The first representative of the globally widespread subdivision 6 Acidobacteria, Vicinamibacter silvestris gen. nov., sp. nov., isolated from subtropical savannah soil

Huber, Katharina J.; Geppert, Alicia; Wanner, Gerhard; Foesel, Bärbel U.; Wüst, Pia K.; Overmann, Jörg

doi:10.1099/ijsem.0.001131

Cited by 66 publications

(40 citation statements)

References 67 publications

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“…Yet the vast majority of acidobacteria detected in soils based on culture dependent and independent approaches are members of subdivisions 1, 2, 3, 4, 5 and 6 (Janssen, 2006;Jones et al, 2009). Many strains in culture collections stem from these aforementioned ubiquitous subdivisions and were originally isolated from soil environments such as tundra soils (M€ annist€ o et al, 2012a), peatland soil Dedysh et al, 2012), agricultural soil or meadow grassland soil Eichorst and Kuske, 2012;Foesel et al, 2013), forest soils Llad o et al, 2016) and subtropical soil (Huber et al, 2016). Therefore, it is particularly pertinent to better understand these environmentally relevant soil strains.…”

Section: Introductionmentioning

confidence: 99%

Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments

Eichorst

Trojan

Roux

et al. 2018

Environmental Microbiology

264

180

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SummaryMembers of the phylum Acidobacteria are abundant and ubiquitous across soils. We performed a large‐scale comparative genome analysis spanning subdivisions 1, 3, 4, 6, 8 and 23 (n = 24) with the goal to identify features to help explain their prevalence in soils and understand their ecophysiology. Our analysis revealed that bacteriophage integration events along with transposable and mobile elements influenced the structure and plasticity of these genomes. Low‐ and high‐affinity respiratory oxygen reductases were detected in multiple genomes, suggesting the capacity for growing across different oxygen gradients. Among many genomes, the capacity to use a diverse collection of carbohydrates, as well as inorganic and organic nitrogen sources (such as via extracellular peptidases), was detected – both advantageous traits in environments with fluctuating nutrient environments. We also identified multiple soil acidobacteria with the potential to scavenge atmospheric concentrations of H2, now encompassing mesophilic soil strains within the subdivision 1 and 3, in addition to a previously identified thermophilic strain in subdivision 4. This large‐scale acidobacteria genome analysis reveal traits that provide genomic, physiological and metabolic versatility, presumably allowing flexibility and versatility in the challenging and fluctuating soil environment.

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Section: Introductionmentioning

confidence: 99%

Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments

Eichorst

Trojan

Roux

et al. 2018

Environmental Microbiology

264

180

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“…RNA gene showed 90% similarity to Mailhella massiliensis (Ndongo et al, 2017). The OTU93 recovered in MSP pool represented a member of Acidobacteria, and its 16S RNA gene showed 94% similarity to Vicinamibacter silvestris (Huber et al, 2016); the OTU97 represented an unclassified member of Phycisphaerae and its closest relative is Tepidisphaera mucosa (Kovaleva et al, 2015) (Their 16S rRNA gene similarity is 91%); More interestingly, the OTU98 recovered from MSP pool in this study together with 16S rRNA gene sequences detected in Formosan subterranean termite (Husseneder et al, 2009) and…”

Section: Discussionmentioning

confidence: 50%

“…The OTU21 represented an unclassified member of Proteobacteria , and its 16S RNA gene showed 90% similarity to Mailhella massiliensis (Ndongo et al., ). The OTU93 recovered in MSP pool represented a member of Acidobacteria , and its 16S RNA gene showed 94% similarity to Vicinamibacter silvestris (Huber et al., ); the OTU97 represented an unclassified member of Phycisphaerae and its closest relative is Tepidisphaera mucosa (Kovaleva et al., ) (Their 16S rRNA gene similarity is 91%); More interestingly, the OTU98 recovered from MSP pool in this study together with 16S rRNA gene sequences detected in Formosan subterranean termite (Husseneder et al., ) and Reticulitermes speratus (Hongoh, Ohkuma, & Kudo, ) clustered to a unique lineage of Verrucomicrobia (Figure e). So far, there is not any bacterial culture showing 16S rRNA gene sequence similarity higher than 80% to this unique lineage.…”

Section: Discussionmentioning

confidence: 53%

Harnessing microfluidic streak plate technique to investigate the gut microbiome of Reticulitermes chinensis

et al. 2018

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The termite gut microbiome is a model system to investigate microbial interactions and their associations with host. For decades, extensive research with molecular tools and conventional cultivation method has been carried out to define the microbial diversity in termite gut. Yet, many bacterial groups of the termite gut microbiome have not been successfully cultivated in laboratory. In this study, we adapted the recently developed microfluidic streak plate (MSP) technique for cultivation of termite gut microbial communities at both aerobic and anaerobic conditions. We found that 99 operational taxonomic units (OTUs) were cultivable by MSP approach and 18 OTUs were documented first time for termite gut microbiota. Further analysis of the bacterial diversities derived by culture-dependent MSP approach and culture-independent 16S rRNA gene typing revealed that both methods have bias in recovery of gut microbiota. In total 396 strains were isolated with MSP technique, and potential new taxa at species and/or genus levels were obtained that were phylogenetically related to Burkholderia, Micrococcus, and Dysgonomonas. Results from this study indicate that MSP technique is applicable for cultivating previously unknown and new microbial groups of termite gut microbiota.

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“…Solibacter usitatus Ellin6076” (DSM 22595) were cultivated at 25°C in VL55 media, Geothrix fermentans (DSM 14018) was grown at 32°C in Geobacter medium (M 826, DSMZ media list) and Holophaga foetida (DSM 6591) at 28°C in TMBS4 medium (M 559 from DSMZ media list). The two species of SD6 Acidobacteria were grown as described earlier (Huber et al, 2016; Vieira et al, 2017). …”

Section: Methodsmentioning

confidence: 99%

Pheno- and Genotyping of Hopanoid Production in Acidobacteria

et al. 2017

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Hopanoids are pentacyclic triterpenoid lipids synthesized by different bacterial groups. Methylated hopanoids were believed to be exclusively synthesized by cyanobacteria and aerobic methanotrophs until the genes encoding for the methylation at the C-2 and C-3 position (hpnP and hpnR) were found to be widespread in the bacterial domain, invalidating their use as specific biomarkers. These genes have been detected in the genome of the Acidobacterium “Ca. Koribacter versatilis,” but our knowledge of the synthesis of hopanoids and the presence of genes of their biosynthetic pathway in other member of the Acidobacteria is limited. We analyzed 38 different strains of seven Acidobacteria subdivisions (SDs 1, 3, 4, 6, 8, 10, and 23) for the presence of C30 hopenes and C30+ bacteriohopane polyols (BHPs) using the Rohmer reaction. BHPs and/or C30 hopenes were detected in all strains of SD1 and SD3 but not in SD4 (excepting Chloracidobacterium thermophilum), 6, 8, 10, and 23. This is in good agreement with the presence of genes required for hopanoid biosynthesis in the 31 available whole genomes of cultivated Acidobacteria. All genomes encode the enzymes involved in the non-mevalonate pathway ultimately leading to farnesyl diphosphate but only SD1 and 3 Acidobacteria and C. thermophilum encode all three enzymes required for the synthesis of squalene, its cyclization (shc), and addition and modification of the extended side chain (hpnG, hpnH, hpnI, hpnJ, hpnO). In almost all strains, only tetrafunctionalized BHPs were detected; three strains contained variable relative abundances (up to 45%) of pentafunctionalized BHPs. Only “Ca. K. versatilis” contained methylated hopanoids (i.e., 2,3-dimethyl bishomohopanol), although in low (<10%) amounts. These genes are not present in any other Acidobacterium, consistent with the absence of methylated BHPs in the other examined strains. These data are in agreement with the scattered occurrence of methylated BHPs in other bacterial phyla such as the Alpha-, Beta-, and Gammaproteobacteria and the Cyanobacteria, limiting their biomarker potential. Metagenomes of Acidobacteria were also examined for the presence of genes required for hopanoid biosynthesis. The complete pathway for BHP biosynthesis was evident in SD2 Acidobacteria and a group phylogenetically related to SD1 and SD3, in line with the limited occurrence of BHPs in acidobacterial cultures.

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The first representative of the globally widespread subdivision 6 Acidobacteria, Vicinamibacter silvestris gen. nov., sp. nov., isolated from subtropical savannah soil

Cited by 66 publications

References 67 publications

Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments

Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments

Harnessing microfluidic streak plate technique to investigate the gut microbiome of Reticulitermes chinensis

Pheno- and Genotyping of Hopanoid Production in Acidobacteria

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