Journal of Microbiology

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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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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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Massilia kyonggiensis sp. nov., Isolated from Forest Soil in Korea: Jaisoo Kim; J. Microbiol. 2014;52(5):378-383. Published online May 9, 2014; DOI: https://doi.org/10.1007/s12275-014-4010-7

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Abstract

A Gram-negative, short, rod-shaped bacterium, TSA1T, was isolated from forest soil collected at Kyonggi University, South Korea. Assessment of 16S rRNA gene sequence sim-ilarity indicated that the strain is related to Massilia niastensis 5516S-1T (98.3%), M. haematophila CCUG 38318T (97.9%), M. aerilata 5516S-11T (97.9%), M. tieshanensis TS3T (97.6%), and M. varians CCUG 3529T (97.1%). Colonies grown on Reasoner’s 2A agar at 30°C for 2 days were transparent, white, round, smooth, and glossy. The cells grew at 10–42°C (optimum: 25–37°C) and pH 5–9 (optimum: 5–9) and in 0–2% NaCl (optimum: 0–1%). TSA1T was able to grow on trypticase soy and nutrient agar, but not on Luria-Bertani or MacConkey agar. The strain was catalase- and oxidase- positive and able to degrade starch and casein, but not car-boxymethyl cellulose. The predominant quinone of TSA1T was Q-8, the major fatty acids were summed feature 3 and C16:0, and the DNA G+C content was 66.7 mol%. Given these findings, we propose that this strain is a novel species of the genus Massilia. We suggest the name Massilia kyonggiensis sp. nov. (type strain, KACC 17471T =KEMB 9005-031T =JCM 19189T).

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Isolation of Paenibacillus pinesoli sp. nov. from Forest Soil in Gyeonggi-Do, Korea: Jeongsuk Moon , Jaisoo Kim; J. Microbiol. 2014;52(4):273-277. Published online March 29, 2014; DOI: https://doi.org/10.1007/s12275-014-3622-2

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Abstract

Using a new culture method for unculturable soil bacteria, strain NB5T was isolated from forest soil at Kyonggi University, and characterized taxonomically on the basis of 16S rRNA gene sequence as well as phenotypic and chemotaxonomic characteristics. The novel strain was a Gram- and catalase-positive, rod-shaped bacterium, which grew in the pH range 6.0–9.5 (optimum, 6.5–9.5) and at temperatures between 15°C and 45°C (optimum, 25–40°C). Growth was possible at 0–5% NaCl (optimum, 0% to 3%) in nutrient, Luria-Bertani, and trypticase soy broths (TSB), as well as R2A medium (with optimal growth in TSB). A phylogenetic analysis of the 16S rRNA gene sequence showed that the novel strain was affiliated with the genus Paenibacillus and had 96.8% and 96.5% similarity to P. nanensis MX2-3T and P. agaridevorans DSM 1355T, respectively. The predominant menaquinone in NB5T was MK-7; the major fatty acids were anteiso-C15:0 and iso-C16:0; and the DNA G+C content was 54.5 mol%. We propose this strain as a novel species of the genus Paenibacillus, and suggest the name Paenibacillus pinesoli sp. nov. (type strain, KACC 17472T =KEMB 9005-025T =JCM 19203T).

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