Soil Metagenome Sequences from a Geothermal Site at Mount Melbourne in Antarctica.
Ontology highlight
ABSTRACT:
SUBMITTER: Park M
PROVIDER: S-EPMC7953305 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Fumarolic Ice caves on Antarctica's Mt. Erebus contain a dark oligotrophic volcanic ecosystem (DOVE) and represent a deep biosphere habitat that can provide insight into microbial communities that utilize energy sources other than photosynthesis. The community assembly and role of fungi in these environments remains largely unknown. However, these habitats could be relatively easily contaminated during human visits. Sixty-one species of fungi were identified from soil clone libraries originating from Warren Cave, a DOVE on Mt. Erebus. The species diversity was greater than has been found in the nearby McMurdo Dry Valleys oligotrophic soil. A relatively large proportion of the clones represented Malassezia species (37% of Basidomycota identified). These fungi are associated with skin surfaces of animals and require high lipid content for growth, indicating that contamination may have occurred through the few and episodic human visits in this particular cave. These findings highlight the importance of fungi to DOVE environments as well as their potential use for identifying contamination by humans. The latter offers compelling evidence suggesting more strict management of these valuable research areas.
| S-EPMC3960884 | biostudies-literature
Project description:The Yellowstone geothermal complex contains over 10,000 diverse geothermal features that host numerous phylogenetically deeply rooted and poorly understood archaea, bacteria, and viruses. Microbial communities in high-temperature environments are generally less diverse than soil, marine, sediment, or lake habitats and therefore offer a tremendous opportunity for studying the structure and function of different model microbial communities using environmental metagenomics. One of the broader goals of this study was to establish linkages among microbial distribution, metabolic potential, and environmental variables. Twenty geochemically distinct geothermal ecosystems representing a broad spectrum of Yellowstone hot-spring environments were used for metagenomic and geochemical analysis and included approximately equal numbers of: (1) phototrophic mats, (2) "filamentous streamer" communities, and (3) archaeal-dominated sediments. The metagenomes were analyzed using a suite of complementary and integrative bioinformatic tools, including phylogenetic and functional analysis of both individual sequence reads and assemblies of predominant phylotypes. This volume identifies major environmental determinants of a large number of thermophilic microbial lineages, many of which have not been fully described in the literature nor previously cultivated to enable functional and genomic analyses. Moreover, protein family abundance comparisons and in-depth analyses of specific genes and metabolic pathways relevant to these hot-spring environments reveal hallmark signatures of metabolic capabilities that parallel the distribution of phylotypes across specific types of geochemical environments.
| S-EPMC3644721 | biostudies-literature
Project description:Active volcanoes in Antarctica contrast with their predominantly cold surroundings, resulting in environmental conditions capable of selecting for versatile and extremely diverse microbial communities. This is especially true on Deception Island, where geothermal, marine, and polar environments combine to create an extraordinary range of environmental conditions. Our main goal in this study was to understand how microbial community structure is shaped by gradients of temperature, salinity, and geochemistry in polar marine volcanoes. Thereby, we collected surface sediment samples associated with fumaroles and glaciers at two sites on Deception, with temperatures ranging from 0 to 98°C. Sequencing of the 16S rRNA gene was performed to assess the composition and diversity of Bacteria and Archaea. Our results revealed that Deception harbors a combination of taxonomic groups commonly found both in cold and geothermal environments of continental Antarctica, and also groups normally identified at deep and shallow-sea hydrothermal vents, such as hyperthermophilic archaea. We observed a clear separation in microbial community structure across environmental gradients, suggesting that microbial community structure is strongly niche driven on Deception. Bacterial community structure was significantly associated with temperature, pH, salinity, and chemical composition; in contrast, archaeal community structure was strongly associated only with temperature. Our work suggests that Deception represents a peculiar "open-air" laboratory to elucidate central questions regarding molecular adaptability, microbial evolution, and biogeography of extremophiles in polar regions.
| S-EPMC5949364 | biostudies-literature
Project description:BackgroundWith genome sequencing becoming more and more affordable, environmental shotgun sequencing of the microorganisms present in an environment generates a challenging amount of sequence data for the scientific community. These sequence data enable the diversity of the microbial world and the metabolic pathways within an environment to be investigated, a previously unthinkable achievement when using traditional approaches. DNA sequence data assembled from extracts of 0.8 microm filtered Sargasso seawater unveiled an unprecedented glimpse of marine prokaryotic diversity and gene content. Serendipitously, many sequences representing picoeukaryotes (cell size <2 microm) were also present within this dataset. We investigated the picoeukaryotic diversity of this database by searching sequences containing homologs of eight nuclear anchor genes that are well conserved throughout the eukaryotic lineage, as well as one chloroplastic and one mitochondrial gene.ResultsWe found up to 41 distinct eukaryotic scaffolds, with a broad phylogenetic spread on the eukaryotic tree of life. The average eukaryotic scaffold size is 2,909 bp, with one gap every 1,253 bp. Strikingly, the AT frequency of the eukaryotic sequences (51.4%) is significantly lower than the average AT frequency of the metagenome (61.4%). This represents 4% to 18% of the estimated prokaryotic diversity, depending on the average prokaryotic versus eukaryotic genome size ratio.ConclusionDespite similar cell size, eukaryotic sequences of the Sargasso Sea metagenome have higher GC content, suggesting that different environmental pressures affect the evolution of their base composition.
| S-EPMC2395239 | biostudies-literature
Project description:Eremiobacterota assembled from Antarctica soils
| PRJNA587560 | ENA
Project description:BackgroundAntarctica and its unique biodiversity are increasingly at risk from the effects of global climate change and other human influences. A significant recent element underpinning strategies for Antarctic conservation has been the development of a system of Antarctic Conservation Biogeographic Regions (ACBRs). The datasets supporting this classification are, however, dominated by eukaryotic taxa, with contributions from the bacterial domain restricted to Actinomycetota and Cyanobacteriota. Nevertheless, the ice-free areas of the Antarctic continent and the sub-Antarctic islands are dominated in terms of diversity by bacteria. Our study aims to generate a comprehensive phylogenetic dataset of Antarctic bacteria with wide geographical coverage on the continent and sub-Antarctic islands, to investigate whether bacterial diversity and distribution is reflected in the current ACBRs.ResultsSoil bacterial diversity and community composition did not fully conform with the ACBR classification. Although 19% of the variability was explained by this classification, the largest differences in bacterial community composition were between the broader continental and maritime Antarctic regions, where a degree of structural overlapping within continental and maritime bacterial communities was apparent, not fully reflecting the division into separate ACBRs. Strong divergence in soil bacterial community composition was also apparent between the Antarctic/sub-Antarctic islands and the Antarctic mainland. Bacterial communities were partially shaped by bioclimatic conditions, with 28% of dominant genera showing habitat preferences connected to at least one of the bioclimatic variables included in our analyses. These genera were also reported as indicator taxa for the ACBRs.ConclusionsOverall, our data indicate that the current ACBR subdivision of the Antarctic continent does not fully reflect bacterial distribution and diversity in Antarctica. We observed considerable overlap in the structure of soil bacterial communities within the maritime Antarctic region and within the continental Antarctic region. Our results also suggest that bacterial communities might be impacted by regional climatic and other environmental changes. The dataset developed in this study provides a comprehensive baseline that will provide a valuable tool for biodiversity conservation efforts on the continent. Further studies are clearly required, and we emphasize the need for more extensive campaigns to systematically sample and characterize Antarctic and sub-Antarctic soil microbial communities. Video Abstract.
| S-EPMC10785390 | biostudies-literature
Project description:The metagenomes of complex microbial communities are rich sources of novel biocatalysts. We exploited the metagenome of a mixed microbial population for isolation of more than 15 different genes encoding novel biocatalysts by using a combined cultivation and direct cloning strategy. A 16S rRNA sequence analysis revealed the presence of hitherto uncultured microbes closely related to the genera Pseudomonas, Agrobacterium, Xanthomonas, Microbulbifer, and Janthinobacterium. Total genomic DNA from this bacterial community was used to construct cosmid DNA libraries, which were functionally searched for novel enzymes of biotechnological value. Our searches in combination with cosmid sequencing resulted in identification of four clones encoding 12 putative agarase genes, most of which were organized in clusters consisting of two or three genes. Interestingly, nine of these agarase genes probably originated from gene duplications. Furthermore, we identified by DNA sequencing several other biocatalyst-encoding genes, including genes encoding a putative stereoselective amidase (amiA), two cellulases (gnuB and uvs080), an alpha-amylase (amyA), a 1,4-alpha-glucan branching enzyme (amyB), and two pectate lyases (pelA and uvs119). Also, a conserved cluster of two lipase genes was identified, which was linked to genes encoding a type I secretion system. The novel gene aguB was overexpressed in Escherichia coli, and the enzyme activities were determined. Finally, we describe more than 162 kb of DNA sequence that provides a strong platform for further characterization of this microbial consortium.
| S-EPMC201203 | biostudies-literature
Project description:Declining soil fertility continues to hinder agricultural production especially among resource-constrained smallholder farmers in sub-Saharan Africa, prompting for evaluation of the strategies used by these farming communities. In this study, we assess soil fertility management among smallholder farmers in Mount Kenya East region. The aim is to examine underlying factors conditioning the uptake of integrated soil fertility management (ISFM) practices in this region; determine the adoption relationship between the practices; and to cluster these techniques. Data for this study was collected between January-March 2019 through a household survey based on a farm household questionnaire and complemented with semi-structured interview with farmers and extension officers. Statistical analyses were generated using SPSS. We use hierarchical clustering analysis to visualize ISFM combination patterns, and correlation matrix in factor analysis to determine the inter-relationship between different ISFM practices. Fisher's exact test and Welch's t-test were used to examine the association between explanatory variables and adoption of ISFM practices. Results show that the decision to invest in fertility practices was correlated with a number of farmers' socio-economic, farm-related factors and institutional characteristics. Fertilizer application correlated significantly with manure use, agroforestry and minimum tillage. ISFM techniques were separated into 3 sets following Ward's hierarchical clustering, namely, manure, fertilizer use and agroforestry (cluster 1 or C1), slash-no-burn, residue burn and fallowing (C2); and residue application and minimum tillage (C3). The study recommends creation of an enabling environment including innovative financing opportunities to facilitate farmers' investment capacities in ISFM and cushion them from potential income loss resulting from implementation of some technologies.
| S-EPMC8010630 | biostudies-literature
Project description:Microbial diversity in geothermal waters of the Unkeshwar hot springs in Maharashtra, India, was studied using 16S rRNA amplicon metagenomic sequencing. Taxonomic analysis revealed the presence of Bacteroidetes, Proteobacteria, Cyanobacteria, Actinobacteria, Archeae, and OD1 phyla. Metabolic function prediction analysis indicated a battery of biological information systems indicating rich and novel microbial diversity, with potential biotechnological applications in this niche.
| S-EPMC4767922 | biostudies-literature
Project description:The Arecibo Observatory (AO) located in Arecibo, Puerto Rico, is the most sensitive, powerful and active planetary radar system in the world [1]. One of its principal components is the 305 m-diameter spherical reflector dish (AORD), which is exposed to high frequency electromagnetic waves. To unravel the microbial communities that inhabit this environment, soil samples from underneath the AORD were collected, DNA extracted, and sequenced using Illumina MiSeq. Taxonomic and functional profiles were generated using the MG-RAST server. The most abundant domain was Bacteria (91%), followed by Virus (8%), Archaea (0.9%) and Eukaryota (0.9%). The most abundant phylum was Proteobacteria (54%), followed by Actinobacteria (8%), Bacteroidetes (5%) and Firmicutes (4%). In terms of functions, the most abundant among the metagenome corresponded to phages, transposable elements and plasmids (16%), followed by clustering-based subsystems (11%), carbohydrates (10%), and amino acids and derivatives (9%). This is the first soil metagenomic dataset from dish antennas and radar systems, specifically, underneath the AORD. Data can be used to explore the effect of high frequency electromagnetic waves in soil microbial composition, as well as the possibility of finding bioprospects with potential biomedical and biotechnological applications.
| S-EPMC6920479 | biostudies-literature