Microbial regulation of the soil carbon cycle: evidence from gene-enzyme relationships

Biotic and abiotic drivers of soil carbon, nitrogen and phosphorus and metal dynamic changes during spontaneous restoration of Pb-Zn mining wastelands

The biotic and abiotic mechanisms that drive important biogeochemical processes (carbon, nitrogen, phosphorus and metals dynamics) in metal mine revegetation remains elusive. Metagenomic sequencing was used to explored vegetation, soil properties, microbial communities, functional genes and their impacts on soil processes during vegetation restoration in a typical Pb-Zn mine. The results showed a clear niche differentiation between bacteria, fungi and archaea. Compared to bacteria and fungi, the archaea richness were more tightly coupled with natural restoration changes. The relative abundances of CAZyme-related, denitrification-related and metal resistance genes reduced, while nitrification, urease, inorganic phosphorus solubilisation, phosphorus transport, and phosphorus regulation -related genes increased. Redundancy analysis, hierarchical partitioning analysis, relative-importance analysis and partial least squares path modelling, indicated that archaea diversity, primarily influenced by available lead, directly impacts carbon dynamics. Functional genes, significantly affected by available cadmium, directly alter nitrogen dynamics. Additionally, pH affects phosphorus dynamics through changes in bacterial diversity, while metal dynamics are directly influenced by vegetation. These insights elucidate natural restoration mechanisms in mine and highlight the importance of archaea in soil processes.

Microbial diversity, enzyme activity, metal contamination, and their responses to environmental drivers in an Indo-Burmese freshwater wetland

Seasonal fluctuations can influence many biotic and abiotic parameters in wetland environments. Present research on wetlands do not serve as a comprehensive model for understanding these seasonal influences, especially in Northeast India, where wetland ecosystems remain understudied. That being, our study investigated the seasonal, spatial, depth-wise variations of enzyme activity (xylanase, invertase, and cellulase), microbial community, and heavy metal concentrations [chromium (Cr), cadmium (Cd), lead (Pb), and iron (Fe)] in the sediments of Deepor Beel. Our results show, seasons rather than sediment layers influence all parameters. Enzyme activities peaked during post-monsoon (POM), with xylanase showing highest activity throughout (0.01-132.94 mmol/min/g). Culture independent bacterial diversity study based on next generation sequence (NGS) analysis revealed a steady decrease in unique amplicon sequence variants (ASVs) from pre-monsoon (PRM) (31), followed by POM (22) and finally monsoon (MON) (2). Bacteria consistently outnumbered archaea throughout the study. Heavy metals peaked during PRM, with Fe reaching 1416-1200 mg kg-1. Cr exceeded US EPA limit in all seasons, while Pb and Cd surpassed the limits during PRM and MON. Pearson's correlation showed that TC, TN, C/N ratio, and EC significantly influenced enzyme activity during PRM and POM. Correlations between microbial community and environmental parameters revealed enzyme activities, C/N ratio and TC to positively influence many microbial genera. In contrast, certain genera showed tolerance to elevated concentrations of Cd, Pb, and Fe. Our findings have considerable implications for predicting the dynamics of abiotic and biotic factors related to the carbon cycle as a consequence of seasonal change.

Comparison of mediating effects of air pollutants on urban morphology and urban heat Island intensity at block scale

The urban heat island effect seriously challenges the sustainability and livability of urban development. Air pollutants (AP) may play a mediating role in the impact of urban morphology (UM) on the canopy layer urban heat island intensity (CLUHII) and the surface urban heat island intensity (SUHII). To verify this hypothesis, taking Urumqi as an example, we use the ridge regression model to reveal the differences in the impacts of UM and AP on the two types of urban heat island intensity (UHII). A structural equation model was established to verify the mediating effect of AP. The results show that: (1) There are differences in the optimal research units for UM and CLUHII and SUHII, which are 500 m and 300 m respectively. (2) Whether it is CLUHII or SUHII, the impact of two - dimensional urban morphology indicators are greater than that of three - dimensional urban morphology indicators. (3) There are similarities and differences in the impact of urban morphology indicators on the two types of UHII. The effects of standard deviation of building height, floor area ratio, and sky view factor on the two are opposite. (4) Air pollutants (PM10, PM2.5, NO2) have significant mediating effects between building density, impervious surface percent, green coverage ratio, mean building height, standard deviation of building height, floor area ratio, sky view factor, and the two types of UHII. This study provides a reliable reference for urban planning aimed at mitigating the urban heat island effect and air pollution.

Adaptation strategies of the soil microbial community to stoichiometric imbalances induced by grassland management measures in the desert steppe of Northwest China

Grassland management measures strongly affect soil resources availability which can not meet microbial elemental demands, potentially resulting in stoichiometric imbalances. This limits microbial metabolic activities and nutrient cycling. However, there is still limiting understanding of the adaptation strategies of soil microbial communities to stoichiometric imbalances. We investigated soil labile resources, microbial biomass stoichiometry, extracellular enzymatic stoichiometry (EES), and microbial communities under three management measures (planting Caragana korshinskii (NTC), moderate-intensity thinning Caragana korshinskii (MTC) and grassland (GL)) in desert steppe of Northwest China, and assessed microbial metabolic limitation. Lower soil labile C:N and C:P values, and higher microbial biomass C:N and C:P values were found in NTC and MTC, leading to lower C:N and C:P imbalances. The microbial communities maintained stoichiometric homeostasis through improving the threshold elemental ratio (TER), adjusting enzymes production and extracellular enzymatic stoichiometry (EES), and increasing microbial biomass P, to store scarce nutrients (N and P), consequently alleviating N and P limitations. Stoichiometric imbalances could better explain the variation of bacterial community compared with fungal community. The C:N imbalance was closely related with bacterial and fungal communities composition and diversity. Partial least squares path modelling highlighted that grassland management measures altered microbial communities, which was directly associated with EES and indirectly associated with high TER. Overall, these results helped to better understand the response of microbial metabolic activities and communities to stoichiometric imbalances changes induced by grassland management measures in the desert steppe. And moderate-intensity thinning C. korshinskii was a promising management measure for Ningxia desert steppe.

Mariculture increases microbially-driven carbon metabolism and sequestration in coastal ecosystems

Mariculture has expanded significantly in recent decades due to rising seafood demand and its contribution to ocean carbon sequestration. While the mechanisms of carbon sequestration in mariculture are well-established, the roles of microorganisms in sedimentary carbon sequestration have rarely been explored. How microorganisms mediate organic carbon metabolism and their effects on coastal carbon pools remain unclear. Here we tested the carbon fraction and contents, as well as extracellular hydrolase activities in macroalgae culture area, fish or abalone culture area, and control area without mariculture. We profiled microbial community composition and carbon metabolism characteristics in sediments through 16S rRNA gene amplicon sequencing and metagenomics. Our findings revealed that macroalgae culture areas exhibited a significantly greater potential for carbon sequestration than the control area, the concentration of TOC in seawater and the contents of SOC, DOC, and ROC in sediments were significantly (p < 0.05) increased by 18.93 %, 6.98 %, 33.98 %, and 18.30 % respectively. These results can be attributed to decreased activities of extracellular hydrolase and a lower abundance of carbon-degrading genes. Moreover, metabolic profiling identified taxa from families such as Alteromonadaceae, Pseudomonadaceae, Rhodobacteraceae, Enterobacteriaceae, and Flavobacteriaceae, which are highly metabolically flexible in utilizing a wide range of organic and inorganic energy sources, playing crucial roles in carbon formation. Their respiratory metabolism, such as sulfate reduction, thiosulfate oxidation, and denitrification as well as secondary metabolism products could also affect the formation and persistence of sedimentary carbon pools. Specifically, increased total nitrogen (TN) and nitrate-nitrogen (NO3-) could potentially enhance microbial degradation of organic carbon, decreasing carbon stock within coastal sediments. This study enhanced our understanding of microbial regulation of the organic carbon pool in the mariculture ecosystem.

Potential of lavender essential oil to inhibit tetracycline resistance and modulate gut microbiota in black soldier fly larvae

The misuse of tetracycline in livestock farming leads to environmental residues that promote the proliferation of antibiotic resistance genes (ARGs), particularly tetracycline resistance (tet) genes. Black soldier fly (BSF) larvae, used for organic waste bioconversion, may carry tetracycline residues in their guts, raising concerns about ARG spread. To address this issue, plant-derived additives such as lavender essential oil (LEO) have been explored as alternative antibiotics. This study investigated the effects of LEO on tet gene suppression and gut microbiota modulation in BSF larvae. Results showed that oxytetracycline treatment increased tet gene relative abundance threefold compared to the control, reaching 1.13 ± 0.29 and enriched pathogens Klebsiella oxytoca and Enterobacter hormaechei. Conversely, LEO treatment (100 mg/kg) reduced tet gene abundance by 46.67 %, from 0.15 ± 0.02 to 0.08 ± 0.02, and enhanced beneficial microorganisms like Leuconostoc pseudomesenteroides. Furthermore, LEO reduced tet gene relative abundance in oxytetracycline-treated larvae from 1.13 ± 0.29 to 0.49 ± 0.19 and 0.70 ± 0.11 in separate treatments. LEO modified fungal composition and nutrient pathways. Network analysis revealed that LEO promoted a more integrated and modular gut microbiota, enhancing functional specialization and resilience. These findings suggest LEO can mitigate ARGs in BSF larvae, offering a sustainable approach for antibiotic resistance management in organic waste recycling and livestock farming.

Water level regimes can regulate the influences of microplastic pollution on carbon loss in paddy soils: Insights from dissolved organic matter and carbon mineralization

The persistence of farmland microplastic (MP) pollution has raised significant concerns regarding its effects on soil organic carbon (SOC) pools in the context of soil pollution but also of global climate change. Nevertheless, the effect of MPs on SOC mineralization as well as dissolved organic carbon (DOC) transformation with different water levels in paddy soils remained uncertain. In this study, we investigated the effect of micro polyethylene (PE) on SOC decomposition in paddy soils under alternating wet and dry (AWD) and continuous flooding (CF) conditions through a 205-day microcosm experiment. Polyethylene addition reduced cumulative CO2 emissions by 5.1-14.8 % under both water conditions. The presence of PE influenced SOC mineralization under CF conditions by diminishing the activity of cellobiohydrolase enzymes and increasing the microbial community diversity. Conversely, at AWD the addition of PE impeded SOC mineralization by reducing the activity of polyphenol oxidase enzymes. However, PE addition resulted in higher DOC content and at low dose of PE addition (0.25 % w/w) increased DOM bioavailability. The most significantly positive effect was found with the addition of 1 % w/w PE, which increased DOC content by 37.2 % and 18.5 % compared to Control (CK) under AWD and CF conditions, respectively. The strong correlation observed between DOC and mineral-associated organic carbon (MAOC) concentrations might result from DOC adsorbed to mineral surfaces to form MAOC and then affect SOC mineralization. Accordingly, AWD is a more efficient management to attenuate the impact of MPs on SOC decomposition compared to CF. Our study is noteworthy in the development of sustainable agricultural practice management in plastic-contaminated soil-crop systems.

Wetland restoration suppresses microbial carbon metabolism by altering keystone species interactions

Soil bacteria play a pivotal role in regulating multifaceted functions of terrestrial ecosystems. Unraveling the succession of bacterial communities and the feedback mechanism on soil organic carbon (SOC) dynamics help embed the ecology of microbiome into C cycling model. However, how wetland restoration drives soil bacterial community assembly and species association to regulate microbial C metabolism remains unclear. Here, we investigated soil bacterial diversity, community structure and co-occurrence network, enzyme activities and SOC decomposition in restored wetlands for one, three, and four years from paddy fields in Northeast China. Wetland restoration for three and four years increased taxonomic (richness) and phylogenetic diversities by 2.39-3.96% and 2.13-3.02%, respectively, and increased the relative contribution of nestedness to community dissimilarity, indicating increased richness changed soil bacterial community structure. However, wetland restoration for three and four years decreased the richness index of aerobic Firmicutes by 5.04-5.74% due to stronger anaerobic condition characterized by increased soil Fe2+/Fe3+ from 0.20 to 0.64. Besides, wetland restoration for four years decreased network complexity (characterized by decreased node number by 2.51%, edge number by 9.62%, positive/negative edge number by 6.37%, average degree by 5.74% and degree centralization by 6.34%). Robustness index decreased with the increase of restoration duration, while vulnerability index increased with the increase of restoration duration, indicating that wetland restoration decreased network stability of soil bacterial communities. These results might be because stronger anaerobic condition induced the decrease of aerobic Bacilli richness index in keystone module, thereby reducing positive association within keystone module. Decreased positive species association within keystone module in turn weakened microbial C metabolism by decreasing hydrolase activities from 7.49 to 5.37 mmol kg SOC-1 h-1 and oxidase activities from 627 to 411 mmol kg SOC-1 h-1, leading to the decrease of SOC decomposition rate from 1.39 to 1.08 g C kg SOC-1 during wetland restoration. Overall, our results suggested that although wetland restoration after agricultural abandonment increased soil bacterial diversity, it decreased positive association within Bacilli-dominated keystone module under stronger anaerobic condition, which weakened microbial C metabolism and SOC decomposition.

Differences in Carbon and Nitrogen Cycling Strategies and Regional Variability in Biological Soil Crust Types

Biological soil crusts (BSCs) play a pivotal role in maintaining ecosystem stability and soil fertility in arid and semi-arid regions. However, the biogeographical differences in soil functional composition between cyanobacterial BSCs (C-BSCs) and moss BSCs (M-BSCs), particularly how environmental changes affect nutrient cycling strategies and microbial community functions, remain poorly understood. In this study, we investigated BSCs across aridity gradients (semi-humid, semi-arid, and arid regions) in China, focusing on carbon and nitrogen cycling pathways, enzyme activities, and nutrient acquisition strategies. It was found that aridity and BSC type had significant effects on the functional characteristics of microorganisms. This was demonstrated by significant differences in various soil microbial activities including enzyme activities and carbon and nitrogen nutrient cycling. With increasing aridity, C-BSCs exhibited reduced carbon cycling activity but enhanced nitrogen cycling processes, whereas M-BSCs displayed diminished activity in both carbon and nitrogen cycling. These divergent strategies were linked to soil properties such as pH and organic carbon content, with C-BSCs adapting through nitrogen-related processes (e.g., nifH, amoA) and M-BSCs relying on C fixation and degradation. These findings provide novel insights into the functional gene diversity of BSCs across different regions, offering valuable references for ecological restoration in arid areas. Specifically, our study highlights the potential of BSC inoculation for carbon and nitrogen enrichment in arid regions, with implications for climate-resilient restoration practices.

Soil organic carbon stabilization is influenced by microbial diversity and temperature

The stabilization of soil organic carbon (SOC) is influenced by soil microbes and environmental factors, particularly temperature, which significantly affects SOC decomposition. This study investigates the effects of temperature (ambient: 25 °C; elevated: 27.5 °C) and soil microbial diversity (low, medium, and high) on the formation of stabilized SOC, focusing on mineral-associated organic carbon (MAOC) and water-stable aggregates, through a 75-day model soil incubation experiment. We measured water-stable aggregates, microbial respiration, and SOC in different fractions. Our results demonstrate that microbial diversity is crucial for SOC mineralization; low diversity resulted in 3.93-6.26% lower total carbon and 8.05-17.32% lower particulate organic carbon (POC) compared to medium and high diversity under the same temperature. While total MAOC was unaffected by temperature and microbial diversity, macroaggregate-occluded MAOC decreased by 8.78%, 38.36% and 9.40% under elevated temperature for low, medium and high diversity, respectively, likely driven by decreased macroaggregate formation. A negative correlation between macroaggregate-occluded POC and microbial respiration (r= -0.37, p < 0.05) suggested microbial decomposition of POC within macroaggregates contributed to respiration, with a portion of the decomposed POC potentially stabilized as microbial-derived MAOC. Notably, soils with medium microbial diversity exhibited the highest levels of both macroaggregate-occluded POC and MAOC at ambient temperature; however, elevated temperature disrupted this stabilization, reducing both POC retention and MAOC accumulation within macroaggregates. These findings underscore the temperature-sensitive interplay between microbial diversity and SOC stabilization, highlighting the need to disentangle microbial pathways governing C dynamics under climate change.

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

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

Sustainable Land Use Enhances Soil Microbial Respiration Responses to Experimental Heat Stress

Soil microbial communities provide numerous ecosystem functions, such as nutrient cycling, decomposition, and carbon storage. However, global change, including land-use and climate changes, affects soil microbial communities and activity. As extreme weather events (e.g., heatwaves) tend to increase in magnitude and frequency, we investigated the effects of heat stress on the activity (e.g., respiration) of soil microbial communities that had experienced four different long-term land-use intensity treatments (ranging from extensive grassland and intensive grassland to organic and conventional croplands) and two climate conditions (ambient vs. predicted future climate). We hypothesized that both intensive land use and future climate conditions would reduce soil microbial respiration (H1) and that experimental heat stress would increase microbial respiration (H2). However, this increase would be less pronounced in soils with a long-term history of high-intensity land use and future climate conditions (H3), and soils with a higher fungal-to-bacterial ratio would show a more moderate response to warming (H4). Our study showed that soil microbial respiration was reduced under high land-use intensity (i.e., -43% between extensive grassland and conventional cropland) and future climate conditions (-12% in comparison to the ambient climate). Moreover, heat stress increased overall microbial respiration (+17% per 1°C increase), while increasing land-use intensity reduced the strength of this response (-25% slope reduction). In addition, increasing soil microbial biomass and fungal-to-bacterial ratio under low-intensity land use (i.e., extensive grassland) enhanced the microbial respiration response to heat stress. These findings show that intensive land use and climate change may compromise the activity of soil microbial communities as well as their respiration under heatwaves. In particular, soil microbial communities under high-intensity land use and future climate are less able to respond to additional stress, such as heatwaves, potentially threatening the critical ecosystem functions driven by soil microbes and highlighting the benefits of more sustainable agricultural practices.

Higher temperature sensitivity of forest soil methane oxidation in colder climates

Forest soils, serving as an important sink for atmospheric methane (CH4), modulate the global CH4 budget. However, the direction and magnitude of the forest soil CH4 sink under warming remain uncertain, partly because the temperature response of microbial CH4 oxidation varies substantially across geographical scales. Here, we reveal the spatial variation in the response of forest soil microbial CH4 oxidation to warming, along with the driving factors, across 84 sites spanning a broad latitudinal gradient in eastern China. Our results show that the temperature sensitivity of soil microbial CH4 oxidation significantly declines with increasing site mean annual temperature, with a range of 0.03 to 0.77 μg CH4 g-1 soil d-1 °C-1. Moreover, soil resources and type II methanotrophs play crucial roles in shaping the temperature sensitivity of soil microbial CH4 oxidation. Our findings highlight the importance of incorporating climate, soil resources, and methanotroph groups into biogeochemical models to more realistically predict forest soil CH4 sink under warming.

Impacts of successive Chinese fir plantations on soil carbon and nitrogen dynamics: Conclusive insights from metagenomic analysis

Chinese fir forests play a significant role both economically and ecologically, contributing to soil and water conservation while also serving as an efficient timber-producing species that brings economic benefits. However, the issue of soil degradation due to continuous Chinese fir planting cannot be overlooked. Continuous planting leads to a decrease in soil nutrients, a reduction in microbial diversity, and changes in microbial community composition, which in turn affect the abundance of carbon and nitrogen cycle functional genes in Chinese fir forest soils. We utilized metagenomic sequencing technology to investigate the dynamics of microbial community composition and carbon and nitrogen-related functional genes in the soils of Chinese fir forests across different plantation generations, exploring their relationship with soil carbon and nitrogen nutrients. We found that the relative abundance of bacterial communities is dominant in both phylum and genus levels within microbial communities. The partial least squares path models (PLS-PM) indicated that planting generations had a negative effect on dissolved organic carbon (DOC), nitrate nitrogen (NO3--N), and microbial biomass nitrogen (MBN), with a significant negative impact on microbial residual carbon (MRC). Easily utilizable carbon nutrient (DOC) in Chinese fir forest soil showed a significant positive effect on the abundance of carbon fixation functional genes (direct effect = 0.91, p < 0.01), and on the abundance of methane metabolism functional genes (direct effect = 1.27, p < 0.01). Nitrogen nutrients (NO3--N, MBN) in the soil also had a significant positive effect on the abundance of carbon fixation functional genes (direct effect = 0.90, p < 0.01). Bacterial communities (Acidobacteria and Verrucomicrobia) had significant negative effects on carbon and nitrogen cycling processes. The abundance of nasA and nirA genes generally showed a decreasing trend with increasing plantation generations. The decrease in available nitrogen nutrients with increased plantation generations was influenced by Assimilatory nitrogen reduction to ammonia (ANRA), an energy-consuming process. In summary, the continuous planting of Chinese fir had significant impacts on the carbon and nitrogen nutrient cycling processes, and it influenced the composition of microbial communities and the spatial distribution of functional genes. Clarifying the changes in carbon and nitrogen nutrient cycling processes in Chinese fir continuous planting provides a reference for maintaining the productivity of Chinese fir plantations.

Impacts of plant root traits and microbial functional attributes on soil respiration components in the desert-oasis ecotone

Dividing soil respiration (Rs) into autotrophic respiration (Ra) and heterotrophic respiration (Rh) represents a pivotal step in deciphering how Rs responds to environmental perturbations. Nevertheless, in arid ecosystems beset by environmental stress, the partitioning of Rs and the underlying mechanisms through which microbial and root traits govern the distinct components remain poorly understood. This study was strategically designed to investigate Rs and its components (Ra and Rh), soil properties, and root traits within the desert-oasis ecotone (encompassing the river bank, transitional zone, and desert margin) of northwest China. Employing metagenomics, we quantitatively characterized microbial taxonomic attributes (i.e., taxonomic composition) and functional attributes (specifically, functional genes implicated in microbial carbon metabolism). Field measurements during the growing season of 2019 unveiled a pronounced decline in soil respiration rates along the environmental gradient from the river bank to the desert margin. The mean soil respiration rate was recorded as 1.82 ± 0.41 μmol m-2 s-1 at the river bank, 0.49 ± 0.15 μmol m-2 s-1 in the transitional zone, and a meager 0.45 ± 0.12 μmol m-2 s-1 in the desert margin. Concomitantly, the Ra and Rh components exhibited a similar trend throughout the study period, with Rh emerging as the dominant driver of Rs. Utilizing random forest modeling, we unearthed significant associations between microbial taxonomic and functional features and Rs components. Notably, both Ra and Rh displayed robust positive correlations with the abundance of phosphatidylinositol glycan A, a key player in microbial carbon metabolism. Partial least squares path modeling further elucidated that soil properties and microbial functions exerted direct and positive influences on both Ra and Rh, whereas taxonomic features failed to register a significant impact. When considering the combined effects of biotic and abiotic factors, microbial functional attributes emerged as the linchpin in dictating Rs composition. Collectively, these findings suggest that a trait-based approach holds great promise in more effectively revealing the response mechanisms of Rs composition to environmental changes, thereby offering novel vistas for future investigations into carbon cycling in terrestrial soils.

Distinct spatiotemporal patterns between fungal alpha and beta diversity of soil-plant continuum in rubber tree

Plant-associated microbial communities strongly relate to host health and productivity. Still, our knowledge of microbial community spatiotemporal patterns in soil-plant continuum is largely limited. Here, we explored the spatiotemporal dynamics of fungal communities across multiple compartments (phyllosphere, leaf endosphere, soil, rhizosphere, rhizoplane, and root endosphere) of rubber tree in two contrasting seasons collected from Hainan Island and Xishuangbanna. Our results demonstrate that the fungal alpha and beta diversity exhibited distinct pattern; the alpha diversity is highly dependent on seasonal changes, while beta diversity only showed a geographical variation pattern. The season-specific environmental factors (e.g., climatic factors) were the most important factors in shaping fungal alpha diversity across the soil-plant continuum. Physicochemical properties explained some of the microbial beta diversity spatiotemporal variation observed, with leaf phosphorus (P) and soil available potassium (AK) likely being the main factors that drove the geographical variation. We further identified the variation of edaphic (e.g., AK) and leaf physicochemical factors (e.g., P) were mainly caused by regional sites (P < 0.05). Taken together, our study provides an empirical evidence that the distinct spatiotemporal patterns of alpha and beta diversity of rubber tree fungal diversity and significantly expand our understanding of ecological drivers of plant-associated microbial communities.

IMPORTANCE

Plants harbor diverse microorganisms in both belowground and aboveground compartments, which play a vital role in plant nitrogen supply and growth promotion. Understanding the spatiotemporal patterns of microbial communities is a prerequisite for harnessing them to promote plant growth. In this study, we show that the alpha and beta diversity of soil-plant continuum in rubber tree exhibited distinct spatiotemporal pattern. Alpha diversity is highly dependent on seasonal changes, while beta diversity only showed a geographical variation pattern. Climatic factors were the most important factors in shaping fungal alpha diversity. Leaf phosphorus (P) and soil available potassium (AK) were major drivers to induce geographical variation.

Phages Affect Soil Dissolved Organic Matter Mineralization by Shaping Bacterial Communities

Viruses are considered to regulate bacterial communities and terrestrial nutrient cycling, yet their effects on bacterial metabolism and the mechanisms of carbon (C) dynamics during dissolved organic matter (DOM) mineralization remain unknown. Here, we added active and inactive bacteriophages (phages) to soil DOM with original bacterial communities and incubated them at 18 or 23 °C for 35 days. Phages initially (1-4 days) reduced CO2 efflux rate by 13-21% at 18 °C and 3-30% at 23 °C but significantly (p < 0.05) increased by 4-29% at 18 °C and 9-41% at 23 °C after 6 days, raising cumulative CO2 emissions by 14% at 18 °C and 21% at 23 °C. Phages decreased dominant bacterial taxa and increased bacterial community diversity (consistent with a "cull-the-winner" dynamic), thus altering the predicted microbiome functions. Specifically, phages enriched some taxa (such as Pseudomonas, Anaerocolumna, and Caulobacter) involved in degrading complex compounds and consequently promoted functions related to C cycling. Higher temperature facilitated phage-bacteria interactions, increased bacterial diversity, and enzyme activities, boosting DOM mineralization by 16%. Collectively, phages impact soil DOM mineralization by shifting microbial communities and functions, with moderate temperature changes modulating the magnitude of these processes but not qualitatively altering their behavior.

Soil microbiome interventions for carbon sequestration and climate mitigation

Mitigating climate change in soil ecosystems involves complex plant and microbial processes regulating carbon pools and flows. Here, we advocate for the use of soil microbiome interventions to help increase soil carbon stocks and curb greenhouse gas emissions from managed soils. Direct interventions include the introduction of microbial strains, consortia, phage, and soil transplants, whereas indirect interventions include managing soil conditions or additives to modulate community composition or its activities. Approaches to increase soil carbon stocks using microbially catalyzed processes include increasing carbon inputs from plants, promoting soil organic matter (SOM) formation, and reducing SOM turnover and production of diverse greenhouse gases. Marginal or degraded soils may provide the greatest opportunities for enhancing global soil carbon stocks. Among the many knowledge gaps in this field, crucial gaps include the processes influencing the transformation of plant-derived soil carbon inputs into SOM and the identity of the microbes and microbial activities impacting this transformation. As a critical step forward, we encourage broadening the current widespread screening of potentially beneficial soil microorganisms to encompass functions relevant to stimulating soil carbon stocks. Moreover, in developing these interventions, we must consider the potential ecological ramifications and uncertainties, such as incurred by the widespread introduction of homogenous inoculants and consortia, and the need for site-specificity given the extreme variation among soil habitats. Incentivization and implementation at large spatial scales could effectively harness increases in soil carbon stocks, helping to mitigate the impacts of climate change.

Long-term climate establishes functional legacies by altering microbial traits

Long-term climate history can influence rates of soil carbon cycling but the microbial traits underlying these legacy effects are not well understood. Legacies may result if historical climate differences alter the traits of soil microbial communities, particularly those associated with carbon cycling and stress tolerance. However, it is also possible that contemporary conditions can overcome the influence of historical climate, particularly under extreme conditions. Using shotgun metagenomics, we assessed the composition of soil microbial functional genes across a mean annual precipitation gradient that previously showed evidence of strong climate legacies in soil carbon flux and extracellular enzyme activity. Sampling coincided with recovery from a regional, multi-year severe drought, allowing us to document how the strength of climate legacies varied with contemporary conditions. We found increased investment in genes associated with resource cycling with historically higher precipitation across the gradient, particularly in traits related to resource transport and complex carbon degradation. This legacy effect was strongest in seasons with the lowest soil moisture, suggesting that contemporary conditions-particularly, resource stress under water limitation-influences the strength of legacy effects. In contrast, investment in stress tolerance did not vary with historical precipitation, likely due to frequent periodic drought throughout the gradient. Differences in the relative abundance of functional genes explained over half of variation in microbial functional capacity-potential enzyme activity-more so than historical precipitation or current moisture conditions. Together, these results suggest that long-term climate can alter the functional potential of soil microbial communities, leading to legacies in carbon cycling.

Microbial functional genes play crucial roles in enhancing soil nutrient availability of halophyte rhizospheres in salinized grasslands

Land degradation due to salinization threatens ecosystem health. Phytoremediation, facilitated by functional microorganisms, has gained attention for improving saline-alkali soils. However, the relationship between the functional potential of rhizosphere microbes involved in multi-element cycling and soil nutrient pools remain unclear. This study focused on the changes in functional genes related to carbon (C), nitrogen (N), and phosphorus (P) cycling in the rhizospheres of various halophytes and bulk soil in the grassland ecosystem of Chaka Salt Lake, Qinghai Province, China. Our evaluation of plant and soil characteristics revealed that halophyte growth increased soil hydrolase activity and nutrient levels, particularly available N. Significant differences were observed in foliage and root nutrients, rhizosphere soil properties, and microbial functional gene composition among plant species. Halophytes significantly altered the abundance of genes involved in C fixation (Calvin and DC/4-HB cycles), C degradation (starch, hemicellulose, cellulose, and pectin degradation), dissimilatory nitrate reduction (nirB), ammonification (ureC), organic P mineralization (phoA and ugpQ), P transport (phnE), and inorganic P dissolution (ppk1). C, N, and P cycling processes were closely related to soil N nutrients, available nutrient ratios, and C/N-cycling enzyme activities. Partial least squares path modeling (PLS-PM) analysis showed that microbial functional genes were directly associated with soil nutrient availability, with soil and plant variables indirectly affecting nutrient pools through the regulation of these genes. These findings enhance our understanding of the biochemical cycling in halophyte rhizospheres and highlight the role of microbial functional genes in saline-alkali soil restoration.

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.

Assembly of soil multitrophic community regulates multifunctionality via multifaceted biotic factors in subtropical ecosystems

Soil biodiversity underpins multiple ecosystem functions and services essential for human well-being. Understanding the determinants of biodiversity-ecosystem function relationships (BEFr) is critical for the conservation and management of soil ecosystems. Community assembly processes determine community diversity and structure. However, there remains limited systematic research on how the assembly processes of multiple organismal groups affect soil ecosystem functions through their influence on biodiversity and species interactions. Here, we analyzed 331 soil samples from different land-use types (cropland, forest, and grassland) in the Qinling-Daba Mountains to investigate the drivers, assembly processes, and network stability of multitrophic organisms. High-throughput sequencing was used to examine archaea, bacteria, fungi, algae, protozoa, and invertebrates, while enzyme activity assays were used to assess ecosystem multifunctionality related to nutrient provisioning. Our results indicated that biotic factors contributed to 62.81-94.97 % of α-diversity and 4.19-52.37 % of β-diversity in multitrophic organisms, even when considering the influence of abiotic factors. Protozoan α- and β-diversity most significantly explained the α- and β-diversity of bacteria, fungi, algae, and invertebrates in soil ecosystems, serving as important indicators for assessing soil multifunctionality and ecosystem health. Furthermore, the assembly processes in prokaryotes were primarily governed by stochasticity (>50 %), whereas those in eukaryotic groups were dominated by deterministic processes (<50 %). Diversity and network stability increased with greater stochasticity in bacterial communities where stochastic processes predominated. Conversely, in fungal and protozoan communities dominated by deterministic processes, diversity and network stability decreased as deterministic processes intensified. Importantly, stochastic processes in soil multitrophic assembly enhanced ecosystem multifunctionality by increasing α-diversity, β-diversity, and network stability. These findings provide valuable insights into the regulation of BEFr by multitrophic assembly processes. Future research should further explore the role of these assembly processes in soil ecosystem functioning under land-use change scenarios.

Integrated microbial activities and isotope analysis unveil the effects of zinc oxide nanoparticles on straw decomposition in agricultural soil

Zinc oxide nanoparticles (ZnONPs) are widely applied across multiple industries and ultimately accumulate in water and soil environments, raising significant concern about their toxicity to organisms in various ecosystems. While the effects of ZnONPs on microflora have been reported, their ecotoxicity to specific biogeochemical process and microbial activities and metabolic functions remains relatively unclear. In this study, a 56-day microcosmic experiment was conducted to explore the toxicity mechanism of ZnONPs (1000 mg kg-1 soil) on straw decomposition, soil organic carbon (SOC) mineralization, and changes in microbial activities and functions in agricultural soil with general wheat straw incorporation using the 13C isotope tracer technique. The results demonstrated that straw incorporation increased the rate of CO2 emission and promoted the straw decomposition. However, the presence of ZnONPs reduced the CO2 release rates during incubation period although the rates were still higher than those under the control due to straw incorporation. CO2 emissions from straw decomposition were dominant before the 7th day of incubation. After day 7, CO2 emissions from the mineralization of original SOC became dominant with their contribution increasing from 17.52 % on day 7 to 60.20 % on day 56 under straw incorporation. ZnONPs affected soil carbon composition and straw decomposition by inhibiting enzyme activity and reducing the abundance of functional genes, indirectly impacting CO2 release. Community Level Physiological Profiles (CLPP) showed ZnONPs reduced functional richness indices, including Shannon-Weiner index (H) and McIntosh index (U), and altered C substrate utilization patterns. This may be due to the direct toxicity of zinc ion (Zn2+) released by ZnONPs to the soil bacterial community. The findings provide insights into the toxicity effects of emerging contaminants on carbon transformation from straw and SOC. Further investigations involving metabolomics are required to reveal the essential effects of ZnONPs on biogeochemical cycle of elements in agricultural soil.

Organic manure rather than chemical fertilization improved dark CO2 fixation by regulating associated microbial functional traits in upland red soils

Dark microbial fixation of CO2 is an indispensable process for soil carbon sequestration. However, the whole genetic information involved in dark CO2 fixation and its influence on dark CO2 fixation rates under diversified fertilization regimes were largely unclear. Here, revealed by 13C-CO2 labeling, dark CO2 fixation rates in upland red soils ranged from 0.029 mg kg-1 d-1 to 0.092 mg kg-1 d-1, and it was 75.49 % higher (P < 0.05) in organic manure (OM) soil but 44.2 % decline (P < 0.05) in chemical nitrogen fertilizer (N) soil compared to unfertilized (CK) soil. In addition, the normalized abundance and Chao1 index of dark CO2 fixation genes (KO level) were significantly different between OM and N soils, showing the highest and lowest, respectively. And they were positively (P < 0.05) correlated with dark CO2 fixation rate. Besides, among the identified CO2 fixation pathways in this study, the DC/4-HB cycle (M00374) was enriched in OM soil, yet the 3-HP cycle (M00376) was enriched in N soil, and their relative abundances were positively and negatively correlated (P < 0.05) with dark CO2 fixation rate, respectively. The PLS-SEM analysis revealed that dark CO2 fixation-related functional traits (i.e. normalized abundance, Chao1 index and gene composition) were directly and positively associated with dark CO2 fixation rate, and organic manure could exert a positive effect on soil dark CO2 fixation rate through enhancing soil properties (e.g., pH and soil organic carbon) and further altering associated microbial functional traits. These results have implications for explaining and predicting the soil CO2 fixation process from the perspective of microbial functional potential.

Microplastic effects on carbon cycling in terrestrial soil ecosystems: Storage, formation, mineralization, and microbial mechanisms

Soil is the largest environmental reservoir of microplastics (MPs) on the earth. Incremental accumulation of MPs in the soil can cause significant changes in soil physicochemical and microbial traits, which may in turn interfere with soil biogeochemical processes such as carbon cycling. With published research regarding MPs impacts on soil carbon cycling growing rapidly, a systematic review summarizing the current knowledge and highlighting future research needs is warranted. As carbon-rich polymers, MPs can contribute to soil organic carbon (SOC) storage via degradation and leaching. MPs can also affect the humification of dissolved organic matters (DOM), consequently influencing the stability of SOC. Exposure to MPs can cause substantial impacts on the growth performance, litter decomposition, and root secretion of terrestrial plants as well as soil microbial carbon turnover, inducing changes in the formation of SOC. The presence of MPs has contrasting effects on the emissions of both CO2 and CH4 from the soil. The diverse effects of MPs on soil carbon metabolism could be partly attributed to the varying changes in soil microbial community structure, functional gene expression, and enzyme activity under MPs exposure. Further research is still highly needed to clarify the pathways of MPs impacts on soil carbon cycling and the driving biological and physicochemical factors behind these processes.

Mechanisms underpinning microplastic effects on the natural climate solutions of wetland ecosystems

Wetland ecosystems are vital carbon dioxide (CO2) sinks, offering significant nature-based solutions for global climate mitigation. However, the recent influx of microplastic (MP) into wetlands substantially impacts key drivers (e.g., plants and microorganisms) underpinning these wetland functions. While MP-induced greenhouse gas (GHG) emissions and effects on soil organic carbon (SOC) mineralization potentially threaten the long-term wetland C-climate feedbacks, the exact mechanisms and linkage are unclear. This review provides a conceptual framework to elaborate on the interplay between MPs, wetland ecosystems, and the atmospheric milieu. We also summarize published studies that validate possible MP impacts on natural climate solutions of wetlands, as well as provide extensive elaboration on underlying mechanisms. We briefly highlight the relationships between MP influx, wetland degradation, and climate change and conclude by identifying key gaps for future research priorities. Globally, plastic production, MP entry into aquatic systems, and wetland degradation-related emissions are predicted to increase. This means that MP-related emissions and wetland-climate feedback should be addressed in the context of the UN Paris Climate Agreement on net-zero emissions by 2050. This overview serves as a wake-up call on the alarming impacts of MPs on wetland ecosystems and urges a global reconsideration of nature-based solutions in the context of climate mitigation.

Bacterial and fungal keystone taxa play different roles in maintaining community resistance and driving soil organic carbon dynamics in response to Solidago Canadensis invasion

The invasion of alien plants has significant implications for vegetation structure and diversity, which could lead to changes in the carbon (C) input from vegetation and change the transformation and decomposition processes of C, thereby altering the dynamics of soil organic carbon (SOC) within ecosystems. Whether alien plant invasion increases the SOC stock and changes SOC fractions consistently within regional scales, and the underlying mechanisms driving these SOC dynamics remain poorly understood. This study investigated SOC dynamics by comparing the plots that suffered invasion and non-invasion of Solidago Canadensis across five ecological function areas in Anhui Province, China, considering climate, edaphic factors, vegetation, and soil microbes. The results demonstrated that the impact of S. Canadensis invasion on SOC storage was not consistent at each site in the 0-20 cm soil layer, as indicated by the range of SOC content (5.94-12.45 g kg-1) observed at non-invaded plots. Stable SOC exhibited similar response patterns with SOC to plant invasion, whereas labile SOC did not. In addition, bacterial and fungal communities were shifted in structure at each site by plant invasion. Bacterial communities exhibited greater resistance to S. Canadensis invasion than did fungal communities, as evidenced by three aspects of the resistance indices-community resistance, phylogenetic conservation, and network complexity. The mechanisms driving SOC dynamics under S. Canadensis invasion were explored using structural equation models. This revealed that fungal keystone taxa responsible for community resistance controlled stable SOC fractions. In contrast, bacterial keystone taxa had the opposite effect on labile and stable SOC. Climatic and edaphic factors were also involved in the labile and stable SOC dynamics. Overall, this study provides novel insights into the dynamics of SOC under S. Canadensis invasion on a regional scale.

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.

Changes in enzyme activity, structure and growth strategies of the rhizosphere microbiome influenced by elevated temperature and CO2

The impacts of global warming and increased CO2 levels on soil processes and crop growth are concerning. Soil enzymes in the rhizosphere, produced mainly by microbes, play a vital role in nutrients mobilization for plants. Nevertheless, a comprehensive understanding of how microbial communities in the rhizosphere respond to increased temperatures and CO2 levels, particularly in relation to nutrient acquisition, is still lacking. Addressing this problem, we grew soybeans under elevated temperature (ET, +2 °C) and CO2 levels (eCO2, +300 ppm), both individually and in combination (eCO2 + eT), in rhizobox mesocosms. Enzyme activity and microbial communities in soybean rhizospheres were investigated using soil zymography. eCO2 increased enzyme activity by 2.5 % to 8.7 %, while eT expanded the hotspot area from 1.8 % to 3.3 %. The combined factors amplified both the hotspot area by 5.3 % to 10.1 % and enzyme activity by 35.4 % to 67.3 %. Compared to ambient conditions, rhizosphere communities under eCO2 were predominantly comprised of r-strategist keystone taxa, including Acidobacteria, Proteobacteria, and Ascomycota. On the contrary, eT induced a shift in the microbial community towards K-selected taxa, characterized by an increased relative abundance of Basidiomycota and Actinobacteria. Furthermore, the combination of eCO2 and eT led to an increase in the relative abundance of key bacterial species (Acidobacteria, Proteobacteria, and Actinobacteria) as well as fungi (Ascomycota and Basidiomycota). These findings indicate the potential significance of enzyme hotspots in modulating responses to climate change. Changes in enzyme activity and hotspot area could indicate the alteration in microbial growth strategies. The treatments exhibited distinct changes in the composition of microbial communities, in network organization, and in the proportion of species designated as r or K-strategists. Overall, these findings highlight the combined effects of global change factors on bacterial and fungal communities, providing insights into their growth strategies and nutrient mobilization under climate change scenarios.

Microbial mechanisms for CO2 and CH4 emissions in Robinia pseudoacacia forests along a North-South transect in the Loess Plateau

Forest soil microbes play a crucial role in regulating atmospheric-soil carbon fluxes. Environmental heterogeneity across forest types and regions may lead to differences in soil CO2 and CH4 emissions. However, the microbial mechanisms underlying these emission variations are currently unclear. In this study, we measured CO2 and CH4 emissions of Robinia pseudoacacia forests along a north-south transect in the Loess Plateau. Using metagenomic sequencing, we investigated the structural and functional profiles of soil carbon cycling microbial communities. Results indicated that the forest CO2 emissions of Robinia pseudoacacia was significantly higher in the north region than in the south region, while the CH4 emission was oppositely. This is mainly attributed to changes in gene abundance driven by soil pH and moisture in participating carbon degradation and methane oxidation processes across different forest regions. The gene differences in carbon fixation processes between regions primarily stem from the Calvin cycle, where the abundance of rbcL, rbcS, and prkB genes dominates microbial carbon fixation in forest soils. Random forest models revealed key genes involved in predicting forest soil CO2 emissions, including SGA1 and amyA for starch decomposition, TYR for lignin decomposition, chitinase for chitin decomposition, and pectinesterase for pectin decomposition. Microbial functional characterization revealed that interregional differences in CH4 emissions during methane metabolism may originate from methane oxidation processes, and the associated gene abundances (glyA, ppc, and pmoB) were key genes for predicting CH4 emissions from forest soils. Our results provide new insights into the microbial mechanisms of CO2 and CH4 emissions from forest soils, which will be crucial for accurate prediction of the forest soil carbon cycle in the future.

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

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

Investigating the bacterial community of gray mangroves (Avicennia marina) in coastal areas of Tabuk region

Mangrove vegetation, a threatened and unique inter-tidal ecosystem, harbours a complex and largely unexplored bacterial community crucial for nutrient cycling and the degradation of toxic pollutants in coastal areas. Despite its importance, the bacterial community composition of the gray mangrove (Avicennia marina) in the Red Sea coastal regions remains under-studied. This study aims to elucidate the structural and functional diversity of the microbiome in the bulk and rhizospheric soils associated with A. marina in the coastal areas of Ras Alshabaan-Umluj (Umluj) and Almunibrah-Al-Wajh (Al-Wajh) within the Tabuk region of Saudi Arabia. Amplicon sequencing targeting the 16S rRNA was performed using the metagenomic DNAs from the bulk and rhizospheric soil samples from Umluj and Al-Wajh. A total of 6,876 OTUs were recovered from all samples, of which 1,857 OTUs were common to all locations while the total number of OTUs unique to Al-wajh was higher (3,011 OTUs) than the total number of OTUs observed (1,324 OTUs) at Umluj site. Based on diversity indices, overall bacterial diversity was comparatively higher in rhizospheric soil samples of both sites. Comparing the diversity indices for the rhizosphere samples from the two sites revealed that the diversity was much higher in the rhizosphere samples from Al-Wajh as compared to those from Umluj. The most dominant genera in rhizosphere sample of Al-Wajh were Geminicoccus and Thermodesulfovibrio while the same habitat of the Umluj site was dominated by Propionibacterium, Corynebacterium and Staphylococcus. Bacterial functional potential prediction analyses showed that bacteria from two locations have almost similar patterns of functional genes including amino acids and carbohydrates metabolisms, sulfate reduction and C-1 compound metabolism and xenobiotics biodegradation. However, the rhizosphere samples of both sites harbour more genes involved in the utilization and assimilation of C-1 compounds. Our results reveal that bacterial communities inhabiting the rhizosphere of A. marina differed significantly from those in the bulk soil, suggesting a possible role of A. marina roots in shaping these bacterial communities. Additionally, not only vegetation but also geographical location appears to influence the overall bacterial composition at the two sites.

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

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

Stockpiling turf alters microbial carbon and nitrogen use efficiency on the Tibetan Plateau

Microbial carbon use efficiency (CUE) and nitrogen use efficiency (NUE) are crucial parameters reflecting soil C and N sequestration. Concerns about how artificial activities disturb alpine meadow ecosystem are increasing, but the knowledge of variances in microbial CUE and NUE in response to turf storage remains scarce. Here, we conducted a turf storage experiment on the Tibetan Plateau with two common storage methods, laying turfs method (LT) and stacking turfs method (ST). Plant litter, aboveground and belowground biomass declined considerably in the LT and ST than those in natural meadow. Soil pH and available phosphorus were significantly lower, but soil organic carbon, total nitrogen, dissolved organic carbon, and available nitrogen were substantially higher in stored turfs (both ST and LT) than in natural meadow. These results led to a differentiation in nutrient status among treatments. Vetor model indicated a stronger C limitation (vector length > 0.61) in ST than that in the LT and a shift from N to P limitation (vector angle >55°) in all stored turfs. Microbial CUE was prominently higher in the LT than those in the ST, signifying that microbes allocated more exogenous C to self-growth in the LT. Microbial NUE declined considerably in stored turfs, indicating a great proportion of N used for catabolic process instead of anabolic process. Microbial CUE and NUE were tightly linked to nutrient content and availability, enzymatic stoichiometry, microbial traits and plant biomass. Our results suggest that variations in microbial CUE and NUE were indirectly regulated by soil physicochemical properties via mediating nutrient imbalance and enzymatic stoichiometry in stored turfs.

Effects of winter soil warming on crop biomass carbon loss from organic matter degradation

Global warming poses an unprecedented threat to agroecosystems. Although temperature increases are more pronounced during winter than in other seasons, the impact of winter warming on crop biomass carbon has not been elucidated. Here we integrate global observational data with a decade-long field experiment to uncover a significant negative correlation between winter soil temperature and crop biomass carbon. For every degree Celsius increase in winter soil temperature, straw and grain biomass carbon decreased by 6.6 ( ± 1.7) g kg-1 and 10.2 ( ± 2.3) g kg-1, respectively. This decline is primarily attributed to the loss of soil organic matter and micronutrients induced by warming. Ignoring the adverse effects of winter warming on crop biomass carbon could result in an overestimation of total food production by 4% to 19% under future warming scenarios. Our research highlights the critical need to incorporate winter warming into agricultural productivity models for more effective climate adaptation strategies.

Small Interfering RNAs (siRNAs) Negatively Impact Growth and Gene Expression of Environmentally Relevant Bacteria in In Vitro Conditions

Rising global populations have amplified food scarcity and ushered in the development of genetically modified (GM) crops containing small interference RNAs (siRNAs) that control gene expression to overcome these challenges. The use of RNA interference (RNAi) in agriculture remains controversial due to uncertainty regarding the unintended release of genetic material and downstream nontarget effects, which have not been assessed in environmental bacteria to date. To evaluate the impacts of siRNAs used in agriculture on environmental bacteria, this study assessed microbial growth and viability as well as transcription activity with and without the presence of environmental stressors. Results showed a statistically significant reduction in growth capacity and maximum biomass achieved when bacteria are exposed to siRNAs alone and with additional external stress (p < 0.05). Further transcriptomic analysis demonstrated that nutrient cycling gene activities were found to be consistently and significantly altered following siRNA exposure, particularly among carbon (xylA, FBPase, limEH, Chitinase, rgl, rgh, rgaE, mannanase, ara) and nitrogen (ureC, nasA, narB, narG, nirK) cycling genes (p < 0.05). Decreases in carbon cycling gene transcription profiles were generally significantly enhanced when siRNA exposure was coupled with nutrient or antimicrobial stress. Collectively, findings suggest that certain conditions facilitate the uptake of siRNAs from their surrounding environments that can negatively affect bacterial growth and gene expression activity, with uncertain downstream impacts on ecosystem homeostasis.

Diversity of Microbial Functional Genes Promotes Soil Nitrogen Mineralization in Boreal Forests

Soil nitrogen (N) mineralization typically governs the availability and movement of soil N. Understanding how factors, especially functional genes, affect N transformations is essential for the protection and restoration of forest ecosystems. To uncover the underlying mechanisms driving soil N mineralization, this study investigated the effects of edaphic environments, substrates, and soil microbial assemblages on net soil N mineralization in boreal forests. Field studies were conducted in five representative forests: Larix principis-rupprechtii forest (LF), Betula platyphylla forest (BF), mixed forest of Larix principis-rupprechtii and Betula platyphylla (MF), Picea asperata forest (SF), and Pinus sylvestris var. mongolica forest (MPF). Results showed that soil N mineralization rates (Rmin) differed significantly among forests, with the highest rate in BF (p < 0.05). Soil properties and microbial assemblages accounted for over 50% of the variability in N mineralization. This study indicated that soil environmental factors influenced N mineralization through their regulatory impact on microbial assemblages. Compared with microbial community assemblages (α-diversity, Shannon and Richness), functional genes assemblages were the most important indexes to regulate N mineralization. It was thus determined that microbial functional genes controlled N mineralization in boreal forests. This study clarified the mechanisms of N mineralization and provided a mechanistic understanding to enhance biogeochemical models for forecasting soil N availability, alongside aiding species diversity conservation and fragile ecosystem revitalization in boreal forests.

Plant diversity is more important than soil microbial diversity in explaining soil multifunctionality in Qinghai-Tibetan plateau wetlands

The Qinghai-Tibetan Plateau harbors rich and diverse wetlands that provide multiple ecological functions simultaneously. Although the relationships between biodiversity and wetland functioning have been well studied in recent decades, the links between the multiple features of plant and microbial communities and soil multifunctionality (SMF) remain unknown in the high-altitude wetlands that are extremely sensitive to human disturbance. Here, using the single function, averaging, weighted, and multiple-threshold methods, we calculated the SMF of Qinghai-Tibetan wetlands based on 15 variables associated with soil nutrient status, nutrient cycle, and greenhouse gas emission. We then related SMF to multidimensional (species, phylogenetic, and functional) diversity of plants and soil microorganisms and microbial network modules. The results showed that plant diversity explained more variance in SMF than soil microbial diversity, and plant species richness and phylogenetic distance were positive predictors of SMF. Bacterial network modules were more positively related to SMF than fungal network modules, and the alpha diversity of bacterial network modules contributed more to SMF than the diversity of the whole bacterial community. Pediococcus, Hirsutella, and Rhodotorula were biomarkers for SMF and had significant relationships with nitrogen mineralization and greenhouse gas emissions. Together, these results highlight the importance of plant diversity and bacterial network modules in determining the SMF, which are crucial to predicting the response of ecosystem functioning to biodiversity loss under intensifying anthropogenic activities.

Soil heavy metal pollution promotes extracellular enzyme production by mediating microbial community structure during vegetation restoration of metallic tailing reservoir

Vegetation restoration in metallic tailing reservoirs is imperative to restore the post-mining degraded ecosystems. Extracellular enzymes determine microbial resource acquisition in soils, yet the mechanisms controlling the enzyme activity and stoichiometry during vegetation restoration in metallic tailing reservoirs remain elusive. Here, we investigated the variations and drivers of C-, N- and P-acquiring enzymes together with microbial community along a 50-year vegetation restoration chronosequence in the China's largest vanadium titano-magnetite tailing reservoir. We found a parabolic pattern in the enzyme activity and efficiency along the chronosequence, peaking at the middle restoration stage (∼30 years) with approximately six-fold increase relative to the initial 1-year site. The enzyme ratios of C:P and N:P decreased by 33 % and 68 % along the chronosequence, respectively, indicating a higher microbial demand of C and N at the early stage and a higher demand of P at the later stage. Soil nutrients directly determined the enzyme activities and stoichiometry, whereas microbial biomass and community structure regulated the temporal pattern of the enzyme efficiency. Surprisingly, increased heavy metal pollution imposed a positive effect on the enzyme efficiency indirectly by altering microbial community structure. This was evidenced by the increased microbial diversity and the conversion of copiotrophic to oligotrophic and stress-tolerant taxa along the chronosequence. Our findings provide new insights into microbial functioning in soil nutrient dynamics during vegetation restoration under increasing heavy metal pollution.

Not all soil carbon is created equal: Labile and stable pools under nitrogen input

Anthropogenic activities have raised nitrogen (N) input worldwide with profound implications for soil carbon (C) cycling in ecosystems. The specific impacts of N input on soil organic matter (SOM) pools differing in microbial availability remain debatable. For the first time, we used a much-improved approach by effectively combining the 13C natural abundance in SOM with 21 years of C3-C4 vegetation conversion and long-term incubation. This allows to distinguish the impact of N input on SOM pools with various turnover times. We found that N input reduced the mineralization of all SOM pools, with labile pools having greater sensitivity to N than stable ones. The suppression in SOM mineralization was notably higher in the very labile pool (18%-52%) than the labile and stable (11%-47%) and the very stable pool (3%-21%) compared to that in the unfertilized control soil. The very labile C pool made a strong contribution (up to 60%) to total CO2 release and also contributed to 74%-96% of suppressed CO2 with N input. This suppression of SOM mineralization by N was initially attributed to the decreased microbial biomass and soil functions. Over the long-term, the shift in bacterial community toward Proteobacteria and reduction in functional genes for labile C degradation were the primary drivers. In conclusion, the higher the availability of the SOM pools, the stronger the suppression of their mineralization by N input. Labile SOM pools are highly sensitive to N availability and may hold a greater potential for C sequestration under N input at global scale.

Plant communication with rhizosphere microbes can be revealed by understanding microbial functional gene composition

Understanding rhizosphere microbial ecology is necessary to reveal the interplay between plants and associated microbial communities. The significance of rhizosphere-microbial interactions in plant growth promotion, mediated by several key processes such as auxin synthesis, enhanced nutrient uptake, stress alleviation, disease resistance, etc., is unquestionable and well reported in numerous literature. Moreover, rhizosphere research has witnessed tremendous progress due to the integration of the metagenomics approach and further shift in our viewpoint from taxonomic to functional diversity over the past decades. The microbial functional genes corresponding to the beneficial functions provide a solid foundation for the successful establishment of positive plant-microbe interactions. The microbial functional gene composition in the rhizosphere can be regulated by several factors, e.g., the nutritional requirements of plants, soil chemistry, soil nutrient status, pathogen attack, abiotic stresses, etc. Knowing the pattern of functional gene composition in the rhizosphere can shed light on the dynamics of rhizosphere microbial ecology and the strength of cooperation between plants and associated microbes. This knowledge is crucial to realizing how microbial functions respond to unprecedented challenges which are obvious in the Anthropocene. Unraveling how microbes-mediated beneficial functions will change under the influence of several challenges, requires knowledge of the pattern and composition of functional genes corresponding to beneficial functions such as biogeochemical functions (nutrient cycle), plant growth promotion, stress mitigation, etc. Here, we focus on the molecular traits of plant growth-promoting functions delivered by a set of microbial functional genes that can be useful to the emerging field of rhizosphere functional ecology.

Tree phylogeny predicts more than litter chemical components in explaining enzyme activities in forest leaf litter decomposition

Litter decomposition is an important process in ecosystem and despite recent research elucidating the significant influence of plant phylogeny on plant-associated microbial communities, it remains uncertain whether a parallel correlation exists between plant phylogeny and the community of decomposers residing in forest litter. In this study, we conducted a controlled litterbag experiment using leaf litter from ten distinct tree species in a central subtropical forest ecosystem in a region characterized by subtropical humid monsoon climate in China. The litterbags were placed in situ using a random experimental design and were collected after 12 months of incubation. Then, the litter chemical properties, microbial community composition and activities of enzyme related to the decomposition of organic carbon (C) and nitrogen (N) were assessed. Across all ten tree species, Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria were identified as the predominant bacterial classes, while the primary fungal classes were Dothideomycetes, Sordariomycetes and Eurotiomycetes. Mantel test revealed significant correlations between litter chemical component and microbial communities, as well as enzyme activities linked to N and C metabolism. However, after controlling for plant phylogenetic distance in partial Mantel test, the relationships between litter chemical component and microbial community structure and enzyme activities were not significant. Random forest and structural equation modeling indicated that plant phylogenetic distance exerted a more substantial influence than litter chemical components on microbial communities and enzyme activities associated with the decomposition of leaf litter. In summary, plant phylogenic divergence was found to be a more influential predictor of enzyme activity variations than microbial communities and litter traits, which were commonly considered reliable indicators of litter decomposition and ecosystem function, thereby highlighting the previously underestimated significance of plant phylogeny in shaping litter microbial communities and enzyme activities associated with degradation processes in forest litter.

Ectomycorrhizal fungi enhance pine growth by stimulating iron-dependent mechanisms with trade-offs in symbiotic performance

Iron (Fe) is crucial for metabolic functions of living organisms. Plants access occluded Fe through interactions with rhizosphere microorganisms and symbionts. Yet, the interplay between Fe addition and plant-mycorrhizal interactions, especially the molecular mechanisms underlying mycorrhiza-assisted Fe processing in plants, remains largely unexplored. We conducted mesocosms in Pinus plants inoculated with different ectomycorrhizal fungi (EMF) Suillus species under conditions with and without Fe coatings. Meta-transcriptomic, biogeochemical, and X-ray fluorescence imaging analyses were applied to investigate early-stage mycorrhizal roots. While Fe addition promoted Pinus growth, it concurrently reduced mycorrhiza formation rate, symbiosis-related metabolites in plant roots, and aboveground plant carbon and macronutrient content. This suggested potential trade-offs between Fe-enhanced plant growth and symbiotic performance. However, the extent of this trade-off may depend on interactions between host plants and EMF species. Interestingly, dual EMF species were more effective at facilitating plant Fe uptake by inducing diverse Fe-related functions than single-EMF species. This subsequently triggered various Fe-dependent physiological and biochemical processes in Pinus roots, significantly contributing to Pinus growth. However, this resulted in a greater carbon allocation to roots, relatively reducing the aboveground plant carbon content. Our study offers critical insights into how EMF communities rebalance benefits of Fe-induced effects on symbiotic partners.

Indirect influence of soil enzymes and their stoichiometry on soil organic carbon response to warming and nitrogen deposition in the Tibetan Plateau alpine meadow

Despite extensive research on the impact of warming and nitrogen deposition on soil organic carbon components, the response mechanisms of microbial community composition and enzyme activity to soil organic carbon remain poorly understood. This study investigated the effects of warming and nitrogen deposition on soil organic carbon components in the Tibetan Plateau alpine meadow and elucidated the regulatory mechanisms of microbial characteristics, including soil microbial community, enzyme activity, and stoichiometry, on organic carbon components. Results indicated that both warming and nitrogen deposition significantly increased soil organic carbon, readily oxidizable carbon, dissolved organic carbon, and microbial biomass carbon. The interaction between warming and nitrogen deposition influenced soil carbon components, with soil organic carbon, readily oxidizable carbon, and dissolved organic carbon reaching maximum values in the W0N32 treatment, while microbial biomass carbon peaked in the W3N32 treatment. Warming and nitrogen deposition also significantly increased soil Cellobiohydrolase, β-1,4-N-acetylglucosaminidase, leucine aminopeptidase, and alkaline phosphatase. Warming decreased the soil enzyme C: N ratio and C:P ratio but increased the soil enzyme N:P ratio, while nitrogen deposition had the opposite effect. The bacterial Chao1 index and Shannon index increased significantly under warming conditions, particularly in the N32 treatment, whereas there were no significant changes in the fungal Chao1 index and Shannon index with warming and nitrogen addition. Structural equation modeling revealed that soil organic carbon components were directly influenced by the negative impact of warming and the positive impact of nitrogen deposition. Furthermore, warming and nitrogen deposition altered soil bacterial community composition, specifically Gemmatimonadota and Nitrospirota, resulting in a positive impact on soil enzyme activity, particularly soil alkaline phosphatase and β-xylosidase, and enzyme stoichiometry, including N:P and C:P ratios. In summary, changes in soil organic carbon components under warming and nitrogen deposition in the alpine meadows of the Tibetan Plateau primarily depend on the composition of soil bacterial communities, soil enzyme activity, and stoichiometric characteristics.

Spatial patterns and drivers of ecosystem multifunctionality in China: Arid vs. humid regions

Ecosystem multifunctionality (EMF) refers to an ecosystem's capacity to simultaneously uphold multiple ecological functions or services. In terrestrial ecosystems, the potential patterns and processes of EMF remain largely unexplored, limiting our comprehension of how ecosystems react to various driving factors. We collected environmental, soil and plant nutrient data, investigate the spatial distribution characteristics of EMF in China's terrestrial ecosystems, differentiating between arid and humid regions and examining the underlying drivers. Our findings reveal substantial spatial heterogeneity in the distribution of EMF across China's terrestrial ecosystems, with pronounced variations between arid and humid regions. In arid regions, the EMF index predominantly falls within the range of -1 to 1, including approximately 66.8 % of the total area, while in humid regions, the EMF index primarily falls within the range of 0 to 2, covering around 55.2 % of the total area. Climate, soil, and vegetation factors account for 61.4 % and 51.9 % of the total EMF variation in arid and humid regions, respectively. Notably, climate emerges as the dominant factor governing EMF variation in arid regions, whereas soil physicochemical properties take precedence in humid regions. Specifically, mean annual temperature (MAT) emerges as the primary factor influencing EMF variation in arid regions, while the normalized difference vegetation index (NDVI) and soil biodiversity index (SBI) play pivotal roles in regulating EMF variation in humid regions. Indeed, climate can exert both direct and indirect influences on EMF. In summary, our study not only compared the disparities in the spatial distribution of EMF in arid and humid regions but also unveiled the distinct controlling factors that govern EMF changes in these different regions. Our research has contributed novel insights for evaluating the drivers responsible for mediating EMF in diverse ecosystems, shedding light on the adaptability and response mechanisms of ecosystems under varying environmental conditions.

The proliferation of beneficial bacteria influences the soil C, N, and P cycling in the soybean-maize intercropping system

Soybean-maize intercropping system can improve the utilization rate of farmland and the sustainability of crop production systems. However, there is a significant gap in understanding the interaction mechanisms between soil carbon (C), nitrogen (N), and phosphorus (P) cycling functional genes, rhizosphere microorganisms, and nutrient availability. To reveal the key microorganisms associated with soil nutrient utilization and C, N, and P cycling function in the soybean-maize intercropping system, we investigated the changes in soil properties, microbial community structure, and abundance of functional genes for C, N, and P cycling under soybean-maize intercropping and monocropping at different fertility stages in a pot experiment. We found that there was no significant difference in the rhizosphere microbial community between soybean-maize intercropping and monocropping at the seeding stage. As the reproductive period progressed, differences in microbial community structure between intercropping and monocropping gradually became significant, manifesting the advantages of intercropping. During the intercropping process of soybean and maize, the relative abundance of beneficial bacteria in soil rhizosphere significantly increased, particularly Streptomycetaceae and Pseudomonadaceae. Moreover, the abundances of C, N, and P cycling functional genes, such as abfA, mnp, rbcL, pmoA (C cycling), nifH, nirS-3, nosZ-2, amoB (N cycling), phoD, and ppx (P cycling), also increased significantly. Redundancy analysis and correlation analysis showed that Streptomycetaceae and Pseudomonadaceae were significantly correlated with soil properties and C, N, and P cycling functional genes. In brief, soybean and maize intercropping can change the structure of microbial community and promote the proliferation of beneficial bacteria in the soil rhizosphere. The accumulation of these beneficial bacteria increased the abundance of C, N, and P cycling functional genes in soil and enhanced the ability of plants to fully utilize environmental nutrients and promoted growth.

Decoupled response of microbial taxa and functions to nutrients: The role of stoichiometry in plantations

The resource quantity and elemental stoichiometry play pivotal roles in shaping belowground biodiversity. However, a significant knowledge gap remains regarding the influence of different plant communities established through monoculture plantations on soil fungi and bacteria's taxonomic and functional dynamics. This study aimed to elucidate the mechanisms underlying the regulation and adaptation of microbial communities at the taxonomic and functional levels in response to communities formed over 34 years through monoculture plantations of coniferous species (Japanese larch, Armand pine, and Chinese pine), deciduous forest species (Katsura), and natural shrubland species (Asian hazel and Liaotung oak) in the temperate climate. The taxonomic and functional classifications of fungi and bacteria were examined for the mineral topsoil (0-10 cm) using MiSeq-sequencing and annotation tools of microorganisms (FAPROTAX and Funguild). Soil bacterial (6.52 ± 0.15) and fungal (4.46 ± 0.12) OTUs' diversity and richness (5.83*103±100 and 1.12*103±46.4, respectively) were higher in the Katsura plantation compared to Armand pine and Chinese pine. This difference was attributed to low soil DOC/OP (24) and DON/OP (11) ratios in the Katsura, indicating that phosphorus availability increased microbial community diversity. The Chinese pine plantation exhibited low functional diversity (3.34 ± 0.04) and richness (45.2 ± 0.41) in bacterial and fungal communities (diversity 3.16 ± 0.15 and richness 56.8 ± 3.13), which could be attributed to the high C/N ratio (25) of litter. These findings suggested that ecological stoichiometry, such as of enzyme, litter C/N, soil DOC/DOP, and DON/DOP ratios, was a sign of the decoupling of soil microorganisms at the genetic and functional levels to land restoration by plantations. It was found that the stoichiometric ratios of plant biomass served as indicators of microbial functions, whereas the stoichiometric ratios of available nutrients in soil regulated microbial genetic diversity. Therefore, nutrient stoichiometry could serve as a strong predictor of microbial diversity and composition during forest restoration.

SOC bioavailability significantly correlated with the microbial activity mediated by size fractionation and soil morphology in agricultural ecosystems

Despite the fact that physical and chemical processes have been widely proposed to explicate the stabilization mechanisms of soil organic carbon (SOC), thebioavailability of SOC linked to soil physical structure, microbial community structure, and functional genes remains poorly understood. This study aims to investigate the SOC division based on bioavailability differences formed by physical isolation, and to clarify the relationships of SOC bioavailability with soil elements, pore characteristics, and microbial activity. Results revealed that soil element abundances such as SOC, TN, and DOC ranked in the same order as the soil porosity as clay > silt ≥ coarse sand > fine sand in both top and sub soil. In contrast to silt and clay, which had reduced SOC bioavailability, fine sand and coarse sand had dramatically enhanced SOC bioavailability compared to the bulk soil. The bacterial and fungal community structure was significantly influenced by particle size, porosity, and soil elements. Copiotrophic bacteria and functional genes were more prevalent in fine sand than clay, which also contained more oligotrophic bacteria. The SOC bioavailability was positively correlated with abundances of functional genes, C degradation genes, and copiotrophic bacteria, but negatively correlated with abundances of soil elements, porosity, oligotrophic bacteria, and microbial biomass (p < 0.05). This indicated that the soil physical structure divided SOC into pools with varying levels of bioavailability, with sand fractions having more bioavailable organic carbon than finer fractions. Copiotrophic Proteobacteria and oligotrophic Acidobacteria, Firmicutes, and Gemmatimonadetes made up the majority of the bacteria linked to SOC mineralization. Additionally, the fungi Mortierellomycota and Mucoromycota, which are mostly involved in SOC mineralization, may have the potential for oligotrophic metabolism. Our results indicated that particle-size fractionation could influence the SOC bioavailability by restricting SOC accessibility and microbial activity, thus having a significant impact on sustaining soil organic carbon reserves in temperate agricultural ecosystems, and provided a new research direction for organic carbon stability.

Molecular insights into the microbial degradation of sediment-derived DOM in a macrophyte-dominated lake under aerobic and hypoxic conditions

The mineralization of dissolved organic matter (DOM) in sediments is an important factor leading to the eutrophication of macrophyte-dominated lakes. However, the changes in the molecular characteristics of sediment-derived DOM during microbial degradation in macrophyte-dominated lakes are not well understood. In this study, the microbial degradation process of sediment-derived DOM in Lake Caohai under aerobic and hypoxic conditions was investigated using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and metagenomics. The results revealed that the microbial degradation of sediment-derived DOM in macrophyte-dominated lakes was more intense under aerobic conditions. The microorganisms mainly metabolized the protein-like substances in the macrophyte-dominated lakes, and the carbohydrate-active enzyme genes and protein/lipid-like degradation genes played key roles in sediment-derived DOM degradation. Organic compounds with high H/C ratios such as lipids, carbohydrates, and protein/lipid-like compounds were preferentially removed by microorganisms during microbial degradation. Meanwhile, there was an increase in the abundance of organic molecular formula with a high aromaticity such as tannins and unsaturated hydrocarbons with low molecular weight and low double bond equivalent. In addition, aerobic/hypoxic environments can alter microbial metabolic pathways of sediment-derived DOM by affecting the relative abundance of microbial communities (e.g., Gemmatimonadetes and Acidobacteria) and functional genes (e.g., ABC.PE.P1 and ABC.PE.P) in macrophyte-dominated lakes. The abundances of lipids, unsaturated hydrocarbons, and protein compounds in aerobic environments decreased by 58 %, 50 %, and 44 %, respectively, compared to in hypoxic environments under microbial degradation. The results of this study deepen our understanding of DOM biodegradation in macrophyte-dominated lakes under different redox environments and provide new insights into nutrients releases from sediment and continuing eutrophication in macrophyte-dominated lakes.

Effects of nitrogen addition on rhizosphere priming: The role of stoichiometric imbalance

Nitrogen (N) input has a significant impact on the availability of carbon (C), nitrogen (N), and phosphorus (P) in the rhizosphere, leading to an imbalanced stoichiometry in microbial demands. This imbalance can result in energy or nutrient limitations, which, in turn, affect C dynamics during plant growth. However, the precise influence of N addition on the C:N:P imbalance ratio and its subsequent effects on rhizosphere priming effects (RPEs) remain unclear. To address this gap, we conducted a 75-day microcosm experiment, varying N addition rates (0, 150, 300 kg N ha-1), to examine how microbes regulate RPE by adapting to stoichiometry and maintaining homeostasis in response to N addition, using the 13C natural method. Our result showed that N input induced a stoichiometric imbalance in C:N:P, leading to P or C limitation for microbes during plant growth. Microbes responded by adjusting enzymatic stoichiometry and functional taxa to preserve homeostasis, thereby modifying the threshold element ratios (TERs) to cope with the C:N:P imbalance. Microbes adapted to the stoichiometric imbalance by reducing TER, which was attributed to a reduction in carbon use efficiency. Consequently, we observed higher RPE under P limitation, whereas the opposite trend was observed under C or N limitation. These results offer novel insights into the microbial regulation of RPE variation under different soil nutrient conditions and contribute to a better understanding of soil C dynamics.