Interactions between microbial diversity and substrate chemistry determine the fate of carbon in soil

Differential responses of plant and microbial respiration to extreme precipitation and drought during spring and summer in the Eurasian meadow steppe

Increasing extreme precipitation and drought events along changes in their seasonal patterns due to climate change are expected to have profound consequences for carbon cycling. However, how these climate extremes impact ecosystem respiration (Reco) and whether these impacts differ between seasons remain unclear. Here, we reveal the responses of Reco and its components to extreme precipitation and drought in spring and summer by conducting a five-year manipulative experiment in a temperate meadow steppe. Based on a 5-year average, the seasonal mean values (±SE) of Reco, Rh, Rroot, Rabg and Rplant significantly increased (p< 0.01) under both extreme precipitation treatments: wet spring (WSP) and wet summer (WSU), and significantly decreased (p< 0.01) under both extreme drought treatments: dry spring (DSP) and dry summer (DSU), except in Rabg under DSU, which remained comparable to the control. The sensitivity of Reco, Rh, Rroot and Rplant to extreme precipitation was significantly higher in spring than in summer. On average, Rplant was the primary contributor of Reco, accounting for 37.18% and 38.31% of the total across all its components under WSP and WSU, respectively during the growing season over the five study years. Moreover, linear models revealed Rplant explained 87% of the variance in Reco. Our findings indicate that future changes in precipitation events, particularly extreme precipitation may lead to increased carbon release from ecosystems, largely driven by enhanced plant respiration rather than microbial respiration. However, due to this study focused solely on respiration and did not measure photosynthesis, the findings represent only the carbon release processes and do not account for potential carbon uptake by plants during the same conditions. These emergent identified contribution to ecosystem respiration provide valuable insights for improving model benchmarks to better predict ecosystem respiration responses to extreme climate in specified season.

Microbial diversity in the arid and semi-arid soils of Botswana

To date, little research has been conducted on the landscape-scale distribution of soil microbial communities and the factors driving their community structures in the drylands of Africa. We investigated the influence of landscape-scale variables on microbial community structure and diversity across different ecological zones in Botswana. We used amplicon sequencing of bacterial 16S rRNA gene and fungal internal transcribed spacers (ITS) and a suite of environmental parameters to determine drivers of microbial community structure. Bacterial communities were dominated by Actinomycetota (21.1%), Pseudomonadota (15.9%), and Acidobacteriota (10.9%). The dominant fungal communities were Ascomycota (57.3%) and Basidiomycota (7.5%). Soil pH, mean annual precipitation, total organic carbon, and soil ions (calcium and magnesium) were the major predictors of microbial community diversity and structure. The co-occurrence patterns of bacterial and fungal communities were influenced by soil pH, with network-specific fungi-bacteria interactions observed. Potential keystone taxa were identified for communities in the different networks. Most of these interactions were between microbial families potentially involved in carbon cycling, suggesting functional redundancy in these soils. Our findings highlight the significance of soil pH in determining the landscape-scale structure of microbial communities in Botswana's dryland soils.

Structure and Function of Soil Bacterial Communities in the Different Wetland Types of the Liaohe Estuary Wetland

Soil bacterial communities play a crucial role in the functioning of estuarine wetlands. Investigating the structure and function of these communities across various wetland types, along with the key factors influencing them, is essential for understanding the relationship between bacteria and wetland ecosystems. The Liaohe Estuary Wetland formed this study's research area, and soil samples from four distinct wetland types were utilized: suaeda wetlands, reed wetlands, pond returning wetlands, and tidal flat wetlands. The structure and function of the soil bacterial communities were examined using Illumina MiSeq high-throughput sequencing technology in conjunction with the PICRUSt analysis method. The results indicate that different wetland types significantly affect the physical and chemical properties of soil, as well as the structure and function of bacterial communities. The abundance and diversity of soil bacterial communities were highest in the suaeda wetland and lowest in the tidal flat wetland. The dominant bacterial phyla identified were Proteobacteria and Bacteroidota. Furthermore, the dominant bacterial genera identified included RSA9, SZUA_442, and SP4260. The primary functional pathways associated with the bacterial communities involved the biosynthesis of valine, leucine, and isoleucine, as well as lipoic acid metabolism, which are crucial for the carbon and nitrogen cycles. This study enhances our understanding of the mutual feedback between river estuary wetland ecosystems and environmental changes, providing a theoretical foundation for the protection and management of wetlands.

Direct Evidence for Microbial Regulation of the Temperature Sensitivity of Soil Carbon Decomposition

Soil physicochemical protection, substrates, and microorganisms are thought to modulate the temperature sensitivity of soil carbon decomposition (Q10), but their regulatory roles have yet to be distinguished because of the confounding effects of concurrent changes of them. Here, we sought to differentiate these effects through microorganism reciprocal transplant and aggregate disruption experiments using soils collected from seven sites along a 5000-km latitudinal transect encompassing a wide range of climatic conditions and from a 4-year laboratory incubation experiment. We found direct microbial regulation of Q10, with a higher Q10 being associated with greater fungal:bacterial ratios. However, no significant direct effects of physicochemical protection and substrate were observed on the variation in Q10 along the latitudinal transect or among different incubation time points. These findings highlight that we should move forward from physicochemical protection and substrate to microbial mechanisms regulating soil carbon decomposition temperature sensitivity to understand and better predict soil carbon-climate feedback.

Recover of Soil Microbial Community Functions in Beech and Turkey Oak Forests After Coppicing Interventions

Forest management influences the occurrence of tree species, the organic matter input to the soil decomposer system, and hence, it can alter soil microbial community and key ecosystem functions it performs. In this study, we compared the potential effect of different forest management, coppice and high forest, on soil microbial functional diversity, enzyme activities and chemical-physical soil properties in two forests, turkey oak and beech, during summer and autumn. We hypothesized that coppicing influences soil microbial functional diversity with an overall decrease. Contrary to our hypothesis, in summer, the functional diversity of soil microbial community was higher in both coppice forests, suggesting a resilience response of the microbial communities in the soil after tree cutting, which occurred 15-20 years ago. In beech forest under coppice management, a higher content of soil organic matter (but also of soil recalcitrant and stable organic carbon) compared to high forest can explain the higher soil microbial functional diversity and metabolic activity. In turkey oak forest, although differences in functional diversity of soil microbial community between management were observed, for the other investigated parameters, the differences were mainly linked to seasonality. The findings highlight that the soil organic matter preservation depends on the type of forest, but the soil microbial community was able to recover after about 15 years from coppice intervention in both forest ecosystems. Thus, the type of management implemented in these forest ecosystems, not negatively affecting soil organic matter pool, preserving microbial community and potentially soil ecological functions, is sustainable in a scenario of climate change.

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

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

Ectomycorrhizal fungi alter soil food webs and the functional potential of bacterial communities

Most of Earth's trees rely on critical soil nutrients that ectomycorrhizal fungi (EcMF) liberate and provide, and all of Earth's land plants associate with bacteria that help them survive in nature. Yet, our understanding of how the presence of EcMF modifies soil bacterial communities, soil food webs, and root chemistry requires direct experimental evidence to comprehend the effects that EcMF may generate in the belowground plant microbiome. To this end, we grew Pinus muricata plants in soils that were either inoculated with EcMF and native forest bacterial communities or only native bacterial communities. We then profiled the soil bacterial communities, applied metabolomics and lipidomics, and linked omics data sets to understand how the presence of EcMF modifies belowground biogeochemistry, bacterial community structure, and their functional potential. We found that the presence of EcMF (i) enriches soil bacteria linked to enhanced plant growth in nature, (ii) alters the quantity and composition of lipid and non-lipid soil metabolites, and (iii) modifies plant root chemistry toward pathogen suppression, enzymatic conservation, and reactive oxygen species scavenging. Using this multi-omic approach, we therefore show that this widespread fungal symbiosis may be a common factor for structuring soil food webs.IMPORTANCEUnderstanding how soil microbes interact with one another and their host plant will help us combat the negative effects that climate change has on terrestrial ecosystems. Unfortunately, we lack a clear understanding of how the presence of ectomycorrhizal fungi (EcMF)-one of the most dominant soil microbial groups on Earth-shapes belowground organic resources and the composition of bacterial communities. To address this knowledge gap, we profiled lipid and non-lipid metabolites in soils and plant roots, characterized soil bacterial communities, and compared soils amended either with or without EcMF. Our results show that the presence of EcMF changes soil organic resource availability, impacts the proliferation of different bacterial communities (in terms of both type and potential function), and primes plant root chemistry for pathogen suppression and energy conservation. Our findings therefore provide much-needed insight into how two of the most dominant soil microbial groups interact with one another and with their host plant.

Mycorrhizal fungi modify decomposition: a meta-analysis

It has been proposed that ectomycorrhizal fungi can reduce decomposition while arbuscular mycorrhizal fungi may enhance it. These phenomena are known as the 'Gadgil effect' and 'priming effect', respectively. However, it is unclear which one predominates globally. We evaluated whether mycorrhizal fungi decrease or increase decomposition, and identified conditions that mediate this effect. We obtained decomposition data from 43 studies (97 trials) conducted in field or laboratory settings that controlled the access of mycorrhizal fungi to substrates colonized by saprotrophs. Across studies, mycorrhizal fungi promoted decomposition of different substrates by 6.7% overall by favoring the priming effect over the Gadgil effect. However, we observed significant variation among studies. The substrate C : N ratio and absolute latitude influenced the effect of mycorrhizal fungi on decomposition and contributed to the variation. Specifically, mycorrhizal fungi increased decomposition at low substrate C : N and absolute latitude, but there was no discernable effect at high values. Unexpectedly, the effect of mycorrhizal fungi was not influenced by the mycorrhizal type. Our findings challenge previous assumptions about the universality of the Gadgil effect but highlight the potential of mycorrhizal fungi to negatively influence soil carbon storage by promoting the priming effect.

Leaf carbon chemistry effectively manipulated soil microbial profiles and induced metabolic adjustments under different revegetation types in the loess Plateau, China

Microorganisms are essential components of underground life systems and drive elemental cycling between plants and soil. Yet, in the ecologically fragile Loess Plateau, scant attention has been paid to the response of microbial communities to organic carbon (C) chemistry of both leaves and soils under different revegetation conditions, as well as subsequent alternation in their C metabolic functions. Here, Fourier transform infrared (FTIR) spectrum, amplicon sequencing of 16S rRNA and ITS, and temporal incubation with Biolog-Eco 96 plates were combined to explore the vegetative heterogeneity of microbial community properties and metabolic functions, as well as their regulatory mechanisms in three typical revegetation types including Robinia pseudoacacia L. (RF), Caragana korshinskii KOM. (SL), and abandoned grassland (AG). We observed higher bacterial-to-fungal ratios (B: F = 270.18) and richer copiotrophic bacteria (Proteobacteria = 33.08%) in RF soil than those in AG soil, suggesting that microbes were dominated by r-strategists in soil under RF treatment, which is mainly related to long-term priming of highly bioavailable leaf C (higher proportion of aromatic and hydrophilic functional groups and lower hydrophobicity). Conversely, microbial taxa in AG soil, which was characterized by higher leaf organic C hydrophobicity (1.39), were dominated by relatively more abundant fungi (lower B: F ratio = 149.49) and oligotrophic bacteria (Actinobacteria = 29.30%). The co-occurrence network analysis showed that microbial interactive associations in RF and AG soil were more complex and connective than in SL soil. Furthermore, Biolog-Eco plate experiments revealed that microorganisms tended to utilize labile C compounds (carbohydrates and amino acids) in RF soil and resistant C compounds (polymers) in AG soil, which were consistent with the substrate adaptation strategies of predominant microbial trophic groups in different revegetation environments. Meanwhile, we observed greater microbial metabolic activity and diversity advantages in RF vegetation. Collectively, we suggest that besides the nutrient variables in the leaf-soil system, the long-term regulation of the microbial community by the C chemistry of the leaf sequentially alters the microbial metabolic profiles in a domino-like manner. RF afforestation is more conducive to restoring soil microbial fertility (including microbial abundance, diversity, interactive association, and metabolic capacity). Our study potentially paves the way for achieving well-managed soil health and accurate prediction of C pool dynamics in areas undergoing ecological restoration of the Loess Plateau.

Nitrogen and Microelements Co-Drive the Decomposition of Typical Grass Litter in the Loess Plateau, China

In grassland ecosystems, the decomposition of litter serves as a vital conduit for nutrient transfer between plants and soil. The aim of this study was to depict the dynamic process of grass litter decomposition and explore its major driver. Three typical grasses [Stipa bungeana Trin (St. B), Artemisia sacrorun Ledeb (Ar. S), and Thymus mongolicus Ronniger (Th. M)] were selected for long-term litter decomposition. Experiments were conducted using three single litters, namely, St. B, Ar. S, and Th. M, and four different compositions of mixed litter: ML1 (55% St. B and 45% Th. M), ML2 (55% St. B and 45% Ar. S), ML3 (75% St. B and 25% Th. M), and ML4 (75% St. B and 25% Ar. S). The dynamic patterns of mass and microelements (Ca, Mg, Fe, Mn, Cu, and Zn) within different litter groups were analyzed. Our findings indicated that, after 1035 days of decomposition, the proportion of residual mass for the single litters was as follows: Th. M (60.6%) > St. B (47.3%) > Ar. S (44.3%), and for the mixed groups it was ML1 (48.0%) > ML3 (41.6%) > ML2 (40.9) > ML4 (38.4%). Mixed cultivation of the different litter groups accelerated the decomposition process, indicating that the mixture of litters had a synergistic effect on litter decomposition. The microelements of the litter exhibited an initial short-term increase followed by long-term decay. After 1035 days of decomposition, the microelements released from the litter were, in descending order, Mg > Ca > Fe > Cu > Mn > Zn. Compared to the separately decomposed St. B litter, mixing led to an inhibition of the release of Ca (antagonistic effect), while it promoted the release of Mg, Cu, and Zn (synergistic effect). For the single litter, the stepwise regression analysis showed that Ca was the dominant factor determining early litter decomposition. Mg, Mn, and Cu were the dominant factors regulating later litter decomposition. For the mixed litter groups, Ca, Mn, and Mg were the dominant factors closely related to early decomposition, and TN emerged as a key factor regulating the mass loss of mixtures during later decomposition. In summary, nitrogen and microelements co-drive the decomposition of typical grass litter. Our study underscores that, in the succession process of grassland, the presence of multiple co-existing species led to a faster loss of plant-derived materials (litter mass and internal elements), which was primarily modulated by species identity and uniformity.

Soil microbial communities regulate the threshold effect of salinity stress on SOM decomposition in coastal salt marshes

Salinity stress is one of the critical environmental drivers of soil organic matter (SOM) decomposition in coastal ecosystems. Although the temperature sensitivity (Q10) of SOM decomposition has been widely applied in Earth system models to forecast carbon processes, the impact of salinity on SOM decomposition by restructuring microbial communities remains uncovered. Here, we conducted a microcosm experiment with soils collected from the coastal salt marsh in the Yellow River Estuary, which is subjected to strong dynamics of salinity due to both tidal flooding and drainage. By setting a gradient of salt solutions, soil salinity was adjusted to simulate salinity stress and soil carbon emission (CO2) rate was measured over the period. Results showed that as salinity increased, the estimated decomposition constants based on first-order kinetics gradually decreased at different temperatures. Below the 20‰ salinity treatments, which doubled the soil salinity, Q10 increased with increasing salinity; but higher salinity constrained the temperature-related response of SOM decomposition by inhibiting microbial growth and carbon metabolisms. Soil bacteria were more sensitive to salinity stress than fungi, which can be inferred from the response of microbial beta-diversity to changing salinity. Among them, the phylotypes assigned to Gammaproteobacteria and Bacilli showed higher salt tolerance, whereas taxa affiliated with Alphaproteobacteria and Bacteroidota were more easily inhibited by the salinity stress. Several fungal taxa belonging to Ascomycota had higher adaptability to the stress. As the substrate was consumed with the incubation, bacterial competition intensified, but the fungal co-occurrence pattern changed weakly during decomposition. Collectively, these findings revealed the threshold effect of salinity on SOM decomposition in coastal salt marshes and emphasized that salt stress plays a key role in carbon sequestration by regulating microbial keystone taxa, metabolisms, and interactions.

Sampling terrigenous diffuse sources in watercourse: Influence of land use and hydrological conditions on dissolved organic matter characteristics

Diffuse and point sources of dissolved organic matter (DOM) in streams influence its composition, interactions and fate in the aquatic ecosystem. These inputs can be very numerous at the scale of a watershed, and their identification remains a challenge, especially for diffuse sources related to land use. The complexity of the transfer mechanisms and the reactivity of DOM throughout the soil-water column continuum raise questions about the sampling of diffuse sources in watercourses. To answer this issue, we compared the characteristics of soil-extracted DOM influenced by a particular land use (homogenous sub-catchment of forest and vineyard) and DOM collected from the watercourse adjacent to the soil samples. A 28-day incubation experiment of soil extracts was designed to remove the labile fraction of DOM. During the first 3 days, between 40 and 70 % of the DOC mass was lost for both types of soils. A set of optical indicators (UV-Visible, EEM fluorescence and HPSEC/UV-fluorescence) showed that the labile fraction was mostly composed by low (<1 kDa) and high (>10 kDa) protein-like molecules. At the end of the incubation, soil-extracted DOM was mainly composed of medium molecules (1-10 kDa) associated to terrigenous humic-like compounds. Its optical and size molecular signature tended towards that in the adjacent watercourses and was specific to land use. However, the characteristics of DOM in watercourses was also influenced by the hydrological conditions, probably due to a transfer of top soil DOM during high water periods and both deep soil and autochthonous DOM during low water periods. These results were obtained by a set of indicators, including novel ones derived from HPSEC/UV-fluorescence. Finally, this study demonstrated that it is possible to sample the DOM representative of a land use directly in the river downstream of the homogeneous sub-basin by multiplying the samples during contrasting hydrological conditions.