WSGMB: weight signed graph neural network for microbial biomarker identification.

The stability of the gut microenvironment is inextricably linked to human health, with the onset of many diseases accompanied by dysbiosis of the gut microbiota. It has been reported that there are differences in the microbial community composition between patients and healthy individuals, and many microbes are considered potential biomarkers. Accurately identifying these biomarkers can lead to more precise and reliable clinical decision-making. To improve the accuracy of microbial biomarker identification, this study introduces WSGMB, a computational framework that uses the relative abundance of microbial taxa and health status as inputs. This method has two main contributions: (1) viewing the microbial co-occurrence network as a weighted signed graph and applying graph convolutional neural network techniques for graph classification; (2) designing a new architecture to compute the role transitions of each microbial taxon between health and disease networks, thereby identifying disease-related microbial biomarkers. The weighted signed graph neural network enhances the quality of graph embeddings; quantifying the importance of microbes in different co-occurrence networks better identifies those microbes critical to health. Microbes are ranked according to their importance change scores, and when this score exceeds a set threshold, the microbe is considered a biomarker. This framework's identification performance is validated by comparing the biomarkers identified by WSGMB with actual microbial biomarkers associated with specific diseases from public literature databases. The study tests the proposed computational framework using actual microbial community data from colorectal cancer and Crohn's disease samples. It compares it with the most advanced microbial biomarker identification methods. The results show that the WSGMB method outperforms similar approaches in the accuracy of microbial biomarker identification.

The application of varying amount of green manure combined with nitrogen fertilizer altered the soil bacterial community and rice yield in karst paddy areas.

Long-term application of green manure (GM) and nitrogen (N) fertilizers markedly improved soil fertility and boosted rice yield in ecologically fragile karst paddy fields. However, the precise response mechanisms of the soil bacterial community to varying amounts of green manure alone and in combination with N fertilizer in such environments remain poorly elucidated. In this study, we investigated the soil bacterial communities, keystone taxa, and their relationship with soil environmental variables across eight fertilization treatments. These treatments included group without N addition (N0M0, no N fertilizer and no GM; N0M22.5, 22.5 t/ha GM; N0M45, 45 t/ha GM, N0M67.5, 67.5 t/ha GM) and group with N addition (NM0, N fertilizer and no GM; NM22.5, N fertilizer and 22.5 t/ha GM; NM45, N fertilizer and 45 t/ha GM; NM67.5, N fertilizer and 67.5 t/ha GM). The results revealed that increasing green manure input significantly boosted rice yield by 15.51-22.08% and 21.84-35% in both the group without and with N addition, respectively, compared to N0M0 treatment. Moreover, with escalating green manure input, soil TN, AN, AK, and AP showed an increasing trend in the group without N addition. However, following the addition of N fertilizer, TN and AN content initially rose, followed by a decline due to the enhanced nutrient availability for rice. Furthermore, the application of a large amount of N fertilizer decreased the C: N ratio in the soil, resulting in significant changes in both the soil microbial community and its function. Particularly noteworthy was the transition of keystone taxa from their original roles as N-fixing and carbon-degrading groups (oligotrophs) to roles in carbon degradation (copiotrophs), nitrification, and denitrification. This shift in soil community and function might serve as a primary factor contributing to enhanced nutrient utilization efficiency in rice, thus significantly promoting rice yield.

Bacterial community structure and co-occurrence networks in the rhizosphere and root endosphere of the grafted apple.

BACKGROUND: Compared with aerial plant tissues (such as leaf, stem, and flower), root-associated microbiomes play an indisputable role in promoting plant health and productivity. We thus explored the similarities and differences between rhizosphere and root endosphere bacterial community in the grafted apple system. RESULTS: Using pot experiments, three microhabitats (bulk soil, rhizosphere and root endosphere) samples were obtained from two-year-old apple trees grafted on the four different rootstocks. We then investigated the bacterial community composition, diversity, and co-occurrence network in three microhabitats using the Illumina sequencing methods. Only 63 amplicon sequence variants (ASVs) out of a total of 24,485 were shared in the rhizosphere and root endosphere of apple grafted on the four different rootstocks (M9T337, Malus hupehensis Rehd., Malus robusta Rehd., and Malus baccata Borkh.). The core microbiome contained 8 phyla and 25 families. From the bulk soil to the rhizosphere to the root endosphere, the members of the phylum and class levels demonstrated a significant enrichment and depletion pattern. Co-occurrence network analysis showed the network complexity of the rhizosphere was higher than the root endosphere. Most of the keystone nodes in both networks were classified as Proteobacteria, Actinobacteriota and Bacteroidetes and were low abundance species. CONCLUSION: The hierarchical filtration pattern existed not only in the assembly of root endosphere bacteria, but also in the core microbiome. Moreover, most of the core ASVs were high-abundance species, while the keystone ASVs of the network were low-abundance species.

Methanogen-methanotroph community has a more consistent and integrated structure in rice rhizosphere than in bulk soil and rhizoplane.

Methanogenic and methanotrophic microbes together determine the net methane flux from rice fields. Despite much research on them as separate communities, there has been little study of combined community patterns, and how these vary between the rhizoplane (root surface), rhizosphere (soil surrounding the root) and bulk soil around rice plants, especially at larger spatial scale. We collected samples from 32 geographically scattered rice fields in east central China, amplicon targeting the mcrA gene for methanogenesis and pmoA gene for methanotrophy by using high-throughput sequencing. Distinct communities of both methanogens and methanotrophs occurred in each of the three compartments, and predominantly positive links were found between methanogens and methanotrophs in all compartments indicating cross-feeding or consortia relationships. Methanogens were acting as the network hub in the bulk soil, and methanotrophs in rhizoplane. Network complexity and stability was greater in the rhizosphere than rhizoplane and bulk soil, with no network hubs detected, suggesting the strongest effect of homeostatic influence by plant occurred in the rhizosphere. The proportion of determinism (homogeneous selection) and distance-decay relation (DDR) in rhizoplane was consistently lower than that in the rhizosphere for both communities, indicating weaker phylogenetic clustering in rice root surface. Our results have provided a better understanding of CH4 oxidation and emission in rice paddy fields and future agriculture management could take into consideration of the subtle variation among different soil compartments and interactions within methanogenic and methanotrophic communities.

Metagenomic analysis revealed the potential of lactic acid bacteria in improving natural saline-alkali land.

Management and improving saline-alkali land is necessary for sustainable agricultural development. We conducted a field experiment to investigate the effects of spraying lactic acid bacteria (LAB) on the cucumber and tomato plant soils. Three treatments were designed, including spraying of water, viable or sterilized LAB preparations to the soils of cucumber and tomato plants every 20 days. Spraying sterilized or viable LAB could reduce the soil pH, with a more obvious effect by using viable LAB, particularly after multiple applications. Metagenomic sequencing revealed that the soil microbiota in LAB-treated groups had higher alpha-diversity and more nitrogen-fixing bacteria compared with the water-treated groups. Both viable and sterilized LAB, but not water application, increased the complexity of the soil microbiota interactive network. The LAB-treated subgroups were enriched in some KEGG pathways compared with water or sterilized LAB subgroups, such as environmental information processing-related pathways in cucumber plant; and metabolism-related pathways in tomato plant, respectively. Redundancy analysis revealed association between some soil physico-chemical parameters (namely soil pH and total nitrogen) and bacterial biomarkers (namely Rhodocyclaceae, Pseudomonadaceae, Gemmatimonadaceae, and Nitrosomonadales). Our study demonstrated that LAB is a suitable strategy for decreasing soil pH and improving the microbial communities in saline-alkali land.

Deciphering Microbial Adaptation in the Rhizosphere: Insights into Niche Preference, Functional Profiles, and Cross-Kingdom Co-occurrences.

Rhizosphere microbial communities are to be as critical factors for plant growth and vitality, and their adaptive differentiation strategies have received increasing amounts of attention but are poorly understood. In this study, we obtained bacterial and fungal amplicon sequences from the rhizosphere and bulk soils of various ecosystems to investigate the potential mechanisms of microbial adaptation to the rhizosphere environment. Our focus encompasses three aspects: niche preference, functional profiles, and cross-kingdom co-occurrence patterns. Our findings revealed a correlation between niche similarity and nucleotide distance, suggesting that niche adaptation explains nucleotide variation among some closely related amplicon sequence variants (ASVs). Furthermore, biological macromolecule metabolism and communication among abundant bacteria increase in the rhizosphere conditions, suggesting that bacterial function is trait-mediated in terms of fitness in new habitats. Additionally, our analysis of cross-kingdom networks revealed that fungi act as intermediaries that facilitate connections between bacteria, indicating that microbes can modify their cooperative relationships to adapt. Overall, the evidence for rhizosphere microbial community adaptation, via differences in gene and functional and co-occurrence patterns, elucidates the adaptive benefits of genetic and functional flexibility of the rhizosphere microbiota through niche shifts.

Core taxa, co-occurrence pattern, diversity, and metabolic pathways contributing to robust anaerobic biodegradation of chlorophenol.

It is hard to achieve robustness in anaerobic biodegradation of trichlorophenol (TCP). We hypothesized that specific combinations of environmental factors determine phylogenetic diversity and play important roles in the decomposition and stability of TCP-biodegrading bacteria. The anaerobic bioreactor was operated at 35 °C (H condition) or 30 °C (L condition) and mainly fed with TCP (from 28 µM to 180 µM) and organic material. Metagenome sequencing was combined with 16S rRNA gene amplicon sequencing for the microbial community analysis. The results exhibited that the property of robustness occurred in specific conditions. The corresponding co-occurrence and diversity patterns suggest high collectivization, degree and evenness for robust communities. Two types of core functional taxa were recognized: dechlorinators (unclassified Anaerolineae, Thermanaerothrix and Desulfovibrio) and ring-opening members (unclassified Proteobacteria, Methanosarcina, Methanoperedens, and Rubrobacter). The deterministic process of the expansion of niche of syntrophic bacteria at higher temperatures was confirmed. The reductive and hydrolytic dechlorination mechanisms jointly lead to C-Cl bond cleavage. H ultimately adapted to the stress of high TCP loading, with more abundant ring-opening enzyme (EC 3.1.1.45, ∼55%) and hydrolytic dechlorinase (EC 3.8.1.5, 26.5%) genes than L (∼47%, 10.5%). The functional structure (based on KEGG) in H was highly stable despite the high loading of TCP (up to 60 µM), but not in L. Furthermore, an unknown taxon with multiple functions (dechlorinating and ring-opening) was found based on genetic sequencing; its functional contribution of EC 3.8.1.5 in H (26.5%) was higher than that in L (10.5%), and it possessed a new metabolic pathway for biodegradation of halogenated aromatic compounds. This new finding is supplementary to the robust mechanisms underlying organic chlorine biodegradation, which can be used to support the engineering, regulation, and design of synthetic microbiomes.

Eutrophication-induced shifts cause diverse responses in the phoD community of a plateau freshwater lake.

Eutrophication is a critical environmental challenge affecting lakes globally. Mitigating trophic level under endogenous phosphorus release is an unsolved problem in eutrophic lakes. However, understanding the dynamics and assembly of microbial communities encoding the alkaline phosphatase (phoD community) and their responses during trophic transitions in eutrophic lakes is limited. In this study, we compared the composition and assembly mechanisms of phoD communities in four seasons in the Yilong Lake, a shallow lake of the Yunnan-Guizhou Plateau. The lake exhibits slightly eutrophic conditions in summer and mesotrophic conditions in spring, autumn, and winter. By analyzing seasonal variations, we observed that during summer, the relative abundance of Pseudomonas in the water had the highest value, while the Shannon-Wiener index of phoD communities was lowest. Mantel tests showed an increased Bray-Curtis dissimilarity of phoD communities in the water with rising eutrophication, a trend not observed in sediment. Notably, eutrophication heightened the homogeneity selection governing the assembly of phoD communities in water. The co-occurrence networks showed that the OTUs in the summer exhibited closer interconnections than those in other seasons. Additionally, the topological parameters from networks indicated that eutrophication is poised to instigate changes and modulate the dynamics of the microbial phoD community, resulting in markedly distinct seasonal behaviors. pH was identified as a critical factor directly influencing phoD community diversity via partial least squares path modeling (PLS-PM). This study shed light on our understanding of the seasonal dynamics of phoD communities and their pivotal role in phosphorus cycling in eutrophic lakes.

Deep insights into the assembly mechanisms, co-occurrence patterns, and functional roles of microbial community in wastewater treatment plants.

The understanding of activated sludge microbial status and roles is imperative for improving and enhancing the performance of wastewater treatment plants (WWTPs). In this study, we conducted a deep analysis of activated sludge microbial communities across five compartments (inflow, effluent, and aerobic, anoxic, anaerobic tanks) over temporal scales, employing high-throughput sequencing of 16S rRNA amplicons and metagenome data. Clearly discernible seasonal patterns, exhibiting cyclic variations, were observed in microbial diversity, assembly, co-occurrence network, and metabolic functions. Notably, summer samples exhibited higher α-diversity and were distinctly separated from winter samples. Our analysis revealed that microbial community assembly is influenced by both stochastic processes (66%) and deterministic processes (34%), with winter samples demonstrating more random assembly compared to summer. Co-occurrence patterns were predominantly mutualistic, with over 96% positive correlations, and summer networks were more organized than those in winter. These variations were significantly correlated with temperature, total phosphorus and sludge volume index. However, no significant differences were found among microbial community across five compartments in terms of ß diversity. A core community of keystone taxa was identified, playing key roles in eight nitrogen and eleven phosphorus cycling pathways. Understanding the assembly mechanisms, co-occurrence patterns, and functional roles of microbial communities is essential for the design and optimization of biotechnological treatment processes in WWTPs.

Chromium contamination affects the fungal community and increases the complexity and stability of the network in long-term contaminated soils.

Chromium (Cr) contamination can adversely affect soil ecology, yet our knowledge of how fungi respond to Cr contamination at heavily contaminated field sites remains relatively limited. This study employed high-throughput sequencing technology to analyze fungal community characteristics in soils with varying Cr concentrations. The results showed that Cr contamination significantly influenced soil fungi's relative abundance and structure. Mantel test analysis identified hexavalent chromium (Cr(VI)) as the primary factor affecting the structure of the soil fungal community. In addition, FUNGuild functional prediction analysis exhibited that Cr contamination reduced the relative abundance of Pathotroph and Symbiotroph trophic types. High concentrations of Cr may lead to a drop in the relative abundance of Animal Pathogens. Molecular ecological network analysis showed that Cr contamination increased interactions among soil fungi, thereby enhancing the stability and complexity of the network. Within these networks, specific keystone taxa, such as the genus Phanerochaete, exhibited properties capable of removing or reducing the toxicity of heavy metals. Our studies suggest that Cr contamination can alter indigenous fungal communities in soil systems, potentially impacting soil ecosystem function.

Short-term continuous monocropping reduces peanut yield mainly via altering soil enzyme activity and fungal community.

Continuous monocropping can lead to soil sickness and increase of soil-borne disease, which finally reduces crop yield. Microorganisms benefit plants by increasing nutrient availability, participating in auxin synthesis, and defending against pathogens. However, little is known about the influence of short-term successive peanuts cropping on soil properties, enzyme activities, its yield, plant-associated microbes, and their potential correlations in peanut production. Here, we examined the community structure, composition, network structure and function of microbes in the rhizosphere and bulk soils under different monocropping years. Moreover, we assessed the impact of changes in the soil micro-environment and associated soil microbes on peanut yield. Our results showed that increase of monocropping year significantly decreased most soil properties, enzyme activities and peanut yield (p < 0.05). Principal co-ordinates analysis (PCoA) and analysis of similarities (ANOSIM) indicated that monocropping year significantly influenced the fungal community structure in the rhizosphere and bulk soils (p < 0.01), while had no effect on the bacterial community. With the increase of continuous monocropping year, peanut selectively decreased (e.g., Candidatus_Entotheonella, Bacillus and Bryobacter) or increased (e.g., Nitrospira, Nocardioides, Ensifer, Gaiella, and Novosphingobium) the abundance of some beneficial bacterial genera in the rhizosphere. Continuous monocropping significantly increased the abundance of plant pathogens (e.g., Plectosphaerella, Colletotrichum, Lectera, Gibberella, Metarhizium, and Microdochium) in the rhizosphere and negatively affected the balance of fungal community. Besides, these species were correlated negatively with L-leucine aminopeptidase (LAP) activity. Network co-occurrence analysis showed that continuous monocropping simplified the interaction network of bacteria and fungi. Random forest and partial least squares path modeling (PLS-PM) analysis further showed that fungal community, pathogen abundance, soil pH, and LAP activity negatively affected peanut yield. In conclusion, short-term continuous monocropping decreased LAP activity and increased potential fungal pathogens abundance, leading to reduction of peanut yield.

Response of TCE biodegradation to elevated H2 and O2: Implication for electrokinetic-enhanced bioremediation.

The study investigated the influences of pure H2 and O2 introduction, simulating gases produced from the electrokinetic-enhanced bioremediation (EK-Bio), on TCE degradation, and the dynamic changes of the indigenous microbial communities. The dissolved hydrogen (DH) and oxygen (DO) concentrations ranged from 0.2 to 0.7 mg/L and 2.6 to 6.6 mg/L, respectively. The biological analysis was conducted by 16S rRNA sequencing and functional gene analyses. The results showed that the H2 introduction enhanced TCE degradation, causing a 90.4% TCE removal in the first 4 weeks, and 131.1 µM was reduced eventually. Accordingly, cis-dichloroethylene (cis-DCE) was produced as the only product. The following three ways should be responsible for this promoted TCE degradation. Firstly, the high DH rapidly reduced the oxidation-reduction potential (ORP) value to around -500 mV, beneficial to TCE microbial dechlorination. Secondly, the high DH significantly changed the community and promoted the enrichment of TCE anaerobic dechlorinators, such as Sulfuricurvum, Sulfurospirillum, Shewanella, Geobacter, and Desulfitobacterium, and increased the abundance of dechlorination gene pceA. Thirdly, the high DH promoted preferential TCE dechlorination and subsequent sulfate reduction. However, TCE bio-remediation did not occur in a high DO environment due to the reduced aerobic function or lack of functional bacteria or co-metabolic substrate. The competitive dissolved organic carbon (DOC) consumption and unfriendly microbe-microbe interactions also interpreted the non-degradation of TCE in the high DO environment. These results provided evidence for the mechanism of EK-Bio. Providing anaerobic obligate dechlorinators, and aerobic metabolic bacteria around the electrochemical cathodes and anodes, respectively, or co-metabolic substrates to the anode can be feasible methods to promote remediation of TCE-contaminated shallow aquifer under EK-Bio technology.

Community assembly and microbial interactions in an alkaline vanadium tailing pond.

Intensive development of vanadium-titanium mines leads to an increasing discharge of vanadium (V) into the environment, imposing potential risks to both environmental system and public health. Microorganisms play a key role in the biogeochemical cycling of V, influencing its transformation and distribution. In addition, the characterization of microbial community patterns serves to assess potential threats imposed by elevated V exposure. However, the impact of V on microbial community remains largely unknown in alkaline V tailing areas with a substantial amounts of V accumulation and nutrient-poor conditions. This study aims to explore the characteristics of microbial community in a wet tailing pond nearby a large-scale V mine. The results reveal V contamination in both water (0.60 mg/L) and sediment tailings (340 mg/kg) in the tailing pond. Microbial community diversity shows distinctive pattern between environmental metrices. Genera with the functional potential of metal reduction\resistance, nitrogen metabolism, and carbon fixation have been identified. In this alkaline V tailing pond, V and pH are major drivers to induce community variation, particularly for functional bacteria. Stochastic processes primarily govern the assemblies of microbial community in the water samples, while deterministic process regulate the community assemblies of sediment tailings. Moreover, the co-occurrence network pattern unveils strong selective pattern for sediment tailings communities, where genera form a complex network structure exhibiting strong competition for limited resource. These findings reveal the patterns of microbial adaptions in wet vanadium tailing ponds, providing insightful guidelines to mitigate the negative impact of V tailing and develop sustainable management for mine-waste reservoir.

Distinct structure, assembly, and gene expression of microplankton in two Arctic estuaries with varied terrestrial inputs.

The Laptev Sea is a major Marginal Sea in the Western Arctic Ocean. The Arctic amplification brought by global warming influences the hydrological properties of rivers passing through the permafrost zone, which would alter the biological community structure at continental margin. In this study, the structure, assembly, and gene expression of planktonic microbial communities in two estuaries (Protoka Ularovskaya River Estuary, PURE; Lena River Estuary, LRE) of Laptev Sea were examined to investigate the environmental effects of polar rivers. PURE and LRE exhibited distinct environmental characteristics: low temperature and high salinity for PURE, and high temperature and low salinity for LRE, influenced by runoff size. Salinity more closely influenced microbial communities in LRE, with freshwater species playing a significant role in community composition. The findings revealed differences between two estuaries in community composition and diversity. Prokaryotes and microeukaryotes had shown different assembly patterns in response to habitat changes caused by terrestrial freshwater input. Furthermore, compared with the PURE, the co-occurrence and inter-domain network of the LRE, which was more affected by terrestrial input, was more complex and stable. Functional gene prediction revealed a higher gene expression of methane metabolism in LRE than in PURE, particularly those related to methane oxidation, and this conclusion could help better explore the impact of global warming on the methane cycle in the Arctic Marginal Seas. This study explored the increased freshwater runoffs under the background of global warming dramatically affect Arctic microplankton communities from community structure, assembly and gene expression aspects.

The influence of soil salinization, induced by the backwater effect of the Yellow River, on microbial community dynamics and ecosystem functioning in arid regions.

Irrigation practices and groundwater levels are critical factors contributing to soil salinization in arid and semi-arid regions. However, the impact of soil salinization resulting from Yellow River water irrigation and recharge on microbial communities and their functions in the Huinong District has not been thoroughly documented. In this study, high-throughput sequencing technology was employed to analyze the diversity, composition, and structure of bacterial and fungal communities across a gradient of salinized soils. The results indicated that the alpha diversity of bacterial communities was significantly higher in slightly saline soils compared to highly saline soils. Soil salinization notably influenced the composition of both bacterial and fungal communities. Highly salinized soils were enriched with bacterial taxa such as Halomonas, Salinimicrobium, Pseudomonas, Solibacillus, and Kocuria, as well as fungal taxa including Emericellopsis, Alternaria, and Podospora. In these highly saline soils, bacterial taxa associated with iron respiration, sulfur respiration, and hydrocarbon degradation were more prevalent, whereas fungal taxa linked to functions such as soil animal pathogens, arbuscular mycorrhizal symbiosis, endophytes, dung saprotrophy, leaf saprotrophy, soil saprotrophy, fungal parasitism, and plant pathogenicity were less abundant. Random forest analysis identified nine bacterial and eighteen fungal taxa as potential biomarkers for salinity discrimination in saline soils. Symbiotic network analysis further revealed that soil salinization pressure reduced the overall complexity and stability of bacterial and fungal communities. Additionally, bacterial community assembly showed a tendency shift from stochastic to deterministic processes in response to increasing salinity, while fungal community assembly remained dominated by deterministic processes. provide robust evidence that soil salinity is a major inhibitor of soil biogeochemical processes in the Huinong District and plays a critical role in shaping bacterial and fungal communities, their symbiotic networks, and their assembly processes.

Organic amendments increased Chinese milk vetch symbiotic nitrogen fixation by enriching Mesorhizobium in rhizosphere.

Symbiotic nitrogen fixation of Chinese milk vetch (Astragalus sinicus L.) can fix nitrogen from the atmosphere and serve as an organic nitrogen source in agricultural ecosystems. Exogenous organic material application is a common practice of affecting symbiotic nitrogen fixation; however, the results of the regulation activities remain under discussion. Studies on the impact of organic amendments on symbiotic nitrogen fixation have focused on dissolved organic carbon content changes, whereas the impact on dissolved organic carbon composition and the underlying mechanism remain unclear. In situ pot experiments were carried out using soils from a 40-year-old field experiment platform to investigate symbiotic nitrogen fixation rate trends, dissolved organic carbon concentration and component, and diazotroph community structure in roots and in rhizosphere soils following long-term application of different exogenous organic substrates, i.e., green manure, green manure and pig manure, and green manure and rice straw. Remarkable increases in rate were observed in and when compared with that in green manure treatment, with the greatest enhancement observed in the treatment. Moreover, organic amendments, particularly pig manure application, altered diazotroph community composition in rhizosphere soils, therefore increasing the abundance of the host-specific genus Mesorhizobium. Furthermore, organic amendments influence the diazotroph communities through two primary mechanisms. Firstly, the components of dissolved organic carbon promote an increase in available iron, facilitated by the presence of humus substrates. Secondly, the elevated content of dissolved organic carbon and available iron expands the niche breadth of Mesorhizobium within the rhizosphere. Consequently, these alterations result in a modified diazotroph community within the rhizosphere, which in turn influences Mesorhizobium nodulation in the root and symbiotic nitrogen fixation rate. The results of the present study enhance our understanding of the impact of organic amendments on symbiotic nitrogen fixation and the underlying mechanism, highlighting the key role of dissolved organic carbon composition on diazotroph community composition in the rhizosphere.

Fungal communities are more sensitive to mildew than bacterial communities during tobacco storage processes.

Mildew poses a significant threat to tobacco production; however, there is limited information on the structure of the abundant and rare microbial subcommunities in moldy tobacco leaves. In this study, we employed high-throughput sequencing technology to discern the disparities in the composition, diversity, and co-occurrence patterns of abundant and rare fungal and bacterial subcommunities between moldy and normal tobacco leaves collected from Guizhou, Shanghai, and Jilin provinces, China. Furthermore, we explored the correlation between microorganisms and metabolites by integrating the metabolic profiles of moldy and normal tobacco leaves. The results showed that the fungi are more sensitive to mildew than bacteria, and that the fungal abundant taxa exhibit greater resistance and environmental adaptability than the rare taxa. The loss of rare taxa results in irreversible changes in the diversity, richness, and composition of the fungal community. Moreover, rare fungal taxa and abundant bacterial taxa played crucial roles in maintaining the stability and functionality of the tobacco microecosystem. In moldy tobacco, however, the disappearance of rare taxa as key nodes resulted in reduced connectivity and stability within the fungal network. In addition, metabolomic analysis showed that the contents of indoles, pyridines, polyketones, phenols, and peptides were significantly enriched in the moldy tobacco leaves, while the contents of amino acids, carbohydrates, lipids, and other compounds were significantly reduced in these leaves. Most metabolites showed negative correlations with Dothideomycetes, Alphaproteobacteria, and Gammaproteobacteria, but showed positive correlations with Eurotiales and Bacilli. This study has demonstrated that abundant fungal taxa are the predominant biological agents responsible for tobacco mildew, while bacteria may indirectly contribute to this process through the production and degradation of metabolites. KEY POINTS: • Fungi exhibited greater sensitivity to mildew of tobacco leaf compared to bacteria • Rare fungal taxa underwent significant damage during the mildew process • Mildew may damage the defense system of the tobacco leaf microecosystem.

Fertilization regime changes rhizosphere microbial community assembly and interaction in Phoebe bournei plantations.

Fertilizer input is one of the effective forest management practices, which improves soil nutrients and microbial community compositions and promotes forest productivity. However, few studies have explored the response of rhizosphere soil microbial communities to various fertilization regimes across seasonal dynamics. Here, we collected the rhizosphere soil samples from Phoebe bournei plantations to investigate the response of community assemblages and microbial interactions of the soil microbiome to the short-term application of four typical fertilizer practices (including chemical fertilizer (CF), organic fertilizer (OF), compound microbial fertilizer (CMF), and no fertilizer control (CK)). The amendments of organic fertilizer and compound microbial fertilizer altered the composition of rhizosphere soil bacterial and fungal communities, respectively. The fertilization regime significantly affected bacterial diversity rather than fungal diversity, and rhizosphere fungi responded more sensitively than bacteria to season. Fertilization-induced fungal networks were more complex than bacterial networks. Stochastic processes governed both rhizosphere soil bacterial and fungal communities, and drift and dispersal limitation dominated soil fungal and bacterial communities, respectively. Collectively, these findings demonstrate contrasting responses to community assemblages and interactions of rhizosphere bacteria and fungi to fertilizer practices. The application of organic fertilization strengthens microbial interactions and changes the succession of key taxa in the rhizosphere habitat. KEY POINTS: • Fertilization altered the key taxa and microbial interaction • Organic fertilizer facilitated the turnover of rhizosphere microbial communities • Stochasticity governed soil fungal and bacterial community assembly.

Similarity of Chinese and Pakistani oral microbiome.

Oral microbiota is vital for human health and can be affected by various factors (i.e. diets, ethnicity). However, few studies have compared oral microbiota of individuals from different nationalities in the same environment. Here, we explored the assembly and interaction of oral microbial communities of Chinese and Pakistanis in one university. Firmicutes and Proteobacteria were the predominant microorganisms in the oral cavity of Chinese and Pakistanis. Streptococcus and Neisseria were the dominant genera of China, while Streptococcus and Haemophilus were the dominant genera of Pakistanis. In addition, the oral community membership and structure were not influenced by season, Chinese/Pakistani student and gender, reflecting the stability of the human oral microbiome. The beta diversity of oral microbiomes between Chinese and Pakistanis significantly differed in winter, but not in spring. The alpha diversity of Chinese students and Pakistani students was similar. Moreover, oral microbial community of both Chinese and Pakistani students was mainly driven by stochastic processes. The microbial network of Chinese was more complexity and stability than that of Pakistanis. Our study uncovers the characteristics of human oral microbiota, which is of great significance for oral and human health.

Searching COVID-19 Clinical Research Using Graph Queries: Algorithm Development and Validation.

BACKGROUND: Since the beginning of the COVID-19 pandemic, >1 million studies have been collected within the COVID-19 Open Research Dataset, a corpus of manuscripts created to accelerate research against the disease. Their related abstracts hold a wealth of information that remains largely unexplored and difficult to search due to its unstructured nature. Keyword-based search is the standard approach, which allows users to retrieve the documents of a corpus that contain (all or some of) the words in a target list. This type of search, however, does not provide visual support to the task and is not suited to expressing complex queries or compensating for missing specifications. OBJECTIVE: This study aims to consider small graphs of concepts and exploit them for expressing graph searches over existing COVID-19-related literature, leveraging the increasing use of graphs to represent and query scientific knowledge and providing a user-friendly search and exploration experience. METHODS: We considered the COVID-19 Open Research Dataset corpus and summarized its content by annotating the publications' abstracts using terms selected from the Unified Medical Language System and the Ontology of Coronavirus Infectious Disease. Then, we built a co-occurrence network that includes all relevant concepts mentioned in the corpus, establishing connections when their mutual information is relevant. A sophisticated graph query engine was built to allow the identification of the best matches of graph queries on the network. It also supports partial matches and suggests potential query completions using shortest paths. RESULTS: We built a large co-occurrence network, consisting of 128,249 entities and 47,198,965 relationships; the GRAPH-SEARCH interface allows users to explore the network by formulating or adapting graph queries; it produces a bibliography of publications, which are globally ranked; and each publication is further associated with the specific parts of the query that it explains, thereby allowing the user to understand each aspect of the matching. CONCLUSIONS: Our approach supports the process of query formulation and evidence search upon a large text corpus; it can be reapplied to any scientific domain where documents corpora and curated ontologies are made available.