Using environmental DNA and particle tracking to uncover the spatial and temporal distribution of elasmobranchs in temperate coastal waters
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PROVIDER: PRJEB79665 | ENA |
REPOSITORIES: ENA
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Project description:Bacterial surface colonization is a universal adaptation strategy in aquatic environments. However, neither the identities of early colonizers nor the temporal changes in surface assemblages are well understood. To determine the identities of the most common bacterial primary colonizers and to assess the succession process, if any, of the bacterial assemblages during early stages of surface colonization in coastal water of the West Pacific Ocean, nonnutritive inert materials (glass, Plexiglas, and polyvinyl chloride) were employed as test surfaces and incubated in seawater off the Qingdao coast in the spring of 2005 for 24 and 72 h. Phylogenetic analysis of the 16S rRNA gene sequences amplified from the recovered surface-colonizing microbiota indicated that diverse bacteria colonized the submerged surfaces. Multivariate statistical cluster analyses indicated that the succession of early surface-colonizing bacterial assemblages followed sequential steps on all types of test surfaces. The Rhodobacterales, especially the marine Roseobacter clade members, formed the most common and dominant primary surface-colonizing bacterial group. Our current data, along with previous studies of the Atlantic coast, indicate that the Rhodobacterales bacteria are the dominant and ubiquitous primary surface colonizers in temperate coastal waters of the world and that microbial surface colonization follows a succession sequence. A conceptual model is proposed based on these findings, which may have important implications for understanding the structure, dynamics, and function of marine biofilms and for developing strategies to harness or control surface-associated microbial communities.
| S-EPMC2223210 | biostudies-literature
Project description:BACKGROUND:Microbial communities present in environmental waters constitute a reservoir for antibiotic-resistant pathogens that impact human health. For this reason, a diverse variety of water environments are being analyzed using metagenomics to uncover public health threats. However, the composition of these communities along the coastal environment of a whole city, where sewage and beach waters are mixed, is poorly understood. RESULTS:We shotgun-sequenced 20 coastal areas from the city of Montevideo (capital of Uruguay) including beach and sewage water samples to characterize bacterial communities and their virulence and antibiotic resistance repertories. As expected, we found that sewage and beach environments present significantly different bacterial communities. This baseline allowed us to detect a higher prevalence and a more diverse repertory of virulence and antibiotic-resistant genes in sewage samples. Many of these genes come from well-known enterobacteria and represent carbapenemases and extended-spectrum betalactamases reported in hospital infections in Montevideo. Additionally, we were able to genotype the presence of both globally disseminated pathogenic clones and emerging antibiotic-resistant bacteria in sewage waters. CONCLUSIONS:Our study represents the first in using metagenomics to jointly analyze beaches and the sewage system from an entire city, allowing us to characterize antibiotic-resistant pathogens circulating in urban waters. The data generated in this initial study represent a baseline metagenomic exploration to guide future longitudinal (time-wise) studies, whose systematic implementation will provide useful epidemiological information to improve public health surveillance.
| S-EPMC6396544 | biostudies-literature
Project description:Bacterioplankton play a key role in marine waters facilitating processes important for carbon cycling. However, the influence of specific bacterial populations and environmental conditions on bacterioplankton community performance remains unclear. The aim of the present study was to identify drivers of bacterioplankton community functions, taking into account the variability in community composition and environmental conditions over seasons, in two contrasting coastal systems. A Least Absolute Shrinkage and Selection Operator (LASSO) analysis of the biological and chemical data obtained from surface waters over a full year indicated that specific bacterial populations were linked to measured functions. Namely, Synechococcus (Cyanobacteria) was strongly correlated with protease activity. Both function and community composition showed seasonal variation. However, the pattern of substrate utilization capacity could not be directly linked to the community dynamics. The overall importance of dissolved organic matter (DOM) parameters in the LASSO models indicate that bacterioplankton respond to the present substrate landscape, with a particular importance of nitrogenous DOM. The identification of common drivers of bacterioplankton community functions in two different systems indicates that the drivers may be of broader relevance in coastal temperate waters.
| S-EPMC5037133 | biostudies-literature
Project description:BackgroundDinoflagellates are a ubiquitous and ecologically important component of marine phytoplankton communities, with particularly notable species including those associated with harmful algal blooms (HABs) and those that bioluminesce. High-throughput sequencing offers a novel approach compared to traditional microscopy for determining species assemblages and distributions of dinoflagellates, which are poorly known especially in Australian waters.ResultsWe assessed the composition of dinoflagellate assemblages in two Australian locations: coastal temperate Port Phillip Bay and offshore tropical waters of Davies Reef (Great Barrier Reef). These locations differ in certain environmental parameters reflecting latitude as well as possible anthropogenic influences. Molecular taxonomic assessment revealed more species than traditional microscopy, and it showed statistically significant differences in dinoflagellate assemblages between locations. Bioluminescent species and known associates of HABs were present at both sites. Dinoflagellates in both areas were mainly represented by the order Gymnodiniales (66%-82% of total sequence reads). In the warm waters of Davies Reef, Gymnodiniales were equally represented by the two superclades, Gymnodiniales sensu stricto (33%) and Gyrodinium (34%). In contrast, in cooler waters of Port Phillip Bay, Gymnodiniales was mainly represented by Gyrodinium (82%). In both locations, bioluminescent dinoflagellates represented up to 0.24% of the total sequence reads, with Protoperidinium the most abundant genus. HAB-related species, mainly represented by Gyrodinium, were more abundant in Port Phillip Bay (up to 47%) than at Davies Reef (28%), potentially reflecting anthropogenic influence from highly populated and industrial areas surrounding the bay. The entire assemblage of dinoflagellates, as well as the subsets of HAB and bioluminescent species, were strongly correlated with water quality parameters (R2 = 0.56-0.92). Significant predictors differed between the subsets: HAB assemblages were explained by salinity, temperature, dissolved oxygen, and total dissolved solids; whereas, bioluminescent assemblages were explained only by salinity and dissolved oxygen, and had greater variability.ConclusionHigh-throughput sequencing and genotyping revealed greater diversity of dinoflagellate assemblages than previously known in both subtropical and temperate Australian waters. Significant correlations of assemblage structure with environmental variables suggest the potential for explaining the distribution and composition of both HAB species and bioluminescent species.
| S-EPMC7885227 | biostudies-literature
Project description:Seagrass meadows play pivotal roles in coastal biochemical cycles, with nitrogen fixation being a well-established process associated with living seagrass. Here, we tested the hypothesis that nitrogen fixation is also associated with seagrass debris in Danish coastal waters. We conducted a 52-day in situ experiment to investigate nitrogen fixation (proxied by acetylene reduction) and dynamics of the microbial community (16S rRNA gene amplicon sequencing) and the nitrogen fixing community (nifH DNA/RNA amplicon sequencing) associated with decomposing Zostera marina leaves. The leaves harboured distinct microbial communities, including distinct nitrogen fixers, relative to the surrounding seawater and sediment throughout the experiment. Nitrogen fixation rates were measurable on most days, but highest on days 3 (dark, 334.8 nmol N g-1 dw h-1) and 15 (light, 194.6 nmol N g-1 dw h-1). Nitrogen fixation rates were not correlated with the concentration of inorganic nutrients in the surrounding seawater or with carbon:nitrogen ratios in the leaves. The composition of nitrogen fixers shifted from cyanobacterial Sphaerospermopsis to heterotrophic genera like Desulfopila over the decomposition period. On the days with highest fixation, nifH RNA gene transcripts were mainly accounted for by cyanobacteria, in particular by Sphaerospermopsis and an unknown taxon (order Nostocales), alongside Proteobacteria. Our study shows that seagrass debris in temperate coastal waters harbours substantial nitrogen fixation carried out by cyanobacteria and heterotrophic bacteria that are distinct relative to the surrounding seawater and sediments. This suggests that seagrass debris constitutes a selective environment where degradation is affected by the import of nitrogen via nitrogen fixation.
| S-EPMC11324715 | biostudies-literature
Project description:In the marine environment, the reactive oxygen species (ROS) superoxide is produced through a diverse array of light-dependent and light-independent reactions, the latter of which is thought to be primarily controlled by microorganisms. Marine superoxide production influences organic matter remineralization, metal redox cycling, and dissolved oxygen concentrations, yet the relative contributions of different sources to total superoxide production remain poorly constrained. Here we investigate the production, steady-state concentration, and particle-associated nature of light-independent superoxide in productive waters off the northeast coast of North America. We find exceptionally high levels of light-independent superoxide in the marine water column, with concentrations ranging from 10 pM to in excess of 2,000 pM. The highest superoxide concentrations were particle associated in surface seawater and in aphotic seawater collected meters off the seafloor. Filtration of seawater overlying the continental shelf lowered the light-independent, steady-state superoxide concentration by an average of 84%. We identify eukaryotic phytoplankton as the dominant particle-associated source of superoxide to these coastal waters. We contrast these measurements with those collected at an off-shelf station, where superoxide concentrations did not exceed 100 pM, and particles account for an average of 40% of the steady-state superoxide concentration. This study demonstrates the primary role of particles in the production of superoxide in seawater overlying the continental shelf and highlights the importance of light-independent, dissolved-phase reactions in marine ROS production.
| S-EPMC7685101 | biostudies-literature
Project description:We investigated the distribution of vibrios in Shenzhen coastal waters in order to obtain valuable information for the aquaculture industry and a health warning system. Quantities of vibrios from surface waters ranged from 0 to 4.40×10(4) CFUs mL(-1) in April (spring), while from 0 to 2.57×10(3) CFUs mL(-1) in September (autumn); the abundance of V. alginolyticus-like species from surface water ranged from 0 to 6.72×10(3) CFUs mL(-1) in April (spring) and from 0 to 1.28×10(3) CFUs mL(-1) in September (autumn); higher counts were observed in spring. The V. alginolyticus-like species was dominant in Shenzhen coastal waters, with the highest abundance in the clean region (stations YMK001 and GDN064) in April, suggesting that Vibrio spp. were naturally occurring bacteria in marine environments. The correlation between the abundance of vibrios (including V. alginolyticus-like species) and environmental factors varied in different regions and different seasons. There were no vibrios detected when the salinity was less than 11.15‰ in the Zhujiang River estuary, which indicated that salinity played a key role in the distribution of vibrios and V. alginolyticus-like species.
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Project description:The presence of human norovirus in the aquatic environment can cause outbreaks related to recreational activities and the consumption of norovirus-contaminated clams. In this study, we investigated the prevalence of norovirus genogroups I (GI) and II (GII) in the coastal aquatic environment in South Korea (March 2014 to February 2015). A total of 504 water samples were collected periodically from four coastal areas (total sites = 63), of which 44 sites were in estuaries (clam fisheries) and 19 were in inflow streams. RT-PCR analysis targeting ORF2 region C revealed that 20.6% of the water samples were contaminated by GI (13.3%) or GII (16.6%). The prevalence of human norovirus was higher in winter/spring than in summer/fall, and higher in inflow streams (50.0%) than in estuaries (7.9%). A total of 229 human norovirus sequences were identified from the water samples, and phylogenetic analysis showed that the sequences clustered into eight GI genotypes (GI.1, 2, 3, 4, 5, 6, 7, and 9) and nine GII genotypes (GII.2, 3, 4, 5, 6, 11, 13, 17, and 21). This study highlighted three issues: 1) a strong correlation between norovirus contamination via inflow streams and coastal areas used in clam fisheries; 2) increased prevalence of certain non-GII.4 genotypes, exceeding that of the GII.4 pandemic variants; 3) seasonal shifts in the dominant genotypes of both GI and GII.
| S-EPMC5040428 | biostudies-literature
Project description:In zooplankton surveys, many smaller taxa or species considered less important are often overlooked. One such example is the actinotrocha larvae of phoronid worms that are rarely quantified in zooplankton samples yet may play important roles in marine food webs. To gain a better understanding of phoronid ecology in coastal waters, we retrospectively analysed 145 plankton samples collected from two coastal sites in Ireland (Lough Hyne and Bantry Bay). Samples were collected using plankton nets from depths of 20 and 40 m. Phoronids were present in 37.7% and 38.2% of samples, with mean abundances of 0.3 ± 0.5 ind. m-3 and 1.2 ± 2.8 ind. m-3, respectively, and were identified as Phoronis muelleri and Phoronis hippocrepia. Phoronids were present consistently each year from April to October at Lough Hyne and from February to October at Bantry Bay. Comparisons with other taxa in Lough Hyne show that abundances are similar to those of fish larvae (1.1 ± 1.8 ind. m-3) and echinoderm larvae (2.3 ± 4.4 ind. m-3). Examination of these samples from Irish waters suggests that phoronids are more abundant in temperate waters than previously reported.Supplementary informationThe online version contains supplementary material available at 10.1007/s10452-022-09982-6.
| S-EPMC9618493 | biostudies-literature
Project description:Cyanobacteria are ubiquitous in marine environments and play an important role as primary producers. Some cyanobacteria, the so-called cyanobionts (cyanobacterial symbionts), have a symbiotic relationship with unicellular organisms. Among these relationships, in particular, the nature (e.g., genetic diversity, host or cyanobiont specificity, and cyanobiont seasonality) of the cyanobiont-dinoflagellate host consortia remains poorly understood. In this study, 16S rDNA of cyanobionts in 138 single host cells isolated over four seasons from temperate waters were sequenced using the MiSeq platform. Genetic analysis of cyanobionts from the dinoflagellate host Ornithocercus revealed that three genetic types of Synechococcales cyanobionts occurred in a wide range of water temperatures (11-24 °C), and their distribution seemed to be closely associated with variations in salinity. Furthermore, a certain degree of host (or cyanobiont) specificity in cyanobionts (or the host) among Ornithocercus species as well as among other dinophysoid species (i.e. Amphisolenia, Citharistes, and Histioneis), was observed. In addition to the Synechococcales cyanobionts, this study identified OTU sequences affiliated with Vampirovibrionales and Chroococcidiopsidales in some Ornithocercus cells, suggesting that Ornithocercus species are an additional habitat for these bacterial groups.
| S-EPMC8097063 | biostudies-literature