Microbial diversity drives carbon use efficiency in a model soil

Core microbial taxonomies that maintain high organic carbon content in upland soil

The accumulation of soil carbon (C) is crucial for the productivity and ecological function of farmland ecosystems. The balance between microbial carbon dioxide (CO2) emission and fixation determines the sustained accumulation potential of C in soil. Microorganisms involved in this process are highly obscure, thus hindering identification and further application of microorganisms with fertile soil function. In this study, a series of typical upland farmland soils were collected from 29 regions and their microbial community structure and soil C fractions were analyzed. Additionally, the rates of CO2 emission and fixation in each soil were measured. The results showed that the correlation between soil CO2 emissions and the SOC concentration was logarithmic, while that between CO2 fixation and SOC was linear. Bacterial and fungal diversity showed an upward trend with increasing soil C, and their α diversity was significantly correlated with CO2 fixation, but not correlated with CO2 emission. Fungi were more associated with soil C than bacteria, and the strength of linkage with soil C varied among the different phyla of microorganisms. Furthermore, the core microbial taxa in soils with low, medium and high SOC levels were identified by discarding redundant amplicon sequence variants, and their community differentiation was significantly driven by soil CO2 emission and fixation based on Mantel analysis. The high abundance of Chloroflexi, Nitrospirota, Actinobacteria, and Mortierellomycota in core taxa might indicate a high level of SOC level. This study highlights that SOC fluctuations are mainly driven by the core microbial taxa, rather than all microbial taxa in the agricultural system. Our research sheds light on the targeted regulation of the soil microbial community structure in upland farmland for soil fertility enhancement.

Enhancement of microbial community dynamics and metabolism in compost through ammonifying cultures inoculation

The efficient use of livestock and poultry manure waste has become a global challenge, with microorganisms playing an important role. To investigate the impact of novel ammonifying microorganism cultures (NAMC) on microbial community dynamics and carbon and nitrogen metabolism, five treatments [5% (v/w) sterilized distilled water, Amm-1, Amm-2, Amm-3, and Amm-4] were applied to cow manure compost. Inoculation with NAMC improved the structure of bacterial and fungal communities, enriched the populations of the functional microorganisms, enhanced the role of specific microorganisms, and promoted the formation of tight modularity within the microbial network. Further functional predictions indicated a significant increase in both carbon metabolism (CMB) and nitrogen metabolism (NMB). During the thermophilic phase, inoculated NAMC treatments boosted carbon metabolism annotation by 10.55%-33.87% and nitrogen metabolism annotation by 26.69%-63.11. Structural equation modeling supported the NAMC-mediated enhancement of NMB and CMB. In conclusion, NAMC inoculation, particularly with Amm-4, enhanced the synergistic interaction between bacteria and fungi. This collaboration promoted enzymatic catabolic and synthetic processes, resultng in positive feedback loops with the endogenous microbial community. Understanding these mechanisms not only unravels how ammonifying microorganisms influence microbial communities but also paves the way for the development of the composting industry and global waste management practices.

Fe oxides simultaneously improve stability of Cd and carbon in paddy soil：The underlying influence at aggregate level

Iron (Fe) oxides have a strong adsorption affinity for Cd and organic carbon (SOC). However, under alternate wet-dry (IF) condition,the influences of Fe oxides on the speciation and disrtribution of Cd and SOC in soil aggregates are unkown. In the present study, soils untreated (S), removed (S-Fe) or added (S+Fe) Fe oxide soils were blended with cadmium chloride solution and cultivated for 56 days under different moisture management practices. Compared with the S-Fe soil, the IF treatment increased the contents of Fe oxide-bound SOC (Fe-OC) and Fe/Mn oxide-bound Cd (Fe/Mn-Cd) by 18.5-29.8-fold and 1.45-2.45-fold, repectively, in the S and S+Fe soils, corresponding to a 36 %-42 % increase in the recalcitrant C pool (RCP) and a 53 %-87 % decrease in the exchangeable Cd content. These results could be attributed to soil particle aggregation and Fe redistribution. Fe addition promoted the transfer of Cd/SOC accumulated in microaggregates to macroaggregates and increased the variable negative charge content in macroaggregates and the adsorption capacity of macroaggregates for Cd/SOC. More Cd/SOC accumulated in macroaggregates in Fe oxide-bound form, which reduced the risk of Cd migration and Cd availability and increased the physical protection of SOC. Therefore, Fe oxide has great potential to simultaneously reduce carbon emissions and cadmium toxicity in paddy soil.

Unveiling the long-term dynamic effects: Biochar mediates bacterial communities to modulate the petroleum hydrocarbon degradation in oil-contaminated sediments

Sediment, as the destination of marine pollutants, often bears much more serious petroleum pollution than water. Biochar is increasingly utilized for remediating organic pollutant-laden sediments, yet its long-term impacts on oil-contaminated sediment remain poorly understood. In this study, simulation experiments adding 2.5 wt% biochars (corn straw and wood chips biochar at different pyrolysis temperatures) were conducted. The effects on petroleum hydrocarbon attenuation, enzyme activities, and microbial community structure were systematically investigated. Results showed enhanced degradation of long-chain alkanes in certain biochar-treated groups. Biochar species and PAH characteristics together lead to the PAHs' attenuation, with low-temperature corn straw biochar facilitating the degradation of phenanthrene, fluorene, and chrysene. Initially, biochars reduced polyphenol oxidase activity but increased urease and dehydrogenase activities. However, there was a noticeable rise in polyphenol oxidase activity for a long time. Biochars influenced bacterial community succession and abundance, likely due to nutrient release stimulating microbial activity. The structural equations model (SEM) reveals that DON affected the enzyme activity by changing the microbial community and thus regulated the degradation of PAHs. These findings shed light on biochar's role in bacterial communities and petroleum hydrocarbon degradation over extended periods, potentially enhancing biochar-based remediation for petroleum-contaminated sediments.

Prediction of As and Cd dissolution in various soils under flooding condition

Although the mobility of arsenic (As) and cadmium (Cd) in soils during the flooding-drainage process has been intensively studied, predicting their dissolution among various soils still remains a challenge. After comprehensively monitoring multiple parameters related to As and Cd dissolution in 8 soils for a 60-day anaerobic incubation, the redundancy analysis (RDA) and structural equation model (SEM) were employed to identify the key factors and influencing pathways controlling the dynamic release of As and Cd. Results showed that pH alone explained 90.5 % Cd dissolution, while the dissolved-Fe(II) and 5 M-HCl extractable Fe(II) jointly only explained 50.6 % As dissolution. After data normalization, the ratio of Fe(II) to 5 M-HCl extracted total Fe (i.e. FetotII/Fetot) significantly improved the correlation to R2 = 0.824 (p < 0.001) with a fixed slope of 0.393 among the 8 soils. Our results highlight the crucial role played by the reduction degree of total iron contents in determining both the reduction and dissolution of As during flooding. In contrast, dissolved-Fe(II) was too vulnerable to soil properties to be a stable indicator of As dissolution. Therefore, we propose to replace the dissolved-Fe(II) with this novel ratio as the key index to quantitatively assess the kinetic change of As solubility potential across various soils under flooding conditions.

Limiting Resources Define the Global Pattern of Soil Microbial Carbon Use Efficiency

Microbial carbon (C) use efficiency (CUE) delineates the proportion of organic C used by microorganisms for anabolism and ultimately influences the amount of C sequestered in soils. However, the key factors controlling CUE remain enigmatic, leading to considerable uncertainty in understanding soil C retention and predicting its responses to global change factors. Here, we investigate the global patterns of CUE estimate by stoichiometric modeling in surface soils of natural ecosystems, and examine its associations with temperature, precipitation, plant-derived C and soil nutrient availability. We found that CUE is determined by the most limiting resource among these four basic environmental resources within specific climate zones (i.e., tropical, temperate, arid, and cold zones). Higher CUE is common in arid and cold zones and corresponds to limitations in temperature, water, and plant-derived C input, while lower CUE is observed in tropical and temperate zones with widespread limitation of nutrients (e.g., nitrogen or phosphorus) in soil. The contrasting resource limitations among climate zones led to an apparent increase in CUE with increasing latitude. The resource-specific dependence of CUE implies that soils in high latitudes with arid and cold environments may retain less organic C in the future, as warming and increased precipitation can reduce CUE. In contrast, oligotrophic soils in low latitudes may increase organic C retention, as CUE could be increased with concurrent anthropogenic nutrient inputs. The findings underscore the importance of resource limitations for CUE and suggest asymmetric responses of organic C retention in soils across latitudes to global change factors.

Regulatory path for soil microbial communities depends on the type and dose of microplastics

To reveal the feedbacks and regulating mechanisms of microplastic types and doses on microbial community, a microcosm experiment was carried out with two non-degradable microplastics [polyethylene (PE) and polyvinyl chloride (PVC)] and four biodegradable microplastics [poly(butylene succinate) (PBS), polyhydroxyalkanoates (PHA), poly(butyleneadipate-co-terephthalate) (PBAT), and polypropylene carbonate (PPC)] at different levels (1 %, 7 %, and 28 %). As a result, the content of total carbon (TC), soil organic carbon (SOC), and microbial biomass carbon (MBC) (expect MBC in PBS soil) increased with increasing doses of microplastics, and increased at the lowest PE dose rate. Biodegradable microplastics created a more active ecological niche while enriching more pathogens than non-degradable microplastics. Structural equation modeling indicated that microbial diversities were in a type-dependent assembly, whereas microbial compositions were more profoundly affected by the microplastic doses, ultimately. The standardized total effect coefficient of microplastic types on bacterial and fungal diversities was - 0.429 and - 0.282, and that of doses on bacterial and fungal compositions was 0.487 and 0.336, respectively. Both microplastic types and doses significantly impacted pH, electrical conductivity, total nitrogen, TC, SOC, and MBC, subsequently inhibiting microbial diversities and stimulating microbial compositions with particular pathways. The results provide a comprehensive understanding for evaluating the potential risk of microplastics.

Effects of exogenous copper on microbial metabolic function and carbon use efficiency of Panax notoginseng planting soil

Soil copper (Cu) pollution is a serious environmental risk in the Panax notoginseng planting area. However, the effect of Cu on soil microbial metabolism and nutrient cycling in this area remains unknown. Therefore, Biolog ECO-plate and enzyme stoichiometry methods were utilized in this study to investigate the impact of exogenous Cu (control: 0 mg·kg-1; Cu100: 100 mg·kg-1; Cu400: 400 mg·kg-1; and Cu600: 600 mg·kg-1) on the metabolic function of soil microbial and nutrient limitation in the P. notoginseng soil. The results indicated that Cu100 significantly increased soil organic carbon (SOC), total phosphorus (TP), soil C:N, microbial biomass carbon (MBC), and microbial biomass nitrogen (MBN) 9.89%, 15.65%, 17.91%, 61.87%, and 90.56% higher than the control, respectively. Moreover, the carbon source utilization ratio of carbohydrates, amino acids, and amphiphilic compounds of Cu100 also increased by 7.16%, 25.47%, and 84.68%, respectively, compared with the control. The activities of β-1,4-glucosidase, cellobiohyrolase, leucine amino peptidase, β-1,4-N-acetylglucosaminidase, and phosphatase significantly decreased with increasing Cu concentration. Soil enzyme stoichiometry showed that all treatments were limited by nitrogen (vector angle < 45°; 19.045-22.081). Cu600 led to the lowest carbon limitation (1.798) and highest carbon use efficiency (CUE:0.267). The PLS-SEM model also showed that MBC, MBN, MBP, and microbial diversity positively affected carbon and nitrogen limitation (0.654 and 0.424). Soil carbon, nitrogen, phosphorus, stoichiometric ratio, MBC, MBN, and MBP positively affected CUE (0.527 and 0.589). The microbial diversity index significantly negatively affected CUE (-1.490). Multiple linear stepwise regression analyses showed that CUE was mainly influenced by MBC, AP, C:P, and LAP. Thus, P. notoginseng soil can benefit soil microbial carbon and nitrogen limitations at low Cu concentrations. Clarifying the metabolic activity and nutritional status of microorganisms under Cu stress can provide some theoretical basis for realizing China's comprehensive and effective management and control policies for environmental risks from metals by 2035.

Contrasting roles of plant, bacterial, and fungal diversity in soil organic carbon accrual during ecosystem restoration: A meta-analysis

Plant and microbial diversity plays vital roles in soil organic carbon (SOC) accumulation during ecosystem restoration. However, how soil microbial diversity mediates the positive effects of plant diversity on carbon accumulation during vegetation restoration remains unclear. We conducted a large-scale meta-analysis with 353 paired observations from 65 studies to examine how plant and microbial diversity changed over 0-160 years of natural restoration and its connection to SOC accrual in the topsoil (0-10 cm). Results showed that natural restoration significantly increased plant aboveground biomass (122.09 %), belowground biomass (153.05 %), and richness (21.99 %) and SOC accumulation (32.34 %) but had no significant impact on microbial diversity. Over time, bacterial and fungal richness increased and then decreased. The responses of major microbial phyla, in terms of relative abundance, varied across restoration and ecosystem types. Specifically, Ascomycota and Zygomycota decreased more under farmland abandonment than under grazing exclusion. In forest, Bacteroidetes, Ascomycota, and Zygomycota significantly decreased after natural restoration. The increase in SOC and Basidiomycota was higher in forest than in grassland. Based on standardized estimates, structural equation modeling showed that plant diversity had the highest positive effect (0.55) on SOC accrual, and while fungal diversity (0.15) also had a positive effective, bacterial diversity (-0.20) had a negative effect. Plant diversity promoted SOC accumulation by directly impacting biomass and soil moisture and total nitrogen and indirectly influencing soil microbial richness. This meta-analysis highlights the significant roles of plant diversity and microbial diversity in carbon accumulation during natural restoration and elucidates their relative contributions to carbon accumulation, thereby aiding in more precise predictions of soil carbon sequestration.

Effects of returning peach branch waste to fields on soil carbon cycle mediated by soil microbial communities

In recent years, the rise in greenhouse gas emissions from agriculture has worsened climate change. Efficiently utilizing agricultural waste can significantly mitigate these effects. This study investigated the ecological benefits of returning peach branch waste to fields (RPBF) through three innovative strategies: (1) application of peach branch organic fertilizer (OF), (2) mushroom cultivation using peach branches as a substrate (MC), and (3) surface mulching with peach branches (SM). Conducted within a peach orchard ecosystem, our research aimed to assess these resource utilization strategies' effects on soil properties, microbial community, and carbon cycle, thereby contributing to sustainable agricultural practices. Our findings indicated that all RPBF treatments enhance soil nutrient content, enriching beneficial microorganisms, such as Humicola, Rhizobiales, and Bacillus. Moreover, soil AP and AK were observed to regulate the soil carbon cycle by altering the compositions and functions of microbial communities. Notably, OF and MC treatments were found to boost autotrophic microorganism abundance, thereby augmenting the potential for soil carbon sequestration and emission reduction. Interestingly, in peach orchard soil, fungal communities were found to contribute more greatly to SOC content than bacterial communities. However, SM treatment resulted in an increase in the presence of bacterial communities, thereby enhancing carbon emissions. Overall, this study illustrated the fundamental pathways by which RPBF treatment affects the soil carbon cycle, providing novel insights into the rational resource utilization of peach branch waste and the advancement of ecological agriculture.

Conceptualizing soil fauna effects on labile and stabilized soil organic matter

Fauna is highly abundant and diverse in soils worldwide, but surprisingly little is known about how it affects soil organic matter stabilization. Here, we review how the ecological strategies of a multitude of soil faunal taxa can affect the formation and persistence of labile (particulate organic matter, POM) and stabilized soil organic matter (mineral-associated organic matter, MAOM). We propose three major mechanisms - transformation, translocation, and grazing on microorganisms - by which soil fauna alters factors deemed essential in the formation of POM and MAOM, including the quantity and decomposability of organic matter, soil mineralogy, and the abundance, location, and composition of the microbial community. Determining the relevance of these mechanisms to POM and MAOM formation in cross-disciplinary studies that cover individual taxa and more complex faunal communities, and employ physical fractionation, isotopic, and microbiological approaches is essential to advance concepts, models, and policies focused on soil organic matter and effectively manage soils as carbon sinks, nutrient stores, and providers of food.

Rare taxa mediate microbial carbon and nutrient limitation in the rhizosphere and bulk soil under sugarcane-peanut intercropping systems

Introduction

Microbial carbon (C) and nutrient limitation exert key influences on soil organic carbon (SOC) and nutrient cycling through enzyme production for C and nutrient acquisition. However, the intercropping effects on microbial C and nutrient limitation and its driving factors between rhizosphere and bulk soil are unclear.

Methods

Therefore, we conducted a field experiment that covered sugarcane-peanut intercropping with sole sugarcane and peanut as controls and to explore microbial C and nutrient limitation based on the vector analysis of enzyme stoichiometry; in addition, microbial diversity was investigated in the rhizosphere and bulk soil. High throughput sequencing was used to analyze soil bacterial and fungal diversity through the 16S rRNA gene and internal transcribed spacer (ITS) gene at a phylum level.

Results

Our results showed that sugarcane-peanut intercropping alleviated microbial C limitation in all soils, whereas enhanced microbial phosphorus (P) limitation solely in bulk soil. Microbial P limitation was also stronger in the rhizosphere than in bulk soil. These results revealed that sugarcane-peanut intercropping and rhizosphere promoted soil P decomposition and facilitated soil nutrient cycles. The Pearson correlation results showed that microbial C limitation was primarily correlated with fungal diversity and fungal rare taxa (Rozellomycota, Chyltridiomycota, and Calcarisporiellomycota) in rhizosphere soil and was correlated with bacterial diversity and most rare taxa in bulk soil. Microbial P limitation was solely related to rare taxa (Patescibacteria and Glomeromycota) in rhizosphere soil and related to microbial diversity and most rare taxa in bulk soil. The variation partitioning analysis further indicated that microbial C and P limitation was explained by rare taxa (7%-35%) and the interactions of rare and abundant taxa (65%-93%).

Conclusion

This study indicated the different intercropping effects on microbial C and nutrient limitation in the rhizosphere and bulk soil and emphasized the importance of microbial diversity, particularly rare taxa.

Microorganisms Directly Affected Sediment Carbon–Nitrogen Coupling in Two Constructed Wetlands

Clarifying the carbon–nitrogen coupling pattern in wetlands is crucial for understanding the driving mechanism of wetland carbon sequestration. However, the impacts of plants and environmental factors on the coupling of carbon–nitrogen in wetland sediments are still unclear. Sediment samples from plant (Typha angustifolia and Phragmites australis)-covered habitats and bare land were collected in two constructed wetlands in northern China. The contents of different forms of carbon and nitrogen in sediments and plants, and the sediment microbial community were detected. It was found that the sediment carbon to nitrogen (C/N) ratios did not differ significantly in the bare sites of different wetlands, but did in the plant-covered sites, which highlighted the different role of plants in shifting the carbon–nitrogen coupling in different constructed wetlands. The effects of plants on the sediment carbon–nitrogen coupling differed in two constructed wetlands, so the structural equation model was used and found that sediment microorganisms directly affected sediment C/N ratios, while water and sediment physicochemical properties indirectly affected sediment C/N ratios by altering sediment microbial functions. Multiple linear regression models showed that water pH, sediment moisture content, water dissolved oxygen, and water depth had a greater influence on the carbon metabolism potential of the sediment microbial community, while sediment moisture content had the greatest impact on the sediment microbial nitrogen metabolism potential. The study indicates that variations in environmental conditions could alter the influence of plants on the carbon and nitrogen cycles of wetland sediments. Water environmental factors mainly affect microbial carbon metabolism functions, while soil physicochemical factors, especially water content, affect microbial carbon and nitrogen metabolism functions.

Mild to moderate drought stress reinforces the role of functional microbiome in promoting growth of a dominant forage species (Neopallasia pectinata) in desert steppe

Background

Desert steppe ecosystems are prone to drought stress, which influences the ecological balance and sustainable development of grasslands. In addition to directly restrict plant growth, drought stress indirectly impacts plant fitness by altering the diversity and function of root-associated microbiomes. This begs the question of whether the functional microbiome of forage plants, represented by synthetic microbial communities (SynComs), can be leveraged to mitigate drought stress in desert steppes and promote the ecological restoration of these fragile ecosystems.

Methods

A pot experiment was conducted to evaluate the role of SynComs in improving the plant growth and drought stress resistance of Neopallasia pectinata (Pall.) Poljak in desert steppe in Inner Mongolia, China. Six SynComs were derived from the rhizosphere and root endosphere of 12 dominant forage species in the desert steppe. Each SynCom comprised two to three bacterial genera (Bacillus, Protomicromonospora, and Streptomyces). We examined the capacities of different SynComs for nutrient solubilization, phytohormone secretion, and enzymatic activity.

Results

Under no water stress (75% soil water holding capacity, WHC), single strains performed better than SynComs in promoting plant growth in terms of stem diameter, root length, and plant dry weight, with the greatest effects observed for Streptomyces coeruleorubidus ATCC 13740 (p < 0.05). However, under mild to moderate drought stress (55% and 35% WHC), SynComs outperformed single strains in enhancing plant biomass accumulation and inducing the production of resistance-related substances (p < 0.05). No significant effect of single strains and SynComs emerged under extreme drought stress (20% WHC).

Conclusion

This study underscores the potential of SynComs in facilitating forage plants to combat drought stress in desert steppe. Mild to moderate drought stress stimulates SynComs to benefit the growth of N. pectinata plants, despite a soil moisture threshold (21% WHC) exists for the microbial effect. The use of SynComs provides a promising strategy for the ecological restoration and sustainable utilization of desert steppes by manipulating the functional microbiome of forage plants.

Thinning enhances forest soil C storage by shifting the soil toward an oligotrophic condition

Forests are significant carbon reservoirs, with approximately one-third of this carbon stored in the soil. Forest thinning, a prevalent management technique, is designed to enhance timber production, preserve biodiversity, and maintain ecosystem functions. Through its influence on biotic and abiotic factors, thinning can profoundly alter soil carbon storage. Yet, the full implications of thinning on forest soil carbon reservoirs and the mechanisms underpinning these changes remain elusive. In this study, we undertook a two-year monitoring initiative, tracking changes in soil extracellular enzyme activities (EEAs), microbial communities, and other abiotic parameters across four thinning intensities within a temperate pine forest. Our results show a marked increase in soil carbon stock following thinning. However, thinning also led to decreased dissolved organic carbon (DOC) content and a reduced DOC to soil organic carbon (SOC) ratio, pointing toward a decline in soil carbon lability. Additionally, fourier transform infrared spectroscopy (FTIR) analysis revealed an augmented relative abundance of aromatic compounds after thinning. There was also a pronounced increase in absolute EEAs (per gram of dry soil) post-thinning, implying nutrient limitations for soil microbes. Concurrently, the composition of bacterial and fungal communities shifted toward oligotrophic dominance post thinning. Specific EEAs (per gram of soil organic matter) exhibit a significant reduction following thinning, indicating a deceleration in organic matter decomposition rates. In essence, our findings reveal that thinning transitions soil toward an oligotrophic state, dampening organic matter decomposition, and thus bolstering the soil carbon storage potential of forest. This study provides enhanced insights into the nuanced relationship between thinning practices and forest soil carbon dynamics, serving as a robust foundation for enlightened forest management strategies.

Soil stoichiometric imbalances constrain microbial-driven C and N dynamics in grassland

Grassland restoration leads to excessive soils with carbon (C) and nitrogen (N) contents that are inadequate to fulfill the requirements of microorganisms. The differences in the stoichiometric ratios of these elements could limit the activity of microorganisms, which ultimately affects the microbial C, N use efficiencies (CUE, NUE) and the dynamics of soil C and N. The present study was aimed at quantifying the soil microbial nutrient limitation and exploring the mechanisms underlying microbial-induced C and N dynamics in chrono-sequence of restored grasslands. It was revealed that grassland restoration increased microbial C, N content, microbial C, N uptake, and microbial CUE and NUE, while the threshold elemental ratio (the C:N ratio) decreased, which is mainly due to the synergistic effect of the microbial biomass and enzymatic stoichiometry imbalance after grassland restoration. Finally, we present a framework for the nutrient limitation strategies that stoichiometric imbalances constrain microbial-driven C and N dynamics. These results are the direct evidence of causal relations between stoichiometric ratios, microbial responses, and soil C, N cycling.

The size and diversity of microbes determine carbon use efficiency in soil

Soil is home to a multitude of microorganisms from all three domains of life. These organisms and their interactions are crucial in driving the cycling of soil carbon. One key indicator of this process is Microbial Carbon Use Efficiency (CUE), which shows how microbes influence soil carbon storage through their biomass production. Although CUE varies among different microorganisms, there have been few studies that directly examine how biotic factors influence CUE. One such factor could be body size, which can impact microbial growth rates and interactions in soil, thereby influencing CUE. Despite this, evidence demonstrating a direct causal connection between microbial biodiversity and CUE is still scarce. To address these knowledge gaps, we conducted an experiment where we manipulated microbial body size and biodiversity through size-selective filtering. Our findings show that manipulating the structure of the microbial community can reduce CUE by approximately 65%. When we restricted the maximum body size of the microbial community, we observed a reduction in bacterial diversity and functional potential, which in turn lowered the community's CUE. Interestingly, when we included large body size micro-eukarya in the soil, it shifted the soil carbon cycling, increasing CUE by approximately 50% and the soil carbon to nitrogen ratio by about 25%. Our metrics of microbial diversity and community structure were able to explain 36%-50% of the variation in CUE. This highlights the importance of microbial traits, community structure and trophic interactions in mediating soil carbon cycling.

Analysis and Functional Prediction of Core Bacteria in the Arabidopsis Rhizosphere Microbiome under Drought Stress

The effects of global warming, population growth, and economic development are increasing the frequency of extreme weather events, such as drought. Among abiotic stresses, drought has the greatest impact on soil biological activity and crop yields. The rhizosphere microbiota, which represents a second gene pool for plants, may help alleviate the effects of drought on crops. In order to investigate the structure and diversity of the bacterial communities on drought stress, this study analyzed the differences in the bacterial communities by high-throughput sequencing and bioinformatical analyses in the rhizosphere of Arabidopsis thaliana under normal and drought conditions. Based on analysis of α and β diversity, the results showed that drought stress had no significant effect on species diversity between groups, but affected species composition. Difference analysis of the treatments showed that the bacteria with positive responses to drought stress were Burkholderia-Caballeronia-Paraburkholderia (BCP) and Streptomyces. Drought stress reduced the complexity of the rhizosphere bacterial co-occurrence network. Streptomyces was at the core of the network in both the control and drought treatments, whereas the enrichment of BCP under drought conditions was likely due to a decrease in competitors. Functional prediction showed that the core bacteria metabolized a wide range of carbohydrates, such as pentose, glycans, and aromatic compounds. Our results provide a scientific and theoretical basis for the use of rhizosphere microbial communities to alleviate plant drought stress and the further exploration of rhizosphere microbial interactions under drought stress.

Biodegradable Mineral Plastics

Mineral plastics are a promising class of bio-inspired materials that offer exceptional properties, like self-heal ability, stretchability in the hydrogel state, and high hardness, toughness, transparency, and non-flammability in the dry state along with reversible transformation into the hydrogel by addition of water. This enables easy reshape-ability and recycling like the solubility in mild acids to subsequently form mineral plastics again by base addition. However, current mineral plastics rely on petrochemistry, are hardly biodegradable, and thus persistent in nature. This work presents the next generation of mineral plastics, which are bio-based and biodegradable, making them a promising, new class of polymers for the development of environmentally friendly materials. Physically cross-linked (poly)glutamic-acid (PGlu)-based mineral plastics are synthesized using various alcohol-water mixtures, metal ion ratios and molecular weights. The rheological properties are easily adjusted using these parameters. The general procedure involves addition of equimolar solution of CaCl2 to PGlu in equal volumes followed by addition of iPrOH (iPrOH:H2O = 1:1) under vigorous stirring conditions. The ready biodegradability of PGlu/CaFe mineral plastic is confirmed in this study where the elements N, Ca, and Fe present in it tend to act as additional nutrients, supporting the growth of microorganisms and consequently, promoting the biodegradation process.

Soil organic matter degradation and methylmercury dynamics in Hg-contaminated soils: Relationships and driving factors

Biodegradation of soil organic matter (SOM), which involves greenhouse gas (GHG) emissions, plays an essential role in the global carbon cycle. Over the past few decades, this has become an important research focus, particularly in natural ecosystems. SOM biodegradation significantly affects contaminants in the environment, such as mercury (Hg) methylation, producing highly toxic methylmercury (MeHg). However, the potential link between GHG production from SOM turnover in contaminated soils and biogeochemical processes involving contaminants remains unclear. In this study, we investigated the dynamics of GHG, MeHg production, and the relationship between biogeochemical processes in soils from two typical Hg mining sites. The two contaminated soils have different pathways, explaining the significant variations in GHG and MeHg production. The divergence of the microbial communities in these two biogeochemical processes is essential. In addition to the microbial role, abiotic factors such as Hg species can significantly affect MeHg production. On the other hand, we found an inverse relationship between CH4 and MeHg, suggesting that carbon emission reduction policies and management could inadvertently increase the MeHg levels. This highlights the need for an eclectic approach to organic carbon sequestration and contaminant containment. These findings suggest that it is difficult to establish a general pattern to describe and explain the SOM degradation and MeHg production in contaminated soils within the specific scenarios. However, this study provides a case study and helpful insights for further understanding the links between environmental risks and carbon turnover in Hg mining areas.

Fungal community composition predicts forest carbon storage at a continental scale

Forest soils harbor hyper-diverse microbial communities which fundamentally regulate carbon and nutrient cycling across the globe. Directly testing hypotheses on how microbiome diversity is linked to forest carbon storage has been difficult, due to a lack of paired data on microbiome diversity and in situ observations of forest carbon accumulation and storage. Here, we investigated the relationship between soil microbiomes and forest carbon across 238 forest inventory plots spanning 15 European countries. We show that the composition and diversity of fungal, but not bacterial, species is tightly coupled to both forest biotic conditions and a seven-fold variation in tree growth rates and biomass carbon stocks when controlling for the effects of dominant tree type, climate, and other environmental factors. This linkage is particularly strong for symbiotic endophytic and ectomycorrhizal fungi known to directly facilitate tree growth. Since tree growth rates in this system are closely and positively correlated with belowground soil carbon stocks, we conclude that fungal composition is a strong predictor of overall forest carbon storage across the European continent.

Active microbial population dynamics and life strategies drive the enhanced carbon use efficiency in high-organic matter soils

Microbial carbon use efficiency (CUE) is a critical parameter that controls carbon storage in soil, but many uncertainties remain concerning adaptations of microbial communities to long-term fertilization that impact CUE. Based on H218O quantitative stable isotope probing coupled with metagenomic sequencing, we disentangled the roles of active microbial population dynamics and life strategies for CUE in soils after a long-term (35 years) mineral or organic fertilization. We found that the soils rich in organic matter supported high microbial CUE, indicating a more efficient microbial biomass formation and a greater carbon sequestration potential. Organic fertilizers supported active microbial communities characterized by high diversity and a relative increase in net growth rate, as well as an anabolic-biased carbon cycling, which likely explains the observed enhanced CUE. Overall, these results highlight the role of population dynamics and life strategies in understanding and predicting microbial CUE and sequestration in soil.IMPORTANCEMicrobial CUE is a major determinant of global soil organic carbon storage. Understanding the microbial processes underlying CUE can help to maintain soil sustainable productivity and mitigate climate change. Our findings indicated that active microbial communities, adapted to long-term organic fertilization, exhibited a relative increase in net growth rate and a preference for anabolic carbon cycling when compared to those subjected to chemical fertilization. These shifts in population dynamics and life strategies led the active microbes to allocate more carbon to biomass production rather than cellular respiration. Consequently, the more fertile soils may harbor a greater microbially mediated carbon sequestration potential. This finding is of great importance for manipulating microorganisms to increase soil C sequestration.

Key Role of Vegetation Cover in Alleviating Microplastic-Enhanced Carbon Emissions

Microplastics (MPs) are considered to influence fundamental biogeochemical processes, but the effects of plant residue-MP interactions on soil carbon turnover in urban greenspaces are virtually unknown. Here, an 84-day incubation experiment was constructed using four types of single-vegetation-covered soils (6 years), showing that polystyrene MP (PSMP) pollution caused an unexpectedly large increase in soil CO2 emissions. The additional CO2 originating from highly bioavailable active dissolved organic matter molecules (<380 °C, predominantly polysaccharides) was converted from persistent carbon (380-650 °C, predominantly aromatic compounds) rather than PSMP derivatives. However, the priming effect of PSMP derivatives was weakened in plant-driven soils (resistivity: shrub > tree > grass). This can be explained from two perspectives: (1) Plant residue-driven humification processes reduced the percentage of bioavailable active dissolved organic matter derived from the priming effects of PSMPs. (2) Plant residues accelerated bacterial community succession (dominated by plant residue types) but slowed fungal community demise (retained carbon turnover-related functional taxa), enabling specific enrichment of glycolysis, the citric acid cycle and the pentose phosphate pathway. These results provide a necessary theoretical basis to understand the role of plant residues in reducing PSMP harm at the ecological level and refresh knowledge about the importance of biodiversity for ecosystem stability.

Humification and fungal community succession during pig manure composting: Membrane covering and mature compost addition

The objective of this study was to elucidate the combined effect of a semi-permeable membrane (M) and mature compost (MC) on humification and fungal community succession in pig manure composting. Compared with the control, the concentrations of humic substances (HSs) increased by 44.54 % (M + 15 % MC) and 43.90 % (M). During the thermophilic phase, Aspergillus (67.26 %) was the dominant genus in the M + 15 % MC treatment. Membrane covering increased the relative abundance (RA) of other phyla (except for Ascomycetes and Basidiomycetes) on the 14th day and Basidiomycetes on the 80th day in M treatment. Humic acid, HSs were positively correlated with the RA of genera Myceliophthora, Kernia, and Mycothermus. Myceliophthora was the key genus in the M + 15 % MC treatment on the 80th day. The results showed that 15 % MC addition under membrane covering optimizes the quality of composting products.

Effects of adding steel slag on humification and characteristics of bacterial community during phosphate-amended composting of municipal sludge

This study aimed to investigate the effects of different proportions (0%, 5%, 7.5%, and 10%) of steel slag (SS) on humification and bacterial community characteristics during phosphate-amended composting of municipal sludge. Compared with adding KH2PO4 alone, co-adding SS significantly promoted the temperature, pH, nitrification, and critical enzyme activities (polyphenol oxidase, cellulase, laccase); especially organic matter (OM) degradation rate (25.5%) and humification degree (1.8) were highest in the 5%-SS treatment. Excitation-emission matrix-parallel factor confirmed that co-adding SS could promote the conversion of protein-like substances or microbial by-products into humic-like substances. Furthermore, adding 5%-SS significantly improved the relative abundances of Actinobacteria, Firmicutes and the genes related to carbohydrate and amino acid metabolism, and enhanced the interactions of bacterial community in stability and complexity. The partial least squares path model indicated that OM was the primary factor affecting humification. These results provided a promising strategy to optimize composting of municipal sludge via SS.

Effect of long-term in-row branch covering on soil microorganisms in pear orchards

Branches covering (BC) is a way to reuse the pruned branches and save the cost of ground cloth. This study investigated the effects of BC and ground-cloth covering on the soil microcosm environment by measuring the chemical properties and microbial communities at different soil depths for 6 years. The results revealed that BC significantly improved soil chemical properties, increased the abundance of bacterial microbial communities and the diversity and homogeneity of bacteria and fungi, while decreased the abundance of fungal microbial communities. There was a threshold value for the regulation of microbial communities by BC, which decreased the high-abundance communities (Proteobacteria, Ascomycota, etc.) and increased the low-abundance communities (Acidobacteriota, Basidiomycota, etc.). Fungi were more sensitive to BC than bacteria. The stability and homogeneity of microorganisms were stronger in the 15-25 cm soil layer. The bacterial phyla were dominated by Proteobacteria, with the top 10 phyla accounting for more than 80% of the relative abundance; the genera were dominated by MND1, with the top 10 genera accounting for about 10%. The fungal phyla were dominated by Ascomycota, with the top 10 phyla accounting for 50-90%; the genera were dominated by unidentified Pyronemataceae sp., with the top 10 genera accounting for 30-60%. The phyla that differed significantly between treatments were mainly Proteobacteria, Ascomycota, Acidobacteriota, and Basidiomycota. In addition, metabolism was the predominant function in bacteria, while Saprotroph was the predominant function in fungi. Bacteroidota correlated strongly with soil chemical properties and bacterial functions, while Chytridiomycota correlated strongly with soil chemical properties and Pathogen-Saprotroph-Symbiotroph. In conclusion, BC can improve soil nutrient content and optimize microbial community structure and function. Through initially assessing the effects of BC on soil nutrients and microorganisms in pear orchard rows, this study provides a reference for excavating key microorganisms and updating the soil row management model.

Unveiling the crucial role of soil microorganisms in carbon cycling: A review

Soil microorganisms, by actively participating in the decomposition and transformation of organic matter through diverse metabolic pathways, play a pivotal role in carbon cycling within soil systems and contribute to the stabilization of organic carbon, thereby influencing soil carbon storage and turnover. Investigating the processes, mechanisms, and driving factors of soil microbial carbon cycling is crucial for understanding the functionality of terrestrial carbon sinks and effectively addressing climate change. This review comprehensively discusses the role of soil microorganisms in soil carbon cycling from three perspectives: metabolic pathways, microbial communities, and environmental influences. It elucidates the roles of different microbial species in carbon cycling and highlights the impact of microbial interactions and environmental factors on carbon cycling. Through the synthesis of 2171 relevant papers in the Web of Science Core database, we elucidated the ecological community structure, activity, and assembly mechanisms of soil microorganisms crucial to the soil carbon cycle that have been widely analyzed. The integration of soil microbial carbon cycle and its driving factors are vital for accurately predicting and modeling biogeochemical cycles and effectively addressing the challenges posed by global climate change. Such integration is vital for accurately predicting and modeling biogeochemical cycles and effectively addressing the challenges posed by global climate change.

Microbially mediated mechanisms underlie soil carbon accrual by conservation agriculture under decade-long warming

Increasing soil organic carbon (SOC) in croplands by switching from conventional to conservation management may be hampered by stimulated microbial decomposition under warming. Here, we test the interactive effects of agricultural management and warming on SOC persistence and underlying microbial mechanisms in a decade-long controlled experiment on a wheat-maize cropping system. Warming increased SOC content and accelerated fungal community temporal turnover under conservation agriculture (no tillage, chopped crop residue), but not under conventional agriculture (annual tillage, crop residue removed). Microbial carbon use efficiency (CUE) and growth increased linearly over time, with stronger positive warming effects after 5 years under conservation agriculture. According to structural equation models, these increases arose from greater carbon inputs from the crops, which indirectly controlled microbial CUE via changes in fungal communities. As a result, fungal necromass increased from 28 to 53%, emerging as the strongest predictor of SOC content. Collectively, our results demonstrate how management and climatic factors can interact to alter microbial community composition, physiology and functions and, in turn, SOC formation and accrual in croplands.

Arbuscular mycorrhizae mitigate negative impacts of soil biodiversity loss on grassland productivity

Grassland degradation decreases ecosystem productivity and diminishes soil biodiversity, leading to the loss of beneficial microorganisms. Arbuscular mycorrhizal fungi (AMF) play a critical role in ecosystem functioning, being a key link between plant and microbial communities, soil, and vegetation. Here, we evaluated the potential of increasing the productivity of degraded grassland by AMF inoculation. A gradient of soil biodiversity: complete sterilization, low, moderate, and high biodiversity was established using the dilution-to-extinction approach. Grassland microcosms under greenhouse conditions were inoculated with three AMF taxa in an increasing diversity: no AMF, single AMF taxa, and all three AMF taxa together. The loss of soil biodiversity decreased plant community productivity, primarily due to reduced biomass of legumes and non-N2-fixing forbs. AMF inoculation raised plant community productivity by 190%, mainly attributed to the greater biomass of legumes and non-N2-fixing forbs. This positive effect of AMF inoculation was particularly pronounced on soils with low biodiversity, where soil mutualists were absent. The biomass of grasses remained independent of AMF inoculation. This differential responsiveness to mycorrhiza was mainly due to the distinctive plant traits of each plant functional group. Inoculating with a single AMF was more beneficial for plant biomass production than inoculation with multiple AMF under lower levels of soil biodiversity, probably due to high functional redundancy among AMF taxa. In conclusion, AMF inoculation reduced the adverse impact of soil degradation and biodiversity loss on plant biomass and vegetation development, highlighting the key roles and importance of AMF for grassland restoration.

Microbial regulation of feedbacks to ecosystem change

Microbes are key biodiversity components of all ecosystems and control vital ecosystem functions. Although we have just begun to unravel the scales and factors that regulate microbial communities, their role in mediating ecosystem stability in response to disturbances remains underexplored. Here, we review evidence of how, when, and where microbes regulate or drive disturbance feedbacks. Negative feedbacks dampen the impacts of disturbance, which maintain ecosystem stability, whereas positive feedbacks instead erode stability by amplifying the disturbance. Here we describe the processes underlying the responses to disturbance using a hierarchy of functional traits, and we exemplify how these may drive biogeochemical feedbacks. We suggest that the feedback potential of functional traits at different hierarchical levels is contingent on the complexity and heterogeneity of the environment.

Effects of uranium mining on soil bacterial communities and functions in the Qinghai-Tibet plateau

The microecological effects of plateau uranium mining are still unknown. In this study, we used 16S rRNA high-throughput sequencing to analyze the impact of plateau uranium mining on the microbial diversity and community structure of tailings soil, tunnel soil, and soil at different depths in an open pit. The results showed that uranium mining significantly reduced soil microbial community richness and diversity indicators, including Chao1, Pielou evenness, and Shannon index (P < 0.05). Uranium mining activities significantly reduced the abundance of RB41, Vicinamidactaceae, and Nitrospira (P < 0.05). Interestingly, the abundance of Thiobacillus, Sphingomonas, and Sulfuriferula significantly increased in the soil samples from various environments and depths during uranium mining (P < 0.05). Beta diversity analysis found that uranium mining resulted in the differentiation of soil microbial communities. Functional enrichment analysis found that uranium mining resulted in the functional enrichment of DNA binding response regulator, DNA helicase, methyl-accepting chemotaxis protein, and Helicase conserved C-terminal domain, whereas cell wall synthesis, nonspecific serine/threonine protein kinase, RNA polymerase sigma-70 factor, and ATP binding cassette transporter were significantly affected by uranium mining (P < 0.05). In addition, we also found that different uranium mining environments and soil depths enriched diverse microbial populations and functions to cope with the environmental pressures that were elicited by uranium mining, including Gaiella, Gemmatimonas, Lysobacter, Pseudomonas, signal transformation histidine kinase, DNA-directed DNA polymerase, and iron complex outer membrane receptor protein functions (P < 0.05). The results have enhanced our understanding of the impact of uranium mining on plateau soil microecological stability and the mechanism of microbial response to uranium mining activities for the first time and aided us in screening microbial strains that can promote the environmental remediation of uranium mining in plateaus.

Can we manage microbial systems to enhance carbon storage?

Climate change is an urgent environmental issue with wide-ranging impacts on ecosystems and society. Microbes are instrumental in maintaining the balance between carbon (C) accumulation and loss in the biosphere, actively regulating greenhouse gas fluxes from vast reservoirs of organic C stored in soils, sediments and oceans. Heterotrophic microbes exhibit varying capacities to access, degrade and metabolise organic C-leading to variations in remineralisation and turnover rates. The present challenge lies in effectively translating this accumulated knowledge into strategies that effectively steer the fate of organic C towards prolonged sequestration. In this article, we discuss three ecological scenarios that offer potential avenues for shaping C turnover rates in the environment. Specifically, we explore the promotion of slow-cycling microbial byproducts, the facilitation of higher carbon use efficiency, and the influence of biotic interactions. The ability to harness and control these processes relies on the integration of ecological principles and management practices, combined with advances in economically viable technologies to effectively manage microbial systems in the environment.

Macrofungi promote SOC decomposition and weaken sequestration by modulating soil microbial function in temperate steppe

Soil organic carbon (SOC) sequestration is a key grassland ecosystem function, and the magnitude of SOC reservoirs depends on microbial involvement, especially that of fungi. Mycelia developed by macrofungi potentially influence carbon (C) fixation and decomposition; however, the mechanisms underlying their effects on SOC storage in grassland ecosystems remain poorly understood. The fairy rings formed by macrofungi in grasslands are natural platform for exploring macrofungal effects on SOC. In this study, we collected topsoil (0-10 cm) from four different fairy ring zones in a temperate steppe to reveal the macrofungal effects on SOC fractions, including particulate organic carbon (POC) and mineral-associated organic carbon (MAOC), and the SOC storage microbial mechanism using metagenomic sequencing technology. Both POC and MAOC decreased after macrofungal passage, resulting in a 7.37 % reduction in SOC. Macrofungal presence reduced microbial biomass carbon (MBC), but significantly enhanced the β-1,4-glucosidase (BG) activity, which increased dissolved organic carbon (DOC). In addition, the abundance of copiotrophs (Proteobacteria and Bacteroidetes) with lower C metabolic rates increased, and that of oligotrophs (Actinobacteria, Acidobacteria, Chloroflexi, and Verrucomicrobia) with higher substrate utilization efficiency decreased in the presence of macrofungi. This may further promote SOC decomposition. Correspondingly, there was a lower abundance of C-fixation genes but more C-degradation genes (especially hemicellulosic degradation genes) during macrofungal passage. Our results indicate that the presence of macrofungi can modulate the soil microbial community and functional genes to reduce SOC storage by inhibiting microbial C sequestration while promoting C decomposition in grassland ecosystems. These findings refine our mechanistic understanding of SOC persistence through the interactions between macrofungi and other microbes.

The efficient solution to decline the greenhouses emission and enrich the bacterial community during pig manure composting: Regulating the particle size of cornstalk

In present study, four lengths of chopped cornstalks were amended with pig manure respectively for 100 days aerobic fermentation, which aimed to evaluate the impact of different length of agricultural solid wastes on gaseous emission and dominating bacterial community succession and connection. The result revealed that the maximum ammonia volatilization was observed in 5 cm of straw samples attributed to the prominent mineralization, which was opposite to the emission of CH4 and N2O. As for global warming potential, the minimum value was detected in 5 cm of straw samples, which decreased by 5.03-24.75% compared with other samples. Additionally, the strongest correlation and complexity of bacterial community could be detected in 5 cm of straw treatment, representing the most vigorous bacterial metabolic ability could be recorded by optimizing the microbial habitat. Therefore, in order to decline the greenhouse effect in livestock manure composting, the 5 cm of corn straw was recommended.

Soil microbial community, dissolved organic matter and nutrient cycling interactions change along an elevation gradient in subtropical China

To identify possible dominating processes involved in soil microbial community assembly, dissolved organic matter (DOM) and multi-nutrient cycling (MNC) interactions and contribute to understanding of climate change effects on these important cycles, we investigated the interaction of soil chemistry, DOM components and microbial communities in five vegetation zones - ranging from evergreen broad-leaved forest to alpine meadow - along an elevation gradient of 290-1960 m in the Wuyi Mountains, Fujian Province, China. Soil DOM composition and microbial community assembly were characterized using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and Illumina MiSeq high-throughput sequencing, respectively. Sloan's neutral model and the modified stochasticity ratio were used to infer community assembly processes. Key microbial drivers of the soil MNC index were identified from partial least squares path models. Our results showed that soil DOM composition is closely related to the vegetation types along an elevation gradient, the structure and composition of the microbial community, and soil nutrient status. Overall, values of the double bond equivalent (DBE), modified aromaticity index (AImod) increased, and H/C ratio and molecular lability boundary (MLBL) percentage decreased with elevation. Lignins/CRAM-like structures compounds dominated soil DOM in each vegetation type and its relative abundance decreased with elevation. Aliphatic/protein and lipids components also decreased, but the relative abundance of aromatic structures and tannin increased with elevation. The alpha diversity index of soil bacteria gradually decreased with elevation, with deterministic processes dominating the microbial community assembly in the highest elevation zone. Bacterial communities were conducive to the decomposition of labile degradable DOM compounds (H/C ≥ 1.5) at low elevation. In the cooler and wetter conditions at higher-elevation sites the relative abundance of potentially resistant soil DOM components (H/C < 1.5) gradually increased. Microbial community diversity and composition were important predictors of potential soil nutrient cycling. Although higher elevation sites have higher nutrient cycling potential, soil DOM was assessed to be a more stable carbon store, with apparent lower lability and bioavailability than at lower elevation sites. Overall, this study increases understanding of the potential linkage between soil microbial community, multiple nutrient cycling and DOM fate in subtropical mountain ecosystems that can help predict the effect of climate change on soil carbon sequestration and thus inform ecosystem management.

Lonicera caerulea L. polyphenols improve short-chain fatty acid levels by reshaping the microbial structure of fermented feces in vitro

Increasing evidence suggests that the pathogenesis of type 2 diabetes mellitus (T2DM) is closely related to the gut microbiota. Polyphenols have been shown to alleviate T2DM, but the effects of L. caerulea L. polyphenols (LPs) on the gut microbiota and metabolites remain elusive. In this study, the inhibitory effects of fermented L. caerulea L. polyphenols (FLPs) and unfermented L. caerulea L. polyphenols (ULPs) on α-amylase and α-glucosidase and the impact of LP on the gut microbiota and metabolites were investigated. Furthermore, the relationship between the two was revealed through correlation analysis. The results showed that ULP and FLP had the highest inhibitory rates against α-amylase and α-glucosidase at 4 mg ml-1, indicating a strong inhibitory ability. In addition, LP plays a regulatory role in the concentration of short-chain fatty acids (SCFAs) and tends to restore them to their normal levels. LP reversed the dysbiosis of the gut microbiota caused by T2DM, as evidenced by an increase in the abundance of bacterial genera such as Lactobacillus, Blautia, and Bacteroides and a decrease in the abundance of bacterial genera such as Escherichia-Shigella and Streptococcus. Similarly, after LP intervention, the relationships among microbial species became more complex and interconnected. In addition, the correlation between the gut microbiota and metabolites was established through correlation analysis. These further findings clarify the mechanism of action of LP against T2DM and provide a new target for T2DM interventions.

Linking Redox Characteristics to Dissolved Organic Matter Derived from Different Biowaste Composts: A Theoretical Modeling Approach Based on FT-ICR MS Analysis

Compost dissolved organic matter (DOM) is a complex mixture of redox-active organic molecules that impact various biogeochemical processes in soil environments. However, the impact of chemical complexity (heterogeneity and chemodiversity) on the electron accepting capacity (EAC) and electron donating capacity (EDC) of DOM molecules remains unclear, which hinders our ability to predict their environmental behavior and redox properties. In this study, the applicability of Vienna Soil Organic Matter Modeler 2 (VSOMM2) to the composting system based on the FT-ICR MS data has been validated. A molecular modeling approach using VSOMM2 and Schrödinger software was developed to quantitatively assess the redox sites and molecular interactions of compost DOM. Compost DOM molecules are categorized into three distinct groups based on their heterogeneous origins. In addition, we have developed 18 molecular models of compost DOM based on the links of molecules to EAC/EDC. Finally, Ar-OH, quinone, Ar-SH, and Ar-NH2 were identified as the redox sites; noncovalent contacts, H bonds, salt bridges, and aromatic-H bonds might be significant electronic transmission channels of compost DOM. Our findings contribute to the development of precise regulatory methods for functional molecules within compost DOM, providing the fine standards for composts matching specific ecosystem service requirements.

Microbial-driven carbon fixation in natural wetland

With the development of global industrialization, carbon neutrality has become an issue that we must be paid attention to. Microorganisms not only have an important impact on the carbon chemical cycle between the Earth's biosphere and biogeography but also play a key role in maintaining the global organic carbon balance. Wetlands are the main reservoir of organic carbon in the mainland of China, and wetland carbon sinks are indispensable for China to achieve the goal of "dual carbon," and China has taken the consolidation and improvement of wetland carbon sink capacity as an important part of the carbon peaking action plan. As a unique low-latitude, high-altitude seasonal plateau wetland in China, Napahai shows high research value. However, the role of microbes in maintaining dissolved organic carbon balance in this area has not been reported. In the study, six carbon fixation genes, accA, aclB, acsA, acsB, cbbL, and rbcL, were analyzed based on metagenomics to elucidate the rich genetic diversity, uniqueness and differences in the Napahai plateau wetland. It was found that the microbial diversity in the Napahai plateau wetland was different from other habitats. In addition, the aclB gene, a rare taxon with high genetic diversity and rich species in the Napahai plateau wetland, played a key role in the microbial metabolic pathway. Finally, the construction of a metabolic pathway through the Kyoto encyclopedia for genes and genomes revealed the contribution of microbes to carbon fixation and the role of microbes in maintaining the organic carbon balance of the Napahai plateau wetland.

Integrating microbial community properties, biomass and necromass to predict cropland soil organic carbon

Manipulating microorganisms to increase soil organic carbon (SOC) in croplands remains a challenge. Soil microbes are important drivers of SOC sequestration, especially via their necromass accumulation. However, microbial parameters are rarely used to predict cropland SOC stocks, possibly due to uncertainties regarding the relationships between microbial carbon pools, community properties and SOC. Herein we evaluated the microbial community properties (diversity and network complexity), microbial carbon pools (biomass and necromass carbon) and SOC in 468 cropland soils across northeast China. We found that not only microbial necromass carbon but also microbial community properties (diversity and network complexity) and biomass carbon were correlated with SOC. Microbial biomass carbon and diversity played more important role in predicting SOC for maize, while microbial network complexity was more important for rice. Models to predict SOC performed better when the microbial community and microbial carbon pools were included simultaneously. Taken together our results suggest that microbial carbon pools and community properties influence SOC accumulation in croplands, and management practices that improve these microbial parameters may increase cropland SOC levels.

Whole-soil-profile warming does not change microbial carbon use efficiency in surface and deep soils

The paucity of investigations of carbon (C) dynamics through the soil profile with warming makes it challenging to evaluate the terrestrial C feedback to climate change. Soil microbes are important engines driving terrestrial biogeochemical cycles; their carbon use efficiency (CUE), defined as the proportion of metabolized organic C allocated to microbial biomass, is a key regulator controlling the fate of soil C. It has been theorized that microbial CUE should decline with warming; however, empirical evidence for this response is scarce, and data from deeper soils are particularly scarce. Here, based on soil samples from a whole-soil-profile warming experiment (0 to 1 m, +4 °C) and 18O tracing approach, we examined the vertical variation of microbial CUE and its response to ~3.3-y experimental warming in an alpine grassland on the Qinghai-Tibetan Plateau. Microbial CUE decreased with soil depth, a trend that was primarily controlled by soil C availability. However, warming had limited effects on microbial CUE regardless of soil depth. Similarly, warming had no significant effect on soil C availability, as characterized by extractable organic C, enzyme-based lignocellulose index, and lignin phenol-based ratios of vanillyls, syringyls, and cinnamyls. Collectively, our work suggests that short-term warming does not alter microbial CUE in either surface or deep soils, and emphasizes the regulatory role of soil C availability on microbial CUE.

Variations of methane fluxes and methane microbial community composition with soil depth in the riparian buffer zone of a sponge city park

Riparian buffers benefit both natural and man-made ecosystems by preventing soil erosion, retaining soil nutrients, and filtering pollutants. Nevertheless, the relationship between vertical methane fluxes, soil carbon, and methane microbial communities in riparian buffers remains unclear. This study examined vertical methane fluxes, soil carbon, and methane microbial communities in three different soil depths (0-5 cm, 5-10 cm, and 10-15 cm) within a riparian buffer of a Sponge City Park for one year. Structural equation model (SEM) results demonstrated that vertical methane fluxes varied with soil depths (λ = -0.37) and were primarily regulated by methanogenic community structure (λ = 0.78). Notably, mathematical regression results proposed that mcrA/pmoA ratio (R² = 0.8) and methanogenic alpha diversity/methanotrophic alpha diversity ratio (R² = 0.8) could serve as valid predictors of vertical variation in methane fluxes in the riparian buffer of urban river. These findings suggest that vertical variation of methane fluxes in riparian buffer soils is mainly influenced by carbon inputs and methane microbial abundance and community diversity. The study's results quantitatively the relationship between methane fluxes in riparian buffer soils and abiotic and biotic factors in the vertical direction, therefore contributing to the further development of mathematical models of soil methane emissions.

Evaluating the role of bacterial diversity in supporting soil ecosystem functions under anthropogenic stress

Ecosystem functions and services are under threat from anthropogenic global change at a planetary scale. Microorganisms are the dominant drivers of nearly all ecosystem functions and therefore ecosystem-scale responses are dependent on responses of resident microbial communities. However, the specific characteristics of microbial communities that contribute to ecosystem stability under anthropogenic stress are unknown. We evaluated bacterial drivers of ecosystem stability by generating wide experimental gradients of bacterial diversity in soils, applying stress to the soils, and measuring responses of several microbial-mediated ecosystem processes, including C and N cycling rates and soil enzyme activities. Some processes (e.g., C mineralization) exhibited positive correlations with bacterial diversity and losses of diversity resulted in reduced stability of nearly all processes. However, comprehensive evaluation of all potential bacterial drivers of the processes revealed that bacterial α diversity per se was never among the most important predictors of ecosystem functions. Instead, key predictors included total microbial biomass, 16S gene abundance, bacterial ASV membership, and abundances of specific prokaryotic taxa and functional groups (e.g., nitrifying taxa). These results suggest that bacterial α diversity may be a useful indicator of soil ecosystem function and stability, but that other characteristics of bacterial communities are stronger statistical predictors of ecosystem function and better reflect the biological mechanisms by which microbial communities influence ecosystems. Overall, our results provide insight into the role of microorganisms in supporting ecosystem function and stability by identifying specific characteristics of bacterial communities that are critical for understanding and predicting ecosystem responses to global change.

Soil nematode assemblages respond to interacting environmental changes

Multi-factor experiments suggest that interactions among environmental changes commonly influence biodiversity and community composition. However, most field experiments manipulate only single factors. Soil food webs are critical to ecosystem health and may be particularly sensitive to interactions among environmental changes that include soil warming, eutrophication, and altered precipitation. Here, we asked how environmental changes interacted to alter soil nematode communities in a northern Chihuahuan Desert grassland. Factorial manipulations of nitrogen, winter rainfall, and nighttime warming matched predictions for regional environmental change. Warming reduced nematode diversity by 25% and genus-level richness by 32%, but declines dissipated with additional winter rain, suggesting that warming effects occurred via drying. Interactions between precipitation and nitrogen also altered nematode community composition, but only weakly affected total nematode abundance, indicating that most change involved reordering of species abundances. Specifically, under ambient precipitation, nitrogen fertilizer reduced bacterivores by 68% and herbivores by 73%, but did not affect fungivores. In contrast, under winter rain addition, nitrogen fertilization increased bacterivores by 95%, did not affect herbivores, and doubled fungivore abundance. Rain can reduce soil nitrogen availability and increase turnover in the microbial loop, potentially promoting the recovery of nematode populations overwhelmed by nitrogen eutrophication. Nematode communities were not tightly coupled to plant community composition and may instead track microbes, including biocrusts or decomposers. Our results highlight the importance of interactions among environmental change stressors for shaping the composition and function of soil food webs in drylands.

Effects of adding corn steep liquor on bacterial community composition and carbon and nitrogen transformation during spent mushroom substrate composting

BACKGROUND

Carbon and nitrogen are essential energy and nutrient substances in the composting process. Corn steep liquor (CSL) is rich in soluble carbon and nitrogen nutrients and active substances and is widely used in the biological industry. Nonetheless, limited research has been done on the effect of CSL on composting. This work firstly reveals the effect of adding CSL to bacterial community composition and carbon and nitrogen conversion during composting. This study provides the choice of auxiliary materials for the spent mushroom substrate compost (SMS) and some novel knowledge about the effect of bacterial community on C and N cycling during composting of SMS and CSL. Two treatments were set up in the experiment: 100% spent mushroom substrate (SMS) as CK and SMS + 0.5% CSL (v/v) as CP.

RESULTS

The results showed that the addition of CSL enhanced the initial carbon and nitrogen content of the compost, altered the bacterial community structure, and increased the bacterial diversity and relative abundance, which might be beneficial to the conversion and retention of carbon and nitrogen in the composting process. In this paper, network analysis was used to screen the core bacteria involved in carbon and nitrogen conversion. In the CP network, the core bacteria were divided into two categories, synthesizing and degrading bacteria, and there were more synthesizing bacteria than degrading bacteria, so the degradation and synthesis of organic matter were carried out simultaneously, while only degrading bacteria were found in the CK network. Functional prediction by Faprotax identified 53 groups of functional bacteria, among which 20 (76.68% abundance) and 14 (13.15% abundance) groups of functional bacteria were related to carbon and nitrogen conversion, respectively. Adding CSL stimulated the compensatory effect of core and functional bacteria, enhanced the carbon and nitrogen transformation ability, stimulated the activity of low-abundance bacteria, and reduced the competitive relationship between the bacterial groups. This may be why the addition of CSL accelerated the organic matter degradation and increased carbon and nitrogen preservation.

CONCLUSIONS

These findings indicate that the addition of CSL promoted the cycling and preservation of carbon and nitrogen in the SMS composts, and the addition of CSL to the compost may be an effective way to dispose of agricultural waste.

Exploring gaseous emissions and pivotal enzymatic activity during co-composting of branch and pig manure: the effect of particle size of bulking agents

The purpose of current study was to probe the effect of various length of branch on gaseous emissions and vital enzymatic activity. Four lengths (<2 cm, 2 cm, 5 cm, and 10 cm) of clipped branch were mingled with collected pig manure for 100 days aerobic fermentation. The consequence demonstrated that the amendment of 2 cm of branch showed conducive to decline the greenhouse gas emissions, which the CH₄ emissions decreased by 1.62-40.10%, and the N₂O emissions decreased by 21.91-34.04% contrasted with other treatments. Furthermore, the peak degree of enzymatic activities was also observed in 2 cm of branch treatment by the optimizing living condition for microbes. In view of microbiological indicators, the most abundant and complex bacterial community could be monitor in 2 cm of branch composting pile, which verified the microbial facilitation. Summing up, the strategy of 2 cm branch amendment would be recommended.

Rhizospheric soil organic carbon accumulated but its molecular groups redistributed via rhizospheric soil microorganisms along multi-root Cerasus humilis plantation chronosequence at the karst rocky desertification control area

Though the relationships between the microorganism communities and the edaphic factors in rhizosphere soil along the plantation chronosequence have been widely reported, few researches have appeared on the interrelationship about rhizospheric soil microorganism community and soil organic carbon (SOC) under multi-root Cerasus humilis plantations of different age. In our study, the rhizospheric soil microbial communities, soil physicochemistry, and SOC molecular groups in plantations of 1-, 3-, and 5-year-old Cerasus humilis were investigated in karst rocky desertification control area of southwest China. It was found that karst rhizospheric soil moisture, total nitrogen, available potassium, and 46-60 ppm N-alkyl/methoxyl C decreased; however, SOC and fungal:bacterial ratio decreased along multi-root Cerasus humilis plantation chronosequence. Proteobacteria, Actinobacteriota, Acidobacteriota, and Ascomycota were recognized as the top 4 phyla in the karst rhizospheric soil microbial co-occurrence network. Moreover, Cerasus humilis plantations exerted significantly direct effect on rhizospheric soil microbial communities and soil physicochemical properties exerted significantly direct effects on SOC molecular groups. Our results suggested that the increased Cerasus humilis plantation years will promote C sequestration (e.g., SOC) with the continued input of root litter, root exudates, and plant litter. The inputted and activated C can be preferentially consumed by rhizospheric soil microorganisms and converted into microbial-derived compounds, which are finally incorporated into recalcitrant SOC pools. Hence, Cerasus humilis redistributed SOC molecular groups via rhizospheric soil microorganisms, and increased ratio of fungi:bacteria in rhizosphere was associated with C sequestration which could not be regarded as a widespread rule. Though our study is the first attempt to recognize the interaction between rhizospheric soil microbial community and SOC molecular groups at the karst rocky desertification control area, it provides a baseline for further research that ecological restoration can promote soil C sequestration via soil microorganisms in the early period of eco-restoration at karst area.

Mechanisms underlying the responses of microbial carbon and nitrogen use efficiencies to nitrogen addition are mediated by topography in a subtropical forest

Microbial carbon use efficiency (CUE) and nitrogen use efficiency (NUE) are key parameters determining the fate of C and N in soils. Atmospheric N deposition has been found to heavily impact multiple soil C and N transformations, but we lack understanding of the responses of CUE and NUE to N deposition, and it remains uncertain whether responses may be mediated by topography. Here, a N addition experiment with three treatment levels (0, 50 and 100 kg N ha^-1 yr^-1) was conducted in the valley and on the slope of a subtropical karst forest. Nitrogen addition increased microbial CUE and NUE at both topographic positions, but the underlying mechanisms differed. In the valley, the increase in CUE was associated with an increase in soil fungal richness:biomass and lower litter C:N, whereas on the slope, the response was linked with a reduced ratio of dissolved soil organic C (DOC) to available phosphorus (AVP) which reduced respiration, and increased root N:P stoichiometry. In the valley, the increase in NUE was explained by stimulated microbial N growth relative to gross N mineralization, which was associated with increased ratios of soil total dissolved N:AVP and fungal richness:biomass. In contrast, on the slope, the increase in NUE was attributed to reduced gross N mineralization, linked to increased DOC:AVP. Overall, our results highlight how topography-driven soil substrate availability and microbial properties can regulate microbial CUE and NUE.

Mini-review: Current and Future Perspectives on Microbially Focused Restoration Strategies in Tallgrass Prairies

Ecosystem restoration is a critical conservation strategy, especially for increasing resilience and resistance to climate change. Current restoration efforts that convert reclaimed agricultural land to native tallgrass prairies typically focus on aboveground communities, but it can take decades to restore soil microbial biodiversity and function using these strategies, if they recover at all. This incomplete restoration can have detrimental impacts on longer-term restoration goals, such as supporting late-successional plant species and facilitating soil carbon sequestration. Soil microorganisms are key components in determining the fate of organic material that enters the soil. They mediate decomposition rates and contribute to plant-microbe-soil interactions, produce microbial biomass, necromass, and metabolic products, and physically protect soil carbon through aggregation. Interactions with plants and controls over soil carbon vary widely depending on the specific microbial taxa present, their physiology, their functional capabilities, and their responses to environmental stressors. Thus, the ability for new restorations, prairie conservation corridors, and prairies planted in marginal lands to act as carbon sinks and help balance greenhouse gas emissions can depend on the success of microbial restoration. Next-generation sequencing approaches can support novel methods for evaluating existing restoration practices and developing microbially focused management strategies. This review summarizes the growing body of literature describing microbially focused tallgrass prairie restoration and considers when and how integrating next-generation sequencing approaches into management efforts can be beneficial. We provide a roadmap for future restoration efforts where microbial ecologists, restoration ecologists, and land managers can work together to meet their goals to promote climate-ready restored ecosystems.

Microbial assemblies with distinct trophic strategies drive changes in soil microbial carbon use efficiency along vegetation primary succession in a glacier retreat area of the southeastern Tibetan Plateau

Soil microbial carbon use efficiency (CUE) is a vital physiological parameter in assessing carbon turnover. Yet, how the microbial assemblies with distinct trophic strategies regulate the soil microbial CUE remains elusive. Based on the oligotrophic-copiotrophic framework, we explored the role of microbial taxa with different trophic strategies in mediating microbial CUE (determined by a ¹³C-labeled approach) along the vegetation primary succession in Hailuogou glacier retreat area of the southeastern Tibetan Plateau. Results showed that soil microbial CUE ranged from 0.54 to 0.72 (averaging 0.62 ± 0.01 across all samples) and increased staggeringly along the vegetation succession. Microbial assemblies with distinct trophic strategies were crucial regulators of soil microbial CUE. Specifically, microbial CUE increased with microbial oligotroph: copiotroph ratios, oligotroph-dominated stage had a higher microbial CUE than copiotroph-dominated ones. The prevalence of oligotrophic members would be the underlying microbial mechanism for the high microbial CUE. Given that oligotrophs predominate in more recalcitrant carbon soils and their higher microbial CUE, we speculate that oligotrophs are likely to potentially enhance carbon sequestration in soils. In addition, the responses of the microbial CUE to fungal oligotroph: copiotroph ratios were higher than bacterial ones. Fungal taxa may play a dominant role in shaping microbial CUE relative to bacterial members. Overall, our results constructed close associations between microbial trophic strategies and CUE and provide direct evidence regarding how microbial trophic strategies regulate microbial CUE. This study is a significant step forward for elucidating the physiological mechanisms regulating microbial CUE and has significant implications for understanding microbial-mediated carbon cycling processes.

Amino Acids Drive the Deterministic Assembly Process of Fungal Community and Affect the Flavor Metabolites in Baijiu Fermentation

Nutrient fluctuation is ubiquitous in fermentation ecosystems. However, the microbial community assembly mechanism and metabolic characteristics in response to nutrient variation are still unclear. Here, we used Baijiu fermentation as a case example to study the responses of microbial community assembly and metabolic characteristics to the variation of amino acids using high-throughput sequencing and metatranscriptomics analyses. We chose two fermentation groups (group A with low amino acid and group B with high amino acid contents). The two groups showed similar succession patterns in the bacterial community, whereas they showed different succession in the fungal community wherein Pichia was dominant in group A and Zygosaccharomyces was dominant in group B. The β-nearest taxon index (βNTI) revealed that bacterial community was randomly formed, whereas fungal community assembly was a deterministic process. Variance partitioning analysis and redundancy analysis revealed that amino acids showed the largest contribution to the fungal community (37.64%, P = 0.005) and were more tightly associated with it in group B. Further study revealed that serine was positively related to Zygosaccharomyces and promoted its growth and ethanol production. Metatranscriptomic analysis revealed that the differential metabolic pathways between the two groups mainly included carbohydrate metabolism and amino acid metabolism, which explained the differences of ethanol production and volatile metabolites (such as isoamylol, isobutanol, and 2-methyl-1-butanol). Then these metabolic pathways were constructed and related gene expression and active microorganisms were listed. Our study provides a systematical understanding of the roles of amino acids in both ecological maintenance and flavor metabolism in fermentation ecosystems. IMPORTANCE In spontaneous fermented foods production, nutrient fluctuation is a critical factor affecting microbial community assembly and metabolic function. Revealing the microbial community assembly mechanism and how it regulates its metabolic characteristics in response to nutrient variation is helpful to the management of the fermentation process. This study provides a systematical understanding of the effect of amino acids on the microbial community assembly and flavor metabolisms using Baijiu fermentation as a case example. The data of this study highlight the importance of the nutrient management in fermentation ecosystems.