Microbial Co-occurrence Networks Research Articles

Biocontrol agents modulate phyllosphere microbiota interactions against pathogen Pseudomonas syringae

The pathogen Pseudomonas syringae, responsible for a variety of diseases, poses a considerable threat to global crop yields. Emerging biocontrol strategies employ antagonistic microorganisms, utilizing phyllosphere microecology and systemic resistance to combat this disease. However, the interactions between phyllosphere microbial dynamics and the activation of the plant defense system remain poorly understood. Here we show significant alterations in phyllosphere microbiota structure and plant gene expression following the application of biocontrol agents. We reveal enhanced collaboration and integration of Sphingomonas and Methylobacterium within the microbial co-occurrence network. Notably, Sphingomonas inhibits P. syringae by disrupting pathogen chemotaxis and virulence. Additionally, both Sphingomonas and Methylobacterium activate plant defenses by upregulating pathogenesis-related gene expression through abscisic acid, ethylene, jasmonate acid, and salicylic acid signaling pathways. Our results highlighted that biocontrol agents promote plant health, from reconstructing beneficial microbial consortia to enhancing plant immunity. The findings enrich our comprehension of the synergistic interplays between phyllosphere microbiota and plant immunity, offering potential enhancements in biocontrol efficacy for crop protection.

Electron-transfer-driven spatial optimisation of anaerobic consortia for efficient methanogenesis: Neglected inductive effect of conductive materials

The inductive effect of conductive materials (CMs) on enhancing methanogenesis metabolism has been overlooked. Herein, we highlight role of CMs in inducing the spatial optimisation of methanogenic consortia by altering the Lewis acid–base (AB) interactions within microbial aggregates. In the presence of CMs and after their removal, the methane production and methane proportion in biogas significantly increase, with no significant difference between the two situations. Analyses of interactions between CMs and extracellular polymer substances (EPSs) with and without D2O reveal that CMs promote release and transfer potential of electron in EPSs, which induce and enhance the role of water molecules being primarily as proton acceptors in the hydrogen bonding between EPSs and water, thereby changing the electron-donor- and electron-acceptor-based AB interactions. Investigations of succession dynamics of microbial communities, co-occurrence networks, and metagenomics further indicate that electron transfer drives the microbial spatial optimisation for efficient methanogenesis through intensive interspecies interactions.

Integrative analyses identify opportunistic pathogens of patients with lower respiratory tract infections based on metagenomic next-generation sequencing

Lower respiratory tract infections (LRTIs) represent some of the most globally prevalent and detrimental diseases. Metagenomic next-generation sequencing (mNGS) technology has effectively addressed the requirement for the diagnosis of clinical infectious diseases. This study aimed at identifying and classifying opportunistic pathogens from the respiratory tract-colonizing microflora in LRTI patients using data acquired from mNGS analyses. A retrospective study was performed employing the mNGS data pertaining to the respiratory samples derived from 394 LRTIs patients. Linear discriminant analysis effect size (LEfSe) analysis was conducted to discern the discriminant bacteria. Receiver operating characteristic curves (ROC) were established to demonstrate discriminant bacterial behavior to distinguish colonization from infection. A total of 443 discriminant bacteria were identified and segregated into three cohorts contingent upon their correlation profiles, detection frequency, and relative abundance in order to distinguish pathogens from colonizing microflora. Among them, 119 emerging opportunistic pathogens (cohort 2) occupied an average area under the curve (AUC) of 0.976 for exhibiting the most prominent predictability in distinguishing colonization from infection, 39 were colonizing bacteria (cohort 1, 0.961), and 285 were rare opportunistic pathogens (cohort 3, 0.887). The LTRIs patients appeared modular in the form of cohorts depicting complex microbial co-occurrence networks, reduced diversity, and a high degree of antagonistic interactions in the respiratory tract microbiome. The study findings indicate that therapeutic interventions should target interaction networks rather than individual microbes, providing an innovative perspective for comprehending and combating respiratory infections. Conclusively, this study reports a profile of LRTIs-associated bacterial colonization and opportunistic pathogens in a relatively large-scale cohort, which might serve as a reference panel for the interpretation of mNGS results in clinical practice.

Enhancing intercropping sustainability: Manipulating soybean rhizosphere microbiome through cropping patterns

Understanding the responses of soybean rhizosphere and functional microbiomes in intercropping scenarios holds promise for optimizing nitrogen utilization in legume-based intercropping systems. This study investigated three cropping layouts under film mulching: sole soybean (S), soybean–maize intercropping in one row (IS), and soybean–maize intercropping in two rows (IIS), each subjected to two nitrogen levels: 110 kg N ha−1 (N110) and 180 kg N ha−1 (N180). Our findings reveal that cropping patterns alter bacterial and nifh communities, with approximately 5 % of soybean rhizosphere bacterial amplicon sequence variants (ASVs) and 42 % of rhizosphere nifh ASVs exhibiting altered abundances (termed sensitive ASVs). Root traits and soil properties shape these communities, with root traits exerting greater influence. Sensitive ASVs drive microbial co-occurrence networks and deterministic processes, predicting 85 % of yield variance and 78 % of partial factor productivity of nitrogen, respectively. These alterations impact bacterial and nifh diversity, complexity, stability, and deterministic processes in legume-based intercropping systems, enhancing performance in terms of yield, nitrogen utilization efficiency, land equivalent ratio, root nodule count, and nodule dry weight under IIS patterns with N110 compared to other treatments. Our findings underscore the importance of field management practices in shaping rhizosphere-sensitive ASVs, thereby altering microbial functions and ultimately impacting the productivity of legume-based intercropping systems. This mechanistic understanding of soybean rhizosphere microbial responses to intercropping patterns offers insights for sustainable intercropping enhancements through microbial manipulation.

Metals and polycyclic aromatic hydrocarbons pollutants in industrial parks under valley landforms in Tibetan Plateau: Spatial pattern, ecological risk and interaction with soil microorganisms

The spatial patterns of pollutants produced by industrial parks are affected by many factors, but the interactions among polycyclic aromatic hydrocarbons (PAHs), metals, and soil microorganisms in the valley landforms of the Tibetan Plateau are poorly understood. Thus, this study systematically investigated the distribution and pollution of metals and PAHs in soil around an industrial park in the typical valley landform of the Tibetan Plateau and analyzed and clarified the interaction among metals, PAHs, and microorganisms. The results were as follows: metal and PAH concentrations were affected by wind direction, especially WN-ES and S-N winds; Cd (2.86–54.64 mg·kg−1) had the highest soil concentrations of the metals screened, followed by variable concentrations of Cu, Pb, and Zn; the pollution levels of metals and PAHs in the S-N wind direction were lower than those in the WN-ES wind direction; the Cd content of Avena sativa in the agricultural soil around the factory exceeded its enrichment ability and food safety standards; the closer to the center of the park, the higher the ecological risk of PAHs; and the TEQ and MEQ values of the PAHs were consistent with their concentration distributions. The results of the soil microbial diversity and co-occurrence network in the dominant wind direction showed that metal and PAH pollution weakened the robustness of soil microbial communities. Additionally, the diversity and robustness of soil microbial communities at the S wind site were higher than those at the ES wind site, which might be attributed to the lower metal content of the former than the latter, which plays a negative role in the biodegradation of PAHs. The results of this study provide insights into the site selection, pollutant supervision, and environmental remediation of industrial parks in typical landforms.

Pre-soil fumigation with ammonium bicarbonate and lime modulates the rhizosphere microbiome to mitigate clubroot disease in Chinese cabbage.

Plasmodiophora brassicae is an ever-increasing threat to cruciferous crop production worldwide. This study investigated the impact of pre-soil fumigation with ammonium bicarbonate (N) and lime (NB) to manage clubroot disease in Chinese cabbage through 16S rRNA gene amplification sequencing. We found that soil fumigation with N and NB suppressed disease incidence by reducing the soil acidity and population of P. brassicae in the rhizosphere. Minimum disease incidence and maximum relative control effect of about 74.68 and 66.28% were achieved in greenhouse and field experiments, respectively, under the combined application of ammonium bicarbonate and lime (LNB) as compared with N, NB, and control (GZ). Microbial diversity analysis through Miseq sequencing proved that pre-soil fumigation with N, NB, and LNB clearly manipulated rhizosphere microbial community composition and changed the diversity and structure of rhizosphere microbes compared with GZ. Bacterial phyla such as Proteobacteria, Bacteriodetes, and Acidobacteria and fungal phyla including Olpidiomycota and Ascomycota were most dominant in the rhizosphere of Chinese cabbage plants. Soil fumigation with N and NB significantly reduced the abundance of clubroot pathogen at genus (Plasmodiophora) level compared with GZ, while decreased further under combined application LNB. Microbial co-occurrence network analysis showed a highly connected and complex network and less competition for resources among microbes under combined application LNB. We conclude that for environmentally friendly and sustainable agriculture, soil fumigation with combined ammonium bicarbonate and lime plays a crucial role in mitigating Chinese cabbage clubroot disease by alleviating soil pH, reducing pathogen population, and manipulating the rhizosphere microbiome.

Contrasting benthic bacterial and fungal communities in two temperate coastal areas affected by different levels of anthropogenic pressure

Benthic microbial communities play a crucial role in maintaining the stability and function of estuarine ecosystems. However, their organization and response to multiple stresses in severely disturbed coastal areas remains to be elucidated. In this study, we revealed the presence of contrasting benthic bacterial and fungal communities in the Liaohe (LH) and Yalujiang (YLJ) estuaries, which are located at similar latitudes and are characterized by similar climates but are subjected to different levels of anthropogenic pressure. The results showed that Firmicutes and Chloroflexi were more abundant in LH, which reflected the influence of anthropogenic pressure in this area. Functional analyses indicated that the functional genes involved in the generation of precursor metabolites and energy pathways were more enriched in the LH community, while genes regulating degradation/utilization/assimilation processes were more enriched in the YLJ community. Distance-dependent similarity analysis showed that the bacterial community in LH was more affected by environmental changes, while that in YLJ was more influenced by geographic dispersion. In contrast, no significant distance-dependent similarity was found for the fungal communities in the two areas. In addition, the network analysis showed that the bacterial-fungal network in YLJ was more complex and stable than that in the LH. Our results highlight the important roles of environmental heterogeneity in controlling microbial community composition, biogeographic patterns, and co-occurrence networks. These findings fill knowledge gaps in the understanding of the different response patterns of benthic communities under varying anthropogenic pressures.

Effects of Conventional Non-Biodegradable Film-Derived Microplastics and New Biodegradable Film-Derived Microplastics on Soil Properties and Microorganisms after Entering Sub-Surface Soil

Plastic film mulching, widely used in agriculture, leads to microplastic (MP) pollution in soils. While biodegradable polybutylene adipate terephthalate (PBAT) films may offer a solution, their impacts on subsurface soils and microorganisms remain unclear. To investigate the effects of conventional non-biodegradable polyethylene (PE) and biodegradable PBAT MPs on the properties of sub-surface soils and microbial communities, MPs were added at varying doses in a field experiment and incubated for 160 days. Physicochemical characteristics, nutrient dynamics, and microbial composition, diversity, and networks of soils were analyzed using standard techniques and 16S rRNA/ITS gene sequencing. Correlations between soil properties and microbes were assessed. Both MP types significantly altered soil characteristics, with PBAT-MP elevating pH and the levels of available phosphorus and potassium more than PE-MP. Microbial composition shifts occurred, with low-addition PBAT-MP promoting plastic-degrading genera. The assessment of α/β-diversity indicated that PBAT-MP predominantly influenced fungi while PE-MP impacted bacteria. An examination of microbial co-occurrence networks highlighted that PE-MP primarily disrupted fungal interactions, whereas PBAT-MP streamlined network complexity. Correlation analyses revealed that PBAT-MP promoted fungal diversity/network resilience correlating to nutrients. PE-MP and PBAT-MP significantly altered native soil/microbe relationships. PBAT-MP may exert greater, yet unknown, impacts over time through its biodegradation into newer and smaller fragments. Future research needs to integrate multi-omics and stable isotope science to elucidate the deep mechanistic impacts of degraded film-derived MPs on microbial ecological functions and biogeochemical cycles. Attention should also be paid to the long-term accumulation/transport of MPs in agricultural soils. Overall, this work deepens the impact and understanding of MPs from plastic film on sub-surface soil ecology. Furthermore, it provides a theoretical foundation for managing ‘white pollution’ in the film-covered farmlands of arid and semi-arid regions in China.

Effect of stress urinary incontinence on vaginal microbial communities

BackgroundPostpartum women often experience stress urinary incontinence (SUI) and vaginal microbial dysbiosis, which seriously affect women’s physical and mental health. Understanding the relationship between SUI and vaginal microbiota composition may help to prevent vaginal diseases, but research on the potential association between these conditions is limited.ResultsThis study employed 16S rRNA gene sequencing to explore the association between SUI and vaginal dysbiosis. In terms of the vaginal microbiota, both species richness and evenness were significantly higher in the SUI group. Additionally, the results of NMDS and species composition indicated that there were differences in the composition of the vaginal microbiota between the two groups. Specifically, compared to postpartum women without SUI (Non-SUI), the relative abundance of bacteria associated with bacterial dysbiosis, such as Streptococcus, Prevotella, Dialister, and Veillonella, showed an increase, while the relative abundance of Lactobacillus decreased in SUI patients. Furthermore, the vaginal microbial co-occurrence network of SUI patients displayed higher connectivity, complexity, and clustering.ConclusionThe study highlights the role of Lactobacillus in maintaining vaginal microbial homeostasis. It found a correlation between SUI and vaginal microbiota, indicating an increased risk of vaginal dysbiosis. The findings could enhance our understanding of the relationship between SUI and vaginal dysbiosis in postpartum women, providing valuable insights for preventing bacterial vaginal diseases and improving women’s health.

Evaluation of lipopeptides biosurfactant from Raoultella planticola for bioremediation in n-hexadecane-contaminated soil

Biosurfactants combined with bioaugmentation for the remediation of petroleum hydrocarbon-contaminated soils proved to be one of the most effective ways. However, research on lipopeptides combined with bioaugmentation is rare, and the biological mechanisms are undefined. Therefore, the effect of Raoultella planticola and the lipopeptides it produces to restore contaminated soils was investigated using n-hexadecane as a model of petroleum hydrocarbons. After 60 d, n-hexadecane removal rate increased from 31.3% in contaminated soil to 39.9% with R. planticola alone and 59.0% with R. planticola together with 1.0 g intracellular lipopeptide (INLS) and 7.5 g sodium gluconate (SG)/kg dry soil. Meanwhile, the nitrogen and phosphorus components of the soil increased by 13.9% and 8% in the experimental group, respectively. Besides, DHA activity was 6.7 times that of the control group at 28 d, indicating a considerable increase in DHA activity. Microbial community analysis revealed a considerable increase in functional genera of Sphingomonas, Nocardia, Pseudoalteromonas, Povalibacter, Apiotrichum, Pseudallecheria, and Ascodesmis. The amount of fungus in the experimental group was more than 30 times that of the control group after 60 d. Microbial co-occurrence networks showed improved interactions of Firmicutes and Ascomycota, encouraging synergistic cooperation among microbes and thereby accelerating n-hexadecane breakdown. At once, the metabolic pathways ko00071 and ko00980 for n-hexadecane degradation were greatly elevated, indicating that functional genes such as alkane 1-monooxygenase and NADPH-cytochrome P450 reductase were activated. These results implied that combining hydrocarbon-degrading microbial with INLS was a promising bioremediation technique to remove soil petroleum hydrocarbons.

Microbial communities outperform extracellular polymeric substances in the reduction of hexavalent chromium by anaerobic granular sludge

The reduction of hexavalent chromium [Cr(VI)] by microbiota agents is a potential method for ecological remediation in heavily contaminated soil. This study investigated the contribution of microbial community and extracellular polymeric substances (EPS) to reduce Cr(VI) using lab-cultured anaerobic granular sludge (AGS). The AGS demonstrated an impressive reduction efficiency of 99.3% for Cr(VI) in soil, operating within an initial Cr(VI) concentration range of 500–3000 mg/kg. The distribution of typical electron acceptors, e.g., SO42-, NO3-, and Fe3+, had a negligible influence on microbial Cr(VI) reduction. The contribution of EPS on Cr(VI) reduction accounted for only 2.1% of the total Cr(VI) reduction, implying that Cr(VI) reduction driven by AGS was primarily caused by the direct effect of microbiota. High-throughput sequencing analysis confirmed that an increasing trend in the relative abundance of Cr reduction bacteria (Sphingopyxis: 0.40–5.54%, Thermonas: 0.41–5.70%, Edaphobaculum: 0.35–6.64%, etc.), and the stability (0.716–4.114) of microbial co-occurrence networks was significantly promoted by the end of the experiment. Materials characterization indicated that successful reduction of Cr(VI) to trivalent chromium [Cr(III)] and formed in Cr(OH)3, and functional groups, O-H, N-H, -CH, and -CH2, of AGS likely played a vital role in Cr(VI) reduction. Overall, these findings offer insights into the remediation technique of microbial Cr(VI) reduction in highly-contaminated soil based on the interaction network stability of the microbial community in AGS.

Drought and vegetation restoration lead to shifts in soil microbial diversity and co-occurrence networks in California coastal prairie

Abstract Background and aims Both drought and vegetation restoration can have dramatic effects on plant community composition, but how they influence soil microbial community diversity, structure, and co-occurrence networks remain less well known. Methods To better understand the regulatory mechanisms of drought and vegetation restoration on soil microorganisms, we planted 12 native species in precipitation manipulation experimental plots in an invaded coastal grassland in California, USA. We measured soil bacterial and fungal community composition by amplicon sequencing, and quantified plant species richness and coverage in the third experimental year. Results Our results showed that drought significantly altered soil bacterial diversity and composition; however, neither drought nor vegetation restoration had significant effects on fungal diversity and composition. The control plots had the most cooperative interactions (greatest number of correlations) among bacterial and/or fungal species, while drought plots yielded the most complex co-occurrence network with the highest modularity and clustering coefficient. Structural equation modeling revealed that plant species richness, net gains, and soil moisture played dominant roles in shaping bacterial community structure. Drought and bacterial community structure directly affected fungal community structure. Plant dominant species cover, common species cover, and bacterial diversity were the key drivers in regulating the microbial co-occurrence network complex. Conclusion We conclude that soil bacterial and fungal communities differ in their responses to abiotic and biotic environmental changes, which may weaken the interspecies interactions among soil microorganisms.

Mechanisms of cadmium release from manganese-rich sediments driven by exogenous DOM and the role of microorganisms

Dissolved organic matter (DOM) is a crucial component of natural sediments that alters Cd sequestration. Nevertheless, how different types of DOM fuel Cd mobilization in Mn-rich sediments has not been elucidated. In the present study, four typical DOM, fluvic acid (FA), bovine serum albumin (BSA), sodium alginate (SA), and sodium dodecyl benzene sulfonate (SDBS), were used to amend Cd-contaminated sediment to study their effects on Cd/Mn biotransformation and microbial community response. The results demonstrated that different DOM drive microbial community shifts and enhance microbially mediated Mn oxide (MnO) reduction and Cd release. The amendment of terrestrial- and anthropogenic-derived DOM (FA and SDBS) mainly contributed to enriching Mn-reducing bacteria phylum Proteobacteria, and its abundance increased by 38.16–74.47 % and 56.41–73.98 %, respectively. Meanwhile, microbial-derived DOM (BSA and SA) mainly stimulated the abundances of metal(loid)-resistant bacteria phylum Firmicutes. Accompanied by microbial community structure, diversity, and co-occurrence network shifts, the DOM concentration and oxidation-reduction potential changed, resulting in enhanced Cd mobilization. Importantly, FA stimulated Cd release most remarkably, probably because of the decreased cooperative interactions between bacterial populations, stronger reduction of MnOs, and higher aromaticity and hydrophobicity of the sediment DOM after amendment. This study linked DOM types to functional microbial communities, and explored the potential roles of different DOM types in Cd biotransformation in lake sediments.

Using kin discrimination to construct synthetic microbial communities of Bacillus subtilis strains impacts the growth of black soldier fly larvae.

Using synthetic microbial communities to promote host growth is an effective approach. However, the construction of such communities lacks theoretical guidance. Kin discrimination is an effective means by which strains can recognize themselves from non-self, and construct competitive microbial communities to produce more secondary metabolites. However, the construction of cooperative communities benefits from the widespread use of beneficial microorganisms. We used kin discrimination to construct synthetic communities (SCs) comprising 13 Bacillus subtilis strains from the surface and gut of black soldier fly (BSF) larvae. We assessed larval growth promotion in a pigeon manure system and found that the synthetic community comprising 4 strains (SC 4) had the most profound effect. Genomic analyses of these 4 strains revealed that their complementary functional genes underpinned the robust functionality of the cooperative synthetic community, highlighting the importance of strain diversity. After analyzing the bacterial composition of BSF larvae and the pigeon manure substrate, we observed that SC 4 altered the bacterial abundance in both the larval gut and pigeon manure. This also influenced microbial metabolic functions and co-occurrence network complexity. Kin discrimination facilitates the rapid construction of synthetic communities. The positive effects of SC 4 on larval weight gain resulted from the functional redundancy and complementarity among the strains. Furthermore, SC 4 may enhance larval growth by inducing shifts in the bacterial composition of the larval gut and pigeon manure. This elucidated how the SC promoted larval growth by regulating bacterial composition and provided theoretical guidance for the construction of SCs.

Characteristics of the oral and gastric microbiome in patients with early-stage intramucosal esophageal squamous cell carcinoma

BackgroundOral microbiome dysbacteriosis has been reported to be associated with the pathogenesis of advanced esophageal cancer. However, few studies investigated the potential role of oral and gastric microbiota in early-stage intramucosal esophageal squamous carcinoma (EIESC).MethodA total of 104 samples were collected from 31 patients with EIESC and 21 healthy controls. The compositions of oral and gastric microbiota were analyzed using 16 S rRNA V3-V4 amplicon sequencing. Linear discriminant analysis effect size (LEfSe) analysis was performed to assess taxonomic differences between groups. The correlation between oral microbiota and clinicopathological factors was evaluated using Spearman correlation analysis. Additionally, co-occurrence networks were established and random forest models were utilized to identify significant microbial biomarkers for distinguishing between the EIESC and control groups.ResultsA total of 292 oral genera and 223 species were identified in both EIESC and healthy controls. Six oral genera were remarkably enriched in EIESC groups, including the genera Porphyromonas, Shigella, Subdoligranulum, Leptotrichia, Paludibacter, and Odoribacter. LEfSe analysis identified genera Porphyromonas and Leptotrichia with LDA scores > 3. In the random forest model, Porphyromonas endodontalis ranked the top microbial biomarker to differentiate EIESC from controls. The elimination rate of Porphyromonas endodontalis from the oral cavity to the stomach was also dramatically decreased in the EIESC group than controls. In the microbial co-occurrence network, Porphyromonas endodontalis was positively correlated with Prevotella tannerae and Prevotella intermedia and was negatively correlated with Veillonella dispar.ConclusionOur study potentially indicates that the dysbacteriosis of both the oral and gastric microbiome was associated with EIESC. Larger scale studies and experimental animal models are urgently needed to confirm the possible role of microbial dysbacteriosis in the pathogenesis of EIESC. (Chinese Clinical Trial Registry Center, ChiCTR2200063464, Registered 07 September 2022, https://www.chictr.org.cn/showproj.html?proj=178563)

Linking ecosystem multifunctionality to microbial community features in rivers along a latitudinal gradient.

Microorganisms regulate numerous ecosystem functions and show considerable differences along a latitudinal gradient. Although studies have revealed the latitudinal patterns of microbial community structure and single ecosystem function, the latitudinal patterns of ecosystem multifunctionality (EMF) and how microbial communities affect EMF along a latitudinal gradient remain unclear. Here, we collected channel sediments, riparian rhizosphere soils, and riparian bulk soils from 30 rivers across China and calculated EMF using 18 variables related to nitrogen cycling, nutrient pool, plant productivity, and water quality. We also determined microbial diversity (taxonomic and functional) and microbial network complexity using metagenomic sequencing. The results showed that EMF significantly decreased with increasing latitude in riparian rhizosphere and bulk soils but not in channel sediments. Microbial taxonomic and functional richness (observed species) in channel sediments were significantly higher in the low-latitude group than in the high-latitude group. However, microbial co-occurrence networks were more complex in the high-latitude group compared with the low-latitude group. Abiotic factors, primarily geographic and climatic factors, contributed more to EMF than microbial diversity and network complexity parameters in which only betweenness centralization had a significant relationship with EMF. Together, this study provides insight into the latitudinal pattern of EMF in rivers and highlights the importance of large-scale factors in explaining such latitudinal patterns.IMPORTANCEEcosystem multifunctionality (EMF) is the capacity of an ecosystem to provide multiple functions simultaneously. Microorganisms, as dominant drivers of belowground processes, have a profound effect on ecosystem functions. Although studies have revealed the latitudinal patterns of microbial community structure and single ecosystem function, the latitudinal patterns of EMF and how microbial communities affect EMF along a latitudinal gradient remain unclear. We collected channel sediments, riparian rhizosphere soils, and riparian bulk soils from 30 rivers along a latitudinal gradient across China and calculated EMF using 18 variables related to nitrogen cycling, nutrient pool, plant productivity, and water quality. This study fills a critical knowledge gap regarding the latitudinal patterns and drivers of EMF in river ecosystems and gives new insights into how microbial diversity and network complexity affect EMF from a metagenomic perspective.

Enhancing soil health and nutrient cycling through soil amendments: Improving the synergy of bacteria and fungi

The synergy between bacteria and fungi is a key determinant of soil health and have a positive effect on plant development under drought conditions, with the potentially enhancing the sustainability of amending soil with natural materials. However, identifying how soil amendments influence plant growth is often difficult due to the complexity of microorganisms and their links with different soil amendment types and environmental factors. To address this, we conducted a field experiment to examine the impact of soil amendments (biochar, Bacillus mucilaginosus, Bacillus subtilis and super absorbent polymer) on plant growth. We also assessed variations in microbial community, links between fungi and bacteria, and soil available nutrients, while exploring how the synergistic effects between fungus and bacteria influenced the response of soil amendments to plant growth. This study revealed that soil amendments reduced soil bacterial diversity but increased the proportion of the family Enterobacteriaceae, Nitrosomonadaceae, and also increased soil fungal diversity and the proportion of the sum of the family Lasiosphaeriaceae, Chaetomiaceae, Pleosporaceae. Changes in soil microbial communities lead to increase the complexity of microbial co-occurrence networks. Furthermore, this heightened network complexity enhanced the synergy of soil bacteria and fungi, supporting bacterial functions related to soil nutrient cycling, such as metabolic functions and genetic, environmental, and cellular processes. Hence, the BC and BS had 3.0-fold and 0.5-fold greater root length densities than CK and apple tree shoot growth were increased by 62.14 %,50.53 % relative to CK, respectively. In sum, our results suggest that the synergistic effect of bacteria and fungi impacted apple tree growth indirectly by modulating soil nutrient cycling. These findings offer a new strategy for enhancing the quality of arable land in arid and semi-arid regions.

Opportunistic pathogens increased and probiotics or short-chain fatty acid-producing bacteria decreased in the intestinal microbiota of pneumonia inpatients during SARS-CoV-2 Omicron variant epidemic.

The global pandemic of COVID-19 has been over four years, and the role of intestinal microbiota in the occurrence and development of COVID-19 needs to be further clarified. During the outbreak of SARS-CoV-2 Omicron variant in China, we analyzed the intestinal microbiome in fecal samples from inpatients with pneumonia and normal individuals in January 2023. The microbiota composition, alpha diversity, beta diversity, differential microbial community, co-occurrence networks, and functional abundance were analyzed. The results showed significant differences in microbiota composition between the two groups. In pneumonia group, the abundance of Bifidobacterium, Blautia, Clostridium, and Coprococcus decreased, while the abundance of Enterococcus, Lactobacillus, and Megamonas increased. Through LEfSe analysis, 37 marker microbiota were identified in pneumonia group. Co-occurrence network analysis found that Lachnospiraceae was critical for the interaction of intestinal microbiota, and the anti-inflammatory bacteria Blautia was negatively correlated with the pro-inflammatory bacteria Ruminococcus. Functional prediction found the up-regulation of steroid biosynthesis, geraniol degradation, and mRNA surveillance pathway in pneumonia group. In conclusion, opportunistic pathogens increased and probiotics, or short-chain fatty acid-producing bacteria, decreased in the intestinal microbiota of pneumonia inpatients during the Omicron epidemic. Blautia could be used as a probiotic in the treatment of pneumonia patients in the future.

Co-Ensiling Whole-Plant Cassava with Corn Stalk for Excellent Silage Production: Fermentation Characteristics, Bacterial Community, Function Profile, and Microbial Ecological Network Features

The objective of this study was to explore excellent silage production through co-ensiling whole-plant cassava and corn stalk, and different ratios of whole-plant cassava (0%, 10%, 20%, 30%, 40%, and 50%, fresh-matter basis) co-ensiled with corn stalk were analyzed based on the silage bacterial community, function profile, and microbial ecological network features. The results demonstrated that co-ensiling 30% whole-plant cassava with 70% corn stalk could be considered an efficient mode of production. The mixed silage showed great quality, as reflected by the reduced pH value and concentrations of acetic acid, butyric acid, and ammonia nitrogen and the enhanced lactic acid concentration, V-score, and nutritional value compared with corn stalk ensiled alone. Meanwhile, co-ensiling restricted the undesirable bacterial Acetobacter fabarum of corn stalk and Pseudomonas aeruginosa of whole-plant cassava and raised the abundance of lactic acid bacteria (LAB) such as Levilactobacillus brevis, Lactiplantibacillus plantarum, Lactobacillus harbinensis, etc. Besides that, the predicted functions of the bacterial community showed large differences in mixed silage compared with whole-plant cassava or corn stalk ensiled alone. Moreover, the analysis of co-occurrence networks showed that mixed silage affected microbial network features, module numbers, and bacterial relative abundances and weakened the complexity and stability of the networks compared with whole-plant cassava single silage. Furthermore, silage microbial community composition had a huge impact on the network properties, and undesirable Pseudomonas aeruginosa played a crucial role in the complexity and stability. Overall, this study revealed the characteristics of whole-plant cassava with corn stalk mixed-silage microbial communities and co-occurrence network modules, complexity, and stability and partly clarified the microbial mechanism of co-ensiling for producing high-quality silage. The findings of this study have important implications for deeply understanding the ensiling process and precisely regulating silage fermentation quality.

Unveiling the driving role of pH on community stability and function during lignocellulose degradation in paddy soil.

Crop straw, a major by-product of agricultural production, is pivotal in maintaining soil health and preserving the ecological environment. While straw incorporation is widely recognized as a sustainable practice, the incomplete decomposition of crop residues poses challenges to plant growth, increasing the risk of pests and diseases. This necessitates a comprehensive investigation. The current study employs a 28-day pot experiment to simulate the degradation of rice straw in paddy soils. The impacts of bioaugmentation and biostimulation on lignocellulose degradation are systematically evaluated. Results indicate a high lignocellulose degradation ability in paddy soil, with over 80% straw weight loss within 28 days. Bioaugmentation with a lignocellulolytic microbial consortium enhances straw degradation during the initial stage (0-14 days). In contrast, biostimulation with readily available nutrients leads to soil acidification, hindering straw degradation and reducing microbial diversity. Furthermore, pH emerges as a critical factor influencing microbial community stability and function during lignocellulose degradation. Microbial co-occurrence network analysis reveals that microorganisms occupy ecological niches associated with different cellulose components. Notably, Module M2, comprising Proteobacteria, Firmicutes, Gemmatimonadota, Actinobacteriota, Bacteroidota, Myxococcota, Halobacterota, and Acidobacteriota, positively correlates with pH and weight loss. This study significantly advances our understanding of microbial mechanisms in soil decomposition, emphasizing the pivotal role of pH in community stability and function in paddy soil. These findings can inform future strategies for managing rice straw while safeguarding soil ecosystem health.