Search

Sampling and sequencing marine environmental DNA (eDNA) provides a tool that can increase our ability to monitor biodiversity, but movement and mixing of eDNA after release from organisms before collection could affect our inference of species distributions. To assess how conditions at differing spatial scales influence the inferred species richness and compositional turnover, we conducted a paired eDNA metabarcoding and capture (beach seining) survey of fishes on the coast of British Columbia. We found more taxa were typically detected using eDNA compared to beach seining. eDNA identified more taxa with alternative habitat preferences, and this richness difference was greater in areas of high seawater movement, suggesting eDNA has a larger spatial grain influenced by water motion. By contrast, we found that eDNA consistently missed low biomass species present in seining surveys. Spatial turnover of communities surveyed using beach seining differed from that of the eDNA and was better explained by factors that vary at small (10–1000s meters) spatial scales. Specifically, vegetation cover and shoreline exposure explained most species turnover from seining, while eDNA turnover was not explained by those factors and showed a distance decay pattern (a change from 10% to 25% similarity from 2 km to 10 km of distance), suggesting unmeasured environmental variation at larger scales drives its turnover. Our findings indicate that the eDNA sample grain is larger than that of capture surveys. Whereas seining can detect differences in fish distributions at scales of 10s–100s of meters, eDNA can best summarize fish biodiversity at larger scales possibly more relevant to regional biodiversity assessments.

Abstract Marine scientific trawl surveys are commonly used to assess the distribution and population size of fisheries‐related species, yet the method is effort‐intensive and can be environmentally destructive. Sequencing environmental DNA (eDNA) from water samples can reveal the presence of organisms in a community without capturing them; however, we expect the detectability of taxa to differ between eDNA and trawl surveys, and understanding how species traits and population variables contribute to detection differences can help calibrate our expectations from each form of sampling. Here, we coupled eDNA metabarcoding and capture trawl surveys in British Columbia, Canada, to examine species traits that explain recurrent differences in detectability between the two methods, including habitat, body size, and biomass. At the regional scale, 17 of 23 fish species (74%) captured by the trawl were detected by eDNA metabarcoding, and 39 additional species were detected by eDNA sampling only. We found that eDNA metabarcoding disproportionately detected trawl‐caught species with greater local biomass (i.e., greater biomass in the adjacent trawl). Fish detected only in eDNA had a greater range of body lengths and a broader range of habitat preferences outside the trawls' target size and sampling areas. Our results suggest that with our level of sampling, eDNA metabarcoding can adequately recapitulate detection of fish communities detected by trawl surveys, but with a bias toward fish of high population biomass and greater inclusion of fish from outside the trawled area.

The rocky reefs of British Columbia’s (BC) coast are a productive ecosystem, home to 38 rockfish species (Genus: Sebastes) that are culturally and economically important. Quantitatively assessing rockfish populations is vital to support conservation and stock assessment needs. Self-contained underwater breathing apparatus (SCUBA) diving surveys are a commonly used monitoring method in BC. However, this resource-intensive approach is challenging, particularly for cryptic or deeper species. Herein, we compared environmental DNA (eDNA) detection methods with SCUBA diving surveys to capture overall rockfish biodiversity. We employed two eDNA methods: 1) a targeted quantitative real-time polymerase chain reaction (qPCR) approach to monitor species of particular importance to First Nations collaborators and decision makers, and 2) a metabarcoding approach for assessing community composition using the previously published MiSebastes assay. Both approaches are confounded by the little DNA sequence divergence among species and high sequence variation within species. Overcoming these challenges using a whole mitochondrial approach with the mtGrasp and unikseq pipelines, we generated highly useful eDNA tools. We found that eDNA methods were highly comparable to dive surveys, as both methods indicated a similar ecological reality, including species detections and distributions. Though there are certain species that cannot be distinguished by the MiSebastes assay, eDNA metabarcoding still detected more rockfish species overall. Both eDNA methods show potential for use alongside conventional methods for scalable incorporation into community-based monitoring programs.

Abstract Marine biodiversity is a key indicator of ecosystem health and can be assessed using a variety of methods, including environmental DNA (eDNA) sampling. However, the ecology of eDNA in physically dynamic nearshore environments remains uncertain, particularly with regards to how eDNA stratifies with depth. Here, we paired eDNA sampling with dive surveys at six sites in Knight Inlet, British Columbia, Canada. eDNA samples were collected from the surface, midwater column and bottom (8–25 m depth) at each site, while dive surveys focused on the bottom (benthic) habitat. Amplicon sequencing using the mitochondrial 12S rRNA gene (targeting fish) and the COI gene (targeting marine invertebrates and algae) resolved significant differences in community composition in surface waters compared with midwater and bottom. Differences by depth were greater than differences across sites, with surface waters dominated by salmon (Oncorhynchus spp.) and rotifer DNA, and midwater and bottom samples largely dominated by Pacific herring, copepods, and mussels. eDNA samples collected at the surface, therefore, may not accurately capture benthic communities, particularly in systems with high levels of freshwater input such as coastal temperate fjords. Over small spatial scales, particularly in systems with strong stratification, adding samples from different depths may be more effective at maximizing inferred diversity rather than sampling more sites. In general, there was low overlap in species detection between dive and eDNA surveys (less than 10% for each taxonomic group – fish, invertebrates, and algae). However, we observed clear strengths for each method – dive surveys provided better taxonomic resolution, while eDNA resolved greater total diversity. These results suggest that the two survey methods can be used in tandem to provide distinct and complementary snapshots of marine biodiversity in the nearshore environment.

Sampling and sequencing marine environmental DNA (eDNA) provides a tool that can increase our ability to monitor biodiversity, but movement and mixing of eDNA after release from organisms before collection could affect our inference of species distributions. To assess how conditions at differing spatial scales influence the inferred species richness and compositional turnover, we conducted a paired eDNA metabarcoding and capture (beach seining) survey of fishes on the coast of British Columbia. We found more taxa were typically detected using eDNA compared to beach seining. eDNA identified more taxa with alternative habitat preferences, and this richness difference was greater in areas of high seawater movement, suggesting eDNA has a larger spatial grain influenced by water motion. By contrast, we found that eDNA consistently missed low biomass species present in seining surveys. Spatial turnover of communities surveyed using beach seining differed from that of the eDNA and was better explained by factors that vary at small (10–1000s meters) spatial scales. Specifically, vegetation cover and shoreline exposure explained most species turnover from seining, while eDNA turnover was not explained by those factors and showed a distance decay pattern (a change from 10% to 25% similarity from 2 km to 10 km of distance), suggesting unmeasured environmental variation at larger scales drives its turnover. Our findings indicate that the eDNA sample grain is larger than that of capture surveys. Whereas seining can detect differences in fish distributions at scales of 10s–100s of meters, eDNA can best summarize fish biodiversity at larger scales possibly more relevant to regional biodiversity assessments. [ABSTRACT FROM AUTHOR]

The seagrass Zostera marina is a widespread foundational species in temperate coastal ecosystems that supports diverse communities of epiphytes and grazers. Bacteria link the production of seagrass to higher trophic levels and are thought to influence seagrass biology and health. Yet, we lack a clear understanding of the factors that structure the seagrass microbiome, or whether there is a consistent microbial community associated with seagrass that underpins functional roles. We sampled surface microbiome (epibiota) from new and old growth seagrass leaves and the surrounding seawater in eight meadows among four regions along the Central Coast of British Columbia, Canada to assess microbiome variability across space and as leaves age. We found that the seagrass leaf microbiome differs strongly from seawater. Microbial communities in new and old growth leaves are different from each other and from artificial seagrass leaves we deployed in one meadow. The microbiome on new leaves is less diverse and there is a small suite of core OTUs (operational taxonomic units) consistently present across regions. The overall microbial community for new leaves is more dispersed but with little regional differentiation, while the epiphytes on old leaves are regionally distinct. Many core OTUs on old leaves are commonly associated with marine biofilms. Together these observations suggest a stronger role for host filtering in new compared to old leaves, and a stronger influence of the environment and environmental colonization in old leaves. We found 11 core microbial taxa consistently present on old and new leaves and at very low relative abundance on artificial leaves and in the water column. These 11 taxa appear to be strongly associated with Z. marina. These core taxa may perform key functions important for the host such as detoxifying seagrass waste products, enhancing plant growth, and controlling epiphyte cover.

The One-to-One program aims to reduce criminal recidivism among prisoners shortly awaiting release, and among probationers. Of 1,484 program participants in Sweden, 776 contained adequate data for analysis. Pre- and post-program scores were available for the Alternative Thinking Test, Levenson's Locus of Control Scale, Skill Survey, Citizen Scale, and Problem Checklist, all areas addressed in the program. This study examined predictive properties of test scores and background characteristics regarding recidivism, as well as differences between sub-groups. All post-tests indicated pro-social changes. Older participants were more likely to complete the program. The most potent predictor for non-recidivism was program completion, with non-completers 64% more likely to re-offend. Significant associations occurred between recidivism and the tests measuring skill improvement over time, chance locus of control pre- and post-program, and attitudes and values (Citizen Scale), partly supporting the theory behind the program.

Colonization by the benign tapeworm, Hymenolepis diminuta, has been associated with a reduction in intestinal inflammation and changes in bacterial microbiota. However, the role of microbiota in the tapeworm anti-inflammatory effect is not yet clear, and the aim of this study was to determine whether disruption of the microflora during worm colonization can affect the course of intestinal inflammation. We added a phase for disrupting the intestinal microbiota using antibiotics to the experimental design for which we previously demonstrated the protective effect of H. diminuta. We monitored the immunological markers, clinical parameters, bacterial microbiota, and histological changes in the colon of rats. After a combination of colonization, antibiotics, and colitis induction, we had four differently affected experimental groups. We observed a different course of the immune response in each group, but no protective effect was found. Rats treated with colonization and antibiotics showed a strong induction of the Th2 response as well as a significant change in microbial diversity. The microbial results also revealed differences in the richness and abundance of some bacterial taxa, influenced by various factors. Our data suggest that interactions between the tapeworm and bacteria may have a major impact on its protective effect.

ABSTRACT Blastocystis is the most prevalent protist of the human intestine, colonizing approximately 20% of the North American population and up to 100% in some nonindustrialized settings. Blastocystis is associated with gastrointestinal and systemic disease but can also be an asymptomatic colonizer in large populations. While recent findings in humans have shown bacterial microbiota changes associated with this protist, it is unknown whether these occur due to the presence of Blastocystis or as a result of inflammation. To explore this, we evaluated the fecal bacterial and eukaryotic microbiota in 156 asymptomatic adult subjects from a rural population in Xoxocotla, Mexico. Colonization with Blastocystis was strongly associated with an increase in bacterial alpha diversity and broad changes in beta diversity and with more discrete changes to the microbial eukaryome. More than 230 operational taxonomic units (OTUs), including those of dominant species Prevotella copri and Ruminococcus bromii, were differentially abundant in Blastocystis-colonized individuals. Large functional changes accompanied these observations, with differential abundances of 202 (out of 266) predicted metabolic pathways (PICRUSt), as well as lower fecal concentrations of acetate, butyrate, and propionate in colonized individuals. Fecal calprotectin was markedly decreased in association with Blastocystis colonization, suggesting that this ecological shift induces subclinical immune consequences to the asymptomatic host. This work is the first to show a direct association between the presence of Blastocystis and shifts in the gut bacterial and eukaryotic microbiome in the absence of gastrointestinal disease or inflammation. These results prompt further investigation of the role Blastocystis and other eukaryotes play within the human microbiome. IMPORTANCE Given the results of our study and other reports of the effects of the most common human gut protist on the diversity and composition of the bacterial microbiome, Blastocystis and, possibly, other gut protists should be studied as ecosystem engineers that drive community diversity and composition.

BackgroundHealth information exchange (HIE) systems are implemented nationwide to integrate health information and facilitate communication among providers. The Nebraska Health Information Initiative is a state-wide HIE launched in 2009. Objective The purpose of this study was to conduct a comprehensive assessment of health care providers’ perspectives on a query-based HIE, including barriers to adoption and important functionality for continued utilization. MethodsWe surveyed 5618 Nebraska health care providers in 2013. Reminder letters were sent 30 days after the initial mailing. ResultsA total of 615 questionnaires (11%) were completed. Of the 100 current users, 63 (63%) indicated satisfaction with HIE. The most common reasons for adoption among current or previous users of an HIE (N = 198) were improvement in patient care (N = 111, 56%) as well as receiving (N = 95, 48%) and sending information (N = 80, 40%) in the referral network. Cost (N = 233, 38%) and loss of productivity (N = 220, 36%) were indicated as the ‘major barriers’ to adoption by all respondents. Accessing a comprehensive patient medication list was identified as the most important feature of the HIE (N = 422, 69%). ConclusionsThe cost of HIE access and workflow integration are significant concerns of health care providers. Additional resources to assist practices plan the integration of the HIE into a sustainable workflow may be required before widespread adoption occurs. The clinical information sought by providers must also be readily available for continued utilization. Query-based HIEs must ensure that medication history, laboratory results and other desired clinical information be present, or long-term utilization of the HIE is unlikely.