Volatile organic compounds from leaf litter decomposition alter soil microbial communities and carbon dynamics

The Role of Soil Microbial Consortia in Sustainable Cereal Crop Residue Management

The global escalation in cereal production, essential to meet growing population demands, simultaneously augments the generation of cereal crop residues, estimated annually at approximately 3107 × 106 Mg/year. Among different crop residue management approaches, returning them to the soil can be essential for various ecological benefits, including nutrient recycling and soil carbon sequestration. However, the recalcitrant characteristics of cereal crop residues pose significant challenges in their management, particularly in the decomposition rate. Therefore, in this review, we aim to summarize the influence of different agricultural practices on enhancing soil microbial decomposer communities, thereby effectively managing cereal crop residues. Moreover, this manuscript provides indirect estimates of cereal crop residue production in Northern Europe and Lithuania, and highlights the diverse roles of lignocellulolytic microorganisms in the decomposition process, with a particular focus on enzymatic activities. This review bridges the knowledge gap and indicates future research directions concerning the influence of agricultural practices on cereal crop residue-associated microbial consortia.

Mechanisms of microbial-driven changes in soil ecological stoichiometry around gold mines

In this study, we used soils with different pollution and nutrient levels (non-polluted S1, highly polluted low-nutrient S2, and highly polluted high nutrient S3) around the gold mine tailing ponds, and combined with metabolic limitation modeling and macro-genomics approaches, aiming to investigate the relationship between soil microbial composition and soil eco-chemometrics characteristics under heavy metal stress. The results showed that heavy pollution resulted in reduced SOC, TN, microbial biomass, and with C- and P- acquisition (BG, CBH, ALP) as well as nitrogen limitation of soil microbial metabolism in soils (S2, S3). Further analysis by macrogenomics showed that heavy metal contamination led to an increase in α-microbial diversity and altered the composition of microbial communities in the soil. The cycling of C, N, and P nutrients was altered by affecting the relative abundance of Anaeromyxobacter, Steroidobacter, Bradyrhizobium, Acidobacterium, Limnochorda (predominantly in the Ascomycetes and Acidobacteria phyla), with the most pronounced effect on the composition of microorganisms synthesizing C-acquiring enzymes, and heavy metals and pH were the main influences on ecological stoichiometry. The results of this study are useful for understanding the sustainability of ecological remediation in heavy metal contaminated areas and for developing ecological restoration strategies.

Changes in soil organic carbon stocks and its physical fractions along an elevation in a subtropical mountain forest

Soil microorganisms are the drivers of soil organic carbon (SOC) mineralization, and the activities of these microorganisms are considered to play a key role in SOC dynamics. However, studies of the relationship between soil microbial carbon metabolism and SOC stocks are rare, especially in different physical fractions (e.g., particulate organic carbon (POC) fraction and mineral-associated organic carbon (MAOC) fraction). In this study, we investigated the changing patterns of SOC stocks, POC stocks, MAOC stocks and microbial carbon metabolism (e.g., microbial growth, carbon use efficiency and biomass turnover time) at 0-20 cm along an elevational gradient in a subtropical mountain forest ecosystem. Our results showed that SOC and POC stocks increased but MAOC stocks remained stable along the elevational gradient. Soil microbial growth increased while microbial turnover time decreased with elevation. Using structural equation modeling, we found that heightened microbial growth is associated with elevated POC stocks. Moreover, MAOC stocks positively correlate with microbial growth but show negative associations with both POC stocks and soil pH. Overall, the increase in SOC stocks along the elevational gradient is primarily driven by changes in POC stocks rather than MAOC stocks. These findings underscore the importance of considering diverse soil carbon fractions and microbial activities in predicting SOC responses to elevation, offering insights into potential climate change feedbacks.

Continuous cropping disorders of eggplants (Solanum melongena L.) and tomatoes (Solanum lycopersicum L.) in suburban agriculture: Microbial structure and assembly processes

Deciphering the intricate relationships between microorganisms and plants remains a formidable challenge in plant microbial ecology, an area that holds promise for optimizing microbial interventions to enhance stress resilience and agricultural yields. In our investigation, we procured samples during 2019 and 2022 from a suburban agricultural greenhouse. Our study delineated the composition of bacterial and fungal communities across various ecological niches-namely, the rhizosphere soil, bulk soil, and phyllosphere of healthy, Ralstonia solanacearum-infected, and dead eggplants and tomatoes. The structure and composition of both fungal and bacterial communities change significantly under the influence of the host genotype across all samples. In the tomato or eggplant groups, bacterial wilt exerts a more pronounced impact on the bacterial community than on the fungal community. We speculate that the rhizosphere of healthy eggplants and tomatoes harbored more antibiotic-producing (e.g., Amycolatopsis and Penicillium) and biocontrol (e.g., Bacillus) strains, which can lead to have lower absolute abundance of R. solanacearum. In the context of R. solanacearum invasion, deterministic processes were responsible for shaping 70.67 % and 80.63 % of the bacterial community assembly in the rhizosphere of eggplants and tomatoes, respectively. Deterministic processes dominated the assembly of fungal communities in the rhizosphere of R. solanacearum-infected eggplants, whereas the opposite was true in the tomatoes. Homogeneous selection emerged as the predominant force governing the bacterial community assembly in the rhizospheres of R. solanacearum-infected eggplants and tomatoes. The bacterial co-occurrence networks in healthy rhizosphere soil were characterized by reduced vulnerability and enhanced stability (i.e., robustness index) and complexity (i.e., cohesion index), compared to their infected counterparts. In summary, complex microbial networks in rhizosphere soils are more resistant to invasion by soil-borne pathogens. The dynamics of bacterial interactions and community assembly processes are pivotal for effective microbiome management and offer predictive insights into the ecological ramifications of R. solanacearum invasions.

Impacts of seasonality, drought, nitrogen fertilization, and litter on soil fluxes of biogenic volatile organic compounds in a Mediterranean forest

Biogenic volatile organic compounds (BVOCs) play critical roles in ecosystems at various scales, influencing above- and below-ground interactions and contributing to the atmospheric environment. Nonetheless, there is a lack of research on soil BVOC fluxes and their response to environmental changes. This study aimed to investigate the impact of drought, nitrogen (N) fertilization, and litter manipulation on soil BVOC fluxes in a Mediterranean forest. We assessed the effects of drought and N fertilization on soil BVOC exchanges and soil CO2 fluxes over two consecutive years using a dynamic chamber method, and solid-phase microextraction was utilized to quantify soil BVOCs in one year. Our findings revealed that the soil acted as an annual net sink for isoprenoids (1.30-10.33 μg m-2 h-1), with the highest uptake rates observed during summers (25.90 ± 9.36 μg m-2 h-1). The increased summer uptake can be attributed to the significant concentration gradient of BVOCs between atmosphere and soil. However, strong seasonal dynamics were observed, as the soil acted as a source of BVOCs in spring and autumn. The uptake rate of isoprenoids exhibited a significant positive correlation with soil temperature and atmospheric isoprenoid concentrations, while displaying a negative correlation with soil moisture and soil CO2 flux. The effects of drought and N fertilization on soil BVOCs were influenced by the type of VOCs, litter layer, and season. Specifically, drought significantly affected the exchange rate and quantities of sesquiterpenes. N fertilization led to increased emissions of specific BVOCs (α-pinene and camphene) due to the stimulation of litter emissions. These findings underscore the importance of the soil as a sink for atmospheric BVOCs in this dry Mediterranean ecosystem. Future drought conditions may significantly impact soil water content, resulting in drier soils throughout the year, which will profoundly affect the exchange of soil BVOCs between the soil and atmosphere.

Disturbance of eucalypt forests alters the composition, function, and assembly of soil microbial communities

Forest disturbance has well-characterized effects on soil microbial communities in tropical and northern hemisphere ecosystems, but little is known regarding effects of disturbance in temperate forests of the southern hemisphere. To address this question, we collected soils from intact and degraded Eucalyptus forests along an east-west transect across Tasmania, Australia, and characterized prokaryotic and fungal communities using amplicon sequencing. Forest degradation altered soil microbial community composition and function, with consistent patterns across soil horizons and regions of Tasmania. Responses of prokaryotic communities included decreased relative abundance of Acidobacteriota, nitrifying archaea, and methane-oxidizing prokaryotes in the degraded forest sites, while fungal responses included decreased relative abundance of some saprotrophic taxa (e.g. litter saprotrophs). Forest degradation also reduced network connectivity in prokaryotic communities and increased the importance of dispersal limitation in assembling both prokaryotic and fungal communities, suggesting recolonization dynamics drive microbial composition following disturbance. Further, changes in microbial functional groups reflected changes in soil chemical properties-reductions in nitrifying microorganisms corresponded with reduced NO3-N pools in the degraded soils. Overall, our results show that soil microbiota are highly responsive to forest degradation in eucalypt forests and demonstrate that microbial responses to degradation will drive changes in key forest ecosystem functions.

Impacts of extreme weather events on terrestrial carbon and nitrogen cycling: A global meta-analysis

Some weather events like drought, increased precipitation, and warming exert substantial impact on the terrestrial C and N cycling. However, it remains largely unclear about the effect of extreme weather events (extreme drought, heavy rainfall, extreme heat, and extreme cold) on terrestrial C and N cycling. This study aims to analyze the responses of pools and fluxes of C and N in plants, soil, and microbes to extreme weather events by conducting a global meta-analysis of 656 pairwise observations. Results showed that extreme weather events (extreme drought, heavy rainfall, and extreme heat) decreased plant biomass and C flux, and extreme drought and heavy rainfall decreased the plant N pool and soil N flux. These results suggest that extreme weather events weaken the C and N cycling process in terrestrial ecosystems. However, this study did not determine the impact of extreme cold on ecosystem C and N cycling. Additional field experiments are needed to reveal the effects of extreme cold on global C and N cycling patterns.

Volatile and Dissolved Organic Carbon Sources Have Distinct Effects on Microbial Activity, Nitrogen Content, and Bacterial Communities in Soil

Variation in microbial use of soil carbon compounds is a major driver of biogeochemical processes and microbial community composition. Available carbon substrates in soil include both low molecular weight-dissolved organic carbon (LMW-DOC) and volatile organic compounds (VOCs). To compare the effects of LMW-DOC and VOCs on soil chemistry and microbial communities under different moisture regimes, we performed a microcosm experiment with five levels of soil water content (ranging from 25 to 70% water-holding capacity) and five levels of carbon amendment: a no carbon control, two dissolved compounds (glucose and oxalate), and two volatile compounds (methanol and α-pinene). Microbial activity was measured throughout as soil respiration; at the end of the experiment, we measured extractable soil organic carbon and total extractable nitrogen and characterized prokaryotic communities using amplicon sequencing. All C amendments increased microbial activity, and all except oxalate decreased total extractable nitrogen. Likewise, individual phyla responded to specific C amendments-e.g., Proteobacteria increased under addition of glucose, and both VOCs. Further, we observed an interaction between moisture and C amendment, where both VOC treatments had higher microbial activity than LMW-DOC treatments and controls at low moisture. Across moisture and C treatments, we identified that Chloroflexi, Nitrospirae, Proteobacteria, and Verrucomicrobia were strong predictors of microbial activity, while Actinobacteria, Bacteroidetes, and Thaumarcheota strongly predicted soil extractable nitrogen. These results indicate that the type of labile C source available to soil prokaryotes can influence both microbial diversity and ecosystem function and that VOCs may drive microbial functions and composition under low moisture conditions.

Changes in Soil Organic C Fractions and C Pool Stability Are Mediated by C-Degrading Enzymes in Litter Decomposition of Robinia pseudoacacia Plantations

Litter decomposition is the main source of soil organic carbon (SOC) pool, regarding as an important part of terrestrial ecosystem C dynamics. The turnover of SOC is mainly regulated by extracellular enzymes secreted by microorganisms. However, the response mechanism of soil C-degrading enzymes and SOC in litter decomposition remains unclear. To clarify how SOC fraction dynamics respond to C-degrading enzymes in litter decomposition, we used field experiments to collect leaf litter and SOC fractions from the underlying layer in Robinia pseudoacacia plantations on the Loess Plateau. Our results showed that SOC, easily oxidizable organic C, dissolved organic C, and microbial biomass C increased significantly during the decomposition process. Litter decomposition significantly decreased soil hydrolase activity, but slightly increased oxidase activity. Correlation analysis results showed that SOC fractions were significantly positively correlated with the litter mass, lignin, soil moisture, and oxidase activity, but significantly negatively correlated with cellulose content and soil pH. Partial least squares path models revealed that soil C-degrading enzymes can directly or indirectly affect the changes of soil C fractions. The most direct factors affecting the SOC fractions of topsoil during litter decomposition were litter lignin and cellulose degradation, soil pH, and C-degrading enzymes. Furthermore, regression analysis showed that the decrease of SOC stability in litter decomposition was closely related to the decrease of soil hydrolase to oxidase ratio. These results highlighted that litter degradation-induced changes in C-degrading enzyme activity significantly affected SOC fractions. Furthermore, the distribution of soil hydrolases and oxidases affected the stability of SOC during litter decomposition. These findings provided a theoretical framework for a more comprehensive understanding of C turnover and stabilization mechanisms between plant and soil.

Effects of Fertilization and Dry-Season Irrigation on Litterfall Dynamics and Decomposition Processes in Subtropical Eucalyptus Plantations

Nutrient management in Eucalyptus plantations is critical for wood production and sustainable development. The biogeochemical mechanisms in Eucalyptus plantations are not fully understood due to changes in the spatiotemporal pattern of precipitation and plantation management. The nutrients released from litterfall are important sources of soil nutrition. We measured the seasonal production of various litterfall types and the proportions of their released nutrients in Eucalyptus urophylla × E. grandis plantations under compound fertilization, dry-season irrigation, and a combined compound fertilization and dry-season irrigation treatment. Our results showed that fertilization increased aboveground biomass and annual litterfall production (except leaf), and that the peak of litterfall production occurred in the rainy season. We found that the decomposition rates of leaf were significantly higher than that of twig, which were mainly controlled by stoichiometric characteristics, followed by soil enzyme activity (β-glucosidase, urease, and polyphenol oxidase). Fertilization decreased the carbon: nitrogen ratio and carbon: phosphorus ratio in litter, and increased soil enzyme activities, which accelerates litter decomposition and nutrient release. Dry-season irrigation increased litter decomposition and only affected the proportion of released potassium by changing the carbon: potassium ratio. Fertilization and dry-season irrigation accelerated the nutrient cycle to enhance compensatory growth. These results help to comprehend the effects of forest management on litterfall dynamics and decomposition processes in Eucalyptus plantations with seasonal drought.

Effect of plant VOCs and light intensity on growth and reproduction performance of an invasive and a native Phytolacca species in China

Invasive plants often pose great threats to the growth of co‐occurring native plant species. Identifying environmental factors that facilitate exotic plant invasion and native species decline are important. In this study, we measured the effects of plant volatile organic compounds (VOCs), light intensity, and their interactions on the growth and reproduction performance of indigenous Phytolacca acinosa, and invasive Phytolacca americana, which has largely replaced the former in China. VOCs of invasive P. americana and low light levels both had negative effects on P. acinosa morphological and reproductive traits (stem length, average leaf number, total number, and length of racemes), and biomass allocation (total biomass, and leaf and flower mass fraction); low light also affected photosynthesis‐related trait (specific leaf area) of P. acinosa. In contrast, VOCs of P. acinosa had no significant effect on P. americana, but low light levels adversely affected its morphological and reproductive traits (stem length, total number, and length of racemes) and biomass allocation (total biomass, stem, and leaf mass fraction). Interactions between plant VOCs and light intensity had no significant effects on P. acinosa or P. americana. Under all experimental treatments, stem length, average leaf area, total number, and length of racemes, Root/Shoot ratio, root and flower mass fraction of P. americana were higher than those of P. acinosa, while average leaf number, specific leaf area, and leaf mass fraction was lower. These results indicated that P. acinosa was sensitive to P. americana VOCs and low light, which might affect the growth of sympatric P. acinosa. P. americana was negatively influenced by low light, but higher plant height and more reproductive organ resource allocation relative to sympatric P. acinosa might contribute to invasion success.

Belowground plant-microbe communications via volatile compounds

Volatile compounds play important roles in rhizosphere biological communications and interactions. The emission of plant and microbial volatiles is a dynamic phenomenon that is affected by several endogenous and exogenous signals. Diffusion of volatiles can be limited by their adsorption, degradation, and dissolution under specific environmental conditions. Therefore, rhizosphere volatiles need to be investigated on a micro and spatiotemporal scale. Plant and microbial volatiles can expand and specialize the rhizobacterial niche not only by improving the root system architecture such that it serves as a nutrient-rich shelter, but also by inhibiting or promoting the growth, chemotaxis, survival, and robustness of neighboring organisms. Root volatiles play an important role in engineering the belowground microbiome by shaping the microbial community structure and recruiting beneficial microbes. Microbial volatiles are appropriate candidates for improving plant growth and health during environmental challenges and climate change. However, some technical and experimental challenges limit the non-destructive monitoring of volatile emissions in the rhizosphere in real-time. In this review, we attempt to clarify the volatile-mediated intra- and inter-kingdom communications in the rhizosphere, and propose improvements in experimental design for future research.

Litter nitrogen concentration changes mediate effects of drought and plant species richness on litter decomposition

Biodiversity loss, exotic plant invasion and climatic change are three important global changes that can affect litter decomposition. These effects may be interactive and these global changes thus need to be considered simultaneously. Here, we assembled herbaceous plant communities with five species richness levels (1, 2, 4, 8 or 16) and subjected them to a drought treatment (no, moderate or intensive drought) that was factorially combined with an invasion treatment (presence or absence of the non-native Symphyotrichum subulatum). We collected litter of these plant communities and let it decompose for 9 months in the plant communities from which it originated. Drought decreased litter decomposition, while invasion by S. subulatum had little impact. Increasing species richness decreased litter decomposition except under intensive drought. A structural equation model showed that drought and species richness affected litter decomposition indirectly through changes in litter nitrogen concentration rather than by altering quantity and diversity of soil meso-fauna or soil physico-chemical properties. The slowed litter decomposition under high species diversity originated from a sampling effect, specifically from low litter nitrogen concentrations in the two dominant species. We conclude that effects on litter decomposition rates that are mediated by changing concentrations of the limiting nutrient in litter need to be considered when predicting effects of global changes such as plant diversity loss.

Phosphorus elevation erodes ectomycorrhizal community diversity and induces divergence of saprophytic community composition between vegetation types

Phosphorus (P) is a critical macronutrient that is essential for many life-sustaining processes. Despite decades of work on plant performance under P deficiency and the importance of microbes in ecosystem processes, little is known about how bacterial and fungal flora respond to P gradients and determine the vegetation health. In current study, we examined soil edaphic conditions and microbial communities in 39 untouched natural forests representing phosphorous deficient (Pp) and phosphorus rich (Pr) soils (due to naturally occurring phosphate rocks) in Yunnan Province, China. We also considered the effect of plant functional types by including the dominant tree species. Bacterial and fungal diversity was greater across the Pp sites compared with Pr sites. The relative abundance of Actinobacteria and Gemmatimonadetes was higher across Pp sites, while Chlamydiae and Verrucomicrobia showed the opposite pattern, with greater relative abundance across the Pr sites. Bacterial taxa that were observed in low P soils were more likely having oligotrophic life history strategies. Interestingly, ectomycorrhizal (ECM) fungal diversity was promoted in the Pp sites, indicating that the decreasing soil P concentration and the increasing host P demand foster stimulated the ECM species for hyphal soil exploration. Moreover, the high P level caused saprophytic fungi (SAP) to diverge, causing its enrichment only under Q. variabilis compared to low P soil, where there is no difference in relative abundance of SAP between the two tree species. This likely resulted in an enhanced decomposition process by SAP and elevation of soil properties (Carbon and Nitrogen) under Q. variabilis across the Pr sites. Taken together, our findings highlight the highly diverse microbiome in low P soils. The higher soil P caused shifts of fungal functional guilds, which likely influence tree growth and health (ECM), along with divergence of ecosystem services between tree functional types.

Corpse decomposition increases the diversity and abundance of antibiotic resistance genes in different soil types in a fish model

As a common natural phenomenon, corpse decomposition may lead to serious environmental pollution such as nitrogen pollution. However, less is known about antibiotic resistance genes (ARGs), an emerging contaminant, during corpse degradation. Here, ARGs and microbiome in three soil types (black, red and yellow soil) have been investigated between experimental and control groups based on next-generation sequencing and high-throughput quantitative PCR techniques. We found that the absolute abundance of total ARGs and mobile genetic elements (MGEs) in the experimental groups were respectively enriched 536.96 and 240.60 times in different soil types, and the number of ARGs in experimental groups was 7-25 more than that in control groups. For experimental groups, the distribution of ARGs was distinct in different soil types, but sulfonamide resistance genes were always enriched. Corpse decomposition was a primary determinant for ARGs profiles. Microbiome, NH₄⁺ concentrates and pH also significantly affected ARGs profiles. Nevertheless, soil types had few effects on ARGs. For soil microbiome, some genera were elevated in experimental groups such as the Ignatzschineria and Myroides. The alpha diversity is decreased in experimental groups and microbial community structures are different between treatments. Additionally, the Escherichia and Neisseria were potential pathogens elevated in experimental groups. Network analysis indicated that most of ARGs like sulfonamide and multidrug resistance genes presented strong positively correlations with NH₄⁺ concentrates and pH, and some genera like Ignatzschineria and Dysgonomonas were positively correlated with several ARGs such as aminoglycoside and sulfonamide resistance genes. Our study reveals a law of ARGs' enrichment markedly during corpse decomposing in different soil types, and these ARGs contaminant maintaining in environment may pose a potential threat to environmental safety and human health.

The Chemistry of Stress: Understanding the 'Cry for Help' of Plant Roots

Plants are faced with various biotic and abiotic stresses during their life cycle. To withstand these stresses, plants have evolved adaptive strategies including the production of a wide array of primary and secondary metabolites. Some of these metabolites can have direct defensive effects, while others act as chemical cues attracting beneficial (micro)organisms for protection. Similar to aboveground plant tissues, plant roots also appear to have evolved “a cry for help” response upon exposure to stress, leading to the recruitment of beneficial microorganisms to help minimize the damage caused by the stress. Furthermore, emerging evidence indicates that microbial recruitment to the plant roots is, at least in part, mediated by quantitative and/or qualitative changes in root exudate composition. Both volatile and water-soluble compounds have been implicated as important signals for the recruitment and activation of beneficial root-associated microbes. Here we provide an overview of our current understanding of belowground chemical communication, particularly how stressed plants shape its protective root microbiome.

Vapor pressure deficit helps explain biogenic volatile organic compound fluxes from the forest floor and canopy of a temperate deciduous forest

Biogenic volatile organic compounds (BVOCs) play critical roles in ecological and earth-system processes. Ecosystem BVOC models rarely include soil and litter fluxes and their accuracy is often challenged by BVOC dynamics during periods of rapid ecosystem change like spring leaf out. We measured BVOC concentrations within the air space of a mixed deciduous forest and used a hybrid Lagrangian/Eulerian canopy transport model to estimate BVOC flux from the forest floor, canopy, and whole ecosystem during spring. Canopy flux measurements were dominated by a large methanol source and small isoprene source during the leaf-out period, consistent with past measurements of leaf ontogeny and theory, and indicative of a BVOC flux situation rarely used in emissions model testing. The contribution of the forest floor to whole-ecosystem BVOC flux is conditional on the compound of interest and is often non-trivial. We created linear models of forest floor, canopy, and whole-ecosystem flux for each study compound and used information criteria-based model selection to find the simplest model with the best fit. Most published BVOC flux models do not include vapor pressure deficit (VPD), but it entered the best canopy, forest floor, and whole-ecosystem BVOC flux model more than any other study variable in the present study. Since VPD is predicted to increase in the future, future studies should investigate how it contributes to BVOC flux through biophysical mechanisms like evaporative demand, leaf temperature and stomatal function.