Global Sequencing: A Review of Current Molecular Data and New Methods Available to Assess Microbial Diversity

Christen, Richard

doi:10.1264/jsme2.me08525

Cited by 68 publications

(54 citation statements)

References 189 publications

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“…Therefore, the genera and species of the bacteria detected in the DGGE analysis seem to be unidentified. DGGE allows the detection of more diverse bacteria than culture-based methods (2,13). To accurately estimate changes in the bacterial community, the identification of these bacteria is very important.…”

Section: Discussionmentioning

confidence: 99%

Distribution of Bacterial Species in Soil with a Vegetational Change from Japanese Black Pine (Pinus thunbergii) to Black Locust (Robinia pseudoacacia)

et al. 2009

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The effects of a nitrogen-fixing tree, black locust (Robinia pseudoacacia), on the distribution of bacterial species were examined in a Japanese black pine (Pinus thunbergii) and black locust-dominated area. DNA was extracted from the soil at depths of 0-5 and 5-10 cm, collected at the border between a Japanese black pine-dominated forest and a black locust-dominated forest, and the distribution of bacterial species was investigated by denaturing gradient gel electrophoresis (DGGE). The bacterial communities did not differ between the two forests. The distribution of some bacterial species correlated significantly with soil pH, soil carbon [C], soil nitrogen [N], and soil N/phosphate [P], but not with soil C/N or soil P. The distributional relationships between ectomycorrhizal (ECM) fungal species and bacterial species were also analyzed. A positive correlation was observed between the distribution of some ECM fungi and bacterial species. These bacteria may have some interactions with ECM fungi in the field.

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Section: Discussionmentioning

confidence: 99%

Distribution of Bacterial Species in Soil with a Vegetational Change from Japanese Black Pine (Pinus thunbergii) to Black Locust (Robinia pseudoacacia)

et al. 2009

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“…The preliminary construction of a phylogenetic tree based on 16S rRNA gene sequences did not permit us to evaluate their relationships clearly with soybean genotypes and isolation media (data not shown). Thus, a statistical approach was adopted for comparing the microbial diversity and phylogenetic composition; such an approach has been used exclusively for culture-independent clone analyses (4,17,19,26).…”

Section: Bacterial Isolationmentioning

confidence: 99%

Nodulation-Dependent Communities of Culturable Bacterial Endophytes from Stems of Field-Grown Soybeans

et al. 2009

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Endophytic bacteria (247 isolates) were randomly isolated from surface-sterilized stems of non-nodulated (Nod − ), wild-type nodulated (Nod + ), and hypernodulated (Nod ++ ) soybeans (Glycine max [L.] Merr) on three agar media (R2A, nutrient agar, and potato dextrose agar). Their diversity was compared on the basis of 16S rRNA gene sequences. The phylogenetic composition depended on the soybean nodulation phenotype, although diversity indexes were not correlated with nodulation phenotype. The most abundant phylum throughout soybean lines tested was Proteobacteria (58-79%). Gammaproteobacteria was the dominant class (21-72%) with a group of Pseudomonas sp. significantly abundant in Nod + soybeans. A high abundance of Alphaproteobacteria was observed in Nod − soybeans, which was explained by the increase in bacterial isolates of the families Rhizobiaceae and Sphingomonadaceae. A far greater abundance of Firmicutes was observed in Nod − and Nod ++ mutant soybeans than in Nod + soybeans. An impact of culture media on the diversity of isolated endophytic bacteria was also observed: The highest diversity indexes were obtained on the R2A medium, which enabled us to access Alphaproteobacteria and other phyla more frequently. The above results indicated that the extent of nodulation changes the phylogenetic composition of culturable bacterial endophytes in soybean stems.

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“…Minamisawa (107) have pointed out the significance of metagenomic analyses of plant-associated microbes to address this issue. Strong support from bioinformatics and rational genome databases (17) are needed to attain this goal.…”

Section: Life Is Not As Simple As It Seemsmentioning

confidence: 99%

A Great Leap forward in Microbial Ecology

et al. 2010

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Ribosomal RNA (rRNA) sequence-based molecular techniques emerged in the late 1980s, which completely changed our general view of microbial life. Coincidentally, the Japanese Society of Microbial Ecology (JSME) was founded, and its official journal "Microbes and Environments (M&E)" was launched, in 1985. Thus, the past 25 years have been an exciting and fruitful period for M&E readers and microbiologists as demonstrated by the numerous excellent papers published in M&E. In this minireview, recent progress made in microbial ecology and related fields is summarized, with a special emphasis on 8 landmark areas; the cultivation of uncultured microbes, in situ methods for the assessment of microorganisms and their activities, biofilms, plant microbiology, chemolithotrophic bacteria in early volcanic environments, symbionts of animals and their ecology, wastewater treatment microbiology, and the biodegradation of hazardous organic compounds.

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Global Sequencing: A Review of Current Molecular Data and New Methods Available to Assess Microbial Diversity

Cited by 68 publications

References 189 publications

Distribution of Bacterial Species in Soil with a Vegetational Change from Japanese Black Pine (Pinus thunbergii) to Black Locust (Robinia pseudoacacia)

Distribution of Bacterial Species in Soil with a Vegetational Change from Japanese Black Pine (Pinus thunbergii) to Black Locust (Robinia pseudoacacia)

Nodulation-Dependent Communities of Culturable Bacterial Endophytes from Stems of Field-Grown Soybeans

A Great Leap forward in Microbial Ecology

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