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Microbial and Functional Diversity within the Phyllosphere of Espeletia sp. in Andean High Mountain Ecosystems

ABSTRACT: Functional profiles predicted based on taxonomic affiliations differed from those obtained by GeoChip microarray analysis, which separated community functional capacity based on plant location. The identified metabolic pathways provided insight regarding microbial strategies for colonization and survival in these ecosystems.

ORGANISM(S): Archaea Eukaryota Bacteria plant metagenome Viruses

PROVIDER: GSE70539 | GEO | 2015/07/09

SECONDARY ACCESSION(S): PRJNA289256

REPOSITORIES: GEO

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Microbial and Functional Diversity within the Phyllosphere of Espeletia sp. in Andean High Mountain Ecosystems

Project description:Functional profiles predicted based on taxonomic affiliations differed from those obtained by GeoChip microarray analysis, which separated community functional capacity based on plant location. The identified metabolic pathways provided insight regarding microbial strategies for colonization and survival in these ecosystems. Sixteen samples analyzed.

2015-07-09 | E-GEOD-70539 | biostudies-arrayexpress

Climate warming and nutrient enrichment jointly affect microbial functional potentials important to nutrient cycling in shallow-lake mesocosms

Project description:Here, we applied a microarray-based metagenomics technology termed GeoChip 5.0 to investigate spring microbial functional genes in mesocosm-simulated shallow lake ecosystems having been undergoing nutrient enrichment and warming for nine years.

2020-12-30 | GSE155582 | GEO

CAZyChip: Dynamic assessment of exploration of glycoside hydrolases in microbial diversity ecosystems.

Project description:Microorganisms constitute a reservoir of enzymes involved in environmental carbon cycling and degradation of plant polysaccharides since they produce a vast variety of glycoside hydrolases. The CAZyChip was developed to allow a rapid characterization at transcriptomic level of these GHs and to identify enzymes acting on hydrolysis of polysaccharide or glycans. This DNA biochip contains the signature of 55,220 bacterial GHs available in the CAZy database. Probes were designed using two softwares and microarrays were directly synthetized using the in situ ink-jet technology. CAZyChip specificity and reproducibility was validated by hybridization of known GHs RNA extracted from recombinant E. coli strains, previously characterized by a functional metagenomic approach. The GHs arsenal was also studied in bioprocess conditions using rumen derived microbiota. The CAZyChip appears to be a user friendly tool for profiling the expression of a large variety of GHs. It can be used to study temporal variations of functional diversity, thereby facilitating the identification of new efficient candidates for enzymatic conversions from various ecosystems.

2016-12-01 | GSE80173 | GEO

Overall functional diversity of microbial communities in three full-scale activated sludge bioreactors

Project description:Understanding microbial community diversity is thought to be crucial for improving process functioning and stabilities of wastewater treatment systems. However, current studies largely focus on taxonomic groups based on 16S rRNA, which are not necessarily linked to functioning, or a few selected functional genes. Here we launched a study to profile the overall functional genes of microbial communities in three full-scale wastewater treatment systems. Triplicate activated sludge samples from each system were analyzed using a high-throughput metagenomics tool named GeoChip 4.2, resulting in the detection of 38,507 to 40,647 functional genes. A high similarity of 75.5% to 79.7% shared genes was noted among the nine samples. Moreover, correlation analyses showed that the abundances of a wide array of functional genes were associated with system performances. For example, the abundances of overall nitrogen cycling genes had a strong correlation to total nitrogen (TN) removal rates (r = 0.7647, P < 0.01). The abundances of overall carbon cycling genes were moderately correlated with COD removal rates (r = 0.6515, P < 0.01). Lastly, we found that influent chemical oxygen demand (COD inf) and total phosphorus concentrations (TP inf), and dissolved oxygen (DO) concentrations were key environmental factors shaping the overall functional genes. Together, the results revealed vast functional gene diversity and some links between the functional gene compositions and microbe-mediated processes.

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The Microbial Gene Diversity along an Elevation Gradient of the Tibetan alpine meadow

Project description:Tibet is one of the most threatened regions by climate warming, thus understanding how its microbial communities function may be of high importance for predicting microbial responses to climate changes. Here, we report a study to profile soil microbial structural genes, which infers functional roles of microbial communities, aiming to explore potential microbial responses to climate changes via a strategy of space-for-time substitution. Using a microarray-based metagenomics tool named GeoChip 4.0, we showed that microbial communities were distinct for most but not all of the sites. Substantial variations were apparent in stress, N and C cycling genes, but they were in line with the functional roles of these genes. sixty-three samples were collected from four elevations (3200,3400,3600 and 3800 m) along a Tibetan alpine meadow; Three replicates in each treatment

2013-11-16 | E-GEOD-52425 | biostudies-arrayexpress

The functional diversity of stream microbes on mountainsides across Eurasia based on Geochip 4.0

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2020-06-22 | GSE128826 | GEO

The microbial functional structure along an elevation gradient of the Shennongjia Mountain as characterized by GeoChip

Project description:Known as “The Oriental Botanic Garden” and the natural gene bank of biological species, Shennongjia is one of the most biologically diverse areas in China and a member of UNESCO's World Network of Biosphere Reserves. The macro-organism resources of shennongjia have been deeply explored. However, the microbial community structure was scarcely detected. In this study, we aim to detedect the microbial community along six sites of Shennonajia Mountain and explore the major controlling factor in shaping microbial community with a microarray-based metagenomics tool named GeoChip 4.2.

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The microbial functional gene diversity in anaerobic digesters under different organic loadings

Project description:Anaerobic digestion is a popular and effective microbial process for waste treatment. The performance of anaerobic digestion processes is contingent on the balance of the microbial food web in utilizing various substrates. Recently, co-digestion, i.e., supplementing the primary substrate with an organic-rich co-substrate has been exploited to improve waste treatment efficiency. Yet the potential effects of elevated organic loading on microbial functional gene community remains elusive. In this study, functional gene array (GeoChip 5.0) was used to assess the response of microbial community to the addition of poultry waste in anaerobic digesters treating dairy manure. Consistent with 16S rRNA gene sequences data, GeoChip data showed that microbial community compositions were significantly shifted in favor of copiotrophic populations by co-digestion, as taxa with higher rRNA gene copy number such as Bacilli were enriched. The acetoclastic methanogen Methanosarcina was also enriched, while Methanosaeta was unaltered but more abundant than Methanosarcina throughout the study period. The microbial functional diversity involved in anaerobic digestion were also increased under co-digestion.

2017-01-12 | GSE93419 | GEO

Geochip data of soil microbial community of biomes from three termperature zones

Project description:Here, we applied a microarray-based metagenomics technology termed GeoChip 5.0 to examined functional gene structure of microbes in three biomes, including boreal, temperate and tropical area.

2024-05-10 | GSE172195 | GEO

The microbial functional structure along an elevation gradient of the Shennongjia Mountain as characterized by GeoChip

Project description:Known as M-bM-^@M-^\The Oriental Botanic GardenM-bM-^@M-^] and the natural gene bank of biological species, Shennongjia is one of the most biologically diverse areas in China and a member of UNESCO's World Network of Biosphere Reserves. The macro-organism resources of shennongjia have been deeply explored. However, the microbial community structure was scarcely detected. In this study, we aim to detedect the microbial community along six sites of Shennonajia Mountain and explore the major controlling factor in shaping microbial community with a microarray-based metagenomics tool named GeoChip 4.2. Seventy-three samples were collected from six sites along the Shennongjia Mountain, with 5-15 replicates in every site

2014-06-13 | E-GEOD-58433 | biostudies-arrayexpress

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