QMEC: a tool for high-throughput quantitative assessment of microbial functional potential in C, N, P, and S biogeochemical cycling

Heterogeneous microstructure induces floatation in high-rate anammox granules

The floatation of anammox granules can be a serious challenge in practical wastewater treatment, as it can deteriorate reactor performance and cause bacterial loss. To deepen the understanding of floatation mechanism, in this study, both the floating (F-AnGS) and settling anammox granules (S-AnGS) from a high-rate anammox reactor were comparatively investigated. F-AnGS demonstrated 1.6 times higher specific anammox activity compared to S-AnGS, but only 65 % of produced gas could be successfully released, as quantified by anaerobic respirometry. In addition to the overall EPS accumulation, F-AnGS exhibited a heterogeneous microstructure distinct from that of S-AnGS, as revealed by 3D X-ray microscopic imaging at the single granule level. The heterogeneous distribution of EPS, which can form a dense surface layer, was the main cause for granule floatation. The heterogeneous microstructure of F-AnGS can reduce the distance between microorganisms and enhance the metabolic interaction between anammox bacteria and heterotrophs. The abundance of community members did not have a significant variation, but the functional genes related to anammox and partial denitrification pathway were significantly increased, indicating the enhanced nitrite loop in F-AnGS. This study proposed new structural insights into mechanism of anammox granule floatation, suggesting the appropriate activity control of granule-based anammox process.

Aluminum and microplastic release from reflective agricultural films disrupt microbial communities and functions in soil

Reflective agricultural films are widely used in vegetable production and orchards to repel pests, accelerate fruit ripening, and boost yields. These films, composed of a plastic base metallized with aluminum (Al), degrade over time in soil, releasing Al and microplastics. This study investigated the aging and weathering of Al-coated reflective films (polyethylene terephthalate, PET-based) under UV radiation, simulated rainfall, and soil burial for up to 120 days, assessing the effects of released Al and microplastics on soil chemistry and microbial communities. Weathering was confirmed by the formation of C-O/CO functional groups, an increasing carbonyl index, and the oxidation of Al to Al₂O₃, as shown by Fourier-transform infrared (FTIR) and X-ray photoelectron spectroscopy (XPS). Faster Al-coated shedding and PET oxidation were observed in the soil environment. Microplastics (0.5 % w/w) from the films reduced soil micronutrient availability (Fe, Mn, Cu), suppressed functional genes involved in carbon, nitrogen, and phosphorus cycling, and shifted microbial communities towards oligotrophic bacteria enrichment (e.g., RB41, Candidatus_Udaeobacter, Gemmatimonadetes, and Chloroflexi) while reducing copiotrophic bacteria (e.g., Sphingomonas, Ellin6067, Dongia, Puia, and Flavisolibacter). Therefore, these findings highlight that reflective film weathering strongly alters soil nutrient content and microbial community composition, with potential implications for soil health and agricultural sustainability.

Distinct vertical profiles of microbial communities and functional genes between different lake sediment layers mediated by nutrients in the sediments and pore waters

Lakes, as vital wetland ecosystems, face increasing anthropogenic pressures, including nutrient pollution, which significantly exacerbates the threat of eutrophication. Microorganisms inhabiting lake sediments are key drivers of biogeochemical cycles of essential elements in aquatic ecosystems. While their roles in eutrophic lakes have been explored, their vertical profiles of community compositions and functional genes in the sediments of eutrophic lakes remain poorly resolved. This study aimed to investigate the spatial distribution patterns of and correlations between nutrient concentrations, microbial communities, and element-cycling-related functional genes in the sediment of Honghu Lake, a representative of shallow lakes located in China's Hubei province. 16S rRNA sequencing was used to explore the microbial community structure, and a high-throughput quantitative-PCR-based gene chip, quantitative microbial element cycling (QMEC), was employed to assess the abundance of functional genes for C, N, P, and S metabolisms. A series of bioinformatic analyses were orchestrated to explore the functional differences between sediment layers. The results indicate that nutrient concentrations, functional gene abundance, and alpha diversity of microbial communities generally decrease with depth from the surface sediment to deeper layers. The main environmental variables correlating with the microbial communities included total phosphorus and total nitrogen in the sediments, and NH4+-N in the pore waters. In the co-occurrence networks, different highly connected species were identified as key members in different sediment layers. Some functional genes were exclusively detected in specific locations and layers, increasing the heterogeneity of the biogeochemical functions, and weakening the functional redundancy of microbial communities. This study showed the connections between environmental variables, microbial community compositions, and element cycling functions in a typical shallow lake, and emphasized the heterogeneity of nutrients, microbial communities, and functional genes in lake sediments and other aquatic ecosystems.

Experimental evidence for viral impact on microbial community, nitrification, and denitrification in an agriculture soil

Viruses are ubiquitous, and their potential impacts on biogeochemical cycles in soil have largely been inferred from correlation evidence and virome studies. Manure has been demonstrated to affect nitrogen cycle by altering soil nutrients and microbial communities. However, the direct impacts of viruses derived from manure on microbial community, nitrification, and denitrification remained exclusive. In this study, concentrated viral extracts obtained from manure were added into an agricultural soil in varying dosages: a one-time addition of 10-fold viruses or a weekly addition of 1-fold viruses for ten weeks. The results showed that both viral extracts and manure significantly changed the microbial community compositions and structures. The effect of manure on microbial diversity was concentration-dependent, differing from the viral impact on microbial diversity in soil. Deterministic processes predominated in the assembly of microbial communities in both viral and manure treatments, with an increased contribution of deterministic processes observed after these treatments. Additionally, a high concentration (10-fold) of viruses enhanced N2O production and reduction in soil. In the control treatment, N2O production was driven by bacterial denitrification, fungal denitrification, and chemo-denitrification. However, bacteria became the dominant driver of N2O production in both virus and manure treatments. Overall, experimental evidence for viral impacts on the composition and assembly of microbial community, as well as on nitrification and denitrification processes, was provided through a 70-day microcosm experiment. These findings highlight the importance of viruses in regulating the distribution and functioning of microbes in terrestrial ecosystems.

Viruses Facilitate Energy Acquisition Potential by Their Bacterial Hosts in Rhizosphere of Grafted Plants

Viruses alter the ecological and evolutionary trajectories of bacterial host communities. Plant grafting is a technique that integrates two species or varietiies and have consequences on the rhizosphere functioning. The grafting effects on the taxonomic and functional assembly of viruses and their bacterial host in the plant rhizosphere remain largely elusive. Using shotgun metagenome sequencing, we recover a total of 1441 viral operational taxonomic units from the rhizosphere of grafted and ungrafted plants after 8-year continuous monoculture. In the grafted and ungrafted rhizosphere, the Myoviridae, Zobellviridae and Kyanoviridae emerged as the predominant viral families, collectively representing around 40% of the viral community in each respective environment. Grafting enriched the members in viral family Kyanoviridae, Tectiviridae, Peduoviridae and Suoliviridae, and auxiliary metabolic genes related to pyruvate metabolism and energy acquisition (e.g., gloB, DNMT1 and dcyD). The virus-bacterial interactions increased the rapid growth potential of bacteria, which explains the strong increase in abundance of specific bacterial hosts (i.e., Chitinophagaceae, Cyclobacteriaceae and Spirosomaceae) in the grafted-plant rhizosphere. Overall, these results deepen our understanding of microbial community assembly and ecological services from the perspective of virus-host interactions.

Bacterially mediated phosphorus cycling favors resource use efficiency of phytoplankton communities in a eutrophic plateau lake

Resource use efficiency has garnered much attention globally owing to its linkage with phytoplankton growth and extinction. However, little is known about how microbially mediated phosphorus (P) cycling affects phytoplankton P resource use efficiency (RUEP), especially in eutrophic plateau lakes. Here, we studied the vertical relationship between bacterial communities and phytoplankton RUEP in water profiles from Hongfeng Lake, a eutrophic lake located in the Guizhou Plateau, and further revealed the influence of bacterially mediated endogenous P release on phytoplankton RUEP. Generally, phytoplankton RUEP increased slightly and then decreased toward deep water layers. Compared to dormancy and recovery periods, outbreak period showed higher RUEP in water profiles and bottom waters. The importance of phytoplankton RUEP in the co-occurrence networks progressively increased from dormancy to outbreak periods. Rhodococcus may affect phytoplankton RUEP in water profiles by dissolving Ca-P or polymerizing excess phosphate. Functional composition of P-related genes was largely affected by NH4Cl-Po, BD-TP and BD-Pi in recovery period, and by NaOH-Po in outbreak period. During phytoplankton growth, bacterial P functional genes promote phytoplankton RUEP mainly by regulating Pi solubilization and Po mineralization in surface sediments. Note that ppk could regulate the formation of polyphosphates and thus reduce phytoplankton RUEP. Taken together, our study revealed the relationship between bacterially mediated P cycling and phytoplankton RUEP, which can effectively monitor the potential risk of phytoplankton blooms and improve eutrophication management.

Active restoration facilitates sedge colonization in degraded alpine meadows on the Qinghai-Tibetan Plateau

Extremely degraded alpine meadow is among the most challenging types of grasslands to restore due to its severely deteriorated habitat and limited self-recovery capability. Since the 2000s, cultivating artificial grasslands has been widely applied as the primary method for restoring theses meadows on the Qinghai-Tibetan Plateau (QTP). However, the performance of climax species (sedges of alpine meadows on the QTP), which is crucial to determine the restoration efforts of alpine meadow, has not received sufficient attention yet. With this context, field data of cultivated grasslands with different restoration stages (S1: 1-6 years, S2: 7-12 years, S3: over 13 years), was collected to examine the change and influencing factors of sedges over restoration time. The results demonstrated that restoration actions facilitated increases in the sedge biomass and the percentage of sedge biomass in S3, though these values remained lower than those in healthy alpine meadow. A clear difference in plant community structure was observed among different grasslands, characterized by an increase in forb abundance and species richness alongside a decrease in grass abundance over restoration time. Soil moisture and organic carbon of S2 and S3, and soil total nitrogen of S3 were significantly improved, while soil available nutrients remained stable compared to the degraded meadow. The relative abundance of most nitrogen- and phosphorus-related functional genes either declined or stabilized during the restoration process. The sedge biomass (77.36 %) and the percentage of sedge biomass (88.35 %) were largely explained by the coupling effects of plant indicators (grass abundance and species richness) and soil indicators (soil bulk density, moisture, organic carbon, and total nitrogen). This study highlights the positive influence of active restoration actions on sedge colonization and the asynchronous dynamics between aboveground (plant community) and belowground components (soil available nutrients and microbial community). These findings imply that accelerating soil nutrients accumulation and cycling should be prioritized in post-restoration management of cultivated grasslands on the QTP and other alpine regions.

Microbial life-history strategies and genomic traits between pristine and cropland soils

Microbial life-history strategies [inferred from ribosomal RNA operon (rrn) gene copy numbers] and associated genomic traits and metabolism potentials in soil significantly influence ecosystem properties and functions globally. Yet, the differences in microbial strategies and traits between disturbed (cropland) and pristine soils, along with their dominant driving factors, remain underexplored. Our large-scale survey of 153 sites, including 84 croplands and 69 pristine soils, combined with long-term field experiments demonstrates that cropland soils support microbial communities with more candidate r-strategies characterized by higher rrn copy numbers and genomic traits conducive to rapid resource utilization. Conversely, pristine soils tend to host communities aligned with more candidate K-strategies marked by high resource use potentials. Elevated nitrogen (N) and phosphorus (P) levels in cropland soils emerge as key factors promoting these candidate r-strategies, overshadowing the influence of organic carbon content, soil structure, or climatic conditions. Results from four long-term field experiments also corroborate that sustained N and P inputs significantly elevate rrn copy numbers, favoring these candidate r-strategists. Our findings highlight that land use and fertilization practices critically shape microbial life-history strategies, with nutrient availability being a decisive factor in increasing the r-strategists in cropland soils.IMPORTANCEMicrobial life-history strategies and genomic traits are key determinants shaping the response of populations to environmental impacts. In this paper, 84 cropland and 69 pristine soil samples were studied, and microorganisms in two ecosystems were categorized into two types of ecological groups using the classical copiotroph-oligotroph dichotomy, promoting a general understanding of the ecological roles of microorganisms. This study is the first to investigate the microbial life-history strategies under different land uses across five climatic zones in China. The results showed that the microbes in cropland soils are more copiotrophic than pristine soils. It also demonstrates that elevated levels of nitrogen and phosphorus in cropland soils are the key factors promoting these r-strategies. This observation emphasizes the critical role of nutrient management in shaping microbial community dynamics and ecosystem functioning and lays the foundation for predicting the response of microbial community composition under resource perturbation.

Bacterial community assembly processes mediate soil functioning under cadmium stress in the agroecosystem

Elucidating the effects of community assembly processes on soil functioning represents a crucial challenge in theoretical ecology, particularly under cadmium (Cd) stress, where our understanding remains limited. In this study, we therefore used amplicon sequencing and a quantitative-PCR-based chip to analyze the changes in bacterial community characteristics, soil functioning and their interrelationships in agroecosystems under different levels of Cd stress. The results indicated that Cd stress led to a decline in community diversity (Z-score), network complexity and stability, an increase in species turnover, and a regulation of community structure. Cd stress significantly increased the relative importance of dispersal limitation and homogeneous selection, reducing community drift and rendering the community more deterministic. Finally, Cd stress significantly reduced soil functional potential (Z-score) and soil functional stability (Z-score), impairing soil carbon, nitrogen, phosphorus, and sulfur cycling. It is noteworthy that correlation and random forest analyses revealed significant effects of specific community assembly processes, including dispersal limitation, homogeneous selection, drift (and others), on changes in soil functional potential (Z-score). The results emphasize the pivotal role of community assembly processes in dictating soil functioning under Cd stress, thereby offering novel insights into the comprehension of microbial-driven mechanisms governing soil functioning.

Warming-Induced Plant Species Shifts Lead to Substantial Losses of Wetland Soil Carbon

Wetlands are large reservoirs of soil organic carbon (SOC), storing one-third of global SOC within 6% of the land surface. However, the feedback direction and magnitude of wetland SOC storage to climate warming remain unclear. Here we present results from an 8-year (2014-2022) wetland warming experiment in the Yellow River Delta, revealing that wetland SOC storage responds to warming in a phase-dependent manner. We found that warming initially reduced both carbon input and output but did not change SOC storage. However, SOC storage abruptly decreased by 21.4% in 2020, which persisted over the following 2 years. This occurred mainly due to shifts in the biomass of dominant plant species (P. australis) under warming, reducing carbon input, increasing microbial carbon degradation, and resulting in microbial necromass carbon loss. These results highlight the critical role of dominant plant species in driving the wetland soil carbon cycle and its feedback to climate change.

A comparative analysis of the microbial community structure and functional gene profile between healthy and diseased Gracilaria lemaneiformis

Marine macroalgae and their associated microbial communities are pivotal in shaping coastal ecosystems and facilitating biogenic elements' biochemical cycles. In this study, we implemented the high-throughput sequencing technology to sequence bacterial 16S rRNA gene to comprehensively analyze the bacterial communities of healthy and diseased macroalgae as well as the surrounding seawaters. The results revealed that Proteobacteria and Bacteroidota were the two main phylum in all samples. Alphaproteobacteria, Gammaproteobacteria and Bacteroidota were the predominant bacterial classes. This observation underscored that the composition of bacterial communities remains comparably consistent at higher taxonomic levels, regardless of variations in their health statuses. The alpha-diversity indices of seawater bacterial communities, epiphytic communities, and endophytic communities showed no significant differences. Epiphytic bacterial communities harbored a greater proportion of colonized bacteria, such as Vibrio and Pseudomonas. While endophytic bacterial communities contained a higher presence of tissue-degrading microbial assemblages, the primary bacterial communities were predominantly affiliated with Rhodobacteraceae and Flavobacteriaceae. Temperature, salinity, nitrate and nitrite concentration were the most significant properties correlated with seawater, epiphytic and endophytic bacterial communities in different health statuses revealed by Canonical correspondence analysis. A PICRUSt analysis demonstrated the metabolic functional prediction. Nitrogen and sulfate reduction genes were mainly concentrated in epiphytic bacterial communities in good health. Endophytic bacterial communities in disease had higher carbon and nitrogen fixation potentials. These results confirmed that bacteria, macroalgae, and environmental properties had an interactive relationship, all related to the momentous ecological benefits of macroalgae.

Dynamic responses in bioaugmentation of petroleum-contaminated soils using thermophilic degrading consortium HT: Hydrocarbons, microbial communities, and functional genes

Bioaugmentation offers an effective strategy for the bioremediation of petroleum-contaminated soils. However, little is known about petroleum hydrocarbons (PHs) degradation with thermophilic consortium application under high temperature. A microcosm was established to study hydrocarbons degradation, microbial communities and functional genes response using a thermophilic petroleum-degrading consortium HT. The results showed that the consortium HT significantly enhanced PHs degradation, particularly for medium (C16-C21) (87.1 %) and long-chain alkanes (C21-C40) (67.2 %) within 140 days under high temperature. Colonization of HT in the soil exhibited lagged characteristics, with a substantial increase in bacterial genera originated from the HT after 60 days. Additionally, LEfSe analysis indicated that the biomarkers of HT treatment were mainly from the HT consortium. Moreover, functional analysis revealed genes related to n-alkane degradation (AlkB, P450, LadA), alkane utilization regulator (AraC, TetR, GntR), as well as several thermotolerance genes were significantly increased in HT treatment. Additionally, network analysis demonstrated distinct co-occurrence patterns induced by nutrient addition and exogenous consortium, with the latter strengthening interactions and stability of bacterial networks under high temperature. This study represents pioneering investigation into the effects of exogenous thermophilic consortium on petroleum degradation, bacterial communities, functional genes and ecological interactions in application of petroleum remediation under thermophilic conditions.

Shifts in fungal communities drive soil profile nutrient cycling during grassland restoration

Soil microbial diversity and community life strategies are crucial for nutrient cycling during vegetation restoration. Although the changes in topsoil microbial communities during restoration have been extensively studied, the structure, life strategies, and function of microbial communities in the subsoil remain poorly understood, especially regarding their role in nutrient cycling during vegetation restoration. In this study, we conducted a comprehensive investigation of the changes in the soil microbial community, assembly process, life strategies, and nutrient cycling functional genes in soil profiles (0-100 cm) across a 36 year chronosequence (5, 15, 28, and 36 years) of fenced grassland and one grazing grassland on the Loess Plateau of China. Our results revealed that soil organic carbon increased by 76.0% in topsoil and 91.6% in subsoil after 36 years of restoration. The bacterial communities were influenced primarily by soil depth, while the fungal communities were highly sensitive to the years of restoration. Microbes in the subsoil recovered faster, and the microbial community structure and functional genes in the soil profiles gradually became more consistent following restoration. In addition, we observed a transition in microbial life history strategies from a persistent K-strategy to a rapid r-strategy during restoration. Notably, the fungal community assembly process played an important role in changes in nutrient cycling genes, which were accompanied by increased carbon fixation and nitrogen mineralization function. Overall, our findings provide several novel insights into the impact of changes in the fungal community on soil nutrient cycling in the soil profile during vegetation restoration.IMPORTANCEOur study revealed that microbes in the subsoil recovered faster than those in the topsoil, which contributed to the reduction in differences in microbial community structure and the distribution of functional genes throughout the soil profile during the restoration process. Importantly, the assembly of fungal communities plays a pivotal role in driving changes in nutrient cycling genes, such as increased carbon fixation and nitrogen mineralization, alongside a reduction in carbon degradation gene abundance. These alterations increase soil organic carbon and nutrient availability during restoration. Our results increase the understanding of the critical role of fungal communities in soil nutrient cycling genes, which facilitate nutrient accumulation in soil profiles during grassland restoration. This insight can guide the development of strategies for manipulating fungal communities to increase soil nutrients in grasslands.

Recoupling of Soil Carbon, Nitrogen, and Phosphorus Cycles along a 30 Year Fire Chronosequence in Boreal Forests of China

The biogeochemical coupling of soil carbon, nitrogen, and phosphorus (C-N-P) cycles is crucial for maintaining the ecological balance of boreal forests. Yet, the current understanding of wildfire disturbance is only based on changes in elemental contents, thereby lacking any within-ecosystem corroboration of biogeochemical coupling. Here, we conducted a field survey of microbial functional associations for 53 genes related to soil C-N-P cycling from 17 locations spanning a 30 year succession period after high-severity forest fires in the Greater Khingan Mountains (Inner Mongolia-China). We found that bacteria proliferated and dominated the competition with fungi by encoding genes for recalcitrant C decomposition, N fixation, and inorganic N cycling during the postfire early succession. Wildfire prominently decoupled the microbial functional associations of soil C-N-P cycling, particularly in organic-inorganic N turnover. However, over the 30 year succession period, these functional associations recoupled in both soil organic and mineral horizons. Notably, the decoupling of microbial functional associations recovered from a wildfire disturbance faster than the soil C-N-P imbalance. This strong resilience of the microbiome will aid in the recovery of the soil elemental balance and ecosystem stability from the increased intensity of wildfires projected for the boreal forests of China.

The relationship between protist consumers and soil functional genes under long-term fertilization

Protists play a crucial role in terrestrial ecosystems by participating in biogeochemical cycles and contributing to ecological balance and stability. However, much remains to be understood about the intricate interactions between soil protists and biogeochemical processes. Here, we collected rhizosphere soil samples from seven distinct fertilization treatments to investigate the responses of bacteria, protists and functional genes to these varying fertilization practices during sorghum's maturity season. The community composition of both protists and bacteria were significantly affected by different fertilization treatments, with organic fertilization increasing protist diversity but not affecting bacterial diversity. There were noticeable variations in the compositions of functional genes across different fertilization treatments, with organic fertilization enhancing the relative abundance of carbon and phosphorus cycling genes. While fertilization generally increased the relative abundance of protistan consumers, it was observed that organic fertilizers decreased the relative abundance of phototrophs. A substantial number of bacterial taxa, including Acidibacter, Steroidobacter, Lysobacter and Agromyces, which correlated positively with functional genes, were found to be prey for protistan consumers, indicating their crucial role in predicting soil functional genes. Altogether, this study highlights the significant impact of fertilization treatments, especially organic fertilization, on the diversity and functional dynamics of protist and bacterial communities, emphasizing the key role of protistan consumers in regulating the soil microbial community and modulating soil biogeochemical cycles.

Dissolved organic carbon can alter coastal sediment phosphorus dynamic: Effects of different carbon forms and concentrations

Coastal waters are receiving increasing loads of dissolved organic carbon (DOC), differing in structural complexity and molecular weights with potential different effects on the phosphorus (P) dynamics in these waters. This study conducted an in-situ investigation in Xiangshan Harbor, China, to explore the patterns of P release in response to DOC inputs. To further elucidate the underlying mechanisms behind the DOC-affected sediment P release, a two-month mesocosm experiment was undertaken with coastal sediment (Xiangshan Harbor) to which acetate, glucose, and humic acid (representing the fermentation product, the simple available carbon, and the refractory humic-like carbon sources, respectively) were separately added to the overlying water at dosages of 0, 5, 10, and 20 mg C L-1. We found that: i) sediment P release showed a non-linear increase with DOC input, a pattern likely due to the diverse forms of DOC in coastal zones, which had varying impacts on P release; ⅱ) significant P release for labile DOC (acetate- and glucose-amended) treatments but retention for humic acid treatments, and the magnitude of P changes mainly depended on the amount of DOC addition; ⅲ) acetate and glucose shared similar P-release-promotion mechanisms, i.e., decreased dissolved oxygen, increased ppk genes in water, and increased P bacteria and alkaline phosphatase activity were the dominant factors behind the P release for both carbon sources, as indicated by piecewise structural equation modelling; ⅳ) humic acid-inhibitory effects on sediment P release, which likely reflect increasing "P-humic acid" complexes that favor P adsorption and sedimentation and form stable "humic acid-enzyme" complexes that reduce the catalytic activity of alkaline phosphatase. Our findings provide new understanding of relationships between loading of DOC with different form/concentration and sediment P dynamics in coastal areas.

Keystone taxa drive the synchronous production of methane and refractory dissolved organic matter in inland waters

The production of both methane (CH4) and refractory dissolved organic matter (RDOM) depends on microbial consortia in inland waters, and it is unclear yet the link of these two processes and the underlying microbial regulation mechanisms. Therefore, a large-scale survey was conducted in China's inland waters, with the measurement of CH4 concentrations, DOM chemical composition, microbial community composition, and relative environmental parameters mainly by chromatographic, optical, mass spectrometric, and high-throughput sequencing analyses, to clarify the abovementioned questions. Here, we found a synchronous production of CH4 and RDOM linked by microbial consortia in inland waters. The increasing microbial cooperation driven by the keystone taxa (mainly Fluviicola and Polynucleobacter) could promote the transformation of labile DOM into RDOM and meanwhile benefit methanogenic microbial communities to produce CH4. As such, CH4 and RDOM showed consistent spatial differences, which were mainly influenced by total nitrogen and dissolved oxygen concentrations. This finding deepened the understanding of microbial-driven carbon transformation and will help to more accurately evaluate the carbon source-sink relationship in inland waters.

Microplastics in agricultural soil: Unveiling their role in shaping soil properties and driving greenhouse gas emissions

Microplastics (MPs) contamination is pervasive in agricultural soils, significantly influencing carbon and nitrogen biogeochemical cycles and altering greenhouse gas (GHG) fluxes. This review examines the sources, status, mechanisms, and ecological consequences of MPs pollution in agricultural soils, with a focus on how MPs modified soil physicochemical properties and microbial gene expression, ultimately impacting GHG emissions. MPs were found to reduce soil water retention, decreasing soil respiration and increasing emissions of CO2, CH₄, and N2O. They also enhanced soil aggregate stability and influenced soil organic carbon (SOC) sequestration, contributing further to GHG emissions. MPs-induced increases in soil pH were associated with suppressed CH₄ and N2O emissions, whereas the abundance of genes encoding enzymes for cellulose and lignin decomposition (e.g., abfA and mnp) stimulated enzyme activity, intensifying N2O release. Additionally, a reduced soil C/N ratio promoted denitrification processes. Changes in microbial communities, including increases in Actinomycetes and Proteobacteria, were observed, with a rise in genes associated with carbon cycling (abfA, manB, xylA) and nitrification-denitrification (nifH, amoA, nirS, nirK), further exacerbating CO2 and N2O emissions. This review provides valuable insights into the complex roles of MPs in GHG dynamics in agricultural soils, offering perspectives for improving environmental management strategies.

Warm growing season activates microbial nutrient cycling to promote fertilizer nitrogen uptake by maize

The influence of nitrogen (N) inputs on soil microbial communities and N uptake by plants is well-documented. Seasonal variations further impact these microbial communities and their nutrient-cycling functions, particularly within multiple cropping systems. Nevertheless, the combined effects of N fertilization and growing seasons on soil microbial communities and plant N uptake remain ambiguous, thereby constraining our comprehension of the optimal growing season for maximizing crop production. In this study, we employed 15N isotope labeling, high-throughput sequencing, and quantitative polymerase chain reaction (qPCR) techniques to investigate the effects of two distinct growing seasons on microbial communities and maize 15N uptake ratios (15NUR). Our results showed that the warm growing season (26.6 °C) increased microbial diversity, reduced network complexity but enhanced stability, decreased microbial associations, and increased modularization compared to the cool growing season (23.1 °C). Additionally, the warm growing season favored oligotrophic species and increased the abundance of microbial guilds and functional genes related to N, phosphorus, and sulfur cycling. Furthermore, alterations in the characteristics of soil microbial keystone taxa were closely linked to variations in maize 15NUR. Overall, our findings demonstrate significant seasonal variations in soil microbial diversity and functioning, with maize exhibiting higher 15NUR during the warm growing season of the double cropping system.

From nature to urbanity: exploring phyllosphere microbiome and functional gene responses to the Anthropocene

The Anthropocene exerts various pressures and influences on the stability and function of the Earth's ecosystems. However, our understanding of how the microbiome responds in form and function to these disturbances is still limited, particularly when considering the phyllosphere, which represents one of the largest microbial reservoirs in the terrestrial ecosystem. In this study, we comprehensively characterized tree phyllosphere bacteria and associated nutrient-cycling genes in natural, rural, suburban, and urban habitats in China. Results revealed that phyllosphere bacterial community diversity, richness, stability, and composition heterogeneity were greatest at the most disturbed sites. Stochastic processes primarily governed the assembly of phyllosphere bacterial communities, although the role of deterministic processes (environmental selection) in shaping these communities gradually increased as we moved from rural to urban sites. Our findings also suggest that human disturbance is associated with the reduced influence of drift as increasingly layered environmental filters deterministically constrain phyllosphere bacterial communities. The intensification of human activity was mirrored in changes in functional gene expression within the phyllosphere microbiome, resulting in enhanced gene abundance, diversity, and compositional variation in highly human-driven disturbed environments. Furthermore, we found that while the relative proportion of core microbial taxa decreased in disturbed habitats, a core set of microbial taxa shaped the distributional characteristics of both microbiomes and functional genes at all levels of disturbance. In sum, this study offers valuable insights into how anthropogenic disturbance may influence phyllosphere microbial dynamics and improves our understanding of the intricate relationship between environmental stressors, microbial communities, and plant function within the Anthropocene.

The effects of different halogenated-pyrethroid pesticides on soil microbial community

The application of pesticides increases crop yields but affects the structure and function of the soil microbial community. Halogens are common functional modification groups in chemical compounds, and innovative pesticides have been developed on the basis of these groups. However, the effects of different halogen substituents on soil microorganisms remain unclear. This study investigated the effects of three pyrethroid pesticides (deltamethrin, cypermethrin, and cyfluthrin) on the soil microbiota. Our results revealed that all these pesticides significantly reduced the stability of the bacterial communities and decreased bacterial diversity at high concentrations. Compared with deltamethrin (Br-) and cypermethrin (Cl-), low concentrations (0.5 mg/kg) of cyfluthrin (F-) increased soil bacterial diversity by 23.14 % and increased the potential for nitrogen fixation by 2.00 % and nitrification by 3.39 %, thus making it a relatively eco-friendly option. Our findings provide new insights into the potential ecological effects of halogenated pyrethroid pesticides on soil ecosystems.

Deciphering Molecular Mechanisms and Diversity of Plant Holobiont Bacteria: Microhabitats, Community Ecology, and Nutrient Acquisition

While gaining increasing attention, plant-microbiome-environment interactions remain insufficiently understood, with many aspects still underexplored. This article explores bacterial biodiversity across plant compartments, including underexplored niches such as seeds and flowers. Furthermore, this study provides a systematic dataset on the taxonomic structure of the anthosphere microbiome, one of the most underexplored plant niches. This review examines ecological processes driving microbial community assembly and interactions, along with the discussion on mechanisms and diversity aspects of processes concerning the acquisition of nitrogen, phosphorus, potassium, and iron-elements essential in both molecular and ecological contexts. These insights are crucial for advancing molecular biology, microbial ecology, environmental studies, biogeochemistry, and applied studies. Moreover, the authors present the compilation of molecular markers for discussed processes, which will find application in (phylo)genetics, various (meta)omic approaches, strain screening, and monitoring. Such a review can be a valuable source of information for specialists in the fields concerned and for applied researchers, contributing to developments in sustainable agriculture, environmental protection, and conservation biology.

Enhanced denitrification by sunlight-hematite: A neglected nitrogen flow pattern in red soil

Mineral-microbe interactions in the Earth's Critical Zone significantly influence elemental biogeochemical cycling and energy flow processes. This study addresses the key scientific question of how semiconducting minerals drive microbial nitrogen cycling. In the red soil environment, the presence of semiconducting minerals enhances the denitrification process mediated by facultative microorganisms (Pseudomonas aeruginosa PAO1) with denitrifying activity. Compared to darkness, light significantly enhanced the synergistic denitrification kinetic process of red soil and Pseudomonas aeruginosa PAO1 (1.87 times). Cyclic voltammetry shows that the P. aeruginosa PAO1-red soil synergistic system exhibits distinct redox peaks under light. The constant potential current curve and electrochemical impedance spectroscopy measurements reveal a high photocurrent density (1.0 μA/cm2) and minimal polarization resistance (102 Ω) under this condition. These findings confirm that the sunlight-red soil-P. aeruginosa PAO1 synergistic process has excellent electron generation and migration capacity, active redox reactions, and good electron compatibility. Additionally, the photoelectrons of semiconductive minerals in red soil profoundly impact the metabolic processes of microbial denitrification functional genes. Using real-time polymerase chain reaction (qPCR) gene array technology, the abundance of nitrogen metabolism functional genes in P. aeruginosa PAO1 increased by 200 % during the light-red soil synergistic process. Notably, denitrification-related genes (ureC, nirS1, gdhA, and nosZ2) were significantly upregulated. This study confirms that semiconducting minerals are involved in the nitrogen cycle pathway of microbial denitrification and supplements the theory of mineral-microbial synergistic element biogeochemical cycling in the natural environment.

Lake ecological restoration of vegetation removal mitigates algal blooms and alters landscape patterns of water and sediment bacteria

Elucidating the influences of ecological restoration measure of lakeshore vegetation removal on water quality and biological community is an important but underestimated subject. We adopted molecular and statistical tools to estimate ecological restoration performance in a plateau lake receiving vegetation removal and simultaneously investigated variabilities of bacterial communities in water and sediment. Significant decreases in lake trophic level and algal bloom degree followed notable decreases in water total nitrogen and total phosphorus after vegetation removal. Non-significant changes in sediment nutrients accompanied remarkable variabilities of abundance and composition of nutrient-cycling functional genes (NCFGs) of sediment bacteria. Taxonomic and phylogenetic α-diversities, functional redundancies, and dispersal potentials of bacteria in water and sediment decreased after vegetation removal, and community successions of water and sediment bacteria were separately significant and non-significant. There were opposite changes in ecological attributes of bacteria in water and sediment in response to vegetation removal, including niche breadth, species replacement, richness difference, community complexity, and community stability. Species replacement rather than richness difference affected more on taxonomic β-diversities of bacteria in water and sediment before and after vegetation removal, and determinism rather than stochasticity dominated bacterial community assemblage. Our results highlighted vegetation removal mitigated algal bloom and affected differently on landscapes of water and sediment bacteria. These findings point to dominant ecological mechanisms underlying landscape shifts in water and sediment bacteria in a disturbed lake receiving vegetation removal and have the potential to guide lake ecological restoration.

Symbiotic bacterial communities and carbon metabolic profiles of Acropora coral with varying health status under thermal stress

Thermal-induced coral bleaching has received substantial research attention; however, the dynamics of symbiotic coral-associated bacterial communities are underexplored and the roles of coral with intermediate health status remain unclear. Using high-throughput sequencing and biochemical analyses, we found that the symbiotic zooxanthellae number gradually decreased with the increase of bleaching degree (non-bleached, semi-bleached, and fully-bleached) in the coral Acropora pruinosa. The semi-bleached host exhibited a relatively more complex microbial interaction network. For the carbon metabolic profiles, relatively higher carbon-fixing abilities observed in non-bleached coral symbiotic bacteria, followed by semi-bleached host, and lowest values appeared in fully-bleached coral. Partial least-squares pathway modeling revealed that bacterial community features and carbon metabolic function were directly related with health status, while temperature exerted a strong influence on the bleaching resilience. These findings can help us better understand the coral microecological feature and carbon metabolic potential under changing environment.

Microbial nitrogen cycling in Microcystis colonies and its contribution to nitrogen removal in eutrophic Lake Taihu, China

Cyanobacterial blooms induced by excessive loadings of nitrogen (N) and other nutrients are a severe ecological problem in aquatic ecosystems. Previous studies of N removal have primarily focused on sediment-water interface, yet the role of cyanobacterial colonies has recently been attracting more research attention. In this study, N cycling processes were quantified for cyanobacterial colonies (primarily Microcystis colonies) and their contribution to N removal was estimated for a large, shallow eutrophic lake in China, Lake Taihu. Various N cycling processes were determined via stable 15N isotope, together with 16S rRNA gene sequencing and quantitative microbial element cycling (QMEC) chip. Denitrification was found to be the most prominent process, estimated to be 36.63, 9.85, 3.35, and 3.15 times higher than dissimilatory nitrate reduction to ammonium (DNRA), nitrification, ammonium (NH4+) uptake and nitrate (NO3-) uptake rates, respectively. Denitrifiers accounted for a large part of the bacterial taxa (35.50 ± 24.65%), and the nirS gene was the most abundant among N cycling-related genes, with (2.54 ± 0.51) × 109 copies g-1Microcystis colonies. A field investigation revealed a positive correlation between the potential denitrification rate and the Chl-a concentration (mostly derived from Microcystis colonies). Based on a multiple stepwise regression model and historical data from 2007 to 2015 for Lake Taihu, the total amount of N removed via denitrification by Microcystis colonies was estimated at 171.72 ± 49.74 t yr-1; this suggests that Microcystis colonies have played an important role in N removal in Lake Taihu since the drinking water crisis in 2007. Overall, this study revealed the importance of denitrification within Microcystis colonies for N removal in eutrophic lakes, like Lake Taihu.

Hydrogeochemical differences drive distinct microbial community assembly and arsenic biotransformation in unconfined and confined groundwater of the geothermal system

High‑arsenic (As) groundwater in geothermal aquifers poses a serious threat to public health. Assembly processes governing groundwater microbial community related to As biotransformation are still unexplored in geothermal groundwater across different aquifers. To fill this gap, groundwater microorganisms, community assembly processes, and microbially metabolic coupling of carbon (C), nitrogen (N), phosphorus (P), sulfur (S), and arsenic (As) were investigated in unconfined and confined groundwater in the thermal reservoirs of the Guide Basin. The difference in groundwater hydrogeochemicals led to the heterogeneity of the microbial community and microbially mediated C, N, P, S, and As cycling between unconfined and confined groundwater. Higher temperature and As concentrations, low nutrient supply, and reduced conditions in confined groundwater supported stronger interspecific coexistence and environmental selection, thus promoting the proliferation of As-resistant microorganisms (ARMs) and simplifying the community assemblage. Abundant available nutrient supply and oxidizing conditions supported an increased species diversity and metabolic functionality in unconfined groundwater. S oxidizers, C fixation, and C degradation bacteria potentially contributed to the decreased As concentrations in unconfined groundwater. However, ARMs, ammonification, and anaerobic ammonia-oxidizing bacteria potentially caused As mobilization in confined groundwater. Overall, our results give a comprehensive insight into the interaction between As and microorganisms in geothermal groundwater.

Impact of Viruses on Prokaryotic Communities and Greenhouse Gas Emissions in Agricultural Soils

Viruses are abundant and ubiquitous in soil, but their importance in modulating greenhouse gas (GHG) emissions in terrestrial ecosystems remains largely unknown. Here, various loads of viral communities are introduced into paddy soils with different fertilization histories via a reciprocal transplant approach to study the role of viruses in regulating greenhouse gas emissions and prokaryotic communities. The results showed that the addition of viruses has a strong impact on methane (CH4) and nitrous oxide (N2O) emissions and, to a minor extent, carbon dioxide (CO2) emissions, along with dissolved carbon and nitrogen pools, depending on soil fertilization history. The addition of a high viral load resulted in a decrease in microbial biomass carbon (MBC) by 31.4%, with changes in the relative abundance of 16.6% of dominant amplicon sequence variants (ASVs) in comparison to control treatments. More specifically, large effects of viral pressure are observed on some specific microbial communities with decreased relative abundance of prokaryotes that dissimilate sulfur compounds and increased relative abundance of Nanoarchaea. Structural equation modeling further highlighted the differential direct and indirect effects of viruses on CO2, N2O, and CH4 emissions. These findings underpin the understanding of the complex microbe-virus interactions and advance current knowledge on soil virus ecology.

Nitrogen enrichment stimulates nutrient cycling genes of rhizosphere soil bacteria in the Phoebe bournei young plantations

Anthropogenic nitrogen (N) deposition is expected to increase substantially and continuously in terrestrial ecosystems, endangering the balance of N and phosphorus (P) in P-deficient subtropical forest soil. Despite the widely reported responses of the microbial community to simulated N deposition, there is limited understanding of how N deposition affects the rhizosphere soil processes by mediating functional genes and community compositions of soil bacteria. Here, five levels of simulated N deposition treatments (N0, 0 g m-2·yr-1; N1, 100 g m-2·yr-1; N2, 200 g m-2·yr-1; N3, 300 g m-2·yr-1; and N4, 400 g m-2·yr-1) were performed in a 10-year-old Phoebe bournei plantation. Quantitative microbial element cycling smart chip technology and 16S rRNA gene sequencing were employed to analyze functional gene compositions involved in carbon (C), N, and P cycling, as well as rhizosphere bacterial community composition. N deposition significantly influenced C cycling relative abundance of genes in the rhizosphere soil, especially those involved in C degradation. Low and moderate levels (100-300 g m-2·yr-1) of N deposition promoted the relative abundance of the C decomposition-related genes (e.g., amyA, abfA, pgu, chiA, cex, cdh, and glx), whereas high N deposition (400 g m-2·yr-1) suppressed enzyme (e.g., soil invertase, soil urease, and soil acid phosphatase) activities, affecting the C cycling processes in the rhizosphere. Simulated N deposition affected the functional genes associated with C, N, and P cycling by mediating soil pH and macronutrients. These findings provide new insights into the management of soil C sequestration in P. bournei young plantations as well as the regulation of C, N, and P cycling and microbial functions within ecosystems.

Depth-dependent effects of forest diversification on soil functionality and microbial community characteristics in subtropical forests

Soil microbes are critical to the maintenance of forest ecosystem function and stability. Forest diversification, such as monocultures versus mixed forests stands, can strongly influence microbial community patterns and processes, as well as their role in soil ecosystem multifunctionality, such as in subtropical forest ecosystems. However, less is known about these patterns and processes vary with soil depth. Here, we investigated the results of an eight-year forest diversification field experiment comparing the soil ecosystem multifunctionality, bacterial and fungal community assembly, and network patterns in mixed versus monoculture plantations along vertical profiles (0-80 cm depth) in a subtropical region. We found that the introduction of broadleaf trees in coniferous monocultures led to enhanced synergies between multiple functions, thus improving soil multifunctionality. The effects of mixed plantations on the functional potential in top soils were greater than in deep soils, especially for carbon degradation genes (apu, xylA, cex, and glx). Microbial community assembly in the top layer, particularly in mixed plantations, was dominated by stochastic processes, whereas deterministic were more important in the deep layer. Soil microbial network complexity and stability were higher in the top layer of mixed plantations, but in the deep layer was monoculture. Interestingly, the changes in microbial communities and multifunctionality in the top layer were mainly related to variation in nutrients, whereas those in the deep were more influenced by soil moisture. Overall, we reveal positive effects of mixed forest stands on soil microbial characteristics and functionality compared to that of monocultures. Our findings highlighted the importance of enhancing functional diversity through the promotion of tree species diversity, and managers can better develop forest management strategies to promote soil health under global change scenarios.

Influence of long-term ecological reclamation on carbon and nitrogen cycling in soil aggregates: The role of bacterial community structure and function

Understanding the influence of microbial taxa and functions on soil carbon (C) and nitrogen (N) cycling, particularly concerning soil aggregate sizes, is crucial for ecosystem management. This study examines the taxonomic and functional dynamics of soil bacterial communities within different aggregate sizes over time. Soil samples from a reclamation forest on the Loess Plateau in North China were collected across reclamation ages of 0, 3, 18, and 28 years. Soil aggregates were categorized into large macro-aggregates (>2000 μm), small macro-aggregates (250-2000 μm), and micro-aggregates (<250 μm) using a modified dry-sieving method. Soil aggregate stability, C and N concentrations, newly derived plant C, enzyme activities, bacterial communities, and functional genes in each aggregate fraction were systematically analyzed. There was a notable increase in soil aggregate stability and a higher proportion of large aggregates was found with increasing forest age. There were significant differences in bacterial community structures, particularly between micro-aggregates and large macro-aggregates and across different forest ages. Reclamation led to an increased abundance of copiotrophic bacterial taxa. Decreases in N-acquiring enzyme activity in micro-aggregates were contrasted by an increase in C, N, and phosphorus (P) acquisition activities in larger aggregates over time. Larger aggregates showed a faster recovery of C and N cycling genes accompanied by a significant enhancement in acetyl-CoA and ammonia oxidation processes, underscoring their importance in soil nutrient cycling. These results highlight the critical role of aggregate size in shaping microbial community structures and functions that influence soil C and N cycling during reclamation and provide new perspectives highlighting the significance of incorporating aggregate size considerations into soil management and reclamation strategies.

Selenium availability in tea: Unraveling the role of microbiota assembly and functions

Tea (Camellia sinensis (L.) O. Kuntze) plants have a strong ability to accumulate selenium (Se). However, the question of how tea plants affect Se availability has received little attention. In this study, five tea cultivars, including Soubei (SB), Aolǜ (AL), Longjing43 (LJ), Zhaori (ZR) and Fenglǜ (FL), were chosen for the study. Quantitative Microbial Ecology Chip and high-throughput sequencing were used to explore the effects of five tea cultivars on soil functions, microbial community structures and Se availability. The results showed that the total soil Se content in the FL garden was lower compared to LJ and SB gardens, whereas available Se was highest in the FL garden. Based on the Bray-Curtis distances, tea cultivar was the main factor affecting bacterial and fungal community structures. The abundance of functional genes concerning carbon, nitrogen, phosphorus and sulfur cycling processes varied among tea gardens. The higher soil NH4+ and NO3- contents, and higher abundance of functional genes like nifH, amoA1 and narG, whereas lower total nitrogen in the FL garden than in the AL and LJ tea gardens demonstrated that the FL tea plants induced microbes to accelerate soil nitrogen cycling processes. Dominant microbes that positively related with functional genes like nifH, narG, and amoA1 were also positively related with the available Se content. In conclusion, tea cultivars could regulate soil functions through affecting microbial community structures and then affecting the soil Se availability. The soil nitrogen cycle processes are suggested to be closely related with Se transformation in tea gardens.

Protists and fungi: Reinforcing urban soil ecological functions against flash droughts

Rising instances of flash droughts are contributing to notable variability in soil moisture across terrestrial ecosystems. These phenomena challenge urban ecosystem services, yet the reaction of soil ecological functions (SEFs) to such events is poorly understood. This study investigates the responses of SEFs (about nutrient metabolism capacity and potential) and the microbiome under two specific scenarios: a flooding-drought sequence and a direct drought condition. Using quantitative microbial element cycling analysis, high-throughput sequencing, and enzyme activity measurements, we found that unlike in forests, the microbial composition in urban soils remained unchanged during flash drought conditions. However, SEFs were affected in both settings. Correlation analysis and Mantel test showed that forest soils exhibited more complex interactions among soil moisture, properties, and microbial communities. Positive linear correlation revealed that bacteria were the sole drivers of SEFs. Interestingly, while multi-threshold results suggested bacterial α diversity impeded the maximization of SEFs in urban soils, fungi and protists had a beneficial impact. Cross-domain network of urban soils had higher number of nodes and edges, but lower average degree and robustness than forest soils. Mantel test revealed that fungi and protist had significant correlations with bacterial composition in forest soils, but not in urban soils. In the urban network, the degree and eigenvector centrality of bacterial, fungal and protistan ASVs were significantly lower compared to those in the forest. These results suggest that the lower robustness of the microbial network in urban soils is attributed to limited interactions among fungi, consumer protists, and bacteria, contributing to the failure of microbial-driven ecological functions. Overall, our findings emphasize the critical role of fungi and protists in shielding urban soils from drought-induced disturbances and in enhancing the resistance of urban ecological functions amidst environmental changes.

Effect of stand age on rhizosphere microbial community assembly of dominant shrubs during sandy desert vegetation restoration

The rhizosphere microbial community helps govern biogeochemical cycling and facilitates complex plant-soil feedback. Understanding the evolutionary dynamics of microbial community structure and functional genes during vegetation succession is crucial for quantifying and understanding ecosystem processes and functions in restored sandy deserts. In this study, the rhizosphere microbial community structure of 11-66-year-old dominant shrubs in a desert revegetation area was examined using shotgun metagenomic sequencing. The interactions between the microbial community structure, functional gene abundances, soil properties, and plant characteristics of different stand ages were comprehensively investigated. The abundance of unique species first increased before subsequently decreasing with stand age, with shared species accounting for only 47.33%-59.42% of the total operational taxonomic units (OTUs). Copiotrophs such as Actinobacteria and Proteobacteria were found to dominate the rhizosphere soil microbial community, with their relative abundance accounting for 75.28%-81.41% of the total OTUs. There was a gradual shift in dominant microbial functional genes being involved in cellular processes towards those involved in environmental information processing and metabolism as stand age increased. Additionally, temporal partitioning was observed in both the microbial co-occurrence network complexity and topological parameters within the rhizosphere soil. Redundancy analysis revealed that dissolved organic carbon was the primary determinant influencing shifts in microbial community structure. Understanding the evolution of microbial community structure and function contributes to identifying potential mechanisms associating the soil microbiome with dominant sand-fixing shrubs as well as understanding the rhizosphere microbiome assembly process. These results shed light on the role of the rhizosphere microbiome in biogeochemical cycling and other ecosystem functions following revegetation of temperate sandy deserts.

Long-term effects of dead algal deposition on sediment surfaces: Behavior of endogenous phosphorus release in sediments

Algae blooms are frequently triggered owing to the improvements in aquatic trophic levels. The aggregated algae from these blooms are eventually dead and accumulate on sediment surfaces, impacting the microenvironment and phosphorus cycling in aquatic systems. However, research on the effects of naturally dead algal deposition on endogenous P release from sediments is lacking. In this study, we investigated the long-term effects of dead algal deposition at varying concentrations on P release from sediments and the underlying mechanisms by assessing microbial metabolism and community structure. The results showed that following the dead algal deposition, the release of P from sediments to the water column peaked on day 40 (0.14±0.017 mg L-1 in Amend12) and the SRP exchange capacity reached maximum (6.09 ± 1.63 mg/(cm2·d) in Amend12) at sediment-water interface in phase1 (0-3 day). This might be primarily attributed to the deposition of dead algae introducing much organic matter (such as organic carbon and organic phosphorus), thus altering the sediment microenvironment, which increased the activity of phosphorus-cycle microorganisms, such as polyphosphate-accumulating organisms, through increasing C source metabolism, reducing intracellular ammonia inhibition, and creating more suitable anaerobic conditions. Therefore, this study has improved our understanding of the management strategies for controlling endogenous phosphorus release in eutrophic shallow lakes, suggesting that the priming effects of freshly deposited algae could be mitigated by harvesting algae at the peak of blooms.

How do glyphosate and AMPA alter the microbial community structure and phosphorus cycle in rice-crayfish systems?

Glyphosate, a commonly used organophosphorus herbicide in rice-crayfish cropping regions, may alter regional phosphorus cycle processes while affecting the structure of microbial communities. However, the effects of glyphosate residues on rice-crayfish systems remain unclear. In this study, we assessed the spatial and temporal distribution characteristics of glyphosate and its primary degradation products, as well as the impact mechanisms of glyphosate on microbial communities and the phosphorus cycle in rice-crayfish systems such as paddy fields, breeding ditches and recharge rivers. The detection rates of glyphosate and aminomethylphosphonic acid (AMPA) were 100% in rice-crayfish systems. Concentrations of glyphosate in the water phase and soil/sediment were as high as 0.012 μg/L and 7.480 μg/kg, respectively, and concentrations of AMPA were as high as 17.435 μg/L and 13.200 μg/kg, respectively. Glyphosate concentrations were not affected by rainfall or sampling site, but concentrations of AMPA in the water phase of recharge rivers were affected by rainfall. The glyphosate concentration was significantly and positively correlated with RBG-16-58-14 abundance, and the AMPA concentration was significantly and positively correlated with Actinobacteria and Lysobacter abundance, and negatively correlated with Cyanobacteria abundance (P < 0.05). The highest abundances of phoD, phnK, and ppx genes were found in all soils/sediments. Glyphosate concentration in soil/sediment was significantly and positively correlated with the abundance of phoD gene encoding an organophosphorus-degrading enzyme and ppx gene encoding poly inorganic phosphate (Pi) hydrolase (P < 0.05). In addition, the glyphosate concentration was significantly and positively correlated with the Ca-bonded Pi content (P < 0.05). This implies that glyphosate may promote the production of stable Pi in rice-crayfish systems by increasing the abundance of phoD and ppx genes. The results of this study reveal the impact mechanism of glyphosate on the phosphorus cycle in rice-crayfish systems and provide a basis for the risk assessment of glyphosate.

Dominant Tree Species and Litter Quality Govern Fungal Community Dynamics during Litter Decomposition

Litter decomposition is a crucial biochemical process regulated by microbial activities in the forest ecosystem. However, the dynamic response of the fungal community during litter decomposition to vegetation changes is not well understood. Here, we investigated the litter decomposition rate, extracellular enzyme activities, fungal community, and nutrient cycling-related genes in leaf and twig litters over a three-year decomposition period in a pure Liquidamabar formosana forest and a mixed L. formosana/Pinus thunbergii forest. The result showed that during the three-year decomposition, twig litter in the mixed forest decomposed faster than that in the pure forest. In both leaf litter and twig litter, β-cellobiosidase and N-acetyl-glucosamidase exhibited higher activities in the mixed forest, whereas phosphatase, β-glucosidase, and β-xylosidase were higher in the pure forest. The fungal α-diversity were higher in both litters in the pure forest compared to the mixed forest, with leaf litter showing higher α-diversity than twig litter. Fungal species richness and α-diversity within leaf litter increased as decomposition progressed. Within leaf litter, Basidiomycota dominated in the mixed forest, while Ascomycota dominated in the pure forest. Funguild analysis revealed that Symbiotroph and ectomycorrhizal fungi were more abundant in the mixed forest compared to the pure forest. In the third-year decomposition, genes related to phosphorus cycling were most abundant in both forests, with the pure forest having a higher abundance of cex and gcd genes. Fungal community structure, predicted functional structure, and gene composition differed between the two forest types and between the two litter types. Notably, the fungal functional community structure during the first-year decomposition was distinct from that in the subsequent two years. These findings suggest that dominant tree species, litter quality, and decomposition time all significantly influence litter decomposition by attracting different fungal communities, thereby affecting the entire decomposition process.

Phosphorus availability influences disease-suppressive soil microbiome through plant-microbe interactions

BACKGROUND

Soil nutrient status and soil-borne diseases are pivotal factors impacting modern intensive agricultural production. The interplay among plants, soil microbiome, and nutrient regimes in agroecosystems is essential for developing effective disease management. However, the influence of nutrient availability on soil-borne disease suppression and associated plant-microbe interactions remains to be fully explored. T his study aims to elucidate the mechanistic understanding of nutrient impacts on disease suppression, using phosphorous as a target nutrient.

RESULTS

A 6-year field trial involving monocropping of tomatoes with varied fertilizer manipulations demonstrated that phosphorus availability is a key factor driving the control of bacterial wilt disease caused by Ralstonia solanacearum. Subsequent greenhouse experiments were then conducted to delve into the underlying mechanisms of this phenomenon by varying phosphorus availability for tomatoes challenged with the pathogen. Results showed that the alleviation of phosphorus stress promoted the disease-suppressive capacity of the rhizosphere microbiome, but not that of the bulk soil microbiome. This appears to be an extension of the plant trade-off between investment in disease defense mechanisms versus phosphorus acquisition. Adequate phosphorus levels were associated with elevated secretion of root metabolites such as L-tryptophan, methoxyindoleacetic acid, O-phosphorylethanolamine, or mangiferin, increasing the relative density of microbial biocontrol populations such as Chryseobacterium in the rhizosphere. On the other hand, phosphorus deficiency triggered an alternate defense strategy, via root metabolites like blumenol A or quercetin to form symbiosis with arbuscular mycorrhizal fungi, which facilitated phosphorus acquisition as well.

CONCLUSION

Overall, our study shows how phosphorus availability can influence the disease suppression capability of the soil microbiome through plant-microbial interactions. These findings highlight the importance of optimizing nutrient regimes to enhance disease suppression, facilitating targeted crop management and boosting agricultural productivity. Video Abstract.

Biofilms in plastisphere from freshwater wetlands: Biofilm formation, bacterial community assembly, and biogeochemical cycles

Microorganisms can colonize to the surface of microplastics (MPs) to form biofilms, termed "plastisphere", which could significantly change their physiochemical properties and ecological roles. However, the biofilm characteristics and the deep mechanisms (interaction, assembly, and biogeochemical cycles) underlying plastisphere in wetlands currently lack a comprehensive perspective. In this study, in situ biofilm formation experiments were performed in a park with different types of wetlands to examine the plastisphere by extrinsic addition of PVC MPs in summer and winter, respectively. Results from the spectroscopic and microscopic analyses revealed that biofilms attached to the MPs in constructed forest wetlands contained the most abundant biomass and extracellular polymeric substances. Meanwhile, data from the high-throughput sequencing showed lower diversity in plastisphere compared with soil bacterial communities. Network analysis suggested a simple and unstable co-occurrence pattern in plastisphere, and the null model indicated increased deterministic process of heterogeneous selection for its community assembly. Based on the quantification of biogeochemical cycling genes by high-throughput qPCR, the relative abundances of genes involving in carbon degradation, carbon fixation, and denitrification were significantly higher in plastisphere than those of soil communities. This study greatly enhanced our understanding of biofilm formation and ecological effects of MPs in freshwater wetlands.

Mixotrophic aerobic denitrification facilitated by denitrifying bacterial-fungal communities assisted with iron in micro-polluted water: Performance, metabolic activity, functional genes abundance, and community co-occurrence

Low-dosage nitrate pollutants can contribute to eutrophication in surface water bodies, such as lakes and reservoirs. This study employed assembled denitrifying bacterial-fungal communities as bio-denitrifiers, in combination with zero-valent iron (ZVI), to treat micro-polluted water. Immobilized bacterial-fungal mixed communities (IBFMC) reactors demonstrated their ability to reduce nitrate and organic carbon by over 43.2 % and 53.7 %, respectively. Compared to IBFMC reactors, IBFMC combined with ZVI (IBFMC@ZVI) reactors exhibited enhanced removal efficiencies for nitrate and organic carbon, reaching the highest of 31.55 % and 17.66 %, respectively. The presence of ZVI in the IBFMC@ZVI reactors stimulated various aspects of microbial activity, including the metabolic processes, electron transfer system activities, abundance of functional genes and enzymes, and diversity and richness of microbial communities. The contents of adenosine triphosphate and electron transfer system activities enhanced more than 5.6 and 1.43 folds in the IBFMC@ZVI reactors compared with IBFMC reactors. Furthermore, significant improvement of crucial genes and enzyme denitrification chains was observed in the IBFMC@ZVI reactors. Iron played a central role in enhancing microbial diversity and activity, and promoting the supply, and transfer of inorganic electron donors. This study presents an innovative approach for applying denitrifying bacterial-fungal communities combined with iron enhancing efficient denitrification in micro-polluted water.

Soil Factors Key to 3,4-Dimethylpyrazole Phosphate (DMPP) Efficacy: EC and SOC Dominate over Biotic Influences

Nitrification inhibitors like 3,4-dimethylpyrazole phosphate (DMPP) are crucial in agriculture to reduce nitrogen losses. However, the efficacy of DMPP varies in different soils. This microcosm incubation study with six soils was conducted to elucidate how soil abiotic factors (physicochemical properties) and biotic factors (nitrogen-cycling microbial abundance and diversity) influence the performance of DMPP. The DMPP efficacy was evaluated through the ammonium-N retention rate (NH4+_RA), inhibition rate of net nitrification rate (NNR_IR), and reduction rate of N2O emissions (N2O_ERR). The results showed that DMPP had significantly different effects on mineral nitrogen conversion and N2O emissions from different soils. NH4+_RA, NNR_IR, and N2O_ERR ranged from -71.15% to 65.37%, 18.77% to 70.23%, and 7.93% to 82.51%, respectively. Correlation analyses and random forest revealed abiotic factors, particularly soil EC and SOC, as the primary determinants of DMPP efficiency compared to microbial diversity. This study sheds new light on the complex interactions between DMPP efficacy and soil environments. The identification of soil EC and SOC as the dominant factors influencing DMPP efficacy provides valuable insights for optimizing its application strategies in agricultural systems. Future research could explore the mechanisms underlying these interactions and develop tailored DMPP formulations that are responsive to specific soil conditions.

Response of microbial communities and biogeochemical cycling functions to sediment physicochemical properties and microplastic pollution under damming and water diversion projects

Understanding the interactions among flow-sediment, microorganisms, and biogeochemical cycles is crucial for comprehending the ecological response mechanisms of dams and water diversion. This study focused on the spatial patterns of carbon, nitrogen, phosphorus, and sulfur (CNPS) cycle functional genes in the water resource for the middle route of the South-to-North Water Diversion Project in China, specifically the Danjiangkou Reservoir (comprising the Han and Dan reservoirs). The investigation incorporated sediment physicochemical properties and microplastic pollution. Numerous microbial species were identified, revealing that microbial communities demonstrated sensitivity to changes in sedimentary mud content. The communities exhibited greater β diversity due to finer sediment particles in the Han Reservoir (HR), whereas in the Dan Reservoir (DR), despite having higher sediment nutrient content and MPs pollution, did not display this pattern. Regarding the composition and structure of microbial communities, the study highlighted that sediment N and P content had a more significant influence compared to particle size and MPs. The quantitative microbial element cycling (QMEC) results confirmed the presence of extensive chemolithotrophic microbes and strong nitrogen cycle activity stemming from long-term water storage and diversion operations. The denitrification intensity in the HR surpassed that of the DR. Notably, near the pre-dam area, biological nitrogen fixation, phosphorus removal, and sulfur reduction exhibited noticeable increases. Dam construction refined sediment, fostering the growth of different biogeochemical cycling bacteria and increasing the abundance of CNPS cycling genes. Furthermore, the presence of MPs exhibited a positive correlation with S cycling genes and a negative correlation with C and N cycling genes. These findings suggest that variations in flow-sediment dynamics and MPs pollution have significant impact the biogeochemical cycle of the reservoir.

Enhancing phosphorus transformation in typical reddish paddy soil from China: Insights on long-term straw return and pig manure application via microbial mechanisms

Effective utilization of organic resources to activate residual phosphorus (P) in soil and enhance its availability is crucial for mitigating P resource scarcity and assessing the sustainable use of P in agricultural practices. However, the mechanisms through which organic resources affect soil P conversion via microorganisms and functional genes remain unknown, particularly in long-term organic-inorganic agricultural systems. In this study, we examined the impact of combined organic-inorganic fertilizer application on P availability, carbon (C) and P cycling genes, and microbial communities (bacterial and fungal) in reddish paddy soil based on a 42-year field experiment. The results indicated that long-term straw returning and pig manure application significantly augmented soil organic carbon (SOC), Olsen-P, microbial biomass carbon (MBC), microbial biomass phosphorus (MBP), enzyme-P, and CaCl2-P levels in paddy soils. Furthermore, these practices increased the abundance of soil C degradation genes, reduced the abundance of soil P cycling genes, and altered microbial community structure and network complexity. Notably, Module #3 ecological clusters in the fungal ecological co-occurrence network were significantly correlated with P cycling genes. Finally, our study demonstrated that long-term straw returning and pig manure application in paddy fields facilitated two robust and contrasting predictive relationships between C degradation (negative relationship) and P cycling (positive relationship) genes, respectively, and enzyme-P and HCl-P changes to improve soil P availability. This study can enhance our understanding of the role of soil microbial communities and functional genes in mediating P transformation to decipher the enhancement in P application efficiency driven by organic resources in reddish paddy soils.

Effect of conventional and biodegradable microplastics on the soil-soybean system: A perspective on rhizosphere microbial community and soil element cycling

As an exogenous carbon input, microplastics (MPs), especially biodegradable MPs, may significantly disrupt soil microbial communities and soil element cycling (CNPS cycling), but few studies have focused on this. Here, we focused on assessing the effects of conventional low-density polyethylene (LDPE), biodegradable polybutylene adipate terephthalate (PBAT), and polylactic acid (PLA) MPs on rhizosphere microbial communities and CNPS cycling in a soil-soybean system. The results showed that PBAT-MPs and PLA-MPs were more detrimental to soybean growth than LDPE-MPs, resulting in a reduction in shoot nitrogen (14.05% and 11.84%) and shoot biomass (33.80% and 28.09%) at the podding stage. In addition, dissolved organic carbon (DOC) increased by 20.91% and 66.59%, while nitrate nitrogen (NO3--N) significantly decreased by 56.91% and 69.65% in soils treated with PBAT-MPs and PLA-MPs, respectively. PBAT-MPs and PLA-MPs mainly enhanced copiotrophic bacteria (Proteobacteria) and suppressed oligotrophic bacteria (Verrucomicrobiota, Gemmatimonadota, etc.), increasing the abundance of CNPS cycling-related functional genes. LDPE-MPs tended to enrich oligotrophic bacteria (Verrucomicrobiota, etc.) and decrease the abundance of CNPS cycling-related functional genes. Correlation analysis revealed that MPs with different degradation properties selectively affected the composition and function of the bacterial community, resulting in changes in the availability of soil nutrients (especially NO3--N). Redundancy analysis further indicated that NO3--N was the primary constraining factor for soybean growth. This study provides a new perspective for revealing the underlying ecological effects of MPs on soil-plant systems.

Seasonal variations affect the ecosystem functioning and microbial assembly processes in plantation forest soils

While afforestation mitigates climate concerns, the impact of afforestation on ecological assembly processes and multiple soil functions (multifunctionality) in afforested areas remains unclear. The Xiong'an New Area plantation forests (Pinus and Sophora forests) in North China were selected to examine the effects of plantation types across four distinct seasons on soil microbiomes. Three functional categories (nutrient stocks, organic matter decomposition, and microbial functional genes) of multifunctionality and the average (net) multifunctionality were quantified. All these categories are directly related to soil functions. The results showed that net soil multifunctionality as a broad function did not change seasonally, unlike other narrow functional categories. Bacterial communities were deterministically (variable selection and homogenous selection) structured, whereas the stochastic process of dispersal limitation was mainly responsible for the assembly and turnover of fungal and protist communities. In Pinus forests, winter initiates a sudden shift from deterministic to stochastic processes in bacterial community assembly, accompanied by decreased Shannon diversity and heightened nutrient cycling (nutrient stocks and organic matter decomposition). This indicates the potential vulnerability of deterministic assembly to seasonal fluctuations, particularly in environments rich in nutrients. The results predicted that protist community composition was uniquely structured with C-related functional activities relative to bacterial and fungal β-diversity variations, which were mostly explained by seasonal variations. Our study highlighted the importance of the protist phagocytosis process on soil microbial interactions through the predicted impact of protist α-diversity on microbial cooccurrence network parameters. This association might be driven by the high abundance of protist consumers as the main predators of bacterial and fungal lineages in our sampling plots. Our findings reveal that the complexity of microbial co-occurrence interactions was considerably higher in spring, perhaps attributing thermal variability and increased resource availability within spring that foster microbial diversity and network complexity. This study contributes to local ecosystem prospects to model the behavior of soil biota seasonally and their implied effects on soil functioning and microbial assembly processes, which will benefit global-scale afforestation programs by promoting novel, precise, and rational plantation forests for future environmental sustainability and self-sufficiency.

A seasonal study on the microbiomes of Diploid vs. Triploid eastern oysters and their denitrification potential

Oyster reefs are hotspots of denitrification mediated removal of dissolved nitrogen (N), however, information on their denitrifier microbiota is scarce. Furthermore, in oyster aquaculture, triploids are often preferred over diploids, yet again, microbiome differences between oyster ploidies are unknown. To address these knowledge gaps, farmed diploid and triploid oysters were collected over an annual growth cycle and analyzed using shotgun metagenomics and quantitative microbial elemental cycling (QMEC) techniques. Regardless of ploidy, Psychrobacter genus was abundant, with positive correlations found for genes of central metabolism, DNA metabolism, and carbohydrate metabolism. MAGs (metagenome-assembled genomes) yielded multiple Psychrobacter genomes harboring norB, narH, narI, and nirK denitrification genes, indicating their functional relevance within the eastern oysters. QMEC analysis indicated the predominance of carbon (C) and nitrogen (N) cycling genes, with no discernable patterns between ploidies. Among the N-cycling genes, the nosZII clade was overrepresented, suggesting its role in the eastern oyster's N removal processes.

Selenium-Mediated Shaping of Citrus Rhizobiome for Promotion in Root Growth and Soil Phosphorus Activation

Selenium (Se) has been widely reported to affect plant growth, nutrient cycling, and the rhizobiome. However, how Se shapes the rhizobiome and interacts with plants remains largely elusive. Pot and hydroponic experiments were employed to elucidate the regulatory mechanism of Se in the citrus rhizobiome. Compared to the control, soil Se application significantly increased the root biomass (34.7%) and markedly reduced rhizosphere HCl-P, H2O-P, NaHCO3-IP, and residual-P of citrus, which were related to the variation of citrus rhizobiome. Se primarily enriched Proteobacteria and Actinobacteria as well as the phosphorus (P) functional genes phod and pqqc. Further study revealed that Se altered the metabolite profile of root exudate, particularly enhancing the abundance of l-cyclopentylglycine, cycloleucine, l-proline, l-pipecolic acid, and inositol, which played a key role in reshaping the citrus rhizobiome. These metabolites could serve as both nutrient sources and signaling molecules, thus supporting the growth or chemotaxis of the functional microbes. These bacterial taxa have the potential to solubilize P or stimulate plant growth. These findings provide a novel mechanistic understanding of the intriguing interactions between Se, root exudate, and rhizosphere microbiomes, and demonstrate the potential for utilizing Se to regulate rhizobiome function and enhance soil P utilization in citrus cultivation.

Metagenomics analysis reveals effects of salinity fluctuation on diversity and ecological functions of high and low nucleic acid content bacteria

Salinity is a critical environmental factor in marine ecosystems and has complex and wide-ranging biological effects. However, the effects of changing salinity on diversity and ecological functions of high nucleic acid (HNA) and low nucleic acid (LNA) bacteria are not well understood. In this study, we used 16S rRNA sequencing and metagenomic sequencing analysis to reveal the response of HNA and LNA bacterial communities and their ecological functions to salinity, which was decreased from 26 ‰ to 16 ‰. The results showed that salinity changes had significant effects on the community composition of HNA and LNA bacteria. Among LNA bacteria, 14 classes showed a significant correlation between relative abundance and salinity. Salinity changes can lead to the transfer of some bacteria from HNA bacteria to LNA bacteria. In the network topology relationship, the complexity of the network between HNA and LNA bacterial communities gradually decreased with decreased salinity. The abundance of some carbon and nitrogen cycling genes in HNA and LNA bacteria varied with salinity. Overall, this study demonstrates the effects of salinity on diversity and ecological functions and suggests the importance of salinity in regulating HNA and LNA bacterial communities and functions.

Ecological effect of microplastics on soil microbe-driven carbon circulation and greenhouse gas emission: A review

Soil organic carbon (SOC) pool, the largest part of terrestrial ecosystem, controls global terrestrial carbon balance and consequently presented carbon cycle-climate feedback in climate projections. Microplastics, (MPs, <5 mm) as common pollutants in soil ecosystems, have an obvious impact on soil-borne carbon circulation by affecting soil microbial processes, which play a central role in regulating SOC conversion. In this review, we initially presented the sources, properties and ecological risks of MPs in soil ecosystem, and then the differentiated effects of MPs on the component of SOC, including dissolved organic carbon, soil microbial biomass carbon and easily oxidized organic carbon varying with the types and concentrations of MPs, the soil types, etc. As research turns into a broader perspective, greenhouse gas emissions dominated by the mineralization of SOC coming into view since it can be significantly affected by MPs and is closely associated with soil microbial respiration. The pathways of MPs impacting soil microbes-driven carbon conversion include changing microbial community structure and composition, the functional enzyme's activity and the abundance and expression of functional genes. However, numerous uncertainties still exist regarding the microbial mechanisms in the deeper biochemical process. More comprehensive studies are necessary to explore the affected footprint and provide guidance for finding the evaluation criterion of MPs affecting climate change.

Forest-to-Cropland Conversion Reshapes Microbial Hierarchical Interactions and Degrades Ecosystem Multifunctionality at a National Scale

Conversion from natural lands to cropland, primarily driven by agricultural expansion, could significantly alter soil microbiome worldwide; however, influences of forest-to-cropland conversion on microbial hierarchical interactions and ecosystem multifunctionality have not been fully understood. Here, we examined the effects of forest-to-cropland conversion on intratrophic and cross-trophic microbial interactions and soil ecosystem multifunctionality and further disclosed their underlying drivers at a national scale, using Illumina sequencing combined with high-throughput quantitative PCR techniques. The forest-to-cropland conversion significantly changed the structure of soil microbiome (including prokaryotic, fungal, and protistan communities) while it did not affect its alpha diversity. Both intrakingdom and interkingdom microbial networks revealed that the intratrophic and cross-trophic microbial interaction patterns generally tended to be more modular to resist environmental disturbance introduced from forest-to-cropland conversion, but this was insufficient for the cross-trophic interactions to maintain stability; hence, the protistan predation behaviors were still disturbed under such conversion. Moreover, key soil microbial clusters were declined during the forest-to-cropland conversion mainly because of the increased soil total phosphorus level, and this drove a great degradation of the ecosystem multifunctionality (by 207%) in cropland soils. Overall, these findings comprehensively implied the negative effects of forest-to-cropland conversion on the agroecosystem, from microbial hierarchical interactions to ecosystem multifunctionality.