Applied and Environmental Microbiology最新文献

{"title":"ChIP-seq and structural analyses delineating the regulatory mechanism of master regulator EsrB in <i>Edwardsiella piscicida</i>.","authors":"Boya Zhang, Yi Zhang, Jingjing Liu, David Reverter, Qiyao Wang, Sang Ho Choi, Bing Liu, Shuai Shao","doi":"10.1128/aem.01805-24","DOIUrl":"10.1128/aem.01805-24","url":null,"abstract":"<p><p>As a response regulator of the EsrA-EsrB two-component system, EsrB is conserved in <i>Hafniaceae</i> and plays a crucial role in virulence and pathogenicity. EsrB possesses DNA binding abilities, enabling it to regulate the transcription of virulence genes to confront different stresses and achieve systematic infections. Here, ChIP-seq analysis of EsrB in Dulbecco's Modified Eagle's Medium (DMEM) (mimicking <i>in vivo</i> environments) revealed that EsrB preferred to bind to virulence-associated promoters with a distinct 7'-4-7'' pseudopalindromic DNA motif and interact with metabolic-related promoters with a high AT DNA motif. The crystal structure of the C-terminal of EsrB (EsrB_C) was solved at 2.20-Å resolution. Specifically, Lys¹⁸¹ enabled the DNA-binding affinity of EsrB and promoted the <i>in vitro</i> and <i>in vivo</i> pathogenicity of <i>Edwardsiella piscicida</i>. Moreover, EsrB directly regulated the expression of genes associated with basal metabolism, including iron and tricarboxylic acid (TCA) cycles. Furthermore, EsrB enhanced iron transport capability and the enzyme activity of succinate dehydrogenase and pyruvate dehydrogenase in DMEM. Collectively, our structural and ChIP-seq analysis provides valuable insights into the DNA binding mechanism of EsrB which will facilitate our understanding of EsrB coordinating virulence and basal metabolism gene expression.</p><p><strong>Importance: </strong>As a crucial virulence regulator, EsrB possesses a LuxR-like superfamily domain at the C-terminal, which is conserved within the canonical NarL family regulators. Due to its critically important role in virulence and pathogenicity in fish hosts, the DNA binding ability has been believed to allow EsrB to regulate genes associated with the invasion process of host cells and basal metabolism in response to environmental stimuli. The lack of EsrB's crystal structure has been a major obstacle in understanding the molecular mechanisms of EsrB-DNA interaction which choreographs EsrB-mediated pathogenic behavior. Here, we conducted ChIP-seq and solved the crystal structure of the C-terminal of EsrB (EsrBC) at 2.20-Å resolution, which revealed that EsrB preferred to bind to virulence-associated promoters with a distinct 7'-4-7' pseudopalindromic DNA motif and interacted with metabolic-related promoters with a high AT DNA motif in Dulbecco's Modified Eagle's Medium (DMEM) (mimicking <i>in vivo</i> environments). Our results facilitate a detailed understanding of EsrB's regulatory role in <i>Edwardsiella piscicida</i> pathogenesis and expand our knowledge of virulence regulators in the family <i>Hafniaceae</i>.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0180524"},"PeriodicalIF":3.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142638567","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 life strategy of bacteria rather than fungi shifts in karst tiankeng island-like systems.","authors":"Cong Jiang, Changchun Qiu, Wei Shui","doi":"10.1128/aem.01581-24","DOIUrl":"10.1128/aem.01581-24","url":null,"abstract":"<p><p>Karst tiankeng is a typical terrestrial habitat island-like system, known as an oasis in a degraded karst landscape. However, we know little about the composition, structure, and life strategies of soil microbial communities in the karst tiankeng ecosystem. In this study, we use amplicon sequencing to investigate the soil bacteria and fungi of 26 karst tiankeng in two typical karst tiankeng groups. The results showed that the composition and structure of bacterial and fungal communities were significantly different at two dimensions (among and within the karst tiankeng group). Bacteria showed more sensitivity to variation in the karst tiankeng area and isolation than fungi. With the increase of karst tiankeng area and isolation, the bacterial life strategies shift from <i>K</i>-strategist to <i>r</i>-strategist, likely due to the changes in soil properties (total phosphorus, Ca, and soil water content). Abundant and rare taxa play different roles in karst tiankeng ecosystems; abundant taxa serve a key role in nutrient cycles and life strategy shifts by occupying the key status in networks. Considering the key role of soil microbes in ecosystems, more attention must be paid to the impact of habitat loss on soil microbial life strategies, particularly in the ecological impact of life strategies change of abundant and rare taxa.</p><p><strong>Importance: </strong>These findings highlight that habitat loss or fragmentation induces a shift in microbial life strategies and improves our understanding of the composition and biogeography of karst ecosystem microorganisms.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0158124"},"PeriodicalIF":3.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142715082","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":"Rhizosphere microbiomes are closely linked to seagrass species: a comparative study of three coastal seagrasses.","authors":"Hao Sun, Xuerui Liu, Tianyu Wang, Shuai Liu, Rui Zhang, Xiangrui Guo, Zhen Yu, Ye Zhao, Pingping Shen, Yanying Zhang","doi":"10.1128/aem.01754-24","DOIUrl":"10.1128/aem.01754-24","url":null,"abstract":"<p><p>Seagrass meadows are important marine ecosystems in coastal areas, offering ecological and economic services to the mankind. However, these ecosystems are facing declines due to climate changes and human activities. Rhizosphere-associated microbiomes play critical roles in the survival and adaptation of seagrasses. While prior studies have explored the general microbial communities and their roles in seagrass meadows, there is a gap in understanding the specific rhizosphere microbiomes of different seagrass species and their interdependent relationships. Our study analyzed the microbial community composition and their metabolism in the rhizosphere of <i>Ruppia sinensis</i> (RS), <i>Zostera japonica</i> (ZJ), and <i>Zostera marina</i> (ZM) obtained from the coastal area of Shandong, China, using high throughput and metagenome sequencing. We found that Rhodobacteraceae, Desulfocapsaceae, and Sulfurovaceae were enriched in RS, ZJ, and ZM samples, respectively, compared with the other two seagrass species, and the bacterial connections were decreased from RS to ZM and ZJ samples. The abundances of <i>nirKS</i> and <i>norBC</i>, mediating denitrification, were higher in RS samples with 2.38% ± 0.59% and 2.14% ± 0.24%, respectively. RS samples also showed a higher level of genes in assimilatory sulfate reduction but lower levels in dissimilatory sulfate reduction and oxidation, with a greater ability to convert sulfide into L-cysteine and acetate. Metagenome-assembled genomes from metagenome of RS rhizosphere had a higher diversity and were assigned to eight phyla. Our study could provide a typical project to analyze the bacterial community structures and metabolic functions in the rhizosphere microbiomes of different seagrasses.</p><p><strong>Importance: </strong>Seagrasses are indispensable in marine ecosystems, offering numerous critical services, with their health significantly influenced by associated rhizosphere microbiomes. Although studies have investigated the microbial communities and their ecological roles in seagrass meadows, the correlations between rhizosphere microbiome and seagrass species from a particular geographic region are limited. Some studies concentrated on the bacterial composition within the rhizosphere of various seagrasses, but the functional aspects of these microbiomes remain unexplored. Our research delves into this void, revealing that <i>Ruppia sinensis</i>, <i>Zostera japonica</i>, and <i>Zostera marina</i> host diverse bacterial community in the composition, connections, functions, and metabolism, such as nitrogen and sulfur metabolism. Our study revealed that seagrass species play an important role in shaping the rhizosphere microbiomes in an equivalent environment, emphasizing the importance of seagrass species in shaping the rhizosphere microbial communities.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0175424"},"PeriodicalIF":3.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142581936","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":"Soil fungal networks exhibit sparser interactions than bacterial networks in diseased banana plantations.","authors":"Peng Chen, Jinku Li, Dandan Wei, Yanlin Chen, Chen He, Huanyu Bao, Zhongjun Jia, Yunze Ruan, Pingshan Fan","doi":"10.1128/aem.01572-24","DOIUrl":"10.1128/aem.01572-24","url":null,"abstract":"<p><p>Soil microorganisms play a crucial role in suppressing soil-borne diseases. Although the composition of microbial communities in healthy versus diseased soils is somewhat understood, the interplay between microbial interactions and disease incidence remains unclear. This study used 16S rRNA and fungal internal transcribed spacer (ITS) sequencing to investigate the bacterial and fungal community composition in three soil types: forest soil (Z), soil from healthy banana plantations (H), and soil from diseased banana plantations (D). Principal coordinate analysis revealed significant differences among the bacterial and fungal community structures of the three soil types. Compared with those in forest soil, bacterial and fungal diversities significantly decreased in diseased banana soil. Key microorganisms, including the bacteria Chloroflexi and Pseudonocardia and the fungi Mortierellomycota and Moesziomyces, were significantly increased in soil from diseased banana plantations. Redundancy analysis revealed that total nitrogen and available phosphorus were the primary drivers of the soil microbial community structure. The neutral community model posited that the bacterial community assembly in banana plantations is predominantly governed by stochastic processes, whereas the fungal community assembly in banana plantations is primarily driven by deterministic processes. Furthermore, co-occurrence network analysis revealed that the proportion of positive edges in the fungal network of soil from diseased banana plantations was 5.92 times lower than that in soil from healthy banana plantations, and its fungal network structure was sparse and simple. In conclusion, reduced interactions within the fungal network were significantly linked to the epidemiology of Fusarium wilt. These findings underscore the critical role of soil fungal communities in modulating pathogens.</p><p><strong>Importance: </strong>Soil microorganisms are pivotal in mitigating soil-borne diseases. The intricate mechanisms underlying the interactions among microbes and their impact on disease occurrence remain enigmatic. This study underscores that a reduction in fungal network interactions correlates with the incidence of soil-borne Fusarium wilt.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0157224"},"PeriodicalIF":3.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142602829","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":"Exploring the interplay between yeast cell membrane lipid adaptation and physiological response to acetic acid stress.","authors":"Fei Wu, Maurizio Bettiga, Lisbeth Olsson","doi":"10.1128/aem.01212-24","DOIUrl":"10.1128/aem.01212-24","url":null,"abstract":"<p><p>Acetic acid is a byproduct of lignocellulose pretreatment and a potent inhibitor of yeast-based fermentation processes. A thicker yeast plasma membrane (PM) is expected to retard the passive diffusion of undissociated acetic acid into the cell. Molecular dynamic simulations suggest that membrane thickness can be increased by elongating glycerophospholipids (GPL) fatty acyl chains. Previously, we successfully engineered <i>Saccharomyces cerevisiae</i> to increase GPL fatty acyl chain length but failed to lower acetic acid net uptake. Here, we tested whether altering the relative abundance of diacylglycerol (DAG) might affect PM permeability to acetic acid in cells with longer GPL acyl chains (DAG<i>^EN</i>). To this end, we expressed diacylglycerol kinase α (<i>DGKα</i>) in DAG<i>^EN</i>. The resulting DAG<i>^EN</i>_Dgkα strain exhibited restored DAG levels, grew in medium containing 13 g/L acetic acid, and accumulated less acetic acid. Acetic acid stress and energy burden were accompanied by increased glucose uptake in DAG<i>^EN</i>_Dgkα cells. Compared to DAG<i>^EN</i>, the relative abundance of several membrane lipids changed in DAG<i>^EN</i>_Dgkα in response to acetic acid stress. We propose that the ability to increase the energy supply and alter membrane lipid composition could compensate for the negative effect of high net acetic acid uptake in DAG<i>^EN</i>_Dgkα under stressful conditions.</p><p><strong>Importance: </strong>In the present study, we successfully engineered a yeast strain that could grow under high acetic acid stress by regulating its diacylglycerol metabolism. We compared how the plasma membrane and total cell membranes responded to acetic acid by adjusting their lipid content. By combining physiological and lipidomics analyses in cells cultivated in the absence or presence of acetic acid, we found that the capacity of the membrane to adapt lipid composition together with sufficient energy supply influenced membrane properties in response to stress. We suggest that potentiating the intracellular energy system or enhancing lipid transport to destination membranes should be taken into account when designing membrane engineering strategies. The findings highlight new directions for future yeast cell factory engineering.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0121224"},"PeriodicalIF":3.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142613487","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 role of serum albumin in <i>Candida albicans</i> filamentation, germ tube formation, and farnesol sequestration.","authors":"Daniel J Gutzmann, Brigid M Toomey, Audrey L Atkin, Kenneth W Nickerson","doi":"10.1128/aem.01626-24","DOIUrl":"10.1128/aem.01626-24","url":null,"abstract":"<p><p><i>Candida albicans</i> is an opportunistic pathogen and colonizer of the human gut and mucosal membranes. <i>C. albicans</i> exhibits morphological plasticity, which is crucial for its fitness within the host and virulence. Morphogenesis in <i>C. albicans</i> is regulated, in part, by its production of farnesol, an autoregulatory molecule that inhibits filamentation. Morphogenesis is also regulated in response to external cues, such as serum, which stimulates hyphal formation by <i>C. albicans</i>. The precise mechanism by which serum stimulates hyphal formation is unknown. The most abundant serum protein is albumin. The binding affinity of albumin for nonpolar, fatty-acid-like molecules suggests that it may interact directly with exogenous farnesol and influence morphogenesis through sequestration of free farnesol. To test this hypothesis, we assessed whether albumin and albumin devoid of fatty acids (i) stimulated farnesol secretion and (ii) influenced the farnesol threshold required to inhibit filamentation. We found that albumin promoted farnesol secretion and filamentation, and the extent of its ability to do so was based on the presence or absence of bound fatty acids. We hypothesize that albumin not bound to fatty acids has the capacity to bind to farnesol and sequester it from <i>C. albicans</i>, encouraging filamentation.IMPORTANCEFor at least 50 years, researchers have wondered about the mechanisms by which serum stimulates germ tube formation (GTF) and hyphal growth in <i>C. albicans</i>. Here, we tested a model (Nickerson et al., Microbiol Mol Biol Rev 88:e00081-22, 2024, https://doi.org/10.1128/mmbr.00081-22) that serum promotes GTF and farnesol synthesis in part by extracting internal farnesol (F_i) from the cells toward the excess binding capacity of the albumins. The data presented here suggests that albumin not bound by fatty acids sequesters free farnesol thereby modulating filamentation and farnesol secretion by altering the equilibrium of internal vs external farnesol. We expect that the influence of secreted farnesol on cell morphology will differ during pathogenesis depending on location within the body, but sequestration of farnesol in the blood could mediate immune cell recruitment and promote hyphal formation.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0162624"},"PeriodicalIF":3.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142613510","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":"Articles of Significant Interest in This Issue.","authors":"","doi":"10.1128/aem.02439-24","DOIUrl":"https://doi.org/10.1128/aem.02439-24","url":null,"abstract":"","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":"90 12","pages":"e0243924"},"PeriodicalIF":3.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142845656","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 phospho-ferrozine assay: a tool to study bacterial redox-active metabolites produced at the plant root.","authors":"David Giacalone, Emilly Schutt, Darcy L McRose","doi":"10.1128/aem.02194-24","DOIUrl":"https://doi.org/10.1128/aem.02194-24","url":null,"abstract":"<p><p>Soil microbial communities are pivotal to plant health and nutrient acquisition. It is becoming increasingly clear that many interactions, both among and between microbes and plants, are governed by small bioactive molecules or \"secondary metabolites\" that can aid in communication, competition, and nutrient uptake. Yet, secondary metabolite biogeography - who makes what, where, and why-is in its infancy. Further, secondary metabolite biosynthesis genes are often silent or weakly expressed under standard laboratory conditions, making it incredibly difficult to study these small molecules. To begin to address these dual challenges, we focused on redox-active metabolites (RAMs), a specific class of small molecules, and took advantage of recent findings that many RAMs aid in acquiring phosphorus and that their production is frequently stimulated by stress for this macronutrient. We developed a screen for RAM-producing bacteria that leverages phosphorus limitation to stimulate metabolite biosynthesis and uses a colorimetric (ferrozine) iron-reduction assay to identify redox activity. We isolated 557 root-associated bacteria from grasses collected at sites across the United States (Santa Rita Experimental Range [AZ], Konza Prairie Biological Station [KS], and Harvard Forest [MA]) and from commercial tomato plants and screened them for RAM production. We identified 128 soil isolates of at least 19 genera across Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes that produced RAMs under phosphorus stress. Our work reveals that the production of RAMs under phosphorus stress is common across diverse soil bacteria and provides an approach to screen for these small molecules rapidly.IMPORTANCEBy secreting secondary metabolites, bacteria at the plant root can defend against diseases and help acquire essential nutrients. However, the genes that synthesize secondary metabolites are typically inactive or are weakly expressed under standard laboratory conditions. This fact makes it difficult to study these small molecules and hinders the discovery of novel small molecules that may play crucial roles in agricultural and biomedical settings. Here, we focus on redox-active metabolites (RAMs), a class of secondary metabolites that can help bacteria solubilize phosphorus and are often produced when phosphorus is limited. We developed a screen that rapidly identifies RAM-producing bacteria by utilizing a colorimetric iron-reduction assay in combination with phosphorus limitation to stimulate biosynthesis. The screen reveals that RAM-producing bacteria are far more prevalent in soil than previously appreciated and that this approach can be used to identify RAM producers.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0219424"},"PeriodicalIF":3.9,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142833769","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":"Ecological features of microbial community linked to stochastic and deterministic assembly processes in acid mine drainage.","authors":"Zhenghua Liu, Chengying Jiang, Zhuzhong Yin, Ibrahim Ahmed Ibrahim, Teng Zhang, Jing Wen, Lei Zhou, Guoping Jiang, Liangzhi Li, Zhendong Yang, Ye Huang, Zhaoyue Yang, Yabing Gu, Delong Meng, Huaqun Yin","doi":"10.1128/aem.01028-24","DOIUrl":"https://doi.org/10.1128/aem.01028-24","url":null,"abstract":"<p><p>Ecological processes greatly shape microbial community assembly, but the driving factors remain unclear. Here, we compiled a metagenomic data set of microbial communities from global acid mine drainage (AMD) and explored the ecological features of microbial community linked to stochastic and deterministic processes from the perspective of species niche position, interaction patterns, gene functions, and viral infection. Our results showed that dispersal limitation (DL) (48.5%~93.5%) dominated the assembly of phylogenetic bin in AMD microbial community, followed by homogeneous selection (HoS) (3.1%~39.2%), heterogeneous selection (HeS) (1.4%~22.2%), and drift (DR) (0.2%~2.7%). The dominant process of dispersal limitation was significantly influenced by niche position in temperature (<i>r</i> = -0.518, <i>P</i> = 0.007) and dissolved oxygen (<i>r</i> = 0.471, <i>P</i> = 0.015). Network stability had a significantly negative correlation with the relative importance of dispersal limitation, while it had a positive correlation with selection processes, implying changes in network properties could be mediated by ecological processes. Furthermore, we found that ecological processes were mostly related to the gene functions of energy production and conversion (C), and amino acid transport and metabolism (E). Meanwhile, our results showed that the number of proviruses and viral genes involved in arsenic (As) resistance is negatively associated with the relative importance of ecological drift in phylogenetic bin assembly, implying viral infection might weaken ecological drift. Taken together, these results highlight that ecological processes are associated with ecological features at multiple levels, providing a novel insight into microbial community assembly in extremely acidic environments.</p><p><strong>Importance: </strong>Unraveling the forces driving community assemblage is a core issue in microbial ecology, but how ecological constraints impose stochasticity and determinism remains unknown. This study presents a comprehensive investigation to uncover the association of ecological processes with species niche position, interaction patterns, microbial metabolisms, and viral infections, which provides novel insights into community assembly in extreme environments.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0102824"},"PeriodicalIF":3.9,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142827224","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":"Applying a polysaccharide lyase from <i>Stenotrophomonas maltophilia</i> to disrupt alginate exopolysaccharide produced by <i>Pseudomonas aeruginosa</i> clinical isolates.","authors":"Samantha M Felton, Nikki Akula, Glynis L Kolling, Parastoo Azadi, Ian Black, Ambrish Kumar, Christian Heiss, Joseph Capobianco, Joseph Uknalis, Jason A Papin, Bryan W Berger","doi":"10.1128/aem.01853-24","DOIUrl":"https://doi.org/10.1128/aem.01853-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Pseudomonas aeruginosa&lt;/i&gt; is considered one of the most challenging, drug-resistant, opportunistic pathogens partly due to its ability to synthesize robust biofilms. Biofilm is a mixture of extracellular polymeric substances (EPS) that encapsulates microbial cells, leading to immune evasion, antibiotic resistance, and thus higher risk of infection. In the cystic fibrosis lung environment, &lt;i&gt;P. aeruginosa&lt;/i&gt; undergoes a mucoid transition, defined by overproduction of the exopolysaccharide alginate. Alginate encapsulation results in bacterial resistance to antibiotics and the host immune system. Given its role in airway inflammation and chronic infection, alginate is an obvious target to improve treatment for &lt;i&gt;P. aeruginosa&lt;/i&gt; infection. Previously, we demonstrated polysaccharide lyase Smlt1473 from &lt;i&gt;Stenotrophomonas maltophilia&lt;/i&gt; strain k279a can catalyze the degradation of multiple polyuronides &lt;i&gt;in vitro&lt;/i&gt;, including D-mannuronic acid (poly-ManA). Poly-ManA is a major constituent of &lt;i&gt;P. aeruginosa&lt;/i&gt; alginate, suggesting that Smlt1473 could have potential application against multidrug-resistant &lt;i&gt;P. aeruginosa&lt;/i&gt; and perhaps other microbes with related biofilm composition. In this study, we demonstrate that Smlt1473 can inhibit and degrade alginate from &lt;i&gt;P. aeruginosa&lt;/i&gt;. Additionally, we show that tested &lt;i&gt;P. aeruginosa&lt;/i&gt; strains are dominant in acetylated alginate and that all but one have similar M-to-G ratios. These results indicate that variation in enzyme efficacy among the isolates is not primarily due to differences in total EPS or alginate chemical composition. Overall, these results demonstrate Smlt1473 can inhibit and degrade &lt;i&gt;P. aeruginosa&lt;/i&gt; alginate and suggest that other factors including rate of EPS production, alginate sequence/chain length, or non-EPS components may explain differences in enzyme efficacy.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;&lt;i&gt;Pseudomonas aeruginosa&lt;/i&gt; is a major opportunistic human pathogen in part due to its ability to synthesize biofilms that confer antibiotic resistance. Biofilm is a mixture of polysaccharides, DNA, and proteins that encapsulate cells, protecting them from antibiotics, disinfectants, and other cleaning agents. Due to its ability to increase antibiotic and immune resistance, the exopolysaccharide alginate plays a large role in airway inflammation and chronic &lt;i&gt;P. aeruginosa&lt;/i&gt; infection. As a result, colonization with &lt;i&gt;P. aeruginosa&lt;/i&gt; is the leading cause of morbidity and mortality in CF patients. Thus, it is an obvious target to improve the treatment regimen for &lt;i&gt;P. aeruginosa&lt;/i&gt; infection. In this study, we demonstrate that polysaccharide lyase, Smlt1473, inhibits alginate secretion and degrades established alginate from a variety of mucoid &lt;i&gt;P. aeruginosa&lt;/i&gt; clinical isolates. Additionally, Smlt1473 differs from other alginate lyases in that it is active against acetylated alginate, which is secreted during chronic lung infection. These resul","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0185324"},"PeriodicalIF":3.9,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142817065","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}