Dataset Information

Whole-genome sequence analysis of environmental Escherichia coli from the faeces of straw-necked ibis (Threskiornis spinicollis) nesting on inland wetlands.

ABSTRACT: Wildlife, and birds in particular, play an increasingly recognized role in the evolution and transmission of Escherichia coli that pose a threat to humans. To characterize these lineages and their potential threat from an evolutionary perspective, we isolated and performed whole-genome sequencing on 11 sequence types (STs) of E. coli recovered from the desiccated faeces of straw-necked ibis (Threskiornis spinicollis) nesting on inland wetlands located in geographically different regions of New South Wales, Australia. Carriage of virulence-associated genes was limited, and no antimicrobial resistance genes were detected, but novel variants of an insertion element that plays an important role in capturing and mobilizing antibiotic resistance genes, IS26, were identified and characterized. The isolates belonged to phylogroups B1 and D, including types known to cause disease in humans and animals. Specifically, we found E. coli ST58, ST69, ST162, ST212, ST446, ST906, ST2520, ST6096 and ST6241, and a novel phylogroup D strain, ST10208. Notably, the ST58 strain hosted significant virulence gene carriage. The sequences of two plasmids hosting putative virulence-associated factors with incompatibility groups I1 and Y, an extrachromosomal integrative/conjugative element, and a variant of a large Escherichia phage of the family Myoviridae, were additionally characterized. We identified multiple epidemiologically relevant gene signatures that link the ibis isolates to sequences from international sources, plus novel variants of IS26 across different sequence types and in different contexts.

SUBMITTER: Wyrsch ER

PROVIDER: S-EPMC7371105 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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Whole-genome sequence analysis of environmental Escherichia coli from the faeces of straw-necked ibis (Threskiornis spinicollis) nesting on inland wetlands.

Wyrsch Ethan R ER Chowdhury Piklu Roy PR Wallis Louise L Cummins Max L ML Zingali Tiziana T Brandis Kate J KJ Djordjevic Steven P SP

Microbial genomics 20200610 6

Wildlife, and birds in particular, play an increasingly recognized role in the evolution and transmission of Escherichia coli that pose a threat to humans. To characterize these lineages and their potential threat from an evolutionary perspective, we isolated and performed whole-genome sequencing on 11 sequence types (STs) of E. coli recovered from the desiccated faeces of straw-necked ibis (Threskiornis spinicollis) nesting on inland wetlands located in geographically diffe ...[more]

PMID: 32519939

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Project description:Headwater streams and inland wetlands provide essential functions that support healthy watersheds and downstream waters. However, scientists and aquatic resource managers lack a comprehensive synthesis of national and state stream and wetland geospatial datasets and emerging technologies that can further improve these data. We conducted a review of existing United States (US) federal and state stream and wetland geospatial datasets, focusing on their spatial extent, permanence classifications, and current limitations. We also examined recent peer-reviewed literature for emerging methods that can potentially improve the estimation, representation, and integration of stream and wetland datasets. We found that federal and state datasets rely heavily on the US Geological Survey's National Hydrography Dataset for stream extent and duration information. Only eleven states (22%) had additional stream extent information and seven states (14%) provided additional duration information. Likewise, federal and state wetland datasets primarily use the US Fish and Wildlife Service's National Wetlands Inventory (NWI) Geospatial Dataset, with only two states using non-NWI datasets. Our synthesis revealed that LiDAR-based technologies hold promise for advancing stream and wetland mapping at limited spatial extents. While machine learning techniques may help to scale-up these LiDAR-derived estimates, challenges related to preprocessing and data workflows remain. High-resolution commercial imagery, supported by public imagery and cloud computing, may further aid characterization of the spatial and temporal dynamics of streams and wetlands, especially using multi-platform and multi-temporal machine learning approaches. Models integrating both stream and wetland dynamics are limited, and field-based efforts must remain a key component in developing improved headwater stream and wetland datasets. Continued financial and partnership support of existing databases is also needed to enhance mapping and inform water resources research and policy decisions.

Project description:BackgroundPlants play a pivotal role in soil stabilization, with above-ground vegetation and roots combining to physically protect soil against erosion. It is possible that diverse plant communities boost root biomass, with knock-on positive effects for soil stability, but these relationships are yet to be disentangled.QuestionWe hypothesize that soil erosion rates fall with increased plant species richness, and test explicitly how closely root biomass is associated with plant diversity.MethodsWe tested this hypothesis in salt marsh grasslands, dynamic ecosystems with a key role in flood protection. Using step-wise regression, the influences of biotic (e.g. plant diversity) and abiotic variables on root biomass and soil stability were determined for salt marshes with two contrasting soil types: erosion-resistant clay (Essex, southeast UK) and erosion-prone sand (Morecambe Bay, northwest UK). A total of 132 (30-cm depth) cores of natural marsh were extracted and exposed to lateral erosion by water in a re-circulating flume.ResultsSoil erosion rates fell with increased plant species richness (R2 = 0.55), when richness was modelled as a single explanatory variable, but was more important in erosion-prone (R2 = 0.44) than erosion-resistant (R2 = 0.18) regions. As plant species richness increased from two to nine species·m-2, the coefficient of variation in soil erosion rate decreased significantly (R2 = 0.92). Plant species richness was a significant predictor of root biomass (R2 = 0.22). Step-wise regression showed that five key variables accounted for 80% of variation in soil erosion rate across regions. Clay-silt fraction and soil carbon stock were linked to lower rates, contributing 24% and 31%, respectively, to variation in erosion rate. In regional analysis, abiotic factors declined in importance, with root biomass explaining 25% of variation. Plant diversity explained 12% of variation in the erosion-prone sandy region.ConclusionOur study indicates that soil stabilization and root biomass are positively associated with plant diversity. Diversity effects are more pronounced in biogeographical contexts where soils are erosion-prone (sandy, low organic content), suggesting that the pervasive influence of biodiversity on environmental processes also applies to the ecosystem service of erosion protection.

Dataset Information

Whole-genome sequence analysis of environmental Escherichia coli from the faeces of straw-necked ibis (Threskiornis spinicollis) nesting on inland wetlands.

Publications

Whole-genome sequence analysis of environmental <i>Escherichia coli</i> from the faeces of straw-necked ibis (<i>Threskiornis spinicollis</i>) nesting on inland wetlands.

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