Molecular Ecology最新文献

{"title":"Field Reduction of Ectomycorrhizal Fungi Has Cascading Effects on Soil Microbial Communities and Reduces the Abundance of Ectomycorrhizal Symbiotic Bacteria.","authors":"Louis Berrios, Kabir G Peay","doi":"10.1111/mec.17585","DOIUrl":"https://doi.org/10.1111/mec.17585","url":null,"abstract":"<p><p>Specific interactions between bacteria and ectomycorrhizal fungi (EcMF) can benefit plant health, and saprotrophic soil fungi represent a potentially antagonistic guild to these mutualisms. Yet there is little field-derived experimental evidence showing how the relationship among these three organismal groups manifests across time. To bridge this knowledge gap, we experimentally reduced EcMF in forest soils and monitored both bacterial and fungal soil communities over the course of a year. Our analyses demonstrate that soil trenching shifts the community composition of fungal communities towards a greater abundance of taxa with saprotrophic traits, and this shift is linked to a decrease in both EcMF and a common ectomycorrhizal helper bacterial genus, Burkholderia, in a time-dependent manner. These results not only reveal the temporal nature of a widespread tripartite symbiosis between bacteria, EcMF and a shared host tree, but they also refine our understanding of the commonly referenced 'Gadgil effect' by illustrating the cascading effects of EcMF suppression and implicating soil saprotrophic fungi as potential antagonists on bacterial-EcMF interactions.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17585"},"PeriodicalIF":4.5,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142613298","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":"The influence of Acetobacter pomorum bacteria on the developmental progression of Drosophila suzukii via gluconic acid secretion","authors":"Xiao-Li Bing,&nbsp;Zi-Jian Liang,&nbsp;Jia Tian,&nbsp;Xue Gong,&nbsp;Shao-Qiu Huang,&nbsp;Jie Chen,&nbsp;Xiao-Yue Hong","doi":"10.1111/mec.17202","DOIUrl":"10.1111/mec.17202","url":null,"abstract":"<p>Insects are rich in various microorganisms, which play diverse roles in affecting host biology. Although most <i>Drosophila</i> species prefer rotten fruits, the agricultural pest <i>Drosophila suzukii</i> attacks ripening fruits before they are harvested. We have reported that the microbiota has positive and negative impacts on the agricultural pest <i>D. suzukii</i> on nutrient-poor and -rich diets, respectively. On nutrient-poor diets, microbes provide protein to facilitate larval development. But how they impede <i>D. suzukii</i> development on nutrient-rich diets is unknown. Here we report that <i>Acetobacter pomorum</i> (Apo), a commensal bacterium in many <i>Drosophila</i> species and rotting fruit, has several detrimental effects in <i>D. suzukii</i>. Feeding <i>D. suzukii</i> larvae nutrient-rich diets containing live Apo significantly delayed larval development and reduced the body weight of emerged adults. Apo induced larval immune responses and downregulated genes of digestion and juvenile hormone metabolism. Knockdown of these genes in germ-free larvae reproduced Apo-like weakened phenotypes. Apo was confirmed to secrete substantial amounts of gluconic acid. Adding gluconic acid to the <i>D. suzukii</i> larval diet hindered larval growth and decreased adult body weight. Moreover, the dose of gluconic acid that adversely affected <i>D. suzukii</i> did not negatively affect <i>Drosophila melanogaster</i>, suggesting that <i>D. suzukii</i> is less tolerant to acid than <i>D. melanogaster</i>. Taken together, these findings indicate that <i>D. suzukii</i> is negatively affected by gluconic acid, which may explain why it prefers ripening fruit over Apo-rich rotting fruit. These results show an insect's tolerance to microbes can influence its ecological niche.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"33 2","pages":""},"PeriodicalIF":4.9,"publicationDate":"2023-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72012760","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":"Distinct patterns of inheritance shape life-history traits in steelhead trout","authors":"Anne K. Beulke,&nbsp;Alicia Abadía-Cardoso,&nbsp;Devon E. Pearse,&nbsp;Laura C. Goetz,&nbsp;Neil F. Thompson,&nbsp;Eric C. Anderson,&nbsp;John Carlos Garza","doi":"10.1111/mec.17182","DOIUrl":"10.1111/mec.17182","url":null,"abstract":"<p>Life-history variation is the raw material of adaptation, and understanding its genetic and environmental underpinnings is key to designing effective conservation strategies. We used large-scale genetic pedigree reconstruction of anadromous steelhead trout (<i>Oncorhynchus mykiss</i>) from the Russian River, CA, USA, to elucidate sex-specific patterns of life-history traits and their heritability. SNP data from adults returning from sea over a 14-year period were used to identify 13,474 parent–offspring trios. These pedigrees were used to determine age structure, size distributions and family sizes for these fish, as well as to estimate the heritability of two key life-history traits, spawn date and age at maturity (first reproduction). Spawn date was highly heritable (<i>h</i>² = 0.73) and had a cross-sex genetic correlation near unity. We provide the first estimate of heritability for age at maturity in ocean-going fish from this species and found it to be highly heritable (<i>h</i>² from 0.29 to 0.62, depending on sex and method), with a much lower genetic correlation across sexes. We also evaluated genotypes at a migration-associated inversion polymorphism and found sex-specific correlations with age at maturity. The significant heritability of these two key reproductive traits in these imperiled fish, and their patterns of inheritance in the two sexes, is consistent with predictions of both natural and sexually antagonistic selection (sexes experience opposing selection pressures). This emphasizes the importance of anthropogenic factors, including hatchery practices and ecosystem modifications, in shaping the fitness of this species, thus providing important guidance for management and conservation efforts.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"32 24","pages":"6896-6912"},"PeriodicalIF":4.9,"publicationDate":"2023-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17182","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71519842","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":"Patterns of chromosome evolution in ruminants.","authors":"Cristina Arias-Sardá, Sarah Quigley, Marta Farré","doi":"10.1111/mec.17197","DOIUrl":"https://doi.org/10.1111/mec.17197","url":null,"abstract":"<p><p>Studying when and where gross genomic rearrangements occurred during evolution is key to understanding changes in genome structure with functional consequences that might eventually lead to speciation. Here we identified chromosome rearrangements in ruminants, a clade characterized by large chromosome differences. Using 26 genome assemblies, we reconstructed five ancestral karyotypes and classified the rearrangement events occurring in each lineage. With these reconstructions, we then identified evolutionary breakpoints regions (EBRs) and synteny fragments. Ruminant karyotype evolution is characterized by inversions, while interchromosomal rearrangements occurred preferentially in the oldest ancestor of ruminants. We found that EBRs are depleted of protein coding genes, including housekeeping genes. Similarly, EBRs are not enriched in high GC regions, suggesting that meiotic double strand breaks might not be their origin. Overall, our results characterize at fine detail the location of chromosome rearrangements in ruminant evolution and provide new insights into the formation of EBRs.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":""},"PeriodicalIF":4.9,"publicationDate":"2023-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71476036","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":"Is there a latitudinal diversity gradient for symbiotic microbes? A case study with sensitive partridge peas","authors":"Tia L. Harrison,&nbsp;Zoe A. Parshuram,&nbsp;Megan E. Frederickson,&nbsp;John R. Stinchcombe","doi":"10.1111/mec.17191","DOIUrl":"10.1111/mec.17191","url":null,"abstract":"<p>Mutualism is thought to be more prevalent in the tropics than temperate zones and may therefore play an important role in generating and maintaining high species richness found at lower latitudes. However, results on the impact of mutualism on latitudinal diversity gradients are mixed, and few empirical studies sample both temperate and tropical regions. We investigated whether a latitudinal diversity gradient exists in the symbiotic microbial community associated with the legume <i>Chamaecrista nictitans</i>. We sampled bacteria DNA from nodules and the surrounding soil of plant roots across a latitudinal gradient (38.64–8.68 °N). Using 16S rRNA sequence data, we identified many non-rhizobial species within <i>C. nictitans</i> nodules that cannot form nodules or fix nitrogen. Species richness increased towards lower latitudes in the non-rhizobial portion of the nodule community but not in the rhizobial community. The microbe community in the soil did not effectively predict the non-rhizobia community inside nodules, indicating that host selection is important for structuring non-rhizobia communities in nodules. We next factorially manipulated the presence of three non-rhizobia strains in greenhouse experiments and found that co-inoculations of non-rhizobia strains with rhizobia had a marginal effect on nodule number and no effect on plant growth. Our results suggest that these non-rhizobia bacteria are likely commensals—species that benefit from associating with a host but are neutral for host fitness. Overall, our study suggests that temperate <i>C. nictitans</i> plants are more selective in their associations with the non-rhizobia community, potentially due to differences in soil nitrogen across latitude.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"33 1","pages":""},"PeriodicalIF":4.9,"publicationDate":"2023-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71519843","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":"Concurrent invasions of European starlings in Australia and North America reveal population-specific differentiation in shared genomic regions.","authors":"Natalie R Hofmeister, Katarina C Stuart, Wesley C Warren, Scott J Werner, Melissa Bateson, Gregory F Ball, Katherine L Buchanan, David W Burt, Adam P A Cardilini, Phillip Cassey, Tim De Meyer, Julia George, Simone L Meddle, Hannah M Rowland, Craig D H Sherman, William B Sherwin, Wim Vanden Berghe, Lee Ann Rollins, David F Clayton","doi":"10.1111/mec.17195","DOIUrl":"https://doi.org/10.1111/mec.17195","url":null,"abstract":"<p><p>A species' success during the invasion of new areas hinges on an interplay between the demographic processes common to invasions and the specific ecological context of the novel environment. Evolutionary genetic studies of invasive species can investigate how genetic bottlenecks and ecological conditions shape genetic variation in invasions, and our study pairs two invasive populations that are hypothesized to be from the same source population to compare how each population evolved during and after introduction. Invasive European starlings (Sturnus vulgaris) established populations in both Australia and North America in the 19th century. Here, we compare whole-genome sequences among native and independently introduced European starling populations to determine how demographic processes interact with rapid evolution to generate similar genetic patterns in these recent and replicated invasions. Demographic models indicate that both invasive populations experienced genetic bottlenecks as expected based on invasion history, and we find that specific genomic regions have differentiated even on this short evolutionary timescale. Despite genetic bottlenecks, we suggest that genetic drift alone cannot explain differentiation in at least two of these regions. The demographic boom intrinsic to many invasions as well as potential inversions may have led to high population-specific differentiation, although the patterns of genetic variation are also consistent with the hypothesis that this infamous and highly mobile invader adapted to novel selection (e.g., extrinsic factors). We use targeted sampling of replicated invasions to identify and evaluate support for multiple, interacting evolutionary mechanisms that lead to differentiation during the invasion process.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":""},"PeriodicalIF":4.9,"publicationDate":"2023-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71476035","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":"The effect of host admixture on wild house mouse gut microbiota is weak when accounting for spatial autocorrelation","authors":"Dagmar Čížková,&nbsp;Lucie Schmiedová,&nbsp;Martin Kváč,&nbsp;Bohumil Sak,&nbsp;Miloš Macholán,&nbsp;Jaroslav Piálek,&nbsp;Jakub Kreisinger","doi":"10.1111/mec.17192","DOIUrl":"10.1111/mec.17192","url":null,"abstract":"<p>The question of how interactions between the gut microbiome and vertebrate hosts contribute to host adaptation and speciation is one of the major problems in current evolutionary research. Using bacteriome and mycobiome metabarcoding, we examined how these two components of the gut microbiota vary with the degree of host admixture in secondary contact between two house mouse subspecies (<i>Mus</i> <i>musculus musculus</i> and <i>M. m. domesticus</i>). We used a large data set collected at two replicates of the hybrid zone and model-based statistical analyses to ensure the robustness of our results. Assuming that the microbiota of wild hosts suffers from spatial autocorrelation, we directly compared the results of statistical models that were spatially naive with those that accounted for spatial autocorrelation. We showed that neglecting spatial autocorrelation can strongly affect the results and lead to misleading conclusions. The spatial analyses showed little difference between subspecies, both in microbiome composition and in individual bacterial lineages. Similarly, the degree of admixture had minimal effects on the gut bacteriome and mycobiome and was caused by changes in a few microbial lineages that correspond to the common symbionts of free-living house mice. In contrast to previous studies, these data do not support the hypothesis that the microbiota plays an important role in host reproductive isolation in this particular model system.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"33 1","pages":""},"PeriodicalIF":4.9,"publicationDate":"2023-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17192","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71475949","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":"Association between the skin microbiome and MHC class II diversity in an amphibian","authors":"M. Cortazar-Chinarro,&nbsp;A. Richter-Boix,&nbsp;P. Rödin-Mörch,&nbsp;P. Halvarsson,&nbsp;J. B. Logue,&nbsp;A. Laurila,&nbsp;J. Höglund","doi":"10.1111/mec.17198","DOIUrl":"10.1111/mec.17198","url":null,"abstract":"<p>Microbiomes play an important role in determining the ecology and behaviour of their hosts. However, questions remain pertaining to how host genetics shape microbiomes, and how microbiome composition influences host fitness. We explored the effects of geography, evolutionary history and host genetics on the skin microbiome diversity and structure in a widespread amphibian. More specifically, we examined the association between bacterial diversity and composition and the major histocompatibility complex class II exon 2 diversity in 12 moor frog (<i>Rana arvalis</i>) populations belonging to two geographical clusters that show signatures of past and ongoing differential selection. We found that while bacterial alpha diversity did not differ between the two clusters, MHC alleles/supertypes and genetic diversity varied considerably depending on geography and evolutionary history. Bacterial alpha diversity was positively correlated with expected MHC heterozygosity and negatively with MHC nucleotide diversity. Furthermore, bacterial community composition showed significant variation between the two geographical clusters and between specific MHC alleles/supertypes. Our findings emphasize the importance of historical demographic events on hologenomic variation and provide new insights into how immunogenetic host variability and microbial diversity may jointly influence host fitness with consequences for disease susceptibility and population persistence.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"33 1","pages":""},"PeriodicalIF":4.9,"publicationDate":"2023-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17198","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71476034","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":"Patterns of speciation in a parapatric pair of Saturnia moths as revealed by target capture","authors":"Maria Khan,&nbsp;Mukta Joshi,&nbsp;Marianne Espeland,&nbsp;Peter Huemer,&nbsp;Carlos Lopez-Vaamonde,&nbsp;Marko Mutanen","doi":"10.1111/mec.17194","DOIUrl":"10.1111/mec.17194","url":null,"abstract":"<p>The focus of this study has been to understand the evolutionary relationships and taxonomy of a widely distributed parapatric species pair of wild silk moths in Europe: <i>Saturnia pavonia</i> and <i>Saturnia pavoniella</i> (Lepidoptera: Saturniidae). To address species delimitation in these parapatric taxa, target enrichment and mtDNA sequencing was employed alongside phylogenetic, admixture, introgression, and species delimitation analyses. The dataset included individuals from both species close to and farther away from the contact zone as well as two hybrids generated in the lab. Nuclear markers strongly supported both <i>S. pavonia</i> and <i>S. pavoniella</i> as two distinct species, with hybrids forming a sister group to <i>S. pavoniella</i>. However, the Maximum Likelihood (ML) tree generated from mtDNA sequencing data presented a different picture, showing both taxa to be phylogenetically intermixed. This inconsistency is likely attributable to mitonuclear discordance, which can arise from biological factors (e.g., introgressive hybridization and/or incomplete lineage sorting). Our analyses indicate that past introgressions have taken place, but that there is no evidence to suggest an ongoing admixture between the two species, demonstrating that the taxa have reached full postzygotic reproductive isolation and hence represent two distinct biological species. Finally, we discuss our results from an evolutionary point of view taking into consideration the past climatic oscillations that have likely shaped the present dynamics between the two species. Overall, our study demonstrates the effectiveness of the target enrichment approach in resolving shallow phylogenetic relationships under complex evolutionary circumstances and that this approach is useful in establishing robust and well-informed taxonomic delimitations involving parapatric taxa.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"33 1","pages":""},"PeriodicalIF":4.9,"publicationDate":"2023-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17194","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71476037","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":"Disentangling the mechanisms underlying phylosymbiosis in mammals","authors":"Elizabeth K. Mallott","doi":"10.1111/mec.17193","DOIUrl":"10.1111/mec.17193","url":null,"abstract":"<p>Mammalian gut microbial communities are frequently found to be host-specific—microbial community compositions are more similar within than between host species—and some individual microbial taxa consistently associate with a single or small set of host species. The ecoevolutionary dynamics that result in this pattern of phylosymbiosis or host specificity have been proposed, but robust tests of the mechanisms driving these relationships are lacking. In this issue of <i>Molecular Ecology</i>, Mazel et al. (2023) combine large amplicon sequencing data sets with bacterial phenotypic traits to test whether microbial dispersal patterns contribute to the host specificity of the gut microbiome. They find that both transmission mode and oxygen tolerance are predictive of how specialized a microbe is. Horizontally transmitted, oxygen-tolerant microbes are more likely to be generalists, and vertically transmitted anaerobes are more likely to be limited to a few host species. This creative use of publicly available data provides a roadmap for testing hypotheses about the mechanisms underlying phylosymbiosis.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"33 1","pages":""},"PeriodicalIF":4.9,"publicationDate":"2023-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71433792","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}