Conexibacter
            
            arvalis sp. nov., isolated from a cultivated field soil sample

Seki, Tamae; Matsumoto, Atsuko; Shimada, Risa; Inahashi, Yuki; Ōmura, Satoshi; Takahashi, Yōko

doi:10.1099/ijs.0.036095-0

Cited by 48 publications

(34 citation statements)

References 23 publications

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“…In fact, our isolates Ap38E and Ap45E have distinct colony morphologies, but both isolates are small rods of 0.6–1.2 μm ( Figures 4A,B ), similar in size with the bacteria to the family Conexibacteraceae (Monciardini, 2003; Seki et al, 2012). The isolates Ap25E, Ap46E, and Ap42E are also composed of small cells, however, they are coccoid in shape and grow in aggregates ( Figures 4C,D ).…”

Section: Resultsmentioning

confidence: 84%

Isolation of Uncultured Bacteria from Antarctica Using Long Incubation Periods and Low Nutritional Media

et al. 2017

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Uncultured microorganisms comprise most of the microbial diversity existing on our planet. Despite advances in environmental sequencing and single-cell genomics, in-depth studies about bacterial metabolism and screening of novel bioproducts can only be assessed by culturing microbes in the laboratory. Here we report uncultured, or recalcitrant, microorganisms from an Antarctic soil sample, using relatively simple methods: oligotrophic media, extended incubation periods, observation under stereo microscopy, and selection of slow-growing bacteria. We managed to isolate several rare microorganisms belonging to infrequently isolated or recently described genera, for example Lapillicoccus, Flavitalea, Quadrisphaera, Motilibacter, and Polymorphobacter. Additionally, we obtained isolates presenting 16S rRNA sequence similarity ranging from 92.08 to 94.46% with any other known cultured species, including two distinct isolates from the class Thermoleophilia, that although common in Antarctic soils (as identified by metagenomics), was never reported to be isolated from such samples. Our data indicates that simple methods are still useful for cultivating recalcitrant microorganisms, even when dealing with samples from extreme environments.

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Section: Resultsmentioning

confidence: 84%

Isolation of Uncultured Bacteria from Antarctica Using Long Incubation Periods and Low Nutritional Media

et al. 2017

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“…The genus Rubrobacter (order Rubrobacteridae) is capable in bioremediating organic and radioactive pollutants, but it is rarely reported in saline habitats (Jurado et al 2012). The genera Conexibacter and Solirubrobacter (order Rubrobacteridae) have been isolated from cultivated field soils, but seldom from saline soils Seki et al 2012). Firmicutes, the third most abundant phylum in the present dataset, accounted for 8.8 % of all sequences.…”

Section: Bacteriamentioning

confidence: 70%

A meta-analysis of the publicly available bacterial and archaeal sequence diversity in saline soils

Gong

2013

World J Microbiol Biotechnol

102

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An integrated view of bacterial and archaeal diversity in saline soil habitats is essential for understanding the biological and ecological processes and exploiting potential of microbial resources from such environments. This study examined the collective bacterial and archaeal diversity in saline soils using a meta-analysis approach. All available 16S rDNA sequences recovered from saline soils were retrieved from publicly available databases and subjected to phylogenetic and statistical analyses. A total of 9,043 bacterial and 1,039 archaeal sequences, each longer than 250 bp, were examined. The bacterial sequences were assigned into 5,784 operational taxonomic units (OTUs, based on C97 % sequence identity), representing 24 known bacterial phyla, with Proteobacteria (44.9 %), Actinobacteria (12.3 %), Firmicutes (10.4 %), Acidobacteria (9.0 %), Bacteroidetes (6.8 %), and Chloroflexi (5.9 %) being predominant. Lysobacter (12.8 %) was the dominant bacterial genus in saline soils, followed by Sphingomonas (4.5 %), Halomonas (2.5 %), and Gemmatimonas (2.5 %). Archaeal sequences were assigned to 602 OTUs, primarily from the phyla Euryarchaeota (88.7 %) and Crenarchaeota (11.3 %).Halorubrum and Thermofilum were the dominant archaeal genera in saline soils. Rarefaction analysis indicated that less than 25 % of bacterial diversity, and approximately 50 % of archaeal diversity, in saline soil habitats has been sampled. This analysis of the global bacterial and archaeal diversity in saline soil habitats can guide future studies to further examine the microbial diversity of saline soils.

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“…; Seki et al . ). Spartobacteria comprises one of the primary groups of Verrucomicrobia and is widely distributed in soil and aquatic environments (Janssen et al .…”

Section: Discussionmentioning

confidence: 97%

Shifts of tundra bacterial and archaeal communities along a permafrost thaw gradient in Alaska

et al. 2014

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Understanding the response of permafrost microbial communities to climate warming is crucial for evaluating ecosystem feedbacks to global change. This study investigated soil bacterial and archaeal communities by Illumina MiSeq sequencing of 16S rRNA gene amplicons across a permafrost thaw gradient at different depths in Alaska with thaw progression for over three decades. Over 4.6 million passing 16S rRNA gene sequences were obtained from a total of 97 samples, corresponding to 61 known classes and 470 genera. Soil depth and the associated soil physical-chemical properties had predominant impacts on the diversity and composition of the microbial communities. Both richness and evenness of the microbial communities decreased with soil depth. Acidobacteria, Verrucomicrobia, Alpha- and Gamma-Proteobacteria dominated the microbial communities in the upper horizon, whereas abundances of Bacteroidetes, Delta-Proteobacteria and Firmicutes increased towards deeper soils. Effects of thaw progression were absent in microbial communities in the near-surface organic soil, probably due to greater temperature variation. Thaw progression decreased the abundances of the majority of the associated taxa in the lower organic soil, but increased the abundances of those in the mineral soil, including groups potentially involved in recalcitrant C degradation (Actinomycetales, Chitinophaga, etc.). The changes in microbial communities may be related to altered soil C sources by thaw progression. Collectively, this study revealed different impacts of thaw in the organic and mineral horizons and suggests the importance of studying both the upper and deeper soils while evaluating microbial responses to permafrost thaw.

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Conexibacter arvalis sp. nov., isolated from a cultivated field soil sample

Cited by 48 publications

References 23 publications

Isolation of Uncultured Bacteria from Antarctica Using Long Incubation Periods and Low Nutritional Media

Isolation of Uncultured Bacteria from Antarctica Using Long Incubation Periods and Low Nutritional Media

A meta-analysis of the publicly available bacterial and archaeal sequence diversity in saline soils

Shifts of tundra bacterial and archaeal communities along a permafrost thaw gradient in Alaska

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