Microbial Habitats Research Articles

Metal tolerance of Río Tinto fungi.

Southwest Spain's Río Tinto is a stressful acidic microbial habitat with a noticeably high concentration of toxic heavy metals. Nevertheless, it has an unexpected degree of eukaryotic diversity in its basin, with a high diversity of fungal saprotrophs. Although some studies on the eukaryotic diversity in Rio Tinto have been published, none of them used molecular methodologies to describe the fungal diversity and taxonomic affiliations that emerge along the river in different seasons. The aim of the present study was to isolate and describe the seasonal diversity of the fungal community in the Río Tinto basin and its correlation with the physicochemical parameters existing along the river's course. The taxonomic affiliation of 359 fungal isolates, based on the complete internal transcribed spacer DNA sequences, revealed a high degree of diversity, identifying species belonging primarily to the phylum Ascomycota, but representatives of the Basidiomycota and Mucoromycota phyla were also present. In total, 40 representative isolates along the river were evaluated for their tolerance to toxic heavy metals. Some of the isolates were able to grow in the presence of 1000 mM of Cu2+, 750 mM of As5+ and Cd2+, and 100 mM of Co2+, Ni2+, and Pb2+.

Diversity of culturable bacterial isolates and their potential as antimicrobial against human pathogens from Afar region, Ethiopia.

Antimicrobial resistance (AMR) is an escalating global health threat affecting humans, animals, and the environment, underscoring the urgent need for alternative pathogen control methods. Natural products, particularly secondary metabolites from bacteria, continue to be a vital source of antibiotics. However, microbial habitats and metabolites in Africa remain largely unexplored. In this study, we isolated and screened bacteria from Ethiopia's Afar region, characterized by extreme conditions like high temperatures, volcanic activity, high salinity, and hot springs to identify potential bioactive compounds. We discovered diverse bacterial isolates with antimicrobial activity against various pathogens, including strain Sl00103 (Bacillus sp. Sl00103), which demonstrated significant antimicrobial and antioxidant activities. GC-MS analysis identified several antimicrobial compounds, highlighting strain Sl00103 as a promising source of secondary metabolites with potential pharmaceutical applications and warranting further investigation.

Oral Microbiota and the Risk of Gastrointestinal Cancers-A Narrative Literature Review.

The human body is colonized by trillions of microorganisms in a symbiotic relationship. The oral cavity represents one of the most abundant microbial habitats in our body. Advances in sequencing techniques provide a more detailed understanding of the oral microbiota and how imbalances between bacteria, the phenomenon of dysbiosis, can affect not only the development of dental caries or inflammation within the oral cavity but also systemic diseases and cancers in distant locations. This narrative review evaluates the relationship between oral microbiota and its impact on gastrointestinal cancers. Using the keywords "oral microbiota 'AND' gastrointestinal cancers", the PubMed Web of Science and Scopus databases were searched for articles published between 2014 and 2024. Based on the review, the relationship between oral microbiota and oral, esophageal, gastric, colorectal, hepatocellular, and pancreatic cancers was described. Potential oncogenic mechanisms exploited by the microbiota such as the production of pro-inflammatory cytokines, induction of abnormal immune responses, and disruption of cell metabolic pathways were assessed. Further research and a thorough understanding of the impact of the oral microbiota on the development of cancers of the gastrointestinal tract may play a key role in their prevention, diagnosis, and treatment in the future.

Oral Microbiocenosis in Cases of Inflammatory Periodontal Diseases in Children with Tuberculosis

Objective — to examine the microbial spectrum of the oral cavity in cases of inflammatory periodontal diseases of children with tuberculosis. Materials and methods. A study of the microbial habitat of oral biotopes and gingival surfaces was conducted in 97 children aged 6 to 17 years with inflammatory periodontal diseases and tuberculosis (treatment group). The control group consisted of 20 practically healthy children of the same age. The periodontal diseases were diagnosed according to M.F. Danilevsky’s classification (2000). The study of oral microbiocenosis and gingival surfaces in the examined groups of children was performed in accordance with Order No. 234 of the Ministry of Health of Ukraine as of 2006. Results and discussion. Aerobic, facultative anaerobic, and anaerobic bacteria persisted in the oral fluid and on the gingival surfaces of children with tuberculosis and inflammatory periodontal diseases. The most frequent colonies of bacteria were Streptococcus, in particular S. mutans, S. salivarius, S. β-haemolyticus, Staphylococcus (S. aureus, S. epidermidis).The significant evidence of Neisseria (N. catarrhalis) and Corynebacterium (C. xerosis) was revealed in the oral cavity and gingival surfaces of the examined children. The microflora of children from the treatment group revealed mostly Lactobacillus genus. The microbial associations of the examined children consisted of Candida, E. coli fungi. Smear microscopy revealed viruses. S. aureus was higher in the children from the treatment group as compared to the healthy children. In addition, the concentration of microorganisms was higher on the gingival surface versus the oral fluid and was more evident in the children from the treatment group. Conclusions. The obtained spectrum of the oral microbial contamination in the children with tuberculosis and inflammatory periodontal diseases revealed the persisting associations of aerobic, facultative anaerobic, and anaerobic bacteria. The inflammatory periodontal diseases in tuberculosis-infected children were accompanied by the evident increase in the frequency and concentration of microorganisms increasing with the higher severity of the specific process.

The sewer advances: How to select eco-friendly pipe materials for environmental protection

Sewer pipe materials exhibit diverse inner-surface features, which can affect the attachment of biofilm and influence microbial metabolic processes. To investigate the role of the type of pipe material on the composition and metabolic capabilities of the adhering microorganisms, three sets of urban sewers (High-Density Polyethylene Pipe (HDPE), Ductile Iron Pipe (DIP), and Concrete Pipe (CP)) were constructed. Measurements of biofilm thickness and environmental factors revealed that the thickest biofilm in CP pipes reached 2000 μm, with ORP values as low as −325 mV, indicating a more suitable anaerobic microbial habitat. High-throughput sequencing showed similar relative abundances of genera related to carbon and sulfur metabolism in the DIP and CP pipes, whereas HDPE exhibited only half the relative abundance compared to that found in the other pipes. To explore the impact of pipe materials on the mechanisms of microbial response, a metagenomic approach was used to investigate the biological transformation of carbon and sulfur in wastewater. The annotations of the crucial enzyme-encoding genes related to methyl coenzyme M and sulfite reductase in DIP and CP were 50 and 110, respectively, whereas HDPE exhibited lower counts (25 and 70, respectively). This resulted in significantly lower carbon and sulfur metabolism capabilities in the HDPE biofilm than in the other two pipes. The stability of wastewater quality during the transmission process in HDPE pipes reduces the metabolic generation of toxic and harmful gases within the pipes, favoring the preservation of carbon sources for sewer systems. This study reveals the variations in carbon and sulfur metabolism in wastewater pipe systems influenced by pipe materials and provides insights for designing future sewers.

Nutrient requirements shape the preferential habitat of Allorhizobium vitis VAR03-1, a commensal bacterium, in the rhizosphere of Arabidopsis thaliana.

A diverse range of commensal bacteria inhabit the rhizosphere, influencing host plant growth and responses to biotic and abiotic stresses. While root-released nutrients can define soil microbial habitats, the bacterial factors involved in plant-microbe interactions are not well characterized. In this study, we investigated the colonization patterns of two plant disease biocontrol agents, Allorhizobium vitis VAR03-1 and Pseudomonas protegens Cab57, in the rhizosphere of Arabidopsis thaliana using Murashige and Skoog (MS) agar medium. VAR03-1 formed colonies even at a distance from the roots, preferentially in the upper part, while Cab57 colonized only the root surface. The addition of sucrose to the agar medium resulted in excessive proliferation of VAR03-1, similar to its pattern without sucrose, whereas Cab57 formed colonies only near the root surface. Overgrowth of both bacterial strains upon nutrient supplementation inhibited host growth, independent of plant immune responses. This inhibition was reduced in the VAR03-1 ΔrecA mutant, which exhibited increased biofilm formation, suggesting that some activities associated with the free-living lifestyle rather than the sessile lifestyle may be detrimental to host growth. VAR03-1 grew in liquid MS medium with sucrose alone, while Cab57 required both sucrose and organic acids. Supplementation of sugars and organic acids allowed both bacterial strains to grow near and away from Arabidopsis roots in MS agar. These results suggest that nutrient requirements for bacterial growth may determine their growth habitats in the rhizosphere, with nutrients released in root exudates potentially acting as a limiting factor in harnessing microbiota.

Greenhouse gases emissions and microbial assembly mechanism in constructed wetlands for treating saline-alkali and fluoride-laden drainage water

The drainage from high fluoride saline-alkali paddy fields exacerbates agricultural non-point source pollution. Constructed wetlands (CWs) have proven effective in treating such drainage, yet most research has focused on the response mechanisms of CWs to either saline-alkali or fluoride stress individually. The impact of combined stress of saline-alkali and fluoride on CW’s purification effects and greenhouse gas emissions, along with the underlying microbial mechanisms, remains unclear. We constructed mesocosm-scale CWs with four treatments varying in influent saline-alkali levels: low (LS-CWs), medium (MS-CWs), high (HS-CWs), and non saline-alkali CWs (Control-CWs). Our results show that CWs were effective in treating low and medium saline-alkali wastewater. Under high saline-alkali condition (pH: 9.5; EC: 5 mS/cm), CWs exhibited the highest global warming potential (GWP), exceeding that of Control-CWs, LS-CWs, and MS-CWs by 2.2, 4.2, and 3.9 times, respectively. The “ infer Community Assembly Mechanisms by Phylogenetic-bin-based null model ” (iCAMP) analysis indicated that stochastic processes, particularly drift and diffusion limitation (DL), dominated the community assembly of CWs. Elevated saline-alkali levels may enhance microbial habitat differentiation, increasing DL’s contribution, and raising the modularity and complexity of co-occurrence networks. This might be a strategy for microbial communities to resist environmental pressure and maintain network stability. We also propose suitable areas for CWs establishment considering both purification efficiency and GWP, in Western Jilin Province, a typical saline-alkali region. This study addresses a research gap in understanding pollutant transformation and microbial response mechanisms during treating saline-alkali and fluoride-laden drainage within CWs, providing a theoretical basis for the integrated treatment of sewage and greenhouse gas control in CWs to maximize their environmental benefits in practical applications.

Bacterial membrane vesicles from swine farm microbial communities harboring and safeguarding diverse functional genes promoting horizontal gene transfer

Antibiotic resistance (AMR) poses a significant global health challenge, with swine farms recognized as major reservoirs of antibiotic resistance genes (ARGs). Recently, bacterial membrane vesicles (BMVs) have emerged as novel carriers mediating horizontal gene transfer. However, little is known about the ARGs carried by BMVs in swine farm environments and their transfer potential. This study investigated the distribution, sources, and microbiological origins of BMVs in three key microbial habitats of swine farms (feces, soil, and fecal wastewater), along with the ARGs and mobile genetic elements (MGEs) they harbor. Characterization of BMVs revealed particle sizes ranging from 20 to 500 nm and concentrations from 108 to 1012 particles/g, containing DNA and proteins. Metagenomic sequencing identified BMVs predominantly composed of members of the Proteobacteria phyla, including Pseudomonadaceae, Moraxellaceae, and Enterobacteriaceae, carrying diverse functional genes encompassing resistance to 14 common antibiotics and 74,340 virulence genes. Notably, multidrug resistance, tetracycline, and chloramphenicol resistance genes were particularly abundant. Furthermore, BMVs harbored various MGEs, primarily plasmids, and demonstrated the ability to protect their DNA cargo from degradation and facilitate horizontal gene transfer, including the transmission of resistance genes. In conclusion, this study reveals widespread presence of BMVs carrying ARGs and potential virulence genes in swine farm feces, soil, and fecal wastewater. These findings not only provide new insights into the role of extracellular DNA in the environment but also highlight concerns regarding the gene transfer potential mediated by BMVs and associated health risks.

Response characteristics of soil microorganisms under strong disturbance conditions in the riparian zone of the three Gorges reservoir Area

The normal operation of the Three Gorges Reservoir, which involves periodic water storage and discharge, has led to strong disturbances in environmental conditions that alter soil microbial habitats in the riparian zones. Riparian zones are an important part of controlling pollution in the Three Gorges Reservoir area, since they act as a final ecological barrier that intercepts pollutants. Meanwhile, monitoring the health of microbial communities in the riparian zone is crucial for maintaining the ecological security of the reservoir area. We specifically investigate the Daning River, which are tributaries of the Three Gorges Reservoir and have typical riparian zones. Soil samples from these areas were subjected to high-throughput sequencing of 16S rRNA genes and 18S rRNA genes, in order to obtain the characteristics of the present microbial communities under strong disturbances in the riparian zones. We studied the characteristics and distribution patterns of microbial communities and their relationship with soil physicochemical properties. The study results indicate that microbial communities exhibit high diversity and evenness, and spatial heterogeneity is present. The ASV dataset contains many sequences not assigned to known genera, suggesting the presence of new fungal genera in the riparian zone. Redundancy analysis (RDA) revealed that pH and NH4+\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${NH}_{4}^{+}$$\\end{document}-N were the primary environmental factors driving bacterial community variation in the riparian zone, while pH, total carbon (TC) content, and NO3-\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${NO}_{3}^{-}$$\\end{document}-N were identified as the main drivers of soil archaeal community variation.

Microbes as marine habitat formers and ecosystem engineers.

Despite their small individual size, marine prokaryotic and eukaryotic microbes can form large 3D structures and complex habitats. These habitats contribute to seafloor heterogeneity, facilitating colonization by animals and protists. They also provide food and refuge for a variety of species and promote novel ecological interactions. Here we illustrate the role of microbes as ecosystem engineers and propose a classification based on five types of habitat: microbial mats, microbial forests, microbial-mineralized habitats, microbial outcrops and microbial nodules. We also describe the metabolic processes of microbial habitat formers and their ecological roles, highlighting current gaps in knowledge. Their biogeography indicates that these habitats are widespread in all oceans and are continuously being discovered across latitudes and depths. These habitats are also expected to expand under future global change owing to their ability to exploit extreme environmental conditions. Given their high ecological relevance and their role in supporting endemic species and high biodiversity levels, microbial habitats should be included in future spatial planning, conservation and management measures.

Assessment of macrozoobenthic community dynamics in the Ijuk River: Implications for freshwater ecosystem health and conservation management

Background: Nestled within the Isau-Isau Wildlife Reserve, the Ijuk River stretches approximately 3 kilometers, serving as a vital conservation area. Its upstream region plays multiple ecological roles, including watershed management, hydrological regulation, microclimate control, soil fertility maintenance, microbial habitat provision, air quality regulation, and carbon sequestration. However, escalating human activities, particularly changes in land use, pose significant threats to its ecological balance. The particular concern is the conversion of forested areas into agricultural lands, primarily for coffee cultivation and mixed gardens, encroaching dangerously close to the riverbanks. This encroachment necessitates a critical reevaluation of the river's water quality, given its crucial role in supporting biodiversity and ecological equilibrium. Benthic insects dwelling in the riverbed serve as invaluable bioindicators, offering insights into the overall health of aquatic ecosystems. Methods: Conducted between January and July 2022 in the Isau-Isau Wildlife Refuge, Lawang Agung Village, Mulak Ulu District, Lahat Regency, the study aimed to assess the macrozoobenthic community structure across three river segments: upstream, midstream, and downstream. Employing field sampling, observational surveys, taxonomic identification, and data analysis, the research aimed to unravel the river's ecological dynamics. Findings: Through meticulous examination of benthic insect communities, the study revealed relatively favorable water quality in the Ijuk River. However, discernible declines in various ecological parameters, as evidenced by evaluation results, highlight the urgency of conservation efforts and proactive management strategies to mitigate further degradation and preserve the river's ecological integrity. Conclusion: Such endeavors are crucial for safeguarding the biodiversity and sustainability of this vital freshwater ecosystem. Novelty/Originality of this Study: The study uniquely assesses the macrozoobenthic community dynamics in the Ijuk River, revealing significant changes over two decades that highlight the river's ecological health and underscore the urgent need for conservation efforts. It offers a comprehensive, updated evaluation of the macrozoobenthic community structure, providing critical insights into the impacts of land use changes and human activities on freshwater ecosystems.

Maize-alfalfa intercropping alleviates the dependence of multiple ecosystem services on nonrenewable fertilization

Phosphorus is a nonrenewable source of fertilization, which will challenge the future of food production and cropland sustainability worldwide. Crop diversity is known to promote greater productivity, yet the capacity of crop diversity to alleviate productivity dependence on nonrenewable fertilization and promote multiple ecosystem services remains virtually unknown. Here, we conducted a field experiment to quantify the contribution of maize-alfalfa intercropping to soil biodiversity and multiple ecosystem services under contrasting phosphorus fertilization levels. Results showed that unfertilized intercropping can support higher levels of ecosystem services such as soil microbial habitat, plant-soil mutualism, nutrient cycling, and soil carbon storage compared to phosphorus-fertilized monoculture. Intercropping could optimize the delivery of soil diversity and multiple ecosystem services override phosphorus, including microbial diversity, weighted ecosystem services, productivity stability and sustainability, and soil microbial habitat were 5–30 times higher, respectively. Unfertilized intercropping also helped to reduce important tradeoffs between productivity and soil microbial diversity compared with fertilized monoculture. Together, our results provide evidence that intercropping can optimize crop use of phosphorus, and promote multiple important ecosystem services, which can help alleviate global dependence on nonrenewable, and often environmentally deleterious fertilizer inputs.

Enzyme induced polymer degradation as a pathway to create microbial habitats for biomanufacturing intensification

Polymer hydrogels are instrumental in cell immobilization for biomanufacturing, yet traditional hydrogel bioreactors often compromise cell viability, function, and mass transfer. This results in uncontrolled microbial proliferation and significant cell leakage, thereby impeding the continuous production of high-value products. To address these challenges, we introduce an innovative liquid microcavity technique employing a blend of Gelatin-methacryloyl (Gel-MA) and Pluronic F127diacrylate (F127-DA) for precision bioprinting, followed by selective enzymatic digestion of gelatin to create microbial habitats. Through tailoring of the hydrogel’s pore structure and integration of diverse networks, our approach facilitates controlled nutrient transfer, efficient waste removal, and stable mechanical support, all while maintaining a leak-free suspension culture of microorganisms. We validated the effectiveness of our method by fabricating yeast-infused Three-dimensional (3D) lattice constructs, successfully achieving continuous fermentation of glucose into ethanol in a flow reactor with minimal efficiency reduction (≥90 % yield) over five cycles. This research not only confronts the spatial limitations inherent in hydrogel-based systems but also demonstrates a foundational potential for revolutionary change in biomanufacturing practices.

Oral microbiota in aging and diseases

Abstract Human microbiomes are microbial populations that form a symbiotic relationship with humans. There are up to 1000 species on the surface of human skin and mucosal system, among which gut microbiota attracts the most interest. As the beginning of the digestive tract, oral cavity is also an important microbial habitat in the human body which is the first line of defense against pathogens entering the body. Many studies have revealed that oral microbial dysbiosis could not only contribute to oral diseases but also whole-body systemic diseases and health status. Oral microorganisms can enter the gastrointestinal tract with saliva and food, or enter the blood circulation through mouth breakage, thus causing systemic inflammation and aging-related diseases including some causal links to Alzheimer’s disease. A series of changes take place in oral microbial composition during development, with different age stages marked by different dominant microbial species. Despite a lack of comprehensive studies on aging oral microbiota, through systemic inflammation, oral pathogenic microbes are likely to contribute inflammatory aging. As inflammaging is a key signature and one of the causes for accelerated aging, improving the structure of oral microbiome may be not only a new strategy for disease prevention and treatment, but also for aging intervention.

The atmosphere: a transport medium or an active microbial ecosystem?

The atmosphere may be Earth's largest microbial ecosystem. It is connected to all of Earth's surface ecosystems and plays an important role in microbial dispersal on local to global scales. Despite this grand scale, surprisingly little is understood about the atmosphere itself as a habitat. A key question remains unresolved: does the atmosphere simply transport microorganisms from one location to another, or does it harbour adapted, resident, and active microbial communities that overcome the physiological stressors and selection pressures the atmosphere poses to life? Advances in extreme microbiology and astrobiology continue to push our understanding of the limits of life towards ever greater extremes of temperature, pressure, salinity, irradiance, pH, and water availability. Earth's atmosphere stands as a challenging, but potentially surmountable, extreme environment to harbour living, active, resident microorganisms. Here, we confront the current understanding of the atmosphere as a microbial habitat, highlighting key advances and limitations. We pose major ecological and mechanistic questions about microbial life in the atmosphere that remain unresolved and frame the problems and technical pitfalls that have largely hindered recent developments in this space, providing evidence-based insights to drive future research in this field. New innovations supported by rigorous technical standards are needed to enable progress in understanding atmospheric microorganisms and their influence on global processes of weather, climate, nutrient cycling, biodiversity, and microbial connectivity, especially in the context of rapid global change.

Microbial ecology of the deep terrestrial subsurface.

The terrestrial subsurface hosts microbial communities that, collectively, are predicted to comprise as many microbial cells as global surface soils. Although initially thought to be associated with deposited organic matter, deep subsurface microbial communities are supported by chemolithoautotrophic primary production, with hydrogen serving as an important source of electrons. Despite recent progress, relatively little is known about the deep terrestrial subsurface compared to more commonly studied environments. Understanding the composition of deep terrestrial subsurface microbial communities and the factors that influence them is of importance because of human-associated activities including long-term storage of used nuclear fuel, carbon capture, and storage of hydrogen for use as an energy vector. In addition to identifying deep subsurface microorganisms, recent research focuses on identifying the roles of microorganisms in subsurface communities, as well as elucidating myriad interactions-syntrophic, episymbiotic, and viral-that occur among community members. In recent years, entirely new groups of microorganisms (i.e. candidate phyla radiation bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoloarchaeota, Nanoarchaeota archaea) have been discovered in deep terrestrial subsurface environments, suggesting that much remains unknown about this biosphere. This review explores the historical context for deep terrestrial subsurface microbial ecology and highlights recent discoveries that shape current ecological understanding of this poorly explored microbial habitat. Additionally, we highlight the need for multifaceted experimental approaches to observe phenomena such as cryptic cycles, complex interactions, and episymbiosis, which may not be apparent when using single approaches in isolation, but are nonetheless critical to advancing our understanding of this deep biosphere.

Ecological and evolutionary processes involved in shaping microbial habitat generalists and specialists in urban park ecosystems.

Urban parks, as an important urban greenspace, play essential roles in ecosystem services and are important hotspots for microbes. Microbial diversity is driven by different ecological and evolutionary processes, while little is currently known about the distinct roles of ecological and evolutionary features in shaping microbial diversity in urban park ecosystems. We explored the ecological and evolutionary characteristics of prokaryotic and microeukaryotic habitat generalists and specialists in urban park ecosystems based on a representative set of different habitats. We found that different ecological and evolutionary drivers jointly maintained and regulated microbial diversity in urban park microbiomes through analyzing the community assembly process, ecological roles in hierarchical interaction, and species diversification potential. These findings significantly advance our understanding regarding the mechanisms governing microbial diversity in urban park ecosystems.

Identification and validation of microbial biomarkers from cross-cohort datasets using xMarkerFinder.

Microbial signatures have emerged as promising biomarkers for disease diagnostics and prognostics, yet their variability across different studies calls for a standardized approach to biomarker research. Therefore, we introduce xMarkerFinder, a four-stage computational framework for microbial biomarker identification with comprehensive validations from cross-cohort datasets, including differential signature identification, model construction, model validation and biomarker interpretation. xMarkerFinder enables the identification and validation of reproducible biomarkers for cross-cohort studies, along with the establishment of classification models and potential microbiome-induced mechanisms. Originally developed for gut microbiome research, xMarkerFinder's adaptable design makes it applicable to various microbial habitats and data types. Distinct from existing biomarker research tools that typically concentrate on a singular aspect, xMarkerFinder uniquely incorporates a sophisticated feature selection process, specifically designed to address the heterogeneity between different cohorts, extensive internal and external validations, and detailed specificity assessments. Execution time varies depending on the sample size, selected algorithm and computational resource. Accessible via GitHub ( https://github.com/tjcadd2020/xMarkerFinder ), xMarkerFinder supports users with diverse expertise levels through different execution options, including step-to-step scripts with detailed tutorials and frequently asked questions, a single-command execution script, a ready-to-use Docker image and a user-friendly web server ( https://www.biosino.org/xmarkerfinder ).

Stochastic microbial dispersal drives local extinction and global diversity.

Airborne dispersal of microorganisms is a ubiquitous migration mechanism, allowing otherwise independent microbial habitats to interact via biomass exchange. Here, we study the ecological implications of such advective transport using a simple spatial model for bacteria-phage interactions: the population dynamics at each habitat are described by classical Lotka-Volterra equations; however, species populations are taken as integer, that is, a discrete, positive extinction threshold exists. Spatially, species can spread from habitat to habitat by stochastic airborne dispersal. In any given habitat, the spatial biomass exchange causes incessant population density oscillations, which, as a consequence, occasionally drive species to extinction. The balance between local extinction events and dispersal-induced migration allows species to persist globally, even though diversity would be depleted by competitive exclusion, locally. The disruptive effect of biomass dispersal thus acts to increase microbial diversity, allowing system-scale coexistence of multiple species that would not coexist locally.

Review on microbial production of exopolysaccharides and its applications

Exopolysaccharides (EPS) are bio-molecules produced by variety of microorganisms by both eukaryotes and prokaryotic. EPS are high molecular weight molecules available in both homopolysaccharide and heteropolysaccharide. Plants are the primary source of exopolysaccharides (EPS); however, microbiological EPS have a diverse range of structures and functions that enable them to endure harsh environmental conditions. Studying the structure and composition of exopolysaccharides is crucial for understanding their beneficial functions and potential applications in different fields such as food, dairy, medical, pharmaceutical, cosmetics and other industries. This review briefly describes how extremities trigger microbes to produce EPS with unique properties. In addition, it covers optimization and strain improvement methods to increase the productivity of microbes, extraction and purification methods. Similarities and differences of solid-state fermentation and submerged fermentation for EPS production from Bacteria and Fungi are sighted in this review. Applications of EPS in different fields owing to their various physicochemical properties are also discussed in this review. This review provides explanations with respect to microbial habitats, fermentation scales, purification methods and recent research on their potential applications.