Microbial Diversity Composition Research Articles

16S rRNA female reproductive microbiome investigation reveals Dalfopristin, Clorgyline, and Hydrazine as potential therapeutics for the treatment of bacterial vaginosis

Bacterial vaginosis (BV) is a prevalent vaginal illness resulting from a disruption in the vaginal microbial equilibrium. The vaginal microbiota has been shown to have a substantial impact on the development and continuation of BV. This work utilized 16S rRNA sequence analysis of vaginal microbiome samples (Control vs BV samples) utilizing Parallel-Meta 3 to investigate the variations in microbial composition. The unique genes identified were used to determine prospective therapeutic targets and their corresponding inhibitory ligands. Further, molecular docking was conducted and then MD simulations were carried out to confirm the docking outcomes. In the BV samples, we detected several anaerobic bacteria recognized for their ability to generate biofilms, namely Acetohalobium, Anaerolineaceae, Desulfobacteraceae, and others. Furthermore, we identified Dalfopristin, Clorgyline, and Hydrazine as potential therapeutic options for the management of BV. This research provides new insights into the causes of BV and shows the potential effectiveness of novel pharmacological treatments.

Analyzing microbial communities and metabolic functions in estuaries affected by human activity to uncover bioelectrochemical system potential

In the context of bioelectrochemical systems (BES), a profound understanding of the taxonomic composition within indigenous microbial communities is crucial. Their metabolic versatility assumes a foundational role in dictating the functionality of BES, yielding diverse applications for bioenergy production and bioremediation in anthropogenically impacted estuaries. Employing high-throughput sequencing of the V3-V4 region of 16S rRNA and predictive metagenomic analyses of three different estuaries samples (eutrophicated urban reservoir, mud volcano impacted river, and its river mouth), this study delves into the intricate interplay between these communities and their metabolic functions in response to human-induced perturbations, with a specific focus on their applicability to BES. Our findings illuminate remarkable distinctions among the three samples, manifesting in variations in microbial composition and functional metabolic pathways within the respective ecosystems. The mud volcano-affected river, characterized by the highest microbial diversity, exhibited the most diverse array of functional metabolic processes, prominently dominated by chemoheterotrophy (67.43%). In contrast, the river mouth displayed a distinct penchant for autotrophy (33.33%). The eutrophicated urban reservoir showcased a balanced coexistence of chemoheterotrophy (41.18%) and autotrophy (35.29%). Regarding metabolic potential for BES application, most of metabolism potential were associated with anodic activity, while cathodic activity was restricted to autotrophy and its relatives. The results suggested that the microbial communities anthropogenically impacted estuaries were potentially used for anodic and cathodic reactions in BES as electrogens to generate bioelectricity and reduce of pollutants.

Features of the lung microbiota in tuberculosis infection

Normal lung microbiota is a small number of transient microbes; however, respiratory pathology may be associated with persistent microbial colonization of the lungs. It remains a poorly understood and mysterious part of the pathogenesis of tuberculosis infection.The review considers the general pathogenetic mechanisms of the effect of lung microbiota in respiratory pathology and presents the main methodological difficulties in the study of the lung microbiome. This review is aimed at analyzing the results of the available studies on diverse microbial composition of human lungs in tuberculosis using metagenomic sequencing methods. Despite high variability of the presented data, we can conclude that dysbiosis in tuberculosis is more often characterized by a decrease in bacterial diversity and enrichment of lung microbiota with anaerobic bacteria. Acinetobacter, Campylobacter, Moraxella, Pseudomonas, Staphylococcus, and Streptococcus, as well as some other microorganisms are indicated as important pathogenetic factors of dysbiosis in pulmonary tuberculosis, the role of which is yet to be elucidated.

Phylosymbiosis and metabolomics resolve phenotypically plastic and cryptic sponge species in the genus Agelas across the Caribbean basin.

Fundamental to holobiont biology is recognising how variation in microbial composition and function relates to host phenotypic variation. Sponges often exhibit considerable phenotypic plasticity and also harbour dense microbial communities that function to protect and nourish hosts. One of the most prominent sponge genera on Caribbean coral reefs is Agelas. Using a comprehensive set of morphological (growth form, spicule), chemical and molecular data on 13 recognised species of Agelas in the Caribbean basin, we were able to define only five species (=clades) and found that many morphospecies designations were incongruent with phylogenomic and population genetic analyses. Microbial communities were also strongly differentiated between phylogenetic species, showing little evidence of cryptic divergence and relatively low correlation with morphospecies assignment. Metagenomic analyses also showed strong correspondence to phylogenetic species, and to a lesser extent, geographical and morphological characters. Surprisingly, the variation in secondary metabolites produced by sponge holobionts was explained by geography and morphospecies assignment, in addition to phylogenetic species, and covaried significantly with a subset of microbial symbionts. Spicule characteristics were highly plastic, under greater impact from geographical location than phylogeny. Our results suggest that while phenotypic plasticity is rampant in Agelas, morphological differences within phylogenetic species affect functionally important ecological traits, including the composition of the symbiotic microbial communities and metabolomic profiles.

Surface Topography, Microbial Adhesion, and Immune Responses in Silicone Mammary Implant-Associated Capsular Fibrosis.

Breast cancer is the most common cancer in women globally, often necessitating mastectomy and subsequent breast reconstruction. Silicone mammary implants (SMIs) play a pivotal role in breast reconstruction, yet their interaction with the host immune system and microbiome remains poorly understood. This study investigates the impact of SMI surface topography on host antimicrobial responses, wound proteome dynamics, and microbial colonization. Biological samples were collected from ten human patients undergoing breast reconstruction with SMIs. Mass spectrometry profiles were analyzed for acute and chronic wound proteomes, revealing a nuanced interplay between topography and antimicrobial response proteins. 16S rRNA sequencing assessed microbiome dynamics, unveiling topography-specific variations in microbial composition. Surface topography alterations influenced wound proteome composition. Microbiome analysis revealed heightened diversity around rougher SMIs, emphasizing topography-dependent microbial invasion. In vitro experiments confirmed staphylococcal adhesion, growth, and biofilm formation on SMI surfaces, with increased texture correlating positively with bacterial colonization. This comprehensive investigation highlights the intricate interplay between SMI topography, wound proteome dynamics, and microbial transmission. The findings contribute to understanding host-microbe interactions on SMI surfaces, essential for optimizing clinical applications and minimizing complications in breast reconstruction.

Two promising candidates for paratransgenesis, Elizabethkingia and Asaia, increase in both sexes of Anopheles gambiae mosquitoes after feeding

BackgroundThe male mosquito microbiome may be important for identifying ideal candidates for disease control. Among other criteria, mosquito-associated symbionts that have high localization in both male and female mosquitoes and are transmissible through both vertical and sexual routes are desirable. However, mosquito microbiome studies have mainly been female-focused. In this study, the microbiota of male and female Anopheles gambiae sensu lato (s.l.) were compared to identify shared or unique bacteria.MethodsLate larval instars of Anopheles mosquitoes were collected from the field and raised to adults. Equal numbers of males and females of 1-day-old non-sugar-fed, 4–5-day-old sugar-fed and post-blood-fed females were randomly selected for whole-body analyses of bacteria 16S rRNA.ResultsResults revealed that male and female mosquitoes generally share similar microbiota except when females were blood-fed. Compared to newly emerged unfed mosquitoes, feeding on sugar and/or blood increased variability in microbial composition (⍺-diversity), with a higher disparity among females (39% P = 0.01) than in males (29% P = 0.03). Elizabethkingia meningoseptica and Asaia siamensis were common discriminants between feeding statuses in both males and females. While E. meningoseptica was particularly associated with sugar-fed mosquitoes of both sexes and sustained after blood feeding in females, A. siamensis was also increased in sugar-fed mosquitoes but decreased significantly in blood-fed females (LDA score > 4.0, P < 0.05). Among males, A. siamensis did not differ significantly after sugar meals.ConclusionsResults indicate the opportunities for stable infection in mosquitoes should these species be used in bacteria-mediated disease control. Further studies are recommended to investigate possible host-specific tissue tropism of bacteria species which will inform selection of the most appropriate microbes for effective transmission-blocking strategies.

Type VI secretion system drives bacterial diversity and functions in multispecies biofilms

Type VI secretion system (T6SS) plays an essential role in interspecies interactions and provides an advantage for a strain with T6SS in multispecies biofilms. However, how T6SS drives the bacterial community structure and functions in multispecies biofilms still needs to be determined. Using gene deletion and Illumina sequencing technique, we estimated bacterial community responses in multispecies biofilms to T6SS by introducing T6SS-containing Pseudomonas putida KT2440. Results showed that the niche structure shifts of multispecies biofilms were remarkably higher in the presence of T6SS than in the absence of T6SS. The presence of T6SS significantly drove the variation in microbial composition, reduced the alpha-diversity of bacterial communities in multispecies biofilms, and separately decreased and increased the relative abundance of Proteobacteria and Bacteroidota. Co-occurrence network analysis with inferred putative bacterial interactions indicated that P. putida KT2440 mainly displayed strong negative associations with the genera of Psychrobacter, Cellvibrio, Stenotrophomonas, and Brevundimonas. Moreover, the function redundancy index of the bacterial community was strikingly higher in the presence of T6SS than in the absence of T6SS, regardless of whether relative abundances of bacterial taxa were inhibited or promoted. Remarkably, the increased metabolic network similarity with T6SS-containing P. putida KT2440 could enhance the antibacterial activity of P. putida KT2440 on other bacterial taxa. Our findings extend knowledge of microbial adaptation strategies to potential bacterial weapons and could contribute to predicting biodiversity loss and change in ecological functions caused by T6SS.

Shaping Diets for Gut Health: Understanding the Microbial Influence

The human gut is home to trillions of microorganisms that constitute a dynamic ecology involved in both health and disease. Although the makeup of the gut microbiota varies from person to person and is often stable over the course of a lifetime, numerous researches have noted daily variations [1]. One important modifiable factor that affects the composition of the gut microbiota is diet. It becomes clear that microbial diversity, composition, and stability can be controlled through therapeutic dietary approaches. A diverse and abundant microbial ecosystem boosts immunological responses, increases mental well-being, and maintains proper metabolic balance. The Western diet that is characterized by the high intake of artificially processed food and low fiber content has been associated with the exponential decrease in microbial diversity and consequent health issues including gastrointestinal disorders, inflammation and metabolic disturbances [2]. Contrary to it, diverse diet which includes all types of natural sources, such as fruits, vegetables, whole grain, nuts seeds and legumes has been proved to introduce an array of nutrients and fibers fueling our gut microbiota. For instance, dietary fiber aid in the growth and activity of beneficial bacteria in the gut. Moreover, polyphenols and antioxidants present in various plant-based foods exhibit pre-biotic effects, and maintain the gut environment favorable for the proliferation of microbiota [3]. This diverse intake provides a spectrum of substrates that are essential for the bacterial metabolism and also contribute in the growth of diverse range of beneficial bacteria. This dietary diversity not just includes the variety of foods but also involves mindful choices, balanced combination and understand the association of diet and microbiota. In addition, other lifestyle factors also influence over the microbial environment. Chronic stress, irregular sleep patterns and sedentary habits impact the activity and growth of the microbial diversity. It is not a ‘one-size-fits-all’ concept and personalized nutrition strategies are required depending upon the individual variations in microbial composition. Future research should incorporate long-term dietary assessments with short-term diet interventions to improve the findings of diet-microbiome relationship. Interdisciplinary collaborations are significant to navigate the complex relationships encompassing the knowledge from different disciplines such as microbiology, nutrition, behavioral and clinical sciences, allowing us to pave the way for dietary recommendations that prioritize gut health and overall well-being.

Effects of stratification and mixing on spatiotemporal dynamics and functional potential of microbial community in a subtropical large-deep reservoir driven by nutrients and ecological niche

Seasonal thermal stratification is a common environmental phenomenon in reservoir water bodies and an important research topic for deep water reservoirs. A thermally stratified reservoir is an ideal system for investigating the interaction between factors affecting the environment and microorganism communities under spatial–temporal variation. However, few studies have focused on the effects of water stratification and mixing periods in microbial communities and nitrogen conversion. Therefore, using metagenomic sequencing and quantitative polymerase chain reaction, we investigated the microbial diversity and function in the Xin'anjiang Reservoir during water stratification and mixing period. Principal component analysis indicated that the bacterial communities were mostly affected by water stratification, mainly at 10-m depths, whereas the archaea community was influenced by the entire water profile. The predominant archaeal phyla changed from Candidatus_Woesearchaeota and Euryarchaeota to Thaumarchaeota with the increasing water depth during water stratification. The stratified variations of the dominant archaeal phyla strongly reflected the seasonal changes and vertical gradient in water temperature, dissolved oxygen, and pH. Linear regression analysis indicated that variations in microbial composition altered the overall functional attributes of the communities, especially in the archaeal community. Regarding nitrogen metabolism across the whole reservoir, the number of nitrification and denitrification genes dropped in the same direction as the river flow in spring and summer, while the opposite trend was observed in autumn and winter. The functional genes of the water profiles in the transitional and lacustrine zones varied considerably except in winter. Additionally, the copies of nitrification-related genes were more during the stratification stage than during the mixing stage, whereas copies of denitrification-related genes showed the opposite trend. Overall, this study provides unique insights regarding the effects of seasonal stratification on the distribution and function of microorganisms in large-deep reservoirs, which should be considered when establishing guidelines for reservoirs management.

Hazardous risk of antibiotic resistance genes: Host occurrence, distribution, mobility and vertical transmission from different environments to corn silage

Antibiotic resistance genes (ARGs) are one of the emerging contaminants posing a great deal of hazardous risk to public health. This study employed metagenomics and deciphered the potential risk of the antibiotic resistome and their vertical transfer to ensiled whole-crop corn silage harvested from six climate zones: 1. Warm temperate-fully humid-hot summer (Cfa), 2. Arid-desert-cold arid (BWk), 3. Snow-desert-cold summer (Dwc), 4. Snow-desert-hot summer (Dwa), 5. Arid-steppe-cold arid (BSk), and 6. Equatorial-desert (Aw) based on the Köppen-Geiger climate classification in China. The findings demonstrate a high diversity of ARGs, which is related to the drug classes of tetracycline, ciprofloxacin, lincosamide, fosfomycin, and beta lactam. Resistome variations are mostly related to variations in microbial composition and fermentation characteristics of the silages from different climate zones, which are indirectly influenced by environmental conditions. The most dominating ARGs in corn silage were tetM, acrA, H-NS, lnuA, emrR, and KpnG, which is primarily hosted by Klebsiella and Lactobacilli. There were 5 high-risk ARGs (tetM, bacA, SHV-1, dfrA17, and QnrS1) in silage from different climate zones, and the tetM was the most prevalent high-risk ARG. However, throughout the ensiling process, the abundance of ARGs, and mobile ARGs were reduced. The resistome contamination in silage from Tibet (Dwc) with high altitude and harsh environment was relatively low due to the low variety and abundance of ARGs, the low abundance of mobile ARGs and high-risk ARGs. In addition, most of the bacteria responsible for the silage fermentation were also found to be the hosts to the ARGs, although their abundance decreased after 90 d of silage fermentation. Hence, we alert the existence of ARGs-related biosafety risk in silages and call for more attention to the silage ARGs, their hosts, and mobile genetic elements in order to curtail their possible risk to public health.

Metagenomic insights into the energy metabolism and immune variation of sea cucumber Apostichopus japonicus during reproduction

Sea cucumber Apostichopus japonicus is important aquatic economic species in Asia. In recent years, due to the decline of wild resources of A. japonicus, in order to ensure the sustainable supply of seedlings, the broodstock rearing is particularly important during seedling production, reproduction is also an essential stage in the life history of A. japonicus. However，the physiology of marine animals undergoes variations during the process of reproduction. It is well known that the energy demand of broodstock increases and their immunity decreases during the reproduction. Intestinal microorganisms participate in host life activities, while the presence of pathogens and probiotics will affect host health. However, the function of intestinal microbiota in the energy and immunity during the reproduction remains unclear. In this study, we performed a metagenomic analysis of the gut microbiota in A. japonicus to investigate variations in microbial composition and KEGG pathways associated with reproductive periods. Results suggested that Firmicutes/Bacteroidetes (F/B) was gradually increasing during reproduction, which increased host energy harvest, and was difference between male and female A. japonicus. Virulence Factors of Pathogenic Bacteria (VFBD) upregulated from the gonadal growth period. The higher expression of VFBD during the gonadal growth period than at other times may be caused by the fact that Flavobacteriaceae and Rhodobacteraceae are most abundant during this period. Lysozyme activity was upregulated during reproduction and peaked during the gonadal mature period, with a similar trend of variability as in VFBD, which carried out immunological protection against A. japonicus. The relative abundance of Saccharomycetaceae, and Bacillaceae was highest during the spawning period, and it has been identified that microorganisms strengthen immune protection against A. japonicus during this period, when A. japonicus was in a weakened state. Based on KEGG analysis, expression of oxidative phosphorylation and the fever pathway increased after spawning, indicating that reproduction causes oxidative stress in A. japonicus. Additionally, the differences in several KEGG pathways were related to sex. Overall, by analyzing the energy and immune systems, the study confirmed that intestinal microorganisms play vital physiological roles in broodstock of A. japonicus during reproduction. This study provided important information for breeding and the application of A. japonicus in aquaculture.

Therapeutic potential of Litsea cubeba essential oil in modulating inflammation and the gut microbiome.

Inflammation, a sophisticated and delicately balanced physiological mechanism, is paramount to the host's immunological defense against pathogens. However, unfettered and excessive inflammation can be instrumental in engendering a plethora of chronic ailments and detrimental health repercussions, notably within the gastrointestinal tract. Lipopolysaccharides (LPS) from bacteria are potent endotoxins capable of instigating intestinal inflammation through the disruption of the intestinal epithelial barrier and the stimulation of a pro-inflammatory immune response. In this study, we sought to investigate the influence of Litsea cubeba essential oil (LCEO) on LPS-induced intestinal inflammation and associated changes in the gut microbiota. We investigated the therapeutic potential of LCEO for gut health, with particular emphasis on its gut protective properties, anti-inflammatory properties and modulation of the gut microbiome. LCEO exhibited protective effects on colonic tissue by protecting crypts and maintaining epithelial integrity, and anti-inflammatory properties by reducing TNF-α, IL-6, and IL-1β levels in the liver and intestine. Citral, a major component of LCEO, showed robust binding to IL-1β, IL-6, and TNF-α, exerting anti-inflammatory effects through hydrogen bonding interactions. Using community barplot and LEfSe analyses, we detected significant variation in microbial composition, identified discrete biomarkers, and highlighted the influence of essential oils on gut microbial communities. Our research suggests that LCEO may be a promising natural compound for ameliorating diarrhea and intestinal inflammation, with potential implications for modulating the gut microbiome. These observations provide invaluable insight into the potential therapeutic role of LCEO as a natural anti-inflammatory agent for treating intestinal inflammatory disorders, particularly in the setting of a dysregulated immune response and altered gut microbiota. Furthermore, our findings highlight the need to understand the complex interplay between the host, the gut microbiome and natural products in the context of inflammatory diseases.

Longitudinal Changes in Milk Microorganisms in the First Two Months of Lactation of Primiparous and Multiparous Cows.

The present experiment was carried out to analyze the longitudinal changes in milk microorganisms. For this purpose, milk samples were collected from 12 healthy cows (n = 96; six primiparous cows and six multiparous cows) at eight different time points. The characteristics and variations in microbial composition were analyzed by 16S rRNA gene high-throughput sequencing. In the primiparous group, higher and more stable alpha diversity was observed in transitional and mature milk compared with the colostrum, with no significant difference in alpha diversity at each time point in the multiparous group. Proteobacteria, Firmicutes, Bacteroidota, and Actinobacteriota were the most dominant phyla, and Pseudomonas, UCG-005, Acinetobacter, Vibrio, Lactobacillus, Bacteroides, Serratia, Staphylococcus, and Glutamicibacter were the most dominant genera in both primiparous and multiparous cow milk. Some typically gut-associated microbes, such as Bacteroides, UCG-005, and Rikenellaceae_RC9_gut_group, etc., were enriched in the two groups. Biomarker taxa with the day in time (DIM) were identified by a random forest algorithm, with Staphylococcus showing the highest degree of interpretation, and the difference in milk microbiota between the two groups was mainly reflected in 0 d-15 d. Additionally, network analysis suggested that there were bacteria associated with the total protein content in milk. Collectively, our results disclosed the longitudinal changes in the milk microbiota of primiparous and multiparous cows, providing further evidence in dairy microbiology.

Improving NH3 and H2S removal efficiency with pilot-scale biotrickling filter by co-immobilizing Kosakonia oryzae FB2-3 and Acinetobacter baumannii L5-4.

In this study, two NH4+-N and S2- removal strains, namely, Kosakonia oryzae (FB2-3) and Acinetobacter baumannii (L5-4), were isolated from the packing materials in a long-running biotrickling filter (BTF). The removal capacities of combined FB2-3 and L5-4 (FB2-3 + L5-4) toward 100mg L-1 of NH4+-N and 200mg L-1 of S2- reached 97.31 ± 1.62% and 98.57 ± 1.12% under the optimal conditions (32.0°C and initial pH = 7.0), which were higher than those of single strain. Then, FB2-3 and L5-4 liquid inoculums were prepared, and their concentrations respectively reached 1.56 × 109CFUmL-1 and 1.05 × 109CFUmL-1 by adding different resuspension solutions and protective agents after 12-week storage at 25°C. Finally, pilot-scale BTF test showed that NH3 and H2S in the real exhaust gases from a pharmaceutical factory were effectively removed with removal rates > 87% and maximum elimination capacities were reached 136g (NH3) m-3h-1 and 176g (H2S) m-3h-1 at 18°C-34 °C and pH 4.0-7.0 in the BTF loaded with bamboo charcoal packing materials co-immobilized with FB2-3 and L5-4. After co-immobilization of FB2-3 and L5-4, in the bamboo charcoal packing materials, the new microbial diversity composition contained the dominant genera of Acinetobacter, Mycobacterium, Kosakonia, and Sulfobacillus was formed, and the diversity of entire bacterial community was decreased, compared to the control. These results indicate that FB2-3 and L5-4 have potential to be developed into liquid ready-to-use inoculums for effectively removing NH3 and H2S from exhaust gases in BTF.

Variation in bacterial composition, diversity, and activity across different subglacial basal ice types

Abstract. Glaciers and ice sheets possess basal ice layers characterized by high amounts of entrained debris that can serve as sources of nutrients and organic matter, providing a habitat for microorganisms adapted to the frozen conditions. Basal ice forms through various mechanisms and is classified based on ice and debris content; however, little is known about variation in microbial composition, diversity, and activity across different basal ice types. We investigated these parameters in four different types of basal ice from a cold-based and temperate glacier and used a meta-analysis to compare our findings with microbiome studies from other frozen environments. We found basal ice environments harbor a diverse range of microbiomes whose composition and activity can vary significantly between basal ice types, even within adjacent facies from the same glacier. In some debris-rich basal ices, elevated ATP concentrations, isotopic gas signatures, and high 16S rRNA/rDNA amplicon ratios implicated certain bacterial taxa (e.g., Paenisporosarcina, Desulfocapsa, Syntrophus, and Desulfosporosinus) as being potentially active, with ice temperature appearing to be an important predictor for the diversity of inferred active taxa. Compared to those of other sympagic environments, the basal ice microbiomes more closely resemble those found in permafrost or perennial cave ice than glacial ice. In contrast, debris-poor basal ices harbored microbiomes more like those found in englacial ice. Collectively, these results suggest that different basal ice types contain distinct microbiomes that are actively structured by physicochemical properties of their habitat.

Age as a primary driver of the gut microbial composition and function in wild harbor seals

Dietary changes are the major variation cause in the composition of the gut microbiota. The short lactation phase in phocids provides an exceptional opportunity to explore the microbiota's response to a quick transition from a milk-based to a solid diet. We investigated the effects of age and sex on the gut microbiota of harbor seals in Mexico using rectal and fecal samples from pups and adults. 16S gene sequencing revealed age explains most of the observed variations in microbial composition. Individuals with frequent contact (pups—female adults) have major microbial similarities than those with little or no contact (pups—male adults). Overall, adults and females (regardless of sex and age, respectively) have a greater microbial richness; as seals grow, the core microbiome shrinks, and microbial diversity increases. We found pathways related to milk and chitin digestion in pups' microbiomes, indicating pups were transitioning to a solid diet. An enrichment of routes related to dramatic weight loss and body mass indicated higher metabolic stress in pups in late breeding season, when they are weaned and start intermittent fasting. Our findings highlight the host-microbiome interaction in harbor seals during late breeding season in response to food shifts and metabolic stress.

Host-Gut Microbiome Metabolic Interactions in PFAS-Impacted Freshwater Turtles (Emydura macquarii macquarii).

Per-and polyfluoroalkyl substances (PFAS) are a growing concern for humans, wildlife, and more broadly, ecosystem health. Previously, we characterised the microbial and biochemical impact of elevated PFAS on the gut microbiome of freshwater turtles (Emydura macquarii macquarii) within a contaminated catchment in Queensland, Australia. However, the understanding of PFAS impacts on this species and other aquatic organisms is still very limited, especially at the host–gut microbiome molecular interaction level. To this end, the present study aimed to apply these leading-edge omics technologies within an integrated framework that provides biological insight into the host turtle–turtle gut microbiome interactions of PFAS-impacted wild-caught freshwater turtles. For this purpose, faecal samples from PFAS-impacted turtles (n = 5) and suitable PFAS-free reference turtles (n = 5) were collected and analysed. Data from 16S rRNA gene amplicon sequencing and metabolomic profiling of the turtle faeces were integrated using MetOrigin to assign host, microbiome, and co-metabolism activities. Significant variation in microbial composition was observed between the two turtle groups. The PFAS-impacted turtles showed a higher relative abundance of Firmicutes and a lower relative abundance of Bacteroidota than the reference turtles. The faecal metabolome showed several metabolites and pathways significantly affected by PFAS exposure. Turtles exposed to PFAS displayed altered amino acid and butanoate metabolisms, as well as altered purine and pyrimidine metabolism. It is predicted from this study that PFAS-impacted both the metabolism of the host turtle and its gut microbiota which in turn has the potential to influence the host’s physiology and health.

Distinct Denitrifying Phenotypes of Predominant Bacteria Modulate Nitrous Oxide Metabolism in Two Typical Cropland Soils.

Denitrifying nitrous oxide (N2O) emissions in agroecosystems result from variations in microbial composition and soil properties. However, the microbial mechanisms of differential N2O emissions in agricultural soils are less understood. In this study, microcosm experiments using two main types of Chinese cropland soil were conducted with different supplements of nitrate and glucose to simulate the varying nitrogen and carbon conditions. The results show that N2O accumulation in black soil (BF) was significantly higher than that in fluvo-aquic soil (FF) independent of nitrogen and carbon. The abundance of most denitrifying genes was significantly higher in FF, but the ratios of genes responsible for N2O production (nirS and nirK) to the gene responsible for N2O reduction (nosZ) did not significantly differ between the two soils. However, the soils showed obvious discrepancies in denitrifying bacterial communities, with a higher abundance of N2O-generating bacteria in BF and a higher abundance of N2O-reducing bacteria in FF. High accumulation of N2O was verified by the bacterial isolates of Rhodanobacter predominated in BF due to a lack of N2O reduction capacity. The dominance of Castellaniella and others in FF led to a rapid reduction in N2O and thus less N2O accumulation, as demonstrated when the corresponding isolate was inoculated into the studied soils. Therefore, the different phenotypes of N2O metabolism of the distinct denitrifiers predominantly colonized the two soils, causing differing N2O accumulation. This knowledge would help to develop a strategy for mitigating N2O emissions in agricultural soils by regulating the phenotypes of N2O metabolism.

Soil aggregate modulates microbial ecological adaptations and community assemblies in agricultural soils

Soil aggregates provide spatially heterogeneous microenvironments for soil microbiome and ecological processes. Revealing the nuances of assembly processes in aggregates is critical for understanding the fine-scale organization of the soil microbiome and associated biogeochemistry. However, the effect of aggregate sizes on microbial assemblies remains poorly explored. In this study, we investigated the mechanism underlying the assembly processes of microbial communities within three different aggregates sizes across five long-term fertilization experimental stations throughout eastern China. Our results showed that although geographic sites explained most of the variations in microbial composition in aggregates, aggregates of the same size selected phylogenetically closely related microbial species with similar ecological preferences for specific nutrient variables. Null model analysis showed that environmental selection and dispersal limitation primarily governed the assembly of aggregate bacterial and fungal communities, respectively. The relative importance of deterministic processes on microbial communities increased with the increasing aggregate size across all sites. Multiple stepwise regression analysis indicated that nutrient variables associated with community assembly are distinct in different aggregate-size fractions. Bacterial assembly is mainly affected by total carbon and soil organic carbon in macro- and micro-aggregates, whereas it is influenced by the C/P ratio in the silt + clay fraction. For fungal community assembly, the C/N ratio was the major factor in macroaggregate and silt + clay fractions, while N/P ratio had stronger effects in the microaggregates. Furthermore, fertilization effects on the microbial community assembly processes varied across aggregate sizes. Organic fertilization led to a decrease for bacteria while an increase for fungi in the sorting/dispersal effect ratio. The magnitude of such an impact was higher for macro- and micro-aggregates. GeoChip and enzymatic results further demonstrated the regulation of ecological clusters and functions by nutrient variables across aggregates. Our findings highlight that microbial assembly and functional traits in large aggregate-size fractions are susceptible to nutrient changes, and thus can act as potential biological indicators for sustainable management of agricultural soils.

Insights into the bacterial, fungal, and phage communities and volatile profiles in different types of Daqu

Daqu has a rich and diverse microbiota, giving them a suitable biotope for phages. However, the absolute abundances of bacteria and fungi, as well as the phage community characteristics in Daqu, remain unclear. In this study, the microbiota absolute abundance, indigenous phage composition and function, and volatile compound profiles of high-temperature Daqu (HTDQ), medium-temperature Daqu (MTDQ), and low-temperature Daqu (LTDQ) were investigated. Absolute microbiota quantification revealed that there were significant variations in microbial composition and absolute abundance across three types of Daqu. The absolute abundances of the top 30 bacterial genera in LTDQ, MTDQ, and HTDQ were 6.0 × 105, 5.3 × 104, 1.4 × 105 copies/ng DNA, while the top 30 fungal genera had 8.5 × 107, 2.1 × 106, and 6.2 × 105 copies/ng DNA, respectively. LTDQ were enriched in Pantoea, Staphylococcus, and Saccharomycopsis; MTDQ were dominated by Saccharopolyspora, Staphylococcus, Saccharomycopsis, and Aspergillus; HTDQ were dominated by Saccharopolyspora, Bacillus, Byssochlamys, and Saccharomycopsis. Volatile profile analysis revealed that LTDQ, MTDQ, and HTDQ comprised 68, 68, and 75 compounds, respectively, with 39 compounds shared by the three types. Fourteen volatile compounds were identified as highly discriminative features among three types of Daqu, which were closely related to Saccharopolyspora, Thermoactinomyces, Kroppenstedtia, Byssochlamys, and Thermomyces. Metaviromics indicated that Genomoviridae, Mimiviridae and Siphoviridae, and Parvoviridae were the dominant viruses in LTDQ, MTDQ, and HTDQ, respectively. The hosts of phages in Daqu mainly included Lactobacillus, Enterobacter, Pantoea, Bacillus, Pediococcus, and Staphylococcus. Phages may prey on numerous microbes living on Daqu via pathways such as genetic information processing, signaling and cellular processes, and replication and repair. This study highlights the use of absolute quantification to avoid misjudgment of differential taxa in comparative microbiome analysis and provides new insights into the phage community and function in Daqu.