Differences In Community Composition Research Articles

Response and Assembly Process of Soil Microbial Communities Under Different Reclamation Measures

Reclamation is essential for restoring the ecological function of soil in mining areas. However, the microbiological mechanism of soil ecological function reconstruction under different reclamation measures still needs to be clarified. Clarifying the characteristics of soil bacterial and fungal communities, assembly mechanisms, and their relationship with physicochemical properties under different reclamation measures is crucial for reshaping the ecological stability of soil in mining areas. Metagenomic sequencing technology was combined with the null model and neutral model to analyze the differences in soil microbial diversity, community composition, network structure, and community assembly process between the reclaimed natural recovery area （LH） and the reclamation fertilization area （MM）. The results suggested that： ① Compared with that in the LH treatment, the MM treatment significantly increased the soil nutrient content, and the total nitrogen （TN）, total phosphorus （TP）, available phosphorus （AP）, and available potassium （AK） contents increased by 34.70%, 72.72%, 468.98%, and 45.74%, respectively （P<0.05）. ② The dominant bacterial and fungal communities did not change under the LH and MM treatments； however, the abundance of bacterial communities changed significantly. Compared with that in the LH treatment, the relative abundance of Acidobacteria increased significantly by 5.4% in the MM treatment, while the relative abundance of Candidatus Rokubacteria decreased significantly by 235.72% （P<0.05）. Under different reclamation measures, the indicator microorganisms of bacterial and fungal communities changed. ③ Compared with that in the LH treatment, the MM treatment increased the complexity of bacterial networks, decreased the complexity of fungal networks, and increased the number of soil bacterial nodes and links. The reclamation measures transformed the key bacterial groups from Proteobacteria to Candidatus Rokubacteria and Planctomycetes. The key group of fungi was Ascomycota. 4.） The deterministic process dominated the assembly of bacterial and fungal communities. Homogeneous selection contributed the most to the bacterial community assembly in the LH treatment, and heterogeneous selection contributed the most to the MM treatment. The fungal communities were all dominated by heterogeneous selection. These results provide new insights into the soil microbial community structure and ecological function restoration in coal mining subsidence reclamation areas.

Evidence of habitat specificity in sponge microbiomes from Antarctica

BackgroundMarine sponges and their microbiomes are ecosystem engineers distributed across the globe. However, most research has focused on tropical and temperate sponges, while polar regions like Antarctica have been largely neglected. Despite its harsh conditions and geographical isolation, Antarctica is densely populated by sponges. In this study, we explored the extent of habitat specificity in the diversity, community composition, and microbial co-occurrence within Antarctic sponge microbiomes, in comparison to those from other marine environments. We used massive sequencing of 16S rRNA genes and integrated multiple databases to incorporate Antarctic sponges as a habitat in global microbiome analyses.ResultsOur study revealed significant differences in microbial diversity and community composition between Antarctic and non-Antarctic sponges. We found that most microorganisms present in Antarctic sponges are unique to the South Shetland Islands. Nitrosomonas oligotropha, Candidatus Nitrosopumilus, Polaribacter, SAR116 clade, and Low Salinity Nitrite-Oxidizing Bacteria (LS-NOB) are microbial members characterizing the Antarctic sponge microbiomes. Based on their exclusivity and presence across different sponges worldwide, we identified habitat-specific and habitat-generalist bacteria associated with each habitat. They are particularly abundant and connected within all the Antarctic sponges, suggesting that they may play a crucial role as keystone species within these sponge ecosystems.ConclusionsThis study provides significant insights into the microbial diversity and community composition of sponges in Antarctica and non-Antarctic ecoregions. Our findings provide evidence for habitat-specific patterns that differentiate the microbiomes of Antarctic sponges from elsewhere, indicating the strong influence of environmental selection and dispersal limitation wrapped into the Antarctic ecoregions to shape more similar microbial communities in distantly related sponges. This study contributes to understanding signatures of microbial community assembly in the Antarctic sponges and has important implications for the ecology and evolution of these unique marine environments.

Comparative analysis of community composition and network structure between phyllosphere endophytic and epiphytic fungal communities of Mussaenda pubescens.

The phyllosphere constitutes a critical habitat for microorganisms, exerting profound influences on host vitality, developmental dynamics, reproductive functions, and stress resilience. However, the diversity and network structure of endophytic and epiphytic fungal communities within this microecosystem have not been thoroughly explored. In this investigation, high-throughput sequencing technologies were employed to assess the diversity, community composition, and network structure of endophytic and epiphytic fungal communities associated with Mussaenda pubescens across six geographically distinct locations in Southeast China. The results revealed significant differences in community composition and diversity between endophytic and epiphytic fungi, with pronounced geographical variation observed within these phyllosphere fungal communities. Network analysis indicated that epiphytic fungal networks possess enhanced complexity compared with their endophytic counterparts, although the latter exhibit greater network stability. Moreover, stochastic processes were identified as pivotal in shaping the composition of these fungal communities. This research substantially enriches our comprehension of the diversity and organizational mechanisms of phyllosphere fungal communities, providing novel insights into the modalities of species coexistence and the stability of community equilibrium within ecosystems.IMPORTANCEThis study employs high-throughput sequencing technologies to explore the fungal communities within the phyllosphere of Mussaenda pubescens across Southeast China, offering significant insights into plant mycobiome. It demonstrates geographical variations in these fungal communities, with epiphytic fungi exhibiting more complex interaction networks compared with the endophytic fungi. Crucially, the research indicates that stochastic processes play a substantial role in the composition of fungal communities. These findings enhance our comprehension of plant-associated microecosystems and underscore the intricate interplay of randomness in maintaining ecosystem stability and diversity.

Symbiotic bacteria play crucial roles in a herbivorous mite host suitability.

The tomato russet mite (TRM), Aculops lycopersici, is a strictly herbivorous and economically significant pest that infests Solanaceae plants, but its host suitability varies, showing high performance on tomatoes. Although symbiotic bacteria have been suggested to play crucial roles in the host adaptation of herbivores, their effects on TRM remain unclear. In this study, using next generation high-throughput sequencing of the bacterial 16S rRNA data, we identified the bacterial diversity and community composition of TRM feeding on tomato, eggplant, and chili. Our results show no significant difference in the bacterial community composition of TRM across three host plants. However, the relative density of Escherichia coli (TRM_Escherichia) showed 9.36-fold higher on tomato than on eggplant and chili. These results align with the observed TRM performance among three host plants. When TRM_Escherichia was reduced using antibiotics, the treated TRM decreased the population density on tomato. However, when we transferred TRM from eggplant to tomato, the population density of TRM increased, coinciding with an increase of the TRM_Escherichia density. These results indicate that TRM_Escherichia may affect the host suitability of TRM. Our fluorescence in situ hybridization (FISH) results further showed that TRM_Escherichia is primarily distributed in the salivary glands. Metagenomic data results suggest that TRM_Escherichia functions in food digestion and energy metabolism. We provided the first comprehensive analysis of TRM bacterial communities. Our findings demonstrate that the symbiotic bacterium TRM_Escherichia may play crucial roles in the suitability of TRM feeding on different Solanaceae hosts. © 2024 Society of Chemical Industry.

Rainfall and Soil Moisture Jointly Drive Differences in Plant Community Composition in Desert Riparian Forests of Northwest China

Extreme rainfall and soil moisture play important roles in the survival, community composition, and ecosystem function of desert plants. This study focused on arid desert riparian forests ecosystems in the Ebinur Lake Basin of Xinjiang, China. We analyzed the effects of rainfall and soil moisture on species composition, indicator species, β diversity, species turnover, and nestedness using three consecutive years of community surveys. A zero-model combined with a Bayesian framework was used to explore the response of species turnover and nestedness to soil moisture and rainfall, and variance decomposition was used to quantify the relative importance of spatial distance, rainfall, and soil factors in determining species composition. The results indicated the following: (1) when rainfall was high, the richness and abundance of annual herbaceous plants increased. The proportion of the community based on richness (32%) and abundance (58.1%) of annual herbaceous plants in 2016 was higher than that in 2015 and 2017. The Jaccard, Bray–Curtis, and Chao indexes of the community in years with higher rainfall were significantly higher than in years with lower rainfall; however, a lag effect was also observed. (2) Soil factors explained 5% of the changes in community composition, rainfall explained 12% of the changes in community composition, and spatial distance, soil factors, and rainfall jointly explained 32% of the changes in community composition. (3) We also showed that high soil moisture leads to greater β diversity than low soil moisture. Rainfall had the greatest explanatory power on the measured values of β diversity (19.6%) and species turnover (38%), and the factor with the greatest explanatory power for species nestedness was the interaction between rainfall and soil moisture (26.2%). Our findings indicate that drought and rainfall drive differences in plant community composition, with rainfall playing a dominant role. These results provide a basis for understanding the impact of extreme rainfall events on arid ecosystem functions.

Soil multifunctionality and nutrient cycling-related genes in Cunninghamia lanceolata plantations: metagenomic perspective insights into ecological restoration

The widespread cultivation of Cunninghamia lanceolata in China has led to soil degradation and decline in microbial diversity, which have a significant impact on supporting forest ecological services. However, little is known about the long-term consequences from forest management practices on the bacterial functional genes associated with soil nutrient cycling. Here, metagenomic sequencing was used to investigate the soil bacterial functional genes involved in carbon (C), nitrogen (N), and phosphorus (P) cycling in a 16-year pair experiment of pure (C. lanceolata) and mixed plantations (C. lanceolata + Betula luminifera). The results showed that the mixed plantations had much higher soil nutrient content as well as enzyme activity, thereby improving soil multifunctionality (SMF). Forest management practices resulted in differences in the structural and functional composition of soil bacterial communities, such as Chloroflexi, Firmicutes and acid metabolism were enriched in pure plantations, while Acidobacteria, Planctomycetes and amino acid metabolism were enriched in mixed plantations. Compared with monocultures, mixed plantations had higher abundance of genes participated in C degradation, C fixation, methanogenesis, N cycling and P solubilization. The CNP cycling genes also varied with taxon-specific responses to forest management. Forty-seven nearly entire bacterial metagenome-assembled genomes (MAGs) were obtained, in which MAGs enriched in mixed plantations had more functional genes involved in CNP cycling. Notably, acidophilic Acidobacteria played important roles in reduction of Fe(III) and the subsequent release of organic P. In all, our results demonstrated that the use of mixed plantations enhances a number of soil functions via its influence on the abundances of keystone taxa and functional genes, providing a foundation for developing forest management strategies in subtropical regions. In future researches, attention should be paid to the effects of mixed plantations on soil microbial diversity and nutrient cycling across various seasons.

Combined application of multi-omics techniques and multivariate statistical analysis reveals the core functional microorganisms of Qula in Tibet, China

Tibetan Qula, a traditional fermented food processed from yak milk, is valued for its high nutritional content and distinctive flavor, but the vast territory of Tibet often results in quality heterogeneity. To identify the core microorganisms with metabolic activities in Qula, we conducted a comprehensive investigation of 10 samples from 7 regions of Tibet using integrated multi-omics techniques and multivariate statistical analysis. All samples were higher in protein content (36.43∼60.25%), acidity (86.72∼216.52 °T) and lactic acid bacteria count (3.69∼6.14 logCFU/g), while lower in fat (2.40∼11.35%) and moisture contents (5.84∼12.02%). High-throughput sequencing showed significant differences in microbial diversity and community composition among samples, but Lactococcus, Lactobacillus, Leuconostoc, Acetobacter, Penicillium and Aspergillus were core microorganisms due to their high abundance and wide distribution. Notably, they also played an important role in maintaining community interactions, especially Acetobacter. Of the 60 volatiles detected by GC-MS, 23 compounds such as hexanal, heptanal, butanoic acid, hexanoic acid and ethyl octanoate were identified as the dominant flavors. In contrast, the 62 non-volatiles obtained from metabolomics were primarily composed of carbohydrates, organic acids, fatty acids and amino acids, with lactose, lactic acid, palmitic acid and alanine being the most abundant metabolites in their respective categories. Correlation analysis indicated that core microorganisms were predominantly involved in the formation and transformation of metabolites, while Lactococcus, Rhodotorula and Trichothecium facilitated the accumulation of various flavors. This study provides a comprehensive analysis of the microbial and metabolic characteristics of Tibetan Qula, offering a scientific foundation for quality enhancement through biofortification technology.

Comparative analysis of intestinal structure, enzyme activity, intestinal microbiota and gene expression in different segments of pufferfish (Takifugu Obscurus)

The structure of fish intestines does not have a clear regional division, while the function of the intestines may be related to their structure. Therefore, in this study, the delimitation of intestinal segments in pufferfish (Takifugu obscurus) was achieved by morphological analysis. Subsequently, enzyme activity, intestinal microbiota, and gene expression were examined to compare the differences among the pufferfish various segments. According to four morphological parameters: height of mucosa folds (HF), width of mucosa folds (WF), thickness of muscularis (TM), and cross-sectional area (CSA), the pufferfish's intestine was divided into anterior intestine (AI), middle intestine (MI), and posterior intestine (PI). The activity levels of amylase, lipase, and trypsin in the AI and MI were significantly higher than these in the PI. According to the analysis of 16S rDNA, the dominant microbiota at the phylum level in the different segments were Epsilonbacteraeota, Spirochaetes, and Proteobacteria. At the genus level, there were variations observed in the relative abundance of Brevinema, Mycobacterium, Bradyrhizobium, and Microvirga. α diversity analysis revealed that the richness indexes (Ace and Chao1) were the lowest in the MI, while β diversity analysis revealed significant difference in intestinal microbial community composition among the three intestinal segments. Furthermore, RNA-Seq was used to identify differential expression genes (DEGs) and biological pathways among the different intestinal segments. The DEGs between the AI and MI were enriched in pancreatic secretion and protein digestion and absorption, those between AI and PI were involved in ascorbate and aldarate metabolism and glutathione metabolism, and those between MI and PI were involved in steroid biosynthesis, fat digestion and absorption, vitamin digestion and absorption, and glycine, serine and threonine metabolism. In conclusion, the presented results compare and analyze the differences in various intestinal segments of pufferfish, which will be conductive to future exploration of the functions of these different segments.

Using machine learning to reveal seasonal nutrient dynamics and their impact on chlorophyll-a levels in lake ecosystems: A focus on nitrogen and phosphorus

Chlorophyll-a (Chl-a) is a pivotal indicator of lake eutrophication. Studies examining nutrients limiting lake eutrophication at large scales have traditionally focused on summer and autumn, potentially limiting the applicability of their findings. This study encompasses 86 state-controlled points in the Eastern China Basin, spanning data collected from January 2020 to July 2023. Furthermore, we focus on the application of three machine-learning models (i.e., eXtreme Gradient Boosting, Support Vector Machines, and Naive Bayes Classifier) to analyze the seasonal nutrient dynamics in lake ecosystems. We categorized the monitoring data by season to eliminate outliers and employed adaptive synthetic sampling to address data imbalance issues. The results reveal that the direct correlations between total nitrogen (TN), total phosphorus (TP), and TP in conjunction with turbidity and Chl-a are broadly weak, possibly because of geographic variations, nutrient lag effects on algae, and differences in algal community composition. However, probabilistic analyses revealed that as TP or TN levels transitioned from oligo-mesotrophic (O) to eutrophic (E), TP exhibited a greater influence on the variation in Chl-a status than TN during spring and winter (p < 0.05). Conversely, the effects of TP and TN on Chl-a (O-E) were comparable during summer and autumn. Seasonal variations in TN and TP thresholds derived from XGBoost modeling for O and E states of Chl-a suggest the need for stricter control measures during periods of high-nutrient levels and cost-effective management strategies to employ during low-nutrient periods. These findings should enhance our understanding of trophic shifts in lakes and provide a foundation for optimizing eutrophication management strategies across all seasons.

Distinct Bacterial Communities Within the Nonrhizosphere, Rhizosphere, and Endosphere of Ammodendron bifolium Under Winter Condition in the Takeermohuer Desert

Due to human activities and severe climatic conditions, the population of Ammodendron bifolium, an excellent sand-fixing plant, has gradually decreased in the Takeermohuer Desert. The plant-associated bacteria community can enhance its survival in harsh environments. However, the understanding of A. bifolium-associated bacterial community is still unclear during the harsh winter. We investigated the bacterial community structure from the A. bifolium rhizosphere and nonrhizosphere at different depths (i.e., 0–40 cm, 40–80 cm, 80–120 cm) and from endosphere (i.e., root endosphere and stem endosphere) in winter. At the same time, we analyzed the impact of different compartments and soil factors on the bacterial community structure. Studies have shown that the A. bifolium rhizosphere exhibits higher levels of SOM (soil organic matter), SOC (soil organic carbon), SAN (soil alkaline nitrogen), and SAK (soil available potassium) compared with the nonrhizosphere. The dominant bacterial phyla were Proteobacteria (19.6%), Cyanobacteria (15.9%), Actinobacteria (13.6%), Acidobacteria (9.0%), and Planctomycetota (5.7%) in the desert. Proteobacteria (24.0–30.2%) had the highest relative abundance in rhizosphere, Actinobacteria (18.3–22.6%) had the highest relative abundance in nonrhizosphere, and Cyanobacteria had the highest relative abundance in endosphere. At the genus level, the relative abundance of Pseudomonas (1.2%) in the root endosphere was the highest and the other genera were mostly unclassified. The Chao1 and PD_whole_tree indices showed that the diversity of the bacterial communities decreased from nonrhizosphere, rhizosphere, root endosphere to stem endosphere. Co-occurrence network analyses identified Proteobacteria and Actinobacteria as key species across the three compartments. Additionally, unique keystone species like Cyanobacteria, Verrucomicrobiota, and Desulfobacterota were found only in the endosphere. The bacterial community in the rhizosphere was influenced by factors such as EC (electrical conductivity), STC (soil total carbon), SOM, SOC, STN (soil total nitrogen), SAN, STP (soil total phosphorus), and SAK, while that of the nonrhizosphere was mainly influenced by pH, C/N (STC/STN), SAP, and distance. The study highlighted differences in bacterial community composition, diversity, and influencing factors across the three compartments, which can provide a better understanding of the association/interactions between A. bifolium and bacterial communities and lay a foundation for revealing its adaptability in winter.

Dynamic changes in gut microbiota and production phenotypes driven by host genetic background in large yellow croaker

The gut microbiota is becoming increasingly important in enhancing aquaculture productivity. However, there are fewer studies on the effect of host genetic background on the gut microbiota of cultured fish. In the current study, we aimed to determine whether the genetic background of large yellow croaker influences differences in gut microbial composition and growth. To address this objective, we conducted a comparative experiment involving the nearshore cage culture of a selected line (SL) of large yellow croaker, which was subjected to genetic selection for swimming performance, alongside a control line (CL). Both lines were reared under identical environmental and dietary conditions for a duration of six weeks. We employed 16S rRNA gene sequencing technology to analyze the gut microbial composition of the large yellow croaker, and utilized bioinformatics methods to assess the abundance and diversity of the gut microbiota. The findings revealed that the core gut microbiota of both lines primarily comprised Proteobacteria, Firmicutes, and Bacteroidetes. However, a significant disparity in gut microbiota abundance was observed between SL and CL following nearshore cage culture. Additionally, the survival rate of SL reached 64.8 %, significantly higher than the 37.3 % observed in CL. The feed conversion efficiency of SL reached 47.7 %, significantly higher than that of CL (28.6 %). These results underscore the influence of host genetic background on driving differences in gut microbial community composition and production phenotypes. This research offers intriguing insights into the interconnectedness of gut microbiota, fish genetics, and production phenotypes.

Exploring the biosynthesis potential of permafrost microbiomes

BackgroundPermafrost microbiomes are of paramount importance for the biogeochemistry of high latitude soils and while endemic biosynthetic domain sequences involved in secondary metabolism have been found in polar surface soils, the biosynthetic potential of permafrost microbiomes remains unexplored. Moreover, the nature of these ecosystems facilitates the unique opportunity to study the distribution and diversity of biosynthetic genes in relic DNA from ancient microbiomes. To explore the biosynthesis potential in permafrost, we used adenylation (AD) domain sequencing to evaluate non-ribosomal peptide (NRP) production in permafrost cores housing microbiomes separated at kilometer and kiloyear scales.ResultsPermafrost microbiomes represented NRP repertoires significantly different from that of temperate soil microbiomes, but as for temperate soils, the estimated domain richness and diversity was strongly correlated to the bacterial taxonomic diversity across locations. Furthermore, we found significant differences in both community composition and AD domain composition across geographical and temporal distances. Overall, the vast majority of biosynthetic domains showed below 90% amino acid similarity to characterized BGCs, confirming the high degree of novelty of NRPs inherent to permafrost microbiomes. Using available metagenomic sequences, we further identified a high biosynthetic diversity beyond NRPs throughout arctic surface soils down to deep and ancient (megayear old) permafrost microbiomes.ConclusionWe have shown that arctic permafrost microbiomes harbor a unique biosynthetic repertoire rich in hitherto undescribed NRPs. This diversity is driven by geographic separation across kilometer scales and by the bacterial taxonomic diversity between microbiomes confined in separate permafrost layers. Hence the permafrost biome represents a unique resource for studying secondary metabolism, and potentially for the discovery of novel drug leads.

Inclusion of Hybrid Pennisetum and Probiotics Enhanced Anaerobic Fermentation Quality and Bacterial Diversity of Alfalfa Silage

This study aims to assess the impact of Bacillus subtilis (BS) and Lactobacillus buchneri (LB) on the fermentation quality, microbial communities, and predicted metabolic pathways in mixed silage made from alfalfa and hybrid Pennisetum. We prepared mixed silage from fresh alfalfa and hybrid Pennisetum in a 1:1 ratio and inoculated it with BS, LB, or a combination of both (BSLB) or left it untreated as a control. The silage was fermented for 30 and 60 days. The results showed that inoculation with BS, LB, or their combination increased the lactic acid and crude-protein content while reducing the fiber content compared to the control. Additionally, BS and LB inoculation raised (p &lt; 0.05) the acetic acid content, and the combination of both strains increased (p &lt; 0.05) the ratio of lactic acid to acetic acid. LB alone and the combined inoculation also increased the relative abundance of Lactobacillus during the pre-silage period. Functional analysis through the Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed considerable variations among the different probiotic treatments. The silage process reduced nucleotide metabolism but enhanced carbohydrate, amino acid, energy, cofactor, and vitamin nucleotide metabolism. High-throughput sequencing combined with KEGG functional prediction demonstrated significant differences in community composition and functional changes at 30 and 60 days of fermentation. These findings enhance our understanding of bacterial communities and functional changes in mixed silage of alfalfa and hybrid Pennisetum, offering valuable insights into the fermentation mechanisms of legume and grass silage and informing practices for producing high-quality mixed silage.

Evidences of the sources of suspended sediments and ecological processes in the Yellow River Basin.

Terrestrial originated suspended sediments from the Yellow River are crucial to understand the sources of the suspended sediment and ecological processes in estuary. This study integrated physicochemical indices, stable isotopes and microbial communities to trace the origin of the suspended sediment, and investigated the importance of ecological processes in community assembly via the null model and neutral community model. Global data revealed that the dissolved and particle ratios of carbon and nitrogen obviously decreased from the headstream to the estuary. A significant positive correlation was detected between δ15N and δ13C from Henan Province to offshore. Notable differences in bacterial community composition were found between Henan Province and offshore in dry season, whereas nearly no remarkable changes were detected throughout the entire YR basin in wet season. Multiple lines of evidence from physicochemical analysis, stable isotopic and genetic tracing revealed the possibility that the terrestrially- derived suspended sediments in the lower reaches contributed the most carbon and nitrogen to the suspended sediment in the estuary. Dispersal limitations for stochastic processes had the greatest relative importance in the community assembly of the two seasons. A greater degree of homogeneous selection for deterministic processes was exhibited in dry but not wet season. Proteobacteria had a remarkable correlation with salinity and conductivity in both dry and wet seasons, while Elusimicrobiota was more strongly related to NO3-N in dry than that in wet season. Therefore, this study elucidates the source of suspended sediment in estuaries and highlights the ecological processes involved in altering the microbial community composition in Yellow River basin.

Effects of reduced flow gradient on benthic biofilm communities' ecological network and community assembly.

The intensification of human activities has led to flow reduction and cut-off in most global rivers, seriously affecting riverine organisms and the biogeochemical processes. As key indicators of river ecosystems' structure and function, benthic biofilms play a critical role in driving primary production and material cycling in rivers. This research aimed to investigate the characteristics of microbial communities' complexity and stability during river flow reduction. Benthic biofilms were grown in artificial channels and subjected to eight gradients of flow reduction (represented by flow velocity from 0.4 to 110 cm/s). Biofilms' biodiversity, ecological networks and community assembly of bacteria, fungi and algae were investigated by high-throughput sequencing. Results showed significant differences in community composition and structure under different flow conditions. The eight flow gradients' microbial communities were divided into three groups: low, medium and high flows. The flow reduction led to significant decreases in bacterial and fungal communities' Chao1 index. Low flow conditions enriched the bacterial phyla Oxyphotobacteria, Alphaproteobacteria and Mollicutes, but significantly decreased the fungal phylum Chytridiomycota. Lowering flow reduced the fungal network's number of nodes and increased the algal network's number of edges. Cross-domain interactions network analysis showed a gradual increase in node and edge numbers with decreasing flow, while decreasing average path length. The neutral model predicted stochastic processes primarily drove biofilm community assembly, and that model's explanations decreased as the flow gradient decreased. The null model analysis revealed diffusion limitation as the most common stochastic ecological process for bacterial and algal communities, with reduced flow reducing heterogeneous selection and increasing diffusion-limited processes. This study provides an in-depth analysis of flow reduction's effects on biofilm communities' ecological networks and community assembly.

Deciphering Phyllomicrobiome of Cauliflower Leaf: Revelation by Metagenomic and Microbiological Analysis of Tolerant and Susceptible Genotypes Against Black Rot Disease.

Understanding the phyllomicrobiome dynamics in cauliflower plants holds significant promise for enhancing crop resilience against black rot disease, caused by Xanthomonas campestris pv. campestris. In this study, the culturable microbiome and metagenomic profile of tolerant (BR-161) and susceptible (Pusa Sharad) cauliflower genotypes were investigated to elucidate microbial interactions associated with disease tolerance. Isolation of phyllospheric bacteria from asymptomatic and black rot disease symptomatic leaves of tolerant and susceptible cultivars yielded 46 diverse bacterial isolates. Molecular identification via 16S rRNA sequencing revealed differences in the diversity of microbial taxa between genotypes and health conditions. Metagenomic profiling using next-generation sequencing elucidated distinct microbial communities, with higher diversity observed in black rot disease symptomatic leaf of BR-161. Alpha and beta diversity indices highlighted differences in microbial community structure and composition between genotypes and health conditions. Taxonomic analysis revealed a core microbiome consisting of genera such as Xanthomonas, Psychrobacillus, Lactobacillus, and Pseudomonas across all the samples. Validation through microbiological methods confirmed the presence of these key genera. The findings provide novel insights into the phyllomicrobiome of black rot-tolerant and susceptible genotypes of cauliflower. Harnessing beneficial microbial communities identified in this study offers promising avenues for developing sustainable strategies to manage black rot disease and enhance cauliflower crop health and productivity.

Hoverfly assemblages in urban farms compared to urban parks in the city of Geneva

This study aims to assess whether urban farms are good providers of ecosystem services compared to other green infrastructures. To assess two services (pollinating and pest control services), hoverflies were monitored in three urban farms (Budé, Lignon and Tissot) and three urban parks (Franchises, Trembley and Beaulieu) in the canton of Geneva in 2017. The results show a large abundance of hoverflies in the parks and farms, particularly at the end of June. In terms of hoverfly diversity, 81 species were recorded, with 10 species accounting for around 80% of the captures. The Shannon index shows that hoverfly diversity is significantly higher in the parks than in the farms at three out of 6 sampling dates. Of the five most abundant species in parks and farms taken together, three are aphidiphagous and can therefore play a biocontrol role in crops. The average proportion of aphidiphagous individuals is significantly higher in the farms than in the parks. In conclusion, studying hoverflies in urban environments has permitted to highlight differences in function and community composition between apparently similar habitats. However, we recommend limiting the sampling period to the month of June, which would reduce the work involved in sampling with Malaise traps, while retaining significant discriminatory power and limiting impact on syrphid fly communities. In order to encourage hoverflies in the city, it is crucial to maintain several stepping stone habitats within the urban matrix, to favor structures that will give them access to diversified food resources and to adopt maintenance practices that have the least impact on these communities. The introduction of native hedges and aquatic habitats could also be a source of diversification for the pool of species found in the city.

Stage dependent microbial dynamics in hepatocellular carcinoma and adjacent normal liver tissues

The interactive pathway of the gut-liver axis underscores the significance of microbiome modulation in the pathogenesis and progression of various liver diseases, including hepatocellular carcinoma (HCC). This study aims to investigate the disparities in the composition and functionality of the hepatic microbiota between tumor tissues and adjacent normal liver tissues, and their implications in the etiology of HCC. We conducted a comparative analysis of the hepatic microbiome between adjacent normal liver tissues and tumor tissues from HCC patients. Samples were categorized according to the modified Union for International Cancer Control (mUICC) staging system into Non-tumor, mUICC stage I, mUICC stage II, and mUICC stage III groups. Microbial richness and community composition were analyzed, and phylogenetic profiles were examined to identify significantly altered microbial taxa among the groups. Predicted metabolic pathways were analyzed using PICRUSt2. Our analysis did not reveal significant differences in microbial richness and community composition with the development of HCC. However, phylogenetic profiling identified significantly altered microbial taxa among the groups. Sphingobium, known for degrading polychlorinated biphenyls (PCBs), exhibited a significantly negative correlation with clinical indices in HCC patients. Conversely, Sphingomonas, a gut bacterium associated with various liver diseases, showed a positive correlation. Predicted metabolic pathways suggested a correlation between atrazine degradation and valine, leucine, and isoleucine biosynthesis with mUICC stage and tumor size. Our results underscore the critical link between hepatic microbial composition and function and the HCC tumor stage, suggesting a potentially pivotal role in the development of HCC. These findings highlight the importance of targeting the hepatic microbiome for therapeutic strategies in HCC.

Microbiome and Resistome Studies of the Lithuanian Baltic Sea Coast and the Curonian Lagoon Waters and Sediments.

the widespread use of antibiotics in human and veterinary medicine has contributed to the global challenge of antimicrobial resistance, posing significant environmental and public health risks. this study aimed to examine the microbiome and resistome dynamics across a salinity gradient, analyzing water and sediment samples from the Baltic Sea coast and the Curonian Lagoon between 2017 and 2023. the composition of the water and sediment bacterial community was determined by Full-Length Amplicon Metagenomics Sequencing, while ARG detection and quantification were performed using the SmartChipTM Real-Time PCR system. the observed differences in bacterial community composition between the Baltic Sea coast and the Curonian Lagoon were driven by variations in salinity and chlorophyll a (chl a) concentration. The genera associated with infectious potential were observed in higher abundances in sediment than in water samples. Over 300 genes encoding antibiotic resistance (ARGs), such as aminoglycosides, beta-lactams, and multidrug resistance genes, were identified. Of particular interest were those ARGs that have previously been detected in pathogens and those currently classified as a potential future threat. Furthermore, our findings reveal a higher abundance and a distinct profile of ARGs in sediment samples from the lagoon compared to water. these results suggest that transitional waters such as lagoons may serve as reservoirs for ARGs, and might be influenced by anthropogenic pressures and natural processes such as salinity fluctuation and nutrient cycling.

Coal mining activities driving the changes in bacterial community

The mechanism of the difference in bacterial community composition caused by environmental factors in the underground coal mine is unclear. In order to reveal the influence of coal mining activities on the characteristics of bacterial community structure in coal seam, 16S rRNA gene amplicon sequencing technology was used to determine the species abundance, biodiversity, and gene abundance of bacterial community in a coal mine in Shanxi Province, and the environmental factors such as metal elements, non-metal elements, pH value, and gas concentration of coal samples were determined. The results showed that environmental factors and bacterial communities had obvious regional characteristics. Mining activities greatly affected the α diversity of bacterial communities, mining working face > main airway > roadway roof > unexposed coal seam > tunneling roadway. The bacterial community composition of each sample point is also very different. The main airway, roadway roof, and unexposed coal seam are dominated by Actinobacteria while the mining working face and tunneling roadway are dominated by Proteobacteria. Among the gene abundances of metabolic pathways in each site, Citrate cycle had the greatest difference, followed by glycine, serine and threonine metabolism, and oxidative phosphorylation and methane metabolism had little difference. RDA analysis showed that the environmental factors affecting the bacterial community were mainly cadmium, oxygen, hydrogen, and gas content. CCA analysis divided the bacterial community into three categories. Degradation functional bacteria are located in mining working face, bacteria that tolerate poor environments are located in main airway and tunneling roadway, and human pathogens are mostly located in roadway roof and unexposed coal seam. The research results would provide support for realizing green and safe mining in coal mines.