Gemmatimonas aurantiaca T-27
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ABSTRACT:
PROVIDER: PRJDA18501 | ENA |
REPOSITORIES: ENA
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Project description:Gemmatimonas phototrophica is the only phototrophic member of the recently discovered bacterial phylum Gemmatimonadetes. It was isolated from a freshwater lake in the Gobi desert and first described in 2014. So far, Gemmatimonas phototrophica is the only bacterium to have received a complete set of photosynthesis-related genes by horizontal gene transfer from an ancient phototrophic species from the phylum Proteobacteria. This organism illustrates the possibility for engineering phototrophic capability in a non-phototrophic organism and is therefore of great interest to the field of synthetic biology. The structure of the photosynthetic reaction center-light harvesting 1 complex is under investigation by cryo-EM. Proteomic analysis verified the identities of the expected protein components of this complex and, additionally revealed polypeptides that were previously undiscovered and could be mapped to the cryo-EM images.
2022-04-04 | PXD024609 | Pride
Project description:Bacteria belonging to phylum Gemmatimonadetes are found in a wide variety of environments and are particularly abundant in soils. To date, only two Gemmatimonadetes strains have been characterized. Here we report the complete genome sequence and methylation pattern of Gemmatirosa kalamazoonensis KBS708 (ATCC BAA-2150; NCCB 100411), the first characterized Gemmatimondetes strain isolated from soil.
2014-03-12 | GSE55390 | GEO
Project description:Bacteria belonging to phylum Gemmatimonadetes are found in a wide variety of environments and are particularly abundant in soils. To date, only two Gemmatimonadetes strains have been characterized. Here we report the complete genome sequence and methylation pattern of Gemmatirosa kalamazoonensis KBS708 (ATCC BAA-2150; NCCB 100411), the first characterized Gemmatimondetes strain isolated from soil. Examination of the methylome of Gemmatirosa kalamazoonenis KBS708 using kinetic data from single-molecule, real-time (SMRT) sequencing on the PacBio RS
2014-03-12 | E-GEOD-55390 | biostudies-arrayexpress
Project description:N2O-reducing organisms with nitrous oxide reductases (NosZ) are known as the only biological sink of N2O in the environment. Among the most abundant nosZ genes found in the environment are nosZ genes affiliated with the understudied Gemmatimonadetes phylum. In this study, a unique regulatory mechanism of N2O reduction in Gemmatimonas aurantiaca strain T-27, an isolate affiliated with the Gemmatimonadetes phylum, was examined. Strain T-27 was incubated with N2O and/or O2 as the electron acceptor. Significant N2O reduction was observed only when O2 was initially present. When batch cultures of strain T-27 were amended with O2 and N2O, N2O reduction commenced after O2 was depleted. In a long-term incubation with the addition of N2O upon depletion, the N2O reduction rate decreased over time and came to an eventual stop. Spiking of the culture with O2 resulted in the resuscitation of N2O reduction activity, supporting the hypothesis that N2O reduction by strain T-27 required the transient presence of O2 The highest level of nosZ transcription (8.97 nosZ transcripts/recA transcript) was observed immediately after O2 depletion, and transcription decreased ∼25-fold within 85 h, supporting the observed phenotype. The observed difference between responses of strain T-27 cultures amended with and without N2O to O2 starvation suggested that N2O helped sustain the viability of strain T-27 during temporary anoxia, although N2O reduction was not coupled to growth. The findings in this study suggest that obligate aerobic microorganisms with nosZ genes may utilize N2O as a temporary surrogate for O2 to survive periodic anoxia.IMPORTANCE Emission of N2O, a potent greenhouse gas and ozone depletion agent, from the soil environment is largely determined by microbial sources and sinks. N2O reduction by organisms with N2O reductases (NosZ) is the only known biological sink of N2O at environmentally relevant concentrations (up to ∼1,000 parts per million by volume [ppmv]). Although a large fraction of nosZ genes recovered from soil is affiliated with nosZ found in the genomes of the obligate aerobic phylum Gemmatimonadetes, N2O reduction has not yet been confirmed in any of these organisms. This study demonstrates that N2O is reduced by an obligate aerobic bacterium, Gemmatimonas aurantiaca strain T-27, and suggests a novel regulation mechanism for N2O reduction in this organism, which may also be applicable to other obligate aerobic organisms possessing nosZ genes. We expect that these findings will significantly advance the understanding of N2O dynamics in environments with frequent transitions between oxic and anoxic conditions.
| S-EPMC5452805 | biostudies-literature
Project description:Agricultural soil is the primary N2O sink limiting the emission of N2O gas into the atmosphere. Although Gemmatimonadetes bacteria are abundant in agricultural soils, limited information is currently available on N2O reduction by Gemmatimonadetes bacteria. Therefore, the effects of pH and temperature on N2O reduction activities and affinity constants for N2O reduction were examined by performing batch experiments using an isolate of Gemmatimonadetes bacteria, Gemmatimonas aurantiaca (NBRC100505T). G. aurantiaca reduced N2O at pH 5-9 and 4-50°C, with the highest activity being observed at pH 7 and 30°C. The affinity constant of G. aurantiaca cells for N2O was 4.4 μM. The abundance and diversity of the Gemmatimonadetes 16S rRNA gene and nosZ encoding nitrous oxide reductase in agricultural soil samples were also investigated by quantitative PCR (qPCR) and amplicon sequencing ana-lyses. Four N2O-reducing agricultural soil samples were assessed, and the copy numbers of the Gemmatimonadetes 16S rRNA gene (clades G1 and G3), nosZ DNA, and nosZ mRNA were 8.62-9.65×108, 5.35-7.15×108, and 2.23-4.31×109 copies (g dry soil)-1, respectively. The abundance of the nosZ mRNA of Gemmatimonadetes bacteria and OTU91, OUT332, and OTU122 correlated with the N2O reduction rates of the soil samples tested, suggesting N2O reduction by Gemmatimonadetes bacteria. Gemmatimonadetes 16S rRNA gene reads affiliated with OTU4572 and OTU3759 were predominant among the soil samples examined, and these Gemmatimonadetes OTUs have been identified in various types of soil samples.
| S-EPMC9530729 | biostudies-literature
Project description:Whole genome sequencing of a bacterium strain T265 affiliated with the phylum Gemmatimonadetes
| PRJDB11738 | ENA
Project description:Nanosynbacter lyticus type strain TM7x was the first cultivated member of the broadly prevelent, but poorly udnerstood Candidate Phylum Radiation super-phylum. TM7x was shown to be an obligate epibiont with a host range including Schaalia odontolyticus strain XH001. The process of infecting a naive host goes through multiple phases, from an initial binding and interaction phase we call the initial encounter, to a rapid die off of infected host cells, killing phase, followed by regrowth of the host cells, regrowth phase, and finally a stable symbiosis between the species, stable symbiosis.To obtain a better understanding of the process by which these species establish a stable symbiosis, we measured the transcriptome using RNA sequencing across the course of infection. We sampled infected host, XH001/TM7x, during the initial interaction, regrowth, and after attaining stable symbiosis, as well as naive host controls grown under the same culture conditions.
2022-07-18 | GSE196744 | GEO
Project description:Methylome of soil bacterium Gemmatirosa kalamazoonensis KBS708, a member of the rarely cultivated Gemmatimonadetes phylum
| PRJNA241014 | ENA
Project description:Mucor species belongs to the Mucorales order within the phylum Mucoromycota, an early diverging fungal lineage. The purpose of this study was to investigate at the transcriptome scale the similarities and differences that could be linked to different lifestyles. Five strains pertaining to five species were studied: M. fuscus and M. lanceolatus, two species used in cheese ripening, M. racemosus, a recurrent cheese spoiler sometimes described as an opportunistic pathogen, M. circinelloides, often described as an opportunistic pathogen and M. endophyticus, a plant endophyte species.
2018-09-01 | E-MTAB-6453 | biostudies-arrayexpress