Microbial communities across strong environmental gradients in the intertidal rocky shore
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB45042 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR6752150_1.fastq.gz | Fastqsanger.gz | |||
| ERR6752150_2.fastq.gz | Fastqsanger.gz | |||
| ERR6752180_1.fastq.gz | Fastqsanger.gz | |||
| ERR6752180_2.fastq.gz | Fastqsanger.gz | |||
| ERR6752190_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 56 |
Similar Datasets
Project description:Although long-term ecological stability is often discussed as a community attribute, it is typically investigated at the species level (e.g. density, biomass), or as a univariate metric (e.g. species diversity). To provide a more comprehensive assessment of long-term community stability, we used a multivariate similarity approach that included all species and their relative abundances. We used data from 74 sites sampled annually from 2006 to 2017 to examine broad temporal and spatial patterns of change within rocky intertidal communities along the west coast of North America. We explored relationships between community change (inverse of stability) and the following potential drivers of change/stability: (a) marine heatwave events; (b) three attributes of biodiversity: richness, diversity and evenness and (c) presence of the mussel, Mytilus californianus, a dominant space holder and foundation species in this system. At a broad scale, we found an inverse relationship between community stability and elevated water temperatures. In addition, we found substantial differences in stability among regions, with lower stability in the south, which may provide a glimpse into the patterns expected with a changing climate. At the site level, community stability was linked to high species richness and, perhaps counterintuitively, to low evenness, which could be a consequence of the dominance of mussels in this system. Synthesis. Assessments of long-term stability at the whole-community level are rarely done but are key to a comprehensive understanding of the impacts of climate change. In communities structured around a spatially dominant species, long-term stability can be linked to the stability of this 'foundation species', as well as to traditional predictors, such as species richness.
| S-EPMC8518646 | biostudies-literature
Project description:Biodiversity loss is driven by interacting factors operating at different spatial scales. Yet, there remains uncertainty as to how fine-scale environmental conditions mediate biological responses to broad-scale stressors. We surveyed intertidal rocky shore kelp beds situated across a local gradient of wave action and evaluated changes in kelp diversity and abundance after more than two decades of broad scale stressors, most notably the 2013-2016 heat wave. Across all sites, species were less abundant on average in 2017 and 2018 than during 1993-1995 but changes in kelp diversity were dependent on wave exposure, with wave exposed habitats remaining stable and wave sheltered habitats experiencing near complete losses of kelp diversity. In this way, wave exposed sites have acted as refugia, maintaining regional kelp diversity despite widespread local declines. Fucoids, seagrasses and two stress-tolerant kelp species (Saccharina sessilis, Egregia menziesii) did not decline as observed in other kelps, and the invasive species Sargassum muticum increased significantly at wave sheltered sites. Long-term monitoring data from a centrally-located moderate site suggest that kelp communities were negatively impacted by the recent heatwave which may have driven observed losses throughout the region. Wave-sheltered shores, which saw the largest declines, are a very common habitat type in the Northeast Pacific and may be especially sensitive to losses in kelp diversity and abundance, with potential consequences for coastal productivity. Our findings highlight the importance of fine-scale environmental heterogeneity in mediating biological responses and demonstrate how incorporating differences between habitat patches can be essential to capturing scale-dependent biodiversity loss across the landscape.
| S-EPMC6435185 | biostudies-literature
Project description:Functional diversity is intimately linked with community assembly processes, but its large-scale patterns of variation are often not well understood. Here, we investigated the spatiotemporal changes in multiple trait dimensions ("trait space") along vertical intertidal environmental stress gradients and across a landscape scale. We predicted that the range of the trait space covered by local assemblages (i.e., functional richness) and the dispersion in trait abundances (i.e., functional dispersion) should increase from high- to low-intertidal elevations, due to the decreasing influence of environmental filtering. The abundance of macrobenthic algae and invertebrates was estimated at four rocky shores spanning ca. 200 km of the coast over a 36-month period. Functional richness and dispersion were contrasted against matrix-swap models to remove any confounding effect of species richness on functional diversity. Random-slope models showed that functional richness and dispersion significantly increased from high- to low-intertidal heights, demonstrating that under harsh environmental conditions, the assemblages comprised similar abundances of functionally similar species (i.e., trait convergence), while that under milder conditions, the assemblages encompassed differing abundances of functionally dissimilar species (i.e., trait divergence). According to the Akaike information criteria, the relationship between local environmental stress and functional richness was persistent across sites and sampling times, while functional dispersion varied significantly. Environmental filtering therefore has persistent effects on the range of trait space covered by these assemblages, but context-dependent effects on the abundances of trait combinations within such range. Our results further suggest that natural and/or anthropogenic factors might have significant effects on the relative abundance of functional traits, despite that no trait addition or extinction is detected.
| S-EPMC5355202 | biostudies-literature
Project description:The biogeography of the Peruvian Eastern Pacific coast has been described based on oceanographic parameters and qualitative species occurrence data. This has generated disagreement about the limits and existence of different biogeographic units. In this study, the distribution of rocky-shore macrobenthic communities were recorded over 41 sites along the Peruvian coastline (3.5°S-13.5°S) and analyzed together with historic abiotic data in order to quantitatively evaluate the biogeographic zonation of rocky intertidal communities throughout the region and its relationship with environmental variables to propose an update bioregionalization. Clusters and non-metric multidimensional scaling were performed using Bray-Curtis dissimilarity matrices from abundance data to evaluate biogeographic patterns of dissimilarities of rocky-shore communities. Significant turnover of taxa among defined biogeographical units was tested using permutational multivariate dispersion. Relationships between of the biogeographical community's structure and environmental factors were examined using Random Forest analysis on datasets available at Bio-Oracle and Jet Propulsion Laboratory-California Institute of Technology. Variation of community structure of 239 taxa depicted three biogeographical units along the region matching Panamic, transitional and Humboldt provinces. Beta diversity analysis indicated a significant turnover of taxa within the transitional unit. Random forest analysis showed a strong correlation between biogeographic units with phosphate, sea surface temperature, nitrate, dissolved oxygen, cloud fraction, and silicates. Our results set the putative limits of three biogeographic units for rocky-shore communities along the coast of Peru, providing base-line information for understanding further biogeographic changes on communities associated with the ongoing regional coastal cooling and impacts of El Niño events.
| S-EPMC6267975 | biostudies-literature
Project description:Interrelations between epiphytic bacteria and macroalgae are multifaceted and complicated, though little is known about the community structure, interaction and functions of those epiphytic bacteria. This study comprehensively characterized the epiphytic bacterial communities associated with eight different common seaweeds collected from a rocky intertidal zone on the Indian Ocean at Cape Vidal, South Africa. High-throughput sequencing analyses indicated that seaweed-associated bacterial communities were dominated by the phyla Proteobacteria, Bacteroidetes, Firmicutes, Cyanobacteria, Planctomycetes, Actinobacteria and Verrucomicrobia. Energy-dispersive X-ray (EDX) analysis showed the presence of elemental composition in the surface of examined seaweeds, in varying concentrations. Cluster analysis showed that bacterial communities of brown seaweeds (SW2 and SW4) were closely resembled those of green seaweeds (SW1) and red seaweeds (SW7) while those of brown seaweeds formed a separate branch. Predicted functional capabilities of epiphytic bacteria using PICRUSt analysis revealed abundance of genes related to metabolic and biosynthetic activities. Further important identified functional interactions included genes for bacterial chemotaxis, which could be responsible for the observed association and network of elemental-microbes interaction. The study concludes that the diversity of epiphytic bacteria on seaweed surfaces is greatly influenced by algal organic exudates as well as elemental deposits on their surfaces, which triggers chemotaxis responses from epiphytic bacteria with the requisite genes to metabolise those substrates.
| S-EPMC6934600 | biostudies-literature
Project description:Metagenomic analysis reveals distinct patterns of denitrification gene abundance across soil moisture, nitrate gradients
| PRJEB28446 | ENA
Project description:Climate change threatens to destabilize ecological communities, potentially moving them from persistently occupied "basins of attraction" to different states. Increasing variation in key ecological processes can signal impending state shifts in ecosystems. In a rocky intertidal meta-ecosystem consisting of three distinct regions spread across 260 km of the Oregon coast, we show that annually cleared sites are characterized by communities that exhibit signs of increasing destabilization (loss of resilience) over the past decade despite persistent community states. In all cases, recovery rates slowed and became more variable over time. The conditions underlying these shifts appear to be external to the system, with thermal disruptions (e.g., marine heat waves, El Niño-Southern Oscillation) and shifts in ocean currents (e.g., upwelling) being the likely proximate drivers. Although this iconic ecosystem has long appeared resistant to stress, the evidence suggests that subtle destabilization has occurred over at least the last decade.
| S-EPMC8784124 | biostudies-literature
Project description:Historical exploitation of the Mediterranean Sea and the absence of rigorous baselines makes it difficult to evaluate the current health of the marine ecosystems and the efficacy of conservation actions at the ecosystem level. Here we establish the first current baseline and gradient of ecosystem structure of nearshore rocky reefs at the Mediterranean scale. We conducted underwater surveys in 14 marine protected areas and 18 open access sites across the Mediterranean, and across a 31-fold range of fish biomass (from 3.8 to 118 g m(-2)). Our data showed remarkable variation in the structure of rocky reef ecosystems. Multivariate analysis showed three alternative community states: (1) large fish biomass and reefs dominated by non-canopy algae, (2) lower fish biomass but abundant native algal canopies and suspension feeders, and (3) low fish biomass and extensive barrens, with areas covered by turf algae. Our results suggest that the healthiest shallow rocky reef ecosystems in the Mediterranean have both large fish and algal biomass. Protection level and primary production were the only variables significantly correlated to community biomass structure. Fish biomass was significantly larger in well-enforced no-take marine reserves, but there were no significant differences between multi-use marine protected areas (which allow some fishing) and open access areas at the regional scale. The gradients reported here represent a trajectory of degradation that can be used to assess the health of any similar habitat in the Mediterranean, and to evaluate the efficacy of marine protected areas.
| S-EPMC3290621 | biostudies-literature
Project description:Plant terrestrialization brought forth the land plants (embryophytes). Embryophytes account for most of the biomass on land and evolved from streptophyte algae in a singular event. Recent advances have unraveled the first full genomes of the closest algal relatives of land plants; among the first such species was Mesotaenium endlicherianum. Here, we used fine-combed RNAseq in tandem with photophysiological assessment on Mesotaenium exposed to a continuous range of temperature and light cues. Our data establish a grid of 42 different conditions, resulting in 128 transcriptomes and ~1.5 Tbp (~9.9 billion reads) of data to study combinatory effects of stress response using clustering along gradients. We describe major hubs in genetic networks underpinning stress response and acclimation in the molecular physiology of Mesotaenium. Our data suggest that lipid droplet formation, plastid and cell wall-derived signals denominate molecular programs since more than 600 million years of streptophyte evolution—before plants made their first steps on land.
2022-11-11 | PXD037847 | Pride
Project description:Long-term patterns in trajectories of natural communities provide insights into ecological resilience, but their assessment requires long-term census data. We analyzed 16-year census data for intertidal communities from 30 rocky shores along Japan's Pacific coast to assign community change to four possible trajectories (stable, reversible, abrupt, or linear) representing different aspects of ecological resilience, and to estimate multiple metrics of temporal invariability (species richness, species composition, and community abundance). We examined (1) how the prevalence of the four trajectories differs among regions, (2) how the features (model coefficients) of each trajectory vary among regions, and (3) how the temporal invariabilities differ among trajectories and regions. We found that the stable trajectory was the most common. Its features differed among regions, with a faster recovery to steady-state equilibrium in low-latitude regions. Furthermore, trajectories and temporal invariabilities both varied among regions, seemingly in association with the strength of ocean current fluctuations. Thus, the relationship between community temporal invariability and trajectory may be weak or absent, at least at the regional scale.
| S-EPMC8352913 | biostudies-literature