GEO DataSets

(Submitter supplied) 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.

Organism:

uncultured soil microorganism; soil metagenome

Type:

Other

Platform:

GPL29739

120 Samples

Download data: TXT

(Submitter supplied) Fire is a crucial event regulating the structure and functioning of many ecosystems. Yet few studies focused on how fire affects both the taxonomic and functional diversity of soil microbial communities, along with plant diversity and soil carbon (C) and nitrogen (N) dynamics. Here, we analyze these effects for a grassland ecosystem 9-months after an experimental fire at the Jasper Ridge Global Change Experiment (JRGCE) site in California, USA. more...

Organism:

soil metagenome; uncultured soil microorganism

Type:

Other

Platform:

GPL24290

64 Samples

Download data: TXT

(Submitter supplied) Arsenic (As) bioavailability in the rice rhizosphere is influenced by many microbial interactions, particularly by metal-transforming functional groups at the root-soil interface. This study was conducted to examine As-transforming microbes and As-speciation in the rice rhizosphere compartments, in response to two different water management practices (continuous and intermittently flooded), established on fields with high to low soil-As concentration. more...

Organism:

soil metagenome

Type:

Expression profiling by array

Platform:

GPL30371

18 Samples

Download data

(Submitter supplied) The spread of antibiotic resistance genes (ARG) into agricultural soils, products, and foods severely limits the use of organic fertilizers in agriculture. In this study, experimental land plots were fertilized, sown, and harvested for two consecutive agricultural cycles using either mineral or three types of organic fertilizers: sewage sludge, pig slurry, or composted organic fraction of municipal solid waste. more...

Organism:

solid waste metagenome; sludge metagenome; feces metagenome; soil metagenome

Type:

Other

4 related Platforms

71 Samples

Download data: CSV, XLSX

(Submitter supplied) The objective of this study was to identify the different functional genes involved in key biogeochemical cycles in thehigh Arctic regions. Understanding the microbial diversity in the Arctic region is an important step to determine the effects of climate change on these areas.

Organism:

uncultured soil microorganism; soil metagenome

Type:

Expression profiling by array; Other

Platform:

GPL29739

10 Samples

Download data: TXT

(Submitter supplied) The objective of this study was to identify the different functional genes involved in key biogeochemical cycles in the sub- Arctic regions. Understanding the microbial diversity in the Arctic region is an important step to determine the effects of climate change on these areas.

Organism:

uncultured soil microorganism; soil metagenome

Type:

Other

Platform:

GPL29739

10 Samples

Download data: TXT

(Submitter supplied) The objective of this study was to identify the different functional genes involved in key biogeochemical cycles in the low Arctic regions. Understanding the microbial diversity in the Arctic region is an important step to determine the effects of climate change on these areas.

Organism:

soil metagenome; uncultured soil microorganism

Type:

Other

Platform:

GPL29739

10 Samples

Download data: TXT

(Submitter supplied) A comparision of soil microbial functional genes of three types of subtropical broad-leaved forests Microbial functional structure was significantly different among SBFs (P < 0.05). Compared to the DBF and the EBF, the MBF had higher alpha-diversity of functional genes but lower beta-diversity, and showed more complex functional gene networks.

Organism:

soil metagenome

Type:

Other

Platform:

GPL29664

27 Samples

Download data: CSV, XLSX

(Submitter supplied) Microbes play key roles in diverse biogeochemical processes including nutrient cycling. However, responses of soil microbial community at the functional gene level to long-term fertilization, especially integrated fertilization (chemical combined with organic fertilization) remain unclear. Here we used microarray-based GeoChip techniques to explore the shifts of soil microbial functional community in a nutrient-poor paddy soil with long-term (21 years).The long-term fertilization experiment site (set up in 1990) was located in Taoyuan agro-ecosystem research station (28°55’N, 111°27’E), Chinese Academy of Sciences, Hunan Province, China, with a double-cropped rice system. more...

Organism:

uncultured soil microorganism; soil metagenome

Type:

Other

Platform:

GPL24031

18 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

soil metagenome

Type:

Other

Platform:

GPL20780

18 Samples

Download data: FASTA, TXT

(Submitter supplied) In this work, we used a functional gene microarray approach (GeoChip) to assess the soil microbial community functional potential related to the different wine quality. In order to minimize the soil variability, this work was conducted at a “within-vineyard” scale, comparing two similar soils (BRO11 and BRO12) previously identified with respect to pedological and hydrological properties within a single vineyard in Central Tuscany and that yielded highly contrasting wine quality upon cultivation of the same Sangiovese cultivar

Organism:

Archaea; Fungi; Bacteria; Viruses; soil metagenome

Type:

Genome variation profiling by array

Platform:

GPL28213

6 Samples

Download data: TXT

(Submitter supplied) Purpose: Deconstructing the soil microbiome into reduced-complexity functional modules represents a novel method of microbiome analysis. The goals of this study are to confirm differences in transcriptomic patterns among five functional module consortia. Methods: mRNA profiles of 3 replicates each of functional module enrichments of soil inoculum in M9 media with either 1) xylose, 2) n-acetylglucosamine, 3) glucose and gentamycin, 4) xylan, or 5) pectin were generated by sequencing using an Illumina platform (GENEWIZ performed sequencing). more...

Organism:

soil metagenome

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20780

15 Samples

Download data: GFF, TXT

(Submitter supplied) Thiabendazole (TBZ), a benzimidazole used against postharvest fungal growth and as anthelmintic in livestock farming, is highly persistent in soil (DT50> 1-2 years) and therefore challenging concerning its environmental management. In our recent copious attempts to isolate organisms that degrade TBZ, at best, we ended up with a soil microbial enrichment capable of accelerated TBZ degradation. Here, we employed a multi-omic approach combined with DNA stable isotope probing (SIP) for elucidating the underlying system complexity. more...

Organism:

soil metagenome

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26937

18 Samples

Download data: FASTA, TXT

(Submitter supplied) A total of 81515 genes belonging to 31 gene categories were detected in a total of 80 samples

Organism:

Archaea; compost metagenome; manure metagenome; Bacteria; Eukaryota; soil metagenome

Type:

Other

Platform:

GPL26791

79 Samples

Download data: TXT

(Submitter supplied) The effects of two years' winter warming on the overall fungal functional gene structure in Alaskan tundra soil were studies by the GeoChip 4.2 Resuts showed that two years' winter warming changed the overall fungal functional gene structure in Alaskan tundra soil.

Organism:

Fungi; soil metagenome

Type:

Genome variation profiling by array

Platform:

GPL26258

12 Samples

Download data: XLSX

(Submitter supplied) The diversity and environmental distribution of the nosZ gene, which encodes the enzyme responsible for the consumption of nitrous oxide, was investigated in marine and terrestrial environments using a functional gene microarray. The microbial communities represented by the nosZ gene probes showed strong biogeographical separation, with communities from surface ocean waters and agricultural soils significantly different from each other and from those in oceanic oxygen minimum zones. more...

Organism:

soil metagenome; seawater metagenome; synthetic construct

Type:

Other

Platform:

GPL25690

25 Samples

Download data: TXT

(Submitter supplied) This study evaluated the ammonium oxidizing communities (COA) associated with a potato crop (Solanum phureja) rhizosphere soil in the savannah of Bogotá (Colombia) by examining the presence and abundance of amoA enzyme genes and transcripts by qPCR and next-generation sequence analysis. amoA gene abundance could not be quantified by qPCR due to problems inherent in the primers; however, the melting curve analysis detected increased fluorescence for Bacterial communities but not for Archaeal communities. more...

Organism:

soil metagenome

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL20780

3 Samples

Download data: TXT

(Submitter supplied) To study long-term elevated CO2 and enriched N deposition interactive effects on microbial community and soil ecoprocess, here we investigated soil microbial community in a grassland ecosystem subjected to ambient CO2 (aCO2, 368 ppm), elevated CO2 (eCO2, 560 ppm), ambient nitrogen deposition (aN) or elevated nitrogen deposition (eN) treatments for a decade. There exist antagonistic CO2×N interactions on microbial functional genes associated with C, N, P S cycling processes. more...

Organism:

Archaea; Bacteria; Eukaryota; Viruses; soil metagenome

Type:

Other

Platform:

GPL23428

296 Samples

Download data: TXT

(Submitter supplied) Anthropogenic activities have dramatically increased the inputs of reactive nitrogen (N) into terrestrial ecosystems, with potentially important effects on the soil microbial community and consequently soil C and N dynamics. Our analysis of microbial communities in soils subjected to 14 years of 7 g N m-2 year-1 Ca(NO3)2 amendment in a Californian grassland showed that the taxonomic composition of bacterial communities, examined by 16S rRNA gene amplicon sequencing, was significantly altered by nitrate amendment, supporting the hypothesis that N amendment- induced increased nutrient availability, yielded more fast-growing bacterial taxa while reduced slow-growing bacterial taxa. more...

Organism:

soil metagenome; uncultured soil microorganism

Type:

Other

Platform:

GPL24290

64 Samples

Download data: TXT

(Submitter supplied) Global warming has shifted climate zones poleward or upward. However, understanding the responses and mechanism of microbial community structure and functions relevant to natural climate zone succession is challenged by the high complexity of microbial communities. Here, we examined soil microbial community in three broadleaved forests located in the Wulu Mountain (WLM, temperate climate), Funiu Mountain (FNM, at the border of temperate and subtropical climate zones), or Shennongjia Mountain (SNJ, subtropical climate).Soils were characterized for geochemistry, Illumina sequencing was used to determine microbial taxonomic communities and GeoChips 5.0 were used to determine microbial functional genes.

Organism:

Eukaryota; Bacteria; soil metagenome; Archaea

Type:

Other

Platform:

GPL20235

30 Samples

Download data: TXT