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Polluted drains across the globe are affected due to reckless disposal of untreated industrial effluents resulting in significant water pollution affecting microbial community structure/dynamics. To elucidate this, polluted samples were collected from Budha Nala (BN) drain, Tung Dhab (TD) drain, and wastewater treatment plant (WWTP) receiving an inflow of organic pollutants as well as heavy metals due to anthropogenic activities. The sample of unpolluted pristine soil (PS) was used as control, as there is no history of usage of organic chemicals at this site. The bacterial diversity of these samples was sequenced using the Illumina MiSeq platform by amplifying the V3/V4 region of 16S rRNA. The majority of operational taxonomic unit (OTUs) at polluted sites belonged to phyla Proteobacteria specifically Gammaproteobacteria class, followed by Actinobacteria, Bacteriodetes, Chloroflexi, Firmicutes, Planctomycetes, WS6, and TM7, whereas unpolluted site revealed the prevalence of Proteobacteria followed by Actinobacteria, Planctomycetes, Firmicutes, Acidobacteria, Chloroflexi, Bacteroidetes, Verrucomicrobia, and Nitrospirae. The data sets decode unclassified species of the phyla Proteobacteria, Bacteriodetes, Chloroflexi, Firmicutes, and WS6, along with some unclassified bacterial species. The study provided a comparative study of changed microbial community structure, their possible functions across diverse geographical locations, and identifying specific bacterial genera as pollution bio‐indicators of aged polluted drains. [ABSTRACT FROM AUTHOR]

Background: Maternal diet quality and quantity have significant impacts on both maternal and fetal health and development. The composition and function of the maternal gut microbiome is also significantly influenced by diet; however, little is known about the impact of gestational nutrient restriction on the bovine maternal microbiome during early gestation, which is a critical stage for maternal microbiome-mediated fetal programming to take place. The objective of the present study was to evaluate the impacts of diet restriction and one-carbon metabolite (OCM) supplementation during early gestation on maternal ruminal, vaginal, and blood microbiota in cattle. Thirty-three beef heifers (approx. 14 months old) were used in a 2 × 2 factorial experiment with main factors of target gain (control [CON]; targeted 0.45 kg/d gain vs restricted [RES]; targeted − 0.23 kg/d gain), and OCM supplementation (+ OCM vs − OCM; n = 8/treatment; except n = 9 for RES–OCM). Heifers were individually fed, starting treatment at breeding (d 0) and concluding at d 63 of gestation. Ruminal fluid and vaginal swabs were collected on d − 2, d 35, and d 63 (at necropsy) and whole blood was collected on d 63 (necropsy). Bacterial microbiota was assessed using 16S rRNA gene (V3–V4) sequencing. Results: Overall ruminal microbiota structure was affected by gain, OCM, time, and their interactions. The RES heifers had greater microbial richness (observed ASVs) but neither Shannon nor Inverse Simpson diversity was significantly influenced by gain or OCM supplementation; however, on d 63, 34 bacterial genera showed differential abundance in the ruminal fluid, with 25 genera enriched in RES heifers as compared to CON heifers. In addition, the overall interaction network structure of the ruminal microbiota changed due to diet restriction. The vaginal microbiota community structure was influenced by gain and time. Overall microbial richness and diversity of the vaginal microbiota steadily increased as pregnancy progressed. The vaginal ecological network structure was distinctive between RES and CON heifers with genera-genera interactions being intensified in RES heifers. A relatively diverse bacterial community was detected in blood samples, and the composition of the blood microbiota differed from that of ruminal and vaginal microbiota. Conclusion: Restricted dietary intake during early gestation induced significant alterations in the ruminal microbiota which also extended to the vaginal microbiota. The composition of these two microbial communities was largely unaffected by OCM supplementation. Blood associated microbiota was largely distinctive from the ruminal and vaginal microbiota. [ABSTRACT FROM AUTHOR]

Introduction: Seagrass-associated microbial communities play a crucial role in the growth and health of seagrasses. However, like seagrass meadows, seagrassassociated microbial communities are often affected by eutrophication. It remains unclear how eutrophication influences the composition and function of microbial communities associated with different parts of seagrass. Methods: We employed prokaryotic 16S rRNA gene high-throughput sequencing combining microbial community structure analysis and co-occurrence network analysis to investigate variances in microbial community compositions, potential functions and complexities across sediment, seagrass leaves, and seawater within different eutrophic areas of two adjacent seagrass meadows on Hainan Island, China. Results: Our results indicated that microbial diversity on seagrass leaves was significantly lower than in sediment but significantly higher than in seawater. Both sediment and phyllosphere microbial diversity showed no significant difference between the highly eutrophic and less eutrophic sites in each lagoon. However, sediment microbial diversity was higher in the more eutrophic lagoon, while phyllosphere microbial diversity was higher in the less eutrophic lagoon. Heavy eutrophication increased the relative abundance of phyllosphere microorganisms potentially involved in anaerobic metabolic processes, while reducing those responsible for beneficial functions like denitrification. The main factor affecting microbial diversity was organic carbon in seawater and sediment, with high organic carbon levels leading to decreased microbial diversity. The co-occurrence network analysis revealed that heavy eutrophication notably reduced the complexity and internal connections of the phyllosphere microbial community in comparison to the sediment and seawater microbial communities. Furthermore, ternary analysis demonstrated that heavy eutrophication diminished the external connections of the phyllosphere microbial community with the sediment and seawater microbial communities. Conclusion: The pronounced decrease in biodiversity and complexity of the phyllosphere microbial community under eutrophic conditions can lead to greater microbial functional loss, exacerbating seagrass decline. This study emphasizes the significance of phyllosphere microbial communities compared to sediment microbial communities in the conservation and restoration of seagrass meadows under eutrophic conditions. [ABSTRACT FROM AUTHOR]

Both regional species pool and local community assembly mechanism drive the microbial diversity patterns across geographical gradients. However, little has been done to separate their effects on the β diversity patterns of microbial communities involved in nitrogen (N) cycling in river ecosystems. Here, we use high‐throughput sequencing of the archaeal amoA, bacterial amoA, nirK, and nirS genes, null model, and neutral community model to distinguish the relative importance of species pool and local assembly processes for ammonia‐oxidizing and denitrifying communities in river wetlands along a latitudinal gradient in eastern China. Results indicated that the β diversity of the nirS‐type denitrifying community co‐varied with γ diversity and environmental heterogeneity, implying that regional species pool and heterogeneous selection explained variation in β diversity. However, the β diversity of ammonia‐oxidizing and nirK‐type denitrifying communities did not correlate with γ diversity and environmental heterogeneity. The continuous hump distribution of β deviation along the latitudinal gradient and the lower species dispersal rate indicated that the dispersal limitation shaped the variation in β diversity of ammonia‐oxidizing and nirK‐type denitrifying communities. Additionally, biotic interactions drove ammonia‐oxidizing and nirS‐type denitrifying communities by influencing species co‐occurrence patterns. Our study highlights the importance of regional species pool and local community assembly processes in shaping geographical patterns of N‐cycling microorganisms and extends knowledge of their adaptability to a continuously changing environment on a large scale. [ABSTRACT FROM AUTHOR]

In recent years, the salmon farming industry has grown significantly worldwide, and in the Faroe Islands, it has become a major industry with an annual production of over 94,000 tonnes, yielding 24% of the GDP. According to environmental regulations, the ocean floor is monitored during every production cycle at all farming sites, involving macrofaunal, sensory, and chemical analyses. However, the impact of farming activity on microorganisms in the Faroe Islands remains unknown. This study aimed to assess the impact of Atlantic salmon farming on benthic microbial communities, giving a better understanding of the effects on the foundation of the benthic food web and to assess if these are more prone to environmental impact than traditional macrofaunal biomonitoring. Sediment cores were sampled along a transect from directly below the salmon cages to a background reference site. The sampling occurred prior to the release of salmon into the cages ('before stocking') and immediately before the salmon were harvested ('peak biomass'). The 16S rRNA (V4-V5) gene was sequenced on an Illumina MiSeq from our sediment samples at the surface, 3 cm, and 10 cm depth. Significant shifts in microbial community composition were observed between 'before stocking' and 'peak biomass', as well as between different depth layers. Microbial diversity increased with increasing distance from the cages and was at its highest 'before stocking', indicating a significant impact of the salmon farming on the microbial community structure. In contrast to the regularly executed environmental monitoring, the results from this study showed an impact on the sediments by the salmon farming, underlining the powerful alternative of DNA-metabarcoding when biomonitoring an aquaculture area. [ABSTRACT FROM AUTHOR]

Vermicomposting utilizes the synergistic effect of earthworms with microorganisms to accelerate the stabilization of organic matter in biowastes. Nevertheless, the exact mechanism behind the maturity of vermicompost and the growth of earthworms exposed to biochar of varying particle sizes remains unclear. This study presents an investigation of the effect of biochar particle size on earthworm (Eisenia fetida) survival, microbial diversity, and the quality of vermicompost products. To address these issues, pelletized dewatered sludge samples from a municipal sewage treatment plant were amended with pine-based biochar with particle sizes of 1–2 mm, 25–75 μm, 200 nm, and 60 nm as the substrate for vermicomposting. This study revealed that the addition of millimeter-scale biochar and micron-scale biochar significantly promoted the degradation of organic matter since the organic matter in the treatment with 1–2 mm biochar at the end of the vermicomposting experiment decreased by 12.6%, which was equivalent to a 1.9-fold increase compared with that of the control. Excessive nanopowdering of nanobiochar significantly affected the survival of earthworms and led to 24.4–33.3% cumulative mortality, while millimeter-scale (mm) biochar and micron-scale (μm) biochar achieved zero mortality. The findings of this study could be used for evaluating the potential impact of nanoscale biochar to earthworms and guiding biochar-augmented vermicomposting. Highlights: The addition of 1–2 mm biochar resulted in a 1.9-fold greater reduction in organic matter compared to the control group. The introduction of 25–75 μm biochar led to a significant 94% increase in earthworm cocoons. The cumulative mortality rates of 200 nm and 60 nm biochar amendment reached peaks of 33.3% and 24.4% at first week, respectively. Earthworms excrete mucus that effectively removes attached nanobiochar. [ABSTRACT FROM AUTHOR]

Simple Summary: Rodents, as the most abundant group of mammals, offer a unique opportunity to study the relationship between diet and host gut microecology. In this study, we focused on two species of the genus Myospalax in the Eurasian steppes in China: M. psilurus and M. aspalax. These specialized herbivorous rodents have adapted to a subterranean lifestyle and exhibit distinct dietary choices. Our study aimed to investigate how their diet composition is related to their gut microbial communities and whether there are unique indicator species for their gut microecology. Using 16S amplicon technology and macro-barcoding technology, we analyzed the gut bacterial communities and diet composition of the two zokor species. We found that M. psilurus had a higher diversity of gut microbial bacterial communities compared to M. aspalax. The two species also possessed different gut bacterial indicator species, with unique relationships between their diet and gut microbes. Our results provide new insights into the adaptation of zokors to long-term subterranean life and shed light on their cellulose degradation abilities and ecological niches. As the most abundant group of mammals, rodents possess a very rich ecotype, which makes them ideal for studying the relationship between diet and host gut microecology. Zokors are specialized herbivorous rodents adapted to living underground. Unlike more generalized herbivorous rodents, they feed on the underground parts of grassland plants. There are two species of the genus Myospalax in the Eurasian steppes in China: one is Myospalax psilurus, which inhabits meadow grasslands and forest edge areas, and the other is M. aspalax, which inhabits typical grassland areas. How are the dietary choices of the two species adapted to long-term subterranean life, and what is the relationship of this diet with gut microbes? Are there unique indicator genera for their gut microbial communities? Relevant factors, such as the ability of both species to degrade cellulose, are not yet clear. In this study, we analyzed the gut bacterial communities and diet compositions of two species of zokors using 16S amplicon technology combined with macro-barcoding technology. We found that the diversity of gut microbial bacterial communities in M. psilurus was significantly higher than that in M. aspalax, and that the two species of zokors possessed different gut bacterial indicator genera. Differences in the feeding habits of the two species of zokors stem from food composition rather than diversity. Based on the results of Mantel analyses, the gut bacterial community of M. aspalax showed a significant positive correlation with the creeping-rooted type food, and there was a complementary relationship between the axis root-type-food- and the rhizome-type-food-dominated (containing bulb types and tuberous root types) food groups. Functional prediction based on KEGG found that M. psilurus possessed a stronger degradation ability in the same cellulose degradation pathway. Neutral modeling results show that the gut flora of the M. psilurus has a wider ecological niche compared to that of the M. aspalax. This provides a new perspective for understanding how rodents living underground in grassland areas respond to changes in food conditions. [ABSTRACT FROM AUTHOR]

Organic management enhances the formation of distinct and stable soil microbial communities, however, its influence on the temporal recovery of microbiome and multifunctionality of sterilized soil remains poorly understood. We used amplicon sequencing and metagenomic sequencing to investigate the effects of microbial communities in long‐term organic and conventional managed soils on restoring soil microbiome and functionality. We calculated multifunctionality of soils at days 30 and 90 of recolonization using the averaging approach. Results showed that organic management (O) significantly increased alpha diversity, niche width and network complexity of microbial community compared to conventional management (C). The alpha diversity, niche width and network complexity of microbial community in soils with organic soil suspension were significantly increased compared to conventional management at days 30 and 90 of recolonization. Soil multifunctionality of sterilized organic managed soil inoculated with organic soil suspension (OO) was 14.6% to 70.6% higher than that of the rest treatments. Macrogenomic analysis revealed that O significantly enriched functional pathways of ABC transporters, carbon metabolism, biosynthesis of amino acids, two‐component and nitrogen metabolism as well as most of the functional genes for carbon degradation, carbon fixation, nitrogen cycling and phosphorus cycles compared to C. These functional pathways and genes were also significantly enriched in soils with organic soil suspension at day 30 and 90 of recolonization. Furthermore, alpha diversity, niche width, network complexity, functional pathways and functional genes of microbiome correlated positively with soil multifunctionality. Synthesis and applications. Our results emphasize the importance of organic management induced changes in diversity, network complexity, and functionality of microbial communities for promoting recovery to soil microbial and functional losses, providing the theoretical basis for sustainable impact of organic management in agronomic production on soil microbiome and function. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

Background: Penicillium oxalicum is an important fungal agent in the composting of cattle manure, but the changes that occur in the microbial community, physicochemical factors, and potential functions of microorganisms at different time points are still unclear. To this end, the dynamic changes occurring in the microbial community and physicochemical factors and their correlations during the composting of cattle manure with Penicillium oxalicum were analysed. Results: The results showed that the main phyla observed throughout the study period were Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, Halanaerobiaeota, Apicomplexa and Ascomycota. Linear discriminant analysis effect size (LEfSe) illustrated that Chitinophagales and Eurotiomycetes were biomarker species of bacteria and eukaryote in samples from Days 40 and 35, respectively. Bacterial community composition was significantly correlated with temperature and pH, and eukaryotic microorganism community composition was significantly correlated with moisture content and NH4+-N according to redundancy analysis (RDA). The diversity of the microbial communities changed significantly, especially that of the main pathogenic microorganisms, which showed a decreasing trend or even disappeared after composting. Conclusions: In conclusion, a combination of high-throughput sequencing and physicochemical analysis was used to identify the drivers of microbial community succession and the composition of functional microbiota during cattle manure composting with Penicillium oxalicum. The results offer a theoretical framework for explaining microecological assembly during cattle manure composting with Penicillium oxalicum. [ABSTRACT FROM AUTHOR]

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This study was undertaken in order to explore the correlation between the quality changes and microbial community in sauced duck necks during cold storage. Commercial sauced duck necks in modified atmosphere packaging were stored at 4 °C for 1, 4, 7, 10, and 13 days, and the changes in pH, thiobarbituric acid reactive substances (TBARS) value, color, texture, total bacterial count, total volatile base nitrogen (TVB-N) content, and microbial community were analyzed. The results showed that the pH initially decreased and then increased with storage time, while brightness (L*), redness (a*), yellowness (b*) and hardness exhibited a decreasing trend, and elasticity, chewiness, cohesiveness and adhesiveness showed an initial increase followed by a decrease. The total bacterial count, TVB-N and TBARS values all gradually increased during storage, with the total bacterial count and TVB-N exceeding the acceptable limits on the 10th day. Microbial diversity diminished gradually with storage time. At the initial stage of storage, the dominant bacteria were Rhodococcus, Acinetobacter, Ureibacillus and Symbiobacterium, while those in the late storage period were Rhodococcus, Acinetobacter, Leuconostoc and Lactobacillus. Principal co-ordinate analysis indicated the two principal coordinates explained 74.03% of the variation, and differences in microbial community composition occurred after 4 days of storage. Correlation analysis showed that Leuconostoc was positively correlated with pH, total bacterial count, TVB-N content and TBARS value during cold storage of sauced duck necks, indicating that Leuconostoc was the primary spoilage bacteria during storage. [ABSTRACT FROM AUTHOR]

Introduction: Inside oil and gas pipelines, native microbial communities and different solid compounds typically coexist and form mixed deposits. However, interactions between these deposits (primarily consisting of mineral phases) and microorganisms in oil and gas systems remain poorly understood. Here, we investigated the influence of magnetite (Fe3O4), troilite (FeS), and silica (SiO2) on the microbial diversity, cell viability, biofilm formation, and EPS composition of an oil-recovered multispecies consortium. Methods: An oilfield-recovered microbial consortium was grown for 2 weeks in separate bioreactors, each containing 10 g of commercially available magnetite (Fe3O4), troilite (FeS), or silica (SiO2) at 40°C ± 1°C under a gas atmosphere of 20% CO2/80% N2. Results: The microbial population formed in troilite significantly differed from those in silica and magnetite, which exhibited significant similarities. The dominant taxa in troilite was the Dethiosulfovibrio genus, whereas Sulfurospirillum dominated in magnetite and silica. Nevertheless, biofilm formation was lowest on troilite and highest on silica, correlating with the observed cell viability. Discussion: The dissolution of troilite followed by the liberation of HS- (H2S) and Fe2+ into the test solution, along with its larger particle size compared to silica, likely contributed to the observed results. Confocal laser scanning microscopy revealed that the EPS of the biofilm formed in silica was dominated by eDNA, while those in troilite and magnetite primarily contained polysaccharides. Although the mechanisms of this phenomenon could not be determined, these findings are anticipated to be particularly valuable for enhancing MIC mitigation strategies currently used in oil and gas systems. [ABSTRACT FROM AUTHOR]

The Yongle blue hole (YBH), situated in the South China Sea, represents a compelling subject of study in marine microbiology due to its unique redoxlayered microbial ecosystems. However, the diversity and ecology of microbial eukaryotes within the YBH remains underexplored. This study endeavors to bridge this gap through the application of the in situ microbial filtration and fixation (ISMIFF) device to collect 0.22-30 µm microbial samples from 21 water layers of YBH. Subsequent extraction of 18S rRNA metagenomic reads of 21 metagenomes and 10 metatranscriptomes facilitated a comprehensive analysis of community structures. Findings revealed a pronounced superiority in the diversity and richness of eukaryotic microorganisms in the oxic zone compared to its suboxic and anoxic counterparts. Notably, Dinophyceae and Maxillopoda emerged as the predominant taxa based on the analysis of the 18S rRNA reads for the V4 and V9 regions, which showed stratification In their relative abundance and suggested their potential role in the thermohalocline boundaries and oxic-anoxic interface. Specifically, In these eukaryotic microbial communities, Dinophyceae exhibited significant abundance at 20 m (20.01%) and 105 m (26.13%) water depths, while Maxillopoda was prevalent at 40 m (22.84%), 80 m (23.19%), and 100 m (15.42%) depths. A part of these organisms, identified as larvae and protists, were likely attracted by swarming chemosynthetic bacterial prey prevailing at the thermo-halocline boundaries and oxic-anoxic interface. Furthermore, the phylogenetic relationships of the major 18S operational taxonomic units (OTUs) showed a close adjacency to known species, except for three Dinophyceae OTUs. In conclusion, this study provides critical insights into the vertical distribution and transcriptional activity of <30-µm eukaryotic microbes, shedding light on the taxonomic novelty of eukaryotic microorganisms within the semi-enclosed blue holes. [ABSTRACT FROM AUTHOR]

The Eastern Pamir, distinguished with high altitude, extremely arid and cold climate, limited nutrients and sparse vegetation, is a unique ecological reservoir. Microbial communities play a central role in maintaining Eastern Pamir's ecosystem functioning. Despite the ecological significance, due to the difficulty of sample collection and microbial isolation, the microbial diversity and its functionality at the Pamir Plateau have been rarely documented. To fill this gap, 80 soil samples from 17 sites across different elevations were collected, performed the rDNA amplicon sequencing to present the first large-scale overview of bacterial, archaeal, and fungal communities in the Eastern Pamir. Microbiome analysis revealed that the bacteria Actinobacteria, Alphaproteobacteria and Bacteroidia, alongside such as archaea Nitrososphaeria and Halobacteria, and fungi including Dothideomycetes, Sordariomycetes and Eurotiomycetes were dominant lineages at class level in soil microbial communities. The community structure and biodiversity of soil microorganisms provided by this dataset would be pivotal for future studies aimed at understanding the biogeographical distribution, ecological functions and environmental responses of microbial communities of the Pamir Plateau. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The single-cycle transient high-concentration organic load shock test was conducted on the micropressure swirl reactor (MPSR) and sequencing batch reactor (SBR) to assess their capability to different levels of transient organic load shock (OLS), including pollutant removal, sludge characteristics, and microbial characteristics. The results indicated that the impact-resistance of biological treatment systems was related to reactor structure and microbial community distribution. When subjected to transient chemical oxygen demand (COD) load of 0.81, 1.28, and 1.70 g / (L · d a y) , respectively, both reactors exhibited effective organic removal capabilities. Compared with MPSR, within a certain shock range, nitrification in the SBR was less affected by shock and had a higher effect on nitrogen and phosphorus removal. However, when shock load reached 1.70 gCOD/(L·day) , the denitrification was sufficient in the MPSR, and microorganisms continued to secrete polysaccharides (PS), which was beneficial for adsorbing pollutants and resisting impacts. Under steady-state conditions, the SBR exhibited excellent nitrification with a relative abundance of 60.7% for nitrifying functional groups such as Thiothrix. Compared with the SBR, the MPSR displayed a higher microbial community diversity, with a variety of phosphorus-removing bacteria and denitrifying bacteria genera occupying aerobic and anoxic partitions within the same space, which was profitable for effective denitrification and phosphorus removal under high OLS. Besides, the enrichment of Flavobacterium and Zoogloea sp. at high concentrations significantly enhanced the MPSR's resistance to OLS. This study provides a theoretical basis for effective measures by different processes in response to organic load shocks. [ABSTRACT FROM AUTHOR]

Atmospheric nitrogen (N) deposition has been substantially reduced due to declines in the reactive N emission in major regions of the world. Nevertheless, the impact of reduced N deposition on soil microbial communities and the mechanisms by which they are regulated remain largely unknown. Here, we examined the effects of N addition and cessation of N addition on plant and soil microbial communities through a 17‐year field experiment in a temperate grassland. We found that extreme N input did not irreversibly disrupt the ecosystem, but ceasing high levels of N addition led to greater resilience in bacterial and fungal communities. Fungi exhibited diminished resilience compared to bacteria due to their heightened reliance on changes in plant communities. Neither bacterial nor fungal diversity fully recovered to their original states. Their sensitivity and resilience were mainly steered by toxic metal ions and soil pH differentially regulating on functional taxa. Specifically, beneficial symbiotic microbes such as N‐fixing bacteria and arbuscular mycorrhizal fungi experienced detrimental effects from toxic metal ions and lower pH, hindering their recovery. The bacterial functional groups involved in carbon decomposition, and ericoid mycorrhizal and saprotrophic fungi were positively influenced by soil metals, and demonstrated gradual recovery. These findings could advance our mechanistic understanding of microbial community dynamics under ongoing global changes, thereby informing management strategies to mitigate the adverse effects of N enrichment on soil function. [ABSTRACT FROM AUTHOR]

Xuanwei ham is a traditional fermented meat product in China with a unique production process and excellent-quality reputation at home and abroad. To reveal the microbial community succession of Xuanwei ham at different post-ripening times (W1-4) and its relationship with flavour formation, the microbial community, free amino acids, and volatile flavour compounds (VOCs) were analysed by high-throughput sequencing, liquid chromatography (LC), and gas chromatography–mass spectrometry (GC-MS), respectively. A total of 25 free amino acids were detected, among which W3 contained the fewest, and most were generally lower than in hams in the other three years. Fifty-nine VOCs were detected, among which 17 were esters, and the highest ester content was found in W4. Analysis of the bacterial community composition revealed that the bacterial community composition of ham samples from W3 and other years differed greatly, and at the gate level, the dominant bacterial group of Xuanwei ham from different years was Pseudomonadota. At the genus level, the most abundant genera in W1, W2, and W4 were all dominated by Sarocladium, Klebsiella, and Vibrio, with Klebsiella being the most abundant in W1. The most abundant genus in W3 was Vibrio, and the second most dominant genera were Sarocladium and Gammaretrovirus. In short, this study provides a theoretical basis for the storage, quality, and improvement of Xuanwei ham. [ABSTRACT FROM AUTHOR]

Coffee is a critical agricultural commodity and is used to produce premium beverages enjoyed by people worldwide. The microbiome of coffee beans has proven to be an essential tool that improves the flavor profile of coffee by creating aromatic flavor compounds through natural fermentation. This study investigated the natural microbial consortium during the wet process fermentation of coffee onsite in Thailand in order to identify the correlation between microbial diversity and biochemical characteristics including flavor, aroma, and metabolic attributes. Our study found 64 genera of bacteria and 59 genera of yeast/fungi present during the fermentation process. Group of microbes, mainly yeast and lactic acid bacteria, that predominated in the process were significantly correlated with preferable flavor and aroma compounds, including linalyl formate, linalool, cis-isoeugenol, trans-geraniol, and (-)-isopulegol. Some of the detected metabolites were found to be active compounds which could play a role in health. [ABSTRACT FROM AUTHOR]

Deschampsia antarctica Desv. and Poa annua L. are two Poaceae plants with enough endurance to successfully establish populations in the Antarctic region. Their adaptation to the Antarctic environment is closely linked to root-associated microbial communities. In this study, we obtained 16S rRNA sequencing data of the root-associated microbial communities of these two Poaceae plants from NCBI. Meta-analysis was used to investigate the similarities and differences between the root endosphere and rhizosphere-dwelling microbial communities in these two Poaceae plants. Here we report that two Poaceae-Poaceae plants' rhizospheric communities were found to be more species diversity than endospheric communities. The species diversity of P. annua was higher than that of D. antarctica in both endosphere and rhizosphere communities. Seven bacterial families form a core microbiome of two Antarctic Poaceae plants' root endosphere, in which Microbacteriaceae appears to be obligatory root endophytes of the two Antarctic Poaceae plants. The core microbiome of the two Poaceae plants' rhizosphere has six bacterial families. Chitinophagaceae, Burkholderiaceae, and Flavobacteriaceae are most likely to play a crucial role in Poaceae plants' adaptation to cold Antarctic conditions. Sphingobacteriaceae, Caulobacteraceae, Gemmatimonadaceae, and Flavobacteriaceae have a great influence on two Antarctic Poaceae plants. [ABSTRACT FROM AUTHOR]

Plant leaves harbor a rich diversity of bacteria and fungi that, through their interactions with host plants, assume an influential role in plant physiological and metabolic processes. The unique phyllosphere environment of different plant species may shape and select distinct phyllosphere microbial communities. While most academic research has focused on the phyllosphere microorganisms within the same plant variety, there is relatively limited research on the phyllosphere microbial communities between different varieties. Populus L. is a typical tree species in temperate monsoon climates, widely distributed in northern China, and it constitutes a crucial component of China's forestry resources. For the purpose of this study, we investigated the community structure and diversity of phyllosphere fungi and bacteria in different poplar varieties under identical growth conditions to elucidate the main factors contributing to differences in phyllosphere microbial communities among these varieties. Our findings revealed variations in nitrogen, phosphorus, starch, and soluble sugar contents among the three poplar species studied. Additionally, there were considerable disparities in both abundance and α diversity index of phyllosphere fungal and bacterial communities among these species. At the phylum level, Ascomycota and Basidiomycota have been identified as the dominant fungal communities; while Proteobacteria and Actinomycetes were dominant bacterial communities. The correlation analysis pointed out that chemical traits in the leaves, in particular the total phosphorus and the quantity of soluble sugar, had a significant correlation with the structure and diversity of the microbial community residing in the phyllosphere. Overall, our results demonstrate that even under identical site conditions, each poplar species harbors its own unique phyllosphere microbial community composition as well as distinct leaf characteristics—highlighting host plant diversity as a crucial factor driving differences in phyllosphere microbial composition. [ABSTRACT FROM AUTHOR]

Growing evidence suggests that the hydrochemical properties of geothermal fumaroles may play a crucial role in shaping the diversity and functions of microbial communities in various environments. In the present study, the impact of geothermal furaneols on the microbial communities and their metabolic functions across the rock‐soil‐plant continuum was explored considering varying distances from the fumarole source. The results revealed that bacterial phylum Proteobacteria was predominant in all sample types, except in the 10 m rock sample, irrespective of the sampling distance. Archaeal phyla, such as Euryarchaeota and Crenarchaeota, were more prevalent in rock and soil samples, whereas bacterial phyla were more prevalent in plant samples. Thermoacidophilic archaeons, including Picrophilus, Ferroplasma, and Thermogymnomonas were dominant in rocks and soil samples of 1 and 5 m distances; acidophilic mesophiles, including Ferrimicrobium and Granulicella were abundant in the rhizoplane samples, whereas rhizosphere‐associated microbes including Pseudomonas, Pedobacter, Rhizobium, and Novosphingobium were found dominant in the rhizosphere samples. The functional analysis highlighted the higher expression of sulfur oxidative pathways in the rock and soil samples; dark iron oxidation and nitrate/nitrogen respiratory functions in the rhizosphere samples. The findings underscore microbial adaptations across the rock‐soil‐plant continuum, emphasizing the intricate relationship between geothermal fumaroles and microbial communities in adjacent ecosystems. These insights offer a crucial understanding of the evolution of microbial life and highlight their pivotal roles in shaping ecosystem dynamics and functions. [ABSTRACT FROM AUTHOR]

Seawater intrusion significantly affects the microbial communities within coastal aquifers. Investigating the spatial distribution of groundwater microbial communities in coastal regions is crucial for understanding seawater intrusion. The primary objective of this study is to develop a novel microbial index-based method for detecting seawater intrusion. Groundwater microbial samples were collected and sent to the laboratory in the west coastal area of Longkou City, Shandong Province. By characterizing the microbial community within the whole interval of seawater intrusion into fresh groundwater and discussing the effects of salt-freshwater displacement intensities on groundwater microbial communities, including diversity, structure, and function, using indoor domestication experiments, we reveal the response of microorganisms to the seawater intrusion process under in situ environmental conditions. The results show that the microbial community diversity is highest in environments with a seawater mixing proportion (P(sm)) of 2.5% and lowest in those with a P(sm) of 75%. When considering species abundance and evolutionary processes, the microbial community structure is similar at higher P(sm) levels, while it is similar at lower P(sm) levels based on the presence or absence of species. Tenericutes, Flavobacteriia, Rhodobacterales, Flavobacteriales, Rhodobacteraceae, Flavobacteriaceae, Cohaesibacteraceae, and Cohaesibacter are significantly positively correlated with the P(sm). Strong salt-freshwater displacement enhanced the richness and evenness of the microbial community, whereas weak displacement showed the opposite trend. Strong displacement affects the functional profiles of the microbial community. This study effectively addressed the challenge of obtaining samples in coastal areas and also incorporated salt-freshwater displacement intensities, which can more comprehensively describe the microbial community characteristics within the groundwater of coastal aquifers. [ABSTRACT FROM AUTHOR]

Simple Summary: After piglet weaning, with the exposure to the inherent stress of this productive stage, the intestinal microbiota experiences an imbalance, resulting in a loss of beneficial microbial diversity and the development of potentially pathogenic or opportunistic bacteria. This leads to diarrhea and a decrease in the productivity and parameters of intestinal integrity and health. To address this issue, growth-promoting antibiotics have been used. However, in recent years, the search for nutraceutical compounds that can improve intestinal microbial balance and, thus, reduce antibiotic use has become important. In this regard, the effect of four nutraceutical compounds on piglet intestinal microbiota was evaluated for 30 days post-weaning. Following bioinformatic analyses, we report that essential oil from Lippia origanoides and short-chain fructo-oligosaccharides showed promising effects in reducing weaning-induced intestinal dysbiosis, with a decrease in potentially pathogenic taxa and an increase in bacteria associated with improved productivity and morphometric variables of the intestine, as well as the expression of intestinal barrier proteins. These findings elucidate the mechanisms of microbiota modulation by these compounds, aiming to reduce the use of prophylactic antibiotics and promoting the development of new studies focused on exploring metabolic changes in intestinal microbial communities. Due to the challenge of weaning pigs and the need to reduce the use of antimicrobials in animal feed, there is a growing need to look for nutraceutical alternatives to reduce the adverse effects of the post-weaning period. We evaluate the effect of different feed nutraceutical additives on the microbial communities, gut health biomarkers, and productivity of pigs during the post-weaning period. The study involved 240 piglets weaned on the 21st day of age and randomized to six different diets: D1-BD commercial standard feed, D2-AGP: D1 + 150 ppm zinc bacitracin, D3-MD: D1 + 550 ppm maltodextrin, D4-FOS: D1 + 300 ppm fructo-oligosaccharides, D5-EO: D1 + 70 ppm Lippia origanoides essential oil, and D6-SH: D1 + 750 ppm sodium humate. On day 30 post-weaning, zootechnical parameters were evaluated, and jejunal samples were taken to obtain morphometric variables, expression of barrier and enzymatic proteins, and analysis of microbial communities. Animals fed D4-FOS and D5-EO had the lowest feed conversion ratio and higher expression of barrier and enzymatic proteins compared to D1-BD, D2-AGP, and D3-MD. The use of the additives modified the gut microbial communities of the piglets. In conclusion, fructo-oligosaccharides and Lippia origanoides essential oil were the best alternatives to zinc bacitracin as antibiotic growth promoters. [ABSTRACT FROM AUTHOR]

Objective Method Results Conclusion Exploring the effects of age on microbial community structure and understanding the effects of chronological ageing as well as sun exposure on microbial community diversity.The microbial characteristics of the facial skin of 98 adult women aged 18–70 years were studied using 16S rRNA gene sequencing, and differences based on age and reported sun exposure were assessed.The cheek skin's bacterial diversity and richness increased with age. The relative abundance of Cutibacterium decreased with age, while the relative abundance of Corynebacterium, Anaerococcus, Paracoccus, Micrococcus, Kocuria, Kytococcus, and Chryseobacterium increased. In addition, an increase in Micrococcus and a decrease in Cutibacterium were observed in volunteers with more than 2 h of daily sun exposure compared to volunteers with <2 h of daily sun exposure. Under low‐sunlight conditions, Cutibacterium was more prevalent in the youth group, and Corynebacterium, Anaerococcus, and Kytococcus were more prevalent in the older group.The diversity and composition of the bacterial community on the cheeks are affected by age and extrinsic factors (sun exposure) may also play a role in this. [ABSTRACT FROM AUTHOR]

Background: The establishment of microbial communities in neonatal mammals plays a pivotal role in shaping their immune responses to infections and other immune-related conditions. This process is influenced by a combination of endogenous and exogenous factors. Previously, we reported that depletion of CD71 + erythroid cells (CECs) results in an inflammatory response to microbial communities in newborn mice. Results: Here, we systemically tested this hypothesis and observed that the small intestinal lamina propria of neonatal mice had the highest frequency of CECs during the early days of life. This high abundance of CECs was attributed to erythropoiesis niches within the small intestinal tissues. Notably, the removal of CECs from the intestinal tissues by the anti-CD71 antibody disrupted immune homeostasis. This disruption was evident by alteration in the expression of antimicrobial peptides (AMPs), toll-like receptors (TLRs), inflammatory cytokines/chemokines, and resulting in microbial dysbiosis. Intriguingly, these alterations in microbial communities persisted when tested 5 weeks post-treatment, with a more notable effect observed in female mice. This illustrates a sex-dependent association between CECs and neonatal microbiome modulation. Moreover, we extended our studies on pregnant mice, observing that modulating CECs substantially alters the frequency and diversity of their microbial communities. Finally, we found a significantly lower proportion of CECs in the cord blood of pre-term human newborns, suggesting a potential role in dysregulated immune responses to microbial communities in the gut. Conclusions: Our findings provide novel insights into pivotal role of CECs in immune homeostasis and swift adaptation of microbial communities in newborns. Despite the complexity of the cellular biology of the gut, our findings shed light on the previously unappreciated role of CECs in the dialogue between the microbiota and immune system. These findings have significant implications for human health. 9S5HPFpJwLA9vyqyoAGSTR Video Abstract [ABSTRACT FROM AUTHOR]

To accurately define the role of the gut microbiota in health and disease pathogenesis, the preservation of stool sample integrity, in terms of microbial community composition and metabolic function, is critical. This presents a challenge for any studies which rely on participants self-collecting and returning stool samples as this introduces variability and uncertainty of sample storage/handling. Here, we tested the performance of three stool sample collection/preservation buffers when storing human stool samples at different temperatures (room temperature [20 °C], 4 °C and – 80 °C) for up to three days. We compared and quantified differences in 16S rRNA sequencing composition and short-chain fatty acid profiles compared against immediately snap-frozen stool. We found that the choice of preservation buffer had the largest effect on the resulting microbial community and metabolomic profiles. Collectively analysis confirmed that PSP and RNAlater buffered samples most closely recapitulated the microbial diversity profile of the original (immediately – 80 °C frozen) sample and should be prioritised for human stool microbiome studies. [ABSTRACT FROM AUTHOR]

Methane-oxidizing bacteria (MOB) is a group of planktonic microorganisms that use methane as their primary source of cellular energy. For tropical lakes in monsoon Asia, there is currently a knowledge gap on MOB community diversity and the factors influencing their abundance. Herewith, we present a preliminary assessment of the MOB communities in three maar lakes in tropical monsoon Asia using Catalyzed Reporter Deposition, Fluorescence In-Situ Hybridization (CARD-FISH), 16S rRNA amplicon sequencing, and pmoA gene sequencing. Correlation analysis between MOB abundances and lakes' physicochemical parameters following seasonal monsoon events were performed to explain observed spatial and temporal patterns in MOB diversity. The CARD-FISH analyses detected the three MOB types (I, II, and NC10) which aligned with the results from 16S rRNA amplicons and pmoA gene sequencing. Among community members based on 16S rRNA genes, Proteobacterial Type I MOB (e.g., Methylococcaceae and Methylomonadaceae), Proteobacterial Type II (Methylocystaceae), Verrucomicrobial (Methylacidiphilaceae), Methylomirabilota/NC10 (Methylomirabilaceae), and archaeal ANME-1a were found to be the dominant methane-oxidizers in three maar lakes. Analysis of microbial diversity and distribution revealed that the community compositions in Lake Yambo vary with the seasons and are more distinct during the stratified period. Temperature, DO, and pH were significantly and inversely linked with type I MOB and Methylomirabilota during stratification. Only MOB type I was influenced by monsoon changes. This research sought to establish a baseline for the diversity and ecology of planktonic MOB in tropical monsoon Asia to better comprehend their contribution to the CH4 cycle in tropical freshwater ecosystems. [ABSTRACT FROM AUTHOR]

Objective: Rhizosphere microorganisms play crucial roles in the growth and development of plants, disease resistance, and environmental adaptability. As the only wild pepper variety resource in China, domesticated Capsicum frutescens Linn. (Xiaomila) exhibits varying beneficial traits and affects rhizosphere microbial composition compared with its wild counterparts. In this study, we aimed to identify specific rhizosphere microbiome and metabolism patterns established during the domestication process. Methods: The rhizosphere microbial diversity and composition of domesticated and wild C. frutescens were detected and analyzed by metagenomics. Non-targeted metabolomics were used to explore the differences of metabolites in rhizosphere soil between wild and domesticated C. frutescens. Results: We found that the rhizosphere microbial diversity of domesticated variety was significantly different from that of the wild variety, with Massilia being its dominant bacteria. However, the abundance of certain beneficial microbes such as Gemmatimonas, Streptomyces, Rambibacter, and Lysobacter decreased significantly. The main metabolites identified in the wild variety included serylthreonine, deoxyloganic acid, vitamin C, among others. In contrast, those identified in the domesticated group were 4-hydroxy-L-glutamic acid and benzoic acid. Furthermore, the differentially enriched pathways were concentrated in tyrosine and tryptophan biosynthesis, histidine and purinederived alkaloids biosynthesis, benzoic acid family, two-component system, etc. Conclusion: This study revealed that C. frutescens established specific rhizosphere microbiota and metabolites during domestication, which has important significance for the efficient utilization of beneficial microorganisms in breeding and cultivation practices. [ABSTRACT FROM AUTHOR]

TGase-7S gels prepared after different HIU pretreatment times were used to intervene in healthy mice to analyze their effects on growth characteristics and intestinal morphology, and 16S rRNA high-throughput sequencing was applied to fecal samples to investigate the effects of the gel on the structure and diversity of intestinal flora in mice. The results showed that the intestinal tissues of mice in different treatment groups showed better integrity, and the intake of gel increased the length of small intestinal villi in mice, among which the 30-gel group had the highest value of villi length (599.27 ± 44.28) μm (p < 0.05) and showed the neatest and tightest arrangement, indicating that the intake of gel did not have adverse effects on the intestinal tract. The effect of gel ingestion on the diversity of the intestinal microbial community structure was more significant, positively promoting the growth of beneficial bacteria such as Desferriobacterium, Synechococcus, and Bifidobacterium. In addition, the ingestion of the gel improved the intestinal health of mice by altering the physiological functions of the intestinal flora and modulating their participation in various metabolic pathways. The above findings provide some theoretical value for the safety of 7S gel in food applications. [ABSTRACT FROM AUTHOR]

The benefits of urban green space are socially widely recognized as a direct link between plant–microbe interactions and the maintenance of biodiversity, community stability, and ecosystem functioning. Nevertheless, there is a lack of knowledge about the factors influencing microbial communities in urban green spaces, especially those related to phyllosphere epiphytes and stem epiphytes. In this study, we analyzed the microbial community assembly in leaf and stem bark samples collected from Square, Road, Campus, and Park. Illumina sequecing of 16S amplicons was performed to characterize microbial diversity and composition. The α-diversity was significantly higher in the bark epiphytic community, compared to the phyllosphere. Moreover, urban greenspaces'type altered the way communities gathered. The main soil and air properties factors of the urban greenhouse (e.g. soil temperature, atmospheric moisture, air temperature) were shaping the characteristics of bacterial communities on the leaf surface and bark epiphytic. In addition, in the co-occurrence network analysis, keystone taxa were not mostly observed in abundant species, which may be necessary to maintain ecosystem functions. Finally, our findings provide a deeper understanding of the ecological dynamics and microbial interactions within plant phyllosphere and stem epiphytes microbiomes. [ABSTRACT FROM AUTHOR]

Background: Microbiomes are generally characterized by high diversity of coexisting microbial species and strains, and microbiome composition typically remains stable across a broad range of conditions. However, under fixed conditions, microbial ecology conforms with the exclusion principle under which two populations competing for the same resource within the same niche cannot coexist because the less fit population inevitably goes extinct. Therefore, the long-term persistence of microbiome diversity calls for an explanation. Results: To explore the conditions for stabilization of microbial diversity, we developed a simple mathematical model consisting of two competing populations that could exchange a single gene allele via horizontal gene transfer (HGT). We found that, although in a fixed environment, with unbiased HGT, the system obeyed the exclusion principle, in an oscillating environment, within large regions of the phase space bounded by the rates of reproduction and HGT, the two populations coexist. Moreover, depending on the parameter combination, all three major types of symbiosis were obtained, namely, pure competition, host-parasite relationship, and mutualism. In each of these regimes, certain parameter combinations provided for synergy, that is, a greater total abundance of both populations compared to the abundance of the winning population in the fixed environment. Conclusions: The results of this modeling study show that basic phenomena that are universal in microbial communities, namely, environmental variation and HGT, provide for stabilization and persistence of microbial diversity, and emergence of ecological complexity. [ABSTRACT FROM AUTHOR]

Soil organisms play a key role in carbon and nutrient cycling in forest ecosystems. While soil organisms are strongly influenced by litter chemistry and are highly sensitive to abiotic conditions, little is known about the interactive effects of these two factors. To address this gap in knowledge, we conducted a 10 week microcosm experiment in which we simulated the effects of climate change on soil ecology. More specifically, we studied relationships among litter nutrient concentration, microbial biomass, Collembola demographic parameters, and litter decomposition, exploring the potential impacts of increasing air temperature and decreasing soil moisture. To develop a gradient of nutrient concentrations, we created six tree litter mixtures with materials gathered from Quercus pubescens and its companion species. In contrast to microbes, we observed that Collembola abundance and litter decomposition were interactively affected by soil moisture and air temperature: the negative effect of increasing air temperature on Collembola abundance was amplified by reduced soil moisture, whereas the positive effect of increasing air temperature on litter decomposition disappeared under reduced soil moisture conditions. In contrast to fungi, the response of bacterial biomass and Collembola abundance to litter nutrient concentration was dependent on abiotic conditions. More specifically, the relationships between nutrients, especially calcium and magnesium, and bacterial biomass and Collembola abundance were less robust or disappeared under drier or warmer conditions. In conclusion, our findings underscore that ongoing climate change could affect soil organisms directly as well as indirectly, by altering their responses to litter nutrient concentrations. In addition, we found that nutrient‐rich habitats might be more affected than nutrient‐poor habitats by altered climatic conditions. [ABSTRACT FROM AUTHOR]

Aim: Climate is widely understood to determine elevational patterns of soil microbial communities, whereas the effects of parental material are uncertain. Changes in the composition of parental materials along elevational transects could also affect soil microbial communities by influencing soil pH and nutrient availability. Here, we aim to illustrate the combined effects of climate and parental material on the biomass and composition of soil microbial communities along an elevational transect. Location: A subtropical forest on a karst mountain (Mt. Jinfo), China. Taxon: Bacteria and Fungi. Methods: We use phospholipid fatty acid analysis (PLFA) and DNA amplicon high‐throughput sequencing to determine biomass and diversity patterns of soil microbial communities along a subtropical elevational gradient with contrasting parental materials (limestone and clasolite). Results: We observed that the microbial communities were more diverse (α‐diversity) and productive (biomass) on limestone than on clasolite. Additionally, we found that parental material played a role in shaping the composition (β‐diversity) of soil microbial communities along the elevational gradient. The impact of climate on soil microbial communities was found to be significant, albeit relatively weak. Structural equation models provided evidence for both direct and indirect effects of climate and parental material on microbial biomass and α‐diversity along the elevational gradient. Notably, the changes in soil pH, influenced by both parental material and climate, were identified as a key factor driving these effects. Main Conclusions: Our results underline the importance of both climate and parental material variations in space‐for‐time studies investigating soil microbial communities along elevational gradients. [ABSTRACT FROM AUTHOR]

Background and aims: The diversity and stability of belowground microbiota communities influence plant health. However, changes over time in the microbiome composition associated with healthy and diseased trees remains poorly understood. The goal of this study is to understand the changes in belowground microbial community associated with Verticillium wilt of smoke trees to provide a basis for the combination of biological agents and chemical measures to combat Verticillium wilt of smoke trees. Methods: In this study, we used an amplicon-based approach to reveal distinct differences in the diversity, structure and composition of the belowground microbial communities of healthy and diseased smoke trees from June to October. Results: The structure, composition and interactions of the belowground microbial communities are different between healthy and diseased smoke trees from June to October. The co-occurrence networks of the belowground microbial community changed with the severity of the disease over time. Additionally, the structural community of healthy and diseased trees showed a shift in keystone OTUs. Conclusions: This study improves our understanding of the belowground microbial community composition associated with smoke trees in healthy and diseased conditions, offering the potential to both manipulate the plant microbiome to promote plant health and to provide an integrated management strategy of smoke tree. [ABSTRACT FROM AUTHOR]

BACKGROUND: Baijiu brewing is a complex and multifaceted multimicrobial co‐fermentation process, in which various microorganisms interact to form an interdependent micro‐ecosystem, subsequently influencing metabolic activities and compound production. Among these microorganisms, Bacillus, an important bacterial genus in the liquor brewing process, remains unclear in its role in shaping the brewing microbial community and its functional metabolism. RESULTS: A baijiu fermentation system was constructed using B. subtilis JP1 isolated from native jiupei (grain mixture) combined with daqu (a saccharifying agent) and huangshui (a fermentation byproduct). Based on high‐throughput amplicon sequencing analysis, it was evident that B. subtilis JP1 significantly influences bacterial microbial diversity and fungal community structure in baijiu fermentation. Of these, Aspergillus and Monascus emerge as the most markedly altered microbial genera in the jiupei community. Based on co‐occurrence networks and bidirectional orthogonal partial least squares discriminant analysis models, it was demonstrated that the addition of B. subtilis JP1 intensified microbial interactions in jiupei fermentation, consequently enhancing the production of volatile flavor compounds such as heptanoic acid, butyl hexanoate and 3‐methylthiopropanol in jiupei. CONCLUSION: B. subtilis JP1 significantly alters the microbial community structure of jiupei, enhancing aroma formation during fermentation. These findings will contribute to a broader application in solid‐state fermentation. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Aquifers are rich in microbial diversity. However, there is a lack of information about sessile communities in these environments because of the difficulty in sampling fresh in situ rock surfaces. Thus, this study's objective was to better understand the sessile community in a fractured aquifer. Additionally, the impact of the rock mineral composition on microbial community composition during colonization was explored. Using a system of bioreactors, we recreated the environmental conditions of a 1.5 m deep aquifer in Covey Hill (QC, Canada) using groundwater samples collected from the site. We carried out 16S/18S rRNA amplicon sequencing of the water and sessile communities after 24 days of incubation. Our data showed that many microbial taxa overlapped between the sessile and planktonic communities, indicating colonization of the solid surfaces. Quartz and feldspar had a significant impact on bacterial community structure. Sessile communities were dominated by Gaillonella, Alkanindiges, unclassified Acetobacteraceae, Apoikiales, Glissomonadida, and Synurales. We could not detect any Archaea in the sessile community. The sessile communities contained bacterial genera involved in iron cycling and adapted to acidic and low-carbon-concentration environments. Eukaryotic predators dominated the sessile community. [ABSTRACT FROM AUTHOR]

Microbial communities play a crucial role in the processes of material cycling, energy conversion, and information transfer in river water. Analyzing the distribution characteristics of microbial community structure is crucial for preserving the long-term stability of river water ecosystems. In order to investigate the structure characteristics of the microbial communities and the relationships between microbial communities and hydrochemical compositions in agricultural region and urban region of Qingshui River, a total of 20 river water samples, including 13 samples from the agricultural region and 7 samples from the urban region, were collected from the River. The hydrogeochemical methods, high-throughput sequencing technology, and bioinformatics analysis were used to determine the relationships between microbial communities and hydrochemical compositions in the different functional regions of the River. The results showed that river water is generally weakly alkaline water (8.35≤pH≤9.44). The chemical type of river water is mainly HCO3-Ca•Mg water (80%), followed by Cl-Ca•Mg water (20%). Hydrochemical compositions in agricultural region were mainly controlled by the carbonate dissolution and agricultural fertilization inputs, while these in the unban region were primarily affected by the upstream hydrochemical characteristics and unban discharges. The hardening of river bottoms and its banks resulted in lower level of microbial diversity in the urban region than that in the agricultural region, and further caused the differences in microbial community structure. Limnohabitans, Rhodobacter and Flavobacterium were identified as the main genus in the agricultural region, and Cyanobium&lowbar;PCC-6307, Limnohabitans and norank&lowbar;f&lowbar;norank&lowbar;o&lowbar;Chloroplast were the primary genus in the urban region. The order of the influence of hydrochemical factors on microbial community structure was NO3- (P=0.001)>SO42- (P=0.003)>DO(P=0.071)>pH(P=0.222), and among these NO3- emitted from agricultural fertilization has the most significant impact on the microbial community structure in the River. NO3- concentrition in river water was increased by the microbial nitrification process in the agricultural region, whereas it was decreased by microbial denitrification process between the agricultural region and the urban region. [ABSTRACT FROM AUTHOR]

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Purpose: Soil quality is crucial for the growth and development of tea plants. Although the tea rhizosphere microbial composition and function have been extensively studied, few comparative studies have been performed to explore the different ecological niches of tea plants' microbes and their response to current global warming. Materials and methods: In this study, we selected a typical tea plant soil located in Chibi city, Hubei Province, China and collected samples during different seasons from rhizosphere and nonrhizosphere of tea plants. Using the Microbial phospholipid fatty acid analysis method and high-throughput sequencing to analyze the functions of dominant bacterial communities and strategies for coping with different environmental pressures. Results and discussion: The results showed that 19:0 cyclo ω7c was the dominant peak in both the rhizosphere and nonrhizosphere environments in winter compared with 16:0 in both the rhizosphere and nonrhizosphere soil in summer. The composition of PLFAs and a series of derived parameters were regulated by environmental factors such as soil pH, redox potential, total organic carbon, total nitrogen and NO3−-N content. In addition, the tea plant soil microorganisms differed significantly under the different temperature stresses, with significant enrichment of Ktedonobacteria and Micrococcaceae in winter and of Gammaproteobacteria and Proteobacteria in summer. Conclusions: The rhizosphere and nonrhizosphere soil microbial communities of tea plants were co-regulated by the root secretions growth conditions of tea plants, the fertilization conditions and the temperature stress. [ABSTRACT FROM AUTHOR]

The sea bottom acts as a key natural archive where the memory of long-term timescale environmental changes is recorded. This study discusses some ecological and chemical features of fjord sediments that were explored during the AREX cruise carried out in the Svalbard archipelago in the summer of 2021. The activity rates of the enzymes leucine aminopeptidase (LAP), beta-glucosidase (GLU), and alkaline phosphatase (AP) and community-level physiological profiles (CLPPs) were studied with the aim of determining the functional diversity of the benthic microbial community, while bacterial isolates were screened for their susceptibility to antibiotics in order to explore the role of these extreme environments as potential reservoirs of antibiotic resistance. Enzyme activity rates were obtained using fluorogenic substrates, and CLPPs were obtained using Biolog Ecoplates; antibiotic susceptibility assays were performed through the standard disk diffusion method. Spatial trends observed in the functional profiles of the microbial community suggested variability in the microbial community's composition, presumably related to the patchy distribution of organic substrates. Complex carbon sources, carbohydrates, and amino acids were the organic polymers preferentially metabolized by the microbial community. Multi-resistance to enrofloxacin and tetracycline was detected in all of the examined samples, stressing the role of sediments as a potential reservoir of chemical wastes ascribable to antibiotic residuals. This study provides new insights on the health status of fjord sediments of West Spitsbergen, applying a dual ecological and biochemical approach. Microbial communities in the fjord sediments showed globally a good functional diversity, suggesting their versatility to rapidly react to changing conditions. The lack of significant diversification among the three studied areas suggests that microbial variables alone cannot be suitable descriptors of sediment health, and that additional measures (i.e., physical–chemical characteristics) should be taken to better define environmental status. [ABSTRACT FROM AUTHOR]

Introduction: The effects of continuous cropping and rotation cropping, two important tobacco cultivation practices, on soil microbial communities at different stages remain unclear. Different planting patterns have been shown to influence soil physical and chemical properties, which in turn can affect the composition and diversity of soil microbial communities. Methods: In order to investigate the impact of different planting methods on soil microbial community structure, we selected two representative planting methods: continuous cropping (tobacco) and rotational cropping (tobacco-maize). These methods were chosen as the focal points of our research to explore the potential effects on soil microbial communities. High-throughput sequencing technology was employed to investigate the structure of soil microbial communities, as well as their relationships with soil environmental factors, by utilizing the 16S rRNA, ITS, and 18S genes. Furthermore, the interaction among microorganisms was explored through the application of the Random Matrix Theory (RMT) molecular ecological network approach. Results: There was no significant difference in a diversity, but significant difference in b diversity based on Jaccard distance test. Compared to continuous cropping, crop rotation significantly increased the abundance of beneficial prokaryotes Verrucomicrobia and Rhodanobacter. These findings indicate that crop rotation promotes the enrichment of Verrucomicrobia and Rhodanobacter in the soil microbial community. AP and NH4-N had a greater effect on the community structure of prokaryotes and fungi in tobacco soil, while only AP had a greater effect on the community structure of protist. Molecular ecological network analysis showed that the network robustness and Cohesion of rotation were significantly higher than that of continuous cropping, indicating that the complexity and stability of molecular ecological networks were higher in the rotational, and the microbial communities cooperated more effectively, and the community structure was more stable. Discussion: From this point of view, rotational cropping is more conducive to changing the composition of soil microbial community, enhancing the stability of microbial network structure, and enhancing the potential ecological functions in soil. [ABSTRACT FROM AUTHOR]

Microbial communities are known to play an important role in maintaining ecological balance and can be used as an indicator for assessing environmental pollution. Numerous studies have revealed that air pollution can alter the structure of microbial communities, which may increase health risks. Nevertheless, the relationships between microbial communities and particulate matter (PM) caused by air pollution in terms of health risk assessment are not well understood. This study aimed to validate the influences of PM chemical compositions on microbial communities and assess the associated health risks. Our results, based on similarity analysis, revealed that the stability structure of the microbial communities had a similarity greater than 73%. In addition, the altered richness and diversity of microbial communities were significantly associated with PM chemical compositions. Volatile organic compounds (VOCs) and polycyclic aromatic hydrocarbons (PAHs) exerted a positive influence on microbial communities in different environmental variables. Additionally, a stronger linear correlation was observed between hydroxyl radicals (·OH) and the richness of microbial communities. All estimated health risks from PM chemical compositions, calculated under different environmental variables, significantly exceeded the acceptable level by a factor of more than 49. Cr and 1,2-Dibromoethane displayed dual adverse effects of non-carcinogenic and carcinogenic risks. Overall, the study provides insights into the fundamental mechanisms of the variability in microbial communities driven by PM, which may support the crucial role of PM chemical compositions in the risk of microorganisms in the atmospheric environment. [ABSTRACT FROM AUTHOR]

Processes driving nutrient retention in stormwater green infrastructure (SGI) are not well quantified in water-limited biomes. We examined the role of plant diversity and physiochemistry as drivers of microbial community physiology and soil N dynamics post precipitation pulses in a semi-arid region experiencing drought. We conducted our study in bioswales receiving experimental water additions and a montane meadow intercepting natural rainfall. Pulses of water generally elevated soil moisture and pH, stimulated ecoenzyme activity (EEA), and increased the concentration of organic matter, proteins, and N pools in both bioswale and meadow soils. Microbial community growth was static, and N assimilation into biomass was limited across pulse events. Unvegetated plots had greater soil moisture than vegetated plots at the bioswale site, yet we detected no clear effect of plant diversity on microbial C:N ratios, EEAs, organic matter content, and N pools. Differences in soil N concentrations in bioswales and the meadow were most directly correlated to changes in organic matter content mediated by ecoenzyme expression and the balance of C, N, and P resources available to microbial communities. Our results add to growing evidence that SGI ecological function is largely comparable to neighboring natural vegetated systems, particularly when soil media and water availability are similar. [ABSTRACT FROM AUTHOR]

For deep underground coal mining ecosystems, research on microbial communities and geochemical characteristics of sediments in different functional zones is lacking, resulting in the knowledge of zone-level mine water pollution prevention and control being narrow. In this study, we surveyed the geochemical distinctions and microbial communities of five typical functional zones in a representative North China coalfield, Xinjulong coal mine. The data indicated that the geochemical compounds and microbial communities of sediments showed distinguishing features in each zone. The microbial community richness and diversity were ranked as follows: surface water > rock roadways > sumps > coal roadways ≥ goafs. Canonical Correlation Analysis (CCA), Spearman correlation and co-occurrence network analysis demonstrated that microbial communities were sensitive and closely related to hydrochemical processes. The microbial community distribution in the underground mine was closely related not only to nutrient elements (i.e., C, S, P and N), but also to redox-sensitive substances (i.e., Fe and As). When it comes to mine water pollution prevention and control, the central zones are goafs. With the increase in goaf closure time, total nitrogen (TN), total organic carbon (TOC) and total sulfur (TS) decreased, but As, Fe and total phosphorus (TP) gradually increased, and the characteristic pollutant SO42− concentration in water samples decreased. Additionally, the sulfate-reducing bacteria (SRB) had relatively higher proportions in goafs, suggesting goafs were able to purify themselves. In practical engineering, in situ nitrogen injection technology used to expel oxygen and create an anaerobic environment can be implemented to enhance SRB reducing sulfate in goafs. Meanwhile, because coal mine pollution discharge generally only discharges mine water and leaves sediment underground, the pollutants can be transferred to the sediment by strengthening the relevant reactions including the heavy metal solidification and stabilization function of bacteria. [ABSTRACT FROM AUTHOR]

Humic acid (HA) is a typical refractory organic matter, so it is of great significance to investigate its effect on the performance of Anammox granular sludge. When the dosage of HA ≤ 50 mg/L, HA promotes the total nitrogen removal rate (NRR) to 1.45 kg/(m3·day). When HA was between 50 and 100 mg/L, the NRR of Anammox was stable. At this time, the adsorption of HA causes the sludge to gradually turn from red to brown, but the activities of heme and enzymes showed that its capacity was not affected. When HA levels reached 250 mg/L, the NRR dropped to 0.11 kg/(m3·day). Moderate HA levels promoted the release of extracellular polymeric substance (EPS), but excessive HA levels lead to a decrease in EPS concentrations. HA inhibited Anammox activity, which indirectly hindered the transmission of substrate and accumulated substrate toxicity. Although HA promoted the increase of heterotrophic microbial abundance in Anammox system, the microbial diversity decreased gradually. With the increase of HA concentration, the abundance of Candidatus_Brocadia , the main functional microorganism of Anammox system, decreased gradually, while the abundance of Candidatus_Kuenenia increased gradually. [ABSTRACT FROM AUTHOR]

• Novel carbon source and corncob had better denitrification efficiency than polycaprolactone and polyvinyl alcohol-sodium alginate. • The taxonomical composition of bacterial, fungal and archaeal communities can be altered by types of solid carbon source. • Some fungi and archaea species were conducive to solid-phase denitrification (SPD) systems. • Co-occurring network showed some potential collaboration between bacterial fungal and archaeal communities in SPD systems. • Amplicon sequence variant (ASV) can identify more taxonomies that operational taxonomic unit (OTU) cannot in this study. There is a lack of understanding about the bacterial, fungal and archaeal communities' composition of solid-phase denitrification (SPD) systems. We investigated four SPD systems with different carbon sources by analyzing microbial gene sequences based on operational taxonomic unit (OTU) and amplicon sequence variant (ASV). The results showed that the corncob-polyvinyl alcohol sodium alginate-polycaprolactone (CPSP, 0.86±0.04 mg NO 3 −-N/(g·day)) and corncob (0.85±0.06 mg NO 3 −-N/(g·day)) had better denitrification efficiency than polycaprolactone (PCL, 0.29±0.11 mg NO 3 −-N/(g·day)) and polyvinyl alcohol-sodium alginate (PVA-SA, 0.24±0.07 mg NO 3 −-N/(g·day)). The bacterial, fungal and archaeal microbial composition was significantly different among carbon source types such as Proteobacteria in PCL (OTU: 83.72%, ASV: 82.49%) and Rozellomycota in PVA-SA (OTU: 71.99%, ASV: 81.30%). ASV methods can read more microbial units than that of OTU and exhibit higher alpha diversity and classify some species that had not been identified by OTU such as Nanoarchaeota phylum, unclassified_ f_ Xanthobacteraceae genus, etc., indicating ASV may be more conducive to understand SPD microbial communities. The co-occurring network showed some correlation between the bacteria fungi and archaea species, indicating different species may collaborate in SPD systems. Similar KEGG function prediction results were obtained in two bioinformatic methods generally and some fungi and archaea functions should not be ignored in SPD systems. These results may be beneficial for understanding microbial communities in SPD systems. [Display omitted] [ABSTRACT FROM AUTHOR]

Forest management influences the occurrence of tree species, the organic matter input to the soil decomposer system, and hence, it can alter soil microbial community and key ecosystem functions it performs. In this study, we compared the potential effect of different forest management, coppice and high forest, on soil microbial functional diversity, enzyme activities and chemical-physical soil properties in two forests, turkey oak and beech, during summer and autumn. We hypothesized that coppicing influences soil microbial functional diversity with an overall decrease. Contrary to our hypothesis, in summer, the functional diversity of soil microbial community was higher in both coppice forests, suggesting a resilience response of the microbial communities in the soil after tree cutting, which occurred 15–20 years ago. In beech forest under coppice management, a higher content of soil organic matter (but also of soil recalcitrant and stable organic carbon) compared to high forest can explain the higher soil microbial functional diversity and metabolic activity. In turkey oak forest, although differences in functional diversity of soil microbial community between management were observed, for the other investigated parameters, the differences were mainly linked to seasonality. The findings highlight that the soil organic matter preservation depends on the type of forest, but the soil microbial community was able to recover after about 15 years from coppice intervention in both forest ecosystems. Thus, the type of management implemented in these forest ecosystems, not negatively affecting soil organic matter pool, preserving microbial community and potentially soil ecological functions, is sustainable in a scenario of climate change. [ABSTRACT FROM AUTHOR]

Background: Past findings demonstrate that arthropods can egest midgut microbiota into the host skin leading to dual colonization of the vertebrate host with pathogens and saliva microbiome. A knowledge gap exists on how the saliva microbiome interacts with the pathogen in the saliva. To fill this gap, we need to first define the microbial composition of mosquito saliva. Methods: The current study aimed at analyzing and comparing the microbial profile of Aedes albopictus saliva and midgut as well as assessing the impact of Zika virus (ZIKV) infection on the midgut and saliva microbial composition. Colony-reared Ae. albopictus strains were either exposed to ZIKV infectious or noninfectious bloodmeal. At 14 ays postinfection, the 16S V3–V4 hypervariable rRNA region was amplified from midgut and saliva samples and sequenced on an Illumina MiSeq platform. The relative abundance and diversity of midgut and saliva microbial taxa were assessed. Results: We observed a richer microbial community in the saliva compared with the midgut, yet some of the microbial taxa were common in the midgut and saliva. ZIKV infection did not impact the microbial diversity of midgut or saliva. Further, we identified Elizabethkingia spp. in the Ae. albopictus saliva. Conclusions: This study provides insights into the microbial community of the Ae. albopictus saliva as well as the influence of ZIKV infection on the microbial composition of its midgut and saliva. The identification of Elizabethkingia spp., an emerging pathogen of global health significance, in Ae. albopictus saliva is of medical importance. Future studies to assess the interactions between Ae. albopictus saliva microbiome and ZIKV could lead to novel strategies for developing transmission barrier tools. [ABSTRACT FROM AUTHOR]

Lily bulbs, which have both nutrient storage and reproductive functions, are a representative group of plants for studying the maintenance and transfer of plant-associated microbiomes. In this study, a comparison of the microbial composition of bulbs and their regenerated seedlings cultured under aseptic conditions, as well as subcultured seedlings that succeeded five times, was examined by amplicon sequencing. A total of 62 bacterial taxa and 56 fungal taxa were found to be transferred to the 5th generation in seedlings, which are the core microbiome of lily. After the regeneration of seedlings from bulbs, there was a significant increase in the number of detectable microbial species, and after 1, 3, and 5 successive generations, there was a decrease in the number of detectable species. Interestingly, some "new" microorganisms appeared in each generation of samples; for instance, 167 and 168 bacterial operational taxonomic units (OTUs) in the 3rd and 5th generations of seedlings that were not detected in either bulbs or seedlings of the previous two generations. These results suggest that bulbs can maintain a high diversity of microorganisms, including some with ultra-low abundance, and have a high transfer capacity to tuck shoots through continuous subculture. The diversity and maintenance of the microbiome can provide the necessary microbial reservoir support for regenerating seedlings. This habit of maintaining low abundance and high diversity may be biologically and ecologically critical for maintaining microbiome stability and function due to the sequestration nature of the plant. [ABSTRACT FROM AUTHOR]