Applied and Environmental Microbiology最新文献

{"title":"Viral concentration method biases in the detection of viral profiles in wastewater.","authors":"Naeema Cheshomi, Absar Alum, Matthew F Smith, Efrem S Lim, Otakuye Conroy-Ben, Morteza Abbaszadegan","doi":"10.1128/aem.01339-24","DOIUrl":"10.1128/aem.01339-24","url":null,"abstract":"<p><p>Viral detection methodologies used for wastewater-based epidemiology (WBE) studies have a broad range of efficacies. The complex matrix and low viral particle load in wastewater emphasize the importance of the concentration method. This study focused on comparing three commonly used virus concentration methods: polyethylene glycol precipitation (PEG), immuno-magnetic nanoparticles (IMNP), and electronegative membrane filtration (EMF). Influent and effluent wastewater samples were processed by the methods and analyzed by DNA/RNA quantification and sequencing for the detection of human viruses. SARS-COV-2, Astrovirus, and Hepatitis C virus were detected by all the methods in both sample types. PEG precipitation resulted in the detection of 20 types of viruses in influent and 16 types in effluent samples. The corresponding number of virus types detected was 21 and 11 for IMNP, and 16 and 8 for EMF. Certain viruses were unique to only one concentration method. For example, PEG detected three types of viruses in influent and six types in effluent compared to IMNP, which detected seven types in influent and one type in effluent samples. However, the EMF method appeared to be the least effective, detecting three types in influent and none in effluent samples. Rotavirus was detected in influent sample using IMNP method, whereas EMF and PEG methods failed to yield a similar outcome. Consequently, the potential false negative results pose a risk to the credibility of WBE applications. Therefore, implementation of a proper concentration technique is critical to minimize method biases and ensure accurate viral profiling in WBE studies.IMPORTANCEIn recent years, significant research efforts have been focused on the development of viral detection methodology for wastewater-based epidemiology studies, showing a range of variability in detection efficacies. A proper methodology is essential for an appropriate evaluation of disease prevalence and community health in such studies and necessitates designing a concentration method based on the target pathogenic virus. There remains a need for comparative performance evaluations of methods in the context of detection efficiencies. This study highlights the significant impact of sample matrix, viral structure, and nucleic acid composition on the efficacy of viral concentration methods. Assessing WBE techniques to ensure accurate detection and understanding of viral presence within wastewater samples is critical for revealing viral profiles in municipality wastewater samples.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0133924"},"PeriodicalIF":3.9,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11784009/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142783495","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbiome dynamics and functional profiles in deep-sea wood-fall micro-ecosystem: insights into drive pattern of community assembly, biogeochemical processes, and lignocellulose degradation.","authors":"Zeming Bao, Biao Chen, Kefu Yu, Yuxin Wei, Xinyue Liang, Huanting Yao, Xianrun Liao, Wei Xie, Kedong Yin","doi":"10.1128/aem.02165-24","DOIUrl":"10.1128/aem.02165-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Wood-fall micro-ecosystems contribute to biogeochemical processes in the oligotrophic deep ocean. However, the community assembly processes and biogeochemical functions of microbiomes in wood fall remain unclear. This study investigated the diversity, community structure, assembly processes, and functional profiles of bacteria and fungi in a deep-sea wood fall from the South China Sea using physicochemical indices, amplicon sequencing, and metagenomics. The results showed that distinct wood-fall contact surfaces exhibit habitat heterogeneity. The bacterial community of all contact surfaces and the fungal community of seawater contact surface (SWCS) were affected by homogeneous selection. In SWCS and transition region (TR), bacterial communities were influenced by dispersal limitation, whereas fungal communities were affected by homogenizing dispersal. The Venn diagram visualization revealed that the shared fungal community between SWCS and TR was dominated by Aspergillaceae. Additionally, the bacterial community demonstrated a higher genetic potential for sulfur, nitrogen, and methane metabolism than fungi. The sediment contact surface enriched modules were associated with dissimilatory sulfate reduction and methanogenesis, whereas the modules related to nitrate reduction exhibited enrichment characteristics in TR. Moreover, fungi showed a stronger potential for lignocellulase production compared to bacteria, with Microascaceae and Nectriaceae identified as potential contributors to lignocellulose degradation. These results indicate that environmental filtering and organism exchange levels regulated the microbial community assembly of wood fall. The biogeochemical cycling of sulfur, nitrogen, and methane was mainly driven by the bacterial community. Nevertheless, the terrestrial fungi Microascaceae and Nectriaceae might degrade lignocellulose via the combined action of multiple lignocellulases.IMPORTANCEThe presence and activity of microbial communities may play a crucial role in the biogeochemical cycle of deep-sea wood-fall micro-ecosystems. Previous studies on wood falls have focused on the microbiome diversity, community composition, and environmental impact, while few have investigated wood-fall micro-ecosystems by distinguishing among distinct contact surfaces. Our study investigated the microbiome dynamics and functional profiles of bacteria and fungi among distinct wood-fall contact surfaces. We found that the microbiome community assembly was regulated by environmental filtering and organism exchange levels. Bacteria drive the biogeochemical cycling of sulfur, nitrogen, and methane in wood fall through diverse metabolic pathways, whereas fungi are crucial for lignocellulose degradation. Ultimately, this study provides new insights into the driving pattern of community assembly, biogeochemical processes, and lignocellulose degradation in the microbiomes of deep-sea wood-fall micro-ecosystems, enhancing our comprehension of the ecolo","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0216524"},"PeriodicalIF":3.9,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11784029/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142783914","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Time-decay patterns and irregular disturbance: contrasting roles of abundant and rare microbial communities in dynamic coastal seawater.","authors":"Yulin Zhang, Derui Song, Peng Yao, Xiao-Hua Zhang, Jiwen Liu","doi":"10.1128/aem.01751-24","DOIUrl":"10.1128/aem.01751-24","url":null,"abstract":"<p><p>Microbial communities in coastal seas experience strong environmental disturbances, yet their response patterns, especially regarding differently abundant subcommunities, remain poorly understood. Here, through 16S rRNA gene amplicon sequencing, we investigated the diversity, time-decay pattern, and assembly process of abundant, conditionally rare taxa (CRT) and rare microbial subcommunities in temperate coastal waters over 60 consecutive weeks. The abundant (50.9%) and CRT (46.1%) communities each comprised approximately half of the planktonic community, while the CRT and rare communities contributed to the extremely high species diversity. Distinct temporal heterogeneity was observed among the three fractions and was associated with taxonomic level. The abundant subcommunity exhibited time-decay patterns at all taxonomic levels, while for CRT, the pattern was found only at finer levels. In contrast, variations of the rare community loosely followed a temporal rhythm and were largely confined within a specific taxonomic range, likely raised from turnovers among closely related taxa. Determinism dominated the community assembly of the abundant fraction, while the rare one was more controlled by stochasticity that may be related to pulse terrigenous inputs and anthropogenic disturbances. The rare subcommunity with narrow niche widths likely represented a stable repository to offer episodic specialists, while the abundant taxa that exhibited broader niche widths were considered the generalists in fluctuating environments. Our study revealed the distinct strategies that abundant and rare communities adopt to maintain community stability in temporal dynamics of prokaryotic plankton in the coastal seawater.</p><p><strong>Importance: </strong>The relative importance of rare and abundant taxa in microbial temporal patterns remains debated. Here, we identified taxonomically associated distinct diversity modes of abundant and rare subcommunities from a year-round time-series study in dynamic coastal seawater. We highlighted the significance of the rare subcommunity in maintaining community stability by serving as a repository to offer specialists driven by stochastic processes over time. The abundant subcommunity, by contrast, contributed mainly to temporal rhythmic variations. This study expands the current understanding of the temporal dynamics and stability of coastal microbial communities by revealing distinct variation patterns of subcommunities with different abundances.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0175124"},"PeriodicalIF":3.9,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11784082/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142798970","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cu- and Ag-mediated inactivation of <i>L. pneumophila</i> in bench- and pilot-scale drinking water systems.","authors":"Chelsea L Hintz, Brian Morris, Sue Witt, Nicole Sojda, Helen Y Buse","doi":"10.1128/aem.01073-24","DOIUrl":"10.1128/aem.01073-24","url":null,"abstract":"<p><p><i>Legionella pneumophila</i> (Lp) is an opportunistic drinking water pathogen that can cause infections through the inhalation of Lp-containing aerosols and can occur in premise plumbing systems. In this work, the use of copper (Cu) and silver (Ag) ions was evaluated at the bench and pilot scale to determine (i) the effective independent concentrations of copper and silver that are efficacious in inactivating Lp, (ii) the impact of various water quality parameters on the efficaciousness of copper and silver ions, and (iii) the effectiveness and practicality of using dissociation to produce ions at the pilot scale. At the bench scale, it was determined that 0.3 ppm and 0.03 ppm of Cu and Ag, respectively, achieved 6-log inactivation of Lp in 5 h in experimental buffer. But, in dechlorinated filter-sterilized tap water, the same concentrations of Cu were not effective, and the effectiveness of Ag was slower. pH and dissolved inorganic carbon content were found to be important parameters in determining if the use of Cu and Ag ions is appropriate. At the pilot scale, dissociation was successfully used to produce Cu and Ag ions. Target levels of ions were met at the pilot scale but were difficult to achieve, and no impact was observed on Lp concentrations. Results from this study suggest that there are important caveats in the application of this technology when applied in a drinking water matrix and prior understanding of a system's water chemistry may be important to determine the effectiveness of Lp disinfection using Cu and Ag.IMPORTANCEThis work sheds light on the effectiveness of using Cu and Ag ions to inactivate (or kill) <i>Legionella pneumophila. Legionella</i> is an opportunistic drinking water pathogen of public health concern. This work demonstrates that there are important caveats in the application of using Cu and Ag ions to inactivate <i>Legionella pneumophila</i>.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0107324"},"PeriodicalIF":3.9,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11784313/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142845653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lactose-assimilating yeasts with high fatty acid accumulation uncovered by untargeted bioprospecting.","authors":"Karl Persson, Vanessa O Onyema, Ijeoma Princess Nwafor, Kameshwara V R Peri, Chika Otti, Priscilla Nnaemeka, Chioma Onyishi, Sylvia Okoye, Anene Moneke, Onyetugo Amadi, Jonas Warringer, Cecilia Geijer","doi":"10.1128/aem.01615-24","DOIUrl":"10.1128/aem.01615-24","url":null,"abstract":"<p><p>Bioprospecting can uncover new yeast strains and species with interesting ecological characteristics and valuable biotechnological traits, such as the capacity to convert different carbon sources from industrial side and waste streams into bioproducts. In this study, we conducted untargeted yeast bioprospecting in tropical West Africa, collecting 1,996 isolates and determining their growth in 70 different environments. While the collection contains numerous isolates with the potential to assimilate several cost-effective and sustainable carbon and nitrogen sources, we focused on characterizing the 203 strains capable of growing on lactose, the main carbon source in the abundant side stream cheese whey from dairy industries. Through internal transcribed spacer sequencing of the lactose-assimilating strains, we identified 30 different yeast species from both the <i>Ascomycota</i> and <i>Basidiomycota</i> phyla, of which several have not previously been shown to grow on lactose, and some are candidates for new species. Observed differences in growth and ratios of intra- and extracellular lactase activities suggest that the yeasts use a range of different strategies to metabolize lactose. Notably, several basidiomycetous yeasts, including <i>Apiotrichum mycotoxinivorans</i>, <i>Papiliotrema laurentii</i>, and <i>Moesziomyces antarcticus</i>, accumulated lipids up to 40% of their cell dry weight, proving that they can convert lactose into a bioproduct of significant biotechnology interest.</p><p><strong>Importance: </strong>This study paves the way to a better understanding of the natural yeast biodiversity in the largely under-sampled biodiversity hotspot area of tropical West Africa. Our discovery of several yeasts capable of efficiently converting lactose into lipids underscores the value of bioprospecting to identify yeast strains with significant biotechnological potential, which can aid the transition to a circular bioeconomy. Furthermore, the extensive strain collection gathered will facilitate future screening and the development of new cell factories.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0161524"},"PeriodicalIF":3.9,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11784187/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142913086","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Novel inhibition of <i>Staphylococcus aureus</i> sortase A by plantamajoside: implications for controlling multidrug-resistant infections.","authors":"Yujia Chen, Wei Li, Li Wang, Bingmei Wang, Jian Suo","doi":"10.1128/aem.01804-24","DOIUrl":"10.1128/aem.01804-24","url":null,"abstract":"<p><p>In confronting the significant challenge posed by multidrug-resistant (MDR) pathogens, particularly methicillin-resistant <i>Staphylococcus aureus</i> (MRSA), the development of innovative anti-infective strategies is essential. Our research focuses on sortase A (SrtA), a vital enzyme for anchoring surface proteins in <i>S. aureus</i>. We discovered that plantamajoside (PMS), a phenylpropanoid glycoside extracted from <i>Plantago asiatica L</i>. (Plantaginaceae), acts as an effective and reversible inhibitor of SrtA, with a notable IC₅₀ value of 22.93 µg/mL. This breakthrough provides a novel approach to combat both resistance and virulence in MRSA. PMS significantly inhibits <i>S. aureus</i> adhesion to fibrinogen, reducing biofilm formation and hindering the anchoring of staphylococcal protein A to the cell wall. Live-dead cell assays demonstrated increased survival rates in PMS-treated MRSA-infected A549 cells. Fluorescence quenching experiments revealed a robust interaction between PMS and SrtA, with mechanistic analyses pinpointing the critical R197 amino acid residue as the target site. <i>In vivo</i>, PMS was highly effective in a <i>Galleria mellonella</i> infection model, reducing mortality rates in MRSA-infected larvae. Additionally, PMS demonstrated therapeutic efficacy in a mouse pneumonia model, improved survival rates, reduced the bacterial load in pulmonary tissues, and mitigated lung damage. These results validate PMS as a promising compound to mitigate MRSA virulence and thwart resistance by targeting SrtA. This study highlights PMS as a leading candidate for controlling MRSA infections, showing the potential of targeting specific bacterial mechanisms in the fight against MDR infections.IMPORTANCEThe increasing issue of antibiotic resistance, particularly in methicillin-resistant <i>Staphylococcus aureus</i> (MRSA), demands innovative solutions. Our study presents plantamajoside (PMS) as a novel inhibitor of sortase A (SrtA), a key enzyme in <i>S. aureus</i> pathogenicity. By targeting SrtA, PMS shows promise in curbing the ability of MRSA to adhere, invade, and form biofilms, thereby reducing its virulence without exerting selective pressure for resistance. This research is significant because it introduces a potential new strategy in the antimicrobial arsenal, aligning with the global effort to combat drug-resistant infections. This study is crucial because it identifies a natural compound that can reduce the harmful effects of MRSA, a type of bacteria that is very hard to treat owing to resistance to many antibiotics. This discovery could lead to new treatments that are less likely to cause bacteria to become resistant, which is a major win in the fight against infections that are difficult to cure.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0180424"},"PeriodicalIF":3.9,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11784452/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142913241","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nitrous oxide is the main product during nitrate reduction by a novel lithoautotrophic iron(II)-oxidizing culture from an organic-rich paddy soil.","authors":"Hanna Grimm, Jennifer Lorenz, Daniel Straub, Prachi Joshi, Jeremiah Shuster, Christiane Zarfl, E Marie Muehe, Andreas Kappler","doi":"10.1128/aem.01262-24","DOIUrl":"10.1128/aem.01262-24","url":null,"abstract":"<p><p>Microbial nitrate reduction coupled to iron(II) oxidation (NRFeOx) occurs in paddy soils due to high levels of dissolved iron(II) and regular application of nitrogen fertilizer. However, to date, there is no lithoautotrophic NRFeOx isolate or enrichment culture available from this soil environment. Thus, resulting impacts on greenhouse gas emissions during nitrate reduction (i.e., nitrous oxide [N₂O]) and on toxic metalloid (i.e., arsenic) mobility can hardly be investigated. We enriched a lithoautotrophic NRFeOx culture, culture HP (Huilongpu paddy, named after its origin), from a paddy soil (Huilongpu Town, China), which was dominated by <i>Gallionella</i> (71%). The culture reduced 0.45 to 0.63 mM nitrate and oxidized 1.76 to 2.31 mM iron(II) within 4 days leading to N₂O as the main N-product (62%-88% N₂O-N of total reduced NO₃^--N). Nitrite was present as an intermediate at a maximum of 0.16 ± 0.1 mM. Cells were associated with, but mostly not encrusted by, poorly crystalline iron(III) minerals (ferrihydrite). Culture HP performed best below an iron(II) threshold of 2.5-3.5 mM and in a pH range of 6.50-7.05. In the presence of 100 µM arsenite, only 0%-18% of iron(II) was oxidized. Due to low iron(II) oxidation, arsenite was not immobilized. However, the proportion of N₂O-N of total reduced NO₃^--N decreased from 77% to 30%. Our results indicate that lithoautotrophic NRFeOx occurs even in organic-rich paddy soils, resulting in denitrification and subsequent N₂O emissions. The obtained novel enrichment culture allows us to study the impact of lithoautotrophic NRFeOx on arsenic mobility and N₂O emissions in paddy soils.IMPORTANCEPaddy soils are naturally rich in iron(II) and regularly experience nitrogen inputs due to fertilization. Nitrogen fertilization increases nitrous oxide emissions as it is an intermediate product during nitrate reduction. Microorganisms can live using nitrate and iron(II) as electron acceptor and donor, respectively, but mostly require an organic co-substrate. By contrast, microorganisms that only rely on nitrate, iron(II), and CO₂ could inhabit carbon-limited ecological niches. So far, no isolate or consortium of lithoautotrophic iron(II)-oxidizing, nitrate-reducing microorganisms has been obtained from paddy soil. Here, we describe a lithoautotrophic enrichment culture, dominated by a typical iron(II)-oxidizer (<i>Gallionella</i>), that oxidized iron(II) and reduced nitrate to nitrous oxide, negatively impacting greenhouse gas dynamics. High arsenic concentrations were toxic to the culture but decreased the proportion of nitrous oxide of the total reduced nitrate. Our results suggest that autotrophic nitrate reduction coupled with iron(II) oxidation is a relevant, previously overlooked process in paddy soils.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0126224"},"PeriodicalIF":3.9,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11784278/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142783916","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nutrient amendments enrich microbial hydrocarbon degradation metagenomic potential in freshwater coastal wetland microcosm experiments.","authors":"Katie E Howland, Jack J Mouradian, Donald R Uzarski, Michael W Henson, Donald G Uzarski, Deric R Learman","doi":"10.1128/aem.01972-24","DOIUrl":"10.1128/aem.01972-24","url":null,"abstract":"<p><p>Biostimulating native microbes with fertilizers has proven to be a highly effective strategy to speed up biodegradation rates in microbial communities. This study investigates the genetic potential of microbes to degrade light synthetic crude oil in a freshwater coastal wetland. Experimental sediment microcosms were exposed to a variety of conditions (biological control, a light synthetic crude oil amendment, and light synthetic crude oil with nutrient amendment) and incubated for 30 days before volatile organic compounds (BTEX) were quantified and DNA was sequenced for metagenomic analysis. The resulting DNA sequences were binned into metagenome-assembled genomes (MAGs). Analyses of MAGs uncovered a 13-fold significant increase in the abundance of rate-limiting hydrocarbon degrading monooxygenases and dioxygenases, identified only in MAGs from the light synthetic crude oil with nutrient amendments. Further, complete degradation pathways for BTEX compounds were found only in MAGs resulting from the light synthetic crude with nutrient amendment. Moreover, volatile organic compounds (BTEX, cyclohexane, and naphthalene) analyses of microcosm sediments in the presence of nutrients documented that benzene was degraded below detection limits, toluene (98%) and ethylbenzene (67%) were predominantly reduced within 30 days. Results indicate that the genetic potential to degrade BTEX compounds in this freshwater wetland can be linked to the functional potential for bioremediation. BTEX compounds are typically more recalcitrant and tougher to degrade than alkanes. This study demonstrated that stimulating a microbial community with nutrients to enhance its ability to biodegrade hydrocarbons, even in a relatively nutrient-rich habitat like a freshwater wetland, is an effective remediation tactic.</p><p><strong>Importance: </strong>The impact of oil spills in a freshwater aquatic environment can pose dire social, economic, and ecological effects on the region. An oil spill in the Laurentian Great Lakes region has the potential to affect the drinking water of more than 30 million people. The light synthetic crude oil used in this experimental microcosm study is transported through an underground pipeline crossing the waterway between two Laurentian Great Lakes. This study collected metagenomic data (experiments in triplicate) and assessed the quantity of BTEX compounds, which connected microbial degradation function to gene potential. The resulting data documented the bioremediation capabilities of native microbes in a freshwater coastal wetland. This study also provided evidence for this region that bioremediation can be a viable remediation strategy instead of invasive physical methods.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0197224"},"PeriodicalIF":3.9,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11784303/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142798960","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Temperature-responsive regulation of the polycyclic aromatic hydrocarbon-degrading mesophilic bacterium <i>Novosphingobium pentaromativorans</i> US6-1 with a temperature adaptation system.","authors":"Zhuangzhuang Liu, Xinran Liu, Haiyan Huang, Feifei Cao, Qiu Meng, Tingheng Zhu, Jianhua Yin, Xiaofei Song, Zhiliang Yu","doi":"10.1128/aem.01484-24","DOIUrl":"10.1128/aem.01484-24","url":null,"abstract":"<p><p>Survivability and tolerance of polycyclic aromatic hydrocarbon (PAH)-degrading bacteria in harsh environments, especially under varying temperatures, are a bottleneck for the effective application of <i>in situ</i> bioremediation. In this study, a temperature adaptation system (TAS) was constructed by combining a customized thermotolerant system with a customized cold-resistant system to realize the temperature-responsive regulation of the PAH-degrading mesophilic bacterium <i>Novosphingobium pentaromativoran</i>s US6-1. The innovative dual-pronged TAS strategy enabled the chassis strain to effectively tackle conditions under varying temperatures, ensuring robust biological activities across a broadened temperature spectrum and exhibiting the potential to realize the high-efficiency PAH degradation of <i>N. pentaromativorans</i> US6-1 in <i>in situ</i> bioremediation. Furthermore, the temperature-responsive regulation achieved using the TAS circuit is likely promising for creating intelligent microbial cell factories and avoiding precise temperature maintenance, making it highly useful for industrial applications.IMPORTANCEEnvironmental temperature is among the extremely important factors that determine the bioactivities of pollutant-degrading microorganisms in <i>in situ</i> bioremediation. Effectively maintaining the survivability and tolerance of mesophilic microorganisms under harsh conditions and varying temperatures remains a challenge in the application of pollutant bioremediation. This study, for the first time, developed a temperature adaptation system by combining a customized thermotolerant system with a customized cold-resistant system to realize the temperature-responsive regulation of the polycyclic aromatic hydrocarbon (PAH)-degrading mesophilic bacterium <i>Novosphingobium pentaromativoran</i>s US6-1, thus diminishing the need for precise temperature control in PAH bioremediation.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0148424"},"PeriodicalIF":3.9,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11784078/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142811859","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigation on L-rhamnose metabolism of <i>Loigolactobacillus coryniformis</i> subsp. <i>coryniformis</i> DSM 20001 and its propionate-containing fermentates.","authors":"Mensure Elvan Gezer, Kathrine Gravlund Fønss, Maria Florencia Bambace, Angeliki Marietou, Sanne Sandberg Overby, Ulrik Sundekilde, Clarissa Schwab","doi":"10.1128/aem.01613-24","DOIUrl":"10.1128/aem.01613-24","url":null,"abstract":"<p><p>Propionate is an important short-chain carboxylic acid (SCCA) that serves as an effective antimicrobial agent for food preservation. Previous research has highlighted that few <i>Lactobacillaceae</i> can synthesize propionate by metabolizing deoxyhexoses via the fermentation intermediate 1,2-propanediol (1,2-PD). In this study, we investigated propionate production by <i>Loigolactobacillus coryniformis</i> subsp. <i>coryniformis</i> DSM 20001 while utilizing L-rhamnose as the primary carbon source. We cultivated <i>L. coryniformis</i> in small-scale anaerobic bioreactors at 30°C and pH 6.5 for 72 h and monitored the expression of key genes associated with deoxyhexose metabolism using quantitative PCR. In addition, we assessed the contribution of individual SCCA to the antimicrobial activity of the fermentate against common foodborne pathogens, including <i>Escherichia coli</i>, <i>Salmonella enterica</i>, <i>Klebsiella oxytoca</i>, <i>Staphylococcus aureus</i>, <i>Candida albicans</i>, <i>Aspergillus niger</i>, <i>Penicillium roqueforti</i>, and <i>Penicillium purpurogenum</i> using broth dilution assays. During cultivation, we observed the production of up to 16 mM propionate, alongside other metabolites such as lactate (26 mM), formate (2 mM), and acetate (4 mM), derived from 32 mM L-rhamnose. Genes related to L-rhamnose utilization were upregulated within the initial 48 h, while genes involved in 1,2-PD utilization remained highly transcribed throughout fermentation. Comparing the antimicrobial efficacy of the fermentates to synthetic SCCA mixtures, bacterial indicator strains were more sensitive than molds and yeast. Propionate was the primary SCCA responsible for inhibitory activity; inhibition was reduced if indicator strains were able to use lactate.IMPORTANCEWorldwide, approximately 30% of food produced is lost. Despite the application of complementary treatment methods, microbial food spoilage can occur along the entire value chain. The rising concern about food waste has led to increasing interest in natural preservation approaches. <i>Lactobacillaceae</i> fermentative systems produce a variety of short-chain carboxylic acid (SCCA) with antimicrobial potential, and we present here fundamental insight into the only recently discovered deoxyhexose metabolism of <i>Loigolactobacillus coryniformis</i> producing the antimicrobial SCCA propionate. We developed a bioprocess to produce propionate from L-rhamnose under controlled conditions as a first step toward the exploitation of L-rhamnose metabolism in the production of antimicrobial fermentates for use in the food industry, potentially replacing chemical alternatives. Our investigations highlight the major contribution of propionate in antimicrobial activity but also indicate the issue of co-occurring fermentable metabolites, which can affect the efficiency of fermentates.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0161324"},"PeriodicalIF":3.9,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11784251/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142845654","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}