Microbial interactions: from networks to models

Dissolved organic matter characteristics linked to bacterial community succession and nitrogen removal performance in woodchip bioreactors

Woodchip bioreactors are an eco-friendly technology for removing nitrogen (N) pollution. However, there needs to be more clarity regarding the dissolved organic matter (DOM) characteristics and bacterial community succession mechanisms and their association with the N removal performance of bioreactors. The laboratory woodchip bioreactors were continuously operated for 360 days under three influent N level treatments, and the results showed that the average removal rate of TN was 45.80 g N/(m3·day) when the influent N level was 100 mg N/L, which was better than 10 mg N/L and 50 mg N/L. Dynamic succession of bacterial communities in response to influent N levels and DOM characteristics was an important driver of TN removal rates. Medium to high N levels enriched a copiotroph bacterial module (Module 1) detected by network analysis, including Phenylobacterium, Xanthobacteraceae, Burkholderiaceae, Pseudomonas, and Magnetospirillaceae, carrying N-cycle related genes for denitrification and ammonia assimilation by the rapid consumption of DOM. Such a process can increase carbon limitation to stimulate local organic carbon decomposition to enrich oligotrophs with fewer N-cycle potentials (Module 2). Together, this study reveals that the compositional change of DOM and bacterial community succession are closely related to N removal performance, providing an ecological basis for developing techniques for N-rich effluent treatment.

Biotic interactions and environmental modifications determine symbiotic microbial diversity and stability

Taking amphibians as island models, we examined the effects of interspecific interaction on the diversity and stability of microbial ecological. As skin area increased, the diversity and stability of skin microbes decreased, but the strength of negative interactions increased significantly. In contrast, as gut area increased, the diversity and stability of gut microbes increased, but the strength of interactions remained constant. These results indicate that microbial interactions are affected by habitat properties. When living in fluctuating environments without strong filtering, microorganisms can enhance their negative interactions with other taxa by changing the pH of their surroundings. In contrast, the pH of the gut is relatively stable, and colonized microorganisms cannot alter the gut pH and inhibit other colonizers. This study demonstrates that in the field of microbiology, diversity and stability are predominantly influenced by the intensity of interspecies interactions. The findings in this study deepen our understanding of microbial diversity and stability and provide a mechanistic link between species interactions, biodiversity, and stability in microbial ecosystems.

Exploring product maturation, microbial communities and antibiotic resistance gene abundances during food waste and cattle manure co-composting

This study proposed combining food waste (FW) and cattle manure (CM) in composting to improve the product maturity. The findings suggested that the inclusion of CM effectively extended the thermophilic stage, facilitated the decomposition of cellulose, and enhanced the production of humus-like substances by enhancing beneficial microbial cooperation. Adding 40 % CW was optimal to reduce the nitrogen loss, increase the cellulose degradation rate to 22.07 %, increase germination index (GI) to 140 %, and reduce normalized antibiotic resistance gene (ARG) abundances. Adding CW could promote the transformation of protein-like compounds, thereby enhancing the humification process of organic substances. Structural equation modeling further verified that the temperature was the key factor affecting humification production, while the main driver for ARGs was physiochemical parameters. This study shows that co-composting of FW and CM offers the potential to promote humification, reduce ARG abundance, and improve fertilizer quality for utilization of both biowastes in the field.

Unveiling the hidden impact: How human disturbances threaten aquatic microorganisms in cities

Urban activity emissions have important ecological significance to bacterial communities' spatial and temporal distribution and the mechanism of bacterial community construction. The mechanism of bacterial community construction is the key to community structure and lifestyle, and the influence of this aspect has not been thoroughly studied. This study analyzed the response of bacteria in water and sediment in different seasons to urban activities in Jinsha River. The results showed that the influence of urban activities on bacterial community structure in sediment was greater than that in water. The input of pollution in different regions changed the diversity and abundance of water and sediments bacteria and promoted bacterial community reconstruction to a certain extent. Co-network analysis found that many metal-mediated species are core species within the same module and can be used to mitigate pollution caused by metal or organic pollutants due to interspecific solid interactions. Different potential pollution sources around urban rivers affect the metabolic function of bacteria in aquatic ecosystems and promote the detoxification function of bacteria in different media. The results of this study supplement our understanding of the characteristics of microbial communities in urban river systems and provide clues for understanding the maintenance mechanism of microbial diversity in multi-pollution environments.

Growth period and variety together drive the succession of phyllosphere microbial communities of grapevine

Phyllosphere microbes play a crucial role in plant health and productivity. However, the influence of abiotic and biotic factors on these communities is poorly understood. Here, we used amplicon sequencing to investigate the microbiome variations across eight grape cultivars and three distinct leaf ages. The diversity and richness of phyllosphere microbiomes were significantly affected by cultivars and leaf age. Young leaves of most grape cultivars had a higher diversity. Beta-diversity analyses revealed notable differences in microbial communities across leaf ages, with bacterial communities varying substantially between cultivars. The main bacterial genera included Staphylococcus, Exiguobacterium, Acinetobacter, Enterococcus, and Erwinia; the principal fungal genera were Cladosporium, Moesziomyces, Alternaria, Didymella, and Coprinellus across all samples. LEfSe analysis revealed significant differences in bacterial and fungal biomarkers at different leaf ages, with no biomarkers identified among different cultivars. Fungal biomarkers were more abundant than bacterial at three leaf ages, and older leaves had more fungal biomarkers. Notably, beneficial microbial taxa with biocontrol potential were present on the phyllosphere at 45 d, whereas certain fungal groups associated with increased disease risk were first detected at 100 d. The bacterial network was more complex than the fungal network, and young leaves had a more complex network in most cultivars. Our study elucidated the dynamics of early grape phyllosphere microbes, providing valuable insights for early detection and prediction of grape diseases and a foundation for leveraging the grape leaf microbiome for agricultural purposes.

Impact of geochemistry and microbes on the methylmercury production in mangrove sediments

Unraveling the geochemical and microbial controls on methylmercury (MeHg) dynamics in mangrove sediments is important, as MeHg can potentially pose risks to marine biota and people that rely on these ecosystems. While the important role of sulfate-reducing bacteria in MeHg formation has been examined in this ecologically important habitat, the contribution of non-Hg methylating communities on MeHg production remains particularly unclear. Here, we collected sediment samples from 13 mangrove forests in south China and examined the geochemical parameters and microbial communities related to the Hg methylation. MeHg concentrations were significantly correlated to the OM-related parameters such as organic carbon content, total nitrogen, and dissolved organic carbon concentrations, suggesting the importance of OM in the MeHg production. Sulfate-reducing bacteria were the major Hg-methylators in mangrove sediments. Desulfobacteraceae and Desulfobulbaceae dominated the Hg-methylating microbes. Classification random forest analysis detected strong co-occurrence between Hg methylators and putative non-Hg methylators, thus suggesting that both types of microorganisms contribute to the MeHg dynamics in the sediments. Our study provides an overview of MeHg contamination in south China and advances our understanding of Hg methylation in mangrove ecosystems.

Effect of microbial interactions on performance of community metabolic modeling algorithms: flux balance analysis (FBA), community FBA (cFBA) and SteadyCom

To explore the impact of microbial interactions on outcomes from three prevalent algorithms (Flux Balance Analysis (FBA), community FBA (cFBA), and SteadyCom) analyzing microbial community metabolic networks, five toy community models representing common microbial interactions were designed. These include commensalism, mutualism, competition, mutualism-competition, and commensalism-competition. Various scenarios, considering different biomass yields and substrate constraints, were examined for each type. In commensal communities, all algorithms consistently produced similar results. However, changes in biomass yields and substrate constraints led to variable abundances (0.33-0.8) and community growth rates (2-5 1/h) within a broad range. For competitive communities, all algorithms predicted growth of fastest-growing member. To comply with the natural coexistence of members, suboptimal solutions over optimal point are recommended. FBA faced challenges in modeling mutualism, consistently predicting growth of only one member. Although cFBA and SteadyCom resulted in a lower community growth rate, coexistence of both members were satisfied. In toy models with dual interactions, more realistic outcomes were achieved contrary to purely competitive model as the dependency fosters the coexistence which was missing in the competitive only scenarios. These findings emphasize the importance of algorithm choice based on specific microbial interaction types for reliable community behavior predictions.​.

Conversion of monocropping to intercropping promotes rhizosphere microbiome functionality and soil nitrogen cycling

Intercropping can increase soil nutrient availability and provide greater crop yields for intensive agroecosystems. Despite its multiple benefits, how intercropping influences rhizosphere microbiome assemblages, functionality, and complex soil nitrogen cycling is not fully understood. Here, a three-year field experiment was carried out on different cropping system with five fertilization treatments at the main soybean production regions. We found that soybean yields in intercropped systems were on average 17 % greater than in monocropping system, regardless of fertilization treatments. We also found that intercropping systems significant increased network modularity (by 46 %) and functional diversity (by 11 %) than monocropping systems. Metagenomics analyses further indicated intercropping promotes microbiome functional adaptation, particularly enriching core functions related to nitrogen metabolism. Cropping patterns had a stronger influence on the functional genes associated with soil nitrogen cycling (R2 = 0.499). Monocropping systems increased the abundance of functional genes related to organic nitrogen ammonification, nitrogen fixation, and denitrification, while functional guilds of nitrate assimilation (by 28 %), nitrification (by 31 %), and dissimilatory nitrate reduction (by 10.1 %) genes were enriched in intercropping systems. Furthermore, we found that abiotic factors (i.e. AP, pH, and Moisture) are important drivers in shaping soil microbial community assemblage and nitrogen cycling. The functional genes include hzsB, and nrfA, and nxrA that affected by these biotic and abiotic variables were strongly related to crop yield (R2 = 0.076 ~ R2 = 0.249), suggesting a key role for maintaining crop production. We demonstrated that land use conversion from maize monocropping to maize-soybean intercropping diversify rhizosphere microbiome and functionality signatures, and intercropping increased key gene abundance related to soil nitrogen cycling to maintain the advantage of crop yield. The results of this study significantly facilitate our understanding of the complex soil nitrogen cycling processes and lay the foundation for manipulating desired specific functional taxa for improved crop productivity under sustainable intensification.

Seasonal variations in soil microbial community co-occurrence network complexity respond differently to field-simulated warming experiments in a northern subtropical forest

Global warming may reshape seasonal changes in microbial community diversity and co-occurrence network patterns, with significant implications for terrestrial ecosystem function. We conducted a 2-year in situ field simulation of the effects of warming on the seasonal dynamics of soil microbial communities in a northern subtropical Quercus acutissima forest. Our study revealed that warming had no significant effect on the richness or diversity of soil bacteria or fungi in the growing season, whereas different warming gradients had different effects on their diversity in the nongrowing season. Warming also changed the microbial community structure, increasing the abundance of some thermophilic microbial species and decreasing the abundance of some symbiotrophic microorganisms. The co-occurrence network analysis of the microbial community showed that warming decreased the complexity of the intradomain network in the soil bacterial community in the growing and nongrowing seasons but increased it in the fungal community. Moreover, increasing warming temperatures increased the complexity of the interdomain network between bacteria and fungi in the growing season but decreased it in the nongrowing season, and the keystone species in the interdomain network changed with warming. Warming also reduced the proportion of positive microbial community interactions, indicating that warming reduced the mutualism, commensalism, and neutralism of microorganisms as they adapted to soil environmental stress. The factors affecting the fungal community varied considerably across warming gradients, with the bacterial community being significantly affected by soil temperature, MBC, NO3--N and NH4+-N, moreover, SOC and TN significantly affected fungal communities in the 4 °C warming treatment. These results suggest that warming increases seasonal differences in the diversity and complexity of soil microbial communities in the northern subtropical region, significantly influencing soil dynamic processes regulating forest ecosystems under global warming.

High biological N fixation potential dominated by heterotrophic diazotrophs in alpine permafrost rivers on the Qinghai‒Tibet Plateau

Biological nitrogen (N) fixation is a pivotal N source in N-deficient ecosystems. The Qinghai‒Tibet Plateau (QTP) region, which is assumed to be N limited and suboxic, is an ideal habitat for diazotrophs. However, the diazotrophic communities and associated N fixation rates in these high-altitude alpine permafrost QTP rivers remain largely unknown. Herein, we examined diazotrophic communities in the sediment and biofilm of QTP rivers via the nitrogenase (nifH) gene sequencing and assessed their N fixing activities via a 15N isotope incubation assay. Strikingly, anaerobic heterotrophic diazotrophs, such as sulfate- and iron-reducing bacteria, had emerged as dominant N fixers. Remarkably, the nifH gene abundance and N fixation rates increased with altitude, and the average nifH gene abundance (2.57 ± 2.60 × 108 copies g-1) and N fixation rate (2.29 ± 3.36 nmol N g-1d-1) surpassed that documented in most aquatic environments (nifH gene abundance: 1.31 × 105 ∼ 2.57 × 108 copies g-1, nitrogen fixation rates: 2.34 × 10-4 ∼ 4.11 nmol N g-1d-1). Such distinctive heterotrophic diazotrophic communities and high N fixation potential in QTP rivers were associated with low-nitrogen, abundant organic carbon and unique C:N:P stoichiometries. Additionally, the significant presence of psychrophilic bacteria within the diazotrophic communities, along with the enhanced stability and complexity of the diazotrophic networks at higher altitudes, clearly demonstrate the adaptability of diazotrophic communities to extreme cold and high-altitude conditions in QTP rivers. We further determined that altitude, coupled with organic carbon and phosphorus, was the predominant driver shaping diazotrophic communities and their N-fixing activities. Overall, our study reveals high N fixation potential in N-deficient QTP rivers, which provides novel insights into nitrogen dynamics in alpine permafrost rivers.

Anthropogenic activity shapes the assemble and co-occurrence pattern of microbial communities in fishing harbors around the Bohai economic circle

This study aimed to elucidate the effects of coastal environmental stress on the composition of sediment bacterial communities and their cooccurrence patterns in fishing harbors around the Bohai Economic Circle, China. Compared with the natural sea area, fishing harbors contained higher levels of organic pollution (organic pollution index = 0.12 ± 0.026) and considerably reduced bacterial richness and evenness. The distributions of sediment microbial communities clustered along the pollutant concentration gradients across fishing harbors. Betaproteobacteria dominated (76%) organically polluted fishing harbors, which were mostly disturbed by anthropogenic activities. However, the harbors also revealed the absence of numerous pathogenic (Coxiella and Legionella) and photosynthetic (Synechococcus and Leptolyngbya) bacteria. Abundant genera, including Thiobacillus and Arenimonas, exhibited a positive correlation with total phosphorus and a negative correlation with total nitrogen in sediments. Meanwhile, Sulfurovum, Psychrobacter, and Woeseia showed the opposite trend. Pollutant accumulation and anthropogenic activities caused the decrease in the sediment microbial diversity and dispersal ability and promoted convergent evolution. Severely polluted harbors with simplified cooccurrence networks revealed the presence of destabilized microbial communities. In addition, the modularity of bacterial networks decreased with organic pollution. Our results provide important insights into the adjustment mechanism of microbial communities to community organization and functions under environmental pollution stress. Overall, this study enhanced our understanding of how microbial communities in coastal sediments adapted and survived amidst anthropogenic activities like oily effluent discharges from large ships, wash water, domestic sewage, garbage, and fisheries wastes. It also examined their resilience to future contamination.

Metabarcoding and co-occurrence network reveal significant effects of mariculture on benthic eukaryotic microalgal community: A case study in Daya Bay of the South China Sea

Benthic eukaryotic microalgae were analyzed by metabarcoding the partial 18S rRNA gene in Daya Bay bi-monthly in 2021. Altogether 941 eukaryotic microalgal OTUs were detected, belonging to 27 classes of 8 phyla. Dinophyta and Chlorophyta were the dominant phyla. Microalgal community in the mariculture zone differed significantly from those in non-mariculture zone, reflected by low alpha diversity indexes and increasing abundance and richness of chlorophytes and correspondingly decreasing of dinoflagellates. The abundant occurrences of the pico- and nano-sized taxa such as the chlorophyte Picochlorum in the mariculture zone suggested that nutrient enrichment might result in the miniaturization of the benthic eukaryotic microalgae. The co-occurrence network suggested more negative interactions between taxa in the mariculture zone. A total of 41 algal bloom and/or harmful algal bloom (HAB) species were detected in this study, suggesting a high potential risk of HABs in Daya Bay, especially for the recurrent bloom species Scrippsiella acuminata.

Combined influence of the nanoplastics and polycyclic aromatic hydrocarbons exposure on microbial community in seawater environment

Nanoplastics (NPs) and polycyclic aromatic hydrocarbons (PAHs) are recognized as persistent organic pollutant (POPs) with demonstrated physiological toxicity. When present in aquatic environments, the two pollutants could combine with each other, resulting in cumulative toxicity to organisms. However, the combined impact of NPs and PAHs on microorganisms in seawater is not well understood. In this study, we conducted an exposure experiment to investigate the individual and synergistic effects of NPs and PAHs on the composition, biodiversity, co-occurrence networks of microbial communities in seawater. Exposure of individuals to PAHs led to a reduction in microbial community richness, but an increase in the relative abundance of species linked to PAHs degradation. These PAHs-degradation bacteria acting as keystone species, maintained a microbial network complexity similar to that of the control treatment. Exposure to individual NPs resulted in a reduction in the complexity of microbial networks. Furthermore, when PAHs and NPs were simultaneously present, the toxic effect of NPs hindered the presence of keystone species involved in PAHs degradation, subsequently limiting the degradation of PAHs by marine microorganisms, resulting in a decrease in community diversity and symbiotic network complexity. This situation potentially poses a heightened threat to the ecological stability of marine ecosystems. Our work strengthened the understanding of the combined impact of NPs and PAHs on microorganisms in seawater.

Feature sequence-based genome mining uncovers the hidden diversity of bacterial siderophore pathways

Microbial secondary metabolites are a rich source for pharmaceutical discoveries and play crucial ecological functions. While tools exist to identify secondary metabolite clusters in genomes, precise sequence-to-function mapping remains challenging because neither function nor substrate specificity of biosynthesis enzymes can accurately be predicted. Here, we developed a knowledge-guided bioinformatic pipeline to solve these issues. We analyzed 1928 genomes of Pseudomonas bacteria and focused on iron-scavenging pyoverdines as model metabolites. Our pipeline predicted 188 chemically different pyoverdines with nearly 100% structural accuracy and the presence of 94 distinct receptor groups required for the uptake of iron-loaded pyoverdines. Our pipeline unveils an enormous yet overlooked diversity of siderophores (151 new structures) and receptors (91 new groups). Our approach, combining feature sequence with phylogenetic approaches, is extendable to other metabolites and microbial genera, and thus emerges as powerful tool to reconstruct bacterial secondary metabolism pathways based on sequence data.

Deciphering soil environmental regulation on reassembly of the soil bacterial community during wetland restoration

Soil bacteria are vital to regulate biogeochemical processes in wetlands, however, little is known about the patterns and mechanisms of soil bacterial re-organization during wetland restoration. Here, we used a space-for-time substitution approach and examined the ecological processes that drive soil bacterial assembly from cultivated to restored to natural wetlands. Results showed a decrease of soil bacterial α diversity and increase of bacterial community similarity and bacterial interaction (cooperation vs. competition) with years of restoration, which was dominantly influenced by deterministic processes. Identified bacterial keystone taxa (e.g. Variibacter, Acidibacter) with nutrient metabolism capacity exerted strong positive effect on bacterial interaction. Furthermore, changes of soil water condition and nutrient status showed dominantly direct positive effects on soil bacterial reassembly, while falling soil pH significantly promoted bacterial reassembly by increasing keystone taxa and bacterial interaction during wetland restoration. Overall, findings highlighted the crucial role of environmental filtering and its pathway in influencing keystone bacterial taxa that promotes the reassembly of bacterial community during wetland restoration. Our work thus provides a new crucial and timely insight for improving the management of soil bacterial community assembly within the plethora of current and future wetland restoration projects.

Networks as tools for defining emergent properties of microbiomes and their stability

The potential promise of the microbiome to ameliorate a wide range of societal and ecological challenges, from disease prevention and treatment to the restoration of entire ecosystems, hinges not only on microbiome engineering but also on the stability of beneficial microbiomes. Yet the properties of microbiome stability remain elusive and challenging to discern due to the complexity of interactions and often intractable diversity within these communities of bacteria, archaea, fungi, and other microeukaryotes. Networks are powerful tools for the study of complex microbiomes, with the potential to elucidate structural patterns of stable communities and generate testable hypotheses for experimental validation. However, the implementation of these analyses introduces a cascade of dichotomies and decision trees due to the lack of consensus on best practices. Here, we provide a road map for network-based microbiome studies with an emphasis on discerning properties of stability. We identify important considerations for data preparation, network construction, and interpretation of network properties. We also highlight remaining limitations and outstanding needs for this field. This review also serves to clarify the varying schools of thought on the application of network theory for microbiome studies and to identify practices that enhance the reproducibility and validity of future work. Video Abstract.

Microbiome regulation for sustainable wastewater treatment

Sustainable wastewater treatment is essential for attaining clean water and sanitation, aligning with UN Sustainable Development Goals. Wastewater treatment plants (WWTPs) have utilized environmental microbiomes in biological treatment processes in this effort for over a century. However, the inherent complexity and redundancy of microbial communities, and emerging chemical and biological contaminants, challenge the biotechnology applications. Over the past decades, understanding and utilization of microbial energy metabolism and interaction relationships have revolutionized the biological system. In this review, we discuss how microbiome regulation strategies are being used to generate actionable performance for low-carbon pollutant removal and resource recovery in WWTPs. The engineering application cases also highlight the real feasibility and promising prospects of the microbiome regulation approaches. In conclusion, we recommend identifying environmental risks associated with chemical and biological contaminants transformation as a prerequisite. We propose the integration of gene editing and enzyme design to precisely regulate microbiomes for the synergistic control of both chemical and biological risks. Additionally, the development of integrated technologies and engineering equipment is crucial in addressing the ongoing water crisis. This review advocates for the innovation of conventional wastewater treatment biotechnology to ensure sustainable wastewater treatment.

Adaptation strategies of soil microorganisms in resource changes and stoichiometric imbalances induced by secondary succession on the loess plateau

Sequestering farmland for secondary succession is an effective method of restoring ecosystem services to degraded farmland, but long-term secondary succession often alters ecosystem environments, resources, and substrate stoichiometry. Currently, it is not known how resource changes and stoichiometric imbalances due to secondary succession affect soil microbial community structure and function, hindering our understanding of the natural resilience for degraded ecosystems. Here, we assessed nutrient limitation elements, community structure, metabolic functions, co-occurrence network complexity, and community stability of soil microorganisms during secondary succession of abandoned farmlands on the Loess Plateau. Results showed that secondary succession significantly altered plant characteristics and soil properties, as well as causing stoichiometry imbalances in nutrient resources. Along the secondary succession chronosequence, microbial nutrient metabolism shifted from phosphorus (P) limitation to carbon (C) and nitrogen (N) co-limitation. Microbial diversity, eutrophic flora, plant growth-promoting bacteria, and metabolism functional groups increased significantly during the 20 years after the abandonment of the farmlands, but decreased significantly with long-term succession. However, oligotrophic flora and P-solubilizing bacteria became dominant after 30 years of secondary succession on abandoned farmlands. The topological features of microbial co-occurring networks, including nodes, degree, closeness, betweenness, and eigenvector complexity, natural connectivity, and community stability first increased and then decreased with secondary succession. Correlation and random forest analyses indicated that secondary succession-induced stoichiometry imbalances in C:N and N:P, as well as changes in soil organic C and lignin phenols, were the key factors influencing microbial community structure and function. Overall, these results enhance our understanding of the adaptation strategies of soil microbial communities in ecologically managed regions to changes in ecosystem resources and stoichiometric imbalances.

Community organization and network complexity and stability: contrasting strategies of prokaryotic versus eukaryotic microbiomes in the Bohai Sea and Yellow Sea

Unraveling the effects of spatial gradients on microbiome assembly and association is a challenging topic that remains understudied in the coastal ecosystem. Here, we aimed to investigate the effects of spatial variation on the network complexity and stability of plankton microbiomes in the Bohai Sea and Yellow Sea. These seas serve as spawning and nursery grounds for economically important fisheries valued at billions of dollars annually. Environmental heterogeneity structures microbial communities into distinct spatial patterns, leading to complex direct/indirect relationships and broader ecological niches of bacterioplankton compared to microeukaryotic communities. Interestingly, salinity gradients positively influenced the richness of rare subgroups of bacterioplankton, while the rare microeukaryotic subgroups showed an opposite trend. Abundant subgroups of prokaryotic/eukaryotic microbiomes exhibited greater environmental niche breadth and lower phylogenetic distance compared to the rare subgroups. Stochastic processes contributed greatly to microbiome dynamics, and deterministic processes governed the bacterioplankton organization with a lower phylogenetic turnover rate. Compared to microeukaryotes, bacterioplankton exhibit higher network modularity, complexity, and robustness and lower fragmentation, and vulnerability. These observations offer vital insights into the anti-interference ability and resistance of plankton microbiomes in response to environmental gradients in terms of organization and survival strategy as well as their adaptability to environmental disturbances.IMPORTANCEAn in-depth understanding of community organization and stability of coastal microbiomes is crucial to determining the sustainability of marine ecosystems, such as the Bohai Sea and Yellow Sea. Distinct responses between prokaryotic and eukaryotic microbiomes to spatial heterogeneity were observed in terms of geographical distribution, phylogenetic distance, niche breadth, and community assembly process. Environmental variations are significantly correlated with the dynamics of rare eukaryotic plankton subcommunities compared to prokaryotic plankton subcommunities. Deterministic processes shaped prokaryotic plankton community organization with a lower phylogenic turnover rate. Rare subgroups had noticeably higher phylogenetic distance and lower niche breadth than the corresponding abundant subgroups. Prokaryotic microbiomes had higher molecular network complexity and stability compared to microeukaryotes. Results presented here show how environmental gradients alter both the geographical characteristics of the microbial organization in coastal seas and also their co-occurrence network complexity and stability and thus have critical implications for nutrient and energy cycling.

A systematic framework for understanding the microbiome in human health and disease: from basic principles to clinical translation

The human microbiome is a complex and dynamic system that plays important roles in human health and disease. However, there remain limitations and theoretical gaps in our current understanding of the intricate relationship between microbes and humans. In this narrative review, we integrate the knowledge and insights from various fields, including anatomy, physiology, immunology, histology, genetics, and evolution, to propose a systematic framework. It introduces key concepts such as the 'innate and adaptive genomes', which enhance genetic and evolutionary comprehension of the human genome. The 'germ-free syndrome' challenges the traditional 'microbes as pathogens' view, advocating for the necessity of microbes for health. The 'slave tissue' concept underscores the symbiotic intricacies between human tissues and their microbial counterparts, highlighting the dynamic health implications of microbial interactions. 'Acquired microbial immunity' positions the microbiome as an adjunct to human immune systems, providing a rationale for probiotic therapies and prudent antibiotic use. The 'homeostatic reprogramming hypothesis' integrates the microbiome into the internal environment theory, potentially explaining the change in homeostatic indicators post-industrialization. The 'cell-microbe co-ecology model' elucidates the symbiotic regulation affecting cellular balance, while the 'meta-host model' broadens the host definition to include symbiotic microbes. The 'health-illness conversion model' encapsulates the innate and adaptive genomes' interplay and dysbiosis patterns. The aim here is to provide a more focused and coherent understanding of microbiome and highlight future research avenues that could lead to a more effective and efficient healthcare system.

Bacterial specialists playing crucial roles in maintaining system stability and governing microbial diversity in bioremediation of oil-polluted sediments under typical deep-sea condition

Ecologically, interactions and contributions of microbiota generalists and specialists remain largely unexplored in remediation of deep-sea oil pollution. Herein, ecological and evolutionary characteristics of the two taxa were comprehensively investigated in restoration of oil-polluted sediment at deep-sea microcosm. Niche-specialized taxa exhibited rapid speciation rate, more complex network structure and highly interspecific mutualism. In contrast, generalists possessed higher richness but with poor local performance, as evidenced by higher extinction rate, lower stability, and more interspecific antagonism. Generalists were the primary oil degraders, while specialists acted as auxiliaries promoting degradation via production of biofilm and biosurfactant. Evolutionarily, the continuous transition from specialists to generalists insured the exclusion of generalist at a relatively constant level for ecological trade-offs. Collectively, the findings emphasize the importance of specialists in facilitating oil degradation by elucidating their vital roles in maintaining system stability and regulating microbial diversity during process, and offer valuable guidance for designing remediation plans.

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 β 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.

Systemic inflammatory response to daily exposure to microcystin-LR and the underlying gut microbial mechanisms

Cyanobacterial toxins have raised global concerns due to potential chronic disease implications from daily drinking water exposure, which remain largely unknown despite extensive research on their acute effects. To understand the mechanisms underlying microcystin-LR (MC-LR)-induced inflammation-associated diseases. Mice were exposed to MC-LR for one year at concentrations comparable to human environmental exposure levels. Comprehensive pathological observation and multi-omics approaches based on 16S rRNA gene sequencing, untargeted metabolomics, transcriptomics and proteomics were conducted across various organs. Daily exposure to MC-LR induced intestinal microbial dysbiosis and colitis-like changes. It also caused systemic chronic inflammation marked by elevated serum levels of inflammatory cytokines, inflammation-associated pathological changes, and identification of infection-related genes/proteins within the gut-brain-spleen-liver axis. Furthermore, multi-omics analysis across organs suggested that Muribaculaceae may promote a systemic infection-inflammatory response, relying on kynurenine metabolites signaling in peripheral tissues. In contrast, Lachnospiraceae may act an opposing role, dependent on intestinal indole derivatives via the neuroimmunomodulation pathway. A fecal microbiota transplantation experiment confirmed that alterations in Muribaculaceae and Lachnospiraceae resulting from exposure to MC-LR triggered the local and systemic chronic inflammation in mice. This study light on the potential strategies employed by gut microbial community in regulating MC-induced inflammation-associated chronic diseases under repeated exposure through drinking water.

Microbiome transition mediated plant immune response to Alternaria solani (Ellis & Martin) Jones & Grout infection in tomato (Solanum lycopersicum L.)

Alternaria solani (Ellis & Martin) Jones & Grout, causing early blight infection in solanaceous crops, is a growing threat influencing sustainable crop production. Understanding the variation in the foliar microbiome, particularly the bacterial community during pathogenesis, can provide critical information on host-pathogen interactions, highlighting the host immune response during pathogen invasion. In the present study, early blight (EB) infection was artificially induced in tomato leaves, and the transition in the foliar bacterial community from healthy leaf tissue to infected leaves was analyzed. The 16s sequencing data revealed a significant shift in alpha and beta diversity, with infected leaf tissue exhibiting considerably lower bacterial abundance and diversity. Further interpretation at the genus level highlighted the possible role of the host immune system in recruiting higher nitrogen-fixing bacteria to resist the pathogen. The study, in addition to analyzing the foliar bacterial community transition during pathogenesis, has also shed light on the possible strategy employed by the host in recruiting selective nutrient-enriching microbes. Further application of this research in developing biocontrol agents with higher microbial host colonizing ability will be of tremendous benefit in achieving sustainable EB control measures.

Extreme trophic tales: deciphering bacterial diversity and potential functions in oligotrophic and hypereutrophic lakes

BACKGROUND

Oligotrophy and hypereutrophy represent the two extremes of lake trophic states, and understanding the distribution of bacterial communities across these contrasting conditions is crucial for advancing aquatic microbial research. Despite the significance of these extreme trophic states, bacterial community characteristics and co-occurrence patterns in such environments have been scarcely interpreted. To bridge this knowledge gap, we collected 60 water samples from Lake Fuxian (oligotrophic) and Lake Xingyun (hypereutrophic) during different hydrological periods.

RESULTS

Employing 16S rRNA gene sequencing, our findings revealed distinct community structures and metabolic potentials in bacterial communities of hypereutrophic and oligotrophic lake ecosystems. The hypereutrophic ecosystem exhibited higher bacterial α- and β-diversity compared to the oligotrophic ecosystem. Actinobacteria dominated the oligotrophic Lake Fuxian, while Cyanobacteria, Proteobacteria, and Bacteroidetes were more prevalent in the hypereutrophic Lake Xingyun. Functions associated with methanol oxidation, methylotrophy, fermentation, aromatic compound degradation, nitrogen/nitrate respiration, and nitrogen/nitrate denitrification were enriched in the oligotrophic lake, underscoring the vital role of bacteria in carbon and nitrogen cycling. In contrast, functions related to ureolysis, human pathogens, animal parasites or symbionts, and phototrophy were enriched in the hypereutrophic lake, highlighting human activity-related disturbances and potential pathogenic risks. Co-occurrence network analysis unveiled a more complex and stable bacterial network in the hypereutrophic lake compared to the oligotrophic lake.

CONCLUSION

Our study provides insights into the intricate relationships between trophic states and bacterial community structure, emphasizing significant differences in diversity, community composition, and network characteristics between extreme states of oligotrophy and hypereutrophy. Additionally, it explores the nuanced responses of bacterial communities to environmental conditions in these two contrasting trophic states.

Enhanced soil microbial stability is associated with soil organic carbon storage under high-altitude forestation

The potential of forestation to mitigate climate warming depends largely on whether it can improve terrestrial carbon (C) storage. Changes in soil microbial stability can cause ecosystem C fluctuations. Unfortunately, it remains unclear whether forestation alters soil microbial stability with cascading effects on C storage in high-altitude ecosystems. In this study, a total of 14 typical planted forests were selected on the Tibetan Plateau. We showed that high-altitude forestation, particularly with poplars, altered the microbial diversity and potentially improved the stability of soil microbial communities. These changes were associated with soil C accumulation and potentially positive feedback on soil organic C storage. Variations in the microbial community stability were mostly caused by changes in soil bulk density and dissolved organic C. Superior network stability was found in fungal community rather than bacterial community. Additionally, there were strong interactions between bacterial and fungal communities that influenced soil C storage. These findings contribute to understand the differences and relationships between bacteria and fungi in plantation soils. This work reveals the potential of high-altitude forestation to mitigate climate warming through insights into the microbial-mediated mechanisms responsible for soil C storage in high-altitude ecosystems.

Bacterial dynamics in the progression of caries to apical periodontitis in primary teeth of children with severe early childhood caries

Background

Early childhood caries (ECC) are a prevalent chronic disease in young children. However, there has been limited research on the microbiota in different tissue levels of the same tooth in children with ECC. This study aimed to investigate the dynamic changes in bacterial diversity during the progression of Severe Early Childhood Caries (S-ECC) within the same tooth, from the tooth surface to the root canal, by collecting tissue samples from different areas of the affected tooth.

Methods

Twenty primary teeth with periapical periodontitis were selected from 20 children aged 3-5 years, with 100 samples collected from the different layers: uncavitated buccal enamel surface without white spot lesion (surface), the outermost layer of the dentin carious lesion (superficial), the inner layer of carious dentin (deep), necrotic pulp tissue (pulp), and root exudate (exudate). The taxonomy of each OTU representative sequence was analyzed against the 16S rRNA database. Comparisons of alpha diversity between groups were performed. The number of shared and unique genera between groups counted. Beta diversity was contrasted to evaluate differences in bacterial community composition, and the relationships between the microbiota and samples were analyzed. The heatmap analysis of the 30 most abundant genera was used, which highlighted their relative distribution and abundance. The significantly abundant taxa (phylum to genera) of bacteria among the different groups were identified. The differences of relative abundance between bacterial genera among the five groups were analyzed. Significant Spearman correlations were noted, and visualization of the co-occurrence network was conducted.

Results

Bacterial 16S rRNA gene sequencing showed that most genera were present in all layers, with the number of shared genera increasing as the disease advanced. The bacterial communities and core genera in the co-occurrence network changed with progression to severe ECC.

Conclusion

An increase in both the quantity and complexity of bacterial interactions was observed. This study emphasized the importance of paying attention to the relationship between microbial species rather than just checking changes in bacterial species structure when investigating the role of bacteria in disease progression.

Networks of human milk microbiota are associated with host genomics, childhood asthma, and allergic sensitization

The human milk microbiota (HMM) is thought to influence the long-term health of offspring. However, its role in asthma and atopy and the impact of host genomics on HMM composition remain unclear. Through the CHILD Cohort Study, we followed 885 pregnant mothers and their offspring from birth to 5 years and determined that HMM was associated with maternal genomics and prevalence of childhood asthma and allergic sensitization (atopy) among human milk-fed infants. Network analysis identified modules of correlated microbes in human milk that were associated with subsequent asthma and atopy in preschool-aged children. Moreover, reduced alpha-diversity and increased Lawsonella abundance in HMM were associated with increased prevalence of childhood atopy. Genome-wide association studies (GWASs) identified maternal genetic loci (e.g., ADAMTS8, NPR1, and COTL1) associated with HMM implicated with asthma and atopy, notably Lawsonella and alpha-diversity. Thus, our study elucidates the role of host genomics on the HMM and its potential impact on childhood asthma and atopy.

Seasonal Dynamics of Eukaryotic Microbial Communities in the Water-Receiving Reservoir of the Long-Distance Water Diversion Project, China

Inter-basin water transfer projects, such as the Yellow River to Qingdao Water Diversion Project (YQWD), are essential for addressing water scarcity, but impact local aquatic ecosystems. This study investigates the seasonal characteristics of eukaryotic microbial communities in the Jihongtan Reservoir, the main water-receiving body of YQWD, over a one-year period using 18S rDNA amplicon sequencing. The results showed that the eukaryotic microbial diversity did not exhibit significant seasonal variation (p > 0.05), but there was a notable variance in the community structure (p < 0.05). Arthropoda and Paracyclopina, representing the most dominant phylum and the most dominant genus, respectively, both exhibited the lowest abundance during the winter. The Chlorophyta, as the second-dominant phylum, demonstrates its higher abundance in the spring and winter. The Mantel test and PLS-PM (Partial Least Squares Path Modeling) revealed that water temperature (WT), dissolved oxygen (DO), and pH influenced the seasonal dynamic of eukaryotic microbial communities significantly, of which WT was the primary driving factor. In addition to environmental factors, water diversion is likely to be an important influencing factor. The results of the co-occurrence network and robustness suggested that the spring network is the most complex and exhibits the highest stability. Moreover, keystone taxa within networks have been identified, revealing that these key groups encompass both abundant and rare species, with specificity to different seasons. These insights are vital for understanding the seasonal variation of microbial communities in the Jihongtan Reservoir during ongoing water diversions.

From nets to networks: tools for deciphering phytoplankton metabolic interactions within communities and their global significance

Our oceans are populated with a wide diversity of planktonic organisms that form complex dynamic communities at the base of marine trophic networks. Within such communities are phytoplankton, unicellular photosynthetic taxa that provide an estimated half of global primary production and support biogeochemical cycles, along with other essential ecosystem services. One of the major challenges for microbial ecologists has been to try to make sense of this complexity. While phytoplankton distributions can be well explained by abiotic factors such as temperature and nutrient availability, there is increasing evidence that their ecological roles are tightly linked to their metabolic interactions with other plankton members through complex mechanisms (e.g. competition and symbiosis). Therefore, unravelling phytoplankton metabolic interactions is the key for inferring their dependency on, or antagonism with, other taxa and better integrating them into the context of carbon and nutrient fluxes in marine trophic networks. In this review, we attempt to summarize the current knowledge brought by ecophysiology, organismal imaging, in silico predictions and co-occurrence networks using 'omics data, highlighting successful combinations of approaches that may be helpful for future investigations of phytoplankton metabolic interactions within their complex communities.This article is part of the theme issue 'Connected interactions: enriching food web research by spatial and social interactions'.

Impact of climate warming on soil microbial communities during the restoration of the inner Mongolian desert steppe

Introduction

Grazer exclosure is widely regarded as an effective measure for restoring degraded grasslands, having positive effects on soil microbial diversity. The Intergovernmental Panel on Climate Change (IPCC) predicts that global surface temperatures will increase by 1.5-4.5°C by the end of the 21st century, which may affect restoration practices for degraded grasslands. This inevitability highlights the urgent need to study the effect of temperature on grassland soil microbial communities, given their critical ecological functions.

Methods

Here, we assessed the effects of heavy grazing (control), grazer exclosure, and grazer exclosure plus warming by 1.5°C on soil microbial community diversity and network properties as well as their relationships to soil physicochemical properties.

Results and discussion

Our results showed that grazer closure increased soil microbial richness relative to heavy grazing controls. Specifically, bacterial richness increased by 7.9%, fungal richness increased by 20.2%, and the number of fungal network nodes and edges increased without altering network complexity and stability. By contrast, grazer exclosure plus warming decreased bacterial richness by 9.2% and network complexity by 12.4% compared to heavy grazing controls, while increasing fungal network complexity by 25.8%. Grazer exclosure without warming increased soil ammonium nitrogen content, while warming increased soil nitrate nitrogen content. Soil pH and organic carbon were not affected by either exclosure strategy, but nitrate nitrogen was the dominant soil factor explaining changes in bacterial communities.

Conclusion

Our findings show that grazer exclosure increases soil microbial diversity which are effective soil restoration measures for degraded desert steppe, but this effect is weakened under warming conditions. Thus, global climate change should be considered when formulating restoration measures for degraded grasslands.

Cadmium contamination decreased bacterial network complexity and stability in coastal reclamation areas

Cadmium(Cd) contamination can exert significantly adverse effects on soil microbiota in reclaimed areas, however, its effects on bacterial network structure are still limitedly understood. Here we collected soil samples from typical reclaimed wetlands (RW) and ditch wetlands (DW) in coastal reclamation areas and examined the effects of Cd contamination on the bacterial network complexity and stability. The results showed that the bacterial networks were destabilized by the Cd contamination, while bacteria in DW soils showed robust invulnerability characterized by higher node constancy and compositional stability compared with RW soils. Soil bacteria resisted Cd stress by forming a network with intensive connections in the module but sparser connections among the modules. Especially, network modularity was higher in DW soils than in RW soils, but made it more vulnerable to nodes removal. In addition, Cd contamination promoted bacterial positive cohesion but decreased negative cohesion in RW soils. Flavobacteriaceae, Xanthomonadaceae, and Alcaligenaceae were identified as core phylotypes, which played pivotal roles in regulating interspecies interactions due to higher contributions to cohesion and significant correlations with soil nutrients. The findings of this work indicate the changes of bacterial network structure and the indispensable role of core phylotypes in regulating interactions and maintaining network sustainability under Cd contamination.

Comprehensive multi-omics investigation of sub-chronic toxicity induced by Cadmium and Triazophos Co-exposure in hook snout carps (Opsariichthys bidens)

The coexistence of heavy metals and pesticides poses a critical challenge in agricultural ecosystems. Traditional toxicity assessments often focus only on the individual impacts of either pesticides or heavy metals. Here, the untargeted metabolomics and 16 S rRNA sequencing were used to assess the individual and combined effects of cadmium (Cd) and triazophos (TRI) on hook snout carps (Opsariichthys bidens). Cd caused much more serious impacts on hepatic metabolism and gut microbiota than those in TRI. Combined Cd and TRI exposure synergistically affected hepatic metabolism, causing mitochondrial dysfunction and even oxidative damage. Simultaneously, 16 S rRNA sequencing highlighted significant variations in the composition and abundance of gut microbiota. A noteworthy connection emerged between these distinct microbiota profiles and disruptions in energy metabolism, ultimately leading to disorders in metabolites. These findings enhanced the understanding of risks posed by heavy metals and pesticides, providing insights for better environmental risk assessments of aquatic organisms.

Differential interactions of Rickettsia species with tick microbiota in Rh. sanguineus and Rh. turanicus

Tick-borne rickettsioses, caused by Gram-negative bacteria of the Rickettsia genus, pose a growing global threat, with various arthropod vectors contributing to their transmission. Understanding the complex interactions within tick microbiota, including the role of Rickettsia species, is crucial for elucidating the dynamics of rickettsial diseases. Here, we investigate the taxonomic profiles and co-occurrence networks of Rickettsia in Rh. sanguineus sensus lato (s.l.) and Rh. turanicus ticks, revealing significant differences in community composition and local connectivity of Rickettsia species. While the microbiota of both tick species share common taxa, distinct differences in relative abundance and network topology suggest unique ecological niches. Moreover, robustness analysis demonstrates varying resilience to perturbations, indicating different strategies for network organization. Our findings also highlight metabolic differences between tick species, suggesting potential implications for Rickettsia interactions. Overall, this study provides insights into the intricate microbial landscape within ticks, shedding light on the functional redundancy and metabolic pathways associated with Rickettsia, thus advancing our understanding of tick-borne diseases.

Deciphering the differences of bacterial communities between high- and low-productive wheat fields using high-throughput sequencing

Microbial communities have been demonstrated to be essential for healthy and productive soil ecosystems. However, an understanding of the relationship between soil microbial community and soil productivity levels is remarkably limited. In this study, bulk soil (BS), rhizosphere soil (RS), and root (R) samples from the historical high-productive (H) and low-productive (L) soil types of wheat in Hebei province of China were collected and analyzed by high-throughput sequencing. The study highlighted the richness, diversity, and structure of bacterial communities, along with the correlation networks among different bacterial genera. Significant differences in the bacterial community structure between samples of different soil types were observed. Compared with the low-productive soil type, the bacterial communities of samples from the high-productive soil type possessed high species richness, low species diversity, complex and stable networks, and a higher relative abundance of beneficial microbes, such as Pseudoxanthomonas, unclassified Vicinamibacteraceae, Lysobacter, Massilia, Pseudomonas, and Bacillus. Further analysis indicated that the differences were mainly driven by soil organic matter (SOM), available nitrogen (AN), and electrical conductivity (EC). Overall, the soil bacterial community is an important factor affecting soil health and crop production, which provides a theoretical basis for the targeted regulation of microbes in low-productivity soil types.

Effect of different vegetation restoration patterns on community structure and co-occurrence networks of soil fungi in the karst region

Introduction

The Grain for Green Project (GGP) by the Chinese government was an important vegetation restoration project in ecologically fragile and severely degraded karst regions. Soil fungi play a facilitating role in the cycling of nutrients both above and below the ground, which is crucial for maintaining ecosystem function and stability. In karst regions, their role is particularly critical due to the unique geological and soil characteristics, as they mitigate soil erosion, enhance soil fertility, and promote vegetation growth. However, little is known about how the implementation of this project shifts the co-occurrence network topological features and assembly processes of karst soil fungi, which limits our further understanding of karst vegetation restoration.

Methods

By using MiSeq high-throughput sequencing combined with null model analysis technology, we detected community diversity, composition, co-occurrence networks, and assembly mechanisms of soil fungi under three GGP patterns (crop, grassland, and plantation) in the southwestern karst region.

Results

Ascomycota and Basidiomycota were the main fungal phyla in all the karst soils. Returning crop to plantation and grassland had no significant effect on α diversity of soil fungi (P > 0.05), but did significantly affect the β diversity (P = 0.001). Soil moisture and total nitrogen (TN) were the main factors affecting the community structure of soil fungi. Compared with crop, soil fungi networks in grassland and plantation exhibited a higher nodes, edges, degree, and relatively larger network size, indicating that vegetation restoration enhanced fungal interactions. The soil fungi networks in grassland and plantation were more connected than those in crop, implying that the interaction between species was further strengthened after returning the crop to plantation and grassland. In addition, null-model analysis showed that the assembly process of soil fungal communities from crop to grassland and plantation shifted from an undominant process to dispersal limitation.

Discussion

These data indicated that GGP in karst region changed the composition and assembly mechanisms of the soil fungal community and enhanced the interaction between fungal species, which can contribute to a better understanding of the fungal mechanisms involved in the restoration of degraded karst soils through vegetation recovery.

Role of bacterial pathogens in microbial ecological networks in hydroponic plants

Plant-associated microbial communities are crucial for plant growth and health. However, assembly mechanisms of microbial communities and microbial interaction patterns remain elusive across vary degrees of pathogen-induced diseases. By using 16S rRNA high-throughput sequencing technology, we investigated the impact of wildfire disease on the microbial composition and interaction network in plant three different compartments. The results showed that pathogen infection significantly affect the phyllosphere and rhizosphere microbial community. We found that the primary sources of microbial communities in healthy and mildly infected plants were from the phyllosphere and hydroponic solution community. Mutual exchanges between phyllosphere and rhizosphere communities were observed, but microbial species migration from the leaf to the root was rarely observed in severely infected plants. Moreover, wildfire disease reduced the diversity and network complexity of plant microbial communities. Interactions among pathogenic bacterial members suggested that Caulobacter and Bosea might be crucial "pathogen antagonists" inhibiting the spread of wildfire disease. Our study provides deep insights into plant pathoecology, which is helpful for the development of novel strategies for phyllosphere disease prediction or prevention.

Exploring optimal incubation conditions and characteristics of methane oxidizing organisms in deep-sea environments

Anaerobic methanotrophic archaea (ANME) play key roles in buffering the methane budget in the deep-sea environment. This study aimed to explore the optimal environmental conditions for ANME enrichment. The result showed that the sample at 10.5 MPa contained the largest copy numbers of methyl-coenzyme M reductase alpha subunit (mcrA) gene (1.1 × 106 copies/g) compared to any other pressures and the sample at 4 °C contained higher mcrA gene (1.6 × 106 copies/g) than other temperatures. The optimal enrichment pressure for ANME-2c is 10.5 MPa at 4 °C, with an optimal subsequent incubation for ANME-2c less than 211days. Moreover, the beta nearest taxon index was significantly correlated with the incubation time (P<0.05). Total inorganic carbon and sulfate ion were key environmental factors driving community construction. This study offers insights into how ANME-2c was enriched and how species coexist in shared habitats during enrichment.

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.

Differential responses of soil bacteria, fungi and protists to root exudates and temperature

The impact of climate warming on soil microbes has been well documented, with studies revealing its effects on diversity, community structure and network dynamics. However, the consistency of soil microbial community assembly, particularly in response to diverse plant root exudates under varying temperature conditions, remains an unresolved issue. To address this issue, we employed a growth chamber to integrate temperature and root exudates in a controlled experiment to examine the response of soil bacteria, fungi, and protists. Our findings revealed that temperature independently regulated microbial diversity, with distinct patterns observed among bacteria, fungi, and protists. Both root exudates and temperature significantly influenced microbial community composition, yet interpretations of these factors varied among prokaryotes and eukaryotes. In addition to phototrophic bacteria and protists, as well as protistan consumers, root exudates determined to varying degrees the enrichment of other microbial functional guilds at specific temperatures. The effects of temperature and root exudates on microbial co-occurrence patterns were interdependent; root exudates primarily simplified the network at low and high temperatures, while responses to temperature varied between single and mixed exudate treatments. Moreover, temperature altered the composition of keystone species within the microbial network, while root exudates led to a decrease in their number. These results emphasize the substantial impact of plant root exudates on soil microbial community responses to temperature, underscoring the necessity for future climate change research to incorporate additional environmental variables.

Graphene oxide inhibits the transfer of ARGs in rice by reducing the root endophytic bacterial complexity

Antibiotic resistance genes (ARGs) as an emerging contaminant have attracted much attention for their transfer in agricultural ecosystems. Meanwhile, graphene oxide (GO), due to its high adsorption capacity and antibacterial properties, poses potential environmental ecological risks to the occurrence of ARGs, bacteria, and plant physiological ecology. However, the impact and mechanism of GO on the transfer of ARGs in host plants remain unclear. Therefore, this study selected rice as the research object and inoculated Bacillus subtilis carrying ARGs to investigate the influence of GO on the migration of ARGs into rice and its microbiological mechanism. The study found that GO had a certain inhibitory effect on the transfer of ARGs in rice. Although GO reduced the rhizosphere pH in rice, leading to a transition in endophytic bacteria from dominance by Burkholderia to dominance by Gordonia, this process did not directly affect the transfer of ARGs in rice. Further analysis of bacterial interactions revealed that GO could inhibit the transfer of ARGs in rice by reducing the network complexity of endophytic bacteria. Additionally, GO inhibited the formation of endophytic bacterial biofilms and mobile elements, which might affect ARGs' migration in rice. This study elucidated the key microbiological ecological processes of GO on the transfer of ARGs in rice, providing fundamental information for the ecological risk assessment of GO.

Disentangling the factors defining Bacillus subtilis group species abundance in natural soils

Bacillus subtilis is ubiquitously and broadly distributed in various environments but is mostly isolated from soil. Given that B. subtilis is known as a plant growth-promoting rhizobacterium in agriculture, we aimed to describe the natural distribution of this species and uncover how biotic and abiotic factors affect its distribution. When comparing different soils, we discovered that B. subtilis group species are most abundant in grasslands but can rarely be isolated from forest soil, even if the soil sample sites are situated in proximity. Differential analysis revealed that spore-forming bacteria exhibited enrichments in the grassland, suggesting niche overlap or synergistic interactions leading to the proliferation of certain Bacillus species in grassland environments. Network analysis further revealed that Bacillus and other Bacillota established a densely interconnected hub module in the grassland, characterised by positive associations indicating co-occurrence, a pattern not observed in the forest soil. Speculating that this difference was driven by abiotic factors, we combined amplicon sequencing with physico-chemical analysis of soil samples and found multiple chemical variables, mainly pH, to affect microbial composition. Our study pinpoints the factors that influence B. subtilis abundance in natural soils and, therefore, offers insights for designing B. subtilis-based biocontrol products in agricultural settings.

Intensified river salinization alters nitrogen-cycling microbial communities in arid and semi-arid regions of China

Freshwater salinization is receiving increasing global attention due to its profound influence on nitrogen cycling in aquatic ecosystems and the accessibility of water resources. However, a comprehensive understanding of the changes in river salinization and the impacts of salinity on nitrogen cycling in arid and semi-arid regions of China is currently lacking. A meta-analysis was first conducted based on previous investigations and found an intensification in river salinization that altered hydrochemical characteristics. To further analyze the impact of salinity on nitrogen metabolism processes, we evaluated rivers with long-term salinity gradients based on in situ observations. The genes and enzymes that were inhibited generally by salinity, especially those involved in nitrogen fixation and nitrification, showed low abundances in three salinity levels. The abundance of genes and enzymes with denitrification and dissimilatory nitrate reduction to ammonium functions still maintained a high proportion, especially for denitrification genes/enzymes that were enriched under medium salinity. Denitrifying bacteria exhibited various relationships with salinity, while dissimilatory nitrate reduction to ammonium bacterium (such as Hydrogenophaga and Curvibacter carrying nirB) were more inhibited by salinity, indicating that diverse denitrifying bacteria could be used to regulate nitrogen concentration. Most genera exhibited symbiotic and mutual relationships, and the highest proportion of significant positive correlations of abundant genera was found under medium salinity. This study emphasizes the role of river salinity on environment characteristics and nitrogen transformation rules, and our results are useful for improving the availability of river water resources in arid and semi-arid regions.

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.

Deciphering the role of rhizosphere microbiota in modulating disease resistance in cabbage varieties

BACKGROUND

Cabbage Fusarium wilt (CFW) is a devastating disease caused by the soil-borne fungus Fusarium oxysporum f. sp. conglutinans (Foc). One of the optimal measures for managing CFW is the employment of tolerant/resistant cabbage varieties. However, the interplay between plant genotypes and the pathogen Foc in shaping the rhizosphere microbial community, and the consequent influence of these microbial assemblages on biological resistance, remains inadequately understood.

RESULTS

Based on amplicon metabarcoding data, we observed distinct differences in the fungal alpha diversity index (Shannon index) and beta diversity index (unweighted Bray-Curtis dissimilarity) within the rhizosphere of the YR (resistant to Foc) and ZG (susceptible to Foc) cabbage varieties, irrespective of Foc inoculation. Notably, the Shannon diversity shifts in the resistant YR variety were more pronounced following Foc inoculation. Disease-resistant plant variety demonstrate a higher propensity for harboring beneficial microorganisms, such as Pseudomonas, and exhibit superior capabilities in evading harmful microorganisms, in contrast to their disease-susceptible counterparts. Furthermore, the network analysis was performed on rhizosphere-associated microorganisms, including both bacteria and fungi. The networks of association recovered from YR exhibited greater complexity, robustness, and density, regardless of Foc inoculation. Following Foc infection in the YR rhizosphere, there was a notable increase in the dominant bacterium NA13, which is also a hub taxon in the microbial network. Reintroducing NA13 into the soil significantly improved disease resistance in the susceptible ZG variety, by directly inhibiting Foc and triggering defense mechanisms in the roots.

CONCLUSIONS

The rhizosphere microbial communities of these two cabbage varieties are markedly distinct, with the introduction of the pathogen eliciting significant alterations in their microbial networks which is correlated with susceptibility or resistance to soil-borne pathogens. Furthermore, we identified a rhizobacteria species that significantly boosts disease resistance in susceptible cabbages. Our results indicated that the induction of resistance genes leading to varied responses in microbial communities to pathogens may partly explain the differing susceptibilities of the cabbage varieties tested to CFW. Video Abstract.

Time-series sewage metagenomics distinguishes seasonal, human-derived and environmental microbial communities potentially allowing source-attributed surveillance

Sewage metagenomics has risen to prominence in urban population surveillance of pathogens and antimicrobial resistance (AMR). Unknown species with similarity to known genomes cause database bias in reference-based metagenomics. To improve surveillance, we seek to recover sewage genomes and develop a quantification and correlation workflow for these genomes and AMR over time. We use longitudinal sewage sampling in seven treatment plants from five major European cities to explore the utility of catch-all sequencing of these population-level samples. Using metagenomic assembly methods, we recover 2332 metagenome-assembled genomes (MAGs) from prokaryotic species, 1334 of which were previously undescribed. These genomes account for ~69% of sequenced DNA and provide insight into sewage microbial dynamics. Rotterdam (Netherlands) and Copenhagen (Denmark) show strong seasonal microbial community shifts, while Bologna, Rome, (Italy) and Budapest (Hungary) have occasional blooms of Pseudomonas-dominated communities, accounting for up to ~95% of sample DNA. Seasonal shifts and blooms present challenges for effective sewage surveillance. We find that bacteria of known shared origin, like human gut microbiota, form communities, suggesting the potential for source-attributing novel species and their ARGs through network community analysis. This could significantly improve AMR tracking in urban environments.

Metagenomic discovery of microbial eukaryotes in stool microbiomes

Host-associated microbiota form complex microbial communities that are increasingly associated with host behavior and disease. While these microbes include bacterial, archaeal, viral, and eukaryotic constituents, most studies have focused on bacteria due to their dominance in the human host and available tools for investigation. Accumulating evidence suggests microbial eukaryotes in the microbiome play pivotal roles in host health, but our understandings of these interactions are limited to a few readily identifiable taxa because of technical limitations in unbiased eukaryote exploration. Here, we combined cell sorting, optimized eukaryotic cell lysis, and shotgun sequencing to accelerate metagenomic discovery and analysis of host-associated microbial eukaryotes. Using synthetic communities with a 1% microbial eukaryote representation, the eukaryote-optimized cell lysis and DNA recovery method alone yielded a 38-fold increase in eukaryotic DNA. Automated sorting of eukaryotic cells from stool samples of healthy adults increased the number of microbial eukaryote reads in metagenomic pools by up to 28-fold compared to commercial kits. Read frequencies for identified fungi increased by 10,000× on average compared to the Human Microbiome Project and allowed for the identification of novel taxa, de novo assembly of contigs from previously unknown microbial eukaryotes, and gene prediction from recovered genomic segments. These advances pave the way for the unbiased inclusion of microbial eukaryotes in deciphering determinants of health and disease in the host-associated microbiome.IMPORTANCEMicrobial eukaryotes are common constituents of the human gut where they can contribute to local ecology and host health, but they are often overlooked in microbiome studies. The lack of attention is due to current technical limitations that are heavily biased or poorly recovered DNA from microbial eukaryotes. We developed a method to increase the representation of these eukaryotes in metagenomic sequencing of microbiome samples that allows to improve their detection compared to prior methods and allows for the identification of new species. Application of the technique to gut microbiome samples improved detection of fungi, protists, and helminths. New eukaryotic taxa and their encoded genes could be identified by sequencing a small number of samples. This approach can improve the inclusion of eukaryotes into microbiome research.

Polysaccharides induce deep-sea Lentisphaerae strains to release chronic bacteriophages

Viruses are ubiquitous in nature and play key roles in various ecosystems. Notably, some viruses (e.g. bacteriophage) exhibit alternative life cycles, such as chronic infections without cell lysis. However, the impact of chronic infections and their interactions with the host organisms remains largely unknown. Here, we found for the first time that polysaccharides induced the production of multiple temperate phages infecting two deep-sea Lentisphaerae strains (WC36 and zth2). Through physiological assays, genomic analysis, and transcriptomics assays, we found these bacteriophages were released via a chronic style without host cell lysis, which might reprogram host polysaccharide metabolism through the potential auxiliary metabolic genes. The findings presented here, together with recent discoveries made on the reprogramming of host energy-generating metabolisms by chronic bacteriophages, shed light on the poorly explored marine virus-host interaction and bring us closer to understanding the potential role of chronic viruses in marine ecosystems.

One-year monitoring of grass-type architectural waterscapes with long-term operation: Water quality and microorganism

Grass-type architectural waterscapes (GAWs) utilize submerged plants to enhance self-purification ability and maintain a clear-water state. However, knowledge about their long-term water quality and microbial community dynamics remains limited. This study monitored the water quality, microbial community composition, and networks in two GAWs. GAW1 consisted solely Hydrilla verticillata with a water depth of 0.70 m, while GAW2 primarily contained Vallisneria natans, Microsorum pteropus, and Aquarius grisebachii with a water depth of 0.30 m. Results show that both water depth and submerged plant species play crucial roles in GAW establishment. The water depth of 0.7 m enabled Hydrilla verticillata to thrive underwater despite temperature variations, which demonstrated excellent nutrient uptake capacity. Thus, GAW1 exhibited superior self-purification ability, consistently meeting Class III standard for surface water in China. In contrast, GAW2 had a shallow water depth and contained ornamental plants, only meeting Class V standard. Furthermore, microbial communities were shaped by water quality, with distinct enriched genera serving as potential "microbial indicators". Enrichment of the hgcI clade and Sporichthyaceae_unclassified indicated superior water quality in GAW1, while prevalence of Comamonadaceae_unclassified, Flavobacterium, Rhodoluna, and Pseudarcicella suggested poor water quality in GAW2. Additionally, highly complex and connected microbial networks suggested elevated pollutant levels in GAWs. This study emphasized the significance of submerged plant species and water depth in GAWs construction and highlighted microbial communities and networks as potential indicators of water quality.

Integration of soil microbiology and metabolomics to elucidate the mechanism of the accelerated infestation of tobacco by the root-knot nematode

Introduction

Tobacco root-knot nematode (TRKN) disease is a soil-borne disease that presents a major hazard to the cultivation of tobacco, causing significant reduction in crop quality and yield, and affecting soil microbial diversity and metabolites. However, differences in rhizosphere soil microbial communities and metabolites between healthy tobacco soils and tobacco soils with varying degrees of TRKN infection remain unclear.

Methods

In this study, diseased rhizosphere soils of tobacco infected with different degrees of TRKN [severally diseased (DH) soils, moderately diseased (DM) soils, and mildly diseased (DL) soils] and healthy (H) rhizosphere soils were collected. Here, we combined microbiology with metabolomics to investigate changes in rhizosphere microbial communities and metabolism in healthy and TRKN-infected tobacco using high-throughput sequencing and LC-MS/MS platforms.

Results

The results showed that the Chao1 and Shannon indices of bacterial communities in moderately and mildly diseased soils were significantly higher than healthy soils. The Proteobacteria, Actinobacteria, Ascomycota, Burkholderia, Bradyrhizobium and Dyella were enriched in the rhizosphere soil of healthy tobacco. Basidiomycota, Agaricales, Pseudeurotiaceae and Ralstonia were enriched in severally diseased soils. Besides, healthy soils exhibited a relatively complex and interconnected network of bacterial molecular ecologies, while in severally and moderately diseased soils the fungal molecular networks are relatively complex. Redundancy analysis showed that total nitrogen, nitrate nitrogen, available phosphorus, significantly affected the changes in microbial communities. In addition, metabolomics results indicated that rhizosphere soil metabolites were significantly altered after tobacco plants were infected with TRKNs. The relative abundance of organic acids was higher in severally diseased soils. Spearman's analyses showed that oleic acid, C16 sphinganine, 16-hydroxyhexadecanoic acid, D-erythro-3-methylmalate were positively correlated with Basidiomycota, Agaricales, Ralstonia.

Discussion

In conclusion, this study revealed the relationship between different levels of TRKN invasion of tobacco root systems with bacteria, fungi, metabolites and soil environmental factors, and provides a theoretical basis for the biological control of TRKN disease.