Microbial Populations Research Articles

Activated sludge microbial community assembly: the role of influent microbial community immigration.

Wastewater treatment plants (WWTPs) are host to diverse microbial communities and receive a constant influx of microbes from influent wastewater. However, the impact of immigrants on the structure and activities of the activated sludge (AS) microbial community remains unclear. To gain insight on this phenomenon known as perpetual community coalescence, the current study utilized controlled manipulative experiments that decoupled the influent wastewater composition from the microbial populations to reveal the fundamental mechanisms involved in immigration between sewers and AS-WWTP. The immigration dynamics of heterotrophs were analyzed by harvesting wastewater biomass solids from three different sewer systems and adding to synthetic wastewater. Immigrating influent populations were observed to contribute up to 14% of the sequencing reads in the AS. By modeling the net growth rate of taxa, it was revealed that immigrants primarily exhibited low or negative net growth rates. By developing a protocol to reproducibly grow AS-WWTP communities in the lab, we have laid down the foundational principles for the testing of operational factors creating community variations with low noise and appropriate replication. Understanding the processes that drive microbial community diversity and assembly is a key question in microbial ecology. In the future, this knowledge can be used to manipulate the structure of microbial communities and improve system performance in WWTPs.IMPORTANCEIn biological wastewater treatment processes, the microbial community composition is essential in the performance and stability of the system. This study developed a reproducible protocol to investigate the impact of influent immigration (or perpetual coalescence of the sewer and activated sludge communities) with appropriate reproducibility and controls, allowing intrinsic definitions of core and immigrant populations to be established. The method developed herein will allow sequential manipulative experiments to be performed to test specific hypothesis and optimize wastewater treatment processes to meet new treatment goals.

Metatranscriptomic response of deep ocean microbial populations to infusions of oil and/or synthetic chemical dispersant.

Oil spills are a frequent perturbation to the marine environment that has rapid and significant impacts on the local microbiome. Previous studies have shown that exposure to synthetic dispersant alone did not enhance heterotrophic microbial activity or oxidation rates of specific hydrocarbon components but increased the abundance of some taxa (e.g., Colwellia). In contrast, exposure to oil, but not dispersants, increased the abundance of other taxa (e.g., Marinobacter) and stimulated hydrocarbon oxidation rates. Here, we advance these findings by interpreting metatranscriptomic data from this experiment to explore how and why specific components of the microbial community responded to distinct organic carbon exposure regimes. Dispersant alone was selected for a unique community and for dominant organisms that reflected treatment- and time-dependent responses. Dispersant amendment also led to diverging functional profiles among the different treatments. Similarly, oil alone was selected for a community that was distinct from treatments amended with dispersants. The presence of oil and dispersants with added nutrients led to substantial differences in microbial responses, likely suggesting increased fitness driven by the presence of additional inorganic nutrients. The oil-only additions led to a marked increase in the expression of phages, prophages, transposable elements, and plasmids (PPTEPs), suggesting that aspects of microbial community response to oil are driven by the "mobilome," potentially through viral-associated regulation of metabolic pathways in ciliates and flagellates that would otherwise throttle the microbial community through grazing.IMPORTANCEMicrocosm experiments simulated the April 2010 Deepwater Horizon oil spill by applying oil and synthetic dispersants (Corexit EC9500A and EC9527A) to deep ocean water samples. The exposure regime revealed severe negative alterations in the treatments' heterotrophic microbial activity and hydrocarbon oxidation rates. We expanded these findings by exploring metatranscriptomic signatures of the microbial communities during the chemical amendments in the microcosm experiments. Here we report how dominant organisms were uniquely associated with treatment- and time-dependent trajectories during the exposure regimes; nutrient availability was a significant factor in driving changes in metatranscriptomic responses. Remarkable signals associated with PPTEPs showed the potential role of mobilome and viral-associated survival responses. These insights underscore the time-dependent environmental perturbations of fragile marine environments under oil and anthropogenic stress.

Tracing Acinetobacter baumannii's Journey from Hospitals to Aquatic Ecosystems.

This study provides a comprehensive analysis of Acinetobacter baumannii in aquatic environments and fish microbiota by integrating culture-dependent methods, 16S metagenomics, and antibiotic resistance profiling. A total of 83 A. baumannii isolates were recovered using culture-dependent methods from intra-hospital infections (IHI) and wastewater (WW) and surface water (SW) samples from two southern Romanian cities in August 2022. The antibiotic susceptibility was screened using disc diffusion, microdilution, PCR, and Whole Genome Sequencing assays. The highest microbial load in the analyzed samples was found in Glina, Bucharest, for both WW and SW samples across all investigated phenotypes. For Bucharest isolates, the resistance levels corresponded to fluoroquinolones > aminoglycosides > β-lactam antibiotics. In contrast, A. baumannii from upstream SW samples in Târgoviște showed the highest resistance to aminoglycosides. The blaOXA-23 gene was frequently detected in IHI, WW, and SW isolates in Bucharest, but was absent in Târgoviște. Molecular phylogeny revealed the presence of ST10 in Târgoviște isolates and ST2 in Bucharest isolates, while other minor STs were not specifically correlated with a sampling point. Using 16S rRNA sequencing, significant differences in microbial populations between the two locations was identified. The low abundance of Alphaproteobacteria and Actinobacteria in both locations suggests environmental pressures or contamination events. These findings indicate significant fecal contamination and potential public health risks, emphasizing the need for improved water quality monitoring and management.

Microbial Community Dynamics and Metabolite Changes during Wheat Starch Slurry Fermentation.

Wheat starch fermentation slurry is the main substrate for producing Ganmianpi, a traditional Chinese fermented wheat starch-based noodle. In the present work, the microbial population dynamics and metabolite changes in wheat starch fermentation slurry at different fermentation times (0, 1, 2, 3, and 4 days) were measured by using high-throughput sequencing analysis and headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME/GC-MS) methods. The texture and sensory properties of Ganmianpi made from fermented starch slurry are also evaluated. The results showed that Latilactobacillus curvatus and Leuconostoc citreum were the dominant bacteria in wheat starch fermentation slurry, while Saccharomyces cerevisiae and Kazachstania wufongensis were identified as the main species of fungi. With the extension of fermentation time, the reducing sugar content first increased and then decreased, when the titratable acidity content showed an increasing trend, and the nonvolatile acid was significantly higher than the volatile acid. A total of 62 volatile flavor compounds were identified, and the highest content is alcohols, followed by acids. Fermentation significantly reduced the hardness and chewiness of Ganmianpi, and increased its resilience and cohesiveness. Ganmianpi made from fermented starch slurry for two and three days showed a higher sensory score than other samples. The present study is expected to provide a theoretical basis for exploiting the strains with potential for commercial application as starter cultures and quality improvement of Ganmianpi.

Fecal microbiota transplantation accelerates restoration of florfenicol-disturbed intestinal microbiota in a fish model

Antibiotic-induced dysbiosis in the fish gut causes significant adverse effects. We use fecal microbiota transplantation (FMT) to accelerate the restoration of florfenicol-perturbed intestinal microbiota in koi carp, identifying key bacterial populations and metabolites involved in the recovery process through microbiome and metabolome analyses. We demonstrate that florfenicol disrupts intestinal microbiota, reducing beneficial genera such as Lactobacillus, Bifidobacterium, Bacteroides, Romboutsia, and Faecalibacterium, and causing mucosal injuries. Key metabolites, including aromatic amino acids and glutathione-related compounds, are diminished. We show that FMT effectively restores microbial populations, repairs intestinal damage, and normalizes critical metabolites, while natural recovery is less effective. Spearman correlation analyses reveal strong associations between the identified bacterial genera and the levels of aromatic amino acids and glutathione-related metabolites. This study underscores the potential of FMT to counteract antibiotic-induced dysbiosis and maintain fish intestinal health. The restored microbiota and normalized metabolites provide a basis for developing personalized probiotic therapies for fish.

New Secondary Metabolites of Mangrove-Associated Strains.

Positioned at the dynamic interface between terrestrial and marine realms, mangroves embody a vibrant tapestry of biodiversity, encompassing an array of plants, animals, and microorganisms. These microbial inhabitants of mangrove habitats have emerged as a pivotal resource for antimicrobials and a plethora of pharmaceutically valuable compounds, spanning enzymes, antineoplastic agents, pesticides, immunosuppressants, and immunomodulators. This review delves into the recent landscape (January 2021 to May 2024, according to the time of publication) of novel secondary metabolites isolated from mangrove-associated microorganisms, analyzing 41 microbial strains that collectively yielded 165 distinct compounds. Our objective is to assess the productivity and potential of natural products derived from microbial populations within mangrove ecosystems in recent times. Notably, fungi stand out as the preeminent contributors to the emergence of these novel natural products, underscoring their pivotal role in the bioprospecting endeavors within these unique environments.

Macrogenomics Reveals Effects on Marine Microbial Communities during Oplegnathus punctatus Enclosure Farming.

(1) Background: Laizhou Bay is an important aquaculture area in the north of China. Oplegnathus punctatus is one of the species with high economic benefits. In recent years, the water environment of Laizhou Bay has reached a mild eutrophication level, while microorganisms are an important group between the environment and species. In this study, we evaluated alterations in environmental elements, microbial populations, and antibiotic resistance genes (ARGs) along with their interconnections during Oplegnathus punctatus net culture. (2) Methods: A total of 142 samples from various water layers were gathered for metagenome assembly analysis. Mariculture increases the abundance of microorganisms in this culture area and makes the microbial community structure more complex. The change had more significant effects on sediment than on seawater. (3) Results: Certain populations of cyanobacteria and Candidatus Micrarchaecta in seawater, and Actinobacteria and Thaumarchaeota in sediments showed high abundance in the mariculture area. Antibiotic resistance genes in sediments were more sensitive to various environmental factors, especially oxygen solubility and salinity. (4) Conclusions: These findings highlight the complex and dynamic nature of microorganism-environment-ARG interactions, characterized by regional specificity and providing insights for a more rational use of marine resources.

Functional Abdominal Bloating and Gut Microbiota: An Update.

(1) Background: Functional abdominal bloating and distension (FAB/FAD) are common disorders of the gut-brain interaction. Their physiopathology is complex and not completely clarified, although gut microbiota imbalances play a central role. The treatment of FAB/FAD still represents a clinical challenge for both patients and healthcare providers. Gut microbiota modulation strategies might play a crucial role in their management. The aim of this narrative review was to update the current evidence on FAB/FAD, with a focus on gut microbiota. (2) Methods: In October 2023, a review was conducted through the Medline, PubMed, and Embase databases. Selected literature included all available English-edited studies (randomized controlled trials and cross-sectional, cohort, and case-control studies). (3) Results: Twelve studies were selected, most of which investigated the relationship between IBS and microbiota, with bloating being one of its symptoms. The studies suggest that restoring a balanced microbiome appears to be the most promising solution for better management of FAB/FAD. Targeted approaches, such as the use of probiotics, prebiotics, antibiotics such as rifaximin or dietary modifications, may hold the key to alleviating symptoms. Other therapeutic options, such as diet, neuromodulators, and brain-gut behavioral therapies (i.e., cognitive-behavioral therapy) have shown promising outcomes, but strong data are still lacking. (4) Conclusions: Targeted approaches that focus on the gut microbiota, such as the use of probiotics, prebiotics, and antibiotics, are essential in managing FAB/FAD. Understanding the complex relationship between gut microbiota and FAB/FAD is crucial for developing effective treatments. Further studies are needed to explore the specific roles of different microbial populations in patients with FAB/FAD to enhance therapeutic strategies.

Rare rather than abundant taxa of soil bacteria and fungi regulate soil multifunctionality in Eucalyptus plantations

Soil multifunctionality not only contributes to the production of ecosystem services (e.g., nutrient cycling, boosts in plant production, and provision of biological processes), but also supports the survival of species (protecting biodiversity) in an ecosystem. Multi-generational planting (sprouting from logging stumps) of Eucalyptus is widely adopted for timber production in southern China, which distinctly induces the decline of soil properties and destroys soil microbial communities. However, research on various Eucalyptus management practices has predominantly concentrated on soil nutrients and microbial populations. The effects of these practices on soil multifunctionality remain unexplored. Furthermore, the underlying mechanisms influencing the abundant and rare microorganisms have not been fully understood. Here, an 18-year Eucalyptus plantation experiment, including single-generation continuous planting (Y18), multiple-generation felling of the same years (D4), and evergreen broadleaf forest control (CK), was designed. Twenty-three parameters associated with soil nutrient cycling were obtained to quantify soil multifunctionality, and partial least squares path modeling (PLS-PM) was used to reveal the main driving force regulating soil multifunctionality. Our results demonstrated that multi-generational Eucalyptus planting significantly reduced soil multifunctionality, microbial diversity, and network stability. Comparatively, single-generational planting showed slight effects on soil multifunctionality and microbial communities. Stochastic processes dominated the assembly of abundant taxa in Eucalyptus plantations, whereas deterministic processes dominated rare taxa. PLS-PM results revealed that soil organic carbon (SOC), dissolved organic carbon (DOC), total nitrogen (TN), and total phosphorus (TP) directly regulated soil multifunctionality or indirectly through modifying the diversity and networks of rare taxa. The total effect analysis showed that the diversity and network of rare taxa had a greater impact on soil multifunctionality than abundant taxa. SOC and DOC played a crucial role in driving changes in soil multifunctionality. Our findings highlight the need to decrease rotation intensity and conserve rare taxa to mitigate soil quality degradation in artificial Eucalyptus plantations.

Accounting for cellular-level variation in lysis: implications for virus-host dynamics.

Viral impacts on microbial populations depend on interaction phenotypes-including viral traits spanning the adsorption rate, latent period, and burst size. The latent period is a key viral trait in lytic infections. Defined as the time from viral adsorption to viral progeny release, the latent period of bacteriophage is conventionally inferred via one-step growth curves in which the accumulation of free virus is measured over time in a population of infected cells. Developed more than 80 years ago, one-step growth curves do not account for cellular-level variability in the timing of lysis, potentially biasing inference of viral traits. Here, we use nonlinear dynamical models to understand how individual-level variation of the latent period impacts virus-host dynamics. Our modeling approach shows that inference of the latent period via one-step growth curves is systematically biased-generating estimates of shorter latent periods than the underlying population-level mean. The bias arises because variability in lysis timing at the cellular level leads to a fraction of early burst events, which are interpreted, artefactually, as an earlier mean time of viral release. We develop a computational framework to estimate latent period variability from joint measurements of host and free virus populations. Our computational framework recovers both the mean and variance of the latent period within simulated infections including realistic measurement noise. This work suggests that reframing the latent period as a distribution to account for variability in the population will improve the study of viral traits and their role in shaping microbial populations.IMPORTANCEQuantifying viral traits-including the adsorption rate, burst size, and latent period-is critical to characterize viral infection dynamics and develop predictive models of viral impacts across scales from cells to ecosystems. Here, we revisit the gold standard of viral trait estimation-the one-step growth curve-to assess the extent to which assumptions at the core of viral infection dynamics lead to ongoing and systematic biases in inferences of viral traits. We show that latent period estimates obtained via one-step growth curves systematically underestimate the mean latent period and, in turn, overestimate the rate of viral killing at population scales. By explicitly incorporating trait variability into a dynamical inference framework that leverages both virus and host time series, we provide a practical route to improve estimates of the mean and variance of viral traits across diverse virus-microbe systems.

Requirement of a Wnt5A-microbiota axis in the maintenance of gut B-cell repertoire and protection from infection.

We investigated the influence of a Wnt5A-gut microbiota axis on gut B-cell repertoire and protection from infection, having previously demonstrated that Wnt5A in association with gut commensals helps shape gut T-cell repertoire. Accordingly, Wnt5A heterozygous mice, which express less than wild-type level of Wnt5A, and their isolated Peyer's patches (PPs) were studied in comparison with the wild-type counterparts. The percentages of IgM- and IgA-expressing B cells were quite similar in the PP of both sets of mice. However, the PP of the Wnt5A heterozygous mice harbored significantly higher than wild-type levels of microbiota-bound B cell-secreted IgA, indicating the prevalence of a microbial population therein, which is significantly altered from that of wild-type. Additionally, the percentage of PP IgG1-expressing B cells was appreciably depressed in the Wnt5A heterozygous mice in comparison to wild-type. Wnt5A heterozygous mice, furthermore, exhibited notably higher than the wild-type levels of morbidity and mortality following infection with Salmonella typhimurium, a common gut pathogen. Differences in morbidity/mortality correlated with considerable disparity between the PP-B-cell repertoires of the Salmonella-infected Wnt5A heterozygous and wild-type mice, in which the percentage of IgG1-expressing B1b cells in the PP of heterozygous mice remains significantly low as compared to wild-type. Overall, these results suggest that a gut Wnt5A-microbiota axis is intrinsically associated with the maintenance of gut B-cell repertoire and protection from infection.IMPORTANCEAlthough it is well accepted that B cells and microbiota are required for protection from infection and preservation of gut health, a lot remains unknown about how the optimum B-cell repertoire and microbiota are maintained in the gut. The importance of this study lies in the fact that it unveils a potential role of a growth factor termed Wnt5A in the safeguarding of the gut B-cell population and microbiota, thereby protecting the gut from the deleterious effect of infections by common pathogens. Documentation of the involvement of a Wnt5A-microbiota axis in the shaping of a protective gut B-cell repertoire, furthermore, opens up new avenues of investigations for understanding gut disorders related to microbial dysbiosis and B-cell homeostasis that, till date, are considered incurable.

Investigating bacterial diversity involved in the production of vegetable-based ethnic fermented food of North Bengal and their metabolic pathways with reverse ecology approach

Endemic fermented vegetables play a crucial role in local cuisine and culture, with traditionally fermented raw green vegetables such as gundruk being a popular practice in North Bengal and Sikkim, India. However, there is a gap in the microbial profiling of these vegetables. This study aimed to explore the diversity of dominant bacterial populations in fermented leafy vegetables using both culture-dependent and culture-independent methods. In addition to isolating bacteria using conventional methods, we conducted phenotypic and biochemical characterization, community DNA isolation, and amplicon sequencing. We also introduced a new approach in bioinformatics analysis: reverse ecology, which analyzes complementation and competition among participant microbes. In conventional culture-dependent techniques, LAB genera such as Lactobacillus, Enterococcus, Leuconostoc, and Pediococcus have been identified as predominant consortia, whereas metagenomic analysis revealed that the microbiome of fermented dried leafy vegetables was mainly composed of Firmicutes, Proteobacteria, Actinobacteria, Bacteroides, and Planctomycetes at the phylum level. Within the Lactobacillaceae family, predominant types included Lactobacillus, Lactococcus, Pediococcus, Leuconostoc, Enterococcus, Vagococcus, Weissella, and Carnobacterium. The microbial metabolism revealed key pathways, such as carbon metabolism, glycolysis, gluconeogenesis, and glyoxylate. Aromatic amino acid degradation, fatty acid metabolism, amino sugar metabolism, nucleotide sugar metabolism, and biosynthesis of nucleotide sugar pathways were also active. The competition index among microbes and human metabolic data was low (0.32–0.44), indicating minimal competition for nutrition. Complementation indices between bacteria and humans were high (0.76–0.88), suggesting a beneficial impact of gundruk microbial populations on human health.

Article Review: Production and Purification of Antibiotics from Environmental Microorganism

The use for antibiotics to treat microbial with bacteria has been for decades a mainstay of contemporary therapy. Nevertheless, extensive antimicrobial abuse or trafficking has resulted in unforeseen effects that need significant policy reforms for prevention. Researchers discuss two major categories of implications of antimicrobial misuse and excess use in this review. Subsequently talk about how antibiotic resistance spreads from hotspot where resistance evolution occurs to the environment, having a focus on possible resistance dissemination channels. Furthermore, they describe how naturally occurring populations of microbes, in addition to crustaceans including vertebrate organisms are impacted by antimicrobial contamination; regardless of the development of susceptibility. Individuals conclude with a summary of the local initiatives that are now being implemented to mitigate the consequences of antimicrobial contamination as well as regions where these strategies are still being developed.

Microbial Diversity Assessment in Soil from Dumping Sites: Isolation, DNA Extraction and Electrophoretic Analysis

This study aims to investigate the microbial diversity present in soil samples collected from various dumping sites, which are known for their complex and heterogeneous waste environments. The primary objective is to isolate and characterize the microbial communities inhabiting these soils, providing insights into their composition and potential ecological roles. Soil samples were collected by digging 5 cm deep at multiple dumping locations to ensure a representative sampling of the microbial populations. The collected soil samples underwent a serial dilution process, extending up to 10^-9 and 10^-10 dilutions, to facilitate the isolation of individual microbial colonies. These diluted samples were then inoculated onto Standard Potato Dextrose Agar (PDA) media, a nutrient-rich medium conducive to microbial growth. Following an incubation period, distinct bacterial colonies were observed and isolated for further analysis. DNA was extracted from the isolated bacterial colonies using a standard DNA extraction protocol. The quality and purity of the extracted DNA were assessed through gel electrophoresis, a technique that separates DNA fragments based on their size. Remarkably, the electrophoretic analysis revealed clear and distinct DNA bands along with RNA bands, indicating successful extraction of high-quality microbial DNA. Notably, this was achieved without the use of proteinase treatment, which is typically employed to remove protein contaminants from DNA samples. The results of this study underscore the robustness of the methodologies employed in isolating and characterizing microbial DNA from soil samples collected at dumping sites. The presence of distinct DNA and RNA bands highlights the effectiveness of the DNA extraction process, even in the absence of proteinase treatment. These findings provide valuable insights into the microbial diversity within dumping site soils, suggesting a rich and varied microbial community that may play significant roles in soil health and waste decomposition.

Multi-stage oxic biofilm system for pilot-scale treatment of coking wastewater: Pollutants removal performance, biofilm properties and microbial community

A multi-stage oxic biofilm system based on hydrophilic polyurethane foam was established and operated for advanced treatment of coking wastewater, in which distinct gradient variations of pollutants removal, biofilm properties and microbial community in the 5 stages were evaluated. The system rapidly achieved NH4+-N removal efficiency of 97.51 ± 2.29 % within 8 days. The biofilm growing attached on the carriers exhibited high biomass (≥10.29 g/L), which ensured sufficient microbial population. Additionally, the rising extracellular polymeric substance and declining proteins/polysaccharides ratios across stages suggested a dense-to-loose transition in the biofilm’s structure, in response to the varying pollutant concentrations. The dominance of Nitrosomonas cluster in the first 3 stages and Nitrospira lineage in the following 2 stages facilitated the complete depletion of high NH4+-N concentration without NO2--N accumulation. Overall, the distinct biofilm property and community at each stage, shaped by the multi-stage configuration, maximized the pollutants removal efficiency.

Changes in performance, cecal microflora counts and intestinal histology of Japanese quails fed diets containing different fibre sources

The purpose of this experiment was to investigate how various fiber sources impact the performance, microbial population, and intestinal histology of Japanese quail that was performed in a completely randomized design for 42 days. The dietary treatments involved a fiber-free corn-soybean meal-based diet (control, CTL), and CTL with added levels of sunflower hulls (SFH) and sugar beet pulp (SBP) (20 and 40 g kg-1). Body weight gain (BWG) and feed intake (FI) were recorded weekly. Carcass characteristics, cecal microbial population, blood variables and intestinal histology were measured on the 42 day of age. Adding 40 g kg-1 of SBP led to a significant decrease in body weight gain and an increase in the feed conversion ratio of birds from 1 to 21 days (P < 0.05). The relative weight of the gastrointestinal tract and gizzard increased significantly in birds that consumed SFH. Blood triglyceride concentration decreased with the inclusion of fiber in the diet. However, there was a notable increase in blood cholesterol concentration in the birds that were fed SBP (20 and 40 g kg-1) in comparison to those fed SFH (P < 0.05). The population of E. Coli in the cecum increased significantly in the birds that were fed 4 g kg-1 of SBP as opposed to those fed 20 and 40 g kg-1 of SFH (P < 0.05). The villus height of the jejunum in birds that were fed 20 g kg-1 and 40 g kg-1 of SFH demonstrated a significant increase in comparison to the other treatments (P < 0.05). In general, the findings of this research indicated that the inclusion of 40 g kg-1 of SBP in the diet had a negative impact on performance and other physiological parameters. However, the use of SFH and 20 g kg-1 of SBP yielded similar results to birds in the CTL, and in some cases, even better outcomes.

Efficient nitrogen removal of decentralized rural sewage: Pilot-scale study of a novel push-flow coupled bio-ecological system

The performance and mechanisms for pollutant removal were investigated in an extended pilot-scale operation. Results demonstrated that the PF-EFB system maintained stable and efficient performance after over 450 days of continuous operation. Under various operating conditions, the total nitrogen (TN) concentration was reduced to <2 mg/L, and the removal rate exceeded 90 %. The effluent chemical oxygen demand (COD) concentration remained below 40 mg/L. Additionally, a combination of nitrogen transformation and molecular biology analyses was conducted to explore the mechanisms. The key bacterial groups driving system performance were aerobic and anoxic nitrifying bacteria, which dominated the microbial population. Microbial community analysis showed that the abundance of aerobic denitrifying bacteria in the middle of the system was 40.5 %, while the abundance of anoxic denitrifying bacteria at the end was 19.0 %. This spatial variation in the distribution of aerobic and anoxic denitrifying bacteria along the flow direction inside the reactor, driven by environmental factors, is key to the system's efficient denitrification. Overall, the PF-EFB system effectively addressed challenges posed by water flow fluctuations and enhanced nitrogen removal efficiency. This innovative system offers significant benefits and serves as a valuable reference for rural sewage treatment.

‘Altruistic’ cooperation among the prokaryotic community of Atlantic salterns assessed by metagenomics

Hypersaline environments are extreme habitats with a limited prokaryotic diversity, mainly restricted to halophilic or halotolerant archaeal and bacterial taxa adapted to highly saline conditions. This study attempts to analyze the taxonomic and functional diversity of the prokaryotes that inhabit a solar saltern located at the Atlantic Coast, in Isla Cristina (Huelva, Southwest Spain), and the influence of salinity on the diversity and metabolic potential of these prokaryotic communities, as well as the interactions and cooperation among the individuals within that community. Brine samples were obtained from different saltern ponds, with a salinity range between 19.5 % and 39 % (w/v). Total prokaryotic DNA was sequenced using the Illumina shotgun metagenomic strategy and the raw sequence data were analyzed using supercomputing services following the MetaWRAP and SqueezeMeta protocols. The most abundant phyla at moderate salinities (19.5–22 % [w/v]) were Methanobacteriota (formerly “Euryarchaeota”), Pseudomonadota and Bacteroidota, followed by Balneolota and Actinomycetota and Uroviricota in smaller proportions, while at high salinities (36–39 % [w/v]) the most abundant phylum was Methanobacteriota, followed by Bacteroidota. The most abundant genera at intermediate salinities were Halorubrum and the bacterial genus Spiribacter, while the haloarchaeal genera Halorubrum, Halonotius, and Haloquadratum were the main representatives at high salinities. A total of 65 MAGs were reconstructed from the metagenomic datasets and different functions and pathways were identified in them, allowing to find key taxa in the prokaryotic community able to synthesize and supply essential compounds, such as biotin, and precursors of other bioactive molecules, like β-carotene, and bacterioruberin, to other dwellers in this habitat, lacking the required enzymatic machinery to produce them. This work shed light on the ecology of aquatic hypersaline environments, such as the Atlantic Coast salterns, and on the dynamics and factors affecting the microbial populations under such extreme conditions.

Microbiota-Derived Extracellular Vesicle as Emerging Actors in Host Interactions.

The human microbiota is an intricate micro-ecosystem comprising a diverse range of dynamic microbial populations mainly consisting of bacteria, whose interactions with hosts strongly affect several physiological and pathological processes. The gut microbiota is being increasingly recognized as a critical player in maintaining homeostasis, contributing to the main functions of the intestine and distal organs such as the brain. However, gut dysbiosis, characterized by composition and function alterations of microbiota with intestinal barrier dysfunction has been linked to the development and progression of several pathologies, including intestinal inflammatory diseases, systemic autoimmune diseases, such as rheumatic arthritis, and neurodegenerative diseases, such as Alzheimer's disease. Moreover, oral microbiota research has gained significant interest in recent years due to its potential impact on overall health. Emerging evidence on the role of microbiota-host interactions in health and disease has triggered a marked interest on the functional role of bacterial extracellular vesicles (BEVs) as mediators of inter-kingdom communication. Accumulating evidence reveals that BEVs mediate host interactions by transporting and delivering into host cells effector molecules that modulate host signaling pathways and cell processes, influencing health and disease. This review discusses the critical role of BEVs from the gut, lung, skin and oral cavity in the epithelium, immune system, and CNS interactions.

Decoupling soil community structure, functional composition, and nitrogen metabolic activity driven by salinity in coastal wetlands

Coastal wetlands, being a multifaceted and crucial global ecosystem, are facing significant impacts from diverse environmental alterations, particularly soil salinization. Concurrently, the escalation of extreme climate events, such as global warming, presents complex challenges for the protection and restoration efforts. Previous researches concerning microbial communities in the context of climate with continous line numbering change have predominantly concentrated on their structural aspects, with limited attention given to establishing relationships between community structure and functional attributes. In this study, a two-year investigation was conducted on conventional coastal wetland ecosystems, considering variations in salinity and seasonal temperature. Utilizing high-throughput 16S rRNA sequencing, isotope technology, and other methods to explore the bacterial community, nitrogen cycling functional groups, and nitrogen reduction process. This research aims to assess the holistic impacts of significant global environmental changes on microbial communities. The results suggest that salinity, acting as an environmental filter, has a significant impact on the microbial community composition. It leads to a decrease in species abundance, an increase in deterministic processes and the nesting of community succession, while also reducing the stability of microbial ecological networks. The mechanism by which soil salinity impacts bacterial communities involves three main aspects: direct effects, positive climate regulation, and negative regulation of soil properties. Surprisingly, soil salinity exerts a mild inhibitory influence on microbial functional genes and metabolic activity. The primary factors involved in the nitrogen reduction process include electron donors/acceptors, types of nitrogen sources, and organic carbon. The three processes are interconnected due to the impact of environmental factors and signal transmission among microbial populations. This study offers a novel scientific framework for the rehabilitation and enhancement of saline-alkali coastal ecosystems in the face of impending global changes. It achieves this by investigating the varied response patterns exhibited by microbial communities and ecological functional metabolism under salinity-induced stress.