Community Structure, Dynamics and Interactions of Bacteria, Archaea and Fungi in Subtropical Coastal Wetland Sediments.
ABSTRACT: 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.
Project description:The stratified distribution of bacterial and archaeal communities has been detected in many sediment profiles from various natural environments. A better understanding of microbial composition and diversity pattern in coastal mangrove wetlands in relation to physicochemical and spatial-temporal influences could provide more insights into the ecological functions of microbes in coastal wetlands. In this study, seasonal variations of microbial communities within sediment profiles from two sediment types (mangrove forest and intertidal mudflats) at three sampling locations in coastal Mai Po wetland were characterized using MiSeq high throughput sequencing and 16S rRNA quantitative PCR methods. Bacterial 16S rRNA gene abundance showed clear decreasing trends with increasing depth for all sites, seasonality and sediment types. There is a weak seasonal dynamic of bacterial and archaeal community abundance in both seasons. Seasonality imposed more influence on the beta diversity pattern of bacterial community than archaeal community. The five most abundant phyla within bacterial and archaeal community remain stable between two distinctive seasons. Sediment depth and seasonality are the most influential factors affecting bacterial community composition and diversity. The pH is the most influential factor on shaping the archaeal community. Stratified distribution of bacterial community including aerobic and anaerobic bacterial taxa is largely represented in the surface layers and the subsurface layers, respectively. For archaeal stratification, Thaumarchaeota Marine Group I is the dominant member in surface sediments while Bathyarchaeota and MBG-B dominate in subsurface sediments. Such stratified distribution patterns are irrespective of sediment types, sampling locations or seasonality, but significantly correlated to the sediment depth, which might be shaped by oxygen availability and the distribution of other terminal electron accepters along the depth profile.
Project description:Anaerobic ammonium-oxidizing (anammox) bacteria, aerobic ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) are three groups of ammonium/ammonia-oxidizing prokaryotes (AOPs) that are involved in the nitrogen cycle. This research compared the AOP communities in a constructed freshwater wetland with a natural coastal marine wetland in the subtropical Hong Kong. Both vegetated/rhizosphere and nonvegetated sediments were investigated to identify the effects of different macrophytes on the AOP communities. The polymerase chain reaction (PCR)-amplified gene fragments of 16S rRNA and archaeal and bacterial amoA (encoding the ammonia monooxygenase alpha subunit) were applied as molecular biomarkers to analyze the AOPs' phylogeny and diversity. Quantitative PCR was used to determine the abundances of AOPs in the sediments. The results showed that the relatively more heterogeneous freshwater wetland contained a broader range of phylotypes, higher diversity, more complex community structures, and more unevenly distributed abundances of AOPs than the coastal wetland. The effects of vegetation on the community structures of AOPs were plant-specific. The exotic Typha angustifolia affected the community structures of all AOPs and enhanced their abundances in the rhizosphere region. Both Phragmites australis and Cyperus malaccensis showed some effects on the community structures of AOB, but minimal effects on those of anammox bacteria or AOA. Kandelia obovata had almost no detectable effect on all AOPs due to their smaller size. This study suggested that the freshwater and coastal marine wetlands may have different contributions to the inorganic N removal due to the variations in AOP communities and plant types.
Project description:BACKGROUND:Since Spartina alterniflora (simplified as Spartina) has strong ecological competitiveness and rapid growth, it has been introduced and living in the coastal wetland regions of China for more than 30 years. Taking coastal wetland in the Beibu Gulf of south China as an example, the effects of Spartina invasion on soil quality were investigated to provide scientific basis for soil management. METHODOLOGY:The soil quality of six different coastal wetlands, i.e. mangrove (vegetation coverage is above 95%), mangrove- Spartina ecotones (vegetation coverage is above 95%), sparse mangrove (vegetation coverage is 10%-20%), sparse mangrove- Spartina ecotones (vegetation coverage is about 80%), Spartina (vegetation coverage is about 80%) and bare beach (no plants), were analyzed using the following indicators: pH, cation exchange capacity, contents of total nitrogen, total phosphorus and organic carbon, microbial biomass carbon, microbial biomass nitrogen, microbial carbon / organic carbon, and activities of urease, acid phosphatase, invertase, polyphenol oxidase and catalase. PRINCIPAL FINDINGS:The results showed that compared to mangrove wetland, most indicators in the mangrove-Spartina wetland showed a decline tendency except pH value, and the contents of total phosphorus and organic carbon, microbial biomass carbon and soil microbial biomass nitrogen, and the activities of acid phosphatase and invertase were significantly reduced (P<0.05). Compared to sparse mangrove wetland and bare beach, the Spartina invasion wetland (sparse mangrove-Spartina wetland and Spartina wetland) had higher contents of total nitrogen, total phosphorus and organic carbon, microbial biomass carbon, microbial biomass nitrogen, cation exchange capacity and the activities of urease and acid phosphatase, so soil quality in the sparse mangrove wetland and bare beach was significantly improved. Factor Analysis and PCA also showed that: the quality of mangrove wetland soil is better than that of mangrove-Spartina ecotones wetland soil; the quality of sparse mangrove-Spartina ecotones wetland soil is better than that of sparse mangrove wetland soil; the quality of Spartina wetland soil is better than that of bare beach wetland soil. CONCLUSIONS/SIGNIFICANCE:Therefore, in the invaded Beibu Gulf wetland ecosystems of south China, for the mangrove wetlands where the productivity of native plant was higher than that of Spartina, the Spartina invasion can cause soil degradation significantly and it must be strictly controlled, while for sparse mangrove wetland and bare beach where the productivity of native plant was lower than that of Spartina, Spartina invasion can improve the soil quality. Thus our study may help to better understand the effect of plant invasion.
Project description:Many natural wetlands have been converted to human-influenced wetlands. In some instances, human-influenced wetlands could provide complementary habitats for waterbirds, compensating for the loss of natural wetlands. Inner Deep Bay in Hong Kong is composed of both natural and human-influenced wetlands and is under immense development pressure. From an ecology perspective, we need to understand if different wetland types play the same ecological role. To achieve this, we tracked nine little egrets (Egretta garzetta) using GPS loggers for 14 months to study their spatial ecology, home range, movement and habitat use. We found that over 88% of the home range of all individuals comprised of wetlands (commercial fishponds, mangrove, gei wai, channel, and intertidal mudflat). Among these wetland types, nearly all (seven of nine) individuals preferred commercial fishponds over other habitats in all seasons. Little egrets exhibited seasonal movement and habitat use among seasons, with largest home range, greatest movement, and most frequent visits to commercial fishponds in winter compared to spring and autumn. Our results highlight the significant role of commercial fishponds, providing a feeding ground for little egrets. However, other wetland types cannot be ignored, as they were also used considerably. These findings underscore the importance of maintaining a diversity of wetland types as alternative foraging and breeding habitats.
Project description:Bacterial and archaeal communities play important roles in wetland ecosystems. Although the microbial communities in the soils and sediments of wetlands have been studied extensively, the comprehensive distributions of planktonic bacterial and archaeal communities and their responses to environmental variables in wetlands remain poorly understood. The present study investigated the spatiotemporal characteristics of the bacterial and archaeal communities in the water of an artificially irrigated estuarine wetland of the Liaohe River, China, explored whether the wetland effluent changed the bacterial and archaeal communities in the Liaohe River, and evaluated the driving environmental factors. Within the study, 16S rRNA quantitative PCR methods and MiSeq high-throughput sequencing were used. The bacterial and archaeal 16S rRNA gene abundances showed significant temporal variation. Meanwhile, the bacterial and archaeal structures showed temporal but not spatial variation in the wetland and did not change in the Liaohe River after wetland drainage. Moreover, the bacterial communities tended to have higher diversity in the wetland water in summer and in the scarce zone, while a relatively higher diversity of archaeal communities was found in autumn and in the intensive zone. DO, pH and PO4-P were proven to be the essential environmental parameters shaping the planktonic bacterial and archaeal community structures in the Liaohe River estuarine wetland (LEW). The LEW had a high potential for methanogenesis, which could be reflected by the composition of the microbial communities.
Project description:Communities of methanogens, anaerobic methanotrophic archaea and aerobic methanotrophic bacteria (MOB) were compared by profiling polymerase chain reaction (PCR)-amplified products of mcrA and pmoA genes encoded by methyl-coenzyme M reductase alpha subunit and particulate methane monooxygenase alpha subunit, respectively, in sediments of northern South China Sea (nSCS) and Mai Po mangrove wetland. Community structures representing by mcrA gene based on 12 clone libraries from nSCS showed separate clusters indicating niche specificity, while, Methanomicrobiales, Methanosarcinales clades 1,2, and Methanomassiliicoccus-like groups of methanogens were the most abundant groups in nSCS sediment samples. Novel clusters specific to the SCS were identified and the phylogeny of mcrA gene-harboring archaea was updated. Quantitative polymerase chain reaction was used to detect mcrA gene abundance in all samples: similar abundance of mcrA gene in the surface layers of mangrove (3.4?3.9 × 10(6) copies per gram dry weight) and of intertidal mudflat (5.5?5.8 × 10(6) copies per gram dry weight) was observed, but higher abundance (6.9 × 10(6) to 1.02 × 10(8) copies per gram dry weight) was found in subsurface samples of both sediment types. Aerobic MOB were more abundant in surface layers (6.7?11.1 × 10(5) copies per gram dry weight) than the subsurface layers (1.2?5.9 × 10(5) copies per gram dry weight) based on pmoA gene. Mangrove surface layers harbored more abundant pmoA gene than intertidal mudflat, but less pmoA genes in the subsurface layers. Meanwhile, it is also noted that in surface layers of all samples, more pmoA gene copies were detected than the subsurface layers. Reedbed rhizosphere exhibited the highest gene abundance of mcrA gene (8.51 × 10(8) copies per gram dry weight) and pmoA gene (1.56 × 10(7) copies per gram dry weight). This study investigated the prokaryotic communities responsible for methane cycling in both marine and coastal wetland ecosystems, showing the distribution characteristics of mcrA gene-harboring communities in nSCS and stratification of mcrA and pmoA gene diversity and abundance in the Mai Po Nature Reserve.
Project description:Microbial communities within the soil of Laurentian Great Lakes coastal wetlands drive biogeochemical cycles and provide several other ecosystem services. However, there exists a lack of understanding of how microbial communities respond to nutrient gradients and human activity in these systems. This research sought to address the lack of understanding through exploration of relationships among nutrient gradients, microbial community diversity, and microbial networks. Significant differences in microbial community structure were found among coastal wetlands within the western basin of Lake Erie and all other wetlands studied (three regions within Saginaw Bay and one region in the Beaver Archipelago). These diversity differences coincided with higher nutrient levels within the Lake Erie region. Site-to-site variability also existed within the majority of the regions studied, suggesting site-scale heterogeneity may impact microbial community structure. Several subnetworks of microbial communities and individual community members were related to chemical gradients among wetland regions, revealing several candidate indicator communities and taxa that may be useful for Great Lakes coastal wetland management. This research provides an initial characterization of microbial communities among Great Lakes coastal wetlands and demonstrates that microbial communities could be negatively impacted by anthropogenic activities.
Project description:<h4>Background and aims</h4>Hydroperiod drives plant community composition in wetlands, resulting in distinct zonation patterns. Here, we explored the role of seed germination traits in shaping wetland community assembly along a hydroperiod gradient. Specifically, we tested the hypothesis that seeds of reed, mudflat, swamp, shallow- and deep-water communities only germinate under a specific set of environmental factors characterized by the community-specific optimal conditions for seedling survival and growth.<h4>Methods</h4>In a three-factorial experiment, we tested the seed germination response of 50 species typical for temperate wetlands of Europe to temperature fluctuations (constant vs. fluctuating temperature), illumination (light vs. darkness) and oxygen availability (aerobic vs. hypoxia). Phylogenetic principal component analysis, cluster analysis and phylogenetic linear regressions were used to confirm the community-specific seed germination niches.<h4>Key results</h4>Our study revealed the presence of five distinct, community-specific seed germination niches that reflect adaptations made by the study communities to decreasing light intensity, temperature fluctuations and oxygen availability along the hydroperiod gradient. Light as a germination trigger was found to be important in mudflats, swamps and shallow water, whereas the seeds of reed and deep-water species were able to germinate in darkness. A fluctuating temperature is only required for seed germination in mudflat species. Germination of species in the communities at the higher end of the hydroperiod gradient (reed and mudflat) demonstrated a strict requirement for oxygen, whereas swamp, shallow- and deep-water species also germinated under hypoxia.<h4>Conclusions</h4>Our study supports the recent argument that the inclusion of seed germination traits in community ecology adds significant insights to community response to the abiotic and biotic environment. Furthermore, the close relationship between seed germination adaptations and community assembly could help reach a better understanding of the existing patterns of wetland plant distribution at local scales and wetland vegetation dynamics, as well as facilitate nature conservation measures and aquatic habitat restoration.
Project description:The flux of terrestrially derived pathogens to coastal waters presents a significant health risk to marine wildlife, as well as to humans who utilize the nearshore for recreation and seafood harvest. Anthropogenic changes in natural habitats may result in increased transmission of zoonotic pathogens to coastal waters. The objective of our work was to evaluate how human-caused alterations of coastal landscapes in California affect the transport of Toxoplasma gondii to estuarine waters. Toxoplasma gondii is a protozoan parasite that is excreted in the feces of infected felids and is thought to reach coastal waters in contaminated runoff. This zoonotic pathogen causes waterborne toxoplasmosis in humans and is a significant cause of death in threatened California sea otters. Surrogate particles that mimic the behavior of T. gondii oocysts in water were released in transport studies to evaluate if the loss of estuarine wetlands is contributing to an increased flux of oocysts into coastal waters. Compared to vegetated sites, more surrogates were recovered from unvegetated mudflat habitats, which represent degraded wetlands. Specifically, in Elkhorn Slough, where a large proportion of otters are infected with T. gondii, erosion of 36% of vegetated wetlands to mudflats may increase the flux of oocysts by more than 2 orders of magnitude. Total degradation of wetlands may result in increased Toxoplasma transport of 6 orders of magnitude or more. Destruction of wetland habitats along central coastal California may thus facilitate pathogen pollution in coastal waters with detrimental health impacts to wildlife and humans.
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.