Project description:Spirosoma montaniterrae DY10T is an uncharacterized radiation-resistanct bacteria isolated from soil in South Korea. In order to identify the underlying mechanisms involved in UVC-resistance, we generated time-series transcriptome data with UVC radiation and analyzed data with computational methods.
Project description:Analysis of aquatic microbial communities revealed that parts of its diversity consist of bacteria with cell sizes of ~0.1 μm. Such bacteria can show genomic reductions and metabolic dependencies with other bacteria. So far, no study investigated if such bacteria exist in terrestrial environments e.g. soil. Here, we show that such bacteria also exist in soil. The isolated bacteria was identified as Hylemonella gracilis.Co-culture assays with phylogenetically different soil bacteria revealed that H. gracilis grows better when co-cultured with other soil bacteria. Transcriptomics and metabolomics showed that H. gracilis was able to change gene expression, behavior, and biochemistry of the interacting bacteria without direct contact. Our study revealed that bacteria are present in soil that can pass through 0.1 µm filters. Such bacteria may have been overlooked in previous research on soil microbial communities and may contribute to the symbiosis of soil bacterial communities.
Project description:Some soil bacteria promote plant growth, including Pseudomonas species. With this approach we detected significant changes in Arabidopsis genes related to primary metabolism that were induced by the bacteria.
Project description:Negatives effects induced by exposure to ultra-violet (UV) radiation are well known. Nevertheless the modes of action of UV radiation are not well understood, in particular in soil invertebrates. In the present work, the effects of two UV doses (mimicking worst case scenarios in earth crust) on gene expression profile of Enchytraeus crypticus (Enchytraeidae, Oligochaeta) were investigated using the high-throughput 4 x 44K microarray developed for the species.
Project description:Commensal bacteria shape the gut immune system. Colonization bacteria increase the frequency of regulatory T cells, however, the molecular mechanisms are not yet known. To reveal the mechanism, we isolated naïve CD4+ T cells from the spleen of C57BL/6 mice and cultured the cells under Treg-inducing condition culture in the presence or absence of butyrate, a metabolite produced by commensal bacteria.
Project description:Commensal bacteria shapes gut immune system. Colonization bacteria increase the frequency of regulatory T cells, however, the molecular mechanisms has not yet been unknown. To reveal the mechanism, we isolated Naïve CD4+ T cells from spleen of C57BL/6 mice and cultured the cells under Treg-inducing condition culture in the presence or absence of butyrate, a metabolite produced by commensal bacteria.
Project description:In search of AP-3 resistant genes, ATCC 31280△ansaA (inactivation of ansamitocin pksA, in avoiding of the interruption of endogenous generated AP-3) were cultured under the addition of 0, 50, 100 and 200 mg/L exogenous AP-3 for 24 h and collected, for strains under 200 mg/L AP-3, samples after 48 h and 72 h were also collected, and the RNA samples were collected and sent for sequencing.
Project description:In prospective human exploration of outer space, the need to maintain a species over several generations under changed gravity conditions may arise. This paper reports the analysis of the third generation of fruit fly Drosophila melanogaster obtained during the 44.5-day space flight (Foton-M4 satellite, 2014, Russia), followed by the fourth generation on Earth and the fifth generation under conditions of a 12-day space flight (2014, in the Russian Segment of the ISS). The obtained results show that it is possible to obtain the third-fifth generations of a complex multicellular Earth organism under changed gravity conditions (in the cycle “weightlessness – Earth – weightlessness”), which preserves fertility and normal development. However, there were a number of changes in the expression levels and content of cytoskeletal proteins that are the key components of the spindle apparatus and the contractile ring of cells.
Project description:Background: The soil environment is responsible for sustaining most terrestrial plant life on earth, yet we know surprisingly little about the important functions carried out by diverse microbial communities in soil. Soil microbes that inhabit the channels of decaying root systems, the detritusphere, are likely to be essential for plant growth and health, as these channels are the preferred locations of new root growth. Understanding the microbial metagenome of the detritusphere and how it responds to agricultural management such as crop rotations and soil tillage will be vital for improving global food production. Methods: The rhizosphere soils of wheat and chickpea growing under + and - decaying root were collected for metagenomics sequencing. A gene catalogue was established by de novo assembling metagenomic sequencing. Genes abundance was compared between bulk soil and rhizosphere soils under different treatments. Conclusions: The study describes the diversity and functional capacity of a high-quality soil microbial metagenome. The results demonstrate the contribution of the microbiome from decaying root in determining the metagenome of developing root systems, which is fundamental to plant growth, since roots preferentially inhabit previous root channels. Modifications in root microbial function through soil management, can ultimately govern plant health, productivity and food security.
Project description:Desert microbial communities live in a pulsed ecosystem shaped by isolated and rare precipitation events. The Namib desert is one of the oldest continuously hyperarid ecosystems on Earth. In this study, surface microbial communities of open soils (without sheltering features like rocks, vegetation or biological soil crusts) are analysed. We designed an artificial rainfall experiment where a 7x7 (3.5 x 3.5 m) plot remained dry while an adjacent one received a 30 mm simulated rain. Samples were taken randomly in parallel from both plots at 10 min, 1 h, 3 h, 7 h, 24 h and 7 days after the watering moment. Duplicate libraries were generated from total (rRNA depleted) RNA and sequenced 2x150 bp in an Illumina Hiseq 4000 instrument.