ISME communications最新文献

{"title":"Genetic mixing and demixing on expanding spherical frontiers.","authors":"Alba García Vázquez, Namiko Mitarai, Liselotte Jauffred","doi":"10.1093/ismeco/ycae009","DOIUrl":"10.1093/ismeco/ycae009","url":null,"abstract":"<p><p>Genetic fluctuation during range expansion is a key process driving evolution. When a bacterial population is expanding on a 2D surface, random fluctuations in the growth of the pioneers at the front line cause a strong demixing of genotypes. Even when there is no selective advantage, sectors of low genetic diversity are formed. Experimental studies of range expansions in surface-attached colonies of fluorescently labelled micro-organisms have contributed significantly to our understanding of fundamental evolutionary dynamics. However, experimental studies on genetic fluctuations in 3D range expansions have been sparse, despite their importance for tumour or biofilm development. We encapsulated populations of two fluorescent <i>Escherichia coli</i> strains in inoculation droplets (volumes [Formula: see text] nl). The confined ensemble of cells grew when embedded in a hydrogel-with nutrients-and developed 3D colonies with well-defined, sector-like regions. Using confocal laser scanning microscopy, we imaged the development of 3D colonies and the emergence of sectors. We characterized how cell concentration in the inoculation droplet controls sectors, growth rate, and the transition from branched colonies to quasi-spherical colonies. We further analysed how sectors on the surface change over time. We complement these experimental results with a modified 3D Eden growth model. The model in 3D spherical growth predicts a phase, where sectors are merging, followed by a steady increase (constant rate), and the experimentally analysed sectors were consistent with this prediction. Therefore, our results demonstrate qualitative differences between radial (2D) and spherical (3D) range expansions and their importance in gene fixation processes.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae009"},"PeriodicalIF":0.0,"publicationDate":"2024-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10958774/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140208425","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Extracellular symbiont colonizes insect during embryo development.","authors":"Miguel Ángel González Porras, Inès Pons, Marleny García-Lozano, Shounak Jagdale, Christiane Emmerich, Benjamin Weiss, Hassan Salem","doi":"10.1093/ismeco/ycae005","DOIUrl":"10.1093/ismeco/ycae005","url":null,"abstract":"<p><p>Insects typically acquire their beneficial microbes early in development. Endosymbionts housed intracellularly are commonly integrated during oogenesis or embryogenesis, whereas extracellular microbes are only known to be acquired after hatching by immature instars such as larvae or nymphs. Here, however, we report on an extracellular symbiont that colonizes its host during embryo development. Tortoise beetles (<i>Chrysomelidae</i>: <i>Cassidinae</i>) host their digestive bacterial symbiont <i>Stammera</i> extracellularly within foregut symbiotic organs and in ovary-associated glands to ensure its vertical transmission. We outline the initial stages of symbiont colonization and observe that although the foregut symbiotic organs develop 3 days prior to larval emergence, they remain empty until the final 24 h of embryo development. Infection by <i>Stammera</i> occurs during that timeframe and prior to hatching. By experimentally manipulating symbiont availability to embryos in the egg, we describe a 12-h developmental window governing colonization by <i>Stammera</i>. Symbiotic organs form normally in aposymbiotic larvae, demonstrating that these <i>Stammera</i>-bearing structures develop autonomously. In adults, the foregut symbiotic organs are already colonized following metamorphosis and host a stable <i>Stammera</i> population to facilitate folivory. The ovary-associated glands, however, initially lack <i>Stammera</i>. Symbiont abundance subsequently increases within these transmission organs, thereby ensuring sufficient titers at the onset of oviposition ~29 days following metamorphosis. Collectively, our findings reveal that <i>Stammera</i> colonization precedes larval emergence, where its proliferation is eventually decoupled in adult beetles to match the nutritional and reproductive requirements of its host.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae005"},"PeriodicalIF":0.0,"publicationDate":"2024-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10910848/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140029709","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Two human milk-like synthetic bacterial communities displayed contrasted impacts on barrier and immune responses in an intestinal quadricellular model.","authors":"Charles Le Bras, Lucie Rault, Nolwenn Jacquet, Nathalie Daniel, Victoria Chuat, Florence Valence, Amandine Bellanger, Latifa Bousarghin, Sophie Blat, Yves Le Loir, Isabelle Le Huërou-Luron, Sergine Even","doi":"10.1093/ismeco/ycad019","DOIUrl":"10.1093/ismeco/ycad019","url":null,"abstract":"<p><p>The human milk (HM) microbiota, a highly diverse microbial ecosystem, is thought to contribute to the health benefits associated with breast-feeding, notably through its impact on infant gut microbiota. Our objective was to further explore the role of HM bacteria on gut homeostasis through a \"disassembly/reassembly\" strategy. HM strains covering the diversity of HM cultivable microbiota were first characterized individually and then assembled in synthetic bacterial communities (SynComs) using two human cellular models, peripheral blood mononuclear cells and a quadricellular model mimicking intestinal epithelium. Selected HM bacteria displayed a large range of immunomodulatory properties and had variable effects on epithelial barrier, allowing their classification in functional groups. This multispecies characterization of HM bacteria showed no clear association between taxonomy and HM bacteria impacts on epithelial immune and barrier functions, revealing the entirety and complexity of HM bacteria potential. More importantly, the assembly of HM strains into two SynComs of similar taxonomic composition but with strains exhibiting distinct individual properties, resulted in contrasting impacts on the epithelium. These impacts of SynComs partially diverged from the predicted ones based on individual bacteria. Overall, our results indicate that the functional properties of the HM bacterial community rather than the taxonomic composition itself could play a crucial role in intestinal homeostasis of infants.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycad019"},"PeriodicalIF":0.0,"publicationDate":"2024-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10897888/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139984738","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A gauge of coral physiology: re-examining temporal changes in <i>Endozoicomonas</i> abundance correlated with natural coral bleaching.","authors":"Po-Shun Chuang, Sheng-Ping Yu, Po-Yu Liu, Ming-Tsung Hsu, Yu-Jing Chiou, Chih-Ying Lu, Sen-Lin Tang","doi":"10.1093/ismeco/ycae001","DOIUrl":"10.1093/ismeco/ycae001","url":null,"abstract":"<p><p>Bacteria contribute to many physiological functions of coral holobionts, including responses to bleaching. The bacterial genus, <i>Endozoicomonas</i>, dominates the microbial flora of many coral species and its abundance appears to be correlated with coral bleaching. However, evidences for decoupling of bleaching and <i>Endozoicomonas</i> abundance changes have also been reported. In 2020, a severe bleaching event was recorded at reefs in Taiwan, providing a unique opportunity to re-examine bleaching-<i>Endozoicomonas</i> association using multiple stony corals in natural environments. In this study, we monitored tissue color and microbiome changes in three coral species (<i>Montipora</i> sp., <i>Porites</i> sp., and <i>Stylophora pistillata</i>) in Kenting National Park, following the bleaching event. All tagged <i>Montipora</i> sp. and <i>Porites</i> sp. recovered from bleaching within 1 year, while high mortality occurred in <i>S. pistillata</i>. Microbiome analysis found no correlation of <i>Endozoicomonas</i> relative abundance and bleaching severity during the sampling period, but found a stronger correlation when the month in which bleaching occurred was excluded. Moreover, <i>Endozoicomonas</i> abundance increased during recovery months in <i>Montipora</i> sp. and <i>Porites</i> sp., whereas in <i>S. pistillata</i> it was nearly depleted. These results suggest that <i>Endozoicomonas</i> abundance may represent a gauge of coral health and reflect recovery of some corals from stress. Interestingly, even though different <i>Endozoicomonas</i> strains predominated in the three corals, these <i>Endozoicomonas</i> strains were also shared among coral taxa. Meanwhile, several <i>Endozoicomonas</i> strains showed secondary emergence during coral recovery, suggesting possible symbiont switching in <i>Endozoicomonas.</i> These findings indicate that it may be possible to introduce <i>Endozoicomonas</i> to non-native coral hosts as a coral probiotic.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae001"},"PeriodicalIF":0.0,"publicationDate":"2024-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10872716/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139900997","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Impact of age on pneumococcal colonization of the nasopharynx and oral cavity: an ecological perspective.","authors":"Willem R Miellet, Rob Mariman, Janieke van Veldhuizen, Paul Badoux, Alienke J Wijmenga-Monsuur, David Litt, Thijs Bosch, Elizabeth Miller, Norman K Fry, Marianne A van Houten, Nynke Y Rots, Elisabeth A M Sanders, Krzysztof Trzciński","doi":"10.1093/ismeco/ycae002","DOIUrl":"10.1093/ismeco/ycae002","url":null,"abstract":"<p><p>Pneumococcal carriage studies have suggested that pneumococcal colonization in adults is largely limited to the oral cavity and oropharynx. In this study, we used total abundance-based β-diversity (dissimilarity) and β-diversity components to characterize age-related differences in pneumococcal serotype composition of respiratory samples. quantitative PCR (qPCR) was applied to detect pneumococcal serotypes in nasopharyngeal samples collected from 946 toddlers and 602 adults, saliva samples collected from a subset of 653 toddlers, and saliva and oropharyngeal samples collected from a subset of 318 adults. Bacterial culture rates from nasopharyngeal samples were used to characterize age-related differences in rates of colonizing bacteria. Dissimilarity in pneumococcal serotype composition was low among saliva and nasopharyngeal samples from children. In contrast, respiratory samples from adults exhibited high serotype dissimilarity, which predominantly consisted of abundance gradients and was associated with reduced nasopharyngeal colonization. Age-related serotype dissimilarity was high among nasopharyngeal samples and relatively low for saliva samples. Reduced nasopharyngeal colonization by pneumococcal serotypes coincided with significantly reduced <i>Moraxella catarrhalis</i> and <i>Haemophilus influenzae</i> and increased <i>Staphylococcus aureus</i> nasopharyngeal colonization rates among adults. Findings from this study suggest that within-host environmental conditions, utilized in the upper airways by pneumococcus and other bacteria, undergo age-related changes. It may result in a host-driven ecological succession of bacterial species colonizing the nasopharynx and lead to competitive exclusion of pneumococcus from the nasopharynx but not from the oral habitat. This explains the poor performance of nasopharyngeal samples for pneumococcal carriage among adults and indicates that in adults saliva more accurately represents the epidemiology of pneumococcal carriage than nasopharyngeal samples.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae002"},"PeriodicalIF":0.0,"publicationDate":"2024-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10881297/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139934515","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"New chemical and microbial perspectives on vitamin B1 and vitamer dynamics of a coastal system","authors":"Meriel J. Bittner, Catherine C. Bannon, Elden Rowland, J. Sundh, Erin M Bertrand, Anders F Andersson, R. Paerl, Lasse Riemann","doi":"10.1093/ismeco/ycad016","DOIUrl":"https://doi.org/10.1093/ismeco/ycad016","url":null,"abstract":"\u0000 Vitamin B1 (thiamin, B1) is an essential micronutrient for cells, yet intriguingly in aquatic systems most bacterioplankton are unable to synthesize it de novo (auxotrophy), requiring an exogenous source. Cycling of this valuable metabolite in aquatic systems has not been fully investigated and vitamers (B1-related compounds) have only begun to be measured and incorporated into the B1 cycle. Here, we identify potential key producers and consumers of B1 and gain new insights into the dynamics of B1 cycling through measurements of B1 and vitamers (HMP: 4-amino-5-hydroxymethyl-2-methylpyrimidine, HET: 4-methyl-5-thiazoleethanol, FAMP: N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine) in the particulate and dissolved pool in a temperate coastal system. Dissolved B1 was not the primary limiting nutrient for bacterial production and was relatively stable across seasons with concentrations ranging from 74–117 pM, indicating a balance of supply and demand. However, vitamer concentration changed markedly with season as did transcripts related to vitamer salvage and transport suggesting use of vitamers by certain bacterioplankton, e.g. Pelagibacterales. Genomic and transcriptomic analyses showed that up to 78% of the bacterioplankton taxa were B1 auxotrophs. Notably, de novo B1 production was restricted to a few abundant bacterioplankton (e.g. Vulcanococcus, BACL14 (Burkholderiales), Verrucomicrobiales) across seasons. In summer, abundant picocyanobacteria were important putative B1 sources, based on transcriptional activity, leading to an increase in the B1 pool. Our results provide a new dynamic view of the players and processes involved in B1 cycling over time in coastal waters, and identify specific priority populations and processes for future study.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139439292","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}

{"title":"Biomolecular profiles of Arctic Sea-ice diatoms highlight the role of under-ice light in cellular energy allocation","authors":"Rebecca J Duncan, Daniel Nielsen, J. Søreide, Øystein Varpe, Mark J Tobin, Vanessa Pitusi, Philip Heraud, K. Petrou","doi":"10.1093/ismeco/ycad010","DOIUrl":"https://doi.org/10.1093/ismeco/ycad010","url":null,"abstract":"\u0000 Arctic sea-ice diatoms fuel polar marine food webs as they emerge from winter darkness into Spring. Through their photosynthetic activity they manufacture the nutrients and energy that underpin secondary production. Sea-ice diatom abundance and biomolecular composition vary in space and time. With climate change causing short-term extremes and long-term shifts in mean environmental conditions, understanding how and in what way diatoms adjust biomolecular stores with environmental perturbation is important to gain insight into future ecosystem energy production and nutrient transfer. Using synchrotron-based Fourier Transform Infra-Red microspectroscopy, we examined the biomolecular composition of five dominant sea-ice diatom taxa from landfast ice communities covering a range of under-ice light conditions during Spring, in Svalbard, Norway. In all five taxa we saw a doubling of lipid and fatty acid content when light transmitted to the ice-water interface was >5% but <15% (85–95% attenuation through snow and ice). We determined a threshold around 15% light transmittance after which biomolecular synthesis plateaued, likely due to photoinhibitory effects, except for Navicula spp, which continued to accumulate lipids. Increasing under-ice light availability led to increased energy allocation towards carbohydrates, but this was secondary to lipid synthesis, while protein content remained stable. It is predicted that under-ice light availability will change in the Arctic, increasing due to sea-ice thinning and potentially decreasing with higher snowfall. Our findings show that the nutritional content of sea-ice diatoms are taxon-specific and linked to these changes, highlighting potential implications for future energy and nutrient supply for the polar marine food web.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"75 21","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139440401","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}

{"title":"Transposon sequencing reveals the essential gene set and genes enabling gut symbiosis in the insect symbiont <i>Caballeronia insecticola</i>.","authors":"Romain Jouan, Gaëlle Lextrait, Joy Lachat, Aya Yokota, Raynald Cossard, Delphine Naquin, Tatiana Timchenko, Yoshitomo Kikuchi, Tsubasa Ohbayashi, Peter Mergaert","doi":"10.1093/ismeco/ycad001","DOIUrl":"10.1093/ismeco/ycad001","url":null,"abstract":"<p><p><i>Caballeronia insecticola</i> is a bacterium belonging to the <i>Burkholderia</i> genus <i>sensu lato</i>, which is able to colonize multiple environments like soils and the gut of the bean bug <i>Riptortus pedestris</i>. We constructed a saturated <i>Himar1</i> mariner transposon library and revealed by transposon-sequencing that 498 protein-coding genes constitute the essential genome of <i>Caballeronia insecticola</i> for growth in free-living conditions. By comparing essential gene sets of <i>Caballeronia insecticola</i> and seven related <i>Burkholderia s.l.</i> strains, only 120 common genes were identified, indicating that a large part of the essential genome is strain-specific. In order to reproduce specific nutritional conditions that are present in the gut of <i>Riptortus pedestris</i>, we grew the mutant library in minimal media supplemented with candidate gut nutrients and identified several condition-dependent fitness-defect genes by transposon-sequencing. To validate the robustness of the approach, insertion mutants in six fitness genes were constructed and their growth deficiency in media supplemented with the corresponding nutrient was confirmed. The mutants were further tested for their efficiency in <i>Riptortus pedestris</i> gut colonization, confirming that gluconeogenic carbon sources, taurine and inositol, are nutrients consumed by the symbiont in the gut. Thus, our study provides insights about specific contributions provided by the insect host to the bacterial symbiont.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycad001"},"PeriodicalIF":0.0,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10809759/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139571965","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metagenome-assembled genomes of deep-sea sediments: changes in microbial functional potential lag behind redox transitions","authors":"Clemens Schauberger, B. Thamdrup, C. Lemonnier, Blandine Trouche, J. Poulain, P. Wincker, Sophie Arnaud-Haond, R. Glud, Loïs Maignien","doi":"10.1093/ismeco/ycad005","DOIUrl":"https://doi.org/10.1093/ismeco/ycad005","url":null,"abstract":"\u0000 Hadal sediments are hotspots of microbial activity in the deep-sea and exhibit strong biogeochemical gradients. But while these gradients are widely assumed to exert selective forces on hadal microbial communities, the actual relationship between biogeochemistry, functional traits, and microbial community structure remains poorly understood. We tested whether the biogeochemical conditions in hadal sediments select for microbes based on their genomic capacity for respiration and carbohydrate utilization via a metagenomic analysis of over 153 samples from the Atacama Trench region (max. Depth 8085 m). The obtained 1357 non-redundant microbial genomes were affiliated with about one third of all known microbial phyla, with more than half belonging to unknown genera. This indicated that the capability to withstand extreme hydrostatic pressure is a phylogenetically widespread trait and that hadal sediments are inhabited by diverse microbial lineages. While community composition changed gradually over sediment depth, these changes were not driven by selection for respiratory or carbohydrate degradation capability in the oxic and nitrogenous zones, except in the case of anammox bacteria and nitrifying archaea. However, selection based on respiration and carbohydrate degradation capacity did structure the communities of the ferruginous zone, where aerobic and nitrogen respiring microbes declined exponentially (half-life 125–419 years) and were replaced by subsurface communities. These results highlight a delayed response of microbial community composition to selective pressure imposed by redox zonation and indicated that gradual changes in microbial composition are shaped by the high-resilience and slow growth of microbes in the seafloor.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"55 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139441128","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}

{"title":"HME, NFE, and HAE-1 efflux pumps in Gram-negative bacteria: a comprehensive phylogenetic and ecological approach.","authors":"Josselin Bodilis, Olwen Simenel, Serge Michalet, Elisabeth Brothier, Thibault Meyer, Sabine Favre-Bonté, Sylvie Nazaret","doi":"10.1093/ismeco/ycad018","DOIUrl":"10.1093/ismeco/ycad018","url":null,"abstract":"<p><p>The three primary resistance-nodulation-cell division (RND) efflux pump families (heavy metal efflux [HME], nodulation factor exporter [NFE], and hydrophobe/amphiphile efflux-1 [HAE-1]) are almost exclusively found in Gram-negative bacteria and play a major role in resistance against metals and bacterial biocides, including antibiotics. Despite their significant societal interest, their evolutionary history and environmental functions are poorly understood. Here, we conducted a comprehensive phylogenetic and ecological study of the RND permease, the subunit responsible for the substrate specificity of these efflux pumps. From 920 representative genomes of Gram-negative bacteria, we identified 6205 genes encoding RND permeases with an average of 6.7 genes per genome. The HME family, which is involved in metal resistance, corresponds to a single clade (21.8% of all RND pumps), but the HAE-1 and NFE families had overlapping distributions among clades. We propose to restrict the HAE-1 family to two phylogenetic sister clades, representing 41.8% of all RND pumps and grouping most of the RND pumps involved in multidrug resistance. Metadata associated with genomes, analyses of previously published metagenomes, and quantitative Polymerase Chain Reaction (qPCR) analyses confirmed a significant increase in genes encoding HME permeases in metal-contaminated environments. Interestingly, and possibly related to their role in root colonization, genes encoding HAE-1 permeases were particularly abundant in the rhizosphere. In addition, we found that the genes encoding these HAE-1 permeases are significantly less abundant in marine environments, whereas permeases of a new proposed HAE-4 family are predominant in the genomes of marine strains. These findings emphasize the critical role of the RND pumps in bacterial resistance and adaptation to diverse ecological niches.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycad018"},"PeriodicalIF":0.0,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10872679/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139900998","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}