Molecular ecological network analyses

Recruiting high-efficiency denitrifying consortia using Pseudomonas aeruginosa

Synthesizing the microbial community with a high denitrifying capacity is the key for achieving efficient removal of nitrogen species in wastewater treatment plants. Here, we integrated the evolutionary top-down enrichment and bottom-up bioaugmentation to construct a high-efficiency Pseudomonas-recruited denitrifying consortium (PRDC). A PRDC with a high specific denitrification rate of 109.49 ± 10.58 mg N/(g MLVSS·h) was enriched after 181 days of microbiota construction with pre-inoculation of Pseudomonas strain onto carriers. The 16S rRNA gene sequencing analysis suggested that the pre-inoculated Pseudomonas was quickly washed out and replaced by dominant denitrifying genera, such as Halomonas and Thauera, under different hydraulic retention times (HRTs). The pre-inoculated Pseudomonas can facilitate PRDC by providing public goods, but compromising its nutrient requirements. The dominant community assembly processes switched from homogeneous selection to ecological drift and dispersal limitation under shortened HRT. Furthermore, a shortened HRT facilitated the colonization of new immigrants and intensified their competition with the pre-existing dominant denitrifiers. The PRDC carriers achieved a 1.65-fold enhancement in sludge denitrification and reduced the corresponding chemical oxygen demand consumption at a carrier filling ratio of 30%. Overall, our study developed a novel technique using Pseudomonas aeruginosa as a trigger to enrich high-efficiency denitrifying consortia for wastewater treatment.

Integrating network and in-silico simulation insights into the ecological interactions shaped by carbon sources in partial denitrification and anammox system

The underlying ecological mechanism of microbial communities shaped by carbon source in partial denitrification and anammox (PDA) systems remains poorly understood, despite the potential of multiple carbon sources to support the partial denitrification process. Herein, the integrated network and in-silico simulation methods were used to evaluate the considerable impact of carbon sources on the dynamics of ecological interactions. The fluctuation of carbon source (from acetate to glucose and ethanol) significantly destabilized the performance of PDA system (total nitrogen removal efficiency decreased from 96.8% to 69.1%). Glucose simultaneously altered the composition of denitrifying bacteria, resulting in a significant enrichment of the genus Elstera (from 0% to 12.7%). By contrast, genus Thauera re-dominated for partial denitrification with ethanol as carbon source. Importantly, heterotrophic bacteria (e.g., genus Calditrichia) gradually enriched by utilizing ethanol. The presence of acetate in phase IV further enhanced the competitive advantage of heterotrophic bacteria over denitrifying bacteria, thereby resulting in the deteriorated performance of the PDA system. The in-silico simulation of co-culture further revealed that the overgrowth of auxotrophic species Calditrichia utilized amounts of nutrients and limited other functional bacteria. Additionally, the whole co-occurrence network indicated that positive interactions likely improved the adaptability of anammox bacteria under the unsteady conditions. This study provides profound insights into the ecological interactions shaped by carbon sources in PDA systems and underscores the necessity of comprehensive review of the external carbon source to ensure optimal performance.

Long-term response mechanism of bacterial communities to chemical oxidation remediation in petroleum hydrocarbon contaminated groundwater

The limited understanding of microbial response mechanism remains as a bottleneck to evaluate the long-term remediation effectiveness of in situ chemical oxidation in contaminated groundwater. In this study, we investigated long-term response of bacterial communities throughout five remediation stages of pre-oxidation, early-oxidation, late-oxidation, early-recovery and late-recovery. By analyzing bacterial biomass, taxa, diversity and metabolic functions, this work identified the consistently suppressed glyceraldehyde-3-phosphate dehydrogenase pathway and the enrichment of naphthalene degradation pathways for secondary products, suggesting persistent oxidation stress and enhanced microbial utilization of lower-molecular weight carbon sources at the oxidation and early-recovery stages. The dominant microbial clusters shifted from r-strategists to K-strategists and then back to r-strategists, indicating their higher degradation efficiency of petroleum hydrocarbons throughout the oxidation process. The changes in stability and stochastic assembly of bacterial communities during in situ chemical oxidation suggested that oxidative stress, carbon source addition and carbon source limitation as the main influential factors of bacterial community succession at the oxidation, early-recovery and late-recovery stage, respectively. Our findings highlighted the complex recovery and underlying mechanisms of groundwater bacterial communities during in situ chemical oxidation process, and provided valuable insights for effective and long-term site management after in situ chemical oxidation practices.

Microbial metabolism in wormcast affected the perturbation on soil organic matter by microplastics under decabromodiphenyl ethane stress

Large-scale plastic wastes annually inevitably induce co-pollution of microplastics (MPs) and novel brominated flame retardants (NBFRs), while gaps remain concerning their effect on terrestrial function. We investigated the impact of polylactic acid (PLA) or polyethylene (PE) MPs after aging in soil-earthworm microcosms under decabromodiphenyl ethane (DBDPE) contamination. MPs altered the food (i.e. soil) of earthworms and affected cast composition, which in turn further affected soil function. After 28 days of exposure, MPs, especially UV-aged MPs, caused the significant enrichment of plastics-degrading bacteria and C/N cycling functions in wormcast, with increased dissolved organic matter consumption after co-exposure (1 % MPs accompanied by 10 mg kg-1 DBDPE). Aging significantly affected soil carbon sequestration, while its effects varied depending on the types of MPs. Notably, soil organic matter was the most impactor affecting wormcast bacteria, highlighting the importance of earthworm's activity on soil carbon. In comparison, PLA-MPs induced stronger responses to the C/N cycling process based on its biodegradable property than PE-MPs, however, aging had a greater effect on PE-MPs due to the formation of oxygen molecules from nothing in the structure. This study expands our current understanding of the interactions of aged MPs and DBDPE in the terrestrial ecosystem. SYNOPSIS: This study highlighted that both MPs before and aging altered the bacterial communities in wormcast and further affected soil ecology during earthworm feeding and excretion.

Effects of herbicide mixtures on the diversity and composition of microbial community and nitrogen cycling function on agricultural soil: A field experiment in Northeast China

Herbicide mixtures application is a widespread and effective practice in modern agriculture; however, a knowledge gap exists regarding the potential ecotoxicological effects of herbicide mixtures in agricultural systems. Here, the effects of various doses of herbicide mixtures (atrazine, nicosulfuron, and mesotrione) under different varieties of maize cultivation on the structure and function of microbial communities and soil chemical parameters were clarified through field experiments. The results showed that the application of herbicide mixtures increased the bacterial and fungal community alpha diversity at jointing and maturity, indicating a prolonged effect of the herbicide mixtures. Moreover, herbicide mixtures alter the composition of bacterial and fungal communities, with sensitive taxa suppressed and herbicide-tolerant taxa enriched. The herbicide mixtures significantly reduced the abundances of Bacillus even at lower doses, but Penicillum was enriched. FAPROTAX analysis and quantitative PCR (qPCR) results showed that herbicide mixtures inhibited the soil nitrogen-cycle process and related genes AOA-amoA, AOB-amoA, and nifH at maize seedling stage. Moreover, network analysis showed that low concentrations of the herbicide mixtures increased bacterial interactions while high concentrations inhibited them, which indicated that the network complexity may be herbicide concentration dependent. A synthetic community (SynCom) consisting of six bacterial strains was established for the biodegradation of the herbicide mixtures based on the analysis of the bacterial network, which resulted in an increase in the degradation efficiency of nicosulfuron by 15.90%. Moreover, potted maize experiment showed that the addition of the SynCom alleviated the toxic effects of herbicide mixtures on the plants. In summary, this study provides a comprehensive perspective for assessing the ecological risk at taxonomic and functional levels and the biodegradation approach of herbicide mixtures residue on agricultural soils in Northeastern China.

The community dynamic alterations mechanisms of traveling plastics in the Pearl River estuary with the salinity influence

Most ocean plastics originate from terrestrial emissions, and the plastisphere on the plastics would alter during the traveling due to the significant differences in biological communities between freshwater and marine ecosystems. Microorganisms are influenced by the increasing salinity during traveling. To understand the contribution of plastic on the alteration in biological communities of plastisphere during traveling, this study investigated the alterations in microbial communities on plastics during the migration from freshwater to brackish water and saltwater. The results revealed that the migrated plastics can form unique microhabitats with high bacterial and eukaryotic diversity. Compared with the natural carrier (stone), the communities in plastisphere had fewer variations with salinity, indicating that plastisphere can offer stronger protection for freshwater organisms. The hydrophobicity of plastics promoted algal colonization, providing a stable nutrient source for the community during salinity fluctuations. This reduced material exchange between the plastisphere and the surrounding high-salinity environment, facilitating greater community stability. Additionally, the abundant Ochrophyta and Bryozoa of eukaryotes on migrated plastics can facilitate further colonization and promote species diversity. Plastisphere microbial networks revealed that the reduction of salt-intolerant organisms during traveling had fewer effects on the abundance of associated organisms. A more stable community on migrated plastics led to the proliferation of pathogens and carbon cycle-degrading microorganisms. And the increasing relative abundance of carbon cycling functions indicated that the traveling plastics could pose higher environmental risks and exhibit enhanced carbon metabolic capabilities. The study highlighted the biofilms on migrated plastics as a unique ecological niche in estuarine environments, offering a crucial reference for evaluating the ecological risks linked to plastic travel from rivers to the ocean.

Deposited dead algae influence the microbial communities and functional potentials on the surface sediment in eutrophic shallow lakes

Dead algae deposition will change the nutrient transformation on the sediment-water interface. However, the key factors that drive nutrient turnover, particularly the influence of sediment microbiota, remain poorly understood. As a result, this study conducted an 80-day simulated incubation to investigate the effect of different deposition of death algae on microbial communities and functional potentials in sediments. It was revealed that dead algae deposition changed the microbial communities and interactions. Changes in the bacteria are not only reflected in community composition and diversity but also in the interrelation among bacteria taxa, while changes in the fungi are mainly reflected in the interrelation among fungi taxa. Meanwhile, dead algae deposition increased the abundance of mostly functional genes related to the C, N, P, and S cycle processes and improved the function potentials of microorganisms. Both of them led to the increase of PO43-, NO3-, NH4+, and TOC content in the overlying water, influencing the nutrient cycle processes. Moreover, partial least squares path modeling indicated which key factors are to influence different nutrient cycle processes. Sediment nutrients directly influenced the P cycle process, whereas the C, N, and S cycle processes were directly affected by the changes in biological properties. These results provide a new perspective on the effects of dead algal deposition on the sediment nutrient cycle processes mediated by the sediment microbiota.

Assessment of planktonic community diversity and stability in lakes and reservoirs based on eDNA metabarcoding--A case study of Minghu National Wetland Park, China

To evaluate the potential differences in plankton diversity and stability within freshwater lake and reservoir ecosystems, this study employed eDNA metabarcoding to analyze the diversity, assembly mechanisms, stability, and environmental drivers of plankton communities in natural water (Y region) and artificial lake water (M region) at Liupanshui Minghu National Wetland Park, Guizhou Province, China. The study revealed notable regional variations in plankton diversity and assembly mechanisms. Specifically, Shannon, Simpson, and Pielou's evenness indices were higher in the M region, suggesting a more complex species composition compared to the Y region. Analysis of community assembly mechanisms indicated that both regions were influenced by a combination of stochastic and deterministic processes, with stochastic processes serving as the dominant driver. Through LEfSe analysis, Random Forest predictions, and molecular ecological network evaluations, certain OTUs identified as "dual-characteristic" species were consistently highlighted. These species may play a critical role in shaping community composition and contributing to stability. Environmental drivers further clarified these differences. Redundancy analysis (RDA) demonstrated that TDS was the primary factor driving regional differences in key zooplankton species, while EC and DO were significant factors influencing the distribution of key phytoplankton species. Stability assessments, which combined molecular ecological network analysis and the coefficient of variation in species population density, revealed higher stability in the Y region. This indicates that the natural water system (Y region) has a greater resistance to disturbances compared to the artificial system in the M region. The findings provide fundamental support for assessing the health of aquatic ecosystems, as well as for the effective monitoring and biodiversity conservation of lake and reservoir ecosystems.

Metagenomic insights into the assembly, function, and key taxa of bacterial community in full-scale pesticide wastewater treatment processes

Pesticide wastewater emerges as a typical refractory wastewater, characterized by complex composition and high toxicity, posing significant treatment challenges. Bacterial communities are responsible for biological treatment of refractory wastewater in full-scale pesticide wastewater treatment plants (PWWTPs), providing important implications for optimizing system performance and improving management strategies. However, the knowledge of their composition, diversity, function, assembly patterns, and biological interactions remains limited. Therefore, this study applied high-throughput sequencing, machine learning models, and statistical analysis to investigate key features of bacterial communities in eight PWWTPs. We found that Proteobacteria and Bacteroidota were the most abundant phyla, with Pseudomonas, Hyphomicrobium, Comamonas, and Thauera being dominant genera. Bacterial community distribution and diversity varied significantly among influents, sludges, and effluents, with sludges and effluents exhibiting higher diversity, richness, and evenness compared to influents. Deterministic processes primarily shaped the bacterial communities, accounting for 77.12%, 61.44%, and 64.05% of variation in influents, sludges, and effluents, respectively. Homogeneous selection explained 47.71%, 31.37%, and 31.37% of variation across these communities. Key modules (Module 1 in influents, Modules 3 and 4 in sludges, and Module 1 in effluents) were significantly associated with various metabolic and degradative functions (p < 0.05). Core taxa identified by Random Forest analysis were strongly linked to key metabolic and degradation functions, such as the metabolism of cofactors and vitamins, carbohydrates, and amino acids as well as the degradation of benzoate, aminobenzoate, nitrotoluene, chloroalkane, and chloroalkene. This study deepens our understanding of bacterial community dynamics and key features in pesticide wastewater treatment systems, offering scientific guidance for process optimization, efficiency improvement, and system stability assessment.

Revealing real impact of microalgae on seasonal dynamics of bacterial community in a pilot-scale microalgal-bacterial consortium system

The microalgal-bacterial consortium (MBC) system is recognized as an advanced approach for nitrogen and phosphorus removal in wastewater treatment. However, the influence of microalgae on bacterial community dynamics and niche differentiation across varying seasonal conditions remains unexplored. In this study, we established a pilot-scale continuous-flow MBC system to disentangle, for the first time, the impact of microalgae on seasonal bacterial community succession by conducting monthly time-series sampling over a full seasonal cycle. Notably, a core microbiome consisting of 528 ASVs displaying significant seasonal rhythms was identified in both activated sludge (AS) and MBC systems. Unlike the random drift-driven assembly observed in the AS system, microalgae can recruit dominant species that respond to environmental fluctuations to form a core microbiome (heterogeneous selection), thereby enhancing community stability. Concurrently, microalgae facilitated niche differentiation within the core microbiome, driving transition from generalist to specialist species, which in turn promoted synergistic interactions that can improve nitrification and denitrification functions. Additionally, microalgae strengthened the correlation between functional species in the core microbiome and seasonal variations in light and temperature, as well as with regulating the efficiency of nitrogen and phosphorus removal by influencing the abundance of these functional species. These findings deepen our understanding of bacterial ecology based on microalgae management and provide a foundation further for the study of community regulation strategy of MBC systems.

Graph-based deep learning for predictions on changes in microbiomes and biogas production in anaerobic digestion systems

Anaerobic digestion (AD), which relies on a complex microbial consortium for efficient biogas generation, is a promising avenue for renewable energy production and organic waste treatment. However, understanding and optimising AD processes are challenging because of the intricate interactions within microbial communities and the impact of volatile fatty acids (VFAs) on biogas production. To address these challenges, this study proposes the application of graph convolutional networks (GCNs) to comprehensively model AD processes. GCN models were developed to predict microbial dynamics and biogas production by integrating network analyses of high-throughput sequencing data and VFA inhibition effects. The models were trained based on the responses of anaerobic digesters to organic loading rate shock, starvation, and bioaugmentation for 281 d under various feeding conditions. Shifts in microbial community composition during AD stages and feeding conditions were successfully identified using next-generation sequencing tools. Graph topological features indicated a significant coupling between VFAs and microbial families, and the hydrogenotrophic archaeal families were most frequently connected to other families or residual acids. The GCN accurately predicted microbial abundances and gas production rates, achieving a mean squared error of 0.11 and 0.01 and a coefficient of determination of 0.72 and 0.87 for the testing dataset. These results provide valuable insights into the effects of starvation and bioaugmentation on the microbiome by utilising GCNs to model anaerobic treatment processes, predict microbial dynamics, and assess reactor productivity. Our study suggests a new modelling framework for understanding and improving AD systems by considering microbial interaction networks in relation to chemical parameter information at relevant operating scales.

Exploring the function of key species in different composting stages for effective waste biotransformation

Composting is a microbial-driven process that plays a vital role in recycling waste and promoting sustainable production. To develop more effective bioaugmentation strategies, this study examined three successive stages in an aerobic composting system, focusing on microbial community adaptation to high-temperature stress (mode_2) and nutrient-poor conditions (mode_3). The results revealed a shift from an r-strategy (rapid growth) to a K-strategy (thriving under resource-limited conditions). Community succession was predominantly driven by deterministic processes (>90 %) and exhibited strong cooperative interactions. Using multiple statistical approaches, key species were identified for each condition. These species enhanced microbial network connectivity under environmental stresses, increasing network edges by 29 %-35 %. Under high-temperature stress, Bacillus and Ureibacillus maintained core functions, while Chelativorans and Aeribacillus contributed to key metabolic pathways, including amino acid metabolism. In nutrient-poor conditions, Saccharomonospora and Pseudoxanthomonas enhanced overall system functionality, and Novibacillus played a key role in carbon and nitrogen cycling, particularly nitrogen fixation. Predictive models for microbial community stability (R2 = 0.68-0.97) were developed based on these key species to enable rapid assessment of system stability. Overall, this study identifies essential microbes involved in composting across different environmental conditions and clarifies their functional roles, providing valuable insights for optimizing aerobic composting efficiency and advancing waste resource management.

Lactobacillus Johnsonii YH1136 alleviates schizophrenia-like behavior in mice: a gut-microbiota-brain axis hypothesis study

Based on the microbiota-gut-brain axis (MGBA) hypothesis, probiotics play an increasingly important role in treating various psychiatric disorders. Schizophrenia (SCZ) is a common mental disease with a complex pathogenesis and is challenging to treat. Although studies have elucidated the mechanisms associated with the interactions between the microbiota-gut-brain axis and SCZ, few have specifically used probiotics as a therapeutic intervention for SCZ. Accordingly, the current study determines whether L. johnsonii YH1136 effectively prevents SCZ-like behavior in mice and identifies the associated key microbes and metabolites. An SCZ mouse model was established by intraperitoneal injection of MK-801; L. johnsonii YH1136 was administered via oral gavage. L. johnsonii YH1136 significantly improves abnormal behaviors, including psychomotor hyperactivity and sociability and alleviates aberrant enzyme expression associated with tryptophan metabolism in SCZ mice. Additionally, L. johnsonii YH1136 upregulates hippocampal brain-derived neurotrophic factor (BDNF) levels while downregulating tryptophan 2,3-dioxygenase (TDO2), indoleamine-pyrrole 2,3-dioxygenase 1 (IDO1), kynurenine aminotransferase 1 (KAT1). Subsequent 16S rRNA sequencing of intestinal contents suggests that L. johnsonii YH1136 modulates the gut flora structure and composition by increasing the relative abundance of Lactobacillus and decreasing Dubosiella in SCZ mice. N-acetylneuraminic acid and hypoxanthine are the key serum metabolites mediating the interaction between the MGBA and SCZ. These results partially reveal the mechanism underlying the effects of L. johnsonii YH1136 on SCZ-like behavior in mice, supporting the development of therapeutic L. johnsonii probiotic formulations against SCZ.

Community organization and network stability of co-occurring microbiota under the influence of Kuroshio Current

The Kuroshio Current structures environmental characteristics and biodiversity in the northwestern Pacific Ocean (NWPO), a region renowned for its dynamic oceanographic processes and rich marine ecosystems. However, the assembly and associations responses of prokaryotes and microeukaryotes to the Kuroshio Current remain largely unknown. Here, co-occurrence properties and stability of prokaryotic and eukaryotic microbiomes from three regions influenced by the Kuroshio: Kuroshio South of Japan (KSJ), Kuroshio Extension (KE), and the Kuroshio-Oyashio interfrontal zone (KOIZ) are systematically investigated. Microbiomes in the KE showed reduced phylogenetic distance and broader niche breadth than those in the KSJ and KOIZ. Microeukaryotic robustness was highest in the KE and lowest in the KOIZ, while prokaryotes showed the opposite pattern. Prokaryotic and microeukaryotic robustness and compositional stability formed complementary stabilizing and phylogenetic distance along vertical gradients in the KOIZ region, helping to maintain community and ecosystem stability. Prokaryotes and microeukaryotes formed complementary stabilizing under the influence of the Kuroshio Current. Overall, the network of prokaryotes was more stable than that of microeukaryotes, and microeukaryotes were more sensitive to environmental variations than prokaryotes. These results show how the Kuroshio Current influences the community organization and co-occurrence stability of prokaryotic and eukaryotic microbiomes, respectively, as well as their contrasting adaptability and survival strategies to environmental variation.

Cross-sectional-dependent microbial assembly and network stability: Bacteria sensitivity response was higher than eukaryotes and fungi in the Danjiangkou Reservoir

Water depth variation can lead to the vertical structure change of microbial communities in reservoirs, and then affect the relationship between the microbial communities along the depth gradient, profoundly affecting the stability of the aquatic ecosystems. However, the interspecific dynamics of microbial communities across different water layers in deep-water low-nutrient drinking water reservoirs remain not well understood. Thus, we assessed microbial communities' dynamic changes in different water layers in this study. The physical and chemical parameters and different planktonic microbial of the surface, middle, and bottom layers were studied from July 2022 to August 2023 in the Danjiangkou Reservoir, China. Based on high-throughput sequencing technology, model analysis and network analysis, the diversity of microbial communities in different water layers, community construction process and co-occurrence network differences were studied. The results showed that the diversity of bacterial communities in the Danjiangkou reservoir was significantly higher than that of fungi and eukaryotic microorganisms in different water depths. The dominant taxa of the bacterial communities in different water depths were Actinobacteriota, Bacteroidota, Proteobacteria and Cyanobacteria. The dominant phyla were Ascomycota, unclassified_k__Fungi and Chytridiomycota. The relative abundance of vertical dominant species in eukaryotic communities was slightly different, including Cryptophyta, Chlorophyta, Dinophyta and Metazoa. Different microbial communities shared the main dominant species on the vertical stratification. The neutral model showed that random processes significantly affected the assembly process of microbial communities in different water layers, and the mobility of fungal communities was much lower than that of bacteria and eukaryotes. The co-occurrence network analysis showed that the number of nodes and edges of the bacterial community was the highest, indicating that the network scale of the bacterial community was the largest. In addition, the map density and average clustering coefficient of bacterial and eukaryotic communities in surface water were the highest, indicating that the surface microbial species had a high degree of connectivity, can better transfer materials and exchange information, and Sensitive to changes in the external environment. In contrast, in fungal communities, microbial interactions were the most complex at the bottom. The interactions between microbial communities in different water depths were mainly positive, and the negative correlation of microbial communities in the middle and bottom water was greater than that in the surface water, indicating that the competition between species increased with the increase of depth. Correlation analysis showed that the key species of microbial community were significantly correlated with TP, PO43--P, NO3--N and ORP. In summary, by analyzing water depth changes' impacts on the spatial distribution pattern, community assembly process and symbiotic network stability of microbial communities in the Danjiangkou Reservoir, we found that bacterial communities were more sensitive to water depth than eukaryotes and fungi. This study revealed the response mechanism of microbial communities to water depth in low-nutrient reservoirs, which is helpful to reflect aquatic ecological processes and provide a theoretical basis for the construction of subsequent reservoir ecological models.

The Same Source of Microbes has a Divergent Assembly Trajectory Along a Hot Spring Flowing Path

Hot spring microbial mats represent intricate biofilms that establish self-sustaining ecosystems, hosting diverse microbial communities which facilitate a range of biochemical processes and contribute to the structural and functional complexity of these systems. While community structuring across mat depth has received substantial attention, mechanisms shaping horizontal spatial composition and functional structure of these communities remain understudied. Here, we explored the contributions of species source, local environment and species interaction to microbial community assembly processes in six microbial mat regions following a flow direction with a temperature decreasing from 73.3°C to 52.8°C. Surprisingly, we found that despite divergent community structures and potential functions across different microbial mats, large proportions of the community members (45.50%-80.29%) in the recipient mat communities originated from the same source community at the upper limit of temperature for photosynthetic life. This finding indicated that the source species were dispersed with water and subsequently filtered and shaped by local environmental factors. Furthermore, critical species with specific functional attributes played a pivotal role in community assembly by influencing potential interactions with other microorganisms. Therefore, species dispersal via water flow, environmental variables, and local species interaction jointly governed microbial assembly, elucidating assembly processes in the horizontal dimension of hot spring microbial mats and providing insights into microbial community assembly within extreme biospheres.

Deciphering the treatment performance, microbial community responses, and behavior of antibiotic resistance genes in anaerobic sequencing batch reactors under graphene exposure

Graphene has garnered significant attention due to its unique and remarkable properties. The widespread application of graphene materials in numerous fields inevitably leads to their release into the environment. This study examines the long-term impacts of graphene on anaerobic sequencing batch reactors. The low-concentration graphene (5 mg L-1) exhibited a significant inhibitory effect on the removal of chemical oxygen demand, while the high-concentration group (100 mg L-1) was less affected. The transmission electron microscopy and Raman spectroscopy results demonstrated that the anaerobic sludge could attack graphene materials, and cell viability tests showed that high concentrations of graphene were more conducive to microbial attachment. High-throughput sequencing revealed significant alterations in the microbial community structure under graphene pressure. Methanobacterium and Actinomyces gradually became the dominant genera in the high-concentration group. Network analysis showed that graphene increased the complexity and interaction of microbial communities. Additionally, high-throughput qPCR analysis demonstrated that graphene influenced the dynamics of antibiotic resistance genes, with most exhibiting increased abundance over time, especially in the low-concentration group. Consequently, when considering the application of graphene in wastewater treatment, it is crucial to evaluate potential risks, including its effects on system performance and the likelihood of antibiotic resistance gene enrichment.

Characteristics of nutrients and microbial communities in proglacial lakes on the Tibetan Plateau and their potential linkages associated with mercury

Glacier shrinkages and evolutions of post-glacial ecosystems due to human-induced climate change represent some of the most rapidly occurring ecosystem shifts with potential ecological and societal cascading consequences on Earth. Glacial meltwater could introduce a substantial amount of nutrients, dissolved organic matter (DOM), and contaminants stored in glaciers into the lakes. However, influence of glacial meltwater on microbial communities and its impacts in the transformation of trace contaminants by microbes are frequently underestimated. This study explored the distribution of nutrients, mercury (Hg), and microbial communities across the meltwaters, surface waters, deep waters, and outflows of three proglacial lakes that formed after 2000 on the Tibetan Plateau. Our results revealed that alterations in the DOM composition, particularly the efficient metabolism of carbohydrates (CHO), may foster growth and activities of microorganisms. This could enhance the abundance of potential Hg methylators, resulting in an increase in the ratio of methylmercury (MeHg) to total mercury (THg) in water. Our findings highlight substantial interaction between microbial community and compositional variabilities of DOM in proglacial lake. It underlines the essentiality of integrating these factors into future risk appraisals of aquatic ecosystems in proglacial lakes in the context of global climate changes.

Bacterium-Phage Interactions Enhance Biofilm Resilience during Membrane Filtration Biofouling under Oxidative and Hydraulic Stresses

Microbial interactions on membrane surfaces can facilitate biofilm formation and biofouling, which poses a significant challenge for pressure-driven membrane filtration systems. This multiomics study investigates the adaptive responses of bacterium-phage interactions under varying oxidative and hydraulic stress during membrane backwashing and their biological contributions to biofouling. Oxidative and hydraulic stress distinctly shaped bacteria and phage diversity and community composition. Under moderate oxidative backwashing (300 ppm of NaClO), diversity was maintained, with increased antioxidant enzyme activities, extracellular polymeric substance (EPS) production, and quorum sensing (QS) signaling, promoting bacterial resilience and biofilm formation. In contrast, excessive oxidative stress (600 ppm of NaClO) reduced bacteria and phage diversity, disrupted antioxidant responses, and increased microbial sensitivity. Hydraulic stress predominantly influenced viral diversity and co-occurrence network topology, favoring the expansion of broad host-range phages and lysogenic lifestyles under combined stresses. Phage-bacterium interaction analyses highlighted phages' adaptive preferences for hosts with high network centrality and broad ecological niches, which enhanced microbial interactions and resilience. Transcriptomic profiling demonstrated the early enrichment of genes associated with energy metabolism, ROS detoxification, and biofilm formation, followed by stabilization as biofilms matured. Phage-encoded auxiliary metabolic genes were involved in DNA repair, QS, and EPS biosynthesis, contributing to microbial adaptation through oxidative stress resistance and biofilm stabilization. Overall, these findings provide mechanistic insights into biofouling dynamics and highlight the need to optimize chlorine dosing to prevent suboptimal levels of microbial adaptation and biofouling.

Temporal dynamics of nutrient release from mulching of legume roots and shoots litter driven by microbial community during decomposition in organic orchards

Grass residue decomposition is crucial for nutrient cycling in agro-ecosystems, enhancing nutrient utilization efficiency and supporting sustainable crop management. While grass mulching has been widely studied for improving orchard soil fertility, the role of soil microbial communities in decomposing different plant organs remains unclear. Before decomposition, the aboveground and belowground plant parts were harvested and placed in separate litterbags, which were later used for evaluating the decomposition rate and chemical characteristics of the shoots and roots for 40 days (at 10 days intervals). The changes in soil fertility, soil microenvironment, soil microbial community were measured after 0, 1 and 3 months, alongside analysis of key microbial taxa under different residues treatments. The remaining mass of root litter treatment was significantly higher than that of other treatments by 72.97%, 17.53% during 1-10 days and 30-40 days, respectively. During the 40-days period, the release of potassium (K) from root litter reached 58.61%, and the decomposition of lignin was recorded at 56.94%, whereas the release of carbon (C), nitrogen (N), and phosphorus (P) remained relatively stable. Despite no significant changes in nodes, edges, and links at 30 and 90 days, the co-occurrence network of root litter exhibited modularity values of 0.774 and 0.773, respectively. The values were higher than those observed in random networks, indicating the presence of functional modules and enhanced stability within the root microbial community. Litter organs enhanced decomposition rates by positively influencing soil fertility and keystone microbial decomposers, while its soil microenvironment affects decomposition rates. Despite its recalcitrance, the chemical composition of root litter plays a key role in regulating soil microbial community structure and improving soil fertility, thereby maintaining orchard ecosystem functionality.

Polystyrene nanoplastics reshape the peatland plants (Sphagnum) bacteriome under simulated wet-deposition pathway: Insights into unequal impact of ecological niches

Nanoplastics (NPs) enter peatlands through atmospheric deposition, yet their effects on Sphagnum bacterial communities (SBCs) and plant-self remain unknown. We hypothesize that NPs alter the composition, structure, and co-occurrence pattern of epiphytes (Epi) and endophytes (En), thereby differentially affecting the growth and physiological performance of Sphagnum. The 30-day simulated wet deposition experiment was conducted to test this. Here, polystyrene NPs reduced the α-diversity of SBCs, unevenly reshaped the structure of Epi and En. Mfuzz clustering was used to reveal the co-abundance behavior of SBCs, and the null model found SBCs relied on stochastic assembly, formed stable Epi molecular ecological network (MEN) and connected En MEN. NPs disrupted symbiosis of SBCs, with high-abundance phyla reductions impacting MENs and low-abundance phyla affecting the inter-domain ecological network (IDEN) between Epi and En. Increasingly positive NPs (from carboxyl-modified to unmodified, and then to amino-modified NPs) further decreased SBCs abundance. Key clusters of Proteobacteria (Pro.), with α-Pro. and γ-Pro. as module hubs of MENs, and β-Pro. as a network hub in the IDEN, could reflect these changes. Additionally, NPs lowered plant spread area (P < 0.05) and chlorophyll content (P < 0.01), but the reduction in biomass was not significant. Structural equation modeling showed reduced SBCs α-diversity alleviated the NPs phytotoxicity (up to 33.31 % offset), as genetic analysis revealed that methane oxidation, carbon fixation, and trace element metabolism may upregulate plant nutrient supply. Our findings offer critical insights into NPs deposition risks in remote areas and highlight the responses of plant-bacteriome symbiosis.

Exploring the structure and assembly of seagrass microbial communities in rhizosphere and phyllosphere

Microbial community assembly and interactions are pivotal research areas within microbial ecology, yet relevant studies in seagrass rhizospheres and phyllosphere remain relatively scarce. In this study, we utilized high-throughput sequencing technology to investigate the microbial communities in different periods and microhabitats (rhizosphere and phyllosphere) of two seagrass species (Zostera marina and Phyllospadix iwatensis). Our findings suggest that microhabitats have a more pronounced impact on the composition of seagrass-associated microbial communities compared to periods and species. Further investigations reveal that the phyllosphere microbial community exhibits a more intricate co-occurrence network and interactions than the rhizosphere microbial community. Keystone taxa show distinct functional roles in different microhabitats of seagrasses. Additionally, we observed that differences in seagrass microhabitats influence community assembly, with the rhizosphere microbial community being more influenced by deterministic processes (heterogeneous selection) compared to the phyllosphere. These findings contribute to our understanding of the intricate interactions between seagrasses and their associated microbial communities, providing valuable insights into their distribution patterns and microhabitat preferences.IMPORTANCEStudying the community structure and assembly of different microhabitats in seagrass beds contributes to revealing the complexity and dynamic processes of seagrass ecosystems. In the rhizosphere microhabitat of seagrasses, microbial communities may assist in disease resistance or enhance nutrient uptake efficiency in seagrasses. On the other hand, in the microhabitat on the surface of seagrass blades, microorganisms may be closely associated with the physiological functions and nutrient cycling of seagrass blades. Therefore, understanding the structure and assembly mechanisms of rhizosphere and phyllosphere microbial communities is crucial for exploring the interactions between seagrass and microbial communities, as well as for enhancing our comprehension of the stability and resilience of seagrass bed ecosystems.

Complex of intratumoral mycobiome and bacteriome predicts the recurrence of laryngeal squamous cell carcinoma

Dysbiosis of intratumoral fungal and bacterial communities is associated with poor prognosis in various cancers. However, the mycobiome characteristics in laryngeal squamous cell carcinoma (LSCC) and its correlation with recurrence have not yet been investigated. The mycobiome in 80 LSCC samples was characterized using internal transcribed spacer sequencing, encompassing both tumor tissues and their matched para-cancerous tissues. The intratumoral bacteriome was further identified using 16S rRNA sequencing. These two microbial communities were analyzed using bioinformatics and statistical methods to determine its potential correlation with LSCC recurrence. The fungal alpha diversity in tumors was higher compared with that in para-cancerous tissues (P < 0.001). A significant difference in the overall fungal community patterns between tumor tissues and para-cancerous tissues was observed based on Bray-Curtis dissimilarity (P < 0.001). The presence of Alloprevotella, Porphyromonas, Candida, and Fusarium in tumors exhibited a correlation with alcohol consumption. The relative abundance of Penicillium, Exophiala, and Aspergillus in the mycobiome, as well as that of Alloprevotella, Porphyromonas, and Peptostreptococcus in the bacteriome significantly increased the risk of LSCC recurrence (P < 0.05). These six microorganisms can combine to form a microbial complex, which may independently contribute to recurrence risk in patients with LSCC when enriched within the tumor (hazard ratio = 6.844, P < 0.01). Intratumoral fungi and bacteria can be valuable indicators for assessing recurrence in patients with LSCC, indicating their potential as valuable targets for therapeutic intervention.

IMPORTANCE

Our results revealed that dysbiosis of intratumoral microbiota, including increased fungal community diversity and overgrowth of several fungal or bacterial organisms, is substantially linked to the recurrence of LSCC. Drinking habits might alter the laryngeal microbiota to influence the recurrence of LSCC. We also explored a method to potentially predict the recurrence of LSCC from a novel perspective. These findings could offer insights into the etiology of LSCC and pave way to prevent and treat LSCC.

Soil fungal community and co-occurrence network patterns at different successional stages of black locust coppice stands

Background and aims

Black locust (Robinia pseudoacacia L.) plantations transition from seedling to multi-generation coppice systems, leading to declines in productivity and biodiversity. However, the structural and functional reorganization of soil fungal communities during this transition remains poorly understood. This study aimed to characterize fungal community dynamics across successional stages of black locust stands and assess their implications for soil health and ecosystem resilience.

Methods

Soil fungal communities in three black locust stands (first-generation seedling forest, first- and second-generation coppice forests) were analyzed over one year using ITS high-throughput sequencing. We evaluated fungal diversity, guild composition, and co-occurrence networks, integrating statistical analyses (PERMANOVA, ANOSIM, FUNGuild) and network theory to assess seasonal and successional shifts.

Results

Fungal richness and diversity remained stable across stand types and seasons. However, these factors dramatically altered the soil fungal community structure. Shifts in fungal community composition were observed from seedling to coppice stands: Ascomycota dominance decreased (72.9 to 57.9%), while Basidiomycota increased (6.5 to 11.6%). Significant changes in the relative abundance of certain fungal guilds were observed by both stand conversion and seasonal variation (p < 0.05). However, the overall fungal guilds composition was only significantly affected by the seasonal variation, rather than stand conversion (p > 0.05). Furthermore, saprotrophic fungi dominated in autumn/winter (66.49-76.01%), whereas symbiotic fungi peaked in spring (up to 7.27%). As forests transition from seeding to coppice stands, the percentage of negative edges, average degree, and relative modularity of the fungal community co-occurrence networks all gradually decreased. Those suggested that the conversion of black locust stands decreased the connectivity between fungal species, formed less organized structure, increased homogeneity of function among microbial communities, reduced ecological functionality, and decreased resistance to environmental changes. Seasonal temperature fluctuations further modulated network complexity, with summer samples showing heightened edge density but reduced cooperation.

Conclusion

Our findings suggest that the conversion of forests can significantly shift the soil fungal community structure and assembly, favoring Basidiomycota over Ascomycota and reducing network stability. These shifts signal progressive soil nutrient depletion and functional homogenization, potentially compromising ecosystem resilience. Seasonal guild dynamics highlight fungi's role in nutrient cycling, with saprotrophs driving litter decomposition in colder months. This understanding suggest that forest management practices must prioritise the preservation of early successional stages. This is vital to support diverse fungal communities and complex community networks and ensure the stability, functionality and resistance of fungal communities. Restoration efforts must focus on promoting fungal resilience through targeted soil amendments and habitat diversification to enhance ecosystem stability and functionality.

Seasonal lake ice cover drives the restructuring of bacteria-archaea and bacteria-fungi interdomain ecological networks across diverse habitats

The coexistence of different microbial communities is fundamental to the sustainability of many ecosystems, yet our understanding of the relationships among microbial communities in plateau cold-region lakes affected by seasonal ice cover remains limited. This research involved investigating three lakes in the Inner Mongolia segment of the Yellow River basin during frozen and unfrozen periods in two habitats: water bodies and sediments. The research examined the composition and function of bacteria, archaea, and fungi across different times and habitats within the basin, their response to environmental variables in water and sediment, and inter-domain interactions between bacteria-archaea and bacteria-fungi were compared using interdomain ecological network (IDEN). The findings indicate significant variations in the structures of bacterial, archaeal, and fungal communities across different periods and habitats, with the pH of the water body being a crucial environmental variable affecting microbial community composition. In the frozen period, the functionality of microbial communities, especially in terms of energy metabolism, was significantly impacted, with water bodies experiencing more pronounced effects than sediments. Archaea and fungi significantly contribute to the stability of bacterial communities across various habitats, especially in ice-covered conditions, where stronger associations between bacterial communities, archaea, and fungi promote the microbial communities' adaptability to cold stress. Furthermore, our results indicate that the primary environmental variable influencing the structure of IDENs is the nutrient salt content in both water bodies and sediments. This study broadens our understanding of the responses and feedback mechanisms of inter-domain microbial interactions in lakes influenced by seasonal ice cover.

Community assembly and succession of the functional membrane biofilm in the anammox dynamic membrane bioreactor: Deterministic assembly of anammox bacteria

The anammox dynamic membrane bioreactor (DMBR) exhibits potential for efficient nitrogen removal via anammox processes. The functional membrane biofilm in the anammox DMBR significantly enhances nitrogen removal, ensuring robust operation. Nevertheless, ecological mechanisms underpinning the nitrogen removal function of the membrane biofilm remain unclear. We investigated the community succession and assembly of the membrane biofilm communities in two anammox DMBRs utilizing distinct inoculated anammox sludges. Anammox bacteria displayed niche differentiation in both DMBRs. Anammox bacteria Candidatus Kuenenia was selectively enriched to 8.5% abundance in the membrane biofilm communities, contributing to 5.2-7.2% of the nitrogen removal load. Membrane biofilm communities were primarily assembled through deterministic processes. Specifically, the selective enrichment of Candidatus Kuenenia on the membrane biofilms was primarily governed by homogenous selection process, explaining 9.67-9.82% of the variance. The deterministic assemblies of anammox bacteria were mainly influenced by the high substrate affinity of Candidatus Kuenenia and the limited availability of substrates (NH4+ and NO2-) in the membrane biofilms. Furthermore, the relatively weak permeate drag force during the DMBR filtration facilitated the preferential colonization of microbes from the anammox sludge to the membrane biofilm, resulting in the deterministic formation of the membrane biofilm communities with nitrogen removal function. Our findings offer insights into the ecological mechanisms driving the deterministic assembly of the functional membrane biofilm communities in the anammox DMBRs, informing the precise regulation of membrane biofilms for improved nitrogen removal in anammox applications of wastewater treatment.

Detritivore identity modulates effects of nutrient enrichment and a common fungicide presence on leaf litter decomposition and fungal community

Understanding the interaction of biotic and abiotic factors on ecosystem function is crucial for freshwater ecosystem management, However, the influence of nutrient enrichment, fungicide presence, and detritivore identity on leaf litter decomposition and associated fungal communities remains poorly understood. We conducted a microcosm experiment to examine: 1) the individual and combined effects of nutrient enrichment and a common fungicide on leaf litter decomposition and fungal communities; and 2) how two types of detritivore invertebrates (scrapers vs. shredders) influence these effects. After 35 days, we assessed: 1) leaf litter decomposition, dissolved organic carbon (DOC) production, and the activities of extracellular enzymes; and 2) the diversity, community structure, and co-occurrence networks of fungal communities. We found that both fungicides and nutrient enrichment increased enzymatic activity but did not significantly impact fungal diversity. However, fungicides changed fungal community structure and reduced detritivore-mediated decomposition and DOC production, while nutrient enrichment had the opposite effect. In combination, nutrient enrichment mitigated the negative effects of fungicides on fungal co-occurrence network stability and decomposition. We found that detritivore identity selectively influenced fungal taxa, resulting in distinct co-occurrence patterns under different stressors. The effects of nutrient enrichment and/or fungicide on leaf litter decomposition also depended on detritivore identity. This research underscores the pivotal role of detritivore identity and the interplay of biotic and abiotic factors in shaping fungal communities and modulating leaf litter decomposition, particularly in multiple stressors settings, and its implications for effective management and biodiversity conservation.

Phyllosphere mycobiome in two Lycopodiaceae plant species: unraveling potential HupA-producing fungi and fungal interactions

Huperzine A (HupA), a lycopodium alkaloid with therapeutic potential for neurodegenerative diseases such as Alzheimer's disease, is found exclusively in some species of the Huperzioideae subfamily of Lycopodiaceae. Fungi associated with Huperzioideae species are potential contributors to HupA biosynthesis, offering promising prospects for HupA production. Despite its medical significance, limited knowledge of fungal diversity in lycophytes and the variability of HupA production in fungal strains have impeded the discovery and applications of HupA-producing fungi. Here, we investigated HupA concentrations and the mycobiome across various tissues of two Lycopodiaceae species, Huperzia asiatica (a HupA producer) and Diphasiastrum complanatum (a non-HupA producer). We aim to unveil the distribution of potential HupA-producing fungi in different plant tissues and elucidate fungal interactions within the mycobiome, aiming to uncover the role of HupA-producing fungi and pinpoint their potential fungal facilitators. Among the tissues, H. asiatica exhibited the highest HupA concentration in apical shoots (360.27 μg/g fresh weight) whereas D. complanatum showed no HupA presence in any tissue. We obtained 441 amplicon sequence variants (ASVs) from H. asiatica and 497 ASVs from D. complanatum. The fungal communities in bulbils and apical shoots of H. asiatica were low in diversity and dominated by Sordariomycetes, a fungal class harboring the majority of reported HupA-producing fungi. Integrating bioinformatics with published experimental reports, we identified 27 potential HupA-producing fungal ASVs, primarily in H. asiatica, with 12 ASVs identified as hubs in the fungal interaction network, underscoring their pivotal roles in mycobiome stability. Members of certain fungal genera, such as Penicillium, Trichoderma, Dioszegia, Exobasidium, Lycoperdon, and Cladosporium, exhibited strong connections with the potential HupA producers in H. asiatica's network rather than in D. complanatum's. This study advances our knowledge of fungal diversity in Lycopodiaceae and provides insights into the search for potential HupA-producing fungi and fungal facilitators. It highlights the importance of exploring young tissues and emphasizes the ecological interactions that may promote the fungi-mediated production of complex bioactive compounds, offering new directions for research in fungal ecology and secondary metabolite production.

The similarity between arbuscular mycorrhizal fungi communities of trees and nearby herbs in a planted forest exhibited within-site spatial variation patterns explained by local soil conditions

The similarity between the arbuscular mycorrhizal fungi (AMF) communities of trees and neighboring understory herbs in forests remains unclear, which we aimed to clarify. We traced and collected basal roots of 20 randomly chosen Cryptomeria japonica (Cupresaceae) trees and the surrounding soil at four microsites in 1 km2 of a Cr. japonica forest. One Chloranthus serratus (Chlorantaceae) herb immediately at the base of each sampled tree was excavated to collect an intact root system. We amplified a partial small subunit of fungal ribosomal DNA (18S) using Illumina MiSeq amplicon sequencing. Soil physicochemical properties were also measured. We detected 670 and 679 AMF operational taxonomic units (OTUs) in Cr. japonica and Ch. serratus, respectively, belonging to Acaulospora, Dominikia, Glomus, Microkamienskia, Rhizophagus, Septoglomus, and Sclerocystis. Seventeen OTUs were detected in the roots of both host species at average relative abundances > 1%. Among them, four dominant OTUs with an average relative abundance > 10% were concurrently detected in the roots of 17 tree-herb sets. The composition and similarity of their AMF communities were spatially varied, significantly driven by spatially varying soil pH, total C, N, C/N, and elevation, but not electroconductivity, supported by the microsite-dependent distributions of their dominant OTUs. We concluded that the similarity of AMF communities between trees and neighboring understory herbs depends on the soil physicochemical conditions that influence the distribution of their dominant AMF.

Differentiated response mechanisms of soil microbial communities to nitrogen deposition driven by tree species variations in subtropical planted forests

Introduction

The increasing rate of atmospheric nitrogen deposition has severely affected the structure and function of these ecosystems. Although nitrogen deposition is increasing globally, the responses of soil microbial communities in subtropical planted forests remain inadequately studied.

Methods

In this study, a four-year experimental simulation was conducted to assess the impacts of varying nitrogen deposition levels (CK: 0 g·N·m-2·a-1; N10: 10 g·N·m-2·a-1; N20: 20 g·N·m-2·a-1; N25: 25 g·N·m-2·a-1) on two subtropical tree species, Pinus yunnanensis Franch. and Pinus armandii Franch. High-throughput sequencing was performed using the Illumina MiSeq platform. Statistical analyses, including analysis of variance (ANOVA), linear mixed-effects models, principal coordinate analysis (PCoA), analysis of similarity (ANOSIM), redundancy analysis (RDA), random forest analysis, and structural equation modeling (SEM), were used to examine the short-term responses of soil nutrients, bacterial communities, and fungal community structures to nitrogen deposition.

Results and discussion

The results showed that species differences led to variations in soil properties between the two forests, particularly a significant increase in soil pH in P. yunnanensis Franch. forests and a significant decrease in soil pH in P. armandii Franch. forests. Nitrogen addition did not significantly affect microbial diversity in either P. yunnanensis Franch. or P. armandii Franch. soils; however, forest type differences had a significant impact on bacterial diversity. The nitrogen addition significantly affected the relative abundance of specific microbial communities in both forest types, particularly altering the fungal community structure in the P. yunnanensis Franch forests, while no significant changes were observed in the bacterial community structure in either forest type. Furthermore, nitrogen addition increased the network complexity of bacterial communities in P. yunnanensis Franch. forests while decreasing network complexity in P. armandii Franch. forests. Structural equation modeling indicated that nitrogen addition regulates soil bacterial and fungal diversity in both forest types by modifying nitrogen availability.

Purpose and significance

These findings provide insights into the potential long-term impacts of nitrogen deposition on subtropical planted forest ecosystems and offer a theoretical basis for sustainable forest management and regulatory practices.

New insights into the assembly processes of biofilm microbiota communities: Taking the world's largest water diversion canal as a case study

Systematic studies on the assembly process and drivers of biofilm microbiota communities are still limited. In this study, we used the artificial concrete channel of the world's largest interbasin water diversion project, the middle route of the South-to-North Water Diversion Project in China, as a model system to investigate the assembly mechanisms of biofilm microbiota communities. Our study revealed that water temperature (p < 0.001) and hydrodynamic disturbance (p < 0.05) significantly influenced biofilm biomass. The bacterial communities exhibited substantial spatial heterogeneity, whereas the eukaryotic communities presented pronounced spatial and seasonal variations (PERMANOVA, p < 0.05). Neutral model and null model analyses indicated that dispersal limitation and homogeneous selection (54.8 %-69.7 % in bacteria and 55.9 %-76.1 % in eukaryotes) predominantly governed community assembly. Deterministic effects such as hydrodynamic conditions and temperature strongly influence eukaryotes (homogeneous selection accounts for 63.9 % of eukaryotes in spring). The metacommunity network could be divided into five primary modules with key nodes, including many species from Proteobacteria, Chlorophyta, Bacillariophyta, and Cyanobacteria. Bacteria, such as Proteobacteria, Chlorophyta, Cyanobacteria, and Bacteroidota, act as connectors and a vital role in maintaining the coexistence of modules. Finally, we confirmed that physicochemical (hydrodynamic conditions, temperature, dissolved oxygen conductivity permanganate index), spatial, and biological factors have significant effects on both bacterial and eukaryotic communities as well as metacommunity networks. Our findings provide new insights into the different assembly processes and drivers of bacterial and eukaryotic communities in biofilms, which is highly important for water quality monitoring and sustainable water diversion.

Cross-validation for training and testing co-occurrence network inference algorithms

BACKGROUND

Microorganisms are found in almost every environment, including soil, water, air and inside other organisms, such as animals and plants. While some microorganisms cause diseases, most of them help in biological processes such as decomposition, fermentation and nutrient cycling. Much research has been conducted on the study of microbial communities in various environments and how their interactions and relationships can provide insight into various diseases. Co-occurrence network inference algorithms help us understand the complex associations of micro-organisms, especially bacteria. Existing network inference algorithms employ techniques such as correlation, regularized linear regression, and conditional dependence, which have different hyper-parameters that determine the sparsity of the network. These complex microbial communities form intricate ecological networks that are fundamental to ecosystem functioning and host health. Understanding these networks is crucial for developing targeted interventions in both environmental and clinical settings. The emergence of high-throughput sequencing technologies has generated unprecedented amounts of microbiome data, necessitating robust computational methods for network inference and validation.

RESULTS

Previous methods for evaluating the quality of the inferred network include using external data, and network consistency across sub-samples, both of which have several drawbacks that limit their applicability in real microbiome composition data sets. We propose a novel cross-validation method to evaluate co-occurrence network inference algorithms, and new methods for applying existing algorithms to predict on test data. Our method demonstrates superior performance in handling compositional data and addressing the challenges of high dimensionality and sparsity inherent in real microbiome datasets. The proposed framework also provides robust estimates of network stability.

CONCLUSIONS

Our empirical study shows that the proposed cross-validation method is useful for hyper-parameter selection (training) and comparing the quality of inferred networks between different algorithms (testing). This advancement represents a significant step forward in microbiome network analysis, providing researchers with a reliable tool for understanding complex microbial interactions. The method's applicability extends beyond microbiome studies to other fields where network inference from high-dimensional compositional data is crucial, such as gene regulatory networks and ecological food webs. Our framework establishes a new standard for validation in network inference, potentially accelerating discoveries in microbial ecology and human health.

Integration of metagenomic analysis and metabolic modeling reveals microbial interactions in activated sludge systems in response to nanoplastics and plasticizers

Nanoplastics and plasticizers are prevalent in activated sludge and pose a potential threat to microbial communities in wastewater treatment systems. However, studies on the effects of nanoplastics and plasticizers on the interaction mechanisms and metabolic functions of microbial communities in activated sludge systems are still scarce. In this study, the responses of microbial interactions and metabolic functions to PVC nanoplastics (PVCNPs) and bis(2-ethylhexyl) phthalate (DEHP) in activated sludge were investigated via a combination of amplicon sequencing, metagenome sequencing, and metabolic modeling. The results revealed that DEHP had a significant effect on the microbial community under short-term exposure. DEHP contamination may increase vitamin B12 producers to enhance species collaboration in communities. Furthermore, community metabolic modeling revealed that DEHP-degrading bacteria could promote positive interactions among community members. The increased metabolic exchange flux of siderophores and glutathione in microbial communities under PVCNPs and DEHP contamination implied that microbial communities may maintain iron homeostasis in response to PVCNPs and DEHP contamination through interspecies collaboration. However, more data are needed to further validate these results. This study provides vital insights into the response mechanisms of microbial interactions to nanoplastic and plasticizer contamination in activated sludge systems.

Discovery of potentially degrading microflora of different types of plastics based on long-term in-situ incubation in the deep sea

Plastic waste that ends up in the deep sea is becoming an increasing concern. However, it remains unclear whether there is any microflora capable of degrading plastic within this vast ecosystem. In this study, we investigated the bacterial communities associated with different types of plastic-polyamide-nylon 4, 6 (PA), polyethylene (PE), polyethylene terephthalate (PET), and polystyrene (PS)-after one year of in situ incubation in the pelagic deep sea of the Western Pacific. The study was conducted via a submarine mooring system, anchored at four sites with water depths ranging from 1167 to 1735 m in an area of seamounts. High-throughput 16S rRNA gene sequencing revealed distinct bacterial diversities associated with specific plastic types and locations. The family Gordoniaceae was enriched by PS and PE plastics, while the abundance of Methyloligellaceae was significantly increased in the presence of PET. In the case of PA, Bdellovibrionaceae was enriched. Additionally, all plastic types promoted the relative abundance of Rhodobacteraceae and Sulfurimonadaceae families. Plastics appeared to stimulate bacterial communities involved in nitrate and sulfur cycling in seawater, suggesting that nitrogen and sulfur potentially play significant roles in plastic degradation in deep-sea environments. The dominant family Kordiimonadaceae was identified as a significantly different taxon in non-plastic seawater. Furthermore, the addition of plastics enhanced negative interactions among the bacterial communities in the surrounding seawater, with Proteobacteria and Bdellovibrionota selected for the core microbiome. Overall, this in situ deep-sea incubation revealed the response of indigenous microflora to man-made polymeric materials and highlighted the bacterial communities that may be involved in plastic degradation in oceanic areas.

Long-term exposure to fly ash leachate enhances the bioavailability of potentially toxic metals and decreases bacterial community diversity in sediments

The interaction between microorganisms and the physicochemical properties of sediments is the key to maintaining the stability of the ecological environment. However, the effect of fly ash stockpiling on the relationship between sediment bacterial communities and their physicochemical properties remains unclear. In this study, the interactions between geophysical and chemical factors, morphological distribution of potentially toxic metals (PTMs), and bacterial community diversity in sediments affected by long-term ash water seepage were examined. The results showed that (1) Ash water seepage markedly lowered the pH and elevated the electrical conductance; available potassium, available phosphorus, organic carbon contents; small particle size (<0.25 mm), and concentrations of eight PTMs, including nickel (P < 0.05); (2) Ash water seepage considerably raised the relative abundance of Proteobacteria in the sediments, reduced bacterial community α-diversity, and altered the community structure; (3) Bacterial communities in sediments were strongly correlated with the contents of available potassium organic carbon, selenium, arsenic (oxidizable and reducible), antimony (extractable with weak acids), and chromium (extractable with weak acids); and (4) Fly ash perturbation reduced the connectivity and cohesion in the molecular ecological network of sediment bacteria and increased the abundance of pollution-degrading metabolic pathways, such as low-toxicity and organic classes, as well as coupled stimulus-response and chemotaxis-avoidance defense mechanisms. In summary, the results of this study reveal the changes in bacterial communities, major physicochemical factors, and the morphological distribution of PTMs in sediments affected by long-term ash water leakage of fly ash landfills and provides a theoretical basis for ecological environmental management.

Responses of microbial communities in coastal sediments exposed to triclocarban and triclosan

Triclocarban (TCC) and triclosan (TCS) are applied in a wide range of pharmaceutical and personal care products to prevent or reduce bacterial growth. Due to their extensive application, they are frequently detected in marine environments. In this study, marine sediment systems exposed to different concentrations of TCC and TCS were established to evaluate their effects on microbial communities. It was found that TCC and TCS increased catalase and protease activities on Day 1, but inhibited after 15 days. Microbial activity, as indicated by increased dehydrogenase activity and polysaccharide production, should be enhanced after a 15-day adaptation period. High-throughput sequencing revealed resilient α-diversity but significant shifts in community structures were observed, particularly on Day 15. Function prediction analysis confirmed that most functional profiles remained stable, and network analysis indicated that TCC and TCS enhanced the complexity of the microbial community. This study provides new insights into the impacts and risks of TCC and TCS on the marine environment.

Revealing the potential of biochar for heavy metal polluted seagrass remediation from microbial perspective

Seagrass meadows are under threat due to climate change and human activities, including heavy metal contamination, which can accumulate in seagrass tissues and harm their health and productivity. Despite extensive research, effective remediation strategies are lacking. This study investigated biochar's potential as a remediation agent for seagrass meadows affected by heavy metal pollution. Heavy metal pollution was simulated by adding copper (Cu) and chromium (Cd) to seagrass Thalassia hemprichii, and the remediation effects of biochar were evaluated by monitoring seagrass physiology, root-associated microbial communities, and heavy metal concentrations. Seagrasses can accumulate heavy metals, which adversely affect their health and alter microbial communities. Seagrasses may resist heavy metal stress by releasing dissolved organic carbon (DOC) and recruiting beneficial bacteria. Biochar reduced heavy metal bioavailability and restored seagrass ecosystem health, as evidenced by restored microbial community dynamics. This study highlights biochar's promising role in seagrass meadow restoration impacted by heavy metal pollution.

Efficacy of black soldier fly larvae in converting kitchen waste and the dynamic alterations of their gut microbiome

The escalating demand for food, driven by population growth and improved living standards, has prompted the development of efficient and eco-friendly kitchen waste (KW) treatment technologies. This study focused on the feasibility of utilizing KW through the application of black soldier fly larvae (BSFL), with a specific interest in the dynamic changes in the intestinal bacterial community during the treatment process. After a 10-day KW processing period, BSFL gained an average of 0.84 g/hundred worms/day, achieving a conversion efficiency of 18.52% for KW. This demonstrated their capacity to efficiently utilize KW nutrients for good growth performance. Additionally, the bioconversion of KW by BSFL could markedly decrease the presence of potentially pathogenic bacteria in the feed matrix within one day (P < 0.001), including Escherichia coli, Shigella spp., Salmonella spp., and Staphylococcus aureus. Notably, the diversity of the intestinal bacterial community in BSFL increased with age and sustained KW consumption (P < 0.05), accompanied by enhanced stability. In particular, the average relative abundance of potential probiotic genera associated with nutrient absorption and antimicrobial compounds synthesis, including Fusobacterium, Phascolarctobacterium, Enterococcus, and Actinomyces, increased. Conversely, the prevalence of pathogenic genera like Morganella and Escherichia-Shigella, decreased. Co-occurrence network analysis identified Lactobacillus, Brevibacterium, Erythrobacter, and Enterobacteriaceae as keystone species. Despite their low abundance in the BSFL intestine, these species were potentially crucial for KW bioconversion. Our findings underscore the potential of BSFL for sustainable KW conversion, providing strong support for effective waste management strategies.

Plant diversity increases diversity and network complexity rather than alters community assembly processes of leaf-associated fungi in a subtropical forest

Plant diversity significantly impacts ecosystem processes and functions, yet its influence on the community assembly of leaf fungi remains poorly understood. In this study, we investigated leaf epiphytic and endophytic fungal communities in a Chinese subtropical tree species richness experiment, ranging from 1 to 16 species, using amplicon sequencing to target the internal transcribed spacer 1 region of the rDNA. We found that the community assembly of epiphytic and endophytic fungi was predominantly governed by stochastic processes, with a higher contribution of dispersal limitation on epiphytic than on endophytic fungal communities but a higher contribution of selection on endophytic than on epiphytic fungal communities. The plant-epiphytic fungus interaction network was more complex (e.g., more highly connected and strongly nested but less specialized and modularized) than the plant-endophytic fungus interaction network. Additionally, tree species richness was positively correlated with the network complexity and diversity of epiphytic (α-, β- and γ-diversity) and endophytic (β- and γ-diversity) fungi, but was not associated with the contribution of the stochastic and deterministic processes on the community assembly of epiphytic and endophytic fungi. This study highlights that tree species diversity enhances the diversity and network complexity, rather than alters the ecological processes in community assembly of leaf-associated fungi.

Long-Term Crop Rotation Revealed the Relationship Between Soil Organic Carbon Physical Fraction and Bacterial Community at Aggregate Scales

Crop rotation enhances soil fertility and health by modulating microbial communities, with soil organic carbon (SOC) dynamics governed by aggregate-microbial interplay. To date, the effects of different crop rotations on SOC fractions and relevant bacterial communities at aggregate scales remain uncertain. Here, a 17-year field experiment was used to reveal the effects of maize monoculture (MM), soybean monoculture (SS), and maize and soybean rotation on the SOC fractions and bacterial communities. Compared with the SS treatment, only the MS treatment significantly increased the particulate organic carbon (POC) content at the aggregate scale. Nevertheless, higher mineral-associated organic carbon (MaOC) contents were observed under the MS and MM treatments than under the SS treatment. The microbial co-occurrence networks for macro- and microaggregates were divided into three main ecological clusters. The specific taxa in Cluster 1 and Cluster 2 are involved in SOC fraction turnover within macro- and microaggregates, respectively. In total, the Vicinamibacteraceae-driven Cluster 1 community dominated the MaOC turnover process within macroaggregates, whereas the Actinobacteria- and Pyrinomonadaceae-driven Cluster 2 communities changed the MaOC turnover process within microaggregates. This study strengthens our understanding of the role of the microbial community in the accumulation of SOC fractions under different crop rotation practices.

Environmental Stress and the Deterministic Assembly of Bacterial Communities in Daqu: The Role of Amino Acid Content Fluctuations

Bacterial communities are highly susceptible to fluctuations in amino acid content. To investigate the response of microbial communities in daqu to environmental perturbations, we employed high-throughput sequencing and statistical analyses. Samples were collected from two workshops (A and B) at distinct stages of daqu fermentation and storage. Our analysis, using the β-nearest taxon index (βNTI), revealed that fungal community assembly is shaped by both stochastic and deterministic processes. In contrast, bacterial communities exhibited a shift towards deterministic assembly under environmental stress, with fluctuations in amino acid content being a primary driver. Notably, communities with active amino acid metabolism displayed a greater involvement of stochastic processes and harbored a higher number of bacterial keystone taxa, which contributed to the stability of microbial networks. This study provides novel insights into the complex interplay between microbial communities and their environment in the context of daqu.

Comparison of Rhizosphere Microbiomes Between Domesticated and Wild Wheat in a Typical Agricultural Field: Insights into Microbial Community Structure and Functional Shifts

While the differences between domesticated crops and their wild relatives have been extensively studied, less is known about their rhizosphere microbiomes, which hold potential for breeding stress-resistant traits. We compared the rhizosphere microbiomes of domesticated wheat (Triticum aestivum L.) and its wild ancestor (Triticum turgidum ssp. dicoccoides) in a typical agricultural field using 16S rRNA and ITS gene sequencing. Our results revealed a high level of conservation in the rhizosphere microbiomes between wild and domesticated wheat, with minimal divergence in community composition and microbial network structure. However, domesticated wheat exhibited a higher prevalence of fungal pathogens and increased functional redundancy, with significant enrichment of genes involved in carbon and nitrogen cycling. The microbial community assemblies in both wheats were predominantly governed by deterministic processes. This suggests that long-term conventional agricultural practices have imposed minor effects on the compositional differences between the microbiomes of wild and domesticated wheat. Nonetheless, the lower abundance of apparent pathogens in the rhizosphere of the wild wheat suggests greater natural biota or innate host plant resistance against pathogenic fungi. This study may provide valuable insights into the host selection, assembly patterns, and functional potential of microbial communities in wild versus domesticated wheat, with implications for manipulating microbial communities in future crop breeding.

Relations Between Core Taxa and Metabolic Characteristics of Bacterial Communities in Litopenaeus vannamei Ponds and Their Probiotic Potential

Microorganisms play a crucial role in purifying aquaculture water bodies. However, there is limited understanding regarding the core species of bacterial communities in aquaculture ponds and their metabolic functions. Using 16S rRNA gene sequencing technology, network analysis, and Biolog EcoPlates, we identified keystone and core taxa of bacterial communities in Litopenaeus vannamei ponds and investigated their correlations with their community's carbon source utilization abilities based on Biolog EcoPlates. We found that keystone and core taxa in bacterial communities were significantly correlated with the carbon source utilization abilities of bacterial communities. The positively correlated core taxa include (1) Bacillus, Flavobacterium, Brevibacillus, and Paenibacillus, which are used as probiotics in aquaculture, and (2) Candidatus Aquiluna, Dechloromonas, Sulfurifustis, Terrimicrobium, Alsobacter, and Gemmobacter, which have been reported to play a role in nitrogen removal. Furthermore, the positively correlated Tropicimonas (Rhodobacterales: Rhodobacteraceae) in aquaculture has not yet been applied. By nitrogen degradation experiments in aquaculture wastewater, we confirmed the synergistic relationship between the genera Tropicimonas and Bacillus. The co-introduction of Tropicimonas sediminicola SDUM182003 and Priestia aryabhattai HG1802 or Bacillus subtilis XQ1804 into the aquaculture tailwater reduced the time required for the removal rates of nitrite nitrogen and nitrate nitrogen to reach over 90% by 24-48 h. Our research reveals the correlation between core taxa and community carbon source utilization, indicating that the core taxa of bacterial communities play a crucial role in the metabolic functions of the community, and offering a reference for exploring new bacterial genera with probiotic potential.

The Response Microbial of the Cucumber Rhizosphere Network Keystone Taxa of the Cucumber Rhizosphere to Continuous Fertilization

Fertilization is a common agricultural practice used to modify the physicochemical properties of soil, which in turn affects plant growth and the rhizosphere microbial community. However, the mechanisms underlying the variation in the cucumber rhizosphere microecosystem have not been thoroughly investigated. In this study, we conducted three rounds of continuous plant growth experiments in pots to test different fertilizers and reveal the evolutionary features of the rhizosphere microecosystem. Through topological analysis of the microbial co-occurrence networks, we identified putative taxa associated with fertilization disturbances. Structural equation models (SEMs) predict plausible mechanistic links between soil physicochemical properties, plant growth and the rhizosphere microbiome. The results suggest that continuous fertilization with single fertilizers reduces microbial diversity and may disrupt the structure of the microbial network. Furthermore, it was found that the predicted distribution of keystone taxa (Bacteroidetes, Ascomycota, etc.) was significantly sensitive to the application of certain fertilizers. Moreover, it was modeled by the SEMs that the accumulation of NO3- and Na+ in fertilized soil was one of the putative principal causes of rhizosphere microbial network deterioration. This study provides new insights into the dynamic changes in the cucumber rhizosphere microbial community under continuous fertilization and highlights the potential utility of SEMs in analyzing causal relationships in agroecosystem studies before experimental validation.

Functional characteristics and mechanisms of microbial community succession and assembly in a long-term moving bed biofilm reactor treating real municipal wastewater

Moving bed biofilm reactor (MBBR) technology with diverse merits is efficient in treating various waste streams whereas their microbial functional properties and ecology still need in-depth investigation, especially in real wastewater treatment systems. Herein, a well-controlled MBBR treating municipal wastewater was established to investigate the long-term system performance and the underlying principles of community succession and assembly. The system successfully achieved ammonium, TN, and chemical oxygen demand (COD) removal of 96.7 ± 2.2%, 75.2 ± 3.6%, and 90.3 ± 3.8%, respectively, under simplified operation and low energy consumption. The effluent TN concentrations achieved 6.2 ± 1.6 mg-N/L despite the influent fluctuations. Diverse functional denitrifiers, such as Denitratisoma, Thermomonas, and Flavobacterium, and the anammox bacteria Candidatus Brocadia successfully enriched in anoxic chamber biofilms. The nitrifiers Nitrosomonas (∼0.73%) and Nitrospira (∼14.0%) exhibited appreciable nitrification capacity in specialized aerobic chambers. Ecological null model and network analysis revealed that microbial community assembly was mainly regulated by niche-based deterministic processes and air diffusion in the aerobic chamber resulted in more intense and complex bacterial interactions. Environmental filters including influent substrate and operating conditions (e.g., reactor configuration, DO, and temperature) greatly shaped the microbial community structure and affected carbon and nitrogen metabolism. The positive ecological roles of influent microflora and functional redundancy in biofilm communities were believed to facilitate functional stability. The anammox process coupled with partial denitrification in a specialized chamber demonstrated positive application implications. These findings provided valuable perspectives in deciphering the microbiological and ecological mechanisms, functional properties, and application potentials of MBBR.

Bt toxins alter bacterial communities and their potential functions in earthworm intestines

The accumulation and persistence of Bt toxins in soils from Bt plants and Bt biopesticides can result in ecological hazards. Earthworms are one of the most frequently used bioindicators for soil ecological monitoring, characterization, and risk assessment. However, the effects of Bt toxins on earthworm bacterial communities have conversely rarely been studied. Here, the dynamics of exposure to exogenous Bt toxins in earthworm intestines were investigated alongside the impacts of Bt toxins on intestinal bacterial community diversity, stability, and potential function. The intestinal concentration of water-dissolved Bt toxins drastically decreased with increased incubation time. Intestinal bacterial community compositions in earthworm intestines were affected by the concentration of Bt toxin that was added and incubation time. Moreover, lower bacterial community α diversity (i.e., based on Sobs and ACE indices) and significantly higher predicted relative abundances of microbial enzymes in the Bt toxin treatment compared with the control were observed alongside differences in bacterial taxonomic and functional compositional profiles after Bt toxin exposure. The observed changes were most strongly associated with variation in overall functional redundancy. Intestinal bacterial taxa probably played pivotal roles in the degradation and transformation of Bt toxins via nitrogen, phosphorus, and polysaccharide hydrolysis metabolic pathways. Although the application of Bt toxin led to lower intestinal community α diversity and stability after 14 days, these community characteristics were restored upon further incubation to 21 days. Thus, these results suggest that earthworm intestinal microbial communities confer strong resilience and the ability to adapt to Bt toxin stress. Consequently, persistent adverse effects of Bt toxins on intestinal microbiomes were not observed after earthworm exposure to Bt toxins.

Dual-Domain Primary Succession of Bacteria in Glacier Forefield Streams and Soils of a Maritime and Continental Glacier

Glaciers retreat rapidly and create newly exposed terrestrial and aquatic habitats in glacier forefields, where primary succession proceeds synchronously in glacier forefields. Here, we introduced the "Dual-Domain Primary Succession" concept to examine the parallel yet distinct primary succession processes in soil and stream ecosystems within glacier forefields, by focusing on Hailuogou Glacier and Urumqi Glacier No.1 in China. Findings showed that soil bacterial communities exhibited higher α-diversity with a decreasing pattern in Hailuogou Glacier, in contrast to Urumqi Glacier No.1, which displayed lower and unimodally distributed α-diversity along the glacier forefield chronosequence (GFC). A similar pattern emerged in streams, except for an increasing α-diversity trend in Urumqi Glacier No.1 stream along the GFC. Additionally, α-diversity in streams changed more rapidly than in soils for Hailuogou Glacier, but more slowly for Urumqi Glacier No.1. Along GFC, both soil and stream bacterial communities experienced spatial variations, primarily due to species turnover. The succession of community composition was evident at the OTU level, with each module in the co-occurrence network consisting of OTUs enriched at specific successional stages. A substantial number of OTUs shared between paired soil and stream samples showed a decreasing trend along the GFC, while β-diversity increased. The results suggested that bacterial communities have a similar succession pattern but in different pace between soil and stream while having distinct successional trajectories between the studied glaciers. This study highlighted the "Dual-Domain Primary Succession" in glacier forefields, but further studies with more glaciers are necessary to make broader generalizations.

Vegetation types shape the soil micro-food web compositions and soil multifunctionality in Loess Plateau

Introduction

Vegetation degradation and soil erosion are severe problems in the Loess hilly region, rendering it one of the most ecologically vulnerable areas in China and globally. Vegetation restoration has been recognized as an effective approach to amending the fragile ecological environment and restoring degraded ecosystems.

Methods

The effects of different vegetation types: Caragana korshinskii, Prunus armeniaca L., Pinus tabuliformis Carrière, Medicago sativa L., and the control vegetation Stipa bungeana on soil micro-food webs and soil multifunctionality, as well as their response mechanisms to soil environmental drivers, were investigated using High-throughput sequencing technology.

Results

C. korshinskii significantly enhanced soil physicochemical properties and soil enzyme activities by facilitating the stability of the soil micro-food web structure driven by soil bacteria and fungi and increasing the soil multifunctionality in contrast to S. bungeana. Prunus armeniaca also improved soil multifunctionality by promoting soil organic carbon and alkaline phosphatase activity. However, the stability of the soil micro-food web structure and soil multifunctionality were suboptimal in P. tabuliformis and M. sativa. Soil pH, along with carbon, nitrogen, and phosphorus cycling nutrients and enzymes, profoundly influences the structure of the soil micro-food web and soil multifunctionality; among these factors, those related to the carbon and phosphorus cycles are identified as key influencing factors.

Discussion

Therefore, a vegetation restoration strategy prioritizing C. korshinskii as the dominant vegetation type, supplemented by P. armeniaca, significantly impacts restoring soil multifunctionality and stabilizing the soil micro-food web in Loess hill regions and comparable ecological areas.

In-Depth Analysis of Soil Microbial Community Succession Model Construction under Microplastics Stress

Although microplastics (MPs) toxicity to soil microorganisms has been preliminarily explored, the underlying reasons affecting the direction of microbial community succession are unclear. This study aimed to investigate the impacts of MPs infer community assembly mechanisms through phylogenetic bin-based null model analysis, network models, and protein function prediction in five typical Northeast China five typical soils. The results show that microbial communities in soils with high organic matter exhibit a stronger response to MPs, with enhanced protein functionality, network regulation, and assembly processes. The presence of MPs increased the drift process in the soil microbial community assembly by 2%, a deterministic process influenced by MPs, and enhanced the complexity and stability of the community assembly. Overall, MPs altered microbial protein function and regulatory networks by affecting diversity and community assembly processes, leading to shifts in microbial community succession. This study provided a theoretical basis for further study of the ecotoxicological effects of MPs in soil.

Soil organic matter composition affects ecosystem multifunctionality by mediating the composition of microbial communities in long-term restored meadows

BACKGROUND

Soil organic matter composition and microbial communities are key factors affecting ecosystem multifunctionality (EMF) during ecosystem restoration. However, there is little information on their interacting mechanisms in degraded and restored meadows. To fill this knowledge gap, plant, root and soil samples from alpine swamp meadows, alpine Kobresia meadows, severely degraded alpine meadows, short-term restored meadows (< 5 years) and long-term restored meadows (6-14 years) were collected. We leveraged high-throughput sequencing, liquid chromatography and mass spectrometry to characterize soil microbial communities and soil organic matter composition, measured microbial carbon metabolism and determined EMF.

RESULTS

It emerged that the similarity of soil microorganisms in meadows decreased with increasing heterogeneity of soil properties. Dispersal limitation and ecological drift led to the homogenization of the bacterial community. Based on co-occurrence network analysis, an increase in microbial network complexity promoted EMF. Root total phosphorus and soil organic matter components were the key predictors of EMF, while organic acids and phenolic acids increased the stability of the microbial network in long-term restored meadows. Carbon metabolism did not increase in restored meadows, but the niche breadth of soil microorganisms and the utilization efficiency of small molecular carbon sources such as amino acids did increase.

CONCLUSIONS

These findings emphasize the importance of soil organic matter composition in ecological restoration and that the composition should be considered in management strategies aimed at enhancing EMF.