M. Cros, Jean-Marc Frigerio, N. Peyrard, Alain Franc
An accurate and complete taxonomic description of the diversity present in an environmental sample is out of reach at this time. Instead, metabarcoding is used today and it is expected that OTUs represent a category relevant for biodiversity inventories on a molecular basis. However, artefacts in the production of OTUs can occur at different stages and may impact ecological conclusions. We propose to evaluate the quality of OTUs in a sample by characterising the deviation of each OTU’s dissimilarity array from that of an ideal OTU where all sequences are at distances smaller than the barcoding gap. We consider two deviations: the creation of composed OTUs, corresponding to the artificial merging of several OTUs and the creation of noisy OTUs that contain some sequences that are loosely associated with the core sequence of the OTUs and that do not form a compact subgroup. We propose a simple and automatic 2-step method that successively categorises the OTUs of a sample as composed or single and then identifies OTUs with noise amongst the single ones. The associated code is available at https://forgemia.inra.fr/alain.franc/otu_shape. We applied the method on 32 samples of diatoms from Arcachon Bay (France) that represent contrasted environmental conditions and we obtained good agreement with expert categorisation of OTUs. We suggest that single OTUs without noise can be used as such for further ecological studies. Composed OTUs should be post-treated with classical clustering or community detection tools. The quality of single OTUs with noise remains to be further tested via supplementary studies on a diversity of organisms.
对环境样本中存在的多样性进行准确而完整的分类描述目前还无法实现。相反，目前使用的是代谢条码，预计 OTU 代表了与分子基础上的生物多样性清单相关的类别。然而，OTU 生成过程中的误差可能发生在不同阶段，并可能影响生态学结论。我们建议通过描述每个 OTU 的异质性阵列与理想 OTU 的异质性阵列之间的偏差来评估样本中 OTU 的质量，在理想 OTU 中，所有序列的距离都小于条码间隙。我们考虑了两种偏差：一种是人为合并多个 OTU 而产生的组成 OTU，另一种是包含一些与 OTU 核心序列关联松散且未形成紧凑亚群的序列的噪声 OTU。我们提出了一种简单、自动的两步法，可将样本中的 OTU 分为组成 OTU 和单一 OTU，然后在单一 OTU 中识别出带有噪声的 OTU。相关代码见 https://forgemia.inra.fr/alain.franc/otu_shape。我们将该方法应用于代表不同环境条件的阿卡雄湾（法国）32 个硅藻样本，结果与专家的 OTU 分类结果非常吻合。我们建议，在进一步的生态学研究中，可以使用无噪声的单个 OTU。合成的 OTU 应使用经典的聚类或群落检测工具进行后处理。有噪声的单个 OTU 的质量还有待通过对多种生物进行补充研究来进一步检验。
{"title":"Simple approaches for evaluation of OTU quality based on dissimilarity arrays","authors":"M. Cros, Jean-Marc Frigerio, N. Peyrard, Alain Franc","doi":"10.3897/mbmg.8.108649","DOIUrl":"https://doi.org/10.3897/mbmg.8.108649","url":null,"abstract":"An accurate and complete taxonomic description of the diversity present in an environmental sample is out of reach at this time. Instead, metabarcoding is used today and it is expected that OTUs represent a category relevant for biodiversity inventories on a molecular basis. However, artefacts in the production of OTUs can occur at different stages and may impact ecological conclusions. We propose to evaluate the quality of OTUs in a sample by characterising the deviation of each OTU’s dissimilarity array from that of an ideal OTU where all sequences are at distances smaller than the barcoding gap. We consider two deviations: the creation of composed OTUs, corresponding to the artificial merging of several OTUs and the creation of noisy OTUs that contain some sequences that are loosely associated with the core sequence of the OTUs and that do not form a compact subgroup. We propose a simple and automatic 2-step method that successively categorises the OTUs of a sample as composed or single and then identifies OTUs with noise amongst the single ones. The associated code is available at https://forgemia.inra.fr/alain.franc/otu_shape. We applied the method on 32 samples of diatoms from Arcachon Bay (France) that represent contrasted environmental conditions and we obtained good agreement with expert categorisation of OTUs. We suggest that single OTUs without noise can be used as such for further ecological studies. Composed OTUs should be post-treated with classical clustering or community detection tools. The quality of single OTUs with noise remains to be further tested via supplementary studies on a diversity of organisms.","PeriodicalId":18374,"journal":{"name":"Metabarcoding and Metagenomics","volume":"16 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140242306","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}
The Store Mosse National Park in the south of Sweden was surveyed for nematode diversity and distribution using DNA metabarcoding. Fifty samples were collected from five vegetation types in the park across a range of habitats (e.g. soil, litter, lichens, sphagnum and roots). The other habitats, aside from soil and litter, were sampled in order to capture the diversity of nematodes that may be uniquely associated with them. Nematodes were characterised using the V7-V8 variable domain (~ 350 bp) of the 18S ribosomal RNA gene. We identified 46 families, 76 genera (21 new to Swedish fauna) and 60 species (31 new to Swedish fauna). Some nematodes showed strong associations with their habitats, especially at the species level. Although soil and litter supported the most diverse nematode communities, our results support a strong justification for sampling across different media types to quantify nematode diversity accurately. Soil and litter communities showed high levels of stability with balanced distribution of all the various trophic and coloniser-persister groups.
{"title":"Assessing the diversity of nematodes in the Store Mosse National Park (Sweden) using metabarcoding","authors":"Mohammed Ahmed, Dieter Slos, Oleksandr Holovachov","doi":"10.3897/mbmg.8.111307","DOIUrl":"https://doi.org/10.3897/mbmg.8.111307","url":null,"abstract":"The Store Mosse National Park in the south of Sweden was surveyed for nematode diversity and distribution using DNA metabarcoding. Fifty samples were collected from five vegetation types in the park across a range of habitats (e.g. soil, litter, lichens, sphagnum and roots). The other habitats, aside from soil and litter, were sampled in order to capture the diversity of nematodes that may be uniquely associated with them. Nematodes were characterised using the V7-V8 variable domain (~ 350 bp) of the 18S ribosomal RNA gene. We identified 46 families, 76 genera (21 new to Swedish fauna) and 60 species (31 new to Swedish fauna). Some nematodes showed strong associations with their habitats, especially at the species level. Although soil and litter supported the most diverse nematode communities, our results support a strong justification for sampling across different media types to quantify nematode diversity accurately. Soil and litter communities showed high levels of stability with balanced distribution of all the various trophic and coloniser-persister groups.","PeriodicalId":18374,"journal":{"name":"Metabarcoding and Metagenomics","volume":" 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139626817","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}
Éva Ács, Tibor Bíró, Emil Boros, Péter Dobosy, Mónika Duleba, A. Földi, K. T. Kiss, Z. Levkov, Péter Orgoványi, Orsolya Pálné Szén, Zsuzsa Trábert, E. Vadkerti, I. Grigorszky
The research presented investigates whether DNA-based metabarcoding can replace the morphology-based identification of diatom taxa in the ecological status assessments of aquatic habitats. When comparing data obtained with microscopy and metabarcoding, significant deviations have been noticed. One of the main reasons includes the incompleteness of the reference database used for taxonomic annotation of sequences. The database library should be complemented with species inhabiting unique habitats and having specific environmental requirements representing environmental endpoints for genetic diversification. Soda pans and soda lakes are examples of an extreme habitat with the loss of sodic character as the main threat; thus, accurate identification of species and exact information on their salinity tolerance is essential for adequate ecological status assessment. In the present study, by using microscopy and metabarcoding, we investigated taxa of the genus Halamphora that are common in soda pans and soda lakes. We detected six species of which Halamphora dominici and H. veneta occurred frequently and often in high abundance (it was often dominant having relative abundance higher than 5%). Analyses of DNA data confirmed the separation of the two species; as a result, the reference database library has been supplemented with sequences of H. dominici. Furthermore, we have confirmed that this species, which is a significant indicator of sodic character, shows a positive correlation with salinity.
本文介绍的研究调查了在水生生境生态状况评估中，以 DNA 为基础的代谢编码能否取代以形态学为基础的硅藻类群鉴定。在比较显微镜和元条码获得的数据时，发现两者之间存在明显偏差。其中一个主要原因是用于序列分类注释的参考数据库不完整。数据库库中应包括栖息在独特栖息地、对环境有特殊要求的物种，这些物种代表了基因多样化的环境终点。苏打盘和苏打湖是极端栖息地的例子，其钠盐特征的丧失是主要威胁；因此，准确鉴定物种并提供有关其耐盐性的确切信息对于适当的生态状况评估至关重要。在本研究中，我们利用显微镜和代谢编码对苏打盘和苏打湖中常见的 Halamphora 属分类群进行了调查。我们发现了 6 个物种，其中 Halamphora dominici 和 H. veneta 频繁出现，且经常出现在高丰度区（它经常是优势种，相对丰度高于 5%）。对 DNA 数据的分析证实了这两个物种的分离；因此，我们在参考数据库库中补充了 H. dominici 的序列。此外，我们还证实，该物种是钠盐特征的重要指标，与盐度呈正相关。
{"title":"Halamphora taxa in Hungarian soda pans and shallow soda lakes detected via metabarcoding and microscopic analyses","authors":"Éva Ács, Tibor Bíró, Emil Boros, Péter Dobosy, Mónika Duleba, A. Földi, K. T. Kiss, Z. Levkov, Péter Orgoványi, Orsolya Pálné Szén, Zsuzsa Trábert, E. Vadkerti, I. Grigorszky","doi":"10.3897/mbmg.7.111679","DOIUrl":"https://doi.org/10.3897/mbmg.7.111679","url":null,"abstract":"The research presented investigates whether DNA-based metabarcoding can replace the morphology-based identification of diatom taxa in the ecological status assessments of aquatic habitats. When comparing data obtained with microscopy and metabarcoding, significant deviations have been noticed. One of the main reasons includes the incompleteness of the reference database used for taxonomic annotation of sequences. The database library should be complemented with species inhabiting unique habitats and having specific environmental requirements representing environmental endpoints for genetic diversification. Soda pans and soda lakes are examples of an extreme habitat with the loss of sodic character as the main threat; thus, accurate identification of species and exact information on their salinity tolerance is essential for adequate ecological status assessment. In the present study, by using microscopy and metabarcoding, we investigated taxa of the genus Halamphora that are common in soda pans and soda lakes. We detected six species of which Halamphora dominici and H. veneta occurred frequently and often in high abundance (it was often dominant having relative abundance higher than 5%). Analyses of DNA data confirmed the separation of the two species; as a result, the reference database library has been supplemented with sequences of H. dominici. Furthermore, we have confirmed that this species, which is a significant indicator of sodic character, shows a positive correlation with salinity.","PeriodicalId":18374,"journal":{"name":"Metabarcoding and Metagenomics","volume":"26 S1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139004758","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}
Lena A. Schallenberg, Georgia Thomson‐Laing, David Kelly, J. Pearman, Jamie D. Howarth, M. Vandergoes, Jonathan Puddick, Sean Fitzsimons, Andrew Rees, Susanna A. Wood
Introduced trout can induce trophic cascades, however, a lack of pre-introduction data limits knowledge on their impact in many lakes. Traditional paleolimnological approaches have been used to study historic species changes, but until recently these have been restricted to taxa with preservable body-parts. To explore the ecosystem effects of Salmo trutta (brown trout) introduction on an oligotrophic lake in Aotearoa-New Zealand, we used a multi-marker sedimentary environmental DNA (sedDNA) approach coupled with pigments to detect changes across multiple trophic levels. DNA was extracted from core depths capturing approximately 100 years before and after the expected arrival of S. trutta, and metabarcoding was undertaken with four primer sets targeting the 12S rRNA (fish), 18S rRNA (eukaryotes) and cytochrome c oxidase (COI; eukaryotes) genes. The earliest detection of S. trutta eDNA was 1906 (1892–1919 CE with 95% high probability density function) suggesting their introduction was shortly before this. Native fish diversity (12S and 18S rRNA) decreased after the detection of S. trutta, albeit the data was patchy. A shift in overall eukaryotic and algal communities (18S rRNA and COI) was observed around 1856 (1841–1871 CE) to 1891 (1877–1904 CE), which aligns with the expected S. trutta introduction. However, taxonomy could not be assigned to many of the 18S rRNA and COI sequences. Pigment concentrations did not change markedly after S. trutta introduction. SedDNA provides a new tool for understanding the impact of disturbances such as the introduction of non-native species; however, there are still several methodological challenges to overcome.
{"title":"Insights into the ecological impact of trout introduction in an oligotrophic lake using sedimentary environmental DNA","authors":"Lena A. Schallenberg, Georgia Thomson‐Laing, David Kelly, J. Pearman, Jamie D. Howarth, M. Vandergoes, Jonathan Puddick, Sean Fitzsimons, Andrew Rees, Susanna A. Wood","doi":"10.3897/mbmg.7.111467","DOIUrl":"https://doi.org/10.3897/mbmg.7.111467","url":null,"abstract":"Introduced trout can induce trophic cascades, however, a lack of pre-introduction data limits knowledge on their impact in many lakes. Traditional paleolimnological approaches have been used to study historic species changes, but until recently these have been restricted to taxa with preservable body-parts. To explore the ecosystem effects of Salmo trutta (brown trout) introduction on an oligotrophic lake in Aotearoa-New Zealand, we used a multi-marker sedimentary environmental DNA (sedDNA) approach coupled with pigments to detect changes across multiple trophic levels. DNA was extracted from core depths capturing approximately 100 years before and after the expected arrival of S. trutta, and metabarcoding was undertaken with four primer sets targeting the 12S rRNA (fish), 18S rRNA (eukaryotes) and cytochrome c oxidase (COI; eukaryotes) genes. The earliest detection of S. trutta eDNA was 1906 (1892–1919 CE with 95% high probability density function) suggesting their introduction was shortly before this. Native fish diversity (12S and 18S rRNA) decreased after the detection of S. trutta, albeit the data was patchy. A shift in overall eukaryotic and algal communities (18S rRNA and COI) was observed around 1856 (1841–1871 CE) to 1891 (1877–1904 CE), which aligns with the expected S. trutta introduction. However, taxonomy could not be assigned to many of the 18S rRNA and COI sequences. Pigment concentrations did not change markedly after S. trutta introduction. SedDNA provides a new tool for understanding the impact of disturbances such as the introduction of non-native species; however, there are still several methodological challenges to overcome.","PeriodicalId":18374,"journal":{"name":"Metabarcoding and Metagenomics","volume":"9 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138590380","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}
Katherina Schimani, Nélida Abarca, O. Skibbe, Heba Mohamad, R. Jahn, Wolf-Henning Kusber, G. Campana, J. Zimmermann
Polar regions are among the most extreme habitats on Earth. However, diatom biodiversity in those regions is much more extensive and ecologically diverse than previously thought. The objective of this study was to add knowledge to benthic diatom biodiversity in Western Antarctic coastal zones via identification by means of morphology, DNA metabarcoding and cultured isolates. In addition, a taxonomically validated reference library for Antarctic benthic diatoms was established with comprehensive information on habitat, morphology and DNA barcodes (rbcL and 18SV4). Benthic samples from marine, brackish and freshwater habitats were taken at the Antarctic Peninsula. A total of 162 clonal cultures were established, resulting in the identification of 60 taxa. The combination of total morphological richness of 174 taxa, including the clones, with an additional 73 taxa just assigned by metabarcoding resulted in 247 infrageneric taxa. Of those taxa, 33 were retrieved by all three methods and 111 only by morphology. The barcode reference library of Antarctic species with the new references obtained through culturing allowed the assignment of 47 taxa in the metabarcoding analyses, which would have been left unassigned because no matching reference sequences were available before. Non–metric multidimensional scaling analyses of morphological as well as molecular data showed a clear separation of diatom communities according to water and substratum types. Many species, especially marine taxa, still have no record in reference databases. This highlights the need for a more comprehensive reference library to further improve routine diatom metabarcoding. Overall, a combination of morphological and molecular methods, along with culturing, provides complementary information on the biodiversity of benthic diatoms in the region.
{"title":"Exploring benthic diatom diversity in the West Antarctic Peninsula: insights from a morphological and molecular approach","authors":"Katherina Schimani, Nélida Abarca, O. Skibbe, Heba Mohamad, R. Jahn, Wolf-Henning Kusber, G. Campana, J. Zimmermann","doi":"10.3897/mbmg.7.110194","DOIUrl":"https://doi.org/10.3897/mbmg.7.110194","url":null,"abstract":"Polar regions are among the most extreme habitats on Earth. However, diatom biodiversity in those regions is much more extensive and ecologically diverse than previously thought. The objective of this study was to add knowledge to benthic diatom biodiversity in Western Antarctic coastal zones via identification by means of morphology, DNA metabarcoding and cultured isolates. In addition, a taxonomically validated reference library for Antarctic benthic diatoms was established with comprehensive information on habitat, morphology and DNA barcodes (rbcL and 18SV4). Benthic samples from marine, brackish and freshwater habitats were taken at the Antarctic Peninsula. A total of 162 clonal cultures were established, resulting in the identification of 60 taxa. The combination of total morphological richness of 174 taxa, including the clones, with an additional 73 taxa just assigned by metabarcoding resulted in 247 infrageneric taxa. Of those taxa, 33 were retrieved by all three methods and 111 only by morphology. The barcode reference library of Antarctic species with the new references obtained through culturing allowed the assignment of 47 taxa in the metabarcoding analyses, which would have been left unassigned because no matching reference sequences were available before. Non–metric multidimensional scaling analyses of morphological as well as molecular data showed a clear separation of diatom communities according to water and substratum types. Many species, especially marine taxa, still have no record in reference databases. This highlights the need for a more comprehensive reference library to further improve routine diatom metabarcoding. Overall, a combination of morphological and molecular methods, along with culturing, provides complementary information on the biodiversity of benthic diatoms in the region.","PeriodicalId":18374,"journal":{"name":"Metabarcoding and Metagenomics","volume":"15 23","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138603294","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}
Wiebke Sickel, V. Zizka, Alice Scherges, Sarah J. Bourlat, Petra Dieker
Biodiversity is declining at alarming rates worldwide and large-scale monitoring is urgently needed to understand changes and their drivers. While classical taxonomic identification of species is time and labour intensive, the combination with DNA-based methods could upscale monitoring activities to achieve larger spatial coverage and increased sampling effort. However, challenges remain for DNA-based methods when the number of individuals per species and/or biomass estimates are required. Several methodological advancements exist to improve the potential of DNA metabarcoding for abundance analysis, which however need further evaluation. Here, we discuss laboratory, as well as some bioinformatic adjustments to DNA metabarcoding workflows regarding their potential to achieve species abundance estimation from arthropod community samples. Our review includes pre-laboratory processing methods such as specimen photography, laboratory methods such as the use of spike-in DNA as an internal standard and bioinformatic advancements like correction factors. We conclude that specimen photography coupled with DNA metabarcoding currently promises the greatest potential to achieve estimates of the number of individuals per species and biomass estimates, but that approaches such as spike-ins and correction factors are promising methods to pursue further.
全球生物多样性正以惊人的速度减少，迫切需要进行大规模监测，以了解生物多样性的变化及其驱动因素。虽然传统的物种分类鉴定需要大量的时间和人力，但与基于 DNA 的方法相结合，可以扩大监测活动的规模，从而实现更大的空间覆盖范围和更多的采样工作。然而，当需要对每个物种的个体数量和/或生物量进行估计时，基于 DNA 的方法仍面临挑战。有几项方法上的进步可以提高 DNA 代谢标码在丰度分析方面的潜力，但还需要进一步评估。在此，我们将讨论实验室以及生物信息学方面对 DNA 元条码工作流程的一些调整，以了解其实现节肢动物群落样本物种丰度估算的潜力。我们的综述包括标本摄影等实验室前处理方法、使用钉标 DNA 作为内标等实验室方法以及校正因子等生物信息学进步。我们的结论是，标本摄影与 DNA 代谢编码相结合目前最有可能实现每个物种的个体数量估计和生物量估计，但尖峰插入和校正因子等方法也是有希望进一步发展的方法。
{"title":"Abundance estimation with DNA metabarcoding – recent advancements for terrestrial arthropods","authors":"Wiebke Sickel, V. Zizka, Alice Scherges, Sarah J. Bourlat, Petra Dieker","doi":"10.3897/mbmg.7.112290","DOIUrl":"https://doi.org/10.3897/mbmg.7.112290","url":null,"abstract":"Biodiversity is declining at alarming rates worldwide and large-scale monitoring is urgently needed to understand changes and their drivers. While classical taxonomic identification of species is time and labour intensive, the combination with DNA-based methods could upscale monitoring activities to achieve larger spatial coverage and increased sampling effort. However, challenges remain for DNA-based methods when the number of individuals per species and/or biomass estimates are required. Several methodological advancements exist to improve the potential of DNA metabarcoding for abundance analysis, which however need further evaluation. Here, we discuss laboratory, as well as some bioinformatic adjustments to DNA metabarcoding workflows regarding their potential to achieve species abundance estimation from arthropod community samples. Our review includes pre-laboratory processing methods such as specimen photography, laboratory methods such as the use of spike-in DNA as an internal standard and bioinformatic advancements like correction factors. We conclude that specimen photography coupled with DNA metabarcoding currently promises the greatest potential to achieve estimates of the number of individuals per species and biomass estimates, but that approaches such as spike-ins and correction factors are promising methods to pursue further.","PeriodicalId":18374,"journal":{"name":"Metabarcoding and Metagenomics","volume":"68 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139246280","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}
Luisa Páez-Triana, Giovanny Herrera, Laura Vega, D. García-Corredor, Martin Orlando Pulido Medellín, A. Paniz‐Mondolfi, M. Muñoz, Juan David Ramírez
Rhipicephalus sanguineus sensu lato (s.l.), commonly known as the domestic dog tick, is a globally distributed tick. This species plays a significant role in human and animal health, as well as in economy due to its ability to infest livestock. The use of shotgun metagenomics has proven valuable in identifying tick-borne pathogens and key members of the tick microbiome, including endosymbionts. However, the application of shotgun metagenomics in R. sanguineus s.l. ticks in Latin America remains largely unexplored. Therefore, our objective aimed to explore and further analyze the metagenome of the tropical lineage of R. sanguineus s.l. ticks in Colombia. Through our analysis, we identified the three most prevalent pathogens harbored by these ticks, namely: Anaplasma phagocytophilum, Francisella tularensis, and Theileria equi. However, the most abundant microorganism detected was not a pathogen but the endosymbiont Coxiella mudrowiae. Interestingly, Coxiella mudrowiae exhibited significant negative correlations with several pathogens and other endosymbionts. Furthermore, we successfully constructed 27 medium-quality metagenome-assembled genomes (MAGs) for this microorganism, enabling us to conduct a pangenome analysis by comparing them with available genomes and identifying proteins of interest, such as those involved in vitamin B synthesis. This study represents the first implementation of shotgun metagenomics as a methodology to expand our understanding of pathogens and endosymbionts in the circulating tropical lineage of R. sanguineus s.l. ticks in Colombia. The findings of this research serve as a foundation for the development of prevention and mitigation strategies against pathogens transmitted by this tick species. Information gained from this study can contribute to the improvement of public health measures and veterinary practices aimed at controlling the impact of tick-borne diseases.
Rhipicephalus sanguineus sensu lato (s.l.)，俗称家犬蜱，是一种分布于全球的蜱虫。由于其侵扰牲畜的能力，该物种在人类和动物健康以及经济方面发挥着重要作用。在鉴定蜱传病原体和蜱微生物组的关键成员（包括内共生体）方面，散弹枪元基因组学的应用已被证明非常有价值。然而，散弹枪元基因组学在拉丁美洲 R. sanguineus s.l.蜱中的应用在很大程度上仍未得到探索。因此，我们的目标是探索并进一步分析哥伦比亚 R. sanguineus s.l. 热带蜱系的元基因组。通过分析，我们确定了这些蜱虫携带的三种最普遍的病原体，即噬细胞嗜血杆菌（Anaplasma phagocytophilum）、土拉弗氏菌（Francisella tularensis）和马蹄癣菌（Theileria equi）。然而，检测到的最多的微生物并不是病原体，而是内生菌泥rowiae Coxiella。有趣的是，泥状柯西氏菌与几种病原体和其他内生菌呈显著负相关。此外，我们还成功地为这种微生物构建了 27 个中等质量的元基因组组装基因组（MAGs），使我们能够通过将它们与现有基因组进行比较来进行泛基因组分析，并鉴定出我们感兴趣的蛋白质，如参与维生素 B 合成的蛋白质。这项研究首次将枪式元基因组学作为一种方法，用于扩大我们对哥伦比亚热带蜱循环系中病原体和内共生体的了解。这项研究的结果为制定针对这种蜱虫传播的病原体的预防和缓解策略奠定了基础。这项研究获得的信息有助于改善公共卫生措施和兽医实践，以控制蜱传疾病的影响。
{"title":"Metagenomic exploration of endosymbionts and pathogens in the tropical lineage of Rhipicephalus sanguineus sensu lato (s.l.) ticks in Colombia","authors":"Luisa Páez-Triana, Giovanny Herrera, Laura Vega, D. García-Corredor, Martin Orlando Pulido Medellín, A. Paniz‐Mondolfi, M. Muñoz, Juan David Ramírez","doi":"10.3897/mbmg.7.109085","DOIUrl":"https://doi.org/10.3897/mbmg.7.109085","url":null,"abstract":"Rhipicephalus sanguineus sensu lato (s.l.), commonly known as the domestic dog tick, is a globally distributed tick. This species plays a significant role in human and animal health, as well as in economy due to its ability to infest livestock. The use of shotgun metagenomics has proven valuable in identifying tick-borne pathogens and key members of the tick microbiome, including endosymbionts. However, the application of shotgun metagenomics in R. sanguineus s.l. ticks in Latin America remains largely unexplored. Therefore, our objective aimed to explore and further analyze the metagenome of the tropical lineage of R. sanguineus s.l. ticks in Colombia. Through our analysis, we identified the three most prevalent pathogens harbored by these ticks, namely: Anaplasma phagocytophilum, Francisella tularensis, and Theileria equi. However, the most abundant microorganism detected was not a pathogen but the endosymbiont Coxiella mudrowiae. Interestingly, Coxiella mudrowiae exhibited significant negative correlations with several pathogens and other endosymbionts. Furthermore, we successfully constructed 27 medium-quality metagenome-assembled genomes (MAGs) for this microorganism, enabling us to conduct a pangenome analysis by comparing them with available genomes and identifying proteins of interest, such as those involved in vitamin B synthesis. This study represents the first implementation of shotgun metagenomics as a methodology to expand our understanding of pathogens and endosymbionts in the circulating tropical lineage of R. sanguineus s.l. ticks in Colombia. The findings of this research serve as a foundation for the development of prevention and mitigation strategies against pathogens transmitted by this tick species. Information gained from this study can contribute to the improvement of public health measures and veterinary practices aimed at controlling the impact of tick-borne diseases.","PeriodicalId":18374,"journal":{"name":"Metabarcoding and Metagenomics","volume":"6 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139257069","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}
Aman Deep, Dana Bludau, Marius Welzel, Sandra Clemens, Dominik Heider, Jens Boenigk, Daniela Beisser
Sequencing of amplified DNA is the first step towards the generation of Amplicon Sequence Variants (ASVs) or Operational Taxonomic Units (OTUs) for biodiversity assessment and comparative analyses of environmental communities and microbiomes. Notably, the rapid advancements in sequencing technologies have paved the way for the growing utilization of third-generation long-read approaches in recent years. These sequence data imply increasing read lengths, higher error rates, and altered sequencing chemistry. Likewise, methods for amplicon classification and reference databases have progressed, leading to the expansion of taxonomic application areas and higher classification accuracy. With Natrix, a user-friendly and reducible workflow solution, processing of prokaryotic and eukaryotic environmental Illumina sequences using 16S or 18S is possible. Here, we present an updated version of the pipeline, Natrix2, which incorporates VSEARCH as an alternative clustering method with better performance for 16S metabarcoding approaches and mothur for taxonomic classification on further databases, including PR 2 , UNITE and SILVA. Additionally, Natrix2 includes the handling of Nanopore reads, which entails initial error correction and refinement of reads using Medaka and Racon to subsequently determine their taxonomic classification.
{"title":"Natrix2 – Improved amplicon workflow with novel Oxford Nanopore Technologies support and enhancements in clustering, classification and taxonomic databases","authors":"Aman Deep, Dana Bludau, Marius Welzel, Sandra Clemens, Dominik Heider, Jens Boenigk, Daniela Beisser","doi":"10.3897/mbmg.7.109389","DOIUrl":"https://doi.org/10.3897/mbmg.7.109389","url":null,"abstract":"Sequencing of amplified DNA is the first step towards the generation of Amplicon Sequence Variants (ASVs) or Operational Taxonomic Units (OTUs) for biodiversity assessment and comparative analyses of environmental communities and microbiomes. Notably, the rapid advancements in sequencing technologies have paved the way for the growing utilization of third-generation long-read approaches in recent years. These sequence data imply increasing read lengths, higher error rates, and altered sequencing chemistry. Likewise, methods for amplicon classification and reference databases have progressed, leading to the expansion of taxonomic application areas and higher classification accuracy. With Natrix, a user-friendly and reducible workflow solution, processing of prokaryotic and eukaryotic environmental Illumina sequences using 16S or 18S is possible. Here, we present an updated version of the pipeline, Natrix2, which incorporates VSEARCH as an alternative clustering method with better performance for 16S metabarcoding approaches and mothur for taxonomic classification on further databases, including PR 2 , UNITE and SILVA. Additionally, Natrix2 includes the handling of Nanopore reads, which entails initial error correction and refinement of reads using Medaka and Racon to subsequently determine their taxonomic classification.","PeriodicalId":18374,"journal":{"name":"Metabarcoding and Metagenomics","volume":"12 11","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135273533","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}
Due to anthropogenic influences, habitat degradation and a continuous loss of biodiversity in freshwater ecosystems are occurring on a large scale, while these ecosystems constitute invaluable natural resources. Therefore, it is essential to study and monitor freshwater ecosystems to guide conservation efforts. Freshwater ecosystems are one of the less-studied fields in Georgia. Studies about the species distribution of many taxa and/or regions carried out during the last century have not been updated for decades. Here, we report the results of an environmental DNA (eDNA) metabarcoding exercise, based on samples collected from the Rioni River, a tributary to the Black Sea and a crucial aquatic ecosystem regionally and globally. The only comprehensive review of the fish of the Rioni River dates back to 1956. We compared the eDNA-based taxonomic composition to the known faunal composition within the Rioni River and found that the eDNA-based taxonomic coverage approached 75% of the expected total fish fauna. A number of new species occurrences were also found, including the first detection of three invasive alien species ( Carassius gibelio , Pseudorasbora parva , Rhinogobius lindbergi ) in the Rionis River Basin and a new country record of the ninespine stickleback (genus Pungitius ) for Georgia. In spite of the usefulness of the eDNA metabarcoding approach, the sparsity of the fish DNA barcode reference library for the region emerged as a limitation to this study. However, our findings still represent a great leap forward in updating fish status on the Rioni River and testing the effectiveness of the eDNA sampling for aquatic species.
{"title":"Fish diversity assessed by eDNA detection methods in the Rioni River","authors":"Tamar Beridze, Bella Japoshvili, Tamar Edisherashvili, Cort Anderson, Levan Mumladze","doi":"10.3897/mbmg.7.96780","DOIUrl":"https://doi.org/10.3897/mbmg.7.96780","url":null,"abstract":"Due to anthropogenic influences, habitat degradation and a continuous loss of biodiversity in freshwater ecosystems are occurring on a large scale, while these ecosystems constitute invaluable natural resources. Therefore, it is essential to study and monitor freshwater ecosystems to guide conservation efforts. Freshwater ecosystems are one of the less-studied fields in Georgia. Studies about the species distribution of many taxa and/or regions carried out during the last century have not been updated for decades. Here, we report the results of an environmental DNA (eDNA) metabarcoding exercise, based on samples collected from the Rioni River, a tributary to the Black Sea and a crucial aquatic ecosystem regionally and globally. The only comprehensive review of the fish of the Rioni River dates back to 1956. We compared the eDNA-based taxonomic composition to the known faunal composition within the Rioni River and found that the eDNA-based taxonomic coverage approached 75% of the expected total fish fauna. A number of new species occurrences were also found, including the first detection of three invasive alien species ( Carassius gibelio , Pseudorasbora parva , Rhinogobius lindbergi ) in the Rionis River Basin and a new country record of the ninespine stickleback (genus Pungitius ) for Georgia. In spite of the usefulness of the eDNA metabarcoding approach, the sparsity of the fish DNA barcode reference library for the region emerged as a limitation to this study. However, our findings still represent a great leap forward in updating fish status on the Rioni River and testing the effectiveness of the eDNA sampling for aquatic species.","PeriodicalId":18374,"journal":{"name":"Metabarcoding and Metagenomics","volume":"43 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135884558","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}
Bird nests are fascinating microcosms harboring a wide range of arthropods parasitizing the nesting birds or feeding on prey remains, feces, and the nest material. Studies of these communities have been entirely based on emergence traps which collect live organisms out of the nests. The analysis of nest contents and environmental DNA (eDNA) via metabarcoding could expand our knowledge and identify prey, exuviae, and other animal remains in bird nests. Here, we investigated the potential of arthropod remains, nest dust, and feathers to better describe arthropod diversity accumulated in 20 bird nests collected in Guelph (Canada). We used subsampling strategies and tested two extraction approaches to investigate the distribution of DNA in nests, account for low-quality DNA, and the presence of inhibitory substances. In total, 103 taxa were detected via metabarcoding. Arthropod remains delivered the highest number of taxa (n = 67), followed by nest dust (n = 29). Extractions with the PowerSoil kit outperformed DNeasy extractions coupled with PowerClean Pro inhibitor removal. Per nest, on average 5.5% taxonomic overlap between arthropod remains of different size classes was detected and subsamples of nest dust extracted with the PowerSoil kit showed 47.3% taxonomic overlap indicating a heterogeneous eDNA distribution in nests. Most detected species were either feeding in the nest, i.e., herbivorous / predatory, or bird food. We also detected molecular traces of 25 bird species, whose feathers were likely used as nest material. Consequently, the metabarcoding of bird nest materials provides a more complete picture of nest communities, which can enable future studies on functional diversity and better comparisons between nesting species.
{"title":"Unravelling bird nest arthropod community structure using metabarcoding","authors":"Valerie Levesque-Beaudin, Dirk Steinke, Mieke Böcker, Bettina Thalinger","doi":"10.3897/mbmg.7.103279","DOIUrl":"https://doi.org/10.3897/mbmg.7.103279","url":null,"abstract":"Bird nests are fascinating microcosms harboring a wide range of arthropods parasitizing the nesting birds or feeding on prey remains, feces, and the nest material. Studies of these communities have been entirely based on emergence traps which collect live organisms out of the nests. The analysis of nest contents and environmental DNA (eDNA) via metabarcoding could expand our knowledge and identify prey, exuviae, and other animal remains in bird nests. Here, we investigated the potential of arthropod remains, nest dust, and feathers to better describe arthropod diversity accumulated in 20 bird nests collected in Guelph (Canada). We used subsampling strategies and tested two extraction approaches to investigate the distribution of DNA in nests, account for low-quality DNA, and the presence of inhibitory substances. In total, 103 taxa were detected via metabarcoding. Arthropod remains delivered the highest number of taxa (n = 67), followed by nest dust (n = 29). Extractions with the PowerSoil kit outperformed DNeasy extractions coupled with PowerClean Pro inhibitor removal. Per nest, on average 5.5% taxonomic overlap between arthropod remains of different size classes was detected and subsamples of nest dust extracted with the PowerSoil kit showed 47.3% taxonomic overlap indicating a heterogeneous eDNA distribution in nests. Most detected species were either feeding in the nest, i.e., herbivorous / predatory, or bird food. We also detected molecular traces of 25 bird species, whose feathers were likely used as nest material. Consequently, the metabarcoding of bird nest materials provides a more complete picture of nest communities, which can enable future studies on functional diversity and better comparisons between nesting species.","PeriodicalId":18374,"journal":{"name":"Metabarcoding and Metagenomics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44561157","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}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：