Microbial Co-occurrence Research Articles

Quantitative microbiome profiling reveals the developmental trajectory of the chicken gut microbiota and its connection to host metabolism.

Revealing the assembly and succession of the chicken gut microbiota is critical for a better understanding of its role in chicken physiology and metabolism. However, few studies have examined dynamic changes of absolute chicken gut microbes using the quantitative microbiome profiling (QMP) method. Here, we revealed the developmental trajectory of the broiler chicken gut bacteriome and mycobiome by combining high-throughput sequencing with a microbial load quantification assay. We showed that chicken gut microbiota abundance and diversity reached a plateau at 7 days posthatch (DPH), forming segment-specific community types after 1 DPH. The bacteriome was more impacted by deterministic processes, and the mycobiome was more affected by stochastic processes. We also observed stage-specific microbes in different gut segments, and three microbial occurrence patterns including "colonization," "disappearance," and "core" were defined. The microbial co-occurrence networks were very different among gut segments, with more positive associations than negative associations. Furthermore, we provided links between the absolute changes in chicken gut microbiota and their serum metabolite variations. Time-course untargeted metabolomics revealed six metabolite clusters with different changing patterns of abundance. The foregut microbiota had more connections with chicken serum metabolites, and the gut microbes were closely related to chicken lipid and amino acid metabolism. The present study provided a full landscape of chicken gut microbiota development in a quantitative manner, and the associations between gut microbes and chicken serum metabolites further highlight the impact of gut microbiota in chicken growth and development.

Long-term organic fertilizer and biofertilizer application strengthens the associations between soil quality index, network complexity, and walnut yield

Although various combinations of organic-inorganic fertilizers can enhance plant yields, the effects of different fertilization regimes on the associations between rhizosphere soil microorganisms and plant productivity are poorly understood. In this study, we investigated the rhizosphere soil microbial composition and structure and the relationships among rhizospheric microorganisms, soil properties, and yield in a walnut (Juglans regia L.) orchard after 7 years of applying different fertilization regimes. The combinations of organic and inorganic fertilizers were found to enhance walnut yield, soil quality index (SQI), and soil biodiversity (bacterial and fungal) (P < 0.05). The soil microbial community composition and co-occurrence networks of rhizosphere soil (RS) and bulk soil (BS) showed different responses to fertilization. Bacillus and Pseudomonas were mainly enriched in RS, whereas Fusarium was significantly more abundant in BS (P < 0.05) under a combined chemical fertilizer, organic fertilizer, and biofertilizer treatment (F + O + BO). Network analysis revealed that organic fertilizer and biofertilizer reduced the competition and network complexity among rhizosphere microbial communities (edges: RS = 388, BS = 967; modularity: RS = 0.790, BS = 0.834). Furthermore, SQI, microbial diversity, and network complexity were significantly correlated with walnut yield (P < 0.01), among which SQI explained the highest proportion of the variation in yield (SOI: RS = 78.02%; BS = 81.18%). In addition, both yields and soil microbial community composition were significantly affected by pH, SOM, TN, and SMBN. Collectively, these findings have important implications for our understanding of the relationship between woody plants and rhizospheric microorganisms.

Environmental changes drive soil microbial community assembly across arid alpine grasslands on the Qinghai-Tibetan Plateau, China

Soil microbes play a key role in regulating ecosystem functions in arid alpine grasslands, which are extremely sensitive to environmental changes. However, the exact mechanism by which multiple environmental factors interact to shape local soil microbial community assembly is unclear. Therefore, exploring how changing environmental factors affect microbial community assembly responds to will help us predict microbial-mediated ecosystem processes under climate change. Here, we conducted large-scale field sampling from 30 alpine grassland sites (e.g., alpine meadow (AM), alpine steppe (AS) and alpine desert steppe (ADS)) across arid ecosystems on the Qinghai-Tibetan Plateau (QTP), China. Soil bacterial and fungal community assembly and their relationships with spatial, climatic, and vegetation-soil factors were studied with the Molecular Ecological Network Analysis Pipeline (MENAP), analysis of variance (ANOVA), canonical correspondence analysis (CCA) and structural equation models (SEMs). The results showed that the soil microbial diversity and co-occurrence network complexity increased significantly from ADS to AS and AM, and bacteria were more susceptible to environmental factors than fungi. The relative abundances of the dominant bacterial phyla, including Acidobacteria, Proteobacteria, Actinobacteria and Gemmatimonadetes, showed a statistically significant increase, while the relative abundance of the fungal phyla Basidiomycota and Glomeromycota showed significant differences across arid alpine grasslands. Variation partitioning analysis (VPA) revealed that vegetation-soil factors contributed the most to explaining the bacterial community composition, whereas spatial factors contributed the most to explaining the variation in the fungal community composition. The results obtained from the SEMs suggested that latitude and soil pH had the greatest impact on the diversity of bacteria and fungi, respectively. Taken together, the results of this study provide a comprehensive perspective on how the soil microbial communities respond to changes in environmental factors across arid alpine grasslands on the QTP, China.

Microbial community and soil enzyme activities driving microbial metabolic efficiency patterns in riparian soils of the Three Gorges Reservoir.

Riparian zones represent important transitional areas between aquatic and terrestrial ecosystems. Microbial metabolic efficiency and soil enzyme activities are important indicators of carbon cycling in the riparian zones. However, how soil properties and microbial communities regulate the microbial metabolic efficiency in these critical zones remains unclear. Thus, microbial taxa, enzyme activities, and metabolic efficiency were conducted in the riparian zones of the Three Gorges Reservoir (TGR). Microbial carbon use efficiency and microbial biomass carbon had a significant increasing trend along the TGR (from upstream to downstream); indicating higher carbon stock in the downstream, microbial metabolic quotient (qCO2) showed the opposite trend. Microbial community and co-occurrence network analysis revealed that although bacterial and fungal communities showed significant differences in composition, this phenomenon was not found in the number of major modules. Soil enzyme activities were significant predictors of microbial metabolic efficiency along the different riparian zones of the TGR and were significantly influenced by microbial α-diversity. The bacterial taxa Desulfobacterota, Nitrospirota and the fungal taxa Calcarisporiellomycota, Rozellomycota showed a significant positive correlation with qCO2. The shifts in key microbial taxa unclassified_k_Fungi in the fungi module #3 are highlighted as essential factors regulating the microbial metabolic efficiency. Structural equation modeling results also revealed that soil enzyme activities had a highly significant negative effect on microbial metabolism efficiency (bacteria, path coefficient = -0.63; fungi, path coefficient = -0.67).This work has an important impact on the prediction of carbon cycling in aquatic-terrestrial ecotones. Graphical abstract.

Structural Characteristics and Assembly Mechanisms of Soil Microbial Communities under Water-Salt Gradients in Arid Regions.

Exploring the structural characteristics of arid soil microbial communities and their assembly mechanisms is important for understanding the ecological characteristics of arid zone soils and promoting ecological restoration. In this study, we used Illumina high-throughput sequencing technology to study soils in the arid zone of the Lake Ebinur basin, determined the differences among soil microbial community structures in the study area under different water-salt gradients, and investigated the effects of environmental factors on microbial community structure and assembly mechanisms. The results show the following: the microbial community alpha diversity exhibited a significantly higher low water-salt gradient (L) than high water-salt gradient (H) and medium water-salt gradient (M). The pH was most strongly correlated with soil microbial community structure, where the alpha diversity indices of the bacterial community and fungal community were significantly negatively correlated with pH, and the Bray-Curtis distance of bacterial community was significantly positively correlated with pH (p < 0.05). The complexity of bacterial community co-occurrence networks showed a significantly higher L than H and M, and the complexity of fungal community co-occurrence network showed a significantly lower L than H and M. The cooperative relationship of H and M in the co-occurrence networks was stronger than that of the L, and the key species of the microbial co-occurrence network were different under different water-salt gradients. Stochastic processes dominated the assembly mechanism of the microbial community structure of soil, and the explanation rates of deterministic and stochastic processes were different under different water-salt gradients, with the highest explanation rate of stochastic processes on the L accounting for more than 90%. In summary, the soil microbial community structure and assembly mechanisms significantly differed across water-salt gradients, and these findings can help provide a reference for further research on soil microbiology in arid zones.

Insight into the soil aggregate-mediated restoration mechanism of degraded black soil via biochar addition: Emphasizing the driving role of core microbial communities and nutrient cycling

Soil microbial communities are responsive to biochar application. However, few studies have investigated the synergistic effects of biochar application in the restoration of degraded black soil, especially soil aggregate-mediated microbial community changes that improve soil quality. From the perspective of soil aggregates, this study explored the potential microbial driving mechanism of biochar (derived from soybean straw) addition in black soil restoration in Northeast China. The results showed that biochar significantly improved the soil organic carbon, cation exchange capacity and water content, which play crucial roles in aggregate stability. The addition of biochar also significantly increased the concentration of the bacterial community in mega-aggregates (ME; 0.25–2 mm) compared with micro-aggregates (MI; <0.25 mm). Microbial co-occurrence networks analysis showed that biochar enhanced microbial interactions in terms of the number of links and modularity, particularly in ME. 16 S rRNA sequencing predicted that the expression of genes related to carbon (rbcL, acsA, gltS, aclB, and mcrA) and nitrogen (nifH and amoA) transformation increased after the addition of biochar. Furthermore, the functional microbes involved in carbon fixation (Firmicutes and Bacteroidetes) and nitrification (Proteobacteria) were significantly enriched and are the key regulators of carbon and nitrogen kinetics. Structural equation model (SEM) analysis further showed that the application of biochar promoted soil aggregates to positively regulate the abundance of soil nutrient conversion-related microorganisms, thereby increasing soil nutrient content and enzyme activities. These results provide new insights into the mechanisms of soil restoration through biochar addition.

Bio-organic fertilizer promoted phytoremediation using native plant leymus chinensis in heavy Metal(loid)s contaminated saline soil

Heavy metal(loid)s (HMs) contaminated saline soil appeared around the world, however, remediation regarding these collected from field conditions remains unknown. Native plants cultivation and bio-organic fertilizer (BOF) application were two efficient tools for soil amelioration. Herein, a pot experiment was conducted to examine the feasibility of a native plant (Leymus chinensis) for phytoremediation, and investigate the impacts of lignite based bio-organic fertilizer (LBOF) and manure based bio-organic fertilizer (MBOF) on phytoremediation of the soil contaminated by Pb, Cd, As, Zn, Cu, Ca2+, and SO42−. The results demonstrated the effectiveness of L. chinensis and highlighted the positive impacts of BOF according to the improved plant growth, HMs phytostabilization, salt removal, and soil properties. LBOF and MBOF changed soil microbiome to assist phytoremediation in addition to physiological modulation. Having enhanced fungal and bacterial richness respectively, LBOF and MBOF recruited various plant growth promoting rhizobacteria with different functions, and shifted microbial co-occurrence networks and keystone taxa towards these different but beneficial forms. Structural equation models comprehensively reveled the strategy discrepancy of LBOF and MBOF to regulate the plant biomass, HMs uptake, and soil salt. In summary, L. chinensis coupled with BOF, especially LBOF, was a effective strategy to remediate HMs contaminated saline soil.

Bacterial co-occurrence patterns are more complex but less stable than archaea in enhanced oil recovery applied oil reservoirs

A complex microbial community exists in oil reservoirs after the application of chemical enhanced oil recovery (EOR) technologies, where the dynamic interactions of microorganisms are thought to be critical to petroleum composition, recovery, and production technologies but are poorly understood. Here, we used the 16S rRNA gene to construct co-occurrence networks for bacterial and archaeal communities associated with water-, polymer-, and alkaline surfactant polymer (ASP)-flooded oil reservoirs. Nonmetric multidimensional scaling analysis showed that bacterial and archaeal community structures differed significantly (p < 0.01) among the oil reservoirs with different EOR compositions. The microbial co-occurrence pattern in water-flooded reservoirs was more complex, with more nodes, edges, and average degrees (i.e., average links per node in the network) than in the polymer- and ASP-flooded reservoirs. However, the archaeal co-occurrence pattern maintained a more robust structure than that of bacteria under the application of polymer and ASP flooding technologies, suggesting that the application of different enhanced oil recovery techniques has diverse effects on the bacterial and archaeal co-occurrence patterns in reservoirs. The pH and [HCO3−] were significantly correlated with the variations in bacterial and archaeal network structures. Our findings provide new insights into the response of microbes to diverse EOR processes by regulating their interactions in deep oil reservoirs. Revealing the effects of water, polymer, and ASP flooding on the co-occurrence patterns of bacteria and archaea in oil reservoirs, which may facilitate the implementation of microbial enhanced oil recovery technology in the future.

Contributions of plant litter to soil microbial activity improvement and soil nutrient enhancement along with herb and shrub colonization expansions in an arid sandy land

Shrubs and herbs are two important types of vegetation that play a pivotal role in combating land desertification in arid sandy land. Yet, the effects of plant litter on sandy soil microbial activities and soil nutrients during the shrub and herb colonization process are still unclear. Here, contributions of plant litter to soil microbial activity improvement and soil nutrient enhancement along herb and shrub colonization expansion interfaces were studied in an arid sandy landscape. Plant litter mass, soil water content, pH, nutrient content, extracellular enzyme activities, and microbial community structure (taxon composition, α-diversity, β-diversity, and co-occurrence pattern) of soils at depths of 0–10 cm were examined relative to the colonization processes of shrubs and herbs (shrub and herb vegetation → sand-shrub and sand-herb interface → a sand dune) in an arid sandy land. We found that the processes of both herb and shrub colonization significantly increased litter cumulative mass at the soil surface to soil depths of 5 cm, and shrub colonization contributed several folds more litter than herb colonization. Plant litter input significantly decreased soil pH, accelerated soil extracellular enzyme activities, increased abundances of some microbial phyla (Actinobacteria, Chloroflexi, Acidobacteria, Gemmatimonadetes, Patescibacteria, Armatimonadetes, Ascomycota, Moritierellomycota, and Chytridiomycota), enhanced both prokaryotic and fungal α-diversities, altered both prokaryotic and fungal communities, and promoted complexity of microbial networks during both herb and shrub colonization. As a result, microorganisms actively participated in litter decomposition and soil nutrient enhancement. Nevertheless, shrub colonization process exhibited greater potential in nutrient input than herb colonization process due to its greater plant litter input, though both colonization played a comparable role in accelerating soil enzyme activity and improving soil microbial community diversity and co-occurrence. Therefore, xeromorphic shrubs are still more important plants than herbs should be used for vegetation construction and ecological restoration in arid sandy land.

Xanthomonas infection and ozone stress distinctly influence the microbial community structure and interactions in the pepper phyllosphere

While the physiological and transcriptional response of the host to biotic and abiotic stresses have been intensely studied, little is known about the resilience of associated microbiomes and their contribution towards tolerance or response to these stresses. We evaluated the impact of elevated tropospheric ozone (O3), individually and in combination with Xanthomonas perforans infection, under open-top chamber field conditions on overall disease outcome on resistant and susceptible pepper cultivars, and their associated microbiome structure, function, and interaction network across the growing season. Pathogen infection resulted in a distinct microbial community structure and functions on the susceptible cultivar, while concurrent O3 stress did not further alter the community structure, and function. However, O3 stress exacerbated the disease severity on resistant cultivar. This altered diseased severity was accompanied by enhanced heterogeneity in associated Xanthomonas population counts, although no significant shift in overall microbiota density, microbial community structure, and function was evident. Microbial co-occurrence networks under simultaneous O3 stress and pathogen challenge indicated a shift in the most influential taxa and a less connected network, which may reflect the altered stability of interactions among community members. Increased disease severity on resistant cultivar may be explained by such altered microbial co-occurrence network, indicating the altered microbiome-associated prophylactic shield against pathogens under elevated O3. Our findings demonstrate that microbial communities respond distinctly to individual and simultaneous stressors, in this case, O3 stress and pathogen infection, and can play a significant role in predicting how plant-pathogen interactions would change in the face of climate change.

Microbial community structure in rice rhizosheaths under drought stress

Abstract Rhizosheaths can form on the surface of rice (Oryza sativa L.) roots and improve the water-use efficiency of rice under drought stress. The microbes in rhizosheaths can also offer the potential to increase the resilience of rice to future drought. However, little is known about the microbial community in rhizosheath of rice under drought stress. In this study, we compared the root traits, rhizosheath formation and microbial community in the rhizosheath under three irrigation regimes, including well-watered and drought treatments I and II. The irrigation plays important roles in influencing the microbial composition and co-occurrence networks. Drought can promote the accumulation of beneficial microorganisms in rhizosheaths, such as bacteria that are members of the phylum Patescibacteria and the Massilia, Nocardioides, Frateuria and Angustibacter genera and fungi in the genus Talaromyces. However, drought can also induce risk factors for harmful fungi in rice rhizosheaths. Our results suggest that both the rhizosheath and microbes in rhizosheath can offer the potential to improve the resistance of rice to drought. In the future, the isolation and application of beneficial microorganisms in rhizosheaths and scientific planting methods should be studied for the green cultivation of rice.

Lignite bioorganic fertilizer enhanced microbial co-occurrence network stability and plant–microbe interactions in saline-sodic soil

Lignite-converted bioorganic fertilizer substantially improves soil physiochemical properties, but little is known about how lignite bioorganic fertilizer (LBF) affects soil microbial communities and how the changed microbial communities impact their stability, functions, and crop growth in saline-sodic soil. Therefore, a two-year field experiment was conducted in saline-sodic soil in the upper Yellow River basin, Northwest China. Three treatments, i.e., the control treatment without organic fertilizer (CK), the farmyard manure treatment (FYM) amended with 21 t ha−1 (same as local farmers) sheep manure, and the LBF treatment amended with the optimal rate of LBF (3.0 and 4.5 t ha−1), were designed in this study. The results showed that after two years of application of LBF and FYM, the percentage of aggregate destruction (PAD) was significantly reduced by 14.4 % and 9.4 %, respectively, while the saturated hydraulic conductivity (Ks) was obviously increased by 114.4 % and 99.7 %, respectively. The LBF treatment significantly increased the contributions of nestedness to total dissimilarity by 101.4 % and 156.2 % in bacterial and fungal communities, respectively. LBF contributed to the shift from stochasticity to variable selection in the assembly of the fungal community. The LBF treatment enriched the bacterial classes of Gammaproteobacteria, Gemmatimonadetes, and Methylomirabilia and fungal classes of Glomeromycetes and GS13, which were mainly driven by PAD and Ks. Additionally, the LBF treatment significantly increased the robustness and positive cohesions and decreased the vulnerability of the bacterial co-occurrence networks in both 2019 and 2020 in comparison with the CK treatment, indicating that the LBF treatment increased stability of bacterial community. The relative abundance of chemoheterotrophy and arbuscular mycorrhizae in the LBF treatment were 89.6 % and 854.4 % higher than those in the CK treatment, respectively, showing that the LBF enhanced sunflower–microbe interactions. The FYM treatment improved the functions mainly regarding sulfur respiration and hydrocarbon degradation by 309.7 % and 212.8 % in comparison with the CK treatment, respectively. The core rhizomicrobiomes in the LBF treatment showed strong positive connections with the stabilities of both bacterial and fungal co-occurrence networks, as well as the relative abundance and potential functions of chemoheterotrophy and arbuscular mycorrhizae. These factors were also linked to the growth of sunflowers. This study reveals that the LBF improved sunflower growth due to enhance microbial community stability and sunflower–microbe interactions through altering core rhizomicrobiomes in saline-sodic farmland.

Functional Potential of Soil Microbial Communities and Their Subcommunities Varies with Tree Mycorrhizal Type and Tree Diversity.

Soil microbial communities play crucial roles in the earth's biogeochemical cycles. Yet, their genomic potential for nutrient cycling in association with tree mycorrhizal type and tree-tree interactions remained unclear, especially in diverse tree communities. Here, we studied the genomic potential of soil fungi and bacteria with arbuscular (AM) and ectomycorrhizal (EcM) conspecific tree species pairs (TSPs) at three tree diversity levels in a subtropical tree diversity experiment (BEF-China). The soil fungi and bacteria of the TSPs' interaction zone were characterized by amplicon sequencing, and their subcommunities were determined using a microbial interkingdom co-occurrence network approach. Their potential genomic functions were predicted with regard to the three major nutrients carbon (C), nitrogen (N), and phosphorus (P) and their combinations. We found the microbial subcommunities that were significantly responding to different soil characteristics. The tree mycorrhizal type significantly influenced the functional composition of these co-occurring subcommunities in monospecific stands and two-tree-species mixtures but not in mixtures with more than three tree species (here multi-tree-species mixtures). Differentiation of subcommunities was driven by differentially abundant taxa producing different sets of nutrient cycling enzymes across the tree diversity levels, predominantly enzymes of the P (n = 11 and 16) cycles, followed by the N (n = 9) and C (n = 9) cycles, in monospecific stands and two-tree-species mixtures, respectively. Fungi of the Agaricomycetes, Sordariomycetes, Eurotiomycetes, and Leotiomycetes and bacteria of the Verrucomicrobia, Acidobacteria, Alphaproteobacteria, and Actinobacteria were the major differential contributors (48% to 62%) to the nutrient cycling functional abundances of soil microbial communities across tree diversity levels. Our study demonstrated the versatility and significance of microbial subcommunities in different soil nutrient cycling processes of forest ecosystems. IMPORTANCE Loss of multifunctional microbial communities can negatively affect ecosystem services, especially forest soil nutrient cycling. Therefore, exploration of the genomic potential of soil microbial communities, particularly their constituting subcommunities and taxa for nutrient cycling, is vital to get an in-depth mechanistic understanding for better management of forest soil ecosystems. This study revealed soil microbes with rich nutrient cycling potential, organized in subcommunities that are functionally resilient and abundant. Such microbial communities mainly found in multi-tree-species mixtures associated with different mycorrhizal partners can foster soil microbiome stability. A stable and functionally rich soil microbiome is involved in the cycling of nutrients, such as carbon, nitrogen, and phosphorus, and their combinations could have positive effects on ecosystem functioning, including increased forest productivity. The new findings could be highly relevant for afforestation and reforestation regimes, notably in the face of growing deforestation and global warming scenarios.

The characteristics of soil microbial co-occurrence networks across a high-latitude forested wetland ecotone in China.

To understand the effect of seasonal variations on soil microbial communities in a forested wetland ecotone, here, we investigated the dynamics of the diversities and functions of both soil bacterial and fungal communities inhabiting three wetland types (forested wetland, shrub wetland and herbaceous vegetation wetland) from forest-wetland ecotone of northern Xiaoxing'an Mountains spanning different seasons. β-diversity of soil microbial communities varied significantly among different vegetation types (Betula platyphylla-Larix gmelinii, Alnus sibirica, Betula ovalifolia, and Carex schmidtii wetlands). We totally detected 34 fungal and 14 bacterial indicator taxa among distinctive groups by using Linear discriminant analysis effect size (LEfSe) analysis, and identified nine network hubs as the most important nodes detected in whole fungi, bacteria, and fungi-bacteria networks. At the vegetation type-level, bacterial and fungal microbiome living in C. schmidtii wetland soil possessed fewer positive interactions and lower modularity than those in other types of wetland soil. Furthermore, we also discovered that ectomycorrhizal fungi were dominant in the fungal microbiota existing in forested and shrub wetland soils, whereas arbuscular mycorrhizal fungi were predominated in those residing in herbaceous vegetation wetland soil. The distribution of the predicted bacterial functional enzymes also obviously varied among different vegetation-types. In addition, the correlation analysis further revealed that the key fungal network modules were significantly affected by the contents of total N and soil water-soluble K, whereas most of the bacterial network modules were remarkably positively driven by the contents of total N, soil water-soluble K, Mg and Na. Our study suggested that vegetation type are substantive factors controlling the diversity, composition and functional group of soil microbiomes from forest-wetland ecotone of northern Xiaoxing'an Mountains.

Diseased-induced multifaceted variations in community assembly and functions of plant-associated microbiomes.

Plant-associated microorganisms are believed to be part of the so-called extended plant phenotypes, affecting plant growth and health. Understanding how plant-associated microorganisms respond to pathogen invasion is crucial to controlling plant diseases through microbiome manipulation. In this study, healthy and diseased (bacterial wilt disease, BWD) tomato (Solanum lycopersicum L.) plants were harvested, and variations in the rhizosphere and root endosphere microbial communities were subsequently investigated using amplicon and shotgun metagenome sequencing. BWD led to a significant increase in rhizosphere bacterial diversity in the rhizosphere but reduced bacterial diversity in the root endosphere. The ecological null model indicated that BWD enhanced the bacterial deterministic processes in both the rhizosphere and root endosphere. Network analysis showed that microbial co-occurrence complexity was increased in BWD-infected plants. Moreover, higher universal ecological dynamics of microbial communities were observed in the diseased rhizosphere. Metagenomic analysis revealed the enrichment of more functional gene pathways in the infected rhizosphere. More importantly, when tomato plants were infected with BWD, some plant-harmful pathways such as quorum sensing were significantly enriched, while some plant-beneficial pathways such as streptomycin biosynthesis were depleted. These findings broaden the understanding of plant-microbiome interactions and provide new clues to the underlying mechanism behind the interaction between the plant microbiome and BWD.

Microbial ecological responses of partial nitritation/anammox granular sludge to real water matrices and its potential application

Granular sludges are commonly microbial aggregates used to apply partial nitritation/anammox (PN/A) processes during efficient biological nitrogen removal from ammonium-rich wastewater. Considering keystone taxa of anammox bacteria (AnAOB) in granules and their sensitivity to unfavorable environments, it is essential to investigate microbial responses of autotrophic PN/A granules to real water matrices containing organic and inorganic pollutants. In this study, tap water, surface water, and biotreated wastewater effluents were fed into a series of continuous PN/A granular reactors, respectively, and the differentiation in functional activity, sludge morphology, microbial community structure, and nitrogen metabolic pathways was analyzed by integrating kinetic batch testing, size characterization, and metagenomic sequencing. The results showed that feeding of biotreated wastewater effluents causes significant decreases in nitrogen removal activity and washout of AnAOB (dominated by Candidatus Kuenenia) from autotrophic PN/A granules due to the accumulation of heavy metals and formation of cavities. Microbial co-occurrence networks and nitrogen cycle-related genes provided evidence for the high dependence of symbiotic heterotrophs (such as Proteobacteria, Chloroflexi, and Bacteroidetes) on anammox metabolism. The enhancement of Nitrosomonas nitritation in the granules would be considered as an important contributor to greenhouse gas (N2O) emissions from real water matrices. In a novel view on the application of microbial responses, we suggest a bioassay of PN/A granules by size characterization of red-color cores in ecological risk assessment of water environments.

Metabolite-Mediated Responses of Phyllosphere Microbiota to Rust Infection in Two Malus Species.

Plants recruit beneficial microbes to enhance their ability to fight pathogens. However, the current understanding of microbial recruitment is largely limited to belowground systems (root exudates and the rhizosphere). It remains unclear whether the changes in leaf metabolites induced by infectious pathogens can actively recruit beneficial microbes to mitigate the growth of foliar pathogens. In this study, we integrated microbiome and metabolomic analyses to systematically explore the dynamics of phyllosphere fungal and bacterial communities and key leaf metabolites in two crabapple species (Malus sp. "Flame" and Malus sp. "Kelsey") at six stages following infection with Gymnosporangium yamadae. Our results showed that the phyllosphere microbiome changed during lesion expansion, as highlighted by a reduction in bacterial alpha-diversity and an increase in fungal alpha-diversity; a decreasing and then an increasing complexity of the microbial co-occurrence network was observed in Kelsey and a decreasing complexity occurred in Flame. In addition, nucleotide sugars, diarylheptanoids, and carboxylic acids with aromatic rings were more abundant in early stages of collection, which positively regulated the abundance of bacterial orders Pseudomonadales (in Kelsey), Acidimicrobiales, Bacillales, and Flavobacteriales (in Flame). In addition, metabolites such as flavonoids, lignin precursors, terpenoids, coumarins, and quaternary ammonium salts enriched with the expansion of lesions had a positive regulatory effect on fungal families Rhynchogastremataceae and Golubeviaceae (in Flame) and the bacterial order Actinomycetales (in Kelsey). Our findings highlight that plants may also influence phyllosphere microorganisms by adjusting leaf metabolites in response to biotic stress. IMPORTANCE Our findings demonstrate the response patterns of bacterial and fungal communities in the Malus phyllosphere to rust fungus G. yamadae infection, and they also reveal how the phyllosphere microbiome changes with the expansion of lesions. We identified several metabolites whose relative abundance varied significantly with lesion expansion. Using a framework for assessing the role of leaf metabolites in shaping the phyllosphere microbiome of the two Malus species, we identified several specific metabolites that have profoundly selective effects on the microbial community. In conclusion, our study provides new evidence of the ecological niche of the phyllosphere in supporting the "cry for help" strategy for plants.

The degradation of subalpine meadows significantly changed the soil microbiome

Grassland degradation seriously affects the health of our planet, thereby weakening the ability of grasslands to provide multiple ecosystem services. Soil microbes have been recognized as game changers in the succession of degraded lands; therefore, the determination of their responses to grassland degradation is crucial for restoring degraded grasslands. However, soil microbial responses to grassland degradation are still far from being well understood, especially for low-latitude meadows. Hence, this study was performed in one natural and two artificial degraded subalpine meadows in Southern China to identify the soil microbial responses to the degradation of low-latitude subalpine meadows. At each site, soils were collected from nondegraded, moderately degraded, and heavily degraded subalpine meadows. Soil microbial abundance and diversity were analyzed via real-time PCR and amplicon NovaSeq sequencing, respectively. We found that the degradation of subalpine meadows significantly decreased the concentrations of almost all of the soil nutrients and considerably changed soil pH and texture. We also found that soil microbes demonstrated almost consistent responses to the degradation of the natural and artificial subalpine meadows. Specifically, degradation did not affect soil microbial abundance but significantly changed microbial community profiles. The relative abundance of most plant growth-promoting microbial taxa significantly decreased with subalpine meadow degradation, whereas the microbial taxa that were adverse to plant health exhibited a reverse trend. Soil microbial richness was also significantly decreased by the heavy degradation of the subalpine meadows. Additionally, the heavy degradation of the subalpine meadows significantly decreased the complexity and stability of the microbial co-occurrence network. The aforementioned soil microbiome changes also showed the significant correlations with plant biomass. Collectively, the changes in the soil microbiome can be critical factors affecting the degradation of subalpine meadows, and the regulation of soil microbiome is a promising restoration strategy.

Community response of soil microorganisms to combined contamination of polycyclic aromatic hydrocarbons and potentially toxic elements in a typical coking plant.

Both polycyclic aromatic hydrocarbons (PAHs) and potentially toxic elements (PTEs) of coking industries impose negative effects on the stability of soil ecosystem. Soil microbes are regarded as an essential moderator of biochemical processes and soil remediation, while their responses to PAHs-PTEs combined contamination are largely unknown. In the present study, soil microbial diversity and community composition in the typical coking plant under the chronic co-exposure of PAHs and PTEs were investigated and microbial interaction networks were built to reveal microbial co-occurrence patterns. The results indicated that the concentrations of PAHs in the soil inside the coking plant were significantly higher than those outside the plant. The mean concentration of ∑16PAHs was 2894.4 ng·g-1, which is 5.58 times higher than that outside the plant. The average Hg concentration inside the coking plant was 22 times higher than the background value of Hebei province. The soil fungal community inside the coking plant showed lower richness compared with that of outside community, and there are significant difference in the bacterial and fungal community composition between inside and outside of coking plant (p < 0.01). Predicted contribution of different environmental factors to each dominant species based on random forest identified 20 and 25 biomarkers in bacteria and fungi, respectively, that were highly sensitive to coking plant soil in operation, such as Betaproteobacteria，Sordariomycetes and Dothideomycetes. Bacterial and fungal communities were shaped by the soil chemical properties (pH), PTEs (Hg), and PAHs together in the coking plant soils. Furthermore, the bacterial and fungal interaction patterns were investigated separately or jointly by intradomain and interdomain networks. Competition is the main strategy based on the co-exclusion pattern in fungal community, and the competitive relationship inside the coking plant is more complex than that outside the plant. In contrast, cooperation is the dominant strategy in bacterial networks based on the co-occurrence pattern. The present study provided insights into microbial response strategies and the interactions between bacteria and fungi under long-term combined contamination.

Habitats Within the Plant Root Differ in Bacterial Network Topology and Taxonomic Assortativity.

The root microbiome is composed of distinct epiphytic (rhizosphere) and endophytic (endosphere) habitats. Differences in abiotic and biotic factors drive differences in microbial community diversity and composition between these habitats, though how they shape the interactions among community members is unknown. Here, we coupled a large-scale characterization of the rhizosphere and endosphere bacterial communities of 30 plant species across two watering treatments with co-occurrence network analysis to understand how root habitats and soil moisture shape root bacterial network properties. We used a novel bootstrapping procedure and null network modeling to overcome some of the limitations associated with microbial co-occurrence network construction and analysis. Endosphere networks had elevated node betweenness centrality versus the rhizosphere, indicating greater overall connectivity among core bacterial members of the root endosphere. Taxonomic assortativity was higher in the endosphere, whereby positive co-occurrence was more likely between bacteria within the same phylum while negative co-occurrence was more likely between bacterial taxa from different phyla. This taxonomic assortativity could be driven by positive and negative interactions among members of the same or different phylum, respectively, or by similar niche preferences associated with phylum rank among root inhabiting bacteria across plant host species. In contrast to the large differences between root habitats, drought had limited effects on network properties but did result in a higher proportion of shared co-occurrences between rhizosphere and endosphere networks. Our study points to fundamentally different ecological processes shaping bacterial co-occurrence across root habitats. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.