• Korean Journal of Soil Science and Fertilizer
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• v.47 no.6
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• pp.451-456
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• 2014

Organic amendment practices can influence diversity and activities of soil microorganisms. There is a need to investigate this impact compared with other types of materials. This study was carried out to evaluate the long term effects of chemical and organic fertilizer on soil microbial community in upland field. During the last 11 years green manure, rice straw compost, rapeseed cake, pig mature compost, NPK, and NPK + pig mature compost were treated in upland soil. Organic fertilizer treatment found with high bacterial colony forming units (CFUs) as compared to chemical and without fertilizer treatment. There was no significant difference in the actinomycetes and fungal population. The average well color development (AWCD) value was the highest in green manure and, the lowest in without fertilizer treatment. Analyses based on the denaturing gradient gel electrophoresis (DGGE) profile showed that rice straw compost and pig mature compost had a similar banding pattern while rapeseed cake, NPK, NPK + pig mature compost and without fertilizer treatment were clustered in another cluster and clearly distinguished from green manure treatment. Bacterial diversity can be highly increased by the application of organic fertilizer while chemical fertilizer had less impact. It can be concluded that green manure had a beneficial impact on soil microbial flora, while, the use of chemical fertilizer could affect the soil bacterial communities adversely.

• Journal of Microbiology and Biotechnology
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• v.20 no.1
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• pp.21-29
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• 2010

The phenolic compounds are a major contaminant class often found in industrial wastewaters and the biological treatment is an alternative tool commonly employed for their removal. In this sense, monitoring microbial community dynamics is crucial for a successful wastewater treatment. This work aimed to monitor the structure and activity of the bacterial community during the operation of a laboratory-scale continuous submerged membrane bioreactor (SMBR), using PCR and RT-PCR followed by denaturing gradient gel electrophoresis (DGGE) and 16S rRNA libraries. Multivariate analyses carried out using DGGE profiles showed significant changes in the total and metabolically active dominant community members during the 4-week treatment period, explained mainly by phenol and ammonium input. Gene libraries were assembled using 16S rDNA and 16S rRNA PCR products from the fourth week of treatment. Sequencing and phylogenetic analyses of clones from the 16S rDNA library revealed a high diversity of taxa for the total bacterial community, with predominance of Thauera genus (ca. 50%). On the other hand, a lower diversity was found for metabolically active bacteria, which were mostly represented by members of Betaproteobacteria (Thauera and Comamonas), suggesting that these groups have a relevant role in the phenol degradation during the final phase of the SMBR operation.

• Proceedings of the Korean Society of Soil and Groundwater Environment Conference
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• 2004.09a
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• pp.175-178
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• 2004

Little study has been published specifically addressing the dynamics of nitrate reducing bacteria (NBR) during the bioremediation of nitrate-contaminated aquifer. In our previous study we successfully quantified fumarate-enhanced microbial nitrate reduction rate in a nitrate-contaminated aquifer by using a series of single-well push-pull tests (PPTs). In this study we analyzed the suspended population during PPTs. To monitor changes in the microbial community, PCR amplification of 16S rDNA genes and denaturing gradient gel electrophoresis (DGGE) were used to study the dynamics of the bacterial community in detail. Before the stimulation of NBR, the dominant DGGE bands obtained by PCR were affiliated with V-Proteobacteria consisting of Acinetobacter spp. and Pseudomonas fluorescens. However, as NBR biostimulation proceeded, the dominant patterns of DGGE bands changed, and they were affiliated with Azoarcus denitrificans Td-3 and Flavobacterium xanthum. Azoarcus denitrificans Td-3 is known to completely reduce nitrate to nitrogen gas. The series of single-well push-pull tests in this study should prove useful for conducting rapid, low-cost feasibility assessments for in situ denitrification and provide important information about which microorganisms play a key role in bioremediation of a nitrate contaminated aquifer.

• Journal of Microbiology and Biotechnology
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• v.22 no.1
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• pp.1-12
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• 2012

The present study examines the effects of 30 mg/kg butachlor on the cyanobacterial diversity of rice fields in Eastern Uttar Pradesh and Western Bihar in India. A total of 40 samples were grouped into three classes [(i) acidic, (ii) neutral, and (iii) alkaline soils], based on physicochemical and principle component analyses. Acidic soils mainly harbored Westillopsis, Trichormus, Anabaenopsis, and unicellular cyanobacteria; whereas Nostoc, Anabaena, Calothrix, Tolypothrix, and Aulosira were found in neutral and alkaline soils. Molecular characterization using 16S rRNA PCR and DGGE revealed the presence of 13 different phylotypes of cyanobacteria in these samples. Butachlor treatment of the soil samples led to the disappearance of 5 and the emergence of 2 additional phylotypes. A total of 40 DGGE bands showed significant reproducible changes upon treatment with butachlor. Phylogenetic analyses divided the phylotypes into five major clusters exhibiting interesting links with soil pH. Aulosira, Anabaena, Trichormus, and Anabaenopsis were sensitive to butachlor treatment, whereas uncultured cyanobacteria, a chroococcalean member, Westillopsis, Nostoc, Calothrix, Tolypothrix, Rivularia, Gloeotrichia, Fischerella, Leptolyngbya, and Cylindrospermum, appeared to be tolerant against butachlor at their native soil pH. Butachlor-induced inhibition of nitrogen fixation was found to be 65% (maximum) and 33% (minimum) in the soil samples of pH 9.23 and 5.20, respectively. In conclusion, low butachlor doses may prove beneficial in paddy fields having a neutral to alkaline soil pH.

• Journal of Microbiology and Biotechnology
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• v.16 no.2
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• pp.232-239
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• 2006

The microbial activity and bacterial community structure of activated sludge reactors, which treated free cyanide (FC), zinc-complexed cyanide (ZC), or nickel-complexed cyanide (NC), were studied. The three reactors (designated as re-FC, re-ZC, and re-NC) were operated for 50 days with a stepwise decrease of hydraulic retention time. In the re-FC and re-ZC reactors, FC or ZC was almost completely removed, whereas approximately 80-87% of NC was removed in re-NC. This result might be attributed to the high toxicity of nickel released after degradation of NC. In the batch test, the sludges taken from re-FC and re-ZC completely degraded FC, ZC, and NC, whereas the sludge from re-NC degraded only NC. Although re-FC and re-ZC showed similar properties in regard to cyanide degradation, denaturing gradient gel electrophoresis (DGGE) analysis of the 16S rRNA gene of the bacterial communities in the three reactors showed that bacterial community was specifically acclimated to each reactor. We found several bacterial sequences in DGGE bands that showed high similarity to known cyanide-degrading bacteria such as Klebsiella spp., Acidovorax spp., and Achromobacter xylosoxidans. Flocforming microorganism might also be one of the major microorganisms, since many sequences related to Zoogloea, Microbacterium, and phylum TM7 were detected in all the reactors.

• Korean Journal of Organic Agriculture
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• v.19 no.3
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• pp.417-425
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• 2011

This study was conducted to investigate the changes in physicochemical and microbiological properties during fermenting process of farm-made organic liquid fertilizer made of the mixture of organic materials such as blood meal and molasse during fermenting process. The pH level of organic liquid fertilizer during the ermentation decreased from 7.2 to 4.3. The EC of organic liquid fertilizer was increased from 13.9 dS/m to 99.3 dS/m during the fermentation. The total population of aerobic bacteria decreased from $8.2{\times}10^5$ cfu/ml to $3{\times}10^4$ cfu/ml, but Bacillus spp. increased from $2.1{\times}10^2$ cfu/ml to $4.2{\times}10^3$ cfu/ml during the fermentation. Bacterial isolates were obtained from organic liquid fertilizers and identified by fatty acid-base typing. The Genus Bacillus was dominant as fermenting proceeded. The denaturing gradient gel electrophoresis (DGGE) profile showed changes of bacterial communities in organic liquid fertilizers.

• Korean Journal of Organic Agriculture
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• v.19 no.spc
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• pp.190-193
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• 2011

Organic and chemical fertilizer amendments are an important agricultural practice for increasing crop yields. In order to maintain the soil sustainability, it is important to monitor the effects of fertilizer applications on the shift of soil microorganism, which control the cycling of many nutrients in the soils. Here, culture-dependent and culture-independent approaches were used to analyze the soil microorganism and community structure under six fertilization treatments, including green manure, rice straw compost, rapeseed cake, pig mature compost, NPK +pig mature compost, NPK and control. Both organic and chemical fertilizers caused a shift of the cultural microorganism CFUs after treatments. Bacterial CFUs of the organic fertilization treatments were significantly higher than that of chemical fertilization treatments. The DGGE profiles of the bacterial communities of the samples showed that the green manure treatment was a distinct difference in bacterial community, with a greater complexity of the band pattern than other treatments. Cluster analyses based on the DGGE profile showed that rice straw compost and pig mature compost had a similar banding pattern and clustered together firstly. Rapeseed cake, NPK, NPK +pig manure compost and control clustered together in other sub-cluster and clearly distinguished from green manure.

• Journal of Environmental Health Sciences
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• v.34 no.6
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• pp.403-413
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• 2008

Toxic effect of methyl tert-butyl ether (MTBE), tert-butyl alcohol (TBA) and formaldehyde (FA) on microbial activity and diversity was compared in rice field, leek patch, and tidal mud flat soil samples. MTBE, TBA and FA with different concentrations were added into microcosms containing these soil samples, and placed at room temperature for 30 days. Then the microbial activities such as dehydrogenase and viable cell numbers and microbial community using a DGGE (Denaturing gradient gel electrophoresis) fingerprinting method were measured. Among the samples, dehydrogenase activity in rice field was inhibited the most by MTBE, TBA and FA. The toxic effect was higher according to the following orders: FA > MTBE > TBA. Dominant species in the microcosms contaminated with MTBE, TBA and FA were Chloroflex, Bacilli, gamma-proteobacteria in the rice field sample, Sphingobacteria, Flavobacteria, Actinobacteria, Bacilli, gamma-proteobacteria in the leek patch sample, and Sphingobacteria, Flavobacteria, delta-proteobacteria, gamma-proteobacteria in the tidal mud flat sample.

• Journal of Microbiology and Biotechnology
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• v.26 no.2
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• pp.364-372
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• 2016

Sand tubules, made up of sand grains cemented by microbe-induced calcium carbonate precipitation, have been found in China's Ningxia Province. Sand tubules grow like a tree's roots about 40-60 cm below the surface. The properties of sand tubules and their bacterial community were examined. X-Ray diffraction analysis revealed that the sand tubules were associated with crystalline calcite. Scanning electron microscopy showed that the crystalline solid had a lamellar structure and lacked the presence of cells, suggesting that no bacteria acted as nucleation sites, nor that the crystalline solid was formed by the aggregation of bacteria. Denaturing gradient gel electrophoresis analysis showed 11 of the 12 detectable bands were uncultured bacteria by BLAST analysis in the GenBank database, and the rest were closely related to Paenibacillus sp. (100% identity). By cultivation techniques, the only strain isolated from the sand tubule was suggested to be related to Paenibacillus sp.; no archaea were found. Furthermore, Paenibacillus sp. was demonstrated to induce calcium carbonate precipitation in vitro.

• Journal of Microbiology and Biotechnology
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• v.17 no.5
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• pp.853-857
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• 2007

The semi-outdoor cultivation of Spirulina platens is was attempted using an underground-water-based medium. Occurrence of contaminant organisms such as Chlorella sp. and Chlamydomonas sp. was not found from a microscopic observation and bacteria were not detected from denaturing gradient gel electrophoresis(DGGE) analysis of PCR-amplified 16S rDNA during the cultivation, owing to pH control and the high quality of the underground water. The mean productivity was high at $10.5g/m^2/d$ with a range of $4.2-12.3g/m^2/d$ despite the unfavorable weather conditions of the rainy season. The cultivated S. platens is included a normal protein content of 58.9%. Consequently, the underground water improved the biomass productivity and the biomass quality because of an abundant supplementation of natural minerals and through a contaminant-free culture.