• Journal of Ecology and Environment
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• v.41 no.9
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• pp.271-280
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• 2017

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, ${\beta}$-1,4-glucosidase, cellobiohydrolase, ${\beta}$-1,4-xylosidase, ${\beta}$-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 $125.9({\pm}5.7({\pm}1SE))$, $30.9({\pm}0.9)$, $15.7({\pm}0.6)$, $6.7({\pm}0.9)$, and $3.3({\pm}0.3)nmol\;g^{-1}\;h^{-1}$ 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.

• Korean Journal of Soil Science and Fertilizer
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• v.44 no.3
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• pp.479-484
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• 2011

Fatty acid methyl ester (FAME) profiles were used to describe differences in soil microbial communities influenced by conventional farming system (CFS), conventional farming system without pesticides (CFSWP), and organic farming system (OFS) for strawberry cultivation in controlled horticultural land. In comparison to the CFS soils, the average soil microbial biomasses of in the OFS soils were approximately 1.2 times for total FAMEs ($195nmol\;g^{-1}$), 1.4 times for total bacteria ($58nmol\;g^{-1}$), 1.5 times for Gram-negative bacteria ($27.3nmol\;g^{-1}$), 1.2 times for Gram-positive bacteria ($26.1nmol\;g^{-1}$), and 1.5 times for actinomycetes ($2.8nmol\;g^{-1}$). The microbial communities of total bacteria (p<0.05) and Gram-negative bacteria (p<0.05) in the OFS and CFSWP soils were significantly higher larger than those in the CFS soils. However, fungal structure was significantly greater in CFS than in OFS and CFSWP (p<0.05). In principal component analyses of soil microbial communities, our findings suggest that actinomycetes should be considered as potential factor responsible for the clear microbial community differentiation observed between OFS and CFS in controlled horticultural land.

• Transactions of the Korean hydrogen and new energy society
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• v.28 no.5
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• pp.440-446
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• 2017

This study was aimed at evaluating the effects of carbohydrate, protein and lipid content of substrate on hydrogen yields and microbial communities. The hydrogen yields were linearly correlated to carbohydrate content of substrates while others (content of proteins and lipids) did not make a significant contribution. The chemical composition of substrates produced effects on the final products of anaerobic hydrogen fermentation. Acetate and butyrate were the main fermentation products, with their concentration proving to correlate with carbohydrate and protein content of substrates. The result of microbial community analysis revealed that the relative abundances of Clostridium butyricum increased and Clostridium perfringens decreased as the carbohydrate content increased.

• Journal of Microbiology
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• v.37 no.1
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• pp.1-9
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• 1999

The Biolog redox technology was carried out for evaluation of acidification effect on microbial communities at each stage of pH gradient microcosm. While the number of heterotrophic bacterial population and activities of extracellular enzyme decreased as the pH decreased, the number of total bacteria in the microcosm was not affected. The average color development of sample at each pH-gradient showed a sigmoidal curve, and at higher pH, more overall color development appeared in Biolog plates. Average color development value in Biolog plates was stabilized at 50 hours as an optimum incubation time. The color production in the Biolog plates was caused by cell density at above pH 5.0, but by cell activity below pH 4.0. Principal component analysis of color responses revealed distinctive patterns among the pH-gradient microcosm samples.

• Korean Journal of Soil Science and Fertilizer
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• v.42 no.2
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• pp.139-143
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• 2009

We examined the vertical distribution of specific microbial groups and the patterns of microbial community structure within the soil profile using phospholipid fatty acid (PLFA). Samples were collected from the soil surface down to 15 cm in depth from paddy and upland fields located in Daegu, Korea. The two fields have been fertilized with only chemical fertilizers N, P, K for 33 years. Principal component analysis of the PLFA signatures indicated that the composition of the soil microbial communities changed significantly with the cultivation practices and soil depth, suggesting that cultivation practices of paddy and upland fields had more significant influence on soil microbial community than the soil depth did. The soil microbial communities changed more drastically with soil depth in upland field than in paddy field, with making thicker soil surface in paddy field in terms of soil microbial community. The ratios of cyclopropyl/monoenoic precursors and total saturated/total monounsaturated fatty acids increased with soil depth, suggesting that the deeper soil horizons are more carbon-limited and anaerobic than surface soil. The community analysis using PLFAs as biomarkers revealed that Gram-positive bacteria and actinomycetes tended to increase in proportional abundance with increasing soil depth, while the abundance of Gram-negative bacteria and fungi were highest at the soil surface and substantially lower in the subsurface.

• Korean Journal of Environmental Agriculture
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• v.40 no.1
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• pp.49-59
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• 2021

BACKGROUND: Soil salinity causes reduction of crop productivity. Rhizosphere microbes have metabolic capabilities and ability to adaptation of plants to biotic and abiotic stresses. Plant growth-promoting bacteria (PGPB) could play a role as elicitors for inducing tolerance to stresses in plants by affecting resident microorganism in soil. This study was conducted to demonstrate the effect of selected strains on rhizosphere microbial community under salinity stress. METHODS AND RESULTS: The experiments were conducted in tomato plants in pots containing field soil. Bacterial suspension was inoculated into three-week-old tomato plants, one week after inoculation, and -1,000 kPa-balanced salinity stress was imposed. The physiological and biochemical attributes of plant under salt stress were monitored by evaluating pigment, malondialdehyde (MDA), proline, soil pH, electrical conductivity (EC) and ion concentrations. To demonstrate the effect of selected Bacillus strains on rhizosphere microbial community, soil microbial diversity and abundance were evaluated with Illumina MiSeq sequencing, and primer sets of 341F/805R and ITS3/ITS4 were used for bacterial and fungal communities, respectively. As a result, when the bacterial strains were inoculated and then salinity stress was imposed, the inoculation decreases the stress susceptibility including reduction in lipid peroxidation, enhanced pigmentation and proline accumulation which subsequently resulted in better plant growth. However, bacterial inoculations did not affect diversity (observed OTUs, ACE, Chao1 and Shannon) and structure (principle coordinate analysis) of microbial communities under salinity stress. Furthermore, relative abundance in microbial communities had no significant difference between bacterial treated- and untreated-soils under salinity stress. CONCLUSION: Inoculation of Bacillus strains could affect plant responses and soil pH of tomato plants under salinity stress, whereas microbial diversity and abundance had no significant difference by the bacterial treatments. These findings demonstrated that Bacillus strains could alleviate plant's salinity damages by regulating pigments, proline, and MDA contents without significant changes of microbial community in tomato plants, and can be used as effective biostimulators against salinity stress for sustainable agriculture.

• Journal of Environmental Health Sciences
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• v.34 no.5
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• pp.387-394
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• 2008

The toxicity of methyl tert-butyl ether (MTBE), tert-butyl alcohol (TBA) and formaldehyde (FA) on the indigenous microbial community in forest soil was studied. MTBE, TBA and FA with different concentrations were added into microcosms containing forest soil samples. After 10 and 30 days, total viable cell number and dehydrogenase activity in the microcosms were evaluated. Bacterial communities in the microcosms were also analyzed using a denaturing gradient gel electrophoresis (DGGE). Dehydrogenase activity and total viable cell number were decreased according to the increase of MTBE, TBA and FA concentrations (P<0.05). FA toxicity was the highest, but TBA toxicity was the lowest. The results of principal component analysis using DGGE fingerprints showed that the microbial communities contaminated MTBE, TBA and FA were grouped by exposure time not exposure concentration. Dominant species in the microcosms were as follows: Photobacterium damselae sub sp. and Bacillus sp. KAR28 for MTBE; Mycobacterium sp. and Uncultured Clostridium sp. for TBA; and Uncultured Paenibacillaceae bacterium and Anxynobacillus, Flavithermus for FA.

• Journal of Microbiology and Biotechnology
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• v.13 no.3
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• pp.385-393
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• 2003

Microbial communities were analyzed in an anaerobic/aerobic sequencing batch reactor (SBR) fed with glucose as a sole carbon source. Scanning electron microscopy (SEM) showed that tetrad or cuboidal packet bacteria dominated the microbial sludge. Quinone, slot hybridization, and 165 rRNA gene sequencing analyses showed that the Proteobacteria beta subclass and the Actinobacteria group were the main microbial species in the SBR sludge. However, according to transmission electron microscopy (TEM), the packet bacteria did not contain polyphosphate granules or glycogen inclusions, but only separate coccus-shaped bacteria contained these, suggesting that coccus-shaped bacteria accumulated polyphosphate directly and the packet bacteria played other role in the enhanced biological phosphorus removal (EBPR). Based on previous reports, the Actinobacteria group and the Proteobacteria beta subclass were very likely responsible for acid formation and polyphosphate accumulation, respectively, and their cooperation achieved the EBPR in the SBR operation which was supplied with glucose.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.7
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• pp.1045-1054
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• 2012

The phylogenetic diversity of the bacteria in hot composting samples collected from three spatial locations was investigated by molecular tools in order to determine the influence of gradient effect on bacterial communities during the thermophilic phase of composting swine manure with rice straw. Total microbial DNA was extracted and bacterial near full-length 16S rRNA genes were subsequently amplified, cloned, restriction fragment length polymorphism-screened and sequenced. The superstratum sample had the highest microbial diversity among the three samples which was possibly related to the surrounding conditions of the sample resulting from the location. The results showed that the sequences related to Bacillus sp. were most common in the composts. In superstratum sample, 45 clones (33%) and 36 clones (27%) were affiliated with the Bacillus sp. and Clostridium sp., respectively; 74 clones (58%) were affiliated with the Clostridium sp. in the middle-level sample; 52 clones (40%) and 29 clones (23%) were affiliated with the Clostridium sp. and Bacillus sp. in substrate sample, respectively. It indicated that the microbial diversity and community in the samples were different for each sampling site, and different locations of the same pile often contained distinct and different microbial communities.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.8
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• pp.1373-1380
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• 2018

Objective: This study was designed to investigate the effects of temperature and storage time on the evolution of bacterial communities in swine manure. Methods: Manure was stored at $-20^{\circ}C$, $4^{\circ}C$, $20^{\circ}C$, or $37^{\circ}C$ and sampled at 7-day intervals over 28 days of storage, for a total of 5 time points. To assess the bacterial species present, 16S ribosomal RNA gene sequences were analyzed using pyrosequencing. Results: After normalization, 113,934 sequence reads were obtained, with an average length of $466.6{\pm}4.4bp$. The diversity indices of the communities reduced as temperature and storage time increased, and the slopes of rarefaction curves decreased from the second week in samples stored at $-20^{\circ}C$ and $4^{\circ}C$. These results indicate that the richness of the bacterial community in the manure reduced as temperature and storage time increased. Firmicutes were the dominant phylum in all samples examined, ranging from 89.3% to 98.8% of total reads, followed by Actinobacteria, which accounted for 0.6% to 7.9%. A change in community composition was observed in samples stored at $37^{\circ}C$ during the first 7 days, indicating that temperature plays an important role in determining the microbiota of swine manure. Clostridium, Turicibacter, Streptococcus, and Lactobacillus within Firmicutes, and Corynebacterium within Actinobacteria were the most dominant genera in fresh manure and all stored samples. Conclusion: Based on our findings, we propose Clostridium as an indicator genus of swine manure decomposition in an anaerobic environment. The proportions of dominant genera changed in samples stored at $20^{\circ}C$ and $37^{\circ}C$ during the fourth week. Based on these results, it was concluded that the microbial communities of swine manure change rapidly as storage time and temperature increase.