Draft Genome Sequence of the Deinococcus-Thermus Bacterium Meiothermus ruber Strain A

Thiel, Vera; Tomsho, Lynn P.; Burhans, Richard; Schuster, Stephan C.; Ward, David M.; Bryant, Donald A.

doi:10.1128/genomea.00202-15

Cited by 8 publications

(7 citation statements)

References 10 publications

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“…For example, the prediction of pathways involved in carbohydrate, energy and amino acid metabolism (Table 3) was consistent with the predicted heterotrophic physiologies of the majority of identified taxa, such as Deinococcus-Thermus, Proteobacteria, Actinobacteria, Chloroflexi and Gemmatimonadetes (Margulis and Chapman, 2009;Oren and Papke, 2010;Shivlata and Tulasi, 2015;Thiel et al, 2015). As heterotrophic microorganisms are known to degrade complex substrates (Kuffner et al, 2012), these correlations suggest the involvement of the identified taxa in these pathways.…”

Section: Microbial Community Potential Functionality Analysissupporting

confidence: 70%

“…The dominant bacterial phyla identified in this study are all known to harbour members highly resistant to extreme environmental conditions (Margulis and Chapman, 2009;Oren and Papke, 2010). The majority of phyla identified also contained members with heterotrophic physiologies (Oren and Papke, 2010;Shivlata and Tulasi, 2015;Thiel et al, 2015), capable of degrading complex organic compounds (Oren and Papke, 2010). Autotrophic taxa were also identified within all treatment groups, which is consistent to previous findings in Antarctic soils (Makhalanyane et al, 2015).…”

Section: Microbial Community Diversity Analysismentioning

confidence: 99%

“…The putative presence of genes involved in environmental adaptation and stress response is correlated to the predicted stress-tolerant physiologies of the observed taxa. For example, members of the phyla Deinococcus-Thermus and Actinobacteria are known to be highly desiccation and stress tolerant (Oren and Papke, 2010;Shivlata and Tulasi, 2015;Thiel et al, 2015), suggesting a correlation between the presence of these taxa and the putative identification of environmental adaptation as well as replication and repair pathways (Table 3). While these predictions are only indicative of the potential presence of the identified genes and cellular pathways, their abundance is consistent with previous functional diversity surveys within Antarctic soils (Pearce et al, 2012;Chan et al, 2013).…”

Section: Microbial Community Potential Functionality Analysismentioning

confidence: 99%

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Antarctic microbial communities are functionally redundant, adapted and resistant to short term temperature perturbations

Scally

Makhalanyane

Frossard

et al. 2016

Soil Biology and Biochemistry

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Climate change has the potential to induce dramatic shifts in the biodiversity and functionality of soil microorganisms in polar hyperarid ecosystems. In these depauperate soil ecosystems, microbial communities are vital as they represent the dominant input sources of essential nutrients. However, the effects of changing climate on extreme edaphic environments, such as the McMurdo Dry Valleys of Antarctica, remain poorly understood. To better understand these effects, we constructed soil microcosms and simulated temperature shifts over a 40-day period. Soil physicochemical analysis revealed low levels of key nutrients, with mean organic carbon and nitrogen contents of <0.1% and 11.55 ppm, respectively. We also applied 16S rRNA gene amplicon sequencing to determine taxonomic composition and enzyme assays to measure in situ activity. Our data showed a prevalence of ubiquitous soil taxa (Actinobacteria, Chloroflexi and Deinococcus-Thermus), with a smaller proportion of autotrophic phyla (i.e. Cyanobacteria). None of the major phyla showed relative abundance changes in response to temperature. We found very low extracellular enzyme activity levels across all samples and observed no significant differences among temperature treatments. Functional predictions (using PICRUSt) revealed the putative presence of key genes implicated in the cycling of carbon (ppc, rbcl) and nitrogen (nifH, nirK), in stress response and in DNA repair throughout all treatments. Overall, our results suggest that short-term temperature fluctuations do not alter microbial biodiversity and functionality in Antarctic soils. This study provides the first evidence that microbial communities within this edaphic extreme environment may be functionally redundant, adapted and resistant to short term climatic perturbations.

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Section: Microbial Community Potential Functionality Analysissupporting

confidence: 70%

Section: Microbial Community Diversity Analysismentioning

confidence: 99%

Section: Microbial Community Potential Functionality Analysismentioning

confidence: 99%

See 1 more Smart Citation

Antarctic microbial communities are functionally redundant, adapted and resistant to short term temperature perturbations

Scally

Makhalanyane

Frossard

et al. 2016

Soil Biology and Biochemistry

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“…Members of both genera have been isolated from these mat communities (Brock and Freeze, 1969 ; Ward et al, 1997 ; Thiel et al, 2015 ). OTU-21 was identified as a relative of Meiothermus ruber , a member of which, strain A, has previously been isolated from an enrichment culture originally obtained from the microbial mats at Octopus Spring and whose genome has been sequenced (Thiel et al, 2015 ). Tetranucleotide frequency-based binning of contigs >10 kb led to a 1.3-Mb partial genome (Bin-18, Table 3 ) for this moderately thermophilic, aerobic, and heterotrophic bacterium.…”

Section: Resultsmentioning

confidence: 99%

The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. I. Microbial Diversity Based on 16S rRNA Gene Amplicons and Metagenomic Sequencing

et al. 2016

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Microbial-mat communities in the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin at Yellowstone National Park have been studied for nearly 50 years. The emphasis has mostly focused on the chlorophototrophic bacterial organisms of the phyla Cyanobacteria and Chloroflexi. In contrast, the diversity and metabolic functions of the heterotrophic community in the microoxic/anoxic region of the mat are not well understood. In this study we analyzed the orange-colored undermat of the microbial community of Mushroom Spring using metagenomic and rRNA-amplicon (iTag) analyses. Our analyses disclosed a highly diverse community exhibiting a high degree of unevenness, strongly dominated by a single taxon, the filamentous anoxygenic phototroph, Roseiflexus spp. The second most abundant organisms belonged to the Thermotogae, which have been hypothesized to be a major source of H 2 from fermentation that could enable photomixotrophic metabolism by Chloroflexus and Roseiflexus spp. Other abundant organisms include two members of the Armatimonadetes (OP10); Thermocrinis sp.; and phototrophic and heterotrophic members of the Chloroflexi. Further, an Atribacteria (OP9/JS1) member; a sulfate-reducing Thermodesulfovibrio sp.; a Planctomycetes member; a member of the EM3 group tentatively affiliated with the Thermotogae, as well as a putative member of the Arminicenantes (OP8) represented ≥1% of the reads. Archaea were not abundant in the iTag analysis, and no metagenomic bin representing an archaeon was identified. A high microdiversity of 16S rRNA gene sequences was identified for the dominant taxon, Roseiflexus spp. Previous studies demonstrated that highly similar Synechococcus variants in the upper layer of the mats represent ecological species populations with specific ecological adaptations. This study suggests that similar putative ecotypes specifically adapted to different niches occur within the undermat community, particularly for Roseiflexus spp.

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“…T. elongatus was isolated from a cyanobacterial mat environment near Beppu, Japan (Yamaoka et al, ). M. ruber Strain A is an aerobic, heterotrophic, thermophile that was isolated from an enrichment culture originally sampled from the cyanobacterial mat inhabiting Octopus Spring in Yellowstone National Park (WY, USA) (Thiel et al, ). It shares 98.6% nucleotide identity to the 16S rRNA gene sequence of M. ruber DSM 1279 (Loginova et al, ) and displays strong functional relatedness with regard to central carbon and energy metabolism genes (Thiel et al, ).…”

Section: Protocols Of Network Reconstruction From Single Genomesmentioning

confidence: 99%

Microbial Community Metabolic Modeling: A Community Data‐Driven Network Reconstruction

et al. 2016

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Metabolic network modeling of microbial communities provides an in‐depth understanding of community‐wide metabolic and regulatory processes. Compared to single organism analyses, community metabolic network modeling is more complex because it needs to account for interspecies interactions. To date, most approaches focus on reconstruction of high‐quality individual networks so that, when combined, they can predict community behaviors as a result of interspecies interactions. However, this conventional method becomes ineffective for communities whose members are not well characterized and cannot be experimentally interrogated in isolation. Here, we tested a new approach that uses community‐level data as a critical input for the network reconstruction process. This method focuses on directly predicting interspecies metabolic interactions in a community, when axenic information is insufficient. We validated our method through the case study of a bacterial photoautotroph–heterotroph consortium that was used to provide data needed for a community‐level metabolic network reconstruction. Resulting simulations provided experimentally validated predictions of how a photoautotrophic cyanobacterium supports the growth of an obligate heterotrophic species by providing organic carbon and nitrogen sources. J. Cell. Physiol. 231: 2339–2345, 2016. © 2016 The Authors. Journal of Cellular Physiology Published by Wiley Periodicals, Inc.

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Draft Genome Sequence of the Deinococcus-Thermus Bacterium Meiothermus ruber Strain A

Cited by 8 publications

References 10 publications

Antarctic microbial communities are functionally redundant, adapted and resistant to short term temperature perturbations

Antarctic microbial communities are functionally redundant, adapted and resistant to short term temperature perturbations

The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. I. Microbial Diversity Based on 16S rRNA Gene Amplicons and Metagenomic Sequencing

Microbial Community Metabolic Modeling: A Community Data‐Driven Network Reconstruction

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