Biology subjects

Andres, K. J.

Publications and source records attributed to Andres, K. J..

3 recordsLinked to original sources

bioRxiv2025

Globally unified analysis of riverine eDNA reveals common associations of fish biodiversity with drainage characteristics

Freshwater biodiversity is declining at a pace that outstrips the capacity of existing monitoring approaches both in temporal and spatial dimensions, highlighting the urgent need for rapid and scalable assessment and attribution of biodiversity states and changes. Here, we present one of the first global assessments and unified analyses of riverine fish biodiversity using environmental DNA (eDNA) collected from 1818 sites across 113 river systems. We quantified species richness, functional redundancy, phylogenetic diversity, and genetic sequence diversity, and related them to drainage characteristics. Our results showed that eDNA effectively captured global patterns of multi-faceted riverine fish biodiversity and disentangled the roles of climate and human activities in shaping biodiversity-area relationships. Catchments in warmer climates consistently enhanced biodiversity accumulation with area, while higher human activity intensity weakened this scaling. Species richness, functional, and genetic sequence diversity exhibited stronger negative responses to human activities in larger catchments. In contrast, phylogenetic diversity showed the strongest negative effects in smaller catchments with these impacts diminishing as catchment area increased, highlighting the facet-dependent nature of biodiversity responses to environmental gradients. Our findings demonstrate the power of eDNA-based datasets for harmonized, multi-faceted biodiversity assessments, offering a scalable approach for detecting and attributing biodiversity change and informing conservation strategies under accelerating global change.

ecology↗

bioRxiv2025

Integrated reanalysis of global riverine fish eDNA datasets shows robustness and congruence of biodiversity conclusions

The analysis of environmental DNA (eDNA) has revolutionized biodiversity assessments in aquatic ecosystems, enabling non-invasive monitoring of fish communities across diverse regions. However, the global comparability of these eDNA datasets remains ambiguous due heterogeneous sampling protocols and bioinformatic workflows across studies, particularly regarding the robustness of their conclusions on biodiversity assessments. Here, we conducted a meta-analysis of 58 riverine fish eDNA metabarcoding datasets, covering 1,818 sampling sites worldwide, to evaluate the robustness of eDNA-derived biodiversity patterns. We found that species richness estimates and metrics of community structure derived under a common bioinformatic workflow were overall consistent with those of original analyses, despite the relatively high variability in bioinformatic analyses in the respective original studies. Contrastingly, congruence of species identity varied more extensively across datasets, mostly reflecting different completeness and regional relevance of reference databases. Restricting taxonomic assignment to basin-specific species pools improved species identification accuracy, while datasets lacking publicly accessible or well-curated reference data were more prone to mismatches. Year of sampling had a positive effect on taxonomic congruence, such that more recent studies showed increased robustness, also reflecting improved reference database coverage and enhanced species-level identification over time and overall method congruence in more recent years. Overall, the suitability and potential of eDNA for global biodiversity monitoring is corroborating overall robust biodiversity estimates, irrespective of the bioinformatic approaches. Our study underlines the effectiveness and need of further harmonization of bioinformatic workflows and strengthened region-specific reference databases for improved taxonomic resolution and comparability across studies.

ecology↗

bioRxiv2023

Life stage and vaccination shape the gut microbiome of hatchery-reared Atlantic salmon (Salmo salar)

Microbiomes play an essential role in promoting host health and fitness, but the factors affecting variation in gut microbiomes among individuals are not fully understood. Investigating the microbiome under different conditions is needed to link gut microbiomes to host physiology and potentially design manipulations to improve rearing success of captive species. In this study, we characterized the gut microbiomes of Atlantic salmon (Salmo salar) in individuals at different life stages, vaccination status, and hatchery origin. Microbiomes differed between age-0 sub-adults and adults, with sub-adults exhibiting higher diversity and more similar communities when compared to adults. We also found that vaccines against bacterial kidney disease reduced gut microbial diversity within individual sub-adult salmon, resulting in dissimilar gut microbial communities among individuals. The diversity and structure of microbiomes did not differ between groups of adults that were reared in two different hatcheries and sampled from the wild. Sub-adults, particularly unvaccinated sub-adults, displayed a strong core microbiome present in the majority of individuals. Our results suggest that life stage and vaccination status are essential factors in the gut microbiome development of salmon. Conditions experienced during early life stages appear to have a strong influence on the microbiome, but differences among individuals at early life stages may be lost due to environmental factors experienced later in life. The plasticity of the microbiome throughout the life of individuals may have important implications for understanding host health, with potential applications for improving the rearing and reintroduction success of the ecologically and economically important Atlantic salmon. IMPORTANCEThe Atlantic salmon (Salmo salar) is a globally important fisheries and aquaculture species, but the factors affecting gut microbiomes of hatchery-reared fish are not fully understood. Our study explores the influence of life stage, vaccination status, and hatchery origin on the composition and structure of the Atlantic salmon gut microbiome. We found that life stage is an important driver of gut microbiome diversity, likely driven by differences in habitat and diet. Vaccination against bacterial kidney disease led to marked declines in gut microbial diversity within individuals, resulting in highly distinct gut microbial communities among individuals. Hatchery origin did not have a strong influence on adult Atlantic salmon captured from the wild. These findings suggest that life stage and vaccination drive variation in Atlantic salmon microbiomes, but the stability and long-term implications of such variation on host health should be considered in future microbiome research.

microbiology↗