Molecular Ecology最新文献

{"title":"Pollinator shifts despite hybridisation in the Cape's hyperdiverse heathers (Erica, Ericaceae)","authors":"Seth D. Musker,&nbsp;Michael D. Pirie,&nbsp;Nicolai M. Nürk","doi":"10.1111/mec.17505","DOIUrl":"10.1111/mec.17505","url":null,"abstract":"<p>Interrogating the ecological and geographic factors that influence population divergence dynamics can reveal why some groups of organisms diversify more prolifically than others. One such group is the heathers (<i>Erica</i>, Ericaceae), the largest plant genus in the Cape Floristic Region. We study <i>Erica abietina</i>, a highly variable species complex with four subspecies differing in geographic range, habitat and pollination syndrome. We test for population differentiation, hybridisation, introgression and pollinator-driven divergence using genotyping-by-sequencing on samples across the entire distribution. We find five variably distinct genetic groups, with one subspecies comprising two independent lineages that are geographically isolated and occur on different soil types. Phylogenetic analysis suggests two independent shifts between bird and insect pollination, with accompanying genetic divergence. However, for one pair of populations with different pollinators, we uncover several individuals of hybrid origin at a site of sympatry. These results suggest that floral differentiation driven by divergent selection acts in concert with geographic isolation to maintain reproductive isolation and promote speciation. Our investigations reveal a highly dynamic system whose diversity has been shaped by a variety of interacting forces. We suggest that such a system could be a model for much of the diversification of the Cape flora.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17505","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142071605","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":"Soil properties predict below-ground community structure, but not nematode microbiome patterns in semi-arid habitats","authors":"Tiago José Pereira,&nbsp;Alejandro De Santiago,&nbsp;Holly M. Bik","doi":"10.1111/mec.17501","DOIUrl":"10.1111/mec.17501","url":null,"abstract":"<p>Microbial and microeukaryotic communities are extremely abundant and diverse in soil habitats where they play critical roles in ecosystem functioning and services that are essential to soil health. Soil biodiversity is influenced by above-ground (vegetation) and below-ground factors (soil properties), which together create habitat-specific conditions. However, the compound effects of vegetation and soil properties on soil communities are less studied or often focused on one component of the soil biota. Here, we integrate metabarcoding (16S and 18S rRNA genes) and nematode morphology to assess the effects of habitat and soil properties shaping microbial and microeukaryotic communities as well as nematode-associated microbiomes. We show that both vegetation and soil properties (soil bulk density) were major factors structuring microbial and microeukaryotic communities in semi-arid soil habitats. Despite having lower nutrients and lower pH, denser soils displayed significantly higher alpha diversity than less dense soils across datasets. Nematode-associated microbiomes have lower microbial diversity, strongly differ from soil microbes and are more likely to respond to microscale variations among samples than to vegetation or soil bulk density. Consequently, different nematode lineages and trophic groups are likely to display similar associated microbiomes when sharing the same microhabitat. Different microbiome taxa were enriched within specific nematode lineages (e.g. <i>Mycobacterium</i>, <i>Candidatus Cardinium</i>) highlighting potentially new species-specific associations that may confer benefits to their soil nematode hosts. Our findings highlight the importance of exploring above- and below-ground effects to assess community structure in terrestrial habitats, and how fine-scale analyses are critical for understanding patterns of host-associated microbiomes.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17501","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142034673","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":"Chromosome-level genome assembly of a deep-sea Venus flytrap sea anemone sheds light upon adaptations to an extremely oligotrophic environment","authors":"Junyuan Li,&nbsp;Zifeng Zhan,&nbsp;Yang Li,&nbsp;Yanan Sun,&nbsp;Tong Zhou,&nbsp;Kuidong Xu","doi":"10.1111/mec.17504","DOIUrl":"10.1111/mec.17504","url":null,"abstract":"<p>The Venus flytrap sea anemone <i>Actinoscyphia liui</i> inhabits the nutrient-limited deep ocean in the tropical western Pacific. Compared with most other sea anemones, it has undergone a distinct modification of body shape similar to that of the botanic flytrap. However, the molecular mechanism by which such a peculiar sea anemone adapts to a deep-sea oligotrophic environment is unknown. Here, we report the chromosomal-level genome of <i>A. liui</i> constructed from PacBio and Hi-C data. The assembled genome is 522 Mb in size and exhibits a continuous scaffold N50 of 58.4 Mb. Different from most other sea anemones, which typically possess 14–18 chromosomes per haplotype, <i>A. liui</i> has only 11. The reduced number of chromosomes is associated with chromosome fusion, which likely represents an adaptive strategy to economize energy in oligotrophic deep-sea environments. Comparative analysis with other deep-sea sea anemones revealed adaptive evolution in genes related to cellular autophagy (TMBIM6, SESN1, SCOCB and RPTOR) and mitochondrial energy metabolism (MDH1B and KAD2), which may aid in <i>A. liui</i> coping with severe food scarcity. Meanwhile, the genome has undergone at least two rounds of expansion in gene families associated with fast synaptic transmission, facilitating rapid responses to water currents and prey. Positive selection was detected on putative phosphorylation sites of muscle contraction-related proteins, possibly further improving feeding efficiency. Overall, the present study provides insights into the molecular adaptation to deep-sea oligotrophic environments and sheds light upon potential effects of a novel morphology on the evolution of Cnidaria.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17504","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142015808","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":"Recurrent selection shapes the genomic landscape of differentiation between a pair of host-specialized haplodiploids that diverged with gene flow","authors":"Ashleigh N. Glover,&nbsp;Vitor C. Sousa,&nbsp;Ryan D. Ridenbaugh,&nbsp;Sheina B. Sim,&nbsp;Scott M. Geib,&nbsp;Catherine R. Linnen","doi":"10.1111/mec.17509","DOIUrl":"10.1111/mec.17509","url":null,"abstract":"<p>Understanding the genetics of adaptation and speciation is critical for a complete picture of how biodiversity is generated and maintained. Heterogeneous genomic differentiation between diverging taxa is commonly documented, with genomic regions of high differentiation interpreted as resulting from differential gene flow, linked selection and reduced recombination rates. Disentangling the roles of each of these non-exclusive processes in shaping genome-wide patterns of divergence is challenging but will enhance our knowledge of the repeatability of genomic landscapes across taxa. Here, we combine whole-genome resequencing and genome feature data to investigate the processes shaping the genomic landscape of differentiation for a sister-species pair of haplodiploid pine sawflies, <i>Neodiprion lecontei</i> and <i>Neodiprion pinetum</i>. We find genome-wide correlations between genome features and summary statistics are consistent with pervasive linked selection, with patterns of diversity and divergence more consistently predicted by exon density and recombination rate than the neutral mutation rate (approximated by dS). We also find that both global and local patterns of <i>F</i>_ST, <i>d</i>_XY and <i>π</i> provide strong support for recurrent selection as the primary selective process shaping variation across pine sawfly genomes, with some contribution from balancing selection and lineage-specific linked selection. Because inheritance patterns for haplodiploid genomes are analogous to those of sex chromosomes, we hypothesize that haplodiploids may be especially prone to recurrent selection, even if gene flow occurred throughout divergence. Overall, our study helps fill an important taxonomic gap in the genomic landscape literature and contributes to our understanding of the processes that shape genome-wide patterns of genetic variation.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142007928","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":"Extremes of snow and temperature affect patterns of genetic diversity and differentiation in the alpine butterfly Parnassius smintheus","authors":"Mel Lucas,&nbsp;Gordana Rašić,&nbsp;Alessandro Filazzola,&nbsp;Steve Matter,&nbsp;Jens Roland,&nbsp;Nusha Keyghobadi","doi":"10.1111/mec.17503","DOIUrl":"10.1111/mec.17503","url":null,"abstract":"<p>Weather is an important short-term, local driver of population size and dispersal, which in turn contribute to patterns of genetic diversity and differentiation within species. Climate change is leading to greater weather variability and more frequent extreme weather events. While the effects of long-term and broad-scale mean climate conditions on genetic variation are well studied, our understanding of the effects of weather variability and extreme conditions on genetic variation is less developed. We assessed the influence of temperature and snow depth on genetic diversity and differentiation of populations of the alpine butterfly, <i>Parnassius smintheus</i>. We examined the relationships between a suite of variables, including those representing extreme conditions, and population-level genetic diversity and differentiation across 1453 single nucleotide polymorphisms, using both linear and gravity models. We additionally examined effects of land cover variables known to influence dispersal and gene flow in this species. We found that extreme low temperature events and the lowest recorded mean snow depth were significant predictors of genetic diversity. Extreme low temperature events, mean snow depth and land cover resistance were significant predictors of genetic differentiation. These results are congruent with known effects of early winter weather on population size and habitat connectivity on dispersal in <i>P. smintheus</i>. Our results demonstrate the potential for changes in the frequency or magnitude of extreme weather events to alter patterns of genetic diversity and differentiation.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17503","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142003199","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":"Genome-wide SNP assessment of contemporary European red deer genetic structure highlights the distinction of peripheral populations and the main admixture zones in Europe","authors":"Juan Carranza,&nbsp;Javier Pérez-González,&nbsp;Gabriel Anaya,&nbsp;Menno de Jong,&nbsp;Camilla Broggini,&nbsp;Frank E. Zachos,&nbsp;Allan D. McDevitt,&nbsp;Magdalena Niedziałkowska,&nbsp;Maciej Sykut,&nbsp;Sándor Csányi,&nbsp;Norber Bleier,&nbsp;Lázló Csirke,&nbsp;Knut Røed,&nbsp;Christine Saint-Andrieux,&nbsp;Aurelie Barboiron,&nbsp;Araceli Gort-Esteve,&nbsp;Jordi Ruiz-Olmo,&nbsp;Jose Manuel Seoane,&nbsp;Jose Antonio Godoy,&nbsp;Paweł Mackiewicz,&nbsp;Eva de la Peña,&nbsp;Giovanni Vedel,&nbsp;S. Eryn McFarlane,&nbsp;Josephine Pemberton,&nbsp;Alberto Membrillo","doi":"10.1111/mec.17508","DOIUrl":"10.1111/mec.17508","url":null,"abstract":"<p>Genome-wide technologies open up new possibilities to clarify questions on genetic structure and phylogeographic history of taxa previously studied with microsatellite loci and mitochondrial sequences. Here, we used 736 individual red deer (<i>Cervus elaphus</i>) samples genotyped at 35,701 single nucleotide polymorphism loci (SNPs) to assess the population structure of the species throughout Europe. The results identified 28 populations, with higher degrees of genetic distinction in peripheral compared to mainland populations. Iberian red deer show high genetic differentiation, with lineages in Western and Central Iberia maintaining their distinctiveness, which supports separate refugial ranges within Iberia along with little recent connection between Iberian and the remaining Western European populations. The Norwegian population exhibited the lowest variability and the largest allele frequency differences from mainland European populations, compatible with a history of bottlenecks and drift during post-glacial colonization from southern refugia. Scottish populations showed high genetic distance from the mainland but high levels of diversity. Hybrid zones were found between Eastern and Western European lineages in Central Europe as well as in the Pyrenees, where red deer from France are in close contact with Iberian red deer. Anthropogenic restocking has promoted the Pyrenean contact zone, admixture events in populations on the Isle of Rum and in the Netherlands, and at least partly the admixture of the two main lineages in central-eastern Europe. Our analysis enabled detailed resolution of population structure of a large mammal widely distributed throughout Europe and contributes to resolving the evolutionary history, which can also inform conservation and management policies.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17508","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142003200","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":"Conservation and selective pressures shaping baleen whale olfactory receptor genes supports their use of olfaction in the marine environment","authors":"April A. Jauhal,&nbsp;Rochelle Constantine,&nbsp;Richard Newcomb","doi":"10.1111/mec.17497","DOIUrl":"10.1111/mec.17497","url":null,"abstract":"<p>The relative importance of various sensory modalities can shift in response to evolutionary transitions, resulting in changes to underlying gene families encoding their reception systems. The rapid birth-and-death process underlying the evolution of the large olfactory receptor (OR) gene family has accelerated genomic-level change for the sense of smell in particular. The transition from the land to sea in marine mammals is an attractive model for understanding the influence of habitat shifts on sensory systems, with the retained OR repertoire of baleen whales contrasting with its loss in toothed whales. In this study, we examine to what extent the transition from a terrestrial to a marine environment has influenced the evolution of baleen whale OR repertoires. We developed Gene Mining Pipeline (GMPipe) (https://github.com/AprilJauhal/GMPipe), which can accurately identify large numbers of candidate OR genes. GMPipe identified 707 OR sequences from eight baleen whale species. These repertoires exhibited distinct family count distributions compared to terrestrial mammals, including signs of relative expansion in families OR10, OR11 and OR13. While many receptors have been lost or show signs of random drift in baleen whales, others exhibit signs of evolving under purifying or positive selection. Over 85% of OR genes could be sorted into orthologous groups of sequences containing at least four homologous sequences. Many of these groups, particularly from family OR10, presented signs of relative expansion and purifying selective pressure. Overall, our results suggest that the relatively small size of baleen whale OR repertoires result from specialisation to novel olfactory landscapes, as opposed to random drift.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17497","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142003226","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":"Ecological filtering drives rapid spatiotemporal dynamics in fish skin microbiomes","authors":"Hanna Berggren,&nbsp;Yeşerin Yıldırım,&nbsp;Oscar Nordahl,&nbsp;Per Larsson,&nbsp;Mark Dopson,&nbsp;Petter Tibblin,&nbsp;Daniel Lundin,&nbsp;Jarone Pinhassi,&nbsp;Anders Forsman","doi":"10.1111/mec.17496","DOIUrl":"10.1111/mec.17496","url":null,"abstract":"<p>Skin microbiomes provide vital functions, yet knowledge about the drivers and processes structuring their species assemblages is limited—especially for non-model organisms. In this study, fish skin microbiome was assessed by high throughput sequencing of amplicon sequence variants from metabarcoding of V3–V4 regions in the 16S rRNA gene on fish hosts subjected to the following experimental manipulations: (i) translocation between fresh and brackish water habitats to investigate the role of environment; (ii) treatment with an antibacterial disinfectant to reboot the microbiome and investigate community assembly and priority effects; and (iii) maintained alone or in pairs to study the role of social environment and inter-host dispersal of microbes. The results revealed that fish skin microbiomes harbour a highly dynamic microbial composition that was distinct from bacterioplankton communities in the ambient water. Microbiome composition first diverged as an effect of translocation to either the brackish or freshwater habitat. When the freshwater individuals were translocated back to brackish water, their microbiome composition converged towards the fish microbiomes in the brackish habitat. In summary, external environmental conditions and individual-specific factors jointly determined the community composition dynamics, whereas inter-host dispersal had negligible effects. The dynamics of the microbiome composition was seemingly non-affected by reboot treatment, pointing towards high resilience to disturbance. The results emphasised the role of inter-individual variability for the unexplained variation found in many host-microbiome systems, although the mechanistic underpinnings remain to be identified.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17496","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142003227","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":"Microbiota-driven vaccination in soft ticks: Implications for survival, fitness and reproductive capabilities in Ornithodoros moubata","authors":"Ana Laura Cano-Argüelles,&nbsp;Elianne Piloto-Sardiñas,&nbsp;Apolline Maitre,&nbsp;Lourdes Mateos-Hernández,&nbsp;Jennifer Maye,&nbsp;Alejandra Wu-Chuang,&nbsp;Lianet Abuin-Denis,&nbsp;Dasiel Obregón,&nbsp;Timothy Bamgbose,&nbsp;Ana Oleaga,&nbsp;Alejandro Cabezas-Cruz,&nbsp;Ricardo Pérez-Sánchez","doi":"10.1111/mec.17506","DOIUrl":"10.1111/mec.17506","url":null,"abstract":"<p>The <i>Ornithodoros moubata</i> (Om) soft tick, a vector for diseases like tick-borne human relapsing fever and African swine fever, poses challenges to conventional control methods. With diminishing insecticide efficacy, harnessing the tick's microbiota through innovative approaches like microbiota-driven vaccination emerges as a promising strategy for sustainable and targeted disease control. This study investigated the intricate relationship between <i>Pseudomonas</i>, a keystone taxon in the Om microbiome, and its impact on tick fitness, microbiome structure and network dynamics. Utilizing in silico analyses and empirical vaccination experiments, the role of <i>Pseudomonas</i> within microbial networks in the tick midguts (MG) and salivary glands (SG) of Om was studied. Additionally, the consequences of anti-microbiota vaccines targeting <i>Pseudomonas</i> and <i>Lactobacillus</i> on tick fitness, microbiome diversity and community assembly were explored. The result of the study shows that in Om, <i>Pseudomonas</i> plays a central role in microbial networks, influencing keystone species despite being categorized as peripheral (interacting with 47 different taxa, 13 of which are keystone species). Anti-microbiota vaccination targeting <i>Pseudomonas</i> and <i>Lactobacillus</i> yields distinct effects on tick fitness, with <i>Pseudomonas</i> vaccination significantly impacting female tick survival, while <i>Lactobacillus</i> significantly reduced oviposition and fertility. Microbiome changes post-vaccination reveal diversity alterations, emphasizing the impact of vaccine choice. Community assembly dynamics and network robustness analyses highlight <i>Pseudomonas</i>' pivotal role, in influencing topological features and network resilience. The findings of the study provide comprehensive insights into the intricate dynamics of Om microbial networks and the potential of targeted microbiota-driven vaccines for tick control.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17506","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142003201","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":"Insights into the evolutionary and ecological adaption strategies of nirS- and nirK-type denitrifying communities","authors":"Yuzhen Ming,&nbsp;Mamun Abdullah Al,&nbsp;Dandan Zhang,&nbsp;Wengen Zhu,&nbsp;Huanping Liu,&nbsp;Lanlan Cai,&nbsp;Xiaoli Yu,&nbsp;Kun Wu,&nbsp;Mingyang Niu,&nbsp;Qinglu Zeng,&nbsp;Zhili He,&nbsp;Qingyun Yan","doi":"10.1111/mec.17507","DOIUrl":"10.1111/mec.17507","url":null,"abstract":"<p>Denitrification is a crucial process in the global nitrogen cycle, in which two functionally equivalent genes, <i>nirS</i> and <i>nirK</i>, catalyse the critical reaction and are usually used as marker genes. The <i>nirK</i> gene can function independently, whereas <i>nirS</i> requires additional genes to encode nitrite reductase and is more sensitive to environmental factors than <i>nirK</i>. However, the ecological differentiation mechanisms of those denitrifying microbial communities and their adaptation strategies to environmental stresses remain unclear. Here, we conducted metagenomic analysis for sediments and bioreactor samples from Lake Donghu, China. We found that <i>nirS</i>-type denitrifying communities had a significantly lower horizontal gene transfer frequency than that of <i>nirK</i>-type denitrifying communities, and <i>nirS</i> gene phylogeny was more congruent with taxonomy than that of <i>nirK</i> gene. Metabolic reconstruction of metagenome-assembled genomes further revealed that <i>nirS</i>-type denitrifying communities have robust metabolic systems for energy conservation, enabling them to survive under environmental stresses. Nevertheless, <i>nirK</i>-type denitrifying communities seemed to adapt to oxygen-limited environments with the ability to utilize various carbon and nitrogen compounds. Thus, this study provides novel insights into the ecological differentiation mechanism of <i>nirS</i> and <i>nirK</i>-type denitrifying communities, as well as the regulation of the global nitrogen cycle and greenhouse gas emissions.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141999006","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}