Vertical distribution of sediment archaeal community
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ABSTRACT:
PROVIDER: PRJEB10387 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:spatial distribution of sediment archaeal community in Lake Taihu
| PRJEB10388 | ENA
Project description:Using the Illumina sequencing technology, we investigated the vertical distribution of archaeal community in the sediment of Zhushan Bay of Lake Taihu, where the black bloom frequently occurred in summer. Overall, the Miscellaneous Crenarchaeotal Group (MCG), Deep Sea Hydrothermal Vent Group 6 (DHVEG-6), and Methanobacterium dominated the archaeal community. However, we observed significant difference in composition of archaeal community among different depths of the sediment. DHVEG-6 dominated in the surface layer (0-3 cm) sediment. Methanobacterium was the dominating archaeal taxa in the L2 (3-6 cm) and L3 (6-10) sediment. MCG was most abundant in the L4 (10-15 cm) and L5 (15-20 cm) sediment. Besides, DHVEG-6 was significantly affected by the concentration of total phosphorus (TP). And loss on ignition (LOI) was an important environmental factor for Methanobacterium. As the typical archaeal taxa in the surface layer sediment, DHVEG-6 and Methanobacterium might be more adapted to abundant substrate supply from cyanobacterial blooms and take active part in the biomass transformation. We propose that DHVEG-6 and Methanobacterium could be the key archaeal taxa correlated with the "black bloom" formation in Zhushan Bay.
| S-EPMC4738990 | biostudies-literature
Project description:Characterization of archaeal community in activated sludge bioreactors along an elevational gradient in China
| PRJEB9052 | ENA
Project description:Ammonia-oxidizing archaeal (AOA) amoA diversity and relative abundance in Gulf of Mexico sediments (0-2 cm) were investigated using a functional gene microarray; a two color array with a universal internal standard
2013-03-01 | GSE42286 | GEO
Project description:Vertical organization of freshwater sediment microbial communities: implications for microbial activities and burial processes
| PRJEB14189 | ENA
Project description:Ammonia-oxidizing archaeal (AOA) amoA diversity and relative abundance in Gulf of Mexico sediments (0-2 cm) were investigated using a functional gene microarray; a two color array with a universal internal standard Two color array (cy3 and cy5): the universal standard 20 bp oligo (fluoresced with cy5) is printed to the slide with a 70-mer. Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer will bind to it. Signal is the cy3/cy5. Up to four arrays per sample, with two biological replicates made into two targets, each run on duplicate arrays.
2013-03-01 | E-GEOD-42286 | biostudies-arrayexpress
Project description:This project characterizes the metabolic consequences of the daily physiological rhythms and diel vertical migration for the model subtropical copepod, Pleuromamma xiphias. P. xiphias were collected near the Bermuda Atlantic Time Series in plankton tows at different times of day, representing different parts of their daily vertical migration. Single copepods were isolated from the tows and flash-frozen for proteomics analysis.
2024-01-14 | PXD021156 | Pride
Project description:Archaeal community across refuse decomposition Raw sequence reads
| PRJNA411954 | ENA
Project description:Anoxic sediments from Rotsee (Switzerland) were analyzed for the presence and diversity of methanogens by using molecular tools and for methanogenic activity by using radiotracer techniques, in addition to the measurement of chemical profiles. After PCR-assisted sequence retrieval of the 16S rRNA genes (16S rDNA) from the anoxic sediment of Rotsee, cloning, and sequencing, a phylogenetic analysis identified two clusters of sequences and four separated clones. The sequences in cluster 1 grouped with those of Methanosaeta spp., whereas the sequences in cluster 2 comprised the methanogenic endosymbiont of Plagiopyla nasuta. Discriminative oligonucleotide probes were constructed against both clusters and two of the separated clones. These probes were used subsequently for the analysis of indigenous methanogens in a core of the sediment, in addition to domain-specific probes against members of the domains Bacteria and Archaea and the fluorescent stain 4', 6-diamidino-2-phenylindole (DAPI), by fluorescent in situ hybridization. After DAPI staining, the highest microbial density was obtained in the upper sediment layer; this density decreased with depth from (1.01 +/- 0.25) x 10(10) to (2.62 +/- 0.58) x 10(10) cells per g of sediment (dry weight). This zone corresponded to that of highest metabolic activity, as indicated by the ammonia, alkalinity, and pH profiles, whereas the methane profile was constant. Probes Eub338 and Arch915 detected on average 16 and 6% of the DAPI-stained cells as members of the domains Bacteria and Archaea, respectively. Probe Rotcl1 identified on average 4% of the DAPI-stained cells as Methanosaeta spp., which were present throughout the whole core. In contrast, probe Rotcl2 identified only 0.7% of the DAPI-stained cells as relatives of the methanogenic endosymbiont of P. nasuta, which was present exclusively in the upper 2 cm of the sediment. Probes Rotp13 and Rotp17 did not detect any cells. The spatial distribution of the two methanogenic populations corresponded well to the methane production rates determined by incubation with either [14C]acetate or [14C]bicarbonate. Methanogenesis from acetate accounted for almost all of the total methane production, which concurs with the predominance of acetoclastic Methanosaeta spp. that represented on average 91% of the archaeal population. Significant hydrogenotrophic methanogenesis was found only in the organically enriched upper 2 cm of the sediment, where the probably hydrogenotrophic relatives of the methanogenic endosymbiont of P. nasuta, accounting on average for 7% of the archaeal population, were also detected.
| S-EPMC91355 | biostudies-literature
Project description:One of the greatest cyclical patterns in the pelagic ecosystem is the daily vertical migration of various zooplankton and fish to depth, a process referred to as diel vertical migration (DVM). DVM is considered to be energetically costly as tiny plankton migrate hundreds of meters in a 24 hour period. To study the metabolic demands of DVM, the copepod Pleuromamma xiphias was collected during upwards and downwards migration off of Bermuda. Data-dependent acquisition on the Q-Exactive detected >1600 proteins, 180 of which were differentially abundant between the two sampling periods.
2017-02-02 | PXD005778 | Pride