Journal of Microbiology

Research Support, Non-U.S. Gov'ts

Microbial communities inhabiting oil-contaminated soils from two major oilfields in Northern China: Implications for active petroleum-degrading capacity: Weimin Sun , Yiran Dong , Pin Gao , Meiyan Fu , Kaiwen Ta , Jiwei Li; J. Microbiol. 2015;53(6):371-378. Published online May 30, 2015; DOI: https://doi.org/10.1007/s12275-015-5023-6

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Although oilfields harbor a wide diversity of microorganisms with various metabolic potentials, our current knowledge about oil-degrading bacteria is limited because the vast majority of oil-degrading bacteria remain uncultured. In the present study, microbial communities in nine oil-contaminated soils collected from Daqing and Changqing, two of the largest oil fields in China, were characterized through highthroughput sequencing of 16S rRNA genes. Bacteria related to the phyla Proteobacteria and Actinobacteria were dominant in four and three samples, respectively. At the genus level, Alkanindiges, Arthrobacter, Pseudomonas, Mycobacterium, and Rhodococcus were frequently detected in nine soil samples. Many of the dominant genera were phylogenetically related to the known oil-degrading species. The correlation between physiochemical parameters within the microbial communities was also investigated. Canonical correspondence analysis revealed that soil moisture, nitrate, TOC, and pH had an important impact in shaping the microbial communities of the hydrocarbon-contaminated soil. This study provided an in-depth analysis of microbial communities in oilcontaminated soil and useful information for future bioremediation of oil contamination.

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Assessment of Microbial Diversity Bias Associated with Soil Heterogeneity and Sequencing Resolution in Pyrosequencing Analyses: Sokhee P. Jung , Hojeong Kang; J. Microbiol. 2014;52(7):574-580. Published online May 13, 2014; DOI: https://doi.org/10.1007/s12275-014-3636-9

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Abstract

It is important to estimate the true microbial diversities accurately for a comparative microbial diversity analysis among various ecological settings in ecological models. Despite drastically increasing amounts of 16S rRNA gene targeting pyrosequencing data, sampling and data interpretation for comparative analysis have not yet been standardized. For more accurate bacterial diversity analyses, the influences of soil heterogeneity and sequence resolution on bacterial diversity estimates were investigated using pyrosequencing data of oak and pine forest soils with focus on the bacterial 16S rRNA gene. Soil bacterial community sets were phylogenetically clustered into two separate groups by forest type. Rarefaction curves showed that bacterial communities sequenced from the DNA mixtures and the DNAs of the soil mixtures had midsize richness compared with other samples. Richness and diversity estimates were highly variable depending on the sequence read numbers. Bacterial richness estimates (ACE, Chao 1 and Jack) of the forest soils had positive linear relationships with the sequence read number. Bacterial diversity estimates NPShannon, Shannon and the inverse Simpson) of the forest soils were also positively correlated with the sequence read number. One-way ANOVA shows that sequence resolution significantly affected the α-diversity indices (P<0.05), but the soil heterogeneity did not (P>0.05). For an unbiased evaluation, richness and diversity estimates should be calculated and compared from subsets of the same size.

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Effects of Nutritional Input and Diesel Contamination on Soil Enzyme Activities and Microbial Communities in Antarctic Soils: Jiwon Han , Jaejoon Jung , Seunghun Hyun , Hyun Park , Woojun Park; J. Microbiol. 2012;50(6):916-924. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2636-x

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Abstract: Pollution of Antarctic soils may be attributable to increased nutritional input and diesel contamination via anthropogenic activities. To investigate the effect of these environmental changes on the Antarctic terrestrial ecosystem, soil enzyme activities and microbial communities in 3 types of Antarctic soils were evaluated. The activities of alkaline phosphomonoesterase and dehydrogenase were dramatically increased, whereas the activities of β-glucosidase, urease, arylsulfatase, and fluorescein diacetate hydrolysis were negligible. Alkaline phosphomonoesterase and dehydrogenase activities in the 3 types of soils increased 3- to 10-fold in response to nutritional input, but did not increase in the presence of diesel contamination. Consistent with the enzymatic activity data, increased copy numbers of the phoA gene, encoding an alkaline phosphomonoesterase, and the 16S rRNA gene were verified using quantitative real-time polymerase chain reaction. Interestingly, dehydrogenase activity and 16S rRNA gene copy number increased slightly after 30 days, even under diesel contamination, probably because of adaptation of the bacterial population. Intact Antarctic soils showed a predominance of Actinobacteria phylum (mostly Pseudonorcarida species) and other phyla such as Proteobacteria, Chloroflexi, Planctomycetes, Firmicutes, and Verrucomicrobia were present in successively lower proportions. Nutrient addition might act as a selective pressure on the bacterial community, resulting in the prevalence of Actinobacteria phylum (mostly Arthrobacter species). Soils contaminated by diesel showed a predominance of Proteobacteria phylum (mostly Phyllobacterium species), and other phyla such as Actinobacteria, Bacteroidetes, Planctomycetes, and Gemmatimonadetes were present in successively lower proportions. Our data reveal that nutritional input has a dramatic impact on bacterial communities in Antarctic soils and that diesel contamination is likely toxic to enzymes in this population.

NOTE] Evaluation of a Fosmid-Clone-Based Microarray for Comparative Analysis of Swine Fecal Metagenomes: Soo-Je Park , Dong-Hwan Kim , Man-Young Jung , So-Jeong Kim , Hongik Kim , Yang-Hoon Kim , Jong-Chan Chae , Sung-Keun Rhee; J. Microbiol. 2012;50(4):684-688. Published online July 21, 2012; DOI: https://doi.org/10.1007/s12275-012-2115-4

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Abstract: Glass slide arrayed with fosmid clone DNAs generated from swine feces as probes were fabricated and used as a metagenome microarray (MGA). MGA appeared to be specific to their corresponding target genomic fragments. The detection limit was 10 ng of genomic DNA (ca. 106 bacterial cells) in the presence of 1000 ng of background DNA. Linear relationships between the signal intensity and the target DNA (20–100 ng) were observed (r2=0.98). Application of MGA to the comparison of swine fecal metagenomes suggested that the microbial community composition of swine intestine could be dependent on the health state of swine.

Comparative Analysis of Cyanobacterial Communities from Polluted Reservoirs in Korea: Jin-Book Kim , Mi-Sook Moon , Dong-Hun Lee , Sung-Taik Lee , Marco Bazzicalupo , Chi-Kyung Kim; J. Microbiol. 2004;42(3):181-187.; DOI: https://doi.org/2092 [pii]

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Abstract: Cyanobacteria are the dominant phototrophic bacteria in water environments. Here, the diversity of cyanobacteria in seven Korean reservoir waters where different levels of algal blooms were observed during the summer of 2002, was examined by T-RFLP analysis. The number of T-RF bands in the HaeIII T-RFLP profiles analyzed from those water samples ranged from 20 to 44. Of these, cyanobacteria accounted for 6.1 to 27.2% of the total bacteria. The water samples could be clustered into 2 groups according to the Dice coefficient of the T-RF profiles. The eutrophic Dunpo and oligotrophic Chungju reservoirs were selected, and several representative clones from both reservoir waters analyzed for the nucleotide sequences of their 16S rDNA. The major clones were found to belong to the Microcystis and Anabaena species in the waters from the Dunpo and Chungju reservoirs, respectively, which was in agreement with the T-RFLP result. That is, the Microcystis and Anabaena species were dominant in the eutrophic and polluted Dunpo and oligotrophic Chungju reservoir waters, respectively. These results indicated that there is a correlation between prevalence of cyanobacterial species and levels of pollution in reservoir waters.

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