Applied and Environmental Microbiology最新文献

{"title":"N_₂O reduction at low pH.","authors":"Lars R Bakken, Åsa Frostegård","doi":"10.1128/aem.01424-26","DOIUrl":"https://doi.org/10.1128/aem.01424-26","url":null,"abstract":"<p><p>Microbial N_₂O reduction in acid soils became a conundrum when NosZ maturation was found to be impaired at pH ≤6 in both model organisms and soil communities. Yet, evolution appears to have repeatedly circumvented this constraint. Examples include the identification of two small proteins that enable maturation of canonical NosZ at low pH, as well as the <i>Schinkia</i> sp. isolated by G. He, M. E. Davin, S. Kolodney, E. Stutzman, et al. (Appl Environ Microbiol 92:e00069-26, 2026, https://doi.org/10.1128/aem.00069-26), which carries a unique repertoire of <i>nosZ</i> genes and grows by N₂O respiration across pH 4.4-8.5. These discoveries help resolve the conundrum and may provide new options for mitigating N₂O emissions.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0142426"},"PeriodicalIF":4.2,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149178844","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":"Epigenetics as a design variable in heterologous expression.","authors":"Adjo E Kadjo, Galen Ptacek, Barbara I Adaikpoh, Stephanie C Heard, Rasha M Bashatwah, Alessandra S Eustáquio","doi":"10.1128/aem.01024-26","DOIUrl":"https://doi.org/10.1128/aem.01024-26","url":null,"abstract":"<p><p>Heterologous expression-the expression of genes from one organism into another-is an important approach to produce value-added chemicals such as proteins and metabolites. The main challenge, however, is achieving high production yields that are commercially viable. Approaches used to improve productivity rely on editing the DNA sequence, including promoters, ribosome binding sites, and codon usage. Epigenetics, in the form of DNA methylation, may offer an additional layer of control to improve production yields but remains unexplored. Moreover, the choice of the host organism is crucial. We have been interested in developing the alternative bacterial host <i>Burkholderia</i> sp. FERM BP-3421. Four DNA methyltransferases were predicted to be encoded in the genome of this strain, one of which was silent under our growth conditions. After performing gene deletions or overexpression, we experimentally assigned the recognition motif of each DNA methyltransferase, one of which was shown to be essential. As expected, modulation of DNA methylation had major impacts on the transcriptome and metabolome of the host, varying depending on which DNA methyltransferase was modified. Two of the methyltransferases that methylate adenine had overlapping profiles, whereas the one methylating cytosine differed. Finally, we probed the role of DNA methylation during heterologous expression using green fluorescence protein and three different promoters. Expression levels varied in a context-dependent manner with mechanisms, in some cases, involving the presence of methylation motifs within promoter regions but also based on global host effects. This work establishes epigenetics as an important design variable to help improve heterologous expression yields.IMPORTANCEImproving heterologous expression currently relies on modifying the DNA sequence. Epigenetics offers an opportunity to improve outcomes but remains unexplored. We first investigated the effect of epigenetic DNA methylation on the growth, transcriptome, and metabolome of an alternative bacterial host we are interested in developing by generating three single, DNA methyltransferase mutants. Next, we showed that epigenetic DNA methylation or the lack thereof can affect heterologous expression outcomes. The effect was context-dependent, reaching 2.4-fold improvement in one instance. This work highlights the importance of being epigenetics-aware during host development for heterologous expression.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0102426"},"PeriodicalIF":4.2,"publicationDate":"2026-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149164129","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":"Nitrate potentiates kanamycin activity in bacteria through metabolic reprogramming and CpxR-associated respiratory activation.","authors":"Xia Li, Ling-Mei Li, Jia-Hui Lu, Yi-Lin Wu, Ming Jiang","doi":"10.1128/aem.01511-26","DOIUrl":"https://doi.org/10.1128/aem.01511-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Antibiotic resistance in foodborne bacteria profoundly compromises the effectiveness of antimicrobial therapies and represents a persistent global threat to public health and livestock production. There is therefore an urgent need to develop adjuvant strategies that can improve the activity of existing antibiotics against drug-resistant pathogens. In this study, comparative proteomic profiling of kanamycin-susceptible and laboratory-passaged kanamycin-resistant &lt;i&gt;Salmonella enterica&lt;/i&gt; serovar Enteritidis (&lt;i&gt;S&lt;/i&gt;. Enteritidis) revealed coordinated differences in the tricarboxylic acid (TCA) cycle, nitrogen metabolism, and the respiratory electron transport chain. The resistant strain displayed reduced NADH production, proton motive force (PMF), and intracellular kanamycin accumulation. Because these proteomic analyses were performed under antibiotic-free conditions and whole-genome sequencing was not conducted, these differences are interpreted as physiological features associated with the resistant phenotype rather than as evidence of the specific genetic mechanism responsible for the increased kanamycin MIC. Mechanistically, nitrate acted as a potent kanamycin adjuvant by increasing cellular bioenergetic activity through the nitrate-glutamine-glutamate-associated pathway. Nitrate increased NADH production, enhanced TCA cycle activity, and elevated PMF, thereby increasing intracellular kanamycin accumulation. Nitrate also altered CpxR-associated regulation of respiratory genes, providing an additional route by which respiratory activity could be enhanced. Genetic disruption of nitrate transport or selected metabolic and regulatory components attenuated nitrate-mediated potentiation, supporting contributions from both metabolic flux and CpxR-associated respiratory regulation. Importantly, nitrate enhanced kanamycin-mediated killing not only in the laboratory-derived Kana-R strain but also in kanamycin-susceptible Kana-S, indicating a general kanamycin-potentiating effect rather than specific reversal of an acquired resistance mechanism. The nitrate-kanamycin combination also improved treatment outcomes against clinically resistant &lt;i&gt;S.&lt;/i&gt; Enteritidis isolates, including increased survival in murine and chicken infection models. Collectively, these findings identify nitrate as a metabolic adjuvant that can potentiate kanamycin activity by increasing bacterial bioenergetics and drug accumulation. They further illustrate how bacterial physiological state can modulate aminoglycoside efficacy without establishing that nitrate reverses the underlying genetic mechanism of kanamycin resistance.IMPORTANCEAntibiotic efficacy is influenced not only by inherited resistance determinants but also by the physiological and metabolic state of bacterial cells. Our study shows that nitrate can potentiate kanamycin activity in &lt;i&gt;Salmonella enterica&lt;/i&gt; serovar Enteritidis by enhancing central metabolism, respiratory activity, proton motive force, and in","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0151126"},"PeriodicalIF":4.2,"publicationDate":"2026-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149163997","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":"Aggregation and toxicity in bacteria of Rep-WH1 prion-like proteins from the phytopathogen <i>Xylella fastidiosa</i>.","authors":"Leticia Lucero-López, Rafael Giraldo","doi":"10.1128/aem.01745-26","DOIUrl":"https://doi.org/10.1128/aem.01745-26","url":null,"abstract":"<p><p><i>Xylella fastidiosa</i> is a global bacterial phytopathogen that colonizes the xylem vessels, leading to their occlusion and thus to plant death. The expression of the amyloidogenic, prion-like WH1 domain of the replication protein RepA from the <i>Pseudomonas savastanoi</i> plasmid pPS10 severely damages <i>Escherichia coli</i> cells. Here, we characterize the WH1 domains in the Rep proteins from the <i>X. fastidiosa</i> plasmids pXF51 and pXF64. The expression of these Rep-WH1 proteins, as happens with the archetypical RepA-WH1 protein from pPS10, decreased the culturability of <i>E. coli in vitro,</i> promoting dormancy. Expression of pXF51 Rep-WH1 causes the conversion of the bacillary cells into large cocci in which this protein forms a hydrogel, whereas pXF64 Rep-WH1 generates compact amyloid-like aggregates, as do those for pPS10 RepA-WH1, thus defining distinct protein-specific phase separations. In <i>X. fastidiosa</i>, the Rep-WH1 proteins also reduce culturability by altering the integrity of the cell envelope, driving bacterial cells into dormancy, while co-aggregation of a subset of the <i>X. fastidiosa</i> host proteins probably contribute to reducing bacterial virulence in plants. These findings open a way to the exploitation of the intrinsic amyloidogenic potential of endogenous plasmid-encoded Rep proteins for the control of <i>X. fastidiosa</i>, aiming to reduce its economic and environmental impact.IMPORTANCE<i>Xylella fastidiosa</i> is a bacterial pathogen that causes the withering of many woody plants. Currently, there is no efficient way to eradicate this phytopathogen, which menaces crops and natural environments worldwide. In this study, we show that the expression in <i>X. fastidiosa</i> and <i>E. coli</i> of Rep-WH1 proteins, originally encoded by plasmids found either in <i>X. fastidiosa</i> or in <i>Pseudomonas</i>, leads to their aggregation as prions (i.e., transmissible protein particles) that impact bacterial cells by significantly reducing their fitness and, potentially, their virulence. These findings on prion-like Rep-WH1 proteins may constitute the grounds for the development of an efficient weapon against <i>X. fastidiosa</i>.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0174526"},"PeriodicalIF":4.2,"publicationDate":"2026-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149164188","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":"Multiple factors contribute to guaiacol production by <i>Alicyclobacillus acidoterrestris</i> and <i>Alicyclobacillus suci</i> in apple juice, as revealed by transcriptomic and phenotypic analyses.","authors":"Katerina Roth, Zoë C Scott, Andre P Kalenak, Gavin L Sacks, Abigail B Snyder","doi":"10.1128/aem.01679-26","DOIUrl":"https://doi.org/10.1128/aem.01679-26","url":null,"abstract":"<p><p><i>Alicyclobacillus acidoterrestris</i> and <i>Alicyclobacillus suci</i> are guaiacol-producing bacteria that can spoil fruit juices. To study the genetic underpinnings of guaiacol production in juice, transcriptomics was performed on multiple strains of <i>A. suci</i> and <i>A. acidoterrestris</i> under guaiacol production conditions. While guaiacol production was consistently higher by <i>A. acidoterrestris</i> than by <i>A. suci</i>, the gene expression levels associated with guaiacol production (e.g., <i>vdcC</i>, <i>vdcB</i>, <i>vdcD</i>) showed significant variability across strains of both species, suggesting that other factors beyond <i>vdcC</i> transcription influence the amount of guaiacol produced. <i>A. acidoterrestris</i> exhibited a maximum growth rate at 40°C, but produced the most guaiacol at 25°C (16.2 ± 0.6 µg/L, day 14), suggesting that guaiacol is not only linked to growth. When adjusting pH, <i>A. acidoterrestris</i> produced the most guaiacol at pH 4.0 at 14 days (3.2 ± 2.2 µg/L). <i>A. suci</i> also showed the highest amount of guaiacol production at 25°C (3.6 ± 0.3 µg/L, day 7). In pH-adjusted apple juice, <i>A. suci</i> showed consistent growth across all pH levels, yet produced the most guaiacol at pH 3.0 (2.1 ± 0.08 µg/L, day 7). Importantly, guaiacol levels did not consistently correlate with bacterial growth, underscoring the limitations of enumeration-based spoilage assessments. Comparative strain analysis revealed species-specific differences, with <i>A. acidoterrestris</i> producing significantly more guaiacol in apple juice than <i>A. suci</i>, a trend not reflected in media-based PECA assays. These findings highlight the need to evaluate spoilage risk in relevant food matrices under realistic storage conditions to provide beverage producers with insights for improved mitigation strategies.</p><p><strong>Importance: </strong>Beverage spoilage caused by microbes such as <i>Alicyclobacillus</i> poses a significant challenge for the food industry, leading to substantial economic losses and increased food waste. While it is known that some species, specifically those that produce the off-flavor compound guaiacol, are responsible for spoilage, current risk assessment practices often fail to accurately predict spoilage potential. These practices are often flawed because they rely on simple bacterial enumeration or use media-based assays without relevance to a specific food matrix, which do not reflect real-world conditions. Testing the presence or absence of these bacteria without assessment of spoilage can lead to false positives and overly conservative product disposition decisions. This study highlights the need for a more nuanced approach by demonstrating that the relationship between bacterial growth, gene expression, and guaiacol production is not straightforward as it impacts juice spoilage.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0167926"},"PeriodicalIF":4.2,"publicationDate":"2026-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149168790","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":"Cobamide-based interactions between soil bacteria can be predicted based on monoculture growth.","authors":"Zoila I Alvarez-Aponte, Hazel I Anagu, Kenny C Mok, Sandy T Nguyen, Valentine V Trotter, Michiko E Taga","doi":"10.1128/aem.01300-26","DOIUrl":"https://doi.org/10.1128/aem.01300-26","url":null,"abstract":"<p><p>Interactions between microbes shape the structure and function of microbial communities. While studying interactions is key to understanding microbial communities as a whole, gaining a detailed mechanistic view is challenging due to the number of co-occurring interactions. Here, we focus on a single class of shared nutrients, the cobalamin (vitamin B₁₂) family of enzyme cofactors known as cobamides, to study nutrient interactions in laboratory consortia of increasing complexity. Measuring cobamide-dependent growth of two soil <i>Caulobacter</i> isolates in monoculture revealed that each grows faster within a distinct range of cobamide concentrations. Co-culturing the two isolates demonstrated that the cobamide concentration predictably determines which isolate predominates. These results suggest that, although the two organisms appear functionally redundant, with identical metabolic capabilities predicted in their genomes, they may occupy distinct niches in their environment based on cobamide concentration. We further examined the ability of cobamide-producing <i>Mesorhizobium</i> and <i>Priestia</i> isolates to share cobamides and found that both support the cobamide-dependent growth of the two <i>Caulobacter</i> isolates. The <i>Caulobacter</i> isolates could coexist in tri-cultures with each producer following serial passaging, indicating the producers can support the growth of multiple cobamide-dependent organisms. We analyzed the metabolic capacity encoded in the genomes of the four isolates and found that cobamides are likely the main shared nutrient in our co- and tri-cultures. These results highlight the utility of cobamides as a model nutrient to characterize and predict interactions in bacterial consortia of increasing complexity.IMPORTANCEInteractions between microbes shape their communities and the world around them. Because microbial communities are physically and chemically complex, predicting microbial interactions is often difficult. Using a set of four bacteria isolated from the same soil environment, we generated and tested predictions about the interactions involving a family of model nutrients related to cobalamin (vitamin B₁₂). Understanding and predicting interactions can lead to greater insights into microbiome function.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0130026"},"PeriodicalIF":4.2,"publicationDate":"2026-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149164563","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":"Degradation of (S)-1,3-butanediol in <i>Pseudomonas putida</i> KT2440 reveals a CoA-activation route and enantiomeric crosstalk between (R)- and (S)-3-hydroxybutyrate catabolism.","authors":"Nandakumar Arumugam, Tayyab Islam, Joon Young Park, Minchang Jang, Mugesh Sankaranarayanan, Donghyuk Kim, Sung Kuk Lee, Sunghoon Park","doi":"10.1128/aem.01295-26","DOIUrl":"https://doi.org/10.1128/aem.01295-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;1,3-Butanediol (1,3-BDO) exists as (R)- and (S)-enantiomers, yet how aerobic bacteria catabolize the (S)-form has been unknown. Here, we define (S)-1,3-BDO degradation pathway in &lt;i&gt;Pseudomonas putida&lt;/i&gt; KT2440 and uncover an enantioselective enzyme that both controls the pathway and enables a chiral resolution. Transcriptomics, quantitative RT-PCR, and systematic gene deletions show that the &lt;i&gt;ped&lt;/i&gt; cluster oxidizes (S)-1,3-BDO to (S)-3-hydroxybutyrate [(S)-3-HB] using the same upstream machinery as (R)-1,3-BDO and 1,4-BDO, but that the downstream route then diverges sharply. Rather than the free-acid dehydrogenase route used for (R)-3-HB, (S)-3-HB is catabolized through an acyl-CoA synthetase, Acs (PP_3458): a Δ&lt;i&gt;acs&lt;/i&gt; mutant cannot grow on (S)-3-HB, and complementation restores growth, establishing that PP_3458 activates (S)-3-HB to (S)-3-hydroxybutyryl-CoA for β-oxidation. This ATP-dependent CoA-activation route is mechanistically distinct from the ATP-independent (S)-3-hydroxybutyrate dehydrogenase (3SHBDH) pathway of anaerobic &lt;i&gt;Clostridia&lt;/i&gt;, identifying a different enzymatic solution to (S)-3-HB assimilation in aerobes. We further show that PP_3458 strongly prefers (S)- over (R)-3-HB and is inhibited by (R)-3-HB, a crosstalk that explains why a (R)-3-HB-accumulating mutant arrests on racemic 3-HB. Two applications follow directly: whole-cell kinetic resolution that converts racemic 3-HB to (S)-3-HB at high enantiomeric excess (ee &gt; 0.99), and, in a strain unable to degrade (S)-3-HB, near-quantitative recovery-providing a chiral pharmaceutical building block; and &lt;i&gt;ped&lt;/i&gt;-based biosensors that report 1,3-BDO across both enantiomers and function in &lt;i&gt;P. putida&lt;/i&gt; and &lt;i&gt;Escherichia coli&lt;/i&gt;. Some mechanistic details-the inhibition mode and the individual downstream β-oxidation steps-remain to be fully resolved.IMPORTANCE1,3-Butanediol is a commercially important C&lt;sub&gt;4&lt;/sub&gt; diol, but the microbial fate of its (S)-enantiomer in aerobic bacteria has been a gap in our understanding of diol metabolism. We show that &lt;i&gt;Pseudomonas putida&lt;/i&gt; KT2440 degrades (S)-1,3-BDO through a route that, after a shared &lt;i&gt;ped&lt;/i&gt;-dependent oxidation to (S)-3-hydroxybutyrate, depends on an acyl-CoA synthetase (PP_3458) to activate the (S)-acid as its CoA thioester. This ATP-dependent CoA-activation step is a distinct enzymatic strategy from the ATP-independent dehydrogenase route that anaerobic bacteria use for the same substrate, showing that aerobes and anaerobes solve (S)-3-HB assimilation differently. The work also turns this enzymology into utility: because PP_3458 is enantioselective and is inhibited by (R)-3-hydroxybutyrate, the strain can be used for whole-cell kinetic resolution that yields enantiopure (S)-3-hydroxybutyrate-a chiral pharmaceutical building block-from racemic 3-hydroxybutyrate, and the &lt;i&gt;ped&lt;/i&gt;-based biosensors reported here detect 1,3-BDO in both &lt;i&gt;P. putida&lt;/i&gt; and &lt;i&gt;Escherichia coli&lt;/i&gt;, providing a portable","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0129526"},"PeriodicalIF":4.2,"publicationDate":"2026-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149134783","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":"Deep-sea siliceous sponges harbor distinct and functionally diverse microbiomes.","authors":"Katherine R Lane, Kirstin S Meyer-Kaiser, Adena B Collens, Camille V Leal, Allen G Collins, Santiago Herrera, Colleen M Hansel","doi":"10.1128/aem.01747-26","DOIUrl":"https://doi.org/10.1128/aem.01747-26","url":null,"abstract":"<p><p>Sponges, phylum Porifera, are long-lived and basal-branching metazoans that play important roles in ocean biogeochemistry and host diverse microbial communities. Siliceous sponges form a major clade of the Porifera; however, their microbiome is not well characterized, particularly in the deep ocean. Here, we used shotgun metagenomics to investigate the composition of the microbial communities of 13 siliceous sponges collected from four sites near Puerto Rico from depths ranging from 400 to 1,900 meters. Nine of the sponges in this study are from five sponge families that have not previously been sequenced using shotgun metagenomics. We assembled a total of 176 metagenome-assembled genomes from 20 bacterial phyla and 1 archaeal phylum. Ammonia-oxidizing archaea (AOA) <i>Nitrosopumilaceae</i> dominated most siliceous sponge microbial communities and was strikingly the sole symbiont associated with one sponge (<i>Farrea</i>). Overall, microbiome diversity was relatively low across siliceous sponges, except for a Phloeodictyidae, which is likely a high microbial abundance (HMA) sponge. Our results suggest that host sponge phylogeny may shape microbial community structure, with limited evidence for an environmental role. The sponge-associated microbial communities contained genetic capabilities for diverse metabolic functions, particularly contributing to the carbon, nitrogen, and sulfur cycles. In addition to the AOA, evidence of potential for microbial autotrophy was found through the presence of genes for RuBisCO, methanotrophy, and ATP citrate lyase. These results reveal both conserved relationships and metabolic flexibility across siliceous sponge lineages, suggesting unique evolutionary dynamics and demonstrating the importance of microbial metabolism to sponge host health and nutrient cycling in the oligotrophic deep ocean.IMPORTANCEMarine sponges, emerging ~600 million years ago, have close relationships with microorganisms, but the microbiome of deep-sea siliceous sponges is not well understood. Siliceous sponges play essential roles in deep-sea ecosystems by providing habitats for other metazoans and mediating carbon, nitrogen, and sulfur cycling; however, they remain some of the least-studied sponges. By shotgun sequencing DNA from 13 siliceous sponges collected near Puerto Rico, this study found that host sponge phylogeny is linked to microbial community composition and structure. Ammonia-oxidizing archaea dominated the microbial communities associated with marine sponges, likely playing key roles in utilizing metabolic byproducts and supporting host health. Other microbes also contributed to nutrient cycling and contained the potential to fix carbon, suggesting metabolic flexibility, which may benefit sponge hosts in low-resource environments. These findings emphasize the ecological importance of siliceous sponge-microbe symbioses and contribute to our understanding of the drivers shaping their structure and function.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0174726"},"PeriodicalIF":4.2,"publicationDate":"2026-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149134798","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":"Integrated genomics and metabolomics survey of steroids from myxobacteria.","authors":"Bing-Jie Fan, Luo Niu, Teng Liu, Xin-Yi Zhao, Wen-Juan Zhang, De-Gao Wang, Jing Feng, Jia-Qi Hu, Li Zhuo, Chao-Yi Wang, Changsheng Wu","doi":"10.1128/aem.01121-26","DOIUrl":"https://doi.org/10.1128/aem.01121-26","url":null,"abstract":"<p><p>Steroids from myxobacteria remain largely underexplored compared to other natural product classes, leaving a significant gap in our understanding of their biosynthetic diversity, evolutionary trajectories, and pharmacological potential. To address this, we conducted a systematic genomic survey of myxobacterial genomes to delineate the distribution and phylogenetic context of sterol biosynthetic genes, which we found to be organized in a dispersed manner across the chromosome rather than clustered into canonical biosynthetic gene clusters. While the sterol biosynthetic machinery is broadly distributed across <i>Myxococcota</i>, its occurrence is strikingly uneven among lineages, with <i>Nannocystaceae</i> exhibiting the highest biosynthetic potential. Sequence similarity network mining of the oxidosqualene cyclases (OSCs) essential for sterol biosynthesis revealed extensive sequence divergence and unexplored space for discovering novel catalytic functions. Motivated by these bioinformatics predictions, we further demonstrated that integrated chromatographic pre-fractionation with NMR-based metabolic profiling streamlines the targeted isolation of steroids. This approach yielded 12 (seco-)steroids from 2 in-house myxobacterial strains, including 4 previously undescribed structures featuring diverse oxidative decorations, skeletal rearrangements, and ring degradation. Bioactivity assays uncovered that a co-produced metabolite alkylglycoside synergistically potentiates the antimicrobial activity of select secosteroids. Collectively, this study establishes an integrated genomics-metabolomics pipeline that not only expands the structural repertoire of myxobacterial steroids but also provides a blueprint for future discovery of cryptic sterol metabolites and their hidden biological functions.IMPORTANCEThis study presents a systematic phylogenomic survey of sterol biosynthetic genes across the phylum <i>Myxococcota</i>, revealing a dispersed genomic architecture that diverges from canonical bacterial secondary metabolite gene clusters. Beyond this conceptual advance, we demonstrate, for the first time, that NMR-based metabolomics coupled with chromatographic pre-fractionation can accelerate steroid discovery from myxobacteria, leading to the discovery of previously undescribed (seco-)steroids that expand the known chemical space. This integrated pipeline not only enables efficient discovery of cryptic sterol metabolites but also establishes a foundation for understanding the ecological roles of steroids in myxobacteria.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0112126"},"PeriodicalIF":4.2,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149126284","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":"Monitoring disease trends and characterization of non-typhoidal <i>Salmonella</i> isolates from community wastewater in a mid-sized city in Florida, USA: a retrospective study.","authors":"Andrew L Rainey, Lisa E Emerson, Terri Tran, Sarah E Schmedes, Namratha Tarigopula, Paul Fiorella, Matthew D Schimenti, Jessica Ribbing, Ashley Pannell, Susanne Crowe, Jason Blanton, Jessy Motes, Omer Tekin, Heather R Rogers, Paul Davis, Jerne Shapiro, Joseph H Bisesi, Mariola J Ferraro, Anthony T Maurelli","doi":"10.1128/aem.01540-26","DOIUrl":"https://doi.org/10.1128/aem.01540-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Non-typhoidal &lt;i&gt;Salmonella&lt;/i&gt; (NTS) poses a serious threat for multi-drug-resistant infections in the United States. However, most infections are not detected through traditional clinical surveillance, which severely underestimates the community disease burden. Wastewater-based epidemiology can overcome barriers in clinical surveillance and fill the gap. We performed a retrospective study to monitor disease trends and characterize viable NTS isolates from a medium-sized city's wastewater treatment plants. Of 106 weekly raw influent samples from September 2020 to September 2021, 81 samples (76.42%) were NTS-positive via qPCR. NTS wastewater trends were a leading indicator of salmonellosis hospitalizations in the community by 1 week. The 27 unique NTS isolates (representing 11 different serotypes) recovered from wastewater revealed the biodiversity of community circulating infections. Wastewater samples showed a lower biodiversity of serotypes than environmental samples. The biodiversity of isolates collected from wastewater and clinical surveillance was similar but also represented serotypes not identified through traditional clinical surveillance approaches. Genotypic profiles of wastewater isolates revealed that many isolates have the potential for multi-drug-resistant infections and contain virulence genes associated with severe disease. This study shows that wastewater-based epidemiology is a valuable tool for monitoring disease trends and can provide early warning signs of salmonellosis in a community. We successfully enriched and cultured viable NTS isolates from raw wastewater samples frozen for over 1 year, further expanding the capabilities of retrospective studies allowing for future characterization of isolates. Overall, wastewater-based epidemiology is a powerful tool for retrospective analysis and for real-time community surveillance of NTS.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;Wastewater-based epidemiology (WBE) is an emerging tool for community-level infectious disease surveillance, yet its application to bacterial pathogens remains largely underexplored. Our study demonstrated that WBE effectively tracks non-typhoidal &lt;i&gt;Salmonella&lt;/i&gt; (NTS) trends, serving as a leading indicator of hospitalizations. We successfully recovered and characterized &lt;i&gt;Salmonella&lt;/i&gt; isolates from wastewater, highlighting its potential for genomic surveillance. We found that NTS remains viable in frozen wastewater samples for up to 1 year, the longest reported storage time to date. Characterizing bacterial isolates allows for studying pathogen evolution, AMR dynamics, and source tracking. Expanding WBE applications to bacteria could significantly enhance our understanding of disease dynamics and inform proactive public health interventions. Further research is needed to validate WBE as an early warning system for bacterial diseases and integration into a One Health framework. Our findings highlight WBE's growing role in infectious disease epidemiol","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0154026"},"PeriodicalIF":4.2,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149126272","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}