Biology subjects

Gante, H. F.

Publications and source records attributed to Gante, H. F..

6 recordsLinked to original sources

bioRxiv2025

Improving eDNA filtration and purification for qPCR detection of Schistosoma mansoni in lakes Albert and Victoria

BackgroundSchistosomiasis, a parasitic disease caused by Schistosoma trematodes, remains a significant public health burden in sub-Saharan Africa, particularly in regions with limited access to clean water, sanitation and hygiene. Effective disease control strategies rely on large-scale surveillance to accurately identify and target high-risk populations. However, traditional methods such as malacological surveys and stool/urine microscopy in humans often lack sensitivity and scalability. Environmental DNA (eDNA) is emerging as a promising tool for non-invasive surveillance of aquatic pathogens, offering enhanced sensitivity and feasibility for large-scale monitoring. MethodsThis study evaluated the efficacy of eDNA-based detection of Schistosoma mansoni in water samples from Lake Albert and Lake Victoria, Uganda. Three eDNA filtration techniques: open membrane, Waterra capsule and Sylphium capsule filters, were compared for DNA yield and detection efficiency. SYBR Green quantitative polymerase chain reaction (qPCR) targeting the mitochondrial cytochrome oxidase subunit I (COI) gene was performed to quantify S. mansoni eDNA, following in silico and in vitro optimisation of primers. Conventional malacological surveys were conducted in parallel to validate eDNA findings, and statistical analyses examined the influence of environmental factors (turbidity and total dissolved solids (TDS)) on eDNA yield and detection rates. ResultsThe SYBR Green S. mansoni qPCR assay had a practical limit of detection (LOD), defined as amplification in >95% of 33 technical replicates, of 100 copies per reaction. The assay amplified in 82% of reactions with 10 DNA copies and 76% with a single copy. The theoretical LOD, determined via amplification probabilities in RStudio, was 83 copies per reaction, which was also the calculated limit of quantification (LOQ). Schistosoma mansoni eDNA was detected in 58.1% (25/43) of filters from Lake Albert and 19.2% (10/52) from Lake Victoria. The Waterra capsule filter yielded the highest eDNA concentrations, while the Sylphium-coupled capsule filter exhibited comparable detection efficiency. Among the DNA purification methods tested, the Sylphium precipitation-based protocol produced significantly higher eDNA yield than column-based kits (DNeasy Blood and Tissue and Zymo Research). Despite significant variation in eDNA recovery across filtration methods, qPCR detection rates were consistent. No significant correlation was observed between turbidity and S. mansoni eDNA detectability. ConclusionOur findings highlight the potential of eDNA as a sensitive, scalable tool for schistosomiasis surveillance. While Waterra filters and Sylphium extraction maximised DNA yield, lower-yield filtration methods still enabled S. mansoni detection in high-transmission settings. These findings support the adaptability of eDNA approaches across varying resource contexts. Future work should prioritise protocol standardisation, ecological validation, and development of field-ready diagnostics such as LAMP to enable broader implementation in endemic regions.

molecular biology↗

bioRxiv2025

Freshwater fish community assessment using eDNA metabarcoding vs. capture-based methods: differences in efficiency and resolution coupled to habitat and ecology

Environmental DNA (eDNA) metabarcoding has revolutionized ecological and environmental research by describing communities without relying on direct observations, making it a powerful, non-invasive, and cost-effective tool in biodiversity monitoring. However, implementation of eDNA as a standard protocol in long-term monitoring programs, that have traditionally relied on capture-based methods, poses challenges in terms of data comparability. Here, we compared freshwater fish communities assessed through eDNA metabarcoding and electrofishing, across 35 sampling sites in the lower Tagus River basin, Portugal. For most species or species-groups analyzed individually (13 out of 17), there was a significant correspondence between electrofishing and eDNA metabarcoding detections. The correspondence was weaker when comparing the number of specimens captured by electrofishing with the number of eDNA metabarcoding reads, with seven out of 13 taxa showing significant relationships. Species richness estimates based on the two methods were very similar at the basin level. The methods yielded significantly different species compositions, although these differences were driven by samples collected in the Tagus main channel, which is wider and has higher flow rates than tributaries. Benthic and shoreline fish communities showed similar species composition in the two methods, but this was not the case for pelagic communities, probably due to the higher water turnover of the pelagic zone and electrofishing inefficiency. Our results highlight the high potential of eDNA metabarcoding as a complementary method to electrofishing for freshwater fish monitoring, though further validation is needed to assess biases related to site-specific hydrological conditions and the ecology of the target species.

ecology↗

bioRxiv2024

Improving whole biodiversity monitoring and discovery with environmental DNA metagenomics

Environmental DNA (eDNA) metagenomics sequences all DNA molecules present in environmental samples and has the potential of identifying virtually any organism from which they are derived. However, due to unacceptable levels of false positives and negatives, this approach is underexplored as a tool for biodiversity monitoring across the tree of life, particularly for non-microscopic eukaryotes. We present SEQIDIST, a framework that combines multilocus BLAST matches against several reference databases followed by analysis of sequence identity distribution patterns to disentangle false positives while revealing new biodiversity and increasing the accuracy of metagenomic approaches. We tested SEQIDIST on an eDNA metagenomic dataset from a riverine site and compare the results to those obtained with an eDNA metabarcoding approach for benchmarking purposes. We start by characterizing the biological community ([~] 2000 taxa) across the tree of life at low taxonomic levels and show that eDNA metagenomics has a higher sensitivity than eDNA metabarcoding in discovering new diversity. We show that limited representation of whole genome sequences in reference databases can lead to false positives. For non-microscopic eukaryotes, eDNA metagenomic data often consist of a few sparse, anonymous sequences scattered across the genome, making metagenome assembly methods unfeasible. Finally, we infer eDNA source and residency time using read length distributions as a measure of decay status. The higher accuracy of SEQIDIST opens the discussion of the archival potential of eDNA metagenomics and its implementation in biodiversity monitoring actions at large planetary and temporal scales.

ecology↗

bioRxiv2024

First evidence of a causal link between genetic variation and thermal adaptation in a schistosome host snail

Freshwater snails are pivotal in transmitting schistosomiasis, a tropical parasitic disease affecting over 150 million people. The adaptive potential of these snails is a critical factor in determining how climate change and other environmental factors influence disease transmission dynamics, yet it has remained unexplored. Bulinus truncatus is the schistosome intermediate host snail with the widest geographic distribution and therefore plays a pivotal role in determining the maximum range of urogenital schistosomiasis. In this study, we assessed the local adaptation capacity of B. truncatus to temperature through an integrative approach encompassing phenotypic, ecophysiological, and genomic data. Ten snail populations from diverse thermal environments were collected in three countries, with eight populations reared in a common garden. The F2 generation (total N= 2592) was exposed to eight chronic temperature treatments and various life-history traits were recorded for over 14 weeks. Subsequently, ecophysiological analyses were conducted on the ten last surviving snails per population. Genotyping the parental generation collected in the field using a genotyping-by-sequencing (GBS) approach, revealed 12,875 single nucleotide polymorphisms (SNPs), of which 4.91 % were potentially under selection. We observed a significant association between these outlier SNPs, temperature, and precipitation. Thermal adaptations in life-history traits were evident, with lower survival rates at high temperatures of warm- origin snails compensated for by higher reproduction rates. Cold-origin snails, on the other hand, exhibited higher growth rates adapted to a shorter growing season. Ecophysiological adaptations included elevated sugar and haemoglobin contents in cold-adapted snails. In contrast, warm-adapted snails displayed increased protein levels but also more oxidative damage. Furthermore, heightened phenoloxidase levels indicated a more robust immune response in snails from parasite-rich regions. The substantial local adaptation capacity of B. truncatus holds profound implications for its response to climate change, future schistosomiasis risk, and the effectiveness of schistosomiasis control measures. HighlightsO_LILocal adaptation influences species responses to climate change C_LIO_LIThe snail Bulinus truncatus showed a high thermal local adaptation (LA) potential C_LIO_LILA is apparent through variations in life history and ecophysiological traits C_LIO_LIWe identified a significant genetic basis underlying this LA C_LIO_LILA of the hosts could sustain schistosomiasis transmission under global warming C_LI

ecology↗

bioRxiv2022

Effects of haemosporidian co-infection and parasitemia on reproductive strategies in a polymorphic species

Host-parasite interactions play a significant role in evolution. Parasite infections impose fitness costs that can trigger trade-off responses in host reproductive strategies. Individuals can invest limited resources in parasite defense, such as stimulating the immune system, or perform terminal reproductive investment. Here, we investigated how haemosporidian co-infection and parasitemia influence different reproductive strategies in a polymorphic bird species (the white-throated sparrow, Zonotrichia albicollis). We provided an account of the impacts of co-infection and parasitemia on host reproductive success and reproductive strategies in response to parasite infection. We tested the effect of co-infection and parasitemia on reproductive success (fledgling number, extra-pair paternity, ratio social/genetic offspring) and the effect of parental infection on nestling quality (mean nestling growth rate and body condition). We found that co-infection increases reproductive extra-pair paternity and nestling mean body condition. Parental high parasitemia positively impacts the ratio of genetic offspring belonging to the social father and has mixed results on nestling quality. We observed that co-infection in females and parasitemia in males might trigger a switch in reproductive strategy towards a terminal investment for co-infected individuals. In contrast, high parasitemia in females negatively impacted their offspring fitness, possibly due to the reallocation of resources for fighting the infection.

ecology↗

bioRxiv2022

Widespread hybridization between invasive bleak (Alburnus alburnus) and native Iberian chubs (Squalius spp.): a neglected threat

Hybridization between native and exotic species is a major conservation issue. In Iberian rivers, which are simultaneously among the most invaded and diverse ecosystems, harboring a high proportion of endemic fishes, this issue is becoming highly concerning. To date, hybridization has been reported to occur between the invasive bleak Alburnus alburnus and the endemic chubs Squalius alburnoides and S. pyrenaicus, in some scattered locations. However, the bleak is increasingly spreading in the region, potentially increasing the risks of hybridization with these and other Squalius species. To gather a more comprehensive picture on the current extension of hybridization, we compiled and mapped records on hybrids between bleak and chubs collected by multiple research teams in different ongoing projects in the Portuguese territory, and genetically assessed the hybrid identity of specimens in an area of sympatry between bleak and S. carolitertii, using nuclear and mitochondrial markers. We found that hybridization with bleak is widespread in several Portuguese river basins and involves at least three endemic chubs, S. alburnoides, S. pyrenaicus and S. carolitertii. This may have serious consequences, including not only waste of reproductive effort and damage of genetic integrity, but also putative shifts on the reproductive dynamics of the Squalius system, which includes endemic hybrids, reproducing sexually and nonsexually. Hybridization should be recognized as a significant impact of biological invasions, and we recommend that future studies should characterize the fitness of hybrids and their ecological and genetic interactions with parental Iberian fish, to elucidate effective conservation measures.

zoology↗