Biology subjects

Czechowski, P.

Publications and source records attributed to Czechowski, P..

4 recordsLinked to original sources

bioRxiv2021

Environmental DNA analysis needs local reference data to inform taxonomy-based conservation policy:A case study from Aotearoa / New Zealand

Effective management of biodiversity requires regular surveillance of multiple species. Analysis of environmental DNA by metabarcoding (eDNA) holds promise to achieve this relatively easily. However, taxonomic inquiries into eDNA data need suitable molecular reference data, which are often lacking. We evaluate the impact of this reference data void in a case study of fish diversity in the remote fiords of New Zealand. We compared eDNA-derived species identifications against Baited Remote Underwater Video (BRUV) data collected at the same time and locations as the eDNA data. Furthermore, we cross referenced both eDNA and BRUV data against species lists for the same region obtained from literature surveys and the Ocean Biodiversity Information System (OBIS). From all four data sources, we obtained a total of 116 species records (106 ray-finned fishes, 10 cartilaginous fishes; 59 from literature, 44 from eDNA, 25 from BRUV, 25 from OBIS). Concordance of taxonomies between the data sources dissolved with lowering taxonomic levels, most decisively so for eDNA data. BRUV agreed with local biodiversity information much better and fared better in detecting regional biodiversity dissimilarities. We provide evidence that eDNA metabarcoding will remain a powerful but impaired tool for species-level biodiversity management without locally generated reference data.

ecology↗

bioRxiv2021

Global port survey quantifies commercial shippings effect on biodiversity

Spread of nonindigenous organisms by shipping is one of the largest threats to coastal ecosystems. Limited monitoring and understanding of this phenomenon currently hinder development of effective prevention policies. Surveying ports in North America, South America, Europe, Southeast Asia, and Australia we explored environmental DNA community profiles evident of ship-born species spread. We found that community similarities between ports increased with the number of ship voyages, particularly if the ports had similar environments, and when indirect stepping-stone connections were considered. We also found 57 known non-indigenous taxa, some in hitherto unreported locations. We demonstrate the usefulness of eDNA-based tools for global biodiversity surveys, and highlight that shipping homogenizes biodiversity in predictable that could inform policy and management.

ecology↗

bioRxiv2021

Tracing boundaries in Eastern Antarctica: Multi-scale drivers of soil microbial communities across the hyperarid Vestfold Hills

Microorganisms are key to sustaining core ecosystem processes across terrestrial Antarctica but they are rarely considered in conservation frameworks. Whilst greater advocacy has been made towards the inclusion of microbial data in this context, there is still a need for better tools to quantify multispecies responses to environmental change. Here, we extend the scope of Gradient Forest modelling beyond macroorganisms and small datasets to the comprehensive polar soil microbiome encompassing >17, 000 sequence variants for bacteria, micro-eukarya and archaea throughout the hyperarid Vestfold Hills of Eastern Antarctica. Quantification of microbial diversity against 79 physiochemical variables revealed that whilst rank-order importance differed, predictors were broadly consistent between domains, with greatest sharing occurring between bacteria and micro-eukarya. Moisture was identified as the most robust predictor for shaping the regional soil microbiome, with highest compositional turnover or "splits" occurring within the 10 - 12 % moisture content range. Often the most responsive taxa were rarer lineages of bacteria and micro-eukarya with phototrophic and nutrient-cycling capacities such as Cyanobacteria (up to 61.81 % predictive capacity), Chlorophyta (62.17 %) and Ochrophyta (57.81 %). These taxa groups are thus at greater risk of biodiversity loss or gain to projected climate trajectories, which will inevitably disturb current ecosystem dynamics. Better understanding of these threshold tipping points will positively aid conservation efforts across Eastern Antarctica. Furthermore, the successful implementation of an improved Gradient Forest model also presents an exciting opportunity to broaden its use on microbial systems globally.

microbiology↗

bioRxiv2021

Antarctic biodiversity predictions through substrate qualities and environmental DNA

Antarctic conservation science is important to enhance Antarctic policy and to understand alterations of terrestrial Antarctic biodiversity. Antarctic conservation will have limited long term effect in the absence of large-scale biodiversity data, but if such data were available, it is likely to improve environmental protection regimes. To enable Antarctic biodiversity prediction across continental spatial scales through proxy variables, in the absence of baseline surveys, we link Antarctic substrate-derived environmental DNA (eDNA) sequence data from the remote Antarctic Prince Charles Mountains to a selected range of concomitantly collected measurements of substrate properties. We achieve this using a statistical method commonly used in machine learning. We find neutral substrate pH, low conductivity, and some substrate minerals to be important predictors of presence for basidiomycetes, chlorophytes, ciliophorans, nematodes, or tardigrades. Our bootstrapped regression reveals how variations of the identified substrate parameters influence probabilities of detecting eukaryote phyla across vast and remote areas of Antarctica. We believe that our work may improve future taxon distribution modelling and aid targeting logistically challenging biodiversity surveys.

ecology↗