Metabarcoding and Metagenomics最新文献

{"title":"Optimising species detection probability and sampling effort in lake fish eDNA surveys","authors":"Graham S. Sellers, C. Jerde, Lynsey R. Harper, Marco Benucci, Cristina Di Muri, Jianlong Li, Graeme Peirson, Kerry Walsh, Tristan Hatton-Ellis, Willie Duncan, Alistair Duguid, Dave Ottewell, Nigel Willby, Alan Law, Colin W. Bean, I. Winfield, Daniel S. Read, Lori-Jayne Lawson Handley, B. Hänfling","doi":"10.3897/mbmg.8.104655","DOIUrl":"https://doi.org/10.3897/mbmg.8.104655","url":null,"abstract":"Environmental DNA (eDNA) metabarcoding is transforming biodiversity monitoring in aquatic environments. Such an approach has been developed and deployed for monitoring lake fish communities in Great Britain, where the method has repeatedly shown a comparable or better performance than conventional approaches. Previous analyses indicated that 20 water samples per lake are sufficient to reliably estimate fish species richness, but it is unclear how reduced eDNA sampling effort affects richness, or other biodiversity estimates and metrics. As the number of samples strongly influences the cost of monitoring programmes, it is essential that sampling effort is optimised for a specific monitoring objective. The aim of this project was to explore the effect of reduced eDNA sampling effort on biodiversity metrics (namely species richness and community composition) using algorithmic and statistical resampling techniques of a data set from 101 lakes, covering a wide spectrum of lake types and ecological quality. The results showed that reliable estimation of lake fish species richness could, in fact, usually be achieved with a much lower number of samples. For example, in almost 90% of lakes, 95% of complete fish richness could be detected with only 10 water samples, regardless of lake area. Similarly, other measures of alpha and beta-diversity were not greatly affected by a reduction in sample size from 20 to 10 samples. We also found that there is no significant difference in detected species richness between shoreline and offshore sampling transects, allowing for simplified field logistics. This could potentially allow the effective sampling of a larger number of lakes within a given monitoring budget. However, rare species were more often missed with fewer samples, with potential implications for monitoring of invasive or endangered species. These results should inform the design of eDNA sampling strategies, so that these can be optimised to achieve specific monitoring goals.","PeriodicalId":506127,"journal":{"name":"Metabarcoding and Metagenomics","volume":"24 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141810130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Improving understanding of nematode communities in agricultural settings: a comparison of mitometagenomics and morphology","authors":"Eli M. S. Gendron, Clemen J. Oliveira, J. Desaeger, D. Porazinska","doi":"10.3897/mbmg.8.123387","DOIUrl":"https://doi.org/10.3897/mbmg.8.123387","url":null,"abstract":"Florida’s strawberry production provides significant economic benefit for the State; however, plant-parasitic nematodes (PPNs) pose a significant barrier to production. A better understanding of the distribution of nematode diversity in these fields could help to evaluate the potential risk to crops in agricultural fields and support more sustainable PPN management, but accurate analysis of constituent nematode species is key. The use of targeted mitometagenomics (mtMG) to identify nematode species has shown promise with nematode mock communities, but it remains unclear how it compares in natural agricultural settings and to the more traditional morphology-based approach. In this study, we performed a diversity survey of nematode communities across four different strawberry fields at four depths in the State of Florida using both mtMG and morphological methods. We observed significant differences in nematode community richness and composition between the two methods. Both methods failed to detect taxa recovered by the other method, due to method-specific biases resulting from differential detection of trophic groups. Importantly, both methods did agree on the detection and distribution of Meloidogyne, the most abundant PPNs with the added benefit of the mtMG precisely describing specific species. Despite significant community differences, both methods pointed to the important role of both field and depth in shaping these communities and provided evidence of PPN migration across the soil profile. In conclusion, our findings support the complementary use of multiple detection/identification methods when evaluating nematode diversity, particularly for PPNs.","PeriodicalId":506127,"journal":{"name":"Metabarcoding and Metagenomics","volume":"3 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141813521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}