Bacteria in a subtropical coastal mangrove wetland 2010-2011
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA823763 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Jiulongjiang estuary Shidi bacteria 2010-2011 raw sequence
| PRJNA415893 | ENA
Project description:Mangrove wetlands are an important ecosystem in tropical and subtropical regions, and the sediments may contain both oxic and anoxic zones. In this study, ammonia/ammonium-oxidizing prokaryotes (AOPs) in yellow and black sediments with vegetation and non-vegetated sediments in a mangrove wetland of subtropical Hong Kong were investigated in winter and summer. The phylogenetic diversity of anammox bacterial 16S rRNA genes and archaeal and bacterial amoA genes (encoding ammonia monooxygenase alpha-subunit) were analyzed using PCR amplification and denaturing gradient gel electrophoresis to reveal their community structures. Quantitative PCR was also used to detect their gene abundances. The results showed that seasonality had little effect, but sediment type had a noticeable influence on the community structures and abundances of anammox bacteria. For ammonia-oxidizing archaea (AOA), seasonality had a small effect on their community structures, but a significant effect on their abundances: AOA amoA genes were significantly higher in winter than in summer. In winter, the vegetated yellow sediments had lower AOA amoA genes than the other types of sediments, but in summer, the vegetated yellow sediments had higher AOA amoA genes than the other types of sediments. Sediment type had no apparent effect on AOA community structures in winter. In summer, however, the vegetated yellow sediments showed obviously different AOA community structures from the other types of sediments. For ammonia-oxidizing bacteria (AOB), seasonality had a significant effect on their community structures and abundances: AOB amoA genes in winter were apparently higher than in summer, and AOB community structures were different between winter and summer. Sediment type had little effect on AOB community structures, but had a noticeable effect on the abundances: AOB amoA genes of the vegetated yellow sediments were obviously lower than the black ones in both seasons. This study has demonstrated that seasonality and sediment type affected community structures and abundances of AOPs differently in oxic and anoxic sediments of the mangrove wetland.
| S-EPMC3745829 | biostudies-literature
Project description:Coastal wetlands around the world have been degraded by human activities. Global declines in the extent of important habitats including mangroves, salt marsh and tidal flats necessitate mitigation and restoration efforts, however some well-meaning management actions, particularly mangrove afforestation and breakwater construction, can inadvertently cause further loss and degradation if these actions are not planned carefully. In particular, there is a potential conflict between mangrove and shorebird conservation, because mangrove afforestation and restoration may occur at the expense of bare tidal flats, which form the main foraging habitats for threatened coastal migratory shorebirds as well as supporting other coastal organisms. Here, we present several case studies that illustrate the trade-off between mangroves and bare tidal flats. To investigate whether these examples reflect an emerging broad-scale issue, we use satellite imagery to develop a detailed quantification of the change in mangrove habitat extent in 22 important shorebird areas in mainland China between 2000 and 2015. Our results indicate that 1) the extent of mangroves across all sites expanded significantly between 2000 and 2015 (p < 0.01, n = 14) while tidal flat extent in the same areas declined significantly within the same period (p < 0.01, n = 21); 2) among the 14 sites where mangroves were present, the dual threat of mangrove expansion and tidal flat loss have considerably reduced shorebird habitat in eight of these sites. To ensure effective conservation of both mangroves and shorebirds, we propose a decision tree framework for resolving this emerging dilemma between mangrove afforestation and shorebird protection, which requires careful consideration of alternative management strategies. This article is protected by copyright. All rights reserved.
| S-EPMC9912193 | biostudies-literature
Project description:Miscanthus sinensis NC-2010-001 Nat Pop 2011-106-3-5 Resequencing
| PRJNA581298 | ENA
Project description:Bacteria, archaea and fungi play crucial roles in wetland biogeochemical processes. However, little is known about their community structure, dynamics and interactions in subtropical coastal wetlands. Here, we examined communities of the three kingdoms in mangrove and mudflat sediments of a subtropical coastal wetland using Ion Torrent amplicon sequencing and co-occurrence network analysis. Bacterial, archaeal and fungal communities comprised mainly of members from the phyla Proteobacteria and Bacteroidetes, Bathyarchaeota and Euryarchaeota, and Ascomycota, respectively. Species richness and Shannon diversity were highest in bacteria, followed by archaea and were lowest in fungi. Distinct spatiotemporal patterns were observed, with bacterial and fungal communities varying, to different extent, between wet and dry seasons and between mangrove and mudflat, and archaeal community remaining relatively stable between seasons and regions. Redundancy analysis revealed temperature as the major driver of the seasonal patterns of bacterial and fungal communities but also highlighted the importance of interkingdom biotic factors in shaping the community structure of all three kingdoms. Potential ecological interactions and putative keystone taxa were identified based on co-occurrence network analysis. These findings facilitate current understanding of the microbial ecology of subtropical coastal wetlands and provide a basis for better modelling of ecological processes in this important ecosystem.
| S-EPMC6158284 | biostudies-other
Project description:The emerging pollutants antibiotic resistance genes (ARGs) are prevalent in aquatic environments such as estuary. Coastal mangrove ecosystems always serve as natural wetlands for receiving sewage which always carry ARGs. Currently, the research considering ARG distribution in mangrove ecosystems gains more interest. In this work, we investigated the diversity of ARGs in an urban estuary containing mangrove and nonmangrove areas of the South China Sea. A total of 163 ARGs that classified into 22 resistance types and six resistance mechanisms were found. ARG abundance of the samples in the estuary is between 0.144 and 0.203. This is within the general range of Chinese estuaries. The difference analysis showed that abundances of total ARGs, six most abundant ARGs (mtrA, rpoB, rpoC, rpsL, ef-Tu, and parY), the most abundant resistance types (elfamycin, multidrug, and peptide), and the most abundant resistance mechanism (target alteration) were significantly lower in mangrove sediment than that in nonmangrove sediment (p < 0.05). Network and partial redundancy analysis showed that sediment properties and mobile genetic elements were the most influential factors impacting ARG distribution rather than microbial community. The two factors collectively explain 51.22% of the differences of ARG distribution. Our study indicated that mangrove sediments have the capacity to remove ARGs. This work provides a research paradigm for analysis of ARG prevalence and proliferation in the subtropical marine coastal mangrove ecosystem.
| S-EPMC6855136 | biostudies-literature
Project description:Coastal wetland restoration is an important activity to achieve greenhouse gas (GHG) reduction targets, improve water quality, and reach the Sustainable Development Goals. However, many uncertainties remain in connection with achieving, measuring, and reporting success from coastal wetland restoration. We measured levels of carbon (C) abatement and nitrogen (N) removal potential of restored coastal wetlands in subtropical Queensland, Australia. The site was originally a supratidal forest composed of Melaleuca spp. that was cleared and drained in the 1990s for sugarcane production. In 2010, tidal inundation was reinstated, and a mosaic of coastal vegetation (saltmarshes, mangroves, and supratidal forests) emerged. We measured soil GHG fluxes (CH4 , N2 O, CO2 ) and sequestration of organic C in the trees and soil to estimate the net C abatement associated with the reference, converted, and restored sites. To assess the influence of restoration on water quality improvement, we measured denitrification and soil N accumulation. We calculated C abatement of 18.5 Mg CO2-eq ha-1 year-1 when sugarcane land transitioned to supratidal forests, 11.0 Mg CO2-eq ha-1 year-1 when the land transitioned to mangroves, and 6.2 Mg CO2-eq ha-1 year-1 when the land transitioned to saltmarshes. The C abatement was due to tree growth, soil accumulation, and reduced N2 O emissions due to the cessation of fertilization. Carbon abatement was still positive, even accounting for CH4 emissions, which increased in the wetlands due to flooding and N2 O production due to enhanced levels of denitrification. Coastal wetland restoration in this subtropical setting effectively reduces CO2 emissions while providing additional cobenefits, notably water quality improvement.
| S-EPMC9285723 | biostudies-literature
Project description:Analysis of microbial gene expression in response to physical and chemical gradients forming in the Columbia River, estuary, plume and coastal ocean was done in the context of the environmental data base. Gene expression was analyzed for 2,234 individual genes that were selected from fully sequenced genomes of 246 prokaryotic species (bacteria and archaea) as related to the nitrogen metabolism and carbon fixation. Seasonal molecular portraits of differential gene expression in prokaryotic communities during river-to-ocean transition were created using freshwater baseline samples (268, 270, 347, 002, 006, 207, 212). Total RNA was isolated from 64 filtered environmental water samples collected in the Columbia River coastal margin during 4 research cruises (14 from August, 2007; 17 from November, 2007; 18 from April, 2008; and 16 from June, 2008), and analyzed using microarray hybridization with the CombiMatrix 4X2K format. Microarray targets were prepared by reverse transcription of total RNA into fluorescently labeled cDNA. All samples were hybridized in duplicate, except samples 212 and 310 (hybridized in triplicate) and samples 336, 339, 50, 152, 157, and 199 (hybridized once). Sample location codes: number shows distance from the coast in km; CR, Columbia River transect in the plume and coastal ocean; NH, Newport Hydroline transect in the coastal ocean at Newport, Oregon; AST and HAM, Columbia River estuary locations near Astoria (river mile 7-9) and Hammond (river mile 5), respectively; TID, Columbia River estuary locations in the tidal basin (river mile 22-23); BA, river location at Beaver Army Dock (river mile 53) near Quincy, Oregon; UP, river location at mile 74.
2010-09-10 | E-GEOD-18303 | biostudies-arrayexpress
Project description:3-Deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHPS) is a key rate-limiting enzyme in aromatic amino acid anabolism. A new Iβ-type DAHPS gene (aro1A) was identified in a metagenomic library from subtropical marine mangrove sediment. The gene encoded a polypeptide composed of 272 amino acids and had a maximum similarity of 52.4% to a known DAHPS at the amino acid level. Multiple sequence alignment, homologous modeling, and molecular docking showed that Aro1A had the typical (β/α)8 barrel-shaped catalytic structural domain of DAHPS. The motifs and amino acid residues involved in the combination of substrates and metal ligand were highly conservative with the known DAHPS. The putative DAHPS gene was subcloned into a pET-30a(+) vector and was overexpressed in Escherichia coli Rosetta (DE3) cells. The recombinant protein was purified to homogeneity. The maximum activity for the recombinant Aro1A protein occurred at pH 8.0 and 40 °C. Ba2+ and Ca2+ stimulated the activity of Aro1A protein. The enzyme showed high affinity and catalytic efficiency (K m PEP = 19.58 μM, V max PEP = 29.02 μM min-1, and k cat PEP /K m PEP = 0.88 s-1 μM-1) under optimal reaction conditions. The enzymatic property of Aro1A indicates its potential in aromatic amino acid industrial production.
| S-EPMC6362186 | biostudies-literature
Project description:Miscanthus sinensis NC-2010-001 Nat Pop 2011-106-3-5 x Miscanthus sacchariflorus lutarioriparius PF30022 Population Resequencing - 14UI-019R.014 genome sequencing
| PRJNA581151 | ENA