Molecular Ecology Resources最新文献

{"title":"The Impact of Whole-Animal Fluid Preservation on the Observed Gut Microbiome of Vertebrates: Implications for the Use of Museum Specimens in Microbiome Research.","authors":"Samantha S Fontaine, Stevie R Kennedy-Gold, Kurt J Regester, Jennifer A Sheridan, Kevin D Kohl","doi":"10.1111/1755-0998.14127","DOIUrl":"https://doi.org/10.1111/1755-0998.14127","url":null,"abstract":"<p><p>The vertebrate gut houses diverse microbial communities that provide insights into their host's ecological and evolutionary histories. Nevertheless, microbiome research has not been distributed equally across host taxonomy, geography and timescales. The millions of fluid-preserved specimens stored in natural history museums worldwide represent a potentially untapped resource for microbiome information. However, it is unknown how fluid preservation and long-term storage change the composition and diversity of the original microbial community across a variety of host taxa. Here, we present the largest study to date aimed at addressing this question. Specifically, we identified an optimal method for extracting DNA from preserved samples using commercially available kits. Next, for 11 host species representing four vertebrate classes, we compared the gut microbiomes between animals dissected freshly and those collected simultaneously but subsequently fixed in formalin and stored in 70% ethanol for 1 year, similar to museum conditions. In a secondary analysis in amphibians, we compared our collected samples with those from decades-old historical museum specimens. We found that while fluid preservation altered the community composition and reduced the diversity of the recovered microbiome inventories, host species identity predominated in shaping the gut microbiome, and differences across species and geographic localities were retained after preservation. Historical specimens had microbiomes that were the most different from fresh specimens, suggesting that over time, changes in the microbiome of populations have occurred, or preservation effects have compounded. Considering these findings, we discuss the potential for use of fluid-preserved museum specimens in future microbiome studies.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14127"},"PeriodicalIF":5.5,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144140953","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ancient Microbiomes as Mirrored by DNA Extracted From Century-Old Herbarium Plants and Associated Soil.","authors":"Gianluca Grasso, Régis Debruyne, Martino Adamo, Olivier Rué, Franck Lejzerowicz, Lucie Bittner, Valeria Bianciotto, Roland Marmeisse","doi":"10.1111/1755-0998.14122","DOIUrl":"https://doi.org/10.1111/1755-0998.14122","url":null,"abstract":"<p><p>Numerous specimens stored in natural history collections have been involuntarily preserved together with their associated microbiomes. We propose exploiting century-old soils occasionally found on the roots of herbarium plants to assess the diversity of ancient soil microbial communities originally associated with these plants. We extracted total DNA and sequenced libraries produced from rhizospheric soils and roots of four plants preserved in herbaria for more than 120 years in order to characterise the preservation and taxonomic diversity that can be recovered in such contexts. Extracted DNA displayed typical features of ancient DNA, with cytosine deamination at the ends of fragments predominantly shorter than 50 bp. When compared to extant microbiomes, herbarium microbial communities clustered with soil communities and were distinct from communities from other environments. Herbarium communities also displayed biodiversity features and assembly rules typical of soil and plant-associated ones. Soil communities were richer than root-associated ones with which they shared most taxa. Regarding community turnover, we detected collection site, soil versus root and plant species effects. Eukaryotic taxa that displayed a higher abundance in roots were mostly plant pathogens that were not identified among soil-enriched ones. Conservation of these biodiversity features and assembly rules in herbarium-associated microbial communities indicates that herbarium-extracted DNA might reflect the composition of the original plant-associated microbial communities and that preservation in herbaria seemingly did not dramatically alter these characteristics. Using this approach, it should be possible to investigate historical soils and herbarium plant roots to explore the diversity and temporal dynamics of soil microbial communities.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14122"},"PeriodicalIF":5.5,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144136121","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<ArticleTitle xmlns:ns0=\"http://www.w3.org/1998/Math/MathML\">Maximising the Potential of Temporal <ns0:math> <ns0:semantics> <ns0:mrow><ns0:msub><ns0:mi>N</ns0:mi> <ns0:mrow><ns0:mi>e</ns0:mi></ns0:mrow> </ns0:msub> </ns0:mrow> <ns0:annotation>$$ {boldsymbol{N}}_{mathbf{e}} $$</ns0:annotation></ns0:semantics> </ns0:math> Estimation in Long-Term Population Monitoring Programmes.","authors":"Tin-Yu J Hui","doi":"10.1111/1755-0998.14125","DOIUrl":"https://doi.org/10.1111/1755-0998.14125","url":null,"abstract":"","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14125"},"PeriodicalIF":5.5,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144126096","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An Accessible Metagenomic Strategy Allows for Better Characterisation of Invertebrate Bulk Samples.","authors":"Martijn Callens, Guillaume Le Berre, Laure Van den Bulcke, Marianne Lolivier, Sofie Derycke","doi":"10.1111/1755-0998.14126","DOIUrl":"https://doi.org/10.1111/1755-0998.14126","url":null,"abstract":"<p><p>DNA-based techniques are a popular approach for assessing biodiversity in ecological research, especially for organisms which are difficult to detect or identify morphologically. Metabarcoding, the most established method for determining species composition and relative abundance in bulk samples, can be more sensitive and time- and cost-effective than traditional morphological approaches. However, one drawback of this method is PCR bias caused by between-species variation in the amplification efficiency of a marker gene. Metagenomics, bypassing PCR amplification, has been proposed as an alternative to overcome this bias. Several studies have already shown the promising potential of metagenomics, but they all indicate the unavailability of reference genomes for most species in any ecosystem as one of the primary bottlenecks preventing its wider implementation. In this study, we present a strategy that combines unassembled reads of low-coverage whole genome sequencing and publicly available reference genomes to construct a genomic reference database, thus circumventing high sequencing costs and intensive bioinformatic processing. We show that this approach is superior to metabarcoding for approximating relative biomass of macrobenthos species from bulk samples. Furthermore, these results can be obtained with a sequencing effort comparable to metabarcoding. The strategy presented here can thus accelerate the implementation of metagenomics in biodiversity assessments, as it should be relatively easy to adopt by laboratories familiar with metabarcoding and can be used as an accessible alternative.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14126"},"PeriodicalIF":5.5,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144118474","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to \"epiGBS2: Improvements and Evaluation of Highly Multiplexed, epiGBS-Based Reduced Representation Bisulfite Sequencing\".","authors":"","doi":"10.1111/1755-0998.14124","DOIUrl":"https://doi.org/10.1111/1755-0998.14124","url":null,"abstract":"","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14124"},"PeriodicalIF":5.5,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144118476","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An Innovative Binding-Protein-Based dsRNA Extraction Method: Comparison of Cost-Effectiveness of Virus Detection Methods Using High-Throughput Sequencing.","authors":"Mamadou L Fall, Dong Xu, Pierre Lemoyne, Geneviève Clément, Peter Moffett, Christophe Ritzenthaler","doi":"10.1111/1755-0998.14111","DOIUrl":"https://doi.org/10.1111/1755-0998.14111","url":null,"abstract":"<p><p>Viral diseases represent a threat to global food production. Managing the impact of viruses on crop production requires the ability to monitor viruses, study their ecology and anticipate outbreaks. Double-stranded RNA (dsRNA) sequencing is a well-established and reliable method of detecting viruses and studying virome-host interactions and ecology. Compared to total RNA extraction, dsRNA extraction eliminates the majority of host RNAs, improving the recovery of viral RNAs. In this study, we developed and evaluated a novel dsRNA extraction method for high-throughput sequencing (HTS) applications based on the Flock House virus (FHV) B2 protein (B2-based method), and compared its performance with that of established cellulose-based and DRB4-based methods (commercial kit), as well as total RNA extraction techniques. The electrostatic properties of B2 have been instrumental in developing a bead-free and resin-free dsRNA extraction method. The B2-based method demonstrated high viral read recovery, achieving proportions exceeding 20% in most samples, and provided better dsRNA purity with less low weight molecule co-extracted RNA than the DRB4-based method and cellulose-based methods. Despite producing overall fewer total reads than the DRB4-based method, the B2-based enrichment for viral-derived dsRNA was better, with a higher percentage of viral reads, making it effective in virome profiling. Furthermore, it had an excellent detection specificity (0.97) and a good detection sensitivity (0.71), minimising false positives and false negatives. In addition, the B2-based method proved to be highly cost-effective, with a per-reaction cost of $4.47, compared to $35.34 for the DRB4-based method. This method offers a practical solution for laboratories with limited resources or for large-scale sampling for viral ecology studies. Future improvements to the B2-based method should focus on optimising sensitivity to Vitivirus species and developing scalable, automated workflows for high-throughput viral detection.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14111"},"PeriodicalIF":5.5,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075119","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Observation Bias in Metabarcoding.","authors":"Megan R Shaffer, Elizabeth Andruszkiewicz Allan, Amy M Van Cise, Kim M Parsons, Andrew Olaf Shelton, Ryan P Kelly","doi":"10.1111/1755-0998.14119","DOIUrl":"https://doi.org/10.1111/1755-0998.14119","url":null,"abstract":"<p><p>DNA metabarcoding is subject to observation bias associated with PCR and sequencing, which can result in observed read proportions differing from actual species proportions in the DNA extract. Here, we amplify and sequence a mock community of known composition containing marine fishes and cetaceans using four different primer sets and a variety of PCR conditions. We first compare metabarcoding observations to two different sets of expected species proportions based on total genomic DNA and on target mitochondrial template DNA. We find that calibrating observed read proportions based on template DNA concentration is most appropriate as it isolates PCR amplification bias; calibration with total genomic DNA results in bias that can be attributed to both PCR amplification bias and differing ratios of template to total genomic DNA. We then model the remaining amplification bias and find that approximately 60% can be explained by inherent species-specific DNA characteristics. These include primer-template mismatches, amplicon fragment length, and GC content, which vary somewhat across Taq polymerases. Finally, we investigate how different PCR protocols influence community composition regardless of expected proportions and find that changing protocols most strongly influence the amplification of templates with primer mismatches. Our findings suggest that using primer-template pairs without mismatches and targeting a narrow taxonomic group can yield more repeatable and accurate estimates of species' true, underlying DNA template proportions. These findings identify key factors that should be considered when designing studies that aim to apply metabarcoding data quantitatively.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14119"},"PeriodicalIF":5.5,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075122","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Designing Epigenetic Clocks for Wildlife Research.","authors":"Levi Newediuk, Evan S Richardson, Alyssa M Bohart, Amélie Roberto-Charron, Colin J Garroway, Meaghan J Jones","doi":"10.1111/1755-0998.14120","DOIUrl":"https://doi.org/10.1111/1755-0998.14120","url":null,"abstract":"<p><p>The applications of epigenetic clocks - statistical models that predict an individual's age based on DNA methylation patterns - are expanding in wildlife conservation and management. This growing interest highlights the need for field-specific design best practices. Here, we provide recommendations for two main applications of wildlife epigenetic clocks: estimating the unknown ages of individuals and assessing their biological ageing rates. Epigenetic clocks were originally developed to measure biological ageing rates of human tissues, which presents challenges for their adoption in wildlife research. Most notably, the estimated chronological ages of sampled wildlife can be unreliable, and sampling restrictions limit the number and variety of tissues with which epigenetic clocks can be constructed, reducing their accuracy. To address these challenges, we present a detailed workflow for designing, validating applying accurate wildlife epigenetic clocks. Using simulations and analyses applied to an extensive polar bear dataset from across the Canadian Arctic, we demonstrate that accurate epigenetic clocks for wildlife can be constructed and validated using a limited number of samples, accommodating projects with small budgets and sampling constraints. The concerns we address are critical for clock design, whether researchers or third-party service providers perform the bioinformatics. With our workflow and examples, we hope to support the accessible and widespread use of epigenetic clocks in wildlife conservation and management.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14120"},"PeriodicalIF":5.5,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143952206","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unrecognised DNA Degradation in Flash-Frozen Genetic Samples in Natural History Collections.","authors":"Alexander T Salis, Zachary Watson, Meghan Forcellati, Nasrin Ali, Shiva Karmakar, Jasleen Kaur, Nirhy Rabibisoa, Christopher J Raxworthy, Brian Tilston Smith","doi":"10.1111/1755-0998.14121","DOIUrl":"https://doi.org/10.1111/1755-0998.14121","url":null,"abstract":"<p><p>Optimal preservation of tissues from the field to long-term cryo-storage is paramount to securing genetic resources for research needs. DNA preservation techniques vary, with flash freezing currently considered the gold standard in tissue preservation. However, flash freezing tissue samples in the field presents challenges, necessitating a more comprehensive understanding of the quantity and quality of preserved DNA from different techniques in archival collections. We compared metrics from DNA extractions from field-collected amphibian, squamate and bird tissues from archival collections that were flash-frozen in liquid nitrogen or fixed in either ethanol or tissue lysis buffer prior to archival cryopreservation. We also included DNA extracted from tissues of known liquid nitrogen tank failures to provide a baseline of DNA degradation under the very worst-case scenario. Flash-frozen tissues often preserved higher yields of DNA, but peak fragment size, the percentage of fragments larger than 10 kb and DNA integrity numbers were all significantly reduced compared to tissues first preserved in fixative buffers. This pattern was observed across independent samples and between flash-frozen and buffer-preserved pair replicates. Degradation seen in flash-frozen tissues was also distinct to tissues from known tank failures. We suggest that degradation in flash-frozen tissues occurred during shipping, sample sorting/accession or during subsequent subsampling when tissues may partially or fully thaw, exposing DNA to damaging freeze-thaw processes. By contrast, tissues in fixative buffers were likely protected from freeze-thaw damage. This study highlights that using multiple field preservation methods and minimising freeze-thaw cycles for flash-frozen tissues may provide the most robust protection against the DNA degradation sources encountered by field collections.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14121"},"PeriodicalIF":5.5,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143956574","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Towards Large-Scale Museomics Projects: A Cost-Effective and High-Throughput Extraction Method for Obtaining Historical DNA From Museum Insect Specimens.","authors":"Anna Holmquist, Holly Tavris, Grace Kim, Lauren Esposito, Brian Fisher, Athena Lam","doi":"10.1111/1755-0998.14117","DOIUrl":"https://doi.org/10.1111/1755-0998.14117","url":null,"abstract":"<p><p>Natural history collections serve as invaluable repositories of biodiversity data. Large-scale genomic analysis would greatly expand the utility and accessibility of museum collections, but the high cost and time-intensive nature of genomic methods limit such projects, particularly for invertebrate specimens. This paper presents an innovative, cost-effective and high-throughput approach for extracting genomic DNA from diverse insect specimens using single-phase reverse immobilisation (SPRI) beads. We optimised PEG-8000 and NaCl concentrations to balance DNA yield and purity, reducing reagent cost to 4.0-11.6¢ per sample, cost dependent on sample type. Our method was validated against three widely used extraction protocols and showed comparable DNA yield and amplification success to the widely used Qiagen DNeasy kit. We successfully applied the protocol in a high-throughput manner, extracting DNA from 3786 insect specimens across a broad range of ages, taxonomies and tissue types. A detailed protocol and instructional video are provided to facilitate the adoption of the method by other researchers. By improving one of the most crucial steps in any molecular project, this SPRI bead-based DNA extraction approach has significant potential for enabling large-scale museomics projects, thereby increasing the utility of historical collections for biodiversity research and conservation efforts.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14117"},"PeriodicalIF":5.5,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143959253","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}