Variation In Microbial Diversity Research Articles

Unraveling the Role of Tissue Colonized Microbiome in Ovarian Cancer Progression

BackgroundOvarian cancer (OC) is found to be the third most common gynecologic malignancy over the world, having the highest mortality rate among such tumors. Emerging studies underscore the presence of microorganisms within tumor tissues, with certain pathogens intricately linked to disease onset and progression. Disruption of the microbiome frequently precipitates disturbances in host metabolic and immune pathways, thereby fostering the development of cancer. MethodsIn this study, we initiated the investigation by conducting microbial reannotation on the RNA sequencing data derived from ovarian cancer tissues. Subsequently, a comprehensive array of analyses on tissue microbes was executed. These analyses encompassed the assessment of intergroup variations in microbial diversity, differential microbiological analysis, exploration of the association between host gene expression and microbial abundance, as well as an enrichment analysis of functional pathways linked to host genes associated with microbes. ResultsThe analysis results revealed that Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes were the main components at phylum level in ovarian tissue. Notably, the microbial composition of ovarian cancer tissue significantly diverged from that of normal ovarian tissue e, exhibiting markedly lower alpha diversity and distinct beta diversity. Besides, pathogenic microorganisms Achromobacter xylosoxidans and Enterobacter hormaechei were enriched in cancer tissue. Host genes associated with these pathogens were enriched in key pathways including “JAK-STAT signaling pathway”, “Transcriptional misregulation in cancer”, and “Th1 and Th2 cell differentiation”, suggesting their role in ovarian cancer progression through microbial dysbiosis and immune response interaction. ConclusionAbundance of pathogenic microorganisms in ovarian cancer tissue could modulate the expression of host genes, consequently impacting cancer-related signaling pathways and fostering cancer progression.

Microbiome mapping in beef processing reveals safety-relevant variations in microbial diversity and genomic features

The microbiome of surfaces along the beef processing chain represents a critical nexus where microbial ecosystems play a pivotal role in meat quality and safety of end products. This study offers a comprehensive analysis of the microbiome along beef processing using whole metagenomics with a particular focus on antimicrobial resistance and virulence-associated genes distribution. Our findings highlighted that microbial communities change dynamically in the different steps along beef processing chain, influenced by the specific conditions of each micro-environment. Brochothrix thermosphacta, Carnobacterium maltaromaticum, Pseudomonas fragi, Psychrobacter cryohalolentis and Psychrobacter immobilis were identified as the key species that characterize beef processing environments. Carcass samples and slaughterhouse surfaces exhibited a high abundance of antibiotic resistance genes (ARGs), mainly belonging to aminoglycosides, β-lactams, amphenicols, sulfonamides and tetracyclines antibiotic classes, also localized on mobile elements, suggesting the possibility to be transmitted to human pathogens.We also evaluated how the initial microbial contamination of raw beef changes in response to storage conditions, showing different species prevailing according to the type of packaging employed. We identified several genes leading to the production of spoilage-associated compounds, and highlighted the different genomic potential selected by the storage conditions.Our results suggested that surfaces in beef processing environments represent a hotspot for beef contamination and evidenced that mapping the resident microbiome in these environments may help in reducing meat microbial contamination, increasing shelf-life, and finally contributing to food waste restraint.

Microbial response to Nature-Based Solutions in urban soils: A comprehensive analysis using Biolog® EcoPlates™

The study presents a comprehensive examination of changes in soil microbial functional diversity (hereafter called microbial activity) following the implementation of Nature-Based Solutions (NBS) in urban areas. Utilizing the Biolog® EcoPlates™ technique, the study explored variations in microbial diversity in urban soil under NBSs implementation across timespan of two years.Significant differences in microbial activity were observed between control location and those with NBS implementations, with seasonal variations playing a crucial role. NBS positively impacted soil microbial activity especially at two locations: infiltration basin and wild flower meadow showing the most substantial increase after NBS implementation. The study links rainfall levels to microbial functional diversity, highlighting the influence of climatic conditions on soil microbiome. The research investigates also the utilization of different carbon sources by soil microorganisms, shedding light on the specificity of substrate utilization across seasons and locations. The results demonstrate that NBSs implementations lead to changes in substrate utilization patterns, emphasizing the positive influence of NBS on soil microbial communities. Likewise, biodiversity indices, such as Shannon-Weaver diversity (H′), Shannon Evenness Index (E), and substrate richness index (S), exhibit significant variations in response to NBS. Notably, NBS implementation positively impacted H′ and E indexes, especially in infiltration basin and wild flower meadow, underlining the benefits of NBS for enhancing microbial diversity.The obtained results demonstrated valuable insight into the dynamic interactions between NBS implementation and soil microbial activity. The findings underscore the potential of NBS to positively influence soil microbial diversity in urban environments, contributing to urban sustainability and soil health. The study emphasizes the importance of monitoring soil microbial activity to assess the effectiveness of NBS interventions and guides sustainable urban development practices.

Exploring the Microbiome Landscape of Dental Plaque: A Cross-Sectional Analysis in Periodontal Health and Disease.

This study aimed to comprehensively analyze the microbiome of dental plaque in individuals with varying periodontal statuses, encompassing both periodontal health and disease. The primary objectives were to identify microbial markers associated with different clinical conditions, explore variations in microbial diversity, and investigate potential correlations between the oral microbiome and clinical parameters. A cross-sectional design was employed, involving 164 participants aged 18 to 65 years. Inclusion criteria comprised individuals with good oral and systemic health for the periodontal health group and those diagnosed with various stages of periodontal disease for the periodontal disease group. Dental plaque samples were meticulously collected from diverse tooth surfaces, and clinical examinations were conducted to assess periodontal health status. High-throughput sequencing of the 16S ribosomal RNA (rRNA) gene was utilized for microbiome analysis. Demographic characteristics revealed a balanced distribution between the periodontal health and disease groups. Clinical parameters, including probing depth, clinical attachment loss, and bleeding on probing, exhibited significant differences between the two groups (p < 0.001). Microbial diversity indices indicated a higher diversity in the periodontal health group compared to the disease group (p < 0.001). Analysis of relative abundance of bacterial phyla identified significant variations, with Firmicutes, Bacteroidetes, and Actinobacteria showing differential prevalence between health and disease (p < 0.05). Differentially abundant taxa analysis highlighted specific species associated with each clinical condition, including Prevotella intermedia and Porphyromonas gingivalis. Network analysis revealed complex microbial interactions within the oral microbiome. Functional predictions indicated variations in metabolic capabilities between health and disease, with potential implications for virulence and antibiotic resistance. This study provides a comprehensive analysis of the oral microbiome in periodontal health and disease, revealing significant associations between microbial composition and clinical parameters. The identification of microbial markers and functional insights enhances our understanding of the complex interplay within the oral ecosystem. These findings hold promise for advancing diagnostic and therapeutic approaches tailored to individual microbial profiles.

Long-term push–pull cropping system shifts soil and maize-root microbiome diversity paving way to resilient farming system

BackgroundThe soil biota consists of a complex assembly of microbial communities and other organisms that vary significantly across farming systems, impacting soil health and plant productivity. Despite its importance, there has been limited exploration of how different cropping systems influence soil and plant root microbiomes. In this study, we investigated soil physicochemical properties, along with soil and maize-root microbiomes, in an agroecological cereal-legume companion cropping system known as push–pull technology (PPT). This system has been used in agriculture for over two decades for insect-pest management, soil health improvement, and weed control in sub-Saharan Africa. We compared the results with those obtained from maize-monoculture (Mono) cropping system.ResultsThe PPT cropping system changed the composition and diversity of soil and maize-root microbial communities, and led to notable improvements in soil physicochemical characteristics compared to that of the Mono cropping system. Distinct bacterial and fungal genera played a crucial role in influencing the variation in microbial diversity within these cropping systems. The relative abundance of fungal genera Trichoderma, Mortierella, and Bionectria and bacterial genera Streptomyces, RB41, and Nitrospira were more enriched in PPT. These microbial communities are associated with essential ecosystem services such as plant protection, decomposition, carbon utilization, bioinsecticides production, nitrogen fixation, nematode suppression, phytohormone production, and bioremediation. Conversely, pathogenic associated bacterial genus including Bryobacter were more enriched in Mono-root. Additionally, the Mono system exhibited a high relative abundance of fungal genera such as Gibberella, Neocosmospora, and Aspergillus, which are linked to plant diseases and food contamination. Significant differences were observed in the relative abundance of the inferred metabiome functional protein pathways including syringate degradation, L-methionine biosynthesis I, and inosine 5'-phosphate degradation.ConclusionPush–pull cropping system positively influences soil and maize-root microbiomes and enhances soil physicochemical properties. This highlights its potential for agricultural and environmental sustainability. These findings contribute to our understanding of the diverse ecosystem services offered by this cropping system where it is practiced regarding the system's resilience and functional redundancy. Future research should focus on whether PPT affects the soil and maize-root microbial communities through the release of plant metabolites from the intercrop root exudates or through the alteration of the soil's nutritional status, which affects microbial enzymatic activities.

Microbial diversity and keystone species drive soil nutrient cycling and multifunctionality following mangrove restoration

Vegetation restoration exerts transformative effects on nutrient cycling, microbial communities, and ecosystem functions. While extensive research has been conducted on the significance of mangroves and their restoration efforts, the effectiveness of mangrove restoration in enhancing soil multifunctionality in degraded coastal wetlands remains unclear. Herein, we carried out a field experiment to explore the impacts of mangrove restoration and its chronosequence on soil microbial communities, keystone species, and soil multifunctionality, using unrestored aquaculture ponds as controls. The results revealed that mangrove restoration enhanced soil multifunctionality, with these positive effects progressively amplifying over the restoration chronosequence. Furthermore, mangrove restoration led to a substantial increase in microbial diversity and a reshaping of microbial community composition, increasing the relative abundance of dominant phyla such as Nitrospirae, Deferribacteres, and Fusobacteria. Soil multifunctionality exhibited positive correlations with microbial diversity, suggesting a link between variations in microbial diversity and soil multifunctionality. Metagenomic screening demonstrated that mangrove restoration resulted in a simultaneous increase in the abundance of nitrogen (N) related genes, such as N fixation (nirD/H/K), nitrification (pmoA-amoA/B/C), and denitrification (nirK, norB/C, narG/H, napA/B), as well as phosphorus (P)-related genes, including organic P mineralization (phnX/W, phoA/D/G, phnJ/N/P), inorganic P solubilization (gcd, ppx-gppA), and transporters (phnC/D/E, pstA/B/C/S)). The relationship between the abundance of keystone species (such as phnC/D/E) and restoration-induced changes in soil multifunctionality indicates that mangrove restoration enhances soil multifunctionality through an increase in the abundance of keystone species associated with N and P cycles. Additionally, it was observed that changes in microbial community and multifunctionality were largely associated with shifts in soil salinity. These findings demonstrate that mangrove restoration positively influences soil multifunctionality and shapes nutrient dynamics, microbial communities, and overall ecosystem resilience. As global efforts continue to focus on ecosystem restoration, understanding the complexity of mangrove-soil interactions is critical for effective nutrient management and mangrove conservation.

Patient-derived pathogenic microbe deposition enhances exposure risk in pediatric clinics

Healthcare-associated infections (HAIs) pose significant risks to pediatric patients in outpatient settings. To prevent HAIs, understanding the sources and transmission routes of pathogenic microorganisms is crucial. This study aimed to identify the sources of opportunistic bacterial pathogens (OBPs) in pediatric outpatient settings and determine their transmission routes. Furthermore, assessing the public health risks associated with the core OBPs is important. We collected 310 samples from various sites in pediatric outpatient areas and quantified the bacteria using qPCR and CFU counting. We also performed 16S rRNA gene and single-bacterial whole-genome sequencing to profile the transmission routes and antibiotic resistance characteristics of OBPs. We observed significant variations in microbial diversity and composition among sampling sites in pediatric outpatient settings, with active communication of the microbiota between linked areas. We found that the primary source of OBPs in multi-person contact areas was the hand surface, particularly in pediatric patients. Five core OBPs, Staphylococcus epidermidis, Acinetobacter baumannii, Pseudomonas aeruginosa, Streptococcus mitis, and Streptococcus oralis, were mainly derived from pediatric patients and spread into the environment. These OBPs accumulated at multi-person contact sites, resulting in high microbial diversity in these areas. Transmission tests confirmed the challenging spread of these pathogens, with S. epidermidis transferring from the patient's hand to the environment, leading to an increased abundance and emergence of related strains. More importantly, S. epidermidis isolated from pediatric patients carried more antibiotic-resistance genes. In addition, two strains of multidrug-resistant A. baumannii were isolated from both a child and a parent, confirming the transmission of the five core OBPs centered around pediatric patients and multi-person contact areas. Our results demonstrate that pediatric patients serve as a significant source of OBPs in pediatric outpatient settings. OBPs carried by pediatric patients pose a high public health risk. To effectively control HAIs, increasing hand hygiene measures in pediatric patients and enhancing the frequency of disinfection in multi-person contact areas remains crucial. By targeting these preventive measures, the spread of OBPs can be reduced, thereby mitigating the risk of HAIs in pediatric outpatient settings.

Combining dredging with modified zeolite thin-layer capping to control nitrogen release from eutrophic lake sediment

Dredging is widely used to control internal sediment nitrogen (N) pollution during eutrophic lake restoration. However, the effectiveness of dredging cannot be maintained for long periods during seasonal temperature variations. This study used modified zeolite (MZ) as a thin-layer capping material to enhance dredging efficiency during a year-long field sediment core incubation period. Our results showed that dredging alone more effectively reduced pore water N, N flux, and sediment N content than MZ capping but showed more dramatic changes during the warm seasons. The N flux in dredged sediment in summer was 1.8 and 2.5 times that in spring and autumn, respectively, indicating a drastic N regeneration process in the short term. In contrast, the combination method reduced the extra 10% pore water N, 22% N flux, and 8% sediment organic N content compared with dredging alone and maintained high stability during seasonal changes. The results indicated that the addition of MZ to the surface of dredged sediment not only enhanced the control effect of dredging by its adsorption capacity but may also smooth the N regeneration process via successive accumulation (in the channel of the material) and activation of bacteria for months, which was evidenced by the variation in microbial diversity in the MZ treatment. As a result, the combination of dredging with modified zeolite simultaneously enhanced the efficiency and stability of the single dredging method in controlling sediment N content and its release, exhibiting great prospects for long-term application in eutrophic lakes with severe pollution from internal N loading.

Effects of Different Altitudes on Castanopsis hystrix, the Top Community-Building Species in Southern Subtropical China: Rhizospheric Soil Chemical Properties and Soil Microbiota

Castanopsis hystrix, a dominant canopy species in the subtropical forests of south China, is renowned for its high natural regeneration ability. Therefore, this paper took C. hystrix as the subject of study. Examining the variations in microbial diversity and community composition within the soil rhizosphere of C. hystrix across different elevation gradients, we explored how this community-forming species impacts soil microbial diversity and community structure and how soil microorganisms respond to changes in soil physicochemical properties due to altitude gradients. The results show: (1) soil samples from five altitudes established 1078 fungal OTU and 5595 bacterial OTUs. (2) Basidiomycota and ascomycota are dominant fungal groups in the soil, with Acidobacteria being the predominant bacteria for C. hystrix. (3) As altitude increases, fungal communities’ richness and diversity index peaks at 849 m; for bacterial communities, the richness index peaks at 387 m and the diversity index at 670 m. (4) Total phosphorus (TP), nitrate nitrogen (NO3−-N), hydrolyzed nitrogen (HN), total nitrogen (TN), and organic matter (SOM) are significant environmental factors affecting fungal community structure. At the same time, available potassium (AK) significantly influences the composition of bacterial communities. The study underscores the intricate relationship between altitude, soil properties, and microbial diversity, offering insights into how C. hystrix contributes to ecosystem resilience. Recommendations include enhancing phosphorus supplementation and controlling nitrogen deposition to maintain forest ecological integrity, additionally, the supply of potassium in the soil should also be a key consideration. Further research is necessary to understand the broader implications for biodiversity conservation and adaptive management strategies in the face of climate change.

Probiotic Lactobacillus plantarum SHY21-2 protected zebrafish against Aeromonas hydrophila infection by maintaining intestinal barrier integrity, inhibiting inflammatory and oxidative stress responses, and regulating intestinal microbiome

Lactic acid bacteria are generally regarded as an effective alternative to antibiotics in aquaculture farming, especially Lactobacillus strains, which are safe and have probiotic potential. However, the mechanism of action of probiotic Lactobacillus in protecting fish against Aeromonas hydrophila infection remains unclear. In this study, a strain of Lactobacillus plantarum SHY21-2, was investigated for its safety and probiotic properties using a combination of phenotypic and whole-genome analysis. The results revealed that SHY21-2 has good safety, antimicrobial activity, and multiple probiotic properties, including tolerance to acid and bile salts, adherence to intestinal epithelial cells, and effective immunomodulatory and anti-inflammatory potential. Furthermore, 240 zebrafish were randomly divided into 4 groups. After 1 week on a basal diet with or without SHY21-2, all zebrafish were exposed to water with or without A. hydrophila AH40 for 12 h; finally, all zebrafish were transferred to freshwater and fed the basal diet for 5 days. The results showed that supplementation with SHY21-2 alleviated the symptoms of zebrafish infected with A. hydrophila, significantly reduced mortality, inhibited intestinal and muscle inflammation, maintained intestinal barrier integrity, and alleviated hepatic oxidative stress responses. Notably, AH40-infection induced variations in microbial diversity and enriched harmful bacteria, such as unclassified-f-Parachlamydiaceae, Rhodococcus, unclassified-f-Microbacteriaceae, and Bosea, whereas supplementation with SHY21-2 reversed this result and significantly increased the abundance of beneficial bacteria, such as Lactiplantibacillus, Leucobacter, and Gemmobacter. In conclusion, these results suggest that SHY21-2 can effectively protect zebrafish against A. hydrophila infection and is an appropriate candidate probiotic for the aquaculture industry.

Variations in microbial diversity and chemical components of raw dark tea under different relative humidity storage conditions.

Raw dark tea (RDT) usually needs to be stored for a long time to improve its quality under suitable relative humidity (RH). However, the impact of RH on tea quality is unclear. In this study, we investigated the metabolites and microbial diversity, and evaluated the sensory quality of RDT stored under three RH conditions (1%, 57%, and 88%). UHPLC-Q-TOF-MS analysis identified 144 metabolites, including catechins, flavonols, phenolic acids, amino acids, and organic acids. 57% RH led to higher levels of O-methylated catechin derivatives, polymerized catechins, and flavonols/flavones when compared to 1% and 88% RH. The best score in sensory evaluation was also obtained by 57% RH. Aspergillus, Gluconobacter, Kluyvera, and Pantoea were identified as the core functional microorganisms in RDT under different RH storage conditions. Overall, the findings provided new insights into the variation of microbial communities and chemical components under different RH storage conditions.

The Variations of Microbial Diversity and Community Structure Along Different Stream Orders in Wuyi Mountains.

The surface water is an important habitat for freshwater microorganisms, but there is a lack of understanding of the pattern of microbial diversity and structure in stream continuums of small subtropical forest watersheds. Therefore, this study aimed to understand the variations in microbial diversity and community structure along stream orders (1-5) in the small subtropical forest catchments of the Wuyi Mountains. Using GIS software, 20 streams were chosen and classified into 5 orders. Illumina sequencing was used to analyze the dynamics of microbial communities, along with stream orders and hydro-chemical properties of stream water were also determined. Our results indicated that the bacterial and fungal richness (ACE index) was higher in low-order (1 and 2 orders) streams than in high-order (3, 4, and 5 orders) streams, with the highest value in the order 2 streams (P < 0.05). The water temperature and dissolved oxygen were positively correlated with fungal richness (P < 0.05). The bacterial rare taxa had a significant correlation with the abundance taxa (P < 0.05). The relative abundances of Bacteroidetes, Actinobacteria, and Chytridiomycota microbial phyla were significantly different among different order streams (P < 0.05). Using the neutral community model, we found that the fungal community structure was significantly shaped by hydro-chemical properties, while the bacterial community structure was largely regulated by stochastic processes. Our findings suggest that variations in microbial community structure in subtropical headwaters are largely shaped by the water temperature and dissolved oxygen.

Fragmentation disrupts microbial effects on native plant community productivity

Abstract Anthropogenic habitat fragmentation—the breaking up of natural landscapes—is a pervasive threat to biodiversity and ecosystem function world‐wide. Fragmentation results in a mosaic of remnant native habitat patches embedded in human‐modified habitat known as the ‘matrix’. By introducing novel environmental conditions in matrix habitats and reducing connectivity of native habitats, fragmentation can dramatically change how organisms experience their environment. The effects of fragmentation can be especially important in urban landscapes, which are expanding across the globe. Despite this surging threat and the importance of microbiomes for ecosystem services, we know very little about how fragmentation affects microbiomes and even less about their consequences for plant–microbe interactions in urban landscapes. By combining field surveys, microbiome sequencing and experimental mesocosms, we (1) investigated how microbial community diversity, composition and functional profiles differed between 15 native pine rockland fragments and the adjacent urban matrix habitat, (2) identified habitat attributes that explained significant variation in microbial diversity of native core habitat compared to urban matrix and (3) tested how changes in urbanized and low connectivity microbiomes affected plant community productivity. We found urban and native microbiomes differed substantively in diversity, composition and functional profiles, including symbiotic fungi decreasing 81% and pathogens increasing 327% in the urban matrix compared to native habitat. Furthermore, fungal diversity rapidly declined as native habitats became increasingly isolated, with ~50% of variation across the landscape explained by habitat connectivity alone. Interestingly, microbiomes from native habitats increased plant productivity by ~300% while urban matrix microbiomes had no effect, suggesting that urbanization may decouple beneficial plant–microbe interactions. In addition, microbial diversity within native habitats explained significant variation in plant community productivity, with higher productivity linked to more diverse microbiomes from more connected, larger fragments. Synthesis. Taken together, our study not only documents significant changes in microbial diversity, composition and functions in the urban matrix, but also supports that two aspects of habitat fragmentation—the introduction of a novel urban matrix and reduced habitat connectivity—disrupt microbial effects on plant community productivity, highlighting preservation of native microbiomes as critical for productivity in remnant fragments.

Vertical variations in microbial diversity, composition, and interactions in freshwater lake sediments on the Tibetan plateau.

Microbial communities in freshwater lake sediments exhibit a distinct depth-dependent variability. Further exploration is required to understand their biodiversity pattern and microbial interactions in vertical sediments. In this study, sediment cores from two freshwater lakes, Mugecuo (MGC) and Cuopu (CP), on the Tibetan plateau were sampled and subsequently sliced into layers at a depth of every centimeter or half a centimeter. Amplicon sequencing was used to analyze the composition, diversity, and interaction of microbial communities. Results showed that sediment samples of both lakes could be clustered into two groups at a sediment depth of about 20 cm, with obvious shifts in microbial community compositions. In lake MGC, the richness component dominated β-diversity and increased with depth, indicating that the microbial communities in the deep layer of MGC was selected from the surface layer. Conversely, the replacement component dominated β-diversity in CP, implying a high turnover rate in the surface layer and inactive seed banks with a high variety in the deep layer. A co-occurrence network analysis showed that negative microbial interactions were prevalent in the surface layers with high nutrient concentrations, while positive microbial interactions were more common in the deep layers with low nutrient concentrations, suggesting that microbial interactions are influenced by nutrient conditions in the vertical sediments. Additionally, the results highlight the significant contributions of abundant and rare taxa to microbial interactions and vertical fluctuations of β-diversity, respectively. Overall, this work deepens our understanding of patterns of microbial interactions and vertical fluctuation in β-diversity in lake sediment columns, particularly in freshwater lake sediments from the Tibetan plateau.

Microbial Biomarkers for Lung Cancer: Current Understandings and Limitations.

As our "hidden organ", microbes widely co-exist at various sites on the human body. These microbes are collectively referred to as the microbiome. A considerable number of studies have already proven that the microbiome has significant impacts on human health and disease progression, including cancers. The recent discovery of cancer-specific microbiomes renders these cancer-associated microbes as potential biomarkers and therapeutic targets. While at low biomass levels, the lung microbiome still dramatically influences the initiation, progression and treatment of lung cancers. However, research on lung cancer-associated microbiomes is emerging, and most profiling studies are performed within three years. Unfortunately, there are substantial inconsistencies across these studies. Variations in microbial diversity were observed, and different microbial biomarkers for lung cancer have been proposed. In this review, we summarized the current findings of lung cancer microbiome studies and attempt to explain the potential reasons for the dissimilarities. Other than lung microbiomes, oral and airway microbiomes are highly related to lung microbiomes and are therefore included as well. In addition, several lung cancer-associated bacterial genera have been detected by different independent studies. These bacterial genera may not be perfect biomarkers, but they still serve as promising risk factors for lung cancers and show great prognostic value.

Crop rotation-driven change in physicochemical properties regulates microbial diversity, dominant components, and community complexity in paddy soils

Crop rotation is a production practice to promote a more diversified plant community in rice field, thereby enhancing agroecosystem sustainability and production efficiency under an increasing demand for food and energy. The regulation of rotations of rice with different crop on soil microbiomes and their relationships with key soil physicochemical drivers has not been understood enough. To address this, soils of 0–20 cm and 20–40 cm layers subjected to four rotation regimes (rice-rice, tobacco-rice, rice-oilseed rape, and rice-rice-oilseed rape) were collected from a long-term (>20 year) field experiment. Compared with the rice-rice, the other three rotations significantly increased surface soil porosity and the content of soil total nitrogen (N), available phosphorus (P), total potassium, and organic matter, as well as improved soil aggregate composition but decreased soil bulk density (P < 0.05). Rotation patterns and soil layers independently or interactively explained the variation in microbial diversity and community composition in soil, with a greater impact of the rotation regimes (9.3–49.7%; P < 0.05). The rotation systems of rice-oilseed rape and rice-rice-oilseed rape showed a higher soil microbial diversity and co-occurrence of the community species compared with other two systems. The components of the genus Clostridium, Pedobacter, and Gp1 were the dominant hubs (with a larger number of edges) in bacterial communities, and the members of the Mortierella, Ascomycota, and Agaricales were the hubs in fungal communities. The co-occurring networks between the members of bacterial and fungal communities in the four systems showed same keystone taxa that mainly belong to fungal genus Mortierella, Fusicolla, Paranamyces, and Pseudeurotium. The microbial diversity and community composition were positively correlated with soil NH4+-N-to-NO3--N ratio, available P content, total N content, and soil aggregates, and meanwhile, those variables were the creadible predictors of the community changes. These findings highlighted the advantage of rice rotations with oilseed rape in improvement of soil fertility and production by mediating soil microbiome and physicochemical property relationships.

Responses of soil microbial diversity, network complexity and multifunctionality to three land-use changes

Land-use change is one of the greatest challenges for natural ecosystem services. Soil microbiomes are essential for modulating multiple ecosystem functions. However, little is known about the impact of land-use changes on soil microbial communities and their associated soil functions. In this study, 150 alpine soil samples representing conversion of forests to shrublands or grasslands, and of shrublands to grasslands were investigated for bacterial, fungal and protistan community diversity, co-occurrence network, as well as their relationships with soil multifunctionality via a sampling strategy of space-for-time substitution. The conversion of forest to grassland increased the diversity of fungi and bacteria, and altered the microbial community structures of bacteria, fungi and protists, resulting a greater impact on soil microbiome than other land-use conversions. Cross-trophic interaction analyses demonstrated this conversion increased microbial network complexity and robustness, whereas forest to shrubland had the opposite trend. The land-use induced changes in soil multifunctionality were related with microbial network modules, but were not always associated with variations of microbial diversity. Random forest modeling further suggested the significant role of microbial modules in explaining soil multifunctionality, together with environmental factors. These findings indicate divergent responses of belowground multitrophic organisms to land-use changes, and the potential role of microbial module in forecasting soil multifunctionality.

Seasonal variations in microbial diversity and metabolite profiles of the gut of sea cucumber (Apostichopus japonicus)

The sea cucumber (Apostichopus japonicus) is the main economic species in China and has a significant role in aquaculture. Gut microbiome composition is closely related to external environments. In this study, we identified the effects of seasonal changes on the composition and main metabolites of symbiotic microorganisms in the intestine of A. japonicus. We used 16S rRNA sequencing to identify the composition of symbiotic microorganisms in different seasons. Intestinal metabolites were determined using liquid chromatography with tandem mass spectrometry, which linked symbiotic microorganisms to intestinal metabolites. Analyzing changes in intestinal microbial composition across different seasons. The results showed that seasonal changes of intestinal microorganisms were significant, A. japonicus were infected by Vibrio easily in summer, Stigmasterol and sitosterol could affect the growth of body wall of A. japonicus. It is vital importance for A. japonicus that the results benefit for the growth, immunity and aquaculture.

Gastrointestinal Biogeography of Luminal Microbiota and Short-Chain Fatty Acids in Sika Deer (Cervus nippon).

The gut microbiota of sika deer has been widely investigated, but the spatial distribution of symbiotic microbes among physical niches in the gastrointestinal tract remains to be established. While feces are the most commonly used biological samples in these studies, the accuracy of fecal matter as a proxy of the microbiome at other gastrointestinal sites is as yet unknown. In the present study, luminal contents obtained along the longitudinal axis of deer gastrointestinal tract (rumen, reticulum, omasum, abomasum, small intestine, cecum, colon, and rectum) were subjected to 16S rRNA gene sequencing for profiling of the microbial composition, and samples from the rumen, small intestine, and cecum were subjected to metabolomic analysis to evaluate short-chain fatty acid (SCFA) profiles. Prevotella bacteria were the dominant gastric core microbes, while Christensenellaceae_R-7_group was predominantly observed in the intestine. While the eight gastrointestinal sites displayed variations in microbial diversity, abundance, and function, they could be clustered into stomach, small intestine, and large intestine segments, and the results further highlighted a specific microbial niche of the small intestine. SCFA levels in the rumen, small intestine, and cecum were significantly different, with Bacteroidetes and Spirochaetes were shown to play a critical role in SCFA production. Finally, the rectal microbial composition was significantly correlated with colonic and cecum communities but not those of the small intestine and four gastric sites. Quantification of the compositions and biogeographic relationships between gut microbes and SCFAs in sika deer should provide valuable insights into the interactions contributing to microbial functions and metabolites. IMPORTANCE Feces or specific segments of the gastrointestinal tract (in particular, the rumen) were sampled to explore the gut microbiome. The gastrointestinal biogeography of the luminal microbiota in ruminants, which is critical to guide accurate sampling for different purposes, is poorly understood at present. The microbial community of the rectal sample (as a proxy of fecal sample) showed higher correlation with those of other large intestinal sites relative to the small intestine or stomach, suggesting that the microbial composition is specifically shaped by the unique physiological characteristics of different gastrointestinal niches. In addition, significant differences in microbiomes and SCFAs were observed among the different gastrointestinal sites.

Diversity of Microbial Communities in Sediment from Yeosu Bay, Republic of Korea, as Determined by 16S rRNA Gene Amplicon Sequencing.

ABSTRACTMonitoring natural variations in microbial diversity is crucial because microorganisms play a major role in the environmental processes in marine sediment. To evaluate the microbial diversity in Yeosu Bay sediment, 16S rRNA gene amplicon sequencing was performed. Proteobacteria, Chloroflexi, and Bacteroidetes were the predominant phyla in all sediment samples observed.