Microbial community diversity of nirK in riparian zones
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA449223 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6961535_1.fastq.gz | Fastqsanger.gz | |||
| SRR6961535_2.fastq.gz | Fastqsanger.gz | |||
| SRR6961536_1.fastq.gz | Fastqsanger.gz | |||
| SRR6961536_2.fastq.gz | Fastqsanger.gz | |||
| SRR6961537_1.fastq.gz | Fastqsanger.gz |
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Project description:microbial community diversity of nirS in riparian zones Raw sequence reads
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Project description:The community composition (in terms of abundance, distribution and contribution of diverse clades) of bacteria involved in nitrogen transformations in the oxygen minimum zones may be related to the rates of fixed N loss in these systems. The abundance of both denirifying and anammox bacteria, and the assemblage composition of denitrifying bacteria were investigated in the Eastern Tropical South Pacific and the Arabian Sea using assays based on molecular markers for the two groups of bacteria. The abundance and distribution of bacteria associated with the fixed N removal processes denitrification and anammox were investigated using quantitative PCR for genes encoding nitrite reductase (nirK and nirS) in denitrifying bacteria and hydrazine oxidase(hzo) and 16S rRNA genesin anammox bacteria. All of these genes had depth distributions with maxima associated with the secondary nitrite maximum in low oxygen waters. NirS was mch more abundant than nirK, and much more abundant than the 16S rRNA gene from anammox bacteria. The ratio of hzo:16S rRNA for anammox was low and variable implying greater unexplored diversity in the the hzo gene. Assemblage composition of the abundant nirS-type denitrifiers was evaluated using a funcitonal gene microarray. Of the nirS archetypes represented on the microarray, very few occurred speficically in one region or depth interval, but the assemblages varied significantly. Community composition of denitrifiers based on microarray analysis of the nirS gene was most different between geographical regions. Within each region, the surface layer and OMZ assemblages clustered distinctly. Thus, in addition to spatial and temporal variation in denitrificaiton and anammox rates, both microbial abundance and community composition also vary between OMZ regions and depths.
2013-09-12 | GSE50787 | GEO
Project description:The community composition (in terms of abundance, distribution and contribution of diverse clades) of bacteria involved in nitrogen transformations in the oxygen minimum zones may be related to the rates of fixed N loss in these systems. The abundance of both denirifying and anammox bacteria, and the assemblage composition of denitrifying bacteria were investigated in the Eastern Tropical South Pacific and the Arabian Sea using assays based on molecular markers for the two groups of bacteria. The abundance and distribution of bacteria associated with the fixed N removal processes denitrification and anammox were investigated using quantitative PCR for genes encoding nitrite reductase (nirK and nirS) in denitrifying bacteria and hydrazine oxidase(hzo) and 16S rRNA genesin anammox bacteria. All of these genes had depth distributions with maxima associated with the secondary nitrite maximum in low oxygen waters. NirS was mch more abundant than nirK, and much more abundant than the 16S rRNA gene from anammox bacteria. The ratio of hzo:16S rRNA for anammox was low and variable implying greater unexplored diversity in the the hzo gene. Assemblage composition of the abundant nirS-type denitrifiers was evaluated using a funcitonal gene microarray. Of the nirS archetypes represented on the microarray, very few occurred speficically in one region or depth interval, but the assemblages varied significantly. Community composition of denitrifiers based on microarray analysis of the nirS gene was most different between geographical regions. Within each region, the surface layer and OMZ assemblages clustered distinctly. Thus, in addition to spatial and temporal variation in denitrificaiton and anammox rates, both microbial abundance and community composition also vary between OMZ regions and depths. Two color array (Cy3 and Cy5): the universal standard 20-mer oligo is printed to the slide with a 70-mer oligo (an archetype). Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer conjugated to a 20-mer oligo (fluoresced with Cy5) complementary to the universal standard will bind to the oligo probes on the array. Signal is the ratio of Cy3 to Cy5. Three replicate probes were printed for each archetype. Two replicate arrays were run on duplicate targets.
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Project description:Understanding the multifaceted plant diversity and its maintenance mechanisms is crucial for biodiversity conservation. Dam-induced water level fluctuations dramatically alter various aspects of riparian diversity, such as taxonomic (TD), phylogenetic (PD), or functional (FD) diversity. However, few studies simultaneously evaluated plant TD, FD, and PD, especially in the subtropical reservoir riparian zone. Here we sampled plant diversity and environmental drivers along inundation gradients of the Three Gorges Reservoir Region in China. We integrated multifaceted plant diversity to assess how distinct ecological processes affect the plant community assembly and how they respond to inundation gradients, spatial variability, climate, and soils in dam-regulated riparian zones. We found that alpha TD, PD, and FD diversity exhibited decreasing trends with increasing inundation gradients and significant positive correlations with soil organic matter. The number of clustering plant communities increases along the inundation gradients. Beta TD and PD diversity were mainly dominated by species turnover with fewer contributions from nestedness, while beta FD diversity was mainly dominated by nestedness with fewer contributions from species turnover. The explainable rates of different dimensions of beta diversity, turnover, and nestedness ranged from 11% to 61%, with spatial factors explaining the highest beta diversity in different dimensions, followed by inundation gradients, soil properties, and climate variables. Our results suggest dispersal limitations are more important for species turnover in dam-regulated riparian zones at regional scales, while inundation gradients and soil fertility are more critical in shaping plant community assemblages at the local scale. This study emphasizes that environmental and spatial gradients are critical for understanding the assembly mechanisms driving multifaceted plant communities at local and regional scales and reinforces the importance of protecting seed sources and dispersal pathways and maintaining river connectivity when implementing restoration projects.
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Project description:Anammox and denitrification separately dominates microbial N-loss in water saturated and unsaturated soils horizons of riparian zones Raw sequence reads
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