Applied and Environmental Microbiology最新文献

{"title":"Erratum for Hu et al., \"Exploring functional genes' correlation with (<i>S</i>)-equol concentration and new daidzein racemase identification\".","authors":"Yun-Fei Hu, Shu Luo, Sheng-Qi Wang, Ke-Xin Chen, Wei-Xuan Zhong, Bai-Yuan Li, Lin-Yan Cao, Hua-Hai Chen, Ye-Shi Yin","doi":"10.1128/aem.02038-24","DOIUrl":"10.1128/aem.02038-24","url":null,"abstract":"","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0203824"},"PeriodicalIF":3.9,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142567930","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial communities associated with marine sponges from diverse geographic locations harbor biosynthetic novelty.","authors":"Vincent V Nowak, Peng Hou, Jeremy G Owen","doi":"10.1128/aem.00726-24","DOIUrl":"https://doi.org/10.1128/aem.00726-24","url":null,"abstract":"<p><p>Marine sponges are a prolific source of biologically active small molecules, many of which originate from sponge-associated bacteria. Identifying the producing bacteria is a key step in developing sustainable routes for the production of these metabolites. To facilitate the required computational analyses, we developed MetaSing, a reproducible singularity-based pipeline for assembly, identification of high-quality metagenome-assembled genomes (MAGs), and analysis of biosynthetic gene clusters (BGCs) from metagenomic short-read data. We applied this pipeline to metagenomic sequencing data from 16 marine sponges collected from New Zealand, Tonga, and the Mediterranean Sea. This analysis yielded 643 MAGs representing 510 species. Of the 2,670 BGCs identified across all samples, 70.8% were linked to a MAG. Comparison of BGCs to those identified from previously sequenced bacteria revealed high biosynthetic novelty in variety of underexplored phyla, including Poribacteria, Acidobacteriota, and Dadabacteria. Alongside the observation that each sample contains unique biosynthetic potential, this holds great promise for natural product discovery and for furthering the understanding of different sponge holobionts.IMPORTANCEDiscovery of new chemical compounds such as natural products is a crucial endeavor to combat the increasing resistance to antibiotics and other drugs. This manuscript demonstrates that microbial communities associated with marine sponges investigated in this work encode the potential to produce novel chemistry. Lesser studied bacterial taxa that are often difficult to cultivate are particularly rich in potential.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0072624"},"PeriodicalIF":3.9,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142674986","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The puzzle of two tandem acyl-CoA ligases of <i>Pseudomonas putida</i> F1.","authors":"Huijuan Dong, Bo Chen, Haihong Wang, John E Cronan","doi":"10.1128/aem.01267-24","DOIUrl":"10.1128/aem.01267-24","url":null,"abstract":"<p><p>The <i>Pseudomonas putida</i> F1 genome and those of many other pseudomonads contain two tandem genes encoding acyl-CoA ligases Pput_1340 (<i>fadD1</i>) and Pput_1339 (<i>fadD2</i>) with Pput_1339 (<i>fadD2</i>) being the upstream gene. The <i>fadD</i> designation was assigned when both genes were found to complement the growth of an <i>Escherichia coli</i> acyl-CoA synthetase <i>fadD</i> deletion strain with oleic acid as sole carbon source. Site-directed mutagenesis showed that residues of the ATP/AMP domain required for function of <i>E. coli</i> FadD were also essential for full function of FadD1 and FadD2. Growth of the constructed ∆<i>fadD1</i>, ∆<i>fadD2,</i> and ∆<i>fadD1</i>∆<i>fadD2</i> strains was tested in minimal medium with different chain length fatty acids as sole carbon sources. Lack of FadD1 significantly retarded growth with different chain length fatty acids and lack of both FadD1 and FadD2 further retarded growth. Derivatives of the ∆<i>fabA</i>∆<i>desA</i> unsaturated fatty acid auxotrophic strain carrying a deletion of either ∆<i>fadD1</i> or ∆<i>fadD2</i> were constructed. Growth of the ∆<i>fabA</i>∆<i>desA</i>∆<i>fadD1</i> strain was very weak, whereas the ∆<i>fabA</i>∆<i>desA</i>∆<i>fadD2</i> strain grew as well as the ∆<i>fabA</i>∆<i>desA</i> parent strain. Overexpression of either <i>fadD1</i> or <i>fadD2</i> restored growth of the ∆<i>fabA</i>∆<i>desA</i>∆<i>fadD1</i> strain with <i>fadD2</i> overexpression having a greater effect than <i>fadD1</i> overexpression. The ∆<i>fadD1</i> or ∆<i>fadD2</i> genes are cotranscribed although the expression level of <i>fadD1</i> is much higher than that of <i>fadD2</i>. This is attributed to a <i>fadD1</i> promoter located within the upstream FadD2 coding sequence.</p><p><strong>Importance: </strong><i>Pseudomonas</i> bacteria demonstrate a great deal of metabolic diversity and consequently colonize a wide range of ecological niches. A characteristic of these bacteria is a pair of genes in tandem annotated as acyl-CoA ligases involved in fatty acid degradation. The <i>Pseudomonas putida</i> F1 genome is annotated as having at least nine genes encoding acyl-CoA ligases which are scattered around the chromosome excepting the tandem pair. Since similar tandem pairs are found in other pseudomonads, we have constructed and characterized deletion mutants of the tandem ligases. We report that the encoded proteins are authentic acyl-CoA ligases involved in fatty acid degradation.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0126724"},"PeriodicalIF":3.9,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142456542","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Turning trash into treasure: <i>Hermetia illucens</i> microbiome and biodegradation of industrial side streams.","authors":"Patrick Klüber, Friscasari F Gurusinga, Sabine Hurka, Andreas Vilcinskas, Dorothee Tegtmeier","doi":"10.1128/aem.00991-24","DOIUrl":"10.1128/aem.00991-24","url":null,"abstract":"<p><p>Black soldier fly larvae (BSFL) have attracted attention due to their ability to upcycle various biological side streams into valuable biomass, such as proteins, lipids, and chitin. In this study, we investigated the impact of high-fiber diets on larval growth performance and the shift of microbes in the gut. We tested empty fruit bunches (EFB), potato pulp (PP), and cottonseed press cake (CPC), with chicken feed (CF) used as a control diet. We found that larvae reared on the EFB, PP, and CPC were smaller than control larvae at the end of development due to the low nutritional value of the diets. However, survival rates of more than 90% were observed regardless of the diet. We used a cultivation-dependent approach to analyze the microbial community in the gut of BSFL, isolated, and identified a total of 329 bacterial strains. <i>Bacillaceae</i> were most frequently isolated from larvae reared on the high-fiber EFB diet. These isolates were predicted to degrade cellulose <i>in silico</i> and this was subsequently confirmed <i>in vitro</i> using the Congo Red assay. Whereas the members of <i>Enterobacteriaceae</i> and <i>Morganellaceae</i> were mostly found in guts of larvae reared on the high-protein diets CPC and CF. We conclude that the gut microbiome plays a crucial role in the digestion of fiber-rich plant organic material, thereby enabling the BSFL to successfully complete their life cycle also on substrates with low nutritional value. As a result, BSFL convert industrial side streams into valuable biomass, reducing waste and promoting sustainability.</p><p><strong>Importance: </strong>Organic side streams from various industries pose a challenge to the environment. They are often present in huge amounts and are mostly discarded, incinerated, used for biogas production, or as feed for ruminant animals. Many plant-based side streams contain difficult-to-digest fiber as well as anti-nutritional or even insecticidal compounds that could harm the animals. These challenges can be addressed using black soldier fly larvae, which are known to degrade various organic substrates and convert them into valuable biomass. This will help mitigate agro-industrial side streams via efficient waste management and will contribute to the more economical and sustainable farming of insects.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0099124"},"PeriodicalIF":3.9,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142456543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Environment, plant genetics, and their interaction shape important aspects of sunflower rhizosphere microbial communities.","authors":"Clifton P Bueno de Mesquita, Corinne M Walsh, Ziv Attia, Brady D Koehler, Zachary J Tarble, David L Van Tassel, Nolan C Kane, Brent S Hulke","doi":"10.1128/aem.01635-24","DOIUrl":"10.1128/aem.01635-24","url":null,"abstract":"<p><p>Associations with soil microorganisms are crucial for plants' overall health and functioning. While much work has been done to understand drivers of rhizosphere microbiome structure and function, the relative importance of geography, climate, soil properties, and plant genetics remains unclear, as results have been mixed and comprehensive studies across many sites and genotypes are limited. Rhizosphere microbiomes are crucial for crop resistance to pathogens, stress tolerance, nutrient availability, and ultimately yield. Here, we quantify the relative roles of plant genotype, environment, and their interaction in shaping soil rhizosphere communities, using 16S and ITS gene sequencing of rhizosphere soils from 10 genotypes of cultivated sunflower (<i>Helianthus annuus</i>) at 15 sites across the Great Plains of the United States. While site generally outweighed genotype overall in terms of effects on archaeal, bacterial, and fungal richness, community composition, and taxa relative abundances, there was also a significant interaction such that genotype exerted a significant influence on archaeal, bacterial, and fungal microbiomes in certain sites. Site effects were attributed to a combination of spatial distance and differences in climate and soil properties. Microbial taxa that were previously associated with resistance to the fungal necrotrophic pathogen <i>Sclerotinia</i> were present in most sites but differed significantly in relative abundance across sites. Our results have implications for plant breeding and agronomic microbiome manipulations for agricultural improvement across different geographic regions.IMPORTANCEDespite the importance of plant breeding in agriculture, we still have a limited understanding of how plant genetic variation shapes soil microbiome composition across broad geographic regions. Using 15 sites across the Great Plains of North America, we show that cultivated sunflower rhizosphere archaeal, bacterial, and fungal communities are driven primarily by site soil and climatic differences, but genotype can interact with site to influence the composition, especially in warmer and drier sites with lower overall microbial richness. We also show that all taxa that were previously found to be associated with resistance to the fungal pathogen <i>Sclerotinia sclerotiorum</i> were widespread but significantly affected by site, while a subset was also significantly affected by genotype. Our results contribute to a broader understanding of rhizosphere archaeal, bacterial, and fungal community assembly and provide foundational knowledge for plant breeding efforts and potential future microbiome manipulations in agriculture.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0163524"},"PeriodicalIF":3.9,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142493387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of a <i>Limosilactobacillus reuteri</i> therapeutic delivery platform with reduced colonization potential.","authors":"Laura M Alexander, Saima Khalid, Gina M Gallego-Lopez, Theresa J Astmann, Jee-Hwan Oh, Mark Heggen, Phil Huss, Renee Fisher, Amitava Mukherjee, Srivatsan Raman, In Young Choi, Morgan N Smith, Claude J Rogers, Michael W Epperly, Laura J Knoll, Joel S Greenberger, Jan-Peter van Pijkeren","doi":"10.1128/aem.00312-24","DOIUrl":"10.1128/aem.00312-24","url":null,"abstract":"<p><p>Bacterial biotherapeutic delivery vehicles have the potential to treat a variety of diseases. This approach obviates the need to purify the recombinant effector molecule, allows delivery of therapeutics <i>in situ</i> via oral or intranasal administration, and protects the effector molecule during gastrointestinal transit. Lactic acid bacteria have been broadly developed as therapeutic delivery vehicles though risks associated with the colonization of a genetically modified microorganism have so-far not been addressed. Here, we present an engineered <i>Limosilactobacillus reuteri</i> strain with reduced colonization potential. We applied a dual-recombineering scheme for efficient barcoding and generated mutants in genes encoding five previously characterized and four uncharacterized putative adhesins. Compared with the wild type, none of the mutants were reduced in their ability to survive gastrointestinal transit in mice. CmbA was identified as a key protein in <i>L. reuteri</i> adhesion to HT-29 and enteroid cells. The nonuple mutant, a single strain with all nine genes encoding adhesins inactivated, had reduced capacity to adhere to enteroid monolayers. The nonuple mutant producing murine IFN-β was equally effective as its wild-type counterpart in mitigating radiation toxicity in mice. Thus, this work established a novel therapeutic delivery platform that lays a foundation for its application in other microbial therapeutic delivery candidates and furthers the progress of the <i>L. reuteri</i> delivery system towards human use.IMPORTANCEOne major advantage to leverage gut microbes that have co-evolved with the vertebrate host is that evolution already has taken care of the difficult task to optimize survival within a complex ecosystem. The availability of the ecological niche will support colonization. However, long-term colonization of a recombinant microbe may not be desirable. Therefore, strategies need to be developed to overcome this potential safety concern. In this work, we developed a single strain in which we inactivated the encoding sortase, and eight genes encoding characterized/putative adhesins. Each individual mutant was characterized for growth and adhesion to epithelial cells. On enteroid cells, the nonuple mutant has a reduced adhesion potential compared with the wild-type strain. In a model of total-body irradiation, the nonuple strain engineered to release murine interferon-β performed comparable to a derivative of the wild-type strain that releases interferon-β. This work is an important step toward the application of recombinant <i>L. reuteri</i> in humans.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0031224"},"PeriodicalIF":3.9,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142543189","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Directed evolution of bacteriophages: thwarted by prolific prophage.","authors":"Tracey Lee Peters, Jacob Schow, Emma Spencer, James T Van Leuven, Holly Wichman, Craig Miller","doi":"10.1128/aem.00884-24","DOIUrl":"10.1128/aem.00884-24","url":null,"abstract":"<p><p>Various directed evolution methods exist that seek to procure bacteriophages with expanded host ranges, typically targeting phage-resistant or non-permissive bacterial hosts. The general premise of these methods involves propagating phage(s) on multiple bacterial hosts, pooling the lysate, and repeating this process until phage(s) can form plaques on the target host(s). In theory, this produces a lysate containing input phages and their evolved phage progeny. However, in practice, this lysate can also include prophages originating from bacterial hosts. Here, we describe our experience implementing one directed evolution method, the Appelmans protocol, to study phage evolution in the <i>Pseudomonas aeruginosa</i> phage-host system, where we observed rapid host-range expansion of the phage cocktail. Further experimentation and sequencing revealed that the observed host-range expansion was due to a <i>Casadabanvirus</i> prophage originating from a lysogenic host that was only included in the first three rounds of the experiment. This prophage could infect five of eight bacterial hosts initially used, allowing it to persist and proliferate until the termination of the experiment. This prophage was represented in half of the sequenced phage samples isolated from the Appelmans experiment, but despite being subjected to directed evolution conditions, it does not appear to have evolved. This work highlights the impact of prophages in directed evolution experiments and the importance of genetically verifying output phages, particularly for those attempting to procure phages intended for phage therapy applications. This study also notes the usefulness of intraspecies antagonism assays between bacterial host strains to establish a baseline for inhibitory activity and determine the presence of prophage.IMPORTANCEDirected evolution is a common strategy for evolving phages to expand the host range, often targeting pathogenic strains of bacteria. In this study, we investigated phage host-range expansion using directed evolution in the <i>Pseudomonas aeruginosa</i> system. We show that prophages are active players in directed evolution and can contribute to observation of host-range expansion. Since prophages are prevalent in bacterial hosts, particularly pathogenic strains of bacteria, and all directed evolution approaches involve iteratively propagating phage on one or more bacterial hosts, the presence of prophage in phage preparations is a factor that needs to be considered in experimental design and interpretation of results. These results highlight the importance of screening for prophages either genetically or through intraspecies antagonism assays during selection of bacterial strains and will contribute to improving the experimental design of future directed evolution studies.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0088424"},"PeriodicalIF":3.9,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142543191","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantifying bacterial efflux within subcellular domains of <i>Pseudomonas aeruginosa</i>.","authors":"Yujie Li, Michael J Wilhelm, Tong Wu, Xiao-Hua Hu, Oscar N Ruiz, Hai-Lung Dai","doi":"10.1128/aem.01447-24","DOIUrl":"10.1128/aem.01447-24","url":null,"abstract":"<p><p>Molecular efflux is a mechanism through which bacteria actively expel undesirable substances. This is a crucial line of defense against toxic chemicals in harsh environments. Understanding how efflux works is critical for designing antimicrobial strategies. Though much is already known about efflux proteins, important details about the mechanisms of efflux (e.g., importance of specific subcellular domains and ejection rates) have yet to be experimentally quantified. Herein, we use the nonlinear optical technique, second harmonic light scattering, to simultaneously measure the efflux rates from the periplasm and cytosol of a Gram-negative bacterium. The influence of efflux on the uptake kinetics of a mild antimicrobial, malachite green (MG), by <i>Pseudomonas aeruginosa</i> was quantified. It is observed that efflux primarily occurs from the periplasm and is two orders of magnitude faster than from the cytosol. Efflux pumps activate to maintain MG concentrations in the periplasm below 1 µM, while efflux from the cytosol maintains MG concentration below 0.1 µM. Efflux pumps are shown to saturate when exogenous MG concentrations are greater than 25 µM, while the cytosol efflux function saturates at >15 µM. Finally, efflux pumps can simultaneously eject different compounds, as proven by experiments with both MG and hexane, a known effluxable compound.IMPORTANCEMolecular efflux pumps are a crucial defense mechanism that protects bacteria from an otherwise unchecked influx of toxic molecules present in the extracellular environment. The efflux functions constitute a significant hindrance to antimicrobial efficacy. While much is now known regarding the structure of these channels, knowledge of the influence of efflux in individual subcellular domains and the associated ejection rates is still lacking. Using the nonlinear optical technique, second-harmonic light scattering, we have measured the threshold concentrations for pump activation, saturation concentrations, and efflux rates from both the periplasm and cytosol in living Gram-negative bacteria. The quantified efflux data in the different subcellular compartments not only provide a clear mechanistic understanding but also are critical for developing antimicrobial strategies.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0144724"},"PeriodicalIF":3.9,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142543209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of biofilm assembly and microbial diversity on a freshwater, ferrous-hulled shipwreck.","authors":"Maggie O Shostak, Meredith A Cox, Nathan Richards, Erin K Field","doi":"10.1128/aem.01770-24","DOIUrl":"10.1128/aem.01770-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Abandoned shipwrecks are sitting at the bottom of oceans, lakes, and rivers around the world. Over time, microbial-comprised biofilms can help protect wrecks against chemical corrosion or contribute to their deterioration through microbiologically influenced corrosion (MIC) by organisms including iron-oxidizing bacteria (FeOB) and sulfate-reducing bacteria (SRB). Assessing the community assembly of these biofilms will give us a better understanding of the role these microbes play in MIC and the factors that influence it. Here, we determine if microbial community composition differs across a shallow freshwater ferrous-hulled shipwreck environment. Results suggest that there was a statistically significant difference among the sample types indicating the wreck environments around &lt;i&gt;Accomac&lt;/i&gt; influenced the community composition. This is consistent with previous observations within an estuarine, shallow-water wreck environment. &lt;i&gt;Bacteroidota&lt;/i&gt;, &lt;i&gt;Chloroflexota&lt;/i&gt;, and &lt;i&gt;Cyanobacteriota&lt;/i&gt; were the primary taxa responsible for differences among these wreck environments. Interestingly, port-side biofilm communities were significantly different than those on the starboard side suggesting physical factors of the environment drove niche partitioning on each side of the wreck. Similarly, FeOB enrichments and known FeOB taxa were found across the entire wreck but were primarily found in samples associated with the port side of the wreck. Amplicon sequencing identified both known FeOB and SRB taxa with a higher proportion of FeOB than SRB. Overall, these results indicate that there is niche partitioning of the microbial communities as well as with corrosion-causing taxa within a shallow freshwater wreck site which may lead to variation in how microbes may contribute to the protection or deterioration of these ferrous-hulled wrecks.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;The overall structure, abundance, and diversity of microbial communities on shipwrecks have recently been studied in marine aquatic environments. While previous studies have looked at the microbial communities associated with shallow-water ferrous-hulled wrecks in marine environments, studies focusing on freshwater wreck systems are limited. The purpose of this study was to determine microbial community diversity and composition trends across the &lt;i&gt;Accomac&lt;/i&gt; shipwreck environment. Furthermore, shipwrecks are colonized by corrosion-causing taxa, such as iron-oxidizing bacteria and sulfate-reducing bacteria which have been shown to influence the biocorrosion of ferrous-hulled structures. Identification of various microbes in biofilms, as well as corrosion-causing microbes, can help researchers identify the role they play in aquatic ecosystem development and persistence as well as artificial reef integrity. Understanding how microbes assemble on wrecks will provide insight into preservation strategies to prevent deterioration of these wrecks over time, as well as limiting biocor","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0177024"},"PeriodicalIF":3.9,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142456517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Convergent reductive evolution in bee-associated lactic acid bacteria.","authors":"Ana Pontes, Marie-Claire Harrison, Antonis Rokas, Carla Gonçalves","doi":"10.1128/aem.01257-24","DOIUrl":"10.1128/aem.01257-24","url":null,"abstract":"<p><p>Distantly related organisms may evolve similar traits when exposed to similar environments or engaging in certain lifestyles. Several members of the Lactobacillaceae [lactic acid bacteria (LAB)] family are frequently isolated from the floral niche, mostly from bees and flowers. In some floral LAB species (henceforth referred to as bee-associated LAB), distinctive genomic (e.g., genome reduction) and phenotypic (e.g., preference for fructose over glucose or fructophily) features were recently documented. These features are found across distantly related species, raising the hypothesis that specific genomic and phenotypic traits evolved convergently during adaptation to the floral environment. To test this hypothesis, we examined representative genomes of 369 species of bee-associated and non-bee-associated LAB. Phylogenomic analysis unveiled seven independent ecological shifts toward the bee environment in LAB. In these species, we observed significant reductions of genome size, gene repertoire, and GC content. Using machine leaning, we could distinguish bee-associated from non-bee-associated species with 94% accuracy, based on the absence of genes involved in metabolism, osmotic stress, or DNA repair. Moreover, we found that the most important genes for the machine learning classifier were seemingly lost, independently, in multiple bee-associated lineages. One of these genes, acetaldehyde-alcohol dehydrogenase (<i>adhE</i>), encodes a bifunctional aldehyde-alcohol dehydrogenase which has been associated with the evolution of fructophily, a rare phenotypic trait that is pervasive across bee-associated LAB species. These results suggest that the independent evolution of distinctive phenotypes in bee-associated LAB has been largely driven by independent losses of the same sets of genes.IMPORTANCESeveral LAB species are intimately associated with bees and exhibit unique biochemical properties with potential for food applications and honeybee health. Using a machine learning-based approach, our study shows that adaptation of LAB to the bee environment was accompanied by a distinctive genomic trajectory deeply shaped by gene loss. Several of these gene losses occurred independently in distantly related species and are linked to some of their unique biotechnologically relevant traits, such as the preference for fructose over glucose (fructophily). This study underscores the potential of machine learning in identifying fingerprints of adaptation and detecting instances of convergent evolution. Furthermore, it sheds light onto the genomic and phenotypic particularities of bee-associated bacteria, thereby deepening the understanding of their positive impact on honeybee health.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0125724"},"PeriodicalIF":3.9,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142493386","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}