Molecular Ecology Resources最新文献

{"title":"Improving Whole Biodiversity Monitoring and Discovery With Environmental DNA Metagenomics","authors":"Manuel Curto,&nbsp;Ana Veríssimo,&nbsp;Giulia Riccioni,&nbsp;Carlos D. Santos,&nbsp;Filipe Ribeiro,&nbsp;Sissel Jentoft,&nbsp;Maria Judite Alves,&nbsp;Hugo F. Gante","doi":"10.1111/1755-0998.14105","DOIUrl":"10.1111/1755-0998.14105","url":null,"abstract":"<p>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 <span>SeqIDist,</span> a framework that combines multilocus BLAST matches against several reference databases followed by an analysis of sequence identity distribution patterns to disentangle false positives while revealing new biodiversity and increasing the accuracy of metagenomic approaches. We tested <span>SeqIDist</span> on an eDNA metagenomic dataset from a riverine site and compared the results to those obtained with an eDNA metabarcoding approach for benchmarking purposes. We start by characterising 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 <span>SeqIDist</span> opens the discussion of the potential of eDNA metagenomics for archived samples and its implementation in long-term biodiversity monitoring at a planetary scale.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 6","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14105","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750368","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Navigating Methodological Trade-Offs in eDNA Metabarcoding Biodiversity Monitoring: Insights From a Mediterranean Watershed","authors":"Joana Veríssimo,&nbsp;Manuel Lopes-Lima,&nbsp;Fábio Amaral,&nbsp;Cátia Chaves,&nbsp;Vasco Fernandes,&nbsp;Mutaleni Kemanja,&nbsp;Amílcar Teixeira,&nbsp;Filipa M. S. Martins,&nbsp;Pedro Beja","doi":"10.1111/1755-0998.14082","DOIUrl":"10.1111/1755-0998.14082","url":null,"abstract":"<p>Environmental DNA (eDNA) metabarcoding technologies promise significant advances in biodiversity monitoring, yet their application requires extensive optimisation and standardisation. Recent research demonstrated that increased sampling and analytical efforts are needed to improve biodiversity estimates, though fully optimising study designs is often hindered by resource constraints. Consequently, researchers must carefully navigate methodological trade-offs to design effective eDNA metabarcoding monitoring studies. We conducted a water eDNA survey of vertebrates in a Mediterranean watershed to identify key methodological factors influencing species richness and composition estimates. We examined the impacts of using high- versus low-capacity filtration capsules, varying levels of biological and technical replication, and the pooling of PCR replicates before indexing. The primary sources of variation identified were capsule filtration capacity and site replication across the watershed. While biological replication within sites and PCR replication also improved biodiversity estimates, their effects were comparatively smaller. Pooling PCR replicates before indexing performed more poorly than analysing them independently. Methodological impacts were stronger on terrestrial than on aquatic species. Based on these results, we recommend that priority should be given to high-capacity filtration and sampling across multiple sites. Site-level replication deserves lower priority, especially when filtering large water volumes. PCR replication is crucial for detecting rare species but should be balanced with increased site sampling and eventually site-level replication. Avoiding the pooling of PCR replicates is important to enhance sensitivity for rare species. Overall, we stress the importance of balancing methodological choices with resource constraints and monitoring goals, and we emphasise the need for research assessing methodological trade-offs in different study systems.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 6","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14082","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143762551","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Strong Signatures of Selection on Candidate Genes Underlying Core Speciation Mechanisms in Desert Tortoises","authors":"Sarah M. Baty,&nbsp;Raúl Araya-Donoso,&nbsp;Avery Paulsen,&nbsp;Avery Williams,&nbsp;Dale F. DeNardo,&nbsp;Kenro Kusumi,&nbsp;Greer A. Dolby","doi":"10.1111/1755-0998.14098","DOIUrl":"10.1111/1755-0998.14098","url":null,"abstract":"<p>Genomic incompatibilities and differential ecological adaptation are thought to be fundamental mechanisms of speciation. In this study, we generated a chromosome-scale reference genome and annotation for <i>Gopherus morafkai</i> , the Sonoran Desert tortoise, and conducted a detailed analysis of genes under positive selection with its sister species, the Mojave Desert tortoise. They occupy desert habitats with differing seasonal rainfall patterns and have considerable behavioural and reproductive differences, yet maintain a narrow hybrid zone. We find high conservation of synteny with other chelonian species. Results show extensive positive selection (422 candidate genes) relating to eye development and function that may reflect differences in UV exposure, as well as core reproductive isolation mechanisms of sperm–egg recognition, spindle assembly checkpoint and sister chromatid pairing. Together, our results offer strong genomic support and speciation genomic resources for processes shaping reproductive isolation in chelonians.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 6","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14098","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699273","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Segregating Sites Enhance Accuracy of Species Abundance Estimates From eDNA","authors":"Kara J. Andres","doi":"10.1111/1755-0998.14108","DOIUrl":"10.1111/1755-0998.14108","url":null,"abstract":"<p>Species abundance is a fundamental metric in ecology and conservation. Assessing how populations change across space time enables the identification of population trends and informs management and conservation decisions. However, measuring species abundance can be a challenging task, with logistical constraints, sampling biases, and detection limits inhibiting meaningful abundance estimates. Environmental DNA (eDNA) approaches have improved our ability to monitor species presence and biodiversity and may also serve as a tool for measuring species abundance. However, abundance estimates from eDNA typically rely on the correlation between species abundance and the concentration of target species' DNA in a sample, which may be hindered by complex interactions including variable amounts of DNA being shed by different individuals and environmental factors affecting DNA persistence. In this issue, Ai et al. (2025) present a new framework for estimating species abundance from eDNA that uses the amount of genetic diversity detected in a sample, specifically the number of segregating sites, to predict species abundance. The approach was developed and validated using in silico, in vitro, and in situ experiments, demonstrating improved correlations with species abundance compared to estimates based on eDNA concentration. With further improvements in detecting rare genetic variants, this approach has the potential to enhance our ability to quantify species abundance using eDNA.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 6","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14108","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143690401","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correcting for Bias in Estimates of \u0000 \u0000 \u0000 \u0000 θ\u0000 w\u0000 \u0000 \u0000 and Tajima's \u0000 \u0000 \u0000 D\u0000 \u0000 From Missing Data in Next-Generation Sequencing","authors":"Nick Bailey,&nbsp;Laurie Stevison,&nbsp;Kieran Samuk","doi":"10.1111/1755-0998.14104","DOIUrl":"10.1111/1755-0998.14104","url":null,"abstract":"<p>Population genetic analyses use information from the site frequency spectrum to infer evolutionary processes. Two summary statistics, Watterson's estimator (<span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mi>θ</mi>\u0000 <mi>w</mi>\u0000 </msub>\u0000 </mrow>\u0000 </semantics></math>) of genetic diversity, and Tajima's <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>D</mi>\u0000 </mrow>\u0000 </semantics></math>, used for detecting non-neutral evolution, are among the most frequently computed statistics utilising this information. However, missing information in genomic data, particularly as encoded in the Variant Call Format (VCF), can bias these estimates, leading to incorrect evolutionary inferences. We assessed the impact of missing data on the estimation of these statistics using various population genetic software packages (<span>VCFtools</span>, <span>PopGenome</span>, <span>pegas</span> and <span>scikit-allel</span>). By simulating neutral genomic data with varying levels of missing genotypes and sites, we found consistent underestimation of <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mi>θ</mi>\u0000 <mi>w</mi>\u0000 </msub>\u0000 </mrow>\u0000 </semantics></math> across programs. We found a consequent bias in estimates of Tajima's <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>D</mi>\u0000 </mrow>\u0000 </semantics></math>, though the direction varied by software. We developed and implemented correction methods as functions in an update of the popular <span>pixy</span> software, significantly reducing these biases. Our findings highlight the need for accurate data handling in population genomics to avoid misinterpretations of evolutionary phenomena.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 6","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14104","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143690398","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Stomach Content DNA (scDNA) Detection and Quantification for Predator Diet Assessment Using High-Throughput Nanofluidic Chip Technology: Species-Specific qPCR Assay Panel Development and Validation.","authors":"Matthew R Charron, Matthew C Yates, Daniel D Heath","doi":"10.1111/1755-0998.14106","DOIUrl":"https://doi.org/10.1111/1755-0998.14106","url":null,"abstract":"<p><p>Stomach content DNA (scDNA) analyses have become the standard practice for measuring trophic interactions. scDNA metabarcoding has provided broadscale diet composition data but can potentially underestimate certain prey species, as many of the recovered sequence reads come from predator-derived DNA, potentially resulting in incomplete diet information. Targeted detection (quantitative real-time PCR-qPCR) strategies allow for single-species detection from complex multispecies scDNA mixtures. A recent advancement in qPCR technology, high-throughput qPCR (HT-qPCR), allows simultaneous multispecies targeted detection and quantification of candidate species. Here, we describe the development and validation of a panel of single-species qPCR assays targeting the CO1 region of 28 prey fishes from the Great Lakes. We performed a three-step validation procedure for all assays using high-throughput OpenArray nanofluidic technology, measuring assay sensitivity, specificity and interference. Specifically, all assays were measured against dilution series of both target and non-target species DNA with detection limits ranging from 0.00503 pg to 0.0221 ng template DNA per reaction. Assays were tested for interference (e.g., PCR inhibitor) effects by creating artificial scDNA samples spiked with serially diluted target species DNA, resulting in a range of reduction in sensitivity (range = 0.0-125x fold). We validated the OpenArray qPCR assays using individual full-reaction TaqMan qPCR for nine of the assays, finding similar sensitivity despite expectations for the loss of sensitivity in the nanoscale reactions. HT-qPCR targeted detection has the potential to revolutionise scDNA (and eDNA) monitoring by significantly reducing laboratory effort to provide sensitive, targeted and quantitative detection data for multiple species simultaneously.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14106"},"PeriodicalIF":5.5,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143672930","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":"Cochlear Cell Atlas of Two Laryngeal Echolocating Bats—New Evidence for the Adaptive Nervous Physiology in Constant Frequency Bat","authors":"Xue Wang,&nbsp;Mingyue Bao,&nbsp;Hui Wang,&nbsp;Ruyi Sun,&nbsp;Wentao Dai,&nbsp;Keping Sun,&nbsp;Yue Zhu,&nbsp;Yingting Pu,&nbsp;Yujia Chu,&nbsp;Xintong Li,&nbsp;Tianhui Wang,&nbsp;Minjie Zhang,&nbsp;Aiqing Lin,&nbsp;Jiqian Li,&nbsp;Jiang Feng","doi":"10.1111/1755-0998.14101","DOIUrl":"10.1111/1755-0998.14101","url":null,"abstract":"<p>Bats have evolved highly adapted auditory mechanisms associated with ecological specialisation. However, there is scattered knowledge about the neurophysiological and cellular basis underlying high-frequency hearing in echolocating bats. Herein, the total cochlear cell atlas of <i>Rhinolophus ferrumequinum</i> (constant frequency (CF) bat) and <i>Myotis pilosus</i> (frequency modulated (FM) bat) was conducted using the 10x Genomics single-nucleus RNA sequencing method. Differences in the proportion of cochlear cell types, especially for the neural cells, were detected between these two bat species. Previously, genes upregulated in the cochlea of CF compared with FM bats, were found to be mostly related to nervous activities. After mapping to the cochlear cell atlas, we found that the upregulated genes were from neural cells, lateral wall cells and neurosensory epithelium cells. A class of specific neurons and associated functions was detected in the cochlea of <i>R. ferrumequinum</i>, revealed by cross-species single-cell transcriptomic analyses. Furthermore, molecular evidence for the differentiation from glial cells to neuronal cells was also uncovered in the cochlea of <i>R. ferrumequinum</i>. Overall, this study identified specific cellular molecular properties that constitute the neuroanatomical evolutionary dynamics underlying distinct echolocating types of bats and provided new molecular evidence for high-frequency hearing of echolocating bats, promoting related studies about ecological adaptation and evolution.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 6","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14101","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143661807","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ParAquaSeq, a Database of Ecologically Annotated rRNA Sequences Covering Zoosporic Parasites Infecting Aquatic Primary Producers in Natural and Industrial Systems","authors":"Silke Van den Wyngaert,&nbsp;Slawek Cerbin,&nbsp;Laura Garzoli,&nbsp;Hans-Peter Grossart,&nbsp;Alena S. Gsell,&nbsp;Alexandra Kraberg,&nbsp;Cécile Lepère,&nbsp;Sigrid Neuhauser,&nbsp;Miloš Stupar,&nbsp;Andrea Tarallo,&nbsp;Michael Cunliffe,&nbsp;Claire Gachon,&nbsp;Ana Gavrilović,&nbsp;Hossein Masigol,&nbsp;Serena Rasconi,&nbsp;Géza B. Selmeczy,&nbsp;Dirk S. Schmeller,&nbsp;Bettina Scholz,&nbsp;Natàlia Timoneda,&nbsp;Ivana Trbojević,&nbsp;Elżbieta Wilk-Woźniak,&nbsp;Albert Reñé","doi":"10.1111/1755-0998.14099","DOIUrl":"10.1111/1755-0998.14099","url":null,"abstract":"<p>Amplicon sequencing tools such as metabarcoding are commonly used for thorough characterisation of microbial diversity in natural samples. They mostly rely on the amplification of conserved universal markers, mainly ribosomal genes, allowing the taxonomic assignment of barcodes. However, linking taxonomic classification with functional traits is not straightforward and requires knowledge of each taxonomic group to confidently assign taxa to a given functional trait. Zoosporic parasites are highly diverse and yet understudied, with many undescribed species and host associations. However, they can have important impacts on host populations in natural ecosystems (e.g., controlling harmful algal blooms), as well as on industrial-scale algae production, e.g. aquaculture, causing their collapse or economic losses. Here, we present ParAquaSeq, a curated database of available molecular ribosomal sequences belonging to zoosporic parasites infecting aquatic vascular plants, macroalgae and photosynthetic microorganisms, i.e. microalgae and cyanobacteria. These sequences are aligned with ancillary data and other information currently available, including details on their hosts, occurrence, culture availability and associated bibliography. The database includes 1131 curated sequences from marine, freshwater and industrial or artificial environments, and belonging to 13 different taxonomic groups, including Chytridiomycota, Oomycota, Phytomyxea, and Syndiniophyceae. The curated database will allow a comprehensive analysis of zoosporic parasites in molecular datasets to answer questions related to their occurrence and distribution in natural communities. Especially through meta-analysis, the database serves as a valuable tool for developing effective mitigation and sustainable management strategies in the algae biomass industry, but it will also help to identify knowledge gaps for future research.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 6","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14099","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143633289","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Possible More Precise Management Unit Delineation Based on Epigenomic Differentiation of a Long-Distance-Migratory Marine Fish Scomberomorus niphonius","authors":"Sailan Liu,&nbsp;Yan Gao,&nbsp;Xinrui Long,&nbsp;Kunhuan Li,&nbsp;Qilin Gutang,&nbsp;Huiying Xie,&nbsp;Jingzhen Wang,&nbsp;Jiashen Tian,&nbsp;Bo Liang,&nbsp;Jianqing Lin,&nbsp;Wenhua Liu","doi":"10.1111/1755-0998.14103","DOIUrl":"10.1111/1755-0998.14103","url":null,"abstract":"<div>\u0000 \u0000 <p>Understanding population structure and adaptive history is critical for designing appropriate management regulations for fisheries and conserving adaptive potential for the future. However, this is not easy for marine fish, especially those with long-distance migration abilities. In this study, we constructed a high-quality reference genome for Japanese Spanish mackerel (<i>Scomberomorus niphonius</i>) and explored its population structure using whole genomic and epigenomic data. Despite the high depth of the sequence data, we failed to identify geographical genetic differentiation of Japanese Spanish mackerel across Chinese coastal waters. However, whole-genome bisulphite sequencing can classify this species into the Bohai–Yellow Sea group and the East China Sea–South China Sea group. Genes involved in embryonic skeletal system development, limb morphogenesis functions, and adult locomotory behaviour were differentially methylated in the southern (Zhanjiang, ZJ) and northern (Western Dalian, WDL) populations and may play important roles as drivers of population structure in Japanese Spanish mackerel. Our study not only provides the first reference genome of the Japanese Spanish mackerel and sheds light on population differentiation at the epigenomic level, but also provides a methylome-based framework for population structure analyses of marine fish with long-distance migration ability. These findings are expected to facilitate the development of scientific programmes for the successful conservation of marine fishery resources.</p>\u0000 </div>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 6","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143623052","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":"Short Read Lengths Recover Ecological Patterns in 16S rRNA Gene Amplicon Data","authors":"Stephanie D. Jurburg","doi":"10.1111/1755-0998.14102","DOIUrl":"10.1111/1755-0998.14102","url":null,"abstract":"<p>16S rRNA gene metabarcoding, the study of amplicon sequences of the 16S rRNA gene from mixed environmental samples, is an increasingly popular and accessible method for assessing bacterial communities across a wide range of environments. As metabarcoding sequence data archives continue to grow, data reuse will likely become an important source of novel insights into the ecology of microbes. While recent work has demonstrated the benefits of longer read lengths for the study of microbial communities from 16S rRNA gene segments, no studies have explored the use of shorter (&lt; 200 bp) read lengths in the context of data reuse. Nevertheless, this information is essential to improve the reuse and comparability of metabarcoding data across existing datasets. This study reanalyzed nine 16S rRNA datasets targeting aquatic, animal-associated and soil microbiomes, and evaluated how processing the sequence data across a range of read lengths affected the resulting taxonomic assignments, biodiversity metrics and differential (i.e., before-after treatment) analyses. Short read lengths successfully recovered ecological patterns and allowed for the use of more sequences. Limited increases in resolution were observed beyond 150 bp reads across environments. Furthermore, abundance-weighted diversity metrics (e.g., Inverse Simpson index, Morisita-Horn dissimilarities or weighted Unifrac distances) were more robust to variation in read lengths. Read lengths alone contributed to consistent increases in the total number of ASVs detected, highlighting the need to consider metabarcoding-derived diversity estimates within the context of the bioinformatics parameters selected. This study provides evidence-based guidelines for the processing of short reads.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 6","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14102","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143623053","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}