Microbiol

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“…That is, a large proportion of fungi resided as indigenous microorganisms in the soils, and the behavior of some representatives contributed to the definition of the fungal community structure. In our previous study on microbial communities, after the application of two types of organic fertilizer, we demonstrated slight changes in the community structure and the intensity of only a portion of bands 31) . Ros et al analyzed the microbial community in soils amended with different types of compost and reported that changes of only several groups of organisms were the main factors contributing to the dissimilarity 29) .…”

Section: Comparison Of Fungal Communitiesmentioning

confidence: 77%

“…Although numerous studies on the differences between ORG and CNV management have been conducted, reports on microbial community structure are limited to a few papers on the bacterial community 34,35,44) . Previously, we compared both the bacterial and fungal community structure along with the application of organic fertilizers, and found a characteristic shift in the fungal community and only a slight change in the bacterial community structure 31) . We concluded that the bacterial community was too diverse to evaluate the difference, and the fungal community was suitable for monitoring the effects of agricultural managements.…”

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confidence: 94%

Comparative Analysis of Environmental Variability and Fungal Community Structure in Soils between Organic and Conventional Commercial Farms of Cherry Tomato in Japan

et al. 2008

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Soil environmental variability and fungal community structures were analyzed to evaluate differences in soils managed under organic (ORG) and conventional (CNV) systems of farming in Fukushima and Yamagata prefectures in Japan. The soils were collected from 8 ORG and 13 CNV farms in 2005, and 6 ORG and 13 CNV farms in 2006. Principal component analysis (PCA) of 26 environmental variables demonstrated that plots of ORG and CNV were separated; however, the differences were unclear. Environmental variability and scores of principal components indicated more MgO, available phosphorous, NO 3 -N, and K 2 O in ORG than in CNV, and more silt, Mn, and Mg/K in CNV than in ORG. The differences were considered distinguishing for these farming systems. The fungal DGGE profiles and characteristic band intensities could not be used to distinguish between ORG and CNV. However, the PCA of band profiles slightly differentiated the plots of each system for both 2005 and 2006, as was the case for environmental variability. Furthermore, analysis of the PCA scores revealed several characteristic bands in DGGE profiles. A sequence analysis of the characteristic bands indicated the genus Mortierella sp. and close relatives of Cheatomium globosum to be characteristic fungi in CNV, although definitive characteristic fungi were not found in ORG. Since these results were obtained from soils differing in the type and amount of fertilizer, the application of pesticide, and management system, they are considered to reflect the general difference between ORG and CNV soils.

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“…The sequencing of the band observed in PCR-DGGE as other studies (18,29), to identify bacteria unique to the BF or common to the BF and lake water, and further analyses of the flora (including eukaryotes) will be the subjects of future studies. …”

Section: Consortiummentioning

confidence: 99%

Nutrient-Rich Microhabitats within Biofilms Are Synchronized with the External Environment

et al. 2009

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The nutrient ion concentrations in the interstitial waters of biofilms (BFs) formed on reed and stone surfaces were investigated in the northern and southern basins of Lake Biwa over several years. The following were observed for both types of BF: 1) Concentrations of ammonium, nitrate, nitrite, and phosphate ions were much (hundreds to thousands of times) higher in the BFs than in the surrounding lake water; 2) the concentration of ions, especially nitrate ions, in the BFs changed seasonally, being higher from winter to spring and lower from summer to autumn, synchronizing with the changes in the lake water; 3) dissolved-form N:P ratios were higher in the lake water than BFs; and 4) the bacterial flora of the BFs differed from that of the lake water, with smaller seasonal variations. The present study reveals for the first time that the inside of BFs in a natural environment is rich in nutrient ions and shows similar seasonal changes as the lake water. The BFs in an aquatic environment provide a microenvironment capable of sustaining a specific bacterial flora different from that in the surrounding lake water.Key words: biofilm, nutrient ions, bacterial flora, Lake Biwa Microbial biofilms (BFs) are ubiquitous in aquatic environments and perform important environmental functions, including nutrient recycling (2, 5, 27) and purification of pollutants (8,14,15). Natural BFs are generally composed of a variety of microbes and their secretory products, such as extracellular polymeric substances (EPS). The EPS-containing matrix confers on the constituent microbes certain advantages over their free-living counterparts (16,17). An important advantage is the ability to trap and retain dissolved nutrients through an entrapment mechanism that has been proposed (4, 7, 11) and proven (9) to depend on ion exchange processes.However, few studies have been conducted on the nutrient conditions inside BFs formed in natural environments over a long period of observation. Therefore, the present study was designed to compare over several years the concentrations of various nutrient ions in the interstitial waters of BFs and the surrounding lake water. An additional aim was to examine the relationship between the nutrient conditions and bacterial flora inside the BFs. Moreover, the BFs formed on reed and stone surfaces were compared, to clarify the influences of the substratum surfaces.Here, we report for the first time that the nutrient conditions in a BF and in the surrounding water are significantly different with respect to concentrations of ions, particularly nitrate ions, while exhibiting similar seasonal variations. The relationships among the nutrient conditions, bacterial flora constitution, and the physicochemical properties of the BFs are discussed. Materials and Methods Study area and samplingLake Biwa is located in the central part of the Japanese Archipelago (Lat. 35°15' N, Long. 136°05' E). The lake has a surface area of 670 km 2 and a total storage volume of 2.75×10 10 m 3 , consisting of two basins that differ in wa...

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Effects of Cattle Manure and Green Manure on the Microbial Community Structure in Upland Soil Determined by Denaturing Gradient Gel Electrophoresis

Cited by 18 publications

References 51 publications

Functional Gene Differences in Soil Microbial Communities from Conventional, Low-Input, and Organic Farmlands

Functional Gene Differences in Soil Microbial Communities from Conventional, Low-Input, and Organic Farmlands

Comparative Analysis of Environmental Variability and Fungal Community Structure in Soils between Organic and Conventional Commercial Farms of Cherry Tomato in Japan

Nutrient-Rich Microhabitats within Biofilms Are Synchronized with the External Environment

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