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Microbial communities exhibit complex behaviors driven by species interactions and individual characteristics. In this study, we delve into the dynamics of a mixed bacterial population comprising two distinct species with different morphology and motility aspects. Employing agent-based modeling and computer simulations, we analyze the impacts of size ratios and packing fractions on dispersal patterns, aggregate formation, clustering, and spatial ordering. Notably, we find that motility and anisotropy of elongated bacteria significantly influence the distribution and spatial organization of nonmotile spherical species. Passive spherical cells display a superdiffusive behavior, particularly at larger size ratios in the ballistic regime. As the size ratio increases, clustering of passive cells is observed, accompanied by enhanced alignment and closer packing of active cells in the presence of higher passive cell area fractions. In addition, we identify the pivotal role of passive cell area fraction in influencing the response of active cells toward nematicity, with its dependence on size ratio. These findings shed light on the significance of morphology and motility in shaping the collective behavior of microbial communities, providing valuable insights into complex microbial behaviors with implications for ecology, biotechnology, and bioengineering. [ABSTRACT FROM AUTHOR]

Many female squids and cuttlefishes have a symbiotic reproductive organ called the accessory nidamental gland (ANG) that hosts a bacterial consortium involved with egg defense against pathogens and fouling organisms. While the ANG is found in multiple cephalopod families, little is known about the global microbial diversity of these ANG bacterial symbionts. We used 16S rRNA gene community analysis to characterize the ANG microbiome from different cephalopod species and assess the relationship between host and symbiont phylogenies. The ANG microbiome of 11 species of cephalopods from four families (superorder: Decapodiformes) that span seven geographic locations was characterized. Bacteria of class Alphaproteobacteria, Gammaproteobacteria, and Flavobacteriia were found in all species, yet analysis of amplicon sequence variants by multiple distance metrics revealed a significant difference between ANG microbiomes of cephalopod families (weighted/unweighted UniFrac, Bray-Curtis, P = 0.001). Despite being collected from widely disparate geographic locations, members of the family Sepiolidae (bobtail squid) shared many bacterial taxa including (~50%) Opitutae (Verrucomicrobia) and Ruegeria (Alphaproteobacteria) species. Furthermore, we tested for phylosymbiosis and found a positive correlation between host phylogenetic distance and bacterial community dissimilarity (Mantel test r = 0.7). These data suggest that closely related sepiolids select for distinct symbionts from similar bacterial taxa. Overall, the ANGs of different cephalopod species harbor distinct microbiomes and thus offer a diverse symbiont community to explore antimicrobial activity and other functional roles in host fitness.IMPORTANCEMany aquatic organisms recruit microbial symbionts from the environment that provide a variety of functions, including defense from pathogens. Some female cephalopods (squids, bobtail squids, and cuttlefish) have a reproductive organ called the accessory nidamental gland (ANG) that contains a bacterial consortium that protects eggs from pathogens. Despite the wide distribution of these cephalopods, whether they share similar microbiomes is unknown. Here, we studied the microbial diversity of the ANG in 11 species of cephalopods distributed over a broad geographic range and representing 15-120 million years of host divergence. The ANG microbiomes shared some bacterial taxa, but each cephalopod species had unique symbiotic members. Additionally, analysis of host-symbiont phylogenies suggests that the evolutionary histories of the partners have been important in shaping the ANG microbiome. This study advances our knowledge of cephalopod-bacteria relationships and provides a foundation to explore defensive symbionts in other systems.

Biogenic methane (BM) production from coal is quite limited due to its complex chemical nature, which makes the responsible microbes sensitive to its denaturation. In the current investigation, wheat straw (WS) at different concentrations as a cosubstrate were used with coal to augment methane generation from coal. Results revealed that the codigestion approach significantly enhanced the cumulative methane generation in CS1 (17.25 mmol) (coal:straw, 75:25), which was 59.52%–256.47% higher than the CS2 (coal:straw, 85:15), and WS single digestion, respectively. Moreover, the lowest methane yield (0.295 mmol/g) was achieved from single coal digestion. Particularly, the highest methane content, 68.37% in the collected biogas, was observed in CS1, followed by CS2 (49.53%), WS (44.92%), and coal (3.53%). Microbial community analysis illustrates that Methanobacteriaceae (51.33%) and Methanosarcinaceae (48.66%) were the leading archaeal communities at the peak methanogenic stage in CS1. While the abundant bacteria at this stage were Hungateiclostridiaceae (40.18%), Rhodobacteriaceae (21.40%), and Lentimicrobiaceae (19.20%) in CS1. According to scanning electron microscopy (SEM) analysis, several microbes were seen to be attached to the coal surface in CS1 and CS2. Moreover, the nontargeted metabolomic results showed that aromatics, aliphatic, long‐chain fatty acids, and alkane (C19–C36) compounds were found to be highly expressed in only coal, CS1, and CS2 reactors compared to WS. In addition, volatile fatty acids (VFAs) analysis showed that acetic acids were abundantly present in CS1 (2,190,175 ng/ml), followed by WS (1,543,492.88 ng/ml), CS2 (1,159,050 ng/ml), and coal (50,998.31 ng/ml). These results promote the significance of using WS as a cosubstrate with coal to enhance methane production, which can be used as a fuel in power plants. Further studies are required to investigate the potential cosubstrate with coal to enhance methane production and identify the specific metabolic pathways involved. [ABSTRACT FROM AUTHOR]

Fermented beverages (FBs) are facing challenges in functional performance and flavor complexity, necessitating the development of new multi-functional options. Traditional fermented beverages (TFBs), both alcoholic and nonalcoholic, have gained increased attention for their health-promoting effects during the COVID-19 pandemic. This review summarized the primary commercially available probiotics of FBs, along with the limitations of single and mixed probiotic FBs. It also examined the recent research progress on TFBs, emphasizing the typical microbial communities (MC) of TFBs, and TFBs made from crops (grains, vegetables, fruits, etc.) worldwide and their associated functions and health benefits. Furthermore, the construction, technical bottlenecks of the synthetic MC involved in developing innovative FBs were presented, and the promising perspective of FBs was described. Drawing inspiration from the MC of TFBs, developing of stable and multifunctional FBs using synthetic MC holds great promise for beverage industry. However, synthetic MC suffers from structural instability and poorly acknowledged interaction mechanisms, resulting in disappointing results in FBs. Future researches should prioritize creating synthetic MC fermentation that closely resemble natural fermentation, tailored to meet the needs of different consumers. Creating personalized FBs with high-tech intelligence is vital in attracting potential consumers and developing novel beverages for the future. [ABSTRACT FROM AUTHOR]

Aquaponic production relies on microbial activity to convert fish wastes into nutrients for plants. An aquaponic system contains multiple compartments that each have varying environmental pressures that can impact the types of microbes living in the compartment. Furthermore, differences in fish and plant species, system startup and management, and water source can impact microbial communities that colonize an aquaponic system. In this study, we sampled two aquaponic facilities that each operated six replicate aquaponic systems. Metataxonomic analyses were performed on the samples to compare the microbial communities of aquaponic facilities in Minnesota (MN) and Wisconsin (WI), assess the consistency of the microbial communities across multiple systems within a single facility, and evaluate the abundance and types of microbes present within each compartment of a system. Proteobacteria, Bacteroidetes, and Actinobacteria were common in both facilities, but nitrifying organisms were in greater abundance at the WI facility. Microbial communities were largely consistent among systems within a facility, but microbial communities among different compartments of the systems varied. Nitrifying organisms were primarily associated with the biofilter compartment of the MN systems but were found throughout the WI systems, which do not have a dedicated biofiltration compartment. While nitrifying organisms have an important role in an aquaponic system, they comprise less than 10% of the total microbial community of the aquaponic systems we sampled. Other taxa are likely to have equally important roles in the productivity of an aquaponic system, but those taxa and their functions have not been well characterized, and it is unclear how system startup, management, and other factors impact colonization and maintenance of these taxa. [ABSTRACT FROM AUTHOR]

ABSTRACT The frequency of emerging disease is growing with ongoing human activity facilitating new host–pathogen interactions. Novel infection outcomes can also be shaped by the host microbiota. Caenorhabditis elegans nematodes experimentally colonised by a wild microbiota community and infected by the widespread animal pathogen, Staphylococcus aureus, have been shown to suffer higher mortality than those infected by the pathogen alone. Understanding the host responses to such microbiota–pathogen ecological interactions is key to pinpointing the mechanism underlying severe infection outcomes. We conducted transcriptomic analyses of C. elegans colonised by its native microbiota, S. aureus and both in combination. Correlations between altered collagen gene expression and heightened mortality in co‐colonised hosts suggest the microbiota modified host resistance to infection. Furthermore, microbiota colonised hosts showed increased expression of immunity genes and variable expression of stress response genes during infection. Changes in host immunity and stress response could encompass both causes and effects of severe infection outcomes. ‘Re‐wilding’ this model nematode host with its native microbiota indicated that typically commensal microbes can mediate molecular changes in the host that are costly when challenged by a novel emerging pathogen. [ABSTRACT FROM AUTHOR]

Bacterial conjugation, wherein DNA is transferred between cells through direct contact, is highly prevalent in complex microbial communities and is responsible for spreading myriad genes related to human and environmental health. Despite their importance, much remains unknown regarding the mechanisms driving the spread and persistence of these plasmids in situ. Studies have demonstrated that transferring, acquiring, and maintaining a plasmid imposes a significant metabolic burden on the host. Simultaneously, emerging evidence suggests that the presence of a conjugative plasmid can also provide both obvious and unexpected benefits to their host and local community. Combined, this highlights a continuous cost‐benefit tradeoff at the population level, likely contributing to overall plasmid abundance and long‐term persistence. Yet, while the metabolic burdens of plasmid conjugation, and their causes, are widely studied, their attendant potential advantages are less clear. Here, we summarize current perspectives on conjugative plasmids’ metabolic burden and then highlight the lesser‐appreciated yet critical benefits that plasmid‐mediated metabolic burdens may provide. We argue that this largely unexplored tradeoff is critical to both a fundamental theory of microbial populations and engineering applications and therefore warrants further detailed study. [ABSTRACT FROM AUTHOR]

Phytochemicals are potent inhibitors of in vivo ruminal microbial activity and methanogenesis of plant materials. However, a knowledge gap exists on the influence of phytochemicals on microbial ecology and biomethane production under anaerobic bioreactor environment. In this study, high-throughput metagenomic sequencing and physicochemical analyses were used to evaluate the effects of phytochemicals on the microbial community structure and methane production efficiency of different avocado oil processing wastes under standard batch anaerobic digestion (AD) over the 30-day period. Results showed that the avocado wastes produced methane yields (MY) ranging from 79 to 247 mL CH4/gVSadded, with skin/peels (AS), cold-pressed pomace (CDP), cold-pressed wastewater (CDW), and hot-pressed pomace (HDP) digestates showing diauxic methane production patterns and peak daily methane production at day 7. Avocado seed (AK) digestate, characterized by high phytochemical content, exhibited a monophasic methane production pattern and the lowest MY. Pseudomonas, Romboutsia, Paeniclostridium, and Methanocorpusculum, Methanosaeta, Methanoregula, and Methanosarcina were the dominant bacterial and archaeal genera in all digesters. Lipolytic Pseudomonas were enriched in the early AD phase (0–15 days), whereas Romboutsia, Paeniclostridium, and Clostridium increased in the late AD stage (days 13–30). Spearman correlation analyses showed that the total polyphenols and saponins exhibited a significant negative influence on biomethane production. Alkaloid level significantly affected Romboutsia, Paeniclostridium, and Methanoregula, while saponins negatively correlated to AC160630, Clostridium, Methanocorpusculum, and Methanoregula. To the best of our knowledge, this is the first report on the potential negative impact of phytochemicals on the microbial community structure and biomethane production from avocado processing wastes. [ABSTRACT FROM AUTHOR]

The increase in marine diseases, particularly in economically important mollusks, is a growing concern. Among them, the Pacific oyster (Crassostrea gigas) production faces challenges from several diseases, such as the Pacific Oyster Mortality Syndrome (POMS) or vibriosis. The microbial education, which consists of exposing the host immune system to beneficial microorganisms during early life stages is a promising approach against diseases. This study explores the concept of microbial education using controlled and pathogen-free bacterial communities and assesses its protective effects against POMS and Vibrio aestuarianus infections, highlighting potential applications in oyster production. We demonstrate that it is possible to educate the oyster immune system by adding microorganisms during the larval stage. Adding culture based bacterial mixes to larvae protects only against the POMS disease while adding whole microbial communities from oyster donors protects against both POMS and vibriosis. The efficiency of immune protection depends both on oyster origin and on the composition of the bacterial mixes used for exposure. No preferential protection was observed when the oysters were stimulated with their sympatric strains. Furthermore, the added bacteria were not maintained into the oyster microbiota, but this bacterial addition induced long term changes in the microbiota composition and oyster immune gene expression. Our study reveals successful immune system education of oysters by introducing beneficial microorganisms during the larval stage. We improved the long-term resistance of oysters against critical diseases (POMS disease and Vibrio aestuarianus infections) highlighting the potential of microbial education in aquaculture. [ABSTRACT FROM AUTHOR]

Microbes are extensively present among various cancer tissues and play critical roles in carcinogenesis and treatment responses. However, the underlying relationships between intratumoral microbes and tumors remain poorly understood. Here, a MIcrobial Cancer‐association Analysis using a Heterogeneous graph transformer (MICAH) to identify intratumoral cancer‐associated microbial communities is presented. MICAH integrates metabolic and phylogenetic relationships among microbes into a heterogeneous graph representation. It uses a graph transformer to holistically capture relationships between intratumoral microbes and cancer tissues, which improves the explainability of the associations between identified microbial communities and cancers. MICAH is applied to intratumoral bacterial data across 5 cancer types and 5 fungi datasets, and its generalizability and reproducibility are demonstrated. After experimentally testing a representative observation using a mouse model of tumor‐microbe‐immune interactions, a result consistent with MICAH's identified relationship is observed. Source tracking analysis reveals that the primary known contributor to a cancer‐associated microbial community is the organs affected by the type of cancer. Overall, this graph neural network framework refines the number of microbes that can be used for follow‐up experimental validation from thousands to tens, thereby helping to accelerate the understanding of the relationship between tumors and intratumoral microbiomes. [ABSTRACT FROM AUTHOR]

Summary The Anthropocene exerts various pressures and influences on the stability and function of the Earth's ecosystems. However, our understanding of how the microbiome responds in form and function to these disturbances is still limited, particularly when considering the phyllosphere, which represents one of the largest microbial reservoirs in the terrestrial ecosystem. In this study, we comprehensively characterized tree phyllosphere bacteria and associated nutrient‐cycling genes in natural, rural, suburban, and urban habitats in China. Results revealed that phyllosphere bacterial community diversity, richness, stability, and composition heterogeneity were greatest at the most disturbed sites. Stochastic processes primarily governed the assembly of phyllosphere bacterial communities, although the role of deterministic processes (environmental selection) in shaping these communities gradually increased as we moved from rural to urban sites. Our findings also suggest that human disturbance is associated with the reduced influence of drift as increasingly layered environmental filters deterministically constrain phyllosphere bacterial communities. The intensification of human activity was mirrored in changes in functional gene expression within the phyllosphere microbiome, resulting in enhanced gene abundance, diversity, and compositional variation in highly human‐driven disturbed environments. Furthermore, we found that while the relative proportion of core microbial taxa decreased in disturbed habitats, a core set of microbial taxa shaped the distributional characteristics of both microbiomes and functional genes at all levels of disturbance. In sum, this study offers valuable insights into how anthropogenic disturbance may influence phyllosphere microbial dynamics and improves our understanding of the intricate relationship between environmental stressors, microbial communities, and plant function within the Anthropocene. [ABSTRACT FROM AUTHOR]

To investigate the effects of various types of farmland shelterbelts on soil quality and soil bacterial community diversity, this study focused on soil samples from four different shelterbelt types in the Alaer reclamation area, including Populus euphratica Oliv.- Populus tomentosa Carrière (PP), Elaeagnus angustifolia L.- Populus euphratica Oliv. (EP), Populus alba var. pyramidalis Bunge (P), and Salix babylonica L. (S). We analyzed their physical, chemical, biological properties as well as the differences in bacterial community structure, and explored the influencing factors on soil microbial community characteristics through microbial correlation network analysis. The results showed that: (1) There were significant differences in soil properties among the four types of farmland shelterbelts (p < 0.05), with P soils exhibiting the highest levels of organic matter, total nitrogen, and total phosphorus contents. (2) The Alpha diversity indices of soil bacteria showed significant differences among the four types of farmland shelterbelts (p < 0.05), with the P soils displayed the highest Chao1 and Shannon indices. (3) There were differences in the composition and abundance of dominant soil bacterial communities among different farmland shelterbelts, notably, the abundances of Verrucomicrobia, Acidobacteria, and Planctomycetes were significantly higher in P soils compared to the other three types. (4) The complexity of the correlation network between microbial species and environmental factors was highest in EP soils, soil microbial biomass nitrogen and available phosphorus were the main influencing factors. These findings indicated that different types of farmland shelterbelts had significant impacts on soil properties and soil bacterial communities. Soil bacterial communities were regulated by soil properties, their changes reflected a combined effect of soil characteristics and tree species. [ABSTRACT FROM AUTHOR]

Objective: The purpose of this experiment was to explore the effect of adding cellulase and laccase on fermentation quality and microbial community in mixed silage of corn stover and wet brewer's grains. Try to a new approach for the proper preservation and utilization of the agro-industrial by-products (corn stover and wet brewer's grains). Methods: The experiment was divided into four groups: CK (control), C (cellulase, 120 U/g fresh matter [FM]), L (laccase, 50 U/g FM), CL (cellulase 120 U/g FW and laccase 50 U/g FM), and the chemical composition, fermentation quality, microbial population and microbial community in mixed silage of corn stover and wet brewer's grains after 30 day's fermentation were determined. Results: Compared to control, the addition of cellulase significantly increased crude protein (CP), water-soluble carbohydrate (WSC), lactic acid bacteria (LAB) counts, while significantly decreased the neutral detergent fiber (NDF), acid detergent fiber (ADF) content (P < 0.05). Adding laccase significantly decreased the acid detergent lignin (ADL) content (P < 0.05). Combined application of cellulase and laccase significantly increased the CP, WSC content and LAB counts, while significantly decreased pH value, NDF, ADF and ADL content (P < 0.05), thereby improving fermentation quality. In addition, the application of cellulase and laccase increased the abundance of Firmicutes and LAB genera, and decreased microbial diversity level of the sample. Conclusion: The combined application of cellulase and laccase further improved fermentation quality and microbial community in mixed silage of corn stover and wet brewer's grains. [ABSTRACT FROM AUTHOR]

Caulerpa is a genus of green macroalgae that lives in tropical and subtropical coastal waters. It is an intriguing organism because, despite having plant-like structures, it is one giant cell – which, next to multiple nuclei, chloroplasts, and mitochondria, also contains endo- and epiphytic bacteria. The role of these bacteria is unknown, but they might impact the growth and development of the host, adaptation to environmental parameters, and, hence, the ecological success of these algae. We hypothesised that increased sulphide concentrations would trigger a significant shift in the microbial community composition associated with C. prolifera rhizoids, favouring sulphide-oxidizing bacteria. To test this hypothesis, we conducted a mesocosm experiment incubating C. prolifera in sediments with different sulphide concentrations and analysed the algal photosynthesis, growth, and microbiome composition. While photosynthesis was not affected, the Caulerpa weight-based growth rate decreased linearly with increasing sulphide concentration. To analyse the microbiome, we extracted DNA and RNA from the fronds, rhizoids, and the accompanying sediments and performed 16S amplicon sequencing. The microbiome of the fronds was unaffected in both the DNA and RNA samples. However, an increase in sulphide concentration coincided with a decrease in the relative abundance of sulphate-reducing bacteria associated with Caulerpa rhizoids, particularly from the family Desulfocapsaceae. In the RNA samples, potential sulphide oxidisers of the rhizoid-associated members of the Beggiatoaceae were detected. Our results suggest that the rhizobiome of Caulerpa plays a significant role in its adaptation to sulphide-rich environments, offering new insights into the complex interactions within marine holobionts. [ABSTRACT FROM AUTHOR]

The spermosphere, a dynamic microenvironment surrounding germinating seeds, is shaped by the complex interactions between natural compounds exuded by seeds and seed-associated microbial communities. While peptides exuded by plants are known to influence microbiota diversity, little is known about those specifically exuded by seeds. In this study, we characterised the peptidome profile of the spermosphere for the first time using seeds from eight genotypes of common bean (Phaseolus vulgaris) grown in two contrasting production regions. An untargeted LC-MS/MS peptidomic analysis revealed 3,258 peptides derived from 414 precursor proteins of common bean in the spermosphere. This comprehensive peptidomic dataset provides valuable insights into the characteristics of peptides exuded by common bean seeds in the spermosphere. It can be used to identify peptides with potential antimicrobial or other biological activities, advancing our understanding of the functional roles of seed-exuded peptides in the spermosphere. [ABSTRACT FROM AUTHOR]

The transition from traditional wastewater treatment plants to biorefineries represents an environmentally and economically sustainable approach to extracting valuable compounds from waste. Sewage sludge produced from wastewater treatment is incinerated or disposed of in specific landfills. Repurposing this waste material to recover valuable resources could help lower disposal costs and reduce environmental impact by producing other beneficial polymers. Microorganisms present in the sewage sludge can ferment organic pollutants, producing volatile fatty acids (VFA), precursors for biopolymers that could be used as an alternative to petroleum-derived plastics. To boost VFA production during sewage sludge fermentation, it is necessary to understand the operating microbial community and its metabolic capacities in anaerobic conditions. This study presents the influence of the headspace volume on the microbial community and the VFA production to define the best operational parameters in a 225 L pilot plant fermenter. The wasted sewage sludge was withdrawn from an oxic-settling-anaerobic plant that collected wastewater from the canteen and dormitory of the UNIPA Campus (Palermo University, Italy) and incubated using a 40% and a 60% headspace volume. The microbial community was analysed before and after the fermentation process through metataxonomic analysis, and VFA yields were determined by gas chromatography analysis. Our results showed that the 40% headspace volume induced a tenfold higher VFA production than the 60% headspace volume, modulating the microbial community's efforts to establish a VFA-producing factory. Notably, at 40% headspace, the relative abundance of bacteria, like Proteobacteria, Firmicutes, Actinobacteria, and Chloroflexi, significantly increased, as well as the relative abundance of Bacteroidetes and Verrucomicrobia decreased during the fermentation process. This result is consistent with the selection of efficient VFA-producing bacteria that lead to increased VFA yields that are not obtained at 60% headspace. Thus, reducing headspace is a promising strategy that can be implemented, even in full-scale plants, to optimise the wastewater reuse process and maximise VFA production to produce bioplastics, like polyhydroxyalkanoate, for the transition from linear wastewater treatment plants to circular biorefineries. [ABSTRACT FROM AUTHOR]

Pine Wilt Disease (PWD) is a devastating pine tree disease characterized by rapid onset, high mortality rate, quick spread, and difficulty in control. Plant microbiome plays a significant role in the development of PWD. However, the endophytic microbial communities of Pinus koraiensis infected by pine wood nematode (PWN) Bursaphelenchus xylophilus remain largely unexplored. In this study, we analyzed the structural changes of endophytic communities of P. koraiensis after infection by the PWN using high-throughput sequencing technology. The results showed that the community structure underwent significant changes as the degree of PWN infection intensified. The diversity and abundance of endophytic fungi in P. koraiensis increased, while those of endophytic bacteria in P. koraiensis decreased during the infection process. Meanwhile, the abundance of some dominant microorganisms has also changed, including species such as Graphilbum and Pseudoalteromonas. Functional prediction analysis showed that the functional composition of endophytic fungi in P. koraiensis was significantly different across the development of PWD, while the composition of endophytic bacteria remained essentially similar. The results indicated that PWN infection had a significant impact on the structure, diversity, abundance, and functional gene composition of endophytic microbial communities in P. koraiensis , and most of the main endophytic microbial groups tended to coordinate with each other. This work provides a better understanding of the changes in endophytic community structure and function caused by PWD infection of P. koraiensis , which may benefit the exploration of potential endophytes for PWN biocontrol. [ABSTRACT FROM AUTHOR]

This study assessed the impacts of wheat straw as a cosubstrate on coal biocoverion into methane and the associated mechanism within methane metabolic pathways. Co-digestion of coal with varying wheat straw concentrations resulted in a remarkable (1246.05%) increase in methane yield compared to that of the control (CK). Moreover, microbial analysis revealed a uniform distribution of Methanosarcinaceae (51.14%) and Methanobacteriaceae (39.90%) in the co-digestion of coal and wheat straw (CWS1) at a ratio of 3:1 (w/w) compared to other treatments such as coal and wheat straw (CWS2) at a ratio of 3:0.5. In addition, Hungatieclostridiaceae and Rhodobacteriaceae were abundant in both co-digesters, whereas the bacterial communities in the CK group were significantly different and more abundant than those in the Peptostreptococcaceae and Enterobacteriaceae groups. The key enzymes related to methanogenic metabolic pathways, including EC: 1.2.99.5 and EC: 2.1.1.86 (facilitating the conversion of CO2 into methane), and EC:1.12.98.1 exhibited significant abundance within CWS1. Aromatic compounds such as 4-(2-chloroanilino)-4-oxobutanoic acid and phthalic acid were substantially more abundant in CWS1 and CWS2 than in CK, indicating the increased bioavailability of coal to microbial activities. This novel approach demonstrates that wheat straw co-digestion with coal during anaerobic digestion modulates microbial communities and their metabolic pathways to enhance methane production from complex substrates such as coal. [ABSTRACT FROM AUTHOR]

Background: Ticks are vectors of numerous pathogens, with their bacterial composition, abundance, diversity, and interaction influencing both their growth and disease transmission efficiency. Despite the abundance of ticks in Inner Mongolia, China, comprehensive data on their microbial communities are lacking. This study aims to analyze the microbial communities within ticks from Inner Mongolia to inform innovative control strategies for interrupting pathogen transmission. Methods: Tick samples were collected from animals and vegetation in multiple locations across Inner Mongolia and stored at − 80 °C. Ticks were identified using morphological keys and molecular biology methods. Full-length 16S rRNA gene sequencing was performed on collected samples. Bacterial community composition and diversity were mainly analyzed using bioinformatic tools such as QIIME, phyloseq, and DESeq2. Alpha diversity was assessed using Chao1, ACE, and Shannon indices, while beta diversity was evaluated using Bray-Curtis dissimilarity matrices. LEfSe analysis was applied to identify taxa associated with ecological and biological variables. Results: A total of 5,048,137 high-quality read counts were obtained, forming an average of 789.3 OTUs per sample. Proteobacteria, Firmicutes, and Bacteroidetes were the most dominant phyla. Bacterial community composition varied significantly with geography, with Dermacentor nuttalli showing a higher abundance of Rickettsia in Xilingol League, while other regions had different dominant genera. The microbial community also differed based on the feeding status of ticks. Additionally, the microbiota of engorged ticks showed organ specificity. Pathogen detection efforts revealed the presence of nine pathogens across all three tick species. D. nuttalli was found to carry a significantly higher burden of pathogenic bacteria, making it the most potentially threatening tick species in Inner Mongolia. Conclusions: The study highlights significant variations in tick microbiomes influenced by geographic location, feeding status, and tick species. It underscores the importance of enhancing tick and tick-borne disease surveillance in Inner Mongolia for early detection and control of emerging pathogens. [ABSTRACT FROM AUTHOR]

The invasion of phytopathogens impacts the composition and associations of the internal microbial inhabitants. Leaf spot is one of the most devastating diseases in eggplant var. Mattu Gulla which is unique in terms of geographic indication (GI) status. Leaf spot samples (asymptomatic and symptomatic) were collected to characterize the fungal community associated with them using culture-based and next-generation ITS rRNA-based metabarcoding approaches. Both methods showed that Ascomycota and Basidiomycota were the predominant phyla in both groups. In the asymptomatic group, Didymosphaeriaceae, Pleosporaceae, Trichomeriaceae, and Capnodiaceae were the most differentially abundant families. In contrast, Phaeosphaeriaceae, Pleosporaceae, Didymellaceae, Rhynchogastremataceae, and Bulleribasidiaceae were the most differentially abundant families in the symptomatic group. At the genus level, Cladosporium was the most differentially abundant genus in the asymptomatic group. In the symptomatic group Alternaria, Remotididymella, Vishniacozyma, Bulleribasidium, Occultifur, Epicoccum, and Loratospora were the abundant genera. The pathotroph-saprotrophic mode was the most common mode identified in both groups, with an increased abundance in the symptomatic group. Seven fungal families and two genera were identified as common according to the culture-based method and NGS analysis based on ITS rRNA metabarcoding. Our study indicated that the composition of the core microbial community varies with plant health status, and a combination of culturable and next-generation ITS rRNA-based metabarcoding approaches could be a reliable option for obtaining a detailed understanding of plant-associated fungal communities. [ABSTRACT FROM AUTHOR]

Biohydrogen production by dark fermentation (DF) can be achieved using only indigenous bacteria from substrates or by adding an external inoculum. This study aims to provide new insights on the role of indigenous bacteria in DF process operation by investigating DF performances and microbiological aspects. DF tests are performed with only indigenous bacteria, with indigenous and exogenous bacteria and with only exogenous bacteria by inactivating indigenous bacteria by gamma irradiation. Sorghum irradiation reduces DF performances for both hydrogen (17.8 ± 12.8 versus 45.2 ± 1.7 mLH 2 /gVS added) and total metabolite (0.22 ± 0.01 versus 0.30 ± 0.01 gCOD/gVS added) yields. In contrast, no difference is observed with the organic fraction of municipal solid waste, suggesting a distinct role of indigenous bacteria for both substrates. Indigenous bacteria inactivation strongly modifies the metabolic routes and final bacterial community composition. This study proves the key role of indigenous bacteria in influencing metabolite production and bacterial composition. [Display omitted] • Successful inactivation of indigenous bacteria by gamma irradiation. • Lower performances of dark fermentation for irradiated sorghum. • No impact OFMSW irradiation on hydrogen yield and biomass bioconversion. • Metabolic and microbiological changes after irradiation of both substrates. • Lower reproducibility of DF experiments after indigenous bacteria inactivation. [ABSTRACT FROM AUTHOR]

Rhizosphere microbial communities strongly affect outbreaks of root-knot nematode (RKN) disease. However, little is known about the interactions among fungi, bacteria and RKN. The bacterial and fungal community compositions in the rhizospheres of four representative tobacco varieties, both resistant and susceptible to RKN, were characterized using 16S rRNA gene sequencing for bacteria and internal transcribed spacer gene sequencing for fungi. Our findings revealed that the fungi played crucial roles in facilitating the cross-kingdom and symbiotic fungal–bacterial interactions to suppress RKN. Moreover, our investigation suggested Microbacterium as a potential microbial antagonist against RKN based on its enhanced presence in RKN-resistant tobacco genotypes, and the relative abundance of Microbacterium was 34.49% greater in the rhizosphere of resistant tobacco than that of susceptible tobacco significantly. Notably, the richness of fungal community enhanced tobacco's microbe-associated resistance to RKN through the positive regulation of the richness and diversity of bacterial community and the relative abundance of Microbacterium. This study underscores the critical role of the fungus–dominated fungal–bacterial community in bolstering tobacco resistance against RKN. The potential antagonistic role of Microbacterium presents promising avenues for innovative RKN management strategies. [ABSTRACT FROM AUTHOR]

The increasing prevalence of non-tuberculous mycobacterium (NTM) infections alongside tuberculosis (TB) underscores a pressing public health challenge. Yet, the mechanisms governing their infection within the lung remain poorly understood. Here, we integrate metagenomic sequencing, metabolomic sequencing, machine learning classifiers, SparCC, and MetOrigin methods to profile bronchoalveolar lavage fluid (BALF) samples from NTM/TB patients. Our aim is to unravel the intricate interplay between lung microbial communities and NTM/ Mycobacterium tuberculosis infections. Our investigation reveals a discernible reduction in the compositional diversity of the lung microbiota and a diminished degree of mutual interaction concomitant with NTM/TB infections. Notably, NTM patients exhibit a distinct microbial community characterized by marked specialization and notable enrichment of Pseudomonas aeruginosa and Staphylococcus aureus , driving pronounced niche specialization for NTM infection. Simultaneously, these microbial shifts significantly disrupt tryptophan metabolism in NTM infection, leading to an elevation of kynurenine. Mycobacterium intracellulare , Mycobacterium paraintracellulare , Mycobacterium abscessus , and Pseudomonas aeruginosa have been implicated in the metabolic pathways associated with the conversion of indole to tryptophan via tryptophan synthase within NTM patients. Additionally, indoleamine-2,3-dioxygenase converts tryptophan into kynurenine, fostering an immunosuppressive milieu during NTM infection. This strategic modulation supports microbial persistence, enabling evasion from immune surveillance and perpetuating a protracted state of NTM infection. The elucidation of these nuanced microbial and metabolic dynamics provides a profound understanding of the intricate processes underlying NTM and TB infections, offering potential avenues for therapeutic intervention and management. [ABSTRACT FROM AUTHOR]

Introduction: The Hainan Dong goat (DG) is a local meat breed widely raised in Hainan, China because of its good adaptability to local hot and humid weather. However, the growth rate of these DG is much slower than that of commercialised breeds improved in European countries, resulting in poor carcase characteristics, including smaller slaughter weight and carcase weight, which have become increasingly prominent. In recent decades, Nubian goats have been continuously imported into China to improve the production performance of local breeds. Methods: In this study, the effects of breed on growth performance, carcase and meat quality, and ruminal microbiota were analysed in 40 goats, including 20 DGs and 20 hybrid F3 offspring generated by crossing the DG and Nubian hybrids (NH). All the goats were averagely aged 90 days and weighed at 11 ± 1.34 kg. They were assigned to two treatments, with three replicates per treatment. The two groups were fed the same diet for 90 days before slaughter. Results: The results showed that the average daily gain, F/G ratio, slaughter weight, and carcase weight of the NH group were higher than those of the DG group (p < 0.05). However, tube circumference, meat-to-bone ratio, and eye muscle pH were lower in the NH group than in the DG group (p < 0.05). The NH group showed a smaller fibre crosssectional area and fibre diameter, but a larger fibre density than the DG group (p < 0.05). Bacteroidetes and Firmicutes were the most dominant phyla in the two groups; however, the two breeds had different ruminal microbial communities. Discussion: In the present study, the differences in growth performance between two groups of goats under the same feeding environment and feed conditions were compared. The correlation between feed sources and rumen flora has been demonstrated, and the results of this study show that the same diet has similar effects on rumen microorganisms, which in turn have related effects on growth and production performance. Conclusion: In summary, hybrids can improve the growth and slaughter performance of local breeds, which may be related to changes in the rumen microorganisms. This study revealed that crossbreeding of Nubian goats with Dong goats has the potential to be used in a wide range of applications owing to its effectiveness in increasing production efficiency. [ABSTRACT FROM AUTHOR]

Polycystic ovary syndrome (PCOS) is a complex endocrine and metabolic disorder characterized by hyperandrogenism, prolonged anovulation and polycystic ovaries. However, there are no effective interventions to treat this disorder. As previously shown, mangiferin modulated the AMPK and NLRP3 signal pathways to alleviate nonalcoholic fatty liver disease (NAFLD). In recent years, mangiferin has emerged as a promising drug candidate for treating metabolic diseases. In this study, we evaluated the effects of mangiferin on a letrozole (LET) combined with high-fat diet (HFD)-induced PCOS rat model through estrous cycle detection, serum/tissue biochemical analysis, and hematoxylin and eosin (HE) staining of ovarian tissue. The mechanisms of mangiferin's effects on PCOS rats were analyzed using 16S rRNA sequencing, RNA-seq, western blotting (WB), and immunohistochemical (IHC) staining. Our results displayed that mangiferin showed a promising effect in PCOS rats. It improved lipid metabolism, glucose tolerance, insulin resistance, hormonal imbalance, ovarian dysfunction, and adipocyte abnormalities. RNA-seq analysis indicated that mangiferin may be involved in several signal pathways, including apoptosis, necrosis, and inflammation. Furthermore, western blot and immunohistochemical staining demonstrated that mangiferin regulates Caspase-3 and Cytc, exhibiting anti-apoptotic activity in the ovaries. Additionally, mangiferin significantly altered the gut microbiota community of PCOS rats, changing the abundance of firmicutes, bacteroidota, proteobacteria, and actinobacteria at the phylum level and the abundance of Blautia , Coprococcus , Roseburia, and Pseudomonas at the genus level. In conclusion, mangiferin is a promising and novel therapeutic agent for PCOS as it ameliorates insulin resistance, gut microbiota and ovarian cell apoptosis. [ABSTRACT FROM AUTHOR]

Background: Gut microbes are important to the health and fitness of many animals. Many factors have been shown to affect gut microbial communities including diet, lifestyle, and age. Most animals have very complex physiologies, lifestyles, and microbiomes, making it virtually impossible to disentangle what factors have the largest impact on microbiota composition. Honeybees are an excellent model to study host-microbe interactions due to their relatively simple gut microbiota, experimental tractability, and eusociality. Worker honey bees have distinct gut microbiota from their queen mothers despite being close genetic relatives and living in the same environment. Queens and workers differ in numerous ways including development, physiology, pheromone production, diet, and behavior. In the prolonged absence of a queen or Queen Mandibular Pheromones (QMP), some but not all workers will develop ovaries and become "queen-like". Using this inducible developmental change, we aimed to determine if diet and/or reproductive development impacts the gut microbiota of honey bee workers. Results: Microbiota-depleted newly emerged workers were inoculated with a mixture of queen and worker gut homogenates and reared under four conditions varying in diet and pheromone exposure. Three weeks post-emergence, workers were evaluated for ovary development and their gut microbiota communities were characterized. The proportion of workers with developed ovaries was increased in the absence of QMP but also when fed a queen diet (royal jelly). Overall, we found that diet, rather than reproductive development or pheromone exposure, led to more "queen-like" microbiota in workers. However, we revealed that diet alone cannot explain the microbiota composition of workers. Conclusion: The hypothesis that reproductive development explains microbiota differences between queens and workers was rejected. We found evidence that diet is one of the main drivers of differences between the gut microbial community compositions of queens and workers but cannot fully explain the distinct microbiota of queens. Thus, we predict that behavioral and other physiological differences dictate microbiota composition in workers and queens. Our findings not only contribute to our understanding of the factors affecting the honey bee microbiota, which is important for bee health, but also illustrate the versatility and benefits of utilizing honeybees as a model system to study host-microbe interactions. [ABSTRACT FROM AUTHOR]

Determining the effects of fermentation duration on the microbial ecosystem, potential pathogenic risks, and metabolite generation during the fermentation of distilled grains is essential for safeguarding the safety and enhancing the nutritional profile of animal feed. This study investigates the effect of varying fermentation times (9, 30, and 60 days) on microbial diversity, pathogenic risk, and metabolite profiles in distiller grains using 16S rDNA sequencing and LC–MS-based metabolomics. The results showed that early fermentation (9–30 days) enhanced the abundance of beneficial bacteria, such as Lactobacillus reuteri and Lactobacillus pontis (p < 0.05), while pathogenic bacteria, like Serratia marcescens and Citrobacter freundii, were significantly reduced (p < 0.05). Metabolomic analysis revealed an increase in unsaturated fatty acids and the degradation of biogenic amines during early fermentation. However, prolonged fermentation (60 days) led to a resurgence of pathogenic bacteria and reduced the synthesis of essential metabolites. These findings suggest that fermentation duration must be optimized to balance microbial safety and nutrient quality, with 30 days being the optimal period to reduce pathogenic risks and enhance feed quality. [ABSTRACT FROM AUTHOR]

Microbes play an important role in human and animal health, as well as animal productivity. The host microbial interactions within ruminants play a critical role in animal health and productivity and provide up to 70% of the animal's energy needs in the form of fermentation products. As such, many studies have investigated microbial community composition to understand the microbial community changes and factors that affect microbial colonization and persistence. Advances in next-generation sequencing technologies and the low cost of sequencing have led many studies to use 16S rDNA-based analysis tools for interrogation of microbiomes at a much finer scale than traditional culturing. However, methods that rely on single base pair differences for bacterial taxa clustering may inflate or underestimate diversity, leading to inaccurate identification of bacterial diversity. Therefore, in this study, we sequenced mock communities of known membership and abundance to establish filtration parameters to reduce the inflation of microbial diversity due to PCR and sequencing errors. Additionally, we evaluated the effect of the resulting filtering parameters proposed using established bioinformatic pipelines on a study consisting of Holstein and Jersey cattle to identify breed and treatment effects on the bacterial community composition and the impact of filtering on global microbial community structure analysis and results. Filtration resulted in a sharp reduction in bacterial taxa identified, yet retain most sequencing data (retaining >79% of sequencing reads) when analyzed using 3 different microbial analysis pipelines (DADA2, Mothur, USEARCH). After filtration, conclusions from α-diversity and β-diversity tests showed very similar results across all analysis methods. The mock community-based filtering parameters proposed in this study help provide a more realistic estimation of bacterial diversity. Additionally, filtration reduced the variation between microbiome analysis methods and helped to identify microbial community differences that could have been missed due to the large animal-to-animal variation observed in the unfiltered data. As such, we believe the new filtering parameters described in this study will help to obtain diversity estimates that are closer to realistic values, improve the ability to detecting microbial community differences, and help to better understand microbial community changes in 16S rDNA-based studies. The list of standard abbreviations for JDS is available at adsa.org/jds-abbreviations-24. Nonstandard abbreviations are available in the Notes. [ABSTRACT FROM AUTHOR]

Leaf litter in coastal wetlands lays the foundation for carbon storage, and the creation of coastal wetland soils. As climate change alters the biogeochemical conditions and macrophyte composition of coastal wetlands, a better understanding of the interactions between microbial communities, changing chemistry, and leaf litter is required to understand the dynamics of coastal litter breakdown in changing wetlands. Coastal wetlands are dynamic systems with shifting biogeochemical conditions, with both tidal and seasonal redox fluctuations, and marine subsidies to inland habitats. Here, we investigated gene expression associated with various microbial redox pathways to understand how changing conditions are affecting the benthic microbial communities responsible for litter breakdown in coastal wetlands. We performed a reciprocal transplant of leaf litter from four distinct plant species along freshwater‐to‐marine gradients in the Florida Coastal Everglades, tracking changes in environmental and litter biogeochemistry, as well as benthic microbial gene expression associated with varying redox conditions, carbon degradation, and phosphorus acquisition. Early litter breakdown varied primarily by species, with highest breakdown in coastal species, regardless of the site they were at during breakdown, while microbial gene expression showed a strong seasonal relationship between sulfate cycling and salinity, and was not correlated with breakdown rates. The effect of salinity is likely a combination of direct effects, and indirect effects from associated marine subsidies. We found a positive correlation between sulfate uptake and salinity during January with higher freshwater inputs to coastal areas. However, we found a peak of dissimilatory sulfate reduction at intermediate salinity during April when freshwater inputs to coastal sites are lower. The combination of these two results suggests that sulfate acquisition is limiting to microbes when freshwater inputs are high, but that when marine influence increases and sulfate becomes more available, dissimilatory sulfate reduction becomes a key microbial process. As marine influence in coastal wetlands increases with climate change, our study suggests that sulfate dynamics will become increasingly important to microbial communities colonizing decomposing leaf litter. [ABSTRACT FROM AUTHOR]

Plant resource allocation strategies are thought to be largely a consequence of changing abiotic conditions and evolutionary history. However, biotic interactions also influence how a plant allocates resources. As a result, plants mediate indirect interactions between organisms above‐ and belowground through resource allocation. Neighboring plants can influence plant fitness directly through competition for resources, and indirectly by altering associated community interactions (associational effects), such as pollination, herbivory, and a suite of belowground interactions. Given the importance of community interactions for plant success, and the known ability for plant neighbors to change these interactions, the goal of this "pandemic project" was to understand how heterospecific plant neighbors alter plant resource allocation, whether this occurred through above‐ or belowground mechanisms, and whether this in turn alters biotic interactions and the relationship between a focal plant and its herbivore and soil community interactions. To do so, we established a common garden experiment, manipulating plant neighbor identity and the extent of interaction among neighbors (aboveground only, vs. above‐ and belowground interactions, using customized pot types), and measured changes to a focal plant and its biotic interactions over two growing seasons. We found evidence of both neighbor effects and pot type, showing that neighbor interactions affect a focal plant through both above‐ and belowground processes, and how the focal plant is affected depends on neighbor identity. Though neighbors did not directly alter herbivory or most soil microbial interactions, they did alter the relationship between belowground microbial communities and a plant response trait (specific leaf area). Plant resource allocation responses were reduced with time, showing the importance of extending experiments beyond a single growing season, and are an important consideration when making predictions about plant responses to changing conditions. This study contributes to a growing body of work showing how community contexts affect the above‐ and belowground interactions of a plant through plant resource allocation strategies. [ABSTRACT FROM AUTHOR]

Background: Cervical ripening is a multifactorial outcome, and the association between cervical ripening and vaginal microbiota remains unexplored in term primiparous women. A new sequencing technology, microbiome 2bRAD sequencing (2bRAD-M) that provides a higher level of species discrimination compared to amplicon sequencing. We applied 2bRAD-M to analyze the vaginal microbiota in a population with variations in cervical ripeness and to explore potential microbiota factors influencing cervical ripening. Methods: A total of 30 full-term primigravid women participated in this study, with 15 belonging to the low scoring group of cervical ripeness and 15 to the high scoring group. Clinical information was collected from the participants, and the vaginal microbiota and community structure of both groups were analyzed using 2bRAD-M sequencing. Microbiota diversity and differential analyses were conducted to explore potential factors influencing cervical ripening. Results: A total of 605 species were detected. There was no difference in vaginal microbiota diversity between the two groups, and the vaginal microbial composition was structurally similar. In the two groups, Lactobacillus crispatus and Lactobacillus iners were identified as the two pivotal species through random forest analysis. Concurrent, extensive and close connections between species within the two groups were observed in the correlation analysis, influencing the aforementioned two species. Pairwise comparisons showed that Sphingomonas (P = 0.0017) and three others were abundant in high scoring group, while Alloprevotella (P = 0.0014), Tannerella (P = 0.0033), Bacteroides (P = 0.0132), Malassezia (P = 0.0296), Catonella (P = 0.0353) and Pseudomonas (P = 0.0353) and so on showed higher abundance in low scoring group. Linear discriminant analysis effect size identified 29 discriminative feature taxa. Conclusion: For the first time, vaginal microbiota was sequenced using 2bRAD-M. With a relatively simple structure, a more stable vaginal microbiota is associated with higher cervical ripeness, and certain microorganisms, such as Sphingomonas, may play a beneficial role in cervical ripening. [ABSTRACT FROM AUTHOR]

Hadal trenches represent the deepest oceanic realm and were once considered to be deprived of life. However, trenches act as important depocenters for organic matter with highly elevated microbial activity. In this forum, we discuss the biogeochemistry of the hadal realm and its microbial communities thriving at extreme hydrostatic pressure. [ABSTRACT FROM AUTHOR]

Increasingly, researchers are interested in quantifying temporal dynamics of host-associated microbiomes, yet an individual-host approach is still rare in the literature. Detailed longitudinal data from wild individual hosts are key to understanding the fitness implications of temporal microbiome stability and dynamics. Whether stability or flexibility of host-associated microbiomes is beneficial to a host will depend on the ecological context, and so incorporating knowledge of host ecology to these individual-level approaches is vital. Recent advances in analytical approaches may provide helpful tools in testing hypotheses of individual variation in microbiome temporal stability and the consequences of this for host fitness. Ignoring the dynamic nature of microbial communities risks underestimating the power of microbes to impact the health of their hosts. Microbiomes are thought to be important for host fitness, yet the coarse temporal scale and population-level focus of many studies precludes the ability to investigate the importance of among-individual variation in stability and identify the ecological contexts in which this variation matters. Here we briefly summarise current knowledge of temporal dynamics in wild host-associated microbial communities. We then discuss the implications of among-individual variation in microbiota stability and suggest analytical approaches for understanding these patterns. One major requirement is for future studies to conduct individual-level longitudinal analyses, with some systems already well set up for answering these questions. [ABSTRACT FROM AUTHOR]

Mine environments in boreal and sub-boreal zones are expected to experience extreme weather events, increases in temperature, and shifts in precipitation patterns. Climate change impacts on geochemical stability of tailings contaminants and reclamation structures have been identified as important climate-related challenges to Canadian mining sector. Adapting current reclamation strategies for climate change will improve long-term efficiency and viability of mine tailings remediation/restoration strategies under a changing climate. Accordingly, mesocosm experiments were conducted to investigate associations of climate-driven shifts in microbial communities and functions with changes in the geochemistry of organic covers and underlying tailings. Our results show that warming appears to significantly reduce C:N of organic cover and promote infiltration of nitrogen into deeper, unoxidized strata of underlying tailings. We also observed an increase in the abundance of some nitrate reducers and sulfide oxidizers in microbial communities in underlying tailings. These results raise the concern that warming might trigger oxidation of sulfide minerals (linked to nitrate reduction) in deeper unoxidized strata where the oxygen has been eliminated. Therefore, it would be necessary to have monitoring programs to track functionality of covers in response to climate change conditions. These findings have implications for development of climate resilient mine tailings remediation/restoration strategies. [ABSTRACT FROM AUTHOR]

The use of wood ash as a soil amendment remains restricted in many parts of Canada. To better understand belowground biogeochemical responses to wood ash, soil solution chemistry was measured over 3 years following the application of wood ash (0, 2.5, 5.0, and 7.5 Mg·ha−1) at a hardwood stand in Ontario, after which soil microbial response was assessed using 16S rRNA gene and internal transcribed spacer sequencing. Metal concentrations in the locally sourced wood ash were below provincial regulatory limits. Significant increases in soil solution pH were observed within the forest floor in the first year of the trial, and significant increases in calcium and magnesium were also observed in later years of the trial. Concentrations of most metals in soil water either decreased or exhibited no significant change in response to wood ash. There was an increase in diversity and richness of soil prokaryotic groups in the FH horizon at the highest wood ash treatment that is most likely linked to the large increase in pH. This study indicates that wood ash has a strong ameliorative effect on soil and soil water chemistry without major changes to soil microbial communities and is a viable amendment to forest soils at dosages below 5 Mg·ha−1. [ABSTRACT FROM AUTHOR]

Stuccoes are very delicate decorative elements of Roman age. Very few of them survived almost intact to present days and, for this reason, they are of great interest to restorers and conservators. In this study, we combined metabarcoding and untargeted metabolomics to characterise the taxonomic and metabolic profiles of the microorganisms forming biofilms on the stuccoes located on the ceiling of the laconicum, a small thermal environment in the archaeological park of Baia (southern Italy). We found that some samples were dominated by bacteria while others by eukaryotes. Additionally, we observed high heterogeneity in the type and abundance of bacterial taxa, while the eukaryotic communities, except in one sample (at prevalence of fungi), were dominated by green algae. The metabolic profiles were comparable across samples, with lipids, lipid-like molecules and carbohydrates accounting for roughly the 50% of metabolites. In vitro and in vivo tests to remove biofilms on stuccoes using essential oils blends were successful at a 50% dilution for one hour and half. This integrative study advanced our knowledge on taxonomic and metabolic profiles of biofilms on ancient stuccoes and highlighted the potential impacts of these techniques in the field of cultural heritage conservation. [ABSTRACT FROM AUTHOR]

Microbial communities thrive through interactions and communication, which are challenging to study as most microorganisms are not cultivable. To address this challenge, researchers focus on the extracellular space where communication events occur. Exometabolomics and interactome analysis provide insights into the molecules involved in communication and the dynamics of their interactions. Advances in sequencing technologies and computational methods enable the reconstruction of taxonomic and functional profiles of microbial communities using high-throughput multi-omics data. Network-based approaches, including community flux balance analysis, aim to model molecular interactions within and between communities. Despite these advances, challenges remain in computer-assisted biosynthetic capacities elucidation, requiring continued innovation and collaboration among diverse scientists. This review provides insights into the current state and future directions of computer-assisted biosynthetic capacities elucidation in studying microbial communities. ONE SENTENCE SUMMARY: Computer-assisted biosynthetic capacities elucidation accelerates our ability to interpret microbial interactions, allowing us to understand better and establish a balance within ecosystems. [ABSTRACT FROM AUTHOR]

Litter decomposition has historically been attributed to soil microbial community at local scale, but which fundamental process directly contributes to carbon release from decomposing litter remains not fully understood. Here we used in situ microcosms to assess the temporal changes in soil microbial biomass, taxonomic composition, alpha and beta diversity, network complexity and carbon-degrading functional genes during litter decomposition of a subtropical dominant species (Castanopsis carlesii) in an older (45-years) and a younger (9-years) evergreen broadleaved forests. The soil phospholipid fatty acids, bacterial and fungal community composition, α-diversity indexes and network topological properties were not changed significantly after short-term litter input when litter was decomposed by approximately 70%. However, the absolute abundance of functional genes involved in the decomposition of starch, pectin, hemicellulose, cellulose, chitin and lignin were up-regulated, and these variations were associated with soil α-1.4-glucosidase, β-glucosidase and cellobiohydrolase activities in contributing to litter carbon release during decomposition. These results suggest that the upregulation of functional genes rather than microbial community composition and diversity controls local-scale litter decomposition by encoding and secreting enzymes in these subtropical forests. [ABSTRACT FROM AUTHOR]

Phytoremediation of oil pollution using free-floating aquatic plants is a promising method for water body cleaning. In this study, the influence of Eichhornia crassipes and Pistia stratiotes on the degradation of oil pollution was investigated. The loss of oil alkanes and the rheological characteristics of water were evaluated, and an analysis of the emerging rhizospheric microbial communities was carried out using high-throughput sequencing. The presence of E. crassipes and P. stratiotes plants in oil-contaminated tanks had no effect on the degradation of oil alkanes. However, the presence of plants promoted the development of rhizospheric bacteria capable of growing in oil-contaminated environments. Alpha diversity of microbial communities in oil-contaminated samples was higher in the presence of plants. Additionally, plants significantly reduced the water/oil interfacial tension, which facilitated the availability of hydrocarbons for biodegradation. A difference was noted in the microbiome between E. crassipes and P. stratiotes. Changes in the composition of microbial communities highlight the potential of E. crassipes and P. stratiotes as rhizospheric hosts for microorganisms in the phytoremediation of water bodies. [ABSTRACT FROM AUTHOR]

Nitrogen is a vital nutrient for rice growth; however, its inefficient use often results in nutrient loss, environmental degradation, and the emission of greenhouse gases. In this study, a rice paddy simulation was conducted under different water levels (1–4 cm), incorporating a comprehensive analysis of nitrogen dynamics, environmental factors, and microbial communities to evaluate the impact of water levels on nitrogen concentrations and microbial composition. The results indicated that the water level had a greater impact on nitrogen concentrations in surface water than in soil water. Compared to low water level conditions (1 cm), the average concentrations of ammonium nitrogen, nitrate nitrogen, and nitrite nitrogen in surface water under 2–4 cm water levels decreased by approximately 53.8%, 36.7%, and 78.9%, respectively. Water levels also influenced the microbial composition and nitrogen cycling in paddy soil, with lower water levels promoting aerobic processes such as nitrification, while higher water levels facilitated anaerobic processes such as denitrification and dissimilatory nitrate reduction to ammonium. Correspondingly, microbial composition shifted, with aerobic bacteria predominating in shallow water conditions and anaerobic bacteria flourishing under deeper water. These findings suggest that optimized water management, particularly through shallow irrigation, may mitigate nitrogen loss and improve nitrogen use efficiency. Nevertheless, additional field studies are necessary to validate these results and explore their interaction with other agricultural practices. [ABSTRACT FROM AUTHOR]

Gray mold, caused by Botrytis cinerea, is a significant threat to tomato production. Traditional chemical control methods have become increasingly ineffective because of the development of resistance. This study aimed to isolate methanol-utilizing bacteria from tomato leaves and evaluate their biocontrol potential against gray mold. To obtain bacterial suspensions, tomato leaf samples were collected and washed. We analyzed the microbial communities of these samples using 16S rRNA amplicon sequencing and identified several methylotrophic strains. Among these, 405 isolated strains were cultivated on a solid low-nutrient inorganic salt medium containing methanol, and 7 strains exhibiting considerable antifungal activity against B. cinerea were identified. Greenhouse tests revealed that two strains--SY163 and SY183--significantly reduced the severity of gray mold on tomato leaves. Disease index scores and the area under the disease progress curve values confirmed the efficacy of these strains as biocontrol agents. Statistical analysis indicated the effectiveness of pre- and co-application of these strains with B. cinerea. Phylogenetic analysis identified Serratia rubidaea as the inhibitory strain. The biocontrol activity is likely mediated through the production of antifungal compounds and suppression of B. cinerea sporulation. This study provides the basis for developing a technology of gray mold suppression by controlling the abundance of S. rubidaea in plant microbial communities. [ABSTRACT FROM AUTHOR]

Introduction: The phenomenon in which the damage of plant diseases is suppressed by continuous cropping is defined as "suppressiveness" and the development of suppressive soils and key beneficial microorganisms have been identified through various previous studies. However, no studies have been conducted on microbial communities related to disease occurrence before the initial occurrence of diseases in crop monoculture. Methods: We aimed to investigate the ecological modifications of pathogen population density in soil, disease occurrence rate, and microbiota community shifting during ginseng monoculture to better understand the tripartite social relationships in the monoculture system. To achieve the study's objectives, a long-term monoculture of ginseng was established. The microbial diversity and community structure were analyzed using high-throughput sequencing, and the pathogen population density and disease occurrence rate were determined using qPCR and observation. Results and discussion: The results showed that the initial rhizosphere bacterial community of ginseng had already collapsed before the development of the root rot disease. The study also identified the crucial role of soil-borne pathogens in causing disease and the loss of initial keystone taxa populations in the early stages of monoculture. Our study revealed a novel aspect of soil microbiota dynamics during ginseng monoculture, with seven distinct microbes (Beijerinckiaceae, Comamonadaceae, Devosiaceae, Rhizobiaceae, Sphingobacteriaceae, Sphingomonadaceae, and Xanthomonadaceae) participating in soil nitrogen metabolism as an 'initial community' that regulates root rot disease through nutritional competition. The findings contribute to ecological research on disease-suppressiveness soil, disease management, and sustainable agriculture. [ABSTRACT FROM AUTHOR]

Prokaryotes play a crucial role in marine ecosystem health and drive biogeochemical processes. The northern Ninety East Ridge (NER) of the Indian Ocean, a pivotal yet understudied area for these cycles, has been the focus of our study. We employed high-throughput 16S rRNA gene sequencing to analyze 35 water samples from five stations along the ridge, categorized into three depth- and dissolved oxygen-level-based groups. Our approach uncovered a clear stratification of microbial communities, with key bioindicators such as Prochlorococcus MIT9313, Sva0996 marine group, and Candidatus Actinomarina in the upper layer; Ketobacter, Pseudophaeobacter, Nitrospina, and SAR324 clade in the middle layer; and Methylobacterium-Methylorubrum, Sphingomonas, Sphingobium, and Erythrobacter in the deep layer. Methylobacterium-Methylorubrum emerged as the most abundant bacterial genus, while Nitrosopumilaceae predominated among archaeal communities. The spatial and depth-wise distribution patterns revealed that Ketobacter was unique to the northern NER, whereas Methylobacterium-Methylorubrum, UBA10353, SAR324 clade, SAR406, Sva0996_marine_group, Candidatus Actinomarina were ubiquitous across various marine regions, exhibiting niche differentiation at the OTU level. Environmental factors, especially dissolved oxygen (DO), silicate, nitrate, and salinity, significantly influence community structure. These findings not only reveal the novelty and adaptability of the microbial ecosystem in the northern NER but also contribute to the broader understanding of marine microbial diversity and its response to environmental heterogeneity. [ABSTRACT FROM AUTHOR]

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Antibiotic resistance genes (ARGs) are an emerging issue which are receiving increasing concerns in drinking water safety. However, the factors (e.g. treatment processes and water quality) affecting the removal efficiency of ARGs in the drinking water treatment plants (DWTPs) is still unclear. This work investigated the ARG profiles in each treatment process of two DWTPs located in a northwest Chinese city. The results showed that tetracycline and sulfonamide resistance genes were predominant among the 14 targeted ARGs. After the treatment, the Z water treatment plant which demonstrated a higher removal rate of ARGs (ranging from 50 to 80%), compared to the S plant (50–75%). And the average removal rate of tetracycline resistance genes (tetA, tetG, tetQ, tetX) was about 49.18% (S plant) and 67.50% (Z plant), as well as the removal rate of 64.2% and 72.9% for sulfonamide resistance (sul1 and sul2) at S and Z water plants, respectively. It was found that the relative abundance of main microbial communities (such as Bacteroidota, Actinobacteria, Verrucomicrobiota, Roseomonas), α-diversity index, as well as the abundance of pathogenic bacteria were all significantly reduced after different treatment processes. Network co-occurrence analysis revealed that Methylocystis possibly was the potential host for most ARGs, and sul1 was found across a broad spectrum of microorganisms in the drinking water environment. Adonis analysis showed that heavy metals and microbial communities explain solely 44.1% and 35.7% of variances of ARGs within DWTPs. This study provides insights into the contamination status and removal efficiencies of ARGs in DWTPs, offering valuable references for future studies on ARG removal, propagation, and diffusion patterns in drinking water treatment. [ABSTRACT FROM AUTHOR]

A potentially fundamental role of termites in influencing the soil properties andprocesses of the terrestrial ecosystems is gapped here. This research on tlandscape of termite soil mounds and soil properties and their influence on microbial groups and communities is focused on the Nallamalla forest ecosystem. The soil samples were obtained from the termite hills and gardens, and then they were examined for texture, moisture level, pH, total organic carbon (TOC), total nitrogen (TN) and available phosphorus (P). Data demonstrate that the sand/clay ratio of mound soils increased to more than twice (45%). 2%), moisture content (15. 2%), pH (7. 0), TOC (2. 0%), TN (0. The doblows (as parabolic shaped discs of plant-like growth is referred to) are deeprooted (up to 2m or 20 cm), exudate P (20.1 mg/kg) to a level that is over three times that of the surrounding soils. While, in the termite mound soil microbial community chains analysis indicates the higher bacterial and fungal diversity (Proteobacteria - the dominant group with a share of 35%, and Actinobacteria - the other most representative group that has 25%), the main fungal groups are Ascomycota (they have 50% share) and Basidiomycota (30%). This implies that the role of termites is that there is a major influence soil properties and microbial communities and this should be known since they play the ecosystem function and maintain resilience. [ABSTRACT FROM AUTHOR]

Saline lakes, characterized by high salinity and limited nutrient availability, provide an ideal environment for studying extreme halophiles and their biogeochemical processes. The present study examined prokaryotic microbial communities and their ecological functions in lentic sediments (with the salinity gradient and time series) using 16S rRNA amplicon sequencing and a metagenomic approach. Our findings revealed a negative correlation between microbial diversity and salinity. The notable predominance of Archaea in high-salinity lakes signified a considerable alteration in the composition of the microbial community. The results indicate that elevated salinity promotes homogeneous selection pressures, causing substantial alterations in microbial diversity and community structure, and simultaneously hindering interactions among microorganisms. This results in a notable decrease in the complexity of microbial ecological networks, ultimately influencing the overall ecological functional responses of microbial communities such as carbon fixation, sulfur, and nitrogen metabolism. Overall, our findings reveal salinity drives a notable predominance of Archaea, selects for species adapted to extreme conditions, and decreases microbial community complexity within saline lake ecosystems. [ABSTRACT FROM AUTHOR]

Pharmaceuticals can directly inhibit the growth of gut bacteria, but the degree to which such interactions manifest in complex community settings is an open question. Here, we compared the effects of 30 drugs on a 32-species synthetic community with their effects on each community member in isolation. While most individual drug-species interactions remained the same in the community context, communal behaviors emerged in 26% of all tested cases. Cross-protection during which drug-sensitive species were protected in community was 6 times more frequent than cross-sensitization, the converse phenomenon. Cross-protection decreased and cross-sensitization increased at higher drug concentrations, suggesting that the resilience of microbial communities can collapse when perturbations get stronger. By metabolically profiling drug-treated communities, we showed that both drug biotransformation and bioaccumulation contribute mechanistically to communal protection. As a proof of principle, we molecularly dissected a prominent case: species expressing specific nitroreductases degraded niclosamide, thereby protecting both themselves and sensitive community members. [Display omitted] • Bacteria can be protected from and sensitized to drugs in a community context • Cross-protection and community resilience dissipate at high drug concentrations • Drug biotransformation and bioaccumulation can partially explain communal protection • Enzyme specificity and expression dictate detoxification of nitroaromatic drugs A comparison of the effects of pharmaceuticals on different gut bacterial species when grown alone or as part of a community shows that complex microbial communities can protect, and less frequently sensitize, community members to the treatment. Both drug biotransformation and bioaccumulation are key to community protection, which can be overwhelmed at high drug concentrations. [ABSTRACT FROM AUTHOR]