Microbially derived inputs to soil organic matter: are current estimates too low?

Fungal necromass contribution to carbon sequestration in global croplands: A meta-analysis of driving factors and conservation practices

Fungal necromass carbon (FNC) contributes significantly to the build-up of soil organic carbon (SOC) by supplying abundant recalcitrant polymeric melanin present in the fungal cell wall. However, the influence of a wide range of conservation practices and associated factors on FNC accumulation and contribution to SOC in global croplands remains unexplored. Here, a meta-analysis was performed using 873 observations across three continents, together with structural equation modeling, to evaluate conservation practices and factors responsible for the enhancement of FNC and SOC. FNC content (8.39 g kg-1) of North American soils was highest compared to FNC content of Asian and European soils. The structural equation models showed a significant (p < 0.05) positive influence of microbial biomass carbon (MBC), soil pH, and clay contents on the accumulation of FNC. Soil C/N ratio and climate factors, however, had only minor influences on FNC accumulation. Notably, the main driver of FNC was MBC, which is mainly influenced by the soil total N and geographic factors in the study areas. Typical 5 cropland practices had significant effect size (p < 0.05) on FNC, leading to an increase of 12 % to 26 %, and the FNC content was greatest under straw amendment (26 %). Fungal necromass accumulation efficiency ranged from 23 % to 45 % depending on cropland practices: non- and reduced tillage was the most efficient (45 %), followed by crop coverage (32 %), straw amendment (30 %), and manure application (27 %), while N fertilization had the lowest efficiency (23 %). We conclude that FNC contributes to over a quarter of SOC, highlighting its major role in enhancing C sequestration worldwide. Conservation practices, particularly non-tillage or reduced tillage, are important to enhance C sequestration from FNC in croplands.

Tipping the plant-microbe competition for nitrogen in agricultural soils

Nitrogen (N) is the most limiting nutrient in agroecosystems, and its indiscriminate application is at the center of the environmental challenges facing agriculture. To solve this dilemma, crops' nitrogen use efficiency (NUE) needs to increase - in other words, more of the applied nitrogen needs to reach humans. Microbes are the key to cracking this problem. Microbes use nitrogen as an energy source, an electron acceptor, or incorporate it in their biomass. These activities change the form and availability of nitrogen for crops' uptake, impacting its NUE, yields and produce quality. Plants (and microbes) have, however, evolved many mechanisms to compete for soil nitrogen. Understanding and harnessing these competitive mechanisms would enable us to tip the nitrogen balance to the advantage of crops. We will review these competitive mechanisms and highlight some approaches that were applied to reduce microbial competition for N in an agricultural context.

Variation of microbial necromass carbon and its potential relationship with humification during composting of chicken manure with and without biochar addition

Microbial necromass carbon (MNC) is an important stable organic C component. However, the variation of MNC and its potential relationship with humus components in composting remains uncertain. During a 45-day chicken manure composting study with and without biochar, MNC ranged from 24.9 to 77.9 g/kg and increased significantly by 80.9 % to 133 %. MNC constituted 5.77 % to 21.3 % of total organic C, with bacterial/fungal necromass C ratio ranging from 0.82 to 1.78. The MNC/humus C ratio ranged from 0.15 to 0.55, and humic acid C showed significant positive associations with bacterial necromass C (R2 = 0.72) and fungal necromass C (R2 = 0.51). Biochar addition reduced electrical conductivity and moisture content, increased pH, and induced microbial phosphorus limitation, thereby enhancing MNC content by 29.2 % and promoting humification. Our study is the first to elucidate the relationship between microbial necromass and humus substances, providing fundamental data for advancing the microbial carbon pump theory in composting.

Reducing the uncertainty in estimating soil microbial-derived carbon storage

Soil organic carbon (SOC) is the largest carbon pool in terrestrial ecosystems and plays a crucial role in mitigating climate change and enhancing soil productivity. Microbial-derived carbon (MDC) is the main component of the persistent SOC pool. However, current formulas used to estimate the proportional contribution of MDC are plagued by uncertainties due to limited sample sizes and the neglect of bacterial group composition effects. Here, we compiled the comprehensive global dataset and employed machine learning approaches to refine our quantitative understanding of MDC contributions to total carbon storage. Our efforts resulted in a reduction in the relative standard errors in prevailing estimations by an average of 71% and minimized the effect of global variations in bacterial group compositions on estimating MDC. Our estimation indicates that MDC contributes approximately 758 Pg, representing approximately 40% of the global soil carbon stock. Our study updated the formulas of MDC estimation with improving the accuracy and preserving simplicity and practicality. Given the unique biochemistry and functioning of the MDC pool, our study has direct implications for modeling efforts and predicting the land-atmosphere carbon balance under current and future climate scenarios.

Biomolecular budget of persistent, microbial-derived soil organic carbon: The importance of underexplored pools

The details of how soil microorganisms contribute to stable soil organic carbon pools are a pressing knowledge gap with direct implications for soil health and climate mitigation. It is now recognized that microbial necromass contributes substantially to the formation of stable soil carbon. However, the quantification of necromass in soils has largely been limited to model molecules such as aminosugar biomarkers. The abundance and chemical composition of other persistent microbial residues remain unresolved, particularly concerning how these pools may vary with microbial community structure, soil texture, and management practices. Here we use yearlong soil incubation experiments with an isotopic tracer to quantify the composition of persistent residues derived from microbial communities inhabiting sand or silt dominated soil with annual (corn) or perennial (switchgrass) monocultures. Persistent microbial residues were recovered in diverse soil biomolecular pools including metabolites, proteins, lipids, and mineral-associated organic matter (MAOM). The relative abundances of microbial contributions to necromass pools were consistent across cropping systems and soil textures. The greatest residue accumulation was not recovered in MAOM but in the light density fraction of soil debris that persisted after extraction by chemical fractionation using organic solvents. Necromass abundance was positively correlated with microbial biomass abundance and revealed a possible role of cell wall morphology in enhancing microbial carbon persistence; while gram-negative bacteria accounted for the greatest contribution to microbial-derived carbon by mass at one year, residues from gram-positive Actinobacteria and Firmicutes showed greater durability. Together these results offer a quantitative assessment of the relative importance of diverse molecular classes for generating durable soil carbon.

Rhizosphere priming promotes plant nitrogen acquisition by microbial necromass recycling

Nitrogen availability in the rhizosphere relies on root-microorganism interactions, where root exudates trigger soil organic matter (SOM) decomposition through the rhizosphere priming effect (RPE). Though microbial necromass contribute significantly to organically bound soil nitrogen (N), the role of RPEs in regulating necromass recycling and plant nitrogen acquisition has received limited attention. We used 15N natural abundance as a proxy for necromass-N since necromass is enriched in 15N compared to other soil-N forms. We combined studies using the same experimental design for continuous 13CO2 labelling of various plant species and the same soil type, but considering top- and subsoil. RPE were quantified as difference in SOM-decomposition between planted and unplanted soils. Results showed higher plant N uptake as RPEs increased. The positive relationship between 15N-enrichment of shoots and roots and RPEs indicated an enhanced necromass-N turnover by RPE. Moreover, our data revealed that RPEs were saturated with increasing carbon (C) input via rhizodeposition in topsoil. In subsoil, RPEs increased linearly within a small range of C input indicating a strong effect of root-released C on decomposition rates in deeper soil horizons. Overall, this study confirmed the functional importance of rhizosphere C input for plant N acquisition through enhanced necromass turnover by RPEs.

Responses of Soil Carbon and Microbial Residues to Degradation in Moso Bamboo Forest

Moso bamboo (Phyllostachys heterocycla cv. Pubescens) is known for its high capacity to sequester atmospheric carbon (C), which has a unique role to play in the fight against global warming. However, due to rising labor costs and falling bamboo prices, many Moso bamboo forests are shifting to an extensive management model without fertilization, resulting in gradual degradation of Moso bamboo forests. However, many Moso bamboo forests are being degraded due to rising labor costs and declining bamboo timber prices. To delineate the effect of degradation on soil microbial carbon sequestration, we instituted a rigorous analysis of Moso bamboo forests subjected to different degradation durations, namely: continuous management (CK), 5 years of degradation (D-5), and 10 years of degradation (D-10). Our inquiry encompassed soil strata at 0-20 cm and 20-40 cm, scrutinizing alterations in soil organic carbon(SOC), water-soluble carbon(WSOC), microbial carbon(MBC)and microbial residues. We discerned a positive correlation between degradation and augmented levels of SOC, WSOC, and MBC across both strata. Furthermore, degradation escalated concentrations of specific soil amino sugars and microbial residues. Intriguingly, extended degradation diminished the proportional contribution of microbial residuals to SOC, implying a possible decline in microbial activity longitudinally. These findings offer a detailed insight into microbial C processes within degraded bamboo ecosystems.

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

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

A stoichiometric approach to estimate sources of mineral-associated soil organic matter

Mineral-associated soil organic matter (MAOM) is the largest, slowest cycling pool of carbon (C) in the terrestrial biosphere. MAOM is primarily derived from plant and microbial sources, yet the relative contributions of these two sources to MAOM remain unresolved. Resolving this issue is essential for managing and modeling soil carbon responses to environmental change. Microbial biomarkers, particularly amino sugars, are the primary method used to estimate microbial versus plant contributions to MAOM, despite systematic biases associated with these estimates. There is a clear need for independent lines of evidence to help determine the relative importance of plant versus microbial contributions to MAOM. Here, we synthesized 288 datasets of C/N ratios for MAOM, particulate organic matter (POM), and microbial biomass across the soils of forests, grasslands, and croplands. Microbial biomass is the source of microbial residues that form MAOM, whereas the POM pool is the direct precursor of plant residues that form MAOM. We then used a stoichiometric approach-based on two-pool, isotope-mixing models-to estimate the proportional contribution of plant residue (POM) versus microbial sources to the MAOM pool. Depending on the assumptions underlying our approach, microbial inputs accounted for between 34% and 47% of the MAOM pool, whereas plant residues contributed 53%-66%. Our results therefore challenge the existing hypothesis that microbial contributions are the dominant constituents of MAOM. We conclude that biogeochemical theory and models should account for multiple pathways of MAOM formation, and that multiple independent lines of evidence are required to resolve where and when plant versus microbial contributions are dominant in MAOM formation.

Drivers of microbially and plant-derived carbon in topsoil and subsoil

Plant- and microbially derived carbon (C) are the two major sources of soil organic matter (SOM), and their ratio impacts SOM composition, accumulation, stability, and turnover. The contributions of and the key factors defining the plant and microbial C in SOM along the soil profile are not well known. By leveraging nuclear magnetic resonance spectroscopy and biomarker analysis, we analyzed the plant and microbial C in three soil types using regional-scale sampling and combined these results with a meta-analysis. Topsoil (0-40 cm) was rich in carbohydrates and lignin (38%-50%), whereas subsoil (40-100 cm) contained more proteins and lipids (26%-60%). The proportion of plant C increases, while microbial C decreases with SOM content. The decrease rate of the ratio of the microbially derived C to plant-derived C (CM:P ) with SOM content was 23%-30% faster in the topsoil than in the subsoil in the regional study and meta-analysis. The topsoil had high potential to stabilize plant-derived C through intensive microbial transformations and microbial necromass formation. Plant C input and mean annual soil temperature were the main factors defining CM:P in topsoil, whereas the fungi-to-bacteria ratio and clay content were the main factors influencing subsoil CM:P . Combining a regional study and meta-analysis, we highlighted the contribution of plant litter to microbial necromass to organic matter up to 1-m soil depth and elucidated the main factors regulating their long-term preservation.

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

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

Elucidating the effects of organic vs. conventional cropping practice and rhizobia inoculation on rhizosphere microbial diversity and yield of peanut

Legumes such as peanut (Arachis hypogea) can fulfill most of their nitrogen requirement by symbiotic association with nitrogen-fixing bacteria, rhizobia. Nutrient availability is largely determined by microbial diversity and activity in the rhizosphere that influences plant health, nutrition, and crop yield, as well as soil quality and soil fertility. However, our understanding of the complex effects of microbial diversity and rhizobia inoculation on crop yields of different peanut cultivars under organic versus conventional farming systems is extremely limited. In this research, we studied the impacts of conventional vs. organic cultivation practices and inoculation with commercial vs. single strain inoculum on peanut yield and soil microbial diversity of five peanut cultivars. The experiment was set up in the field following a split-split-plot design. Our results from the 16 S microbiome sequencing showed considerable variations of microbial composition between the cultivation types and inoculum, indicating a preferential association of microbes to peanut roots with various inoculum and cropping system. Alpha diversity indices (chao1, Shannon diversity, and Simpson index) of soil microbiome were generally higher in plots with organic than conventional inorganic practices. The cultivation type and inoculum explained significant differences among bacterial communities. Taxonomic classification revealed two phyla, TM6 and Firmicutes were significantly represented in inorganic as compared to organic soil, where significant phyla were Armatimonadetes, Gemmatimonadetes, Nitrospirae, Proteobacteria, Verrucomicrobia, and WS3. Yields in the organic cultivation system decreased by 10-93% of the yields in the inorganic cultivation system. Cultivar G06 and T511 consistently showed relative high yields in both organic and inorganic trials. Our results show significant two-way interactions between cultivation type and genotype for most of the trait data collected. Therefore, it is critical for farmers to choose varieties based on their cultivation practices. Our results showed that bacterial structure was more uniform in organic fields and microbial diversity in legumes was reduced in inorganic fields. This research provided guides for farmers and scientists to improve peanut yield while promoting microbial diversity and increasing sustainability.

Compositional changes in the humin fraction resulting from the long-term cultivation of an Irish grassland soil: Evidence from FTIR and multi-NMR spectroscopies

Soil humin (HN), a major long-term sink for carbon in the pedosphere, plays a key role in the global carbon cycle, and has been less extensively studied than the humic and fulvic acids components. There are increasing concerns about the depletions of soil organic matter (SOM) arising from modern soil cultivation practices but there has been little focus on how HN can be altered as the result. This study has compared the HN components in a soil under cultivation for wheat for >30 years with those from an adjacent contiguous soil that had been under long-term grass for all that time. A urea-fortified basic solution isolated additional humic fractions from soils that had been exhaustively extracted in basic media. Then further exhaustive extractions of the residual soil material with dimethyl sulfoxide, amended with sulphuric acid isolated what may be called the "true" HN fraction. The long-term cultivation resulted in a loss of 53 % soil organic carbon in the surface soil. Infrared and multi-NMR spectroscopies showed the "true" HN to be dominated by aliphatic hydrocarbons and carboxylated structures, but with clear evidence for lesser amounts of carbohydrate and peptide materials, and with weaker evidence for lignin-derived substances. These lesser-amount structures can be sorbed on the soil mineral colloid surfaces and/or covered by the hydrophobic HN component or entrained within these which have strong affinities for the mineral colloids. HN from the cultivated site contained less carbohydrate and more carboxyl groups suggesting slow transformations took place resulting from the cultivation, but these were much slower than for the other components of SOM. It is recommended that a study be made of the HN in a soil under long-term cultivation for which the SOM content has reached a steady state and where HN will be expected to dominate the components of SOM.

Deciphering the contribution of microbial biomass to the properties of dissolved and particulate organic matter in anaerobic digestates

The recalcitrant structures either from substrate or microbial biomass contained in digestates after anaerobic digestion (AD) highly influence digestate valorization. To properly assess the microbial biomass contribution to the digested organic matter (OM), a combination of characterization methods and the use of various substrate types in anaerobic continuous reactors was required. The use of totally biodegradable substrates allowed detecting soluble microbial products via fluorescence spectroscopy at emission wavelengths of 420 and 460 nm while the protein-like signature was enhanced by the whey protein. During reactors' operation, a transfer of complex compounds to the dissolved OM from the particulate OM was observed through fluorescence applied on biochemical fractionation. Consequently, the fluorescence complexity index of the dissolved OM increased from 0.59-0.60 to 1.06-1.07, whereas it decreased inversely for the extractable soluble from the particulate OM from 1.16-1.19 to 0.42-0.54. Accordingly, fluorescence regional integration showed differences among reactors based on visual inspection and orthogonal partial latent structures (OPLS) analysis. Similarly, the impact of the substrate type and operation time on the particulate OM was revealed by ¹³C nuclear magnetic resonance using OPLS, providing a good model (R²X = 0.93 and Q² = 0.8) with a clear time-trend. A high signal resonated at ∼30 ppm attributed to CH₂-groups in the aliphatic chain of lipid-like structure besides carbohydrates intensities at 60-110 ppm distinguished the reactor fed with whey protein from the other, which was mostly biomass related. Indeed, this latter displayed a higher presence of peptidoglycan (δH/C: 1.6-2.0/20-25 ppm) derived from microbial biomass by ¹H-¹³C heteronuclear single-quantum coherence (HSQC) nuclear magnetic resonance. Interestingly, the sample distribution obtained by non-metric multidimensional scaling of bacterial communities resembled the attained using ¹³C NMR properties, opening new research perspectives. Overall, this study discloses the microbial biomass contribution to digestates composition to improve the OM transformation mechanism knowledge.

The Invasive Tradescantia zebrina Affects Litter Decomposition, but It Does Not Change the Lignocellulolytic Fungal Community in the Atlantic Forest, Brazil

Invasive plants affect ecosystems across various scales. In particular, they affect the quality and quantity of litter, which influences the composition of decomposing (lignocellulolytic) fungal communities. However, the relationship among the quality of invasive litter, lignocellulolytic cultivated fungal community composition, and litter decomposition rates under invasive conditions is still unknown. We evaluated whether the invasive herbaceous Tradescantia zebrina affects the litter decomposition in the Atlantic Forest and the lignocellulolytic cultivated fungal community composition. We placed litter bags with litter from the invader and native plants in invaded and non-invaded areas, as well as under controlled conditions. We evaluated the lignocellulolytic fungal communities by culture method and molecular identification. Litter from T. zebrina decomposed faster than litter from native species. However, the invasion of T. zebrina did not alter decomposition rates of either litter type. Although the lignocellulolytic fungal community composition changed over decomposition time, neither the invasion of T. zebrina nor litter type influenced lignocellulolytic fungal communities. We believe that the high plant richness in the Atlantic Forest enables a highly diversified and stable decomposing biota formed in conditions of high plant diversity. This diversified fungal community is capable of interacting with different litter types under different environmental conditions.

Long-term plastic mulching decreases rhizoplane soil carbon sequestration by decreasing microbial anabolism

Ridge-furrow with plastic mulching (RFPM) is a widely used agricultural practice in rain-fed farmlands. However, the impact of microbial related metabolism on soil organic carbon (SOC) is not fully understood. Amino sugar analysis, high-throughput sequencing, and high-throughput qPCR approaches are combined to investigate this topic, based on a long-term experiment. Treatments include flat planting without mulching (FP), ridge-furrow without mulching (RF), and RFPM. RFPM significantly decreases rhizoplane SOC contents, while bulk SOC contents change insignificantly across treatments. In terms of microbial metabolic pathways, RFPM decreases indicators of the in vivo metabolic pathway, whereas those of the ex vivo pathway are increased. In terms of microbial community features, core taxa module #1 is dominated by Sphingomonadaceae. These are putative high yield (Y) strategists, according to the microbial life-history strategy framework. They are closely related to the in vivo pathway and are most predictive for SOC; their abundance is highest under FP and lowest under RFPM. Core taxa module #2 is dominated by Chitinophagaceae, putative resource acquisition (A) strategists, that are closely related to the ex vivo pathway. Their abundance in the rhizoplane is highest under RFPM and lowest under FP. The RFPM-induced decline in SOC occurs simultaneously with the abundance of A-strategists with in vivo pathway but not the Y-strategists with ex vivo pathway. Overall, the result of this study shows a trade-off. In RFPM practice, the ex vivo microbial pathway is enhanced along with the abundance of A-strategists. This is not the case for the in vivo pathway and associated abundance of Y-strategists, which are closely associated with SOC. Our findings underlined the impact of rhizoplane microbial metabolic pathways on SOC status is key to agricultural practices in drylands such as RFPM, and advanced our understanding of how microbes affect the carbon cycling in dryland farming.

Unboxing the black box-one step forward to understand the soil microbiome: A systematic review

Soil is one of the most important assets of the planet Earth, responsible for maintaining the biodiversity and managing the ecosystem services for both managed and natural ecosystems. It encompasses large proportion of microscopic biodiversity, including prokaryotes and the microscopic eukaryotes. Soil microbiome is critical in managing the soil functions, but their activities have diminutive recognition in few systems like desert land and forest ecosystems. Soil microbiome is highly dependent on abiotic and biotic factors like pH, carbon content, soil structure, texture, and vegetation, but it can notably vary with ecosystems and the respective inhabitants. Thus, unboxing this black box is essential to comprehend the basic components adding to the soil systems and supported ecosystem services. Recent advancements in the field of molecular microbial ecology have delivered commanding tools to examine this genetic trove of soil biodiversity. Objective of this review is to provide a critical evaluation of the work on the soil microbiome, especially since the advent of the NGS techniques. The review also focuses on advances in our understanding of soil communities, their interactions, and functional capabilities along with understanding their role in maneuvering the biogeochemical cycle while underlining and tapping the unprecedented metagenomics data to infer the ecological attributes of yet undiscovered soil microbiome. This review focuses key research directions that could shape the future of basic and applied research into the soil microbiome. This review has led us to understand that it is difficult to generalize that soil microbiome plays a substantiated role in shaping the soil networks and it is indeed a vital resource for sustaining the ecosystem functioning. Exploring soil microbiome will help in unlocking their roles in various soil network. It could be resourceful in exploring and forecasting its impacts on soil systems and for dealing with alleviating problems like rapid climate change.

Tradeoffs of microbial life history strategies drive the turnover of microbial-derived organic carbon in coastal saline soils

Stable soil organic carbon (SOC) formation in coastal saline soils is important to improve arable land quality and mitigate greenhouse gas emissions. However, how microbial life-history strategies and metabolic traits regulate SOC turnover in coastal saline soils remains unknown. Here, we investigated the effects of microbial life history strategy tradeoffs on microbial carbon use efficiency (CUE) and microbial-derived SOC formation using metagenomic sequencing technology in different salinity soils. The results showed that high-salinity is detrimental to microbial CUE and microbial-derived SOC formation. Moreover, the regulation of nutrients stoichiometry could not mitigate adverse effects of salt stress on microbial CUE, which indicated that microbial-derived SOC formation is independent of stoichiometry in high-salinity soil. Low-salinity soil is dominated by a high growth yield (Y) strategy, such as higher microbial biomass carbon and metabolic traits which are related to amino acid metabolism, carbohydrate metabolism, and cell processes. However, high-salinity soil is dominated by stress tolerance (S) (e.g., higher metabolic functions of homologous recombination, base excision repair, biofilm formation, extracellular polysaccharide biosynthesis, and osmolytes production) and resource acquisition (A) strategies (e.g., higher alkaline phosphatase activity, transporters, and flagellar assembly). These trade-offs of strategies implied that resource reallocation took place. The high-salinity soil microbes diverted investments away from growth yield to microbial survival and resource capture, thereby decreasing biomass turnover efficiency and impeding microbial-derived SOC formation. Moreover, altering the stoichiometry in low-salinity soil caused more investment in the A-strategy, such as the production of more β-glucosidase and β-N-acetyl-glucosaminidase, and increasing bacterial chemotaxis, which thereby reduced microbial-derived SOC formation. Our research reveals that shift the microbial community from S- and A- strategies to the Y-strategy is important to increase the microbial CUE, and thus enhance SOC turnover in coastal saline soils.

Clarifying the evidence for microbial- and plant-derived soil organic matter, and the path toward a more quantitative understanding

Predicting and mitigating changes in soil carbon (C) stocks under global change requires a coherent understanding of the factors regulating soil organic matter (SOM) formation and persistence, including knowledge of the direct sources of SOM (plants vs. microbes). In recent years, conceptual models of SOM formation have emphasized the primacy of microbial-derived organic matter inputs, proposing that microbial physiological traits (e.g., growth efficiency) are dominant controls on SOM quantity. However, recent quantitative studies have challenged this view, suggesting that plants make larger direct contributions to SOM than is currently recognized by this paradigm. In this review, we attempt to reconcile these perspectives by highlighting that variation across estimates of plant- versus microbial-derived SOM may arise in part from methodological limitations. We show that all major methods used to estimate plant versus microbial contributions to SOM have substantial shortcomings, highlighting the uncertainty in our current quantitative estimates. We demonstrate that there is significant overlap in the chemical signatures of compounds produced by microbes, plant roots, and through the extracellular decomposition of plant litter, which introduces uncertainty into the use of common biomarkers for parsing plant- and microbial-derived SOM, especially in the mineral-associated organic matter (MAOM) fraction. Although the studies that we review have contributed to a deeper understanding of microbial contributions to SOM, limitations with current methods constrain quantitative estimates. In light of recent advances, we suggest that now is a critical time to re-evaluate long-standing methods, clearly define their limitations, and develop a strategic plan for improving the quantification of plant- and microbial-derived SOM. From our synthesis, we outline key questions and challenges for future research on the mechanisms of SOM formation and stabilization from plant and microbial pathways.

Effects of environmental factors on anthocyanin accumulation in the fruits of Lycium ruthenicum Murray across different desert grasslands

Anthocyanins can help plants adapt and resist adverse environments and have important nutritional and medicinal effects on human beings. However, how environmental factors affect the anthocyanins accumulation of plants and how to improve the anthocyanins content of plants in different soils needs further exploration. Hence, this study aimed to investigate the effects of environmental factors on the accumulation of cyanidin, petunidin, malvidin, and delphinidin in the fruits of Lycium ruthenicum in sandy desert grassland (SS), gravel desert grassland (GD), and saline-alkali desert grassland (SD) in the lower reaches of the Shiyang River Basin. The variable importance screened the key environmental factors affecting anthocyanin accumulation in projection (VIP) and multiple stepwise regressions. The structural equation model (SEM) was established to understand how the climate and soil factors affect the total anthocyanin accumulation. For establishing soil nutrient optimization schemes by partial least squares regression (PLS) and the simplex algorithm used to improve the anthocyanin content in different types of desert grassland. In SS, electrical conductivity (EC) and microbial biomass carbon (SMBC) showed highly significant and positive effects on the content of total anthocyanin, cyanidin, and petunidin. In GD, soil moisture and microbial biomass nitrogen (SNBN) significantly negatively affected total anthocyanin content. In SD, catalase (CAT), phosphatase (PHO), and total potassium (TK) had the greatest impact on total anthocyanin content. It is indicated that the targeted improvement measures are necessary to increase anthocyanin content in the fruit of Lycium ruthenicum.

Contrasting response of fungal versus bacterial residue accumulation within soil aggregates to long-term fertilization

Soil microorganisms are critical for soil carbon (C) cycling. They primarily regulate the turnover of the soil organic C (SOC) by adjusting their community structure, and contributing residues with a considerable amount to the resistant SOC. Nevertheless, how long-term fertilization (e.g., the combination of manure and chemical fertilizer) affects the spatial distribution of both living microbial communities and dead microbial residue within soil aggregate fractions remains largely unclear. In this study, we analyzed changes in microbial community (lipid biomarkers) and microbial residue retention (amino sugar biomarkers), and also calculated the contribution of microbial residue to organic C in bulk soil and different soil aggregates (> 2 mm, 1-2 mm, 0.25-1 mm, and < 0.25 mm) in Alfisols treated with 29 years fertilization or no fertilization (control). Our results showed that long-term fertilization significantly increased the mean weight diameter (MWD) of aggregates and organic C contents in all aggregate fractions. The fertilization treatment increased the contents of PLFAs and microbial residue C, but the relative contribution of microbial residue to SOC was higher in the control (56.8% vs. 49.0%), due to the low SOC background caused by much lower level of non-microbially derived C input. These results suggested that long-term fertilization could increase SOC by accumulating both plant- and microbial-derived C, while the C deficient soil is more dependent on the accumulation of microbial residues. Long-term fertilization promoted the enrichment of bacterial-derived muramic acid in micro aggregates, but increased the proportion of fungal-derived glucosamine in macro aggregates. Meanwhile, the contribution of bacterial residue to organic C in the fertilization treatment was higher in micro aggregates (7.6% for > 2 mm vs. 9.2% for < 0.25 mm aggregate), while the contribution of fungal residue was higher in macro aggregate fractions (40.9% for > 2 mm vs. 35.7% for < 0.25 mm aggregate). The above results indicated that long-term fertilization could drive the differentiation of heterogeneous microbial residue accumulation patterns that significantly alter the contribution of fungal- versus bacterial-derived C to organic C within soil aggregate fractions.

Gypsum, crop rotation, and cover crop impacts on soil organic carbon and biological dynamics in rainfed transitional no-till corn-soybean systems

Soil organic carbon (SOC), a core soil quality indicator, is influenced by management practices. The objective of our 2012–2016 study was to elucidate the impact of gypsum, crop rotation, and cover crop on SOC and several of its biological indicators under no-till in Alabama (Shorter), Indiana (Farmland), and Ohio (Hoytville and Piketon) in the USA. A randomized complete block design in factorial arrangement with gypsum (at 0, 1.1, and 2.2 Mg/ha annually), rye (Secale cereal L.) vs no cover crop, and rotation (continuous soybean [Glycine max (L) Merr., SS] vs corn [Zea mays, L.]-soybean, both the CS and SC phases) was conducted. Composite soils were collected (0–15 cm and 15–30 cm) in 2016 to analyze microbial biomass C (SMBC), SOC, total N, active C, cold and hot-water extractable C, C and N pool indices (CPI and NPI), and C management index (CMI). Results varied for main effects of gypsum, crop rotation, and cover crop on SOC pools, total N, and SOC lability within and across the sites. Gypsum at 2.2 Mg/ha increased SMBC within sites and by 41% averaged across sites. Likewise, gypsum increased SMBC:SOC, active C, and hot-water C (as indicators of labile SOC) averaged across sites. CS rotation increased SOC, active C, CPI, and CMI compared to SS, but decreased SMBC and SMBC:SOC within and across sites. CPI had a significant relationship with NPI across all sites (R² = 0.90). Management sensitive SOC pools that responded to the combined gypsum (2.2 Mg/ha), crop rotation (CS), and cover crop (rye) were SMBC, SMBC:SOC, active C, and CMI via SMBC. These variables can provide an early indication of management-induced changes in SOC storage and its lability. Our results show that when SOC accumulates, its lability has decreased, presumably because the SMBC has processed all readily available C into a less labile form.

The impact of biochar on wood-inhabiting bacterial community and its function in a boreal pine forest

Biochar is considered to be a possible means of carbon sequestration to alleviate climate change. However, the dynamics of the microbial community during wood decomposition after biochar application remain poorly understood. In this study, the wood-inhabiting bacterial community composition and its potential functions during a two-year decomposition period after the addition of different amounts of biochar (0.5 kg m^-2 and 1.0 kg m^-2), and at different biochar pyrolysis temperatures (500 °C and 650 °C), in a boreal Scots pine forest, were analyzed using Illumina NovaSeq sequencing combined with Functional Annotation of Prokaryotic Taxa (FAPROTAX). The results showed that the wood decomposition rates increased after biochar addition to the soil surface in the second year. Treatment with biochar produced at high temperatures increased the diversity of wood-inhabiting bacteria more than that produced at low temperatures (P < 0.05). The wood-inhabiting bacterial diversity and species richness decreased with decomposition time. The biochar treatments changed the wood-inhabiting bacterial community structure during the decomposition period. The pyrolysis temperature and the amount of applied biochar had no effect on the bacterial community structure but shifted the abundance of certain bacterial taxa. Similarly, biochar application shifted the wood-inhabiting bacterial community function in the first year, but not in the second year. The wood-inhabiting bacterial community and function were affected by soil pH, soil water content, and soil total nitrogen. The results provide useful information on biochar application for future forest management practices. Long-term monitoring is needed to better understand the effects of biochar application on nutrient cycling in boreal forests.

Extraction methods for untargeted metabolomics influence enzymatic activity in diverse soils

Soil organic matter (SOM) is the largest carbon pool in terrestrial ecosystems and underpins the health and productivity of soil. Accurate characterization of its chemical composition will improve our understanding of biotic and abiotic processes regulating its stabilization. Our purpose in this study was to estimate the loss of SOM by microbial and exoenzymatic activity that might occur when soil is extracted for analysis of representative low molecular weight mass features using untargeted metabolomics. Two mined clays (kaolinite, montmorillonite) and three diverse soils (varying in texture, specific surface area and cation exchange capacity) were used to assess the extraction efficiency and loss of three enzymatic activity indicators (2,6-dichloroindophenol sodium salt hydrate [DCIP], 4-methylumbelliferyl phosphate [MUBph] and 3,4-dihydroxy-L-phenylalanine [LDOPA]) during extraction with two different solvents (water and methanol). Losses of the indicators were attributed to extraction method (ultrasonication, shaking, or shaking following chloroform fumigation), physical properties associated with the soil/clay type, and microbial activity. Soil/clay type strongly influenced indicator recovery and hence, SOM recovery. Choice of extraction method strongly influenced the composition and recovery of representative SOM mass features, while the choice of solvent determined whether the soil type or extraction method had a greater influence of compositional differences in the SOM mass features extracted. Extraction following chloroform fumigation had the greatest loss of the indicators, due to enzymatic activity and/or adsorption onto the soil matrix. Minimal variation in composition and loss of SOM mass features occurred during extraction by shaking for the soils tested; we therefore recommend it as the method of choice for untargeted SOM extraction studies.

Speciation of heavy metals in soils and their immobilization at micro-scale interfaces among diverse soil components

Heavy metal (HM) pollution of soils is a globally important ecological and environmental problem. Previous studies have focused on i) tracking pollution sources in HM-contaminated soils, ii) exploring the adsorption capacity and distribution of HMs, and iii) assessing phyto-uptake of HMs and their ecotoxicity. However, few reviews have systematically summarized HM pollution in soil-plant systems over the past decade. Understanding the mechanisms of interaction between HMs and solid soil components is consequently key to effectively controlling and remediating HM pollution. However, the compositions of solid soil phases are diverse, their structures are complex, and their spatial arrangements are heterogeneous, all leading to the formation of soil micro-domains that exhibit different particle sizes and surface properties. The various soil components and their interactions ultimately control the speciation, transformation, and bioavailability of HMs in soils. Over the past few decades, the extensive application of advanced instrumental techniques and methods has greatly expanded our understanding of the behavior of HMs in organic mineral assemblages. In this review, studies investigating the immobilization of HMs by minerals, organic compounds, microorganisms, and their associated complexes are summarized, with a particular emphasis on the interfacial adsorption and immobilization of HMs. In addition, methods for analyzing the speciation and distribution of HMs in aggregates of natural soils with different particle sizes are also discussed. Moreover, we also review the methods for speciating HMs at mineral-organic micro-scale interfaces. Lastly, developmental prospects for HM research at inorganic-organic interfaces are outlined. In future research, the most advanced methods should be used to characterize the interfaces and in situ characteristics of metals and metal complexes. In particular, the roles and contributions of microorganisms in the immobilization of HMs at complex mineral-organic interfaces require significant further investigation.

Characterizing Natural Organic Matter Transformations by Microbial Communities in Terrestrial Subsurface Ecosystems: A Critical Review of Analytical Techniques and Challenges

Determining the mechanisms, traits, and pathways that regulate microbial transformation of natural organic matter (NOM) is critical to informing our understanding of the microbial impacts on the global carbon cycle. The capillary fringe of subsurface soils is a highly dynamic environment that remains poorly understood. Characterization of organo-mineral chemistry combined with a nuanced understanding of microbial community composition and function is necessary to understand microbial impacts on NOM speciation in the capillary fringe. We present a critical review of the popular analytical and omics techniques used for characterizing complex carbon transformation by microbial communities and focus on how complementary information obtained from the different techniques enable us to connect chemical signatures with microbial genes and pathways. This holistic approach offers a way forward for the comprehensive characterization of the formation, transformation, and mineralization of terrestrial NOM as influenced by microbial communities.

Hyphae move matter and microbes to mineral microsites: Integrating the hyphosphere into conceptual models of soil organic matter stabilization

Associations between soil minerals and microbially derived organic matter (often referred to as mineral-associated organic matter or MAOM) form a large pool of slowly cycling carbon (C). The rhizosphere, soil immediately adjacent to roots, is thought to control the spatial extent of MAOM formation because it is the dominant entry point of new C inputs to soil. However, emphasis on the rhizosphere implicitly assumes that microbial redistribution of C into bulk (non-rhizosphere) soils is minimal. We question this assumption, arguing that because of extensive fungal exploration and rapid hyphal turnover, fungal redistribution of soil C from the rhizosphere to bulk soil minerals is common, and encourages MAOM formation. First, we summarize published estimates of fungal hyphal length density and turnover rates and demonstrate that fungal C inputs are high throughout the rhizosphere-bulk soil continuum. Second, because colonization of hyphal surfaces is a common dispersal mechanism for soil bacteria, we argue that hyphal exploration allows for the non-random colonization of mineral surfaces by hyphae-associated taxa. Third, these bacterial communities and their fungal hosts determine the chemical form of organic matter deposited on colonized mineral surfaces. Collectively, our analysis demonstrates that omission of the hyphosphere from conceptual models of soil C flow overlooks key mechanisms for MAOM formation in bulk soils. Moving forward, there is a clear need for spatially explicit, quantitative research characterizing the environmental drivers of hyphal exploration and hyphosphere community composition across systems, as these are important controls over the rate and organic chemistry of C deposited on minerals.

Functional group diversity for the adsorption of lead(Pb) to bacterial cells and extracellular polymeric substances

Bacteria and their secreted extracellular polymeric substances (EPS) are widely distributed in ecosystems and have high capacity for heavy metal immobilization. The knowledge about the molecular-level interactions with heavy metal ions is essential for predicting the behavior of heavy metals in natural and engineering systems. This comprehensive study using potentiometric titration, Fourier-transform infrared (FTIR) spectroscopy, isothermal titration calorimetry (ITC) and X-ray absorption fine structure (XAFS) was able to reveal the functional diversity and adsorption mechanisms for Pb onto bacteira and the EPS in greater detail than ever before. We identified mono-carboxylic, multi-carboxylic, phosphodiester, phosphonic and sulfhydryl sites and found the partitioning of Pb to these functional groups varied between gram-negative and gram-positive bacterial strains, the soluble and cell-bound EPS and Pb concentrations. The sulfhydryl and phosphodiester groups preferentially complexed with Pb in P. putida cells, while multifunctional carboxylic groups promoted Pb adsorption in B. subtilis cells and the protein fractions in EPS. Though the functional site diversity, the adsorption of Pb to organic ligands occurred spontaneously through a universal entropy increase and inner-sphere complexation mechanism. The functional group scale knowledge have implications for the modeling of heavy metal behavior in the environment and application of these biological resources.

Effect of high soil C/N ratio and nitrogen limitation caused by the long-term combined organic-inorganic fertilization on the soil microbial community structure and its dominated SOC decomposition

The application of organic fertilizers, such as straw and manure, is an efficient approach to maintain soil productivity. However, the effect of these organic fertilizers on soil microbial nutrient balance has not yet been established. In this study, the effects of the long-term combined organic-inorganic fertilization on microbial community were investigated by conducting a 30-year-long field test. Overall, the following five fertilizer groups were employed: inorganic NP fertilizer (NP), inorganic NK fertilizer (NK), inorganic NPK fertilizer (NPK), NPK + manure (MNPK), and NPK + straw (SNPK). The results indicated that the mean natural logarithm of the soil C:N:P acquisition enzyme ratio was 1.04:1.11:1.00 under organic-inorganic treatments, which showed a deviation from its overall mean ratio of 1:1:1. This indicates that microbial resources do not have a balance. Vector analysis (vector angle <45°) and threshold elemental ratio analysis (R_C:N-TER_C:N > 0) further demonstrated that the microbial metabolism was limited by Nitrogen (N) under SNPK and MNPK treatments. N limitation further influenced soil microbial community structure and its dominated SOC decomposition. Specifically, Microbial communities transformed into a more oligotrophic-dominant condition (fungal, Acidobacteria, Chloroflexi) from copiotrophic-dominant (Proteobacteria, Actinobacteria) condition with increasing N limitation. Lysobacter genus and Blastocatellaceae family, in the bacterial communities along with the Mortierella elongata species in fungal communities, were markedly associated with the N limitation, which could be the critical biomarker that represented N limitation. Both correlation analysis and partial least squares path modeling showed significant positive effects of N limitation on the ratio of bacterial functional genes (Cellulase/Amylase), involved in recalcitrant SOC degradation.

Increased microbial expression of organic nitrogen cycling genes in long-term warmed grassland soils

Global warming increases soil temperatures and promotes faster growth and turnover of soil microbial communities. As microbial cell walls contain a high proportion of organic nitrogen, a higher turnover rate of microbes should also be reflected in an accelerated organic nitrogen cycling in soil. We used a metatranscriptomics and metagenomics approach to demonstrate that the relative transcription level of genes encoding enzymes involved in the extracellular depolymerization of high-molecular-weight organic nitrogen was higher in medium-term (8 years) and long-term (>50 years) warmed soils than in ambient soils. This was mainly driven by increased levels of transcripts coding for enzymes involved in the degradation of microbial cell walls and proteins. Additionally, higher transcription levels for chitin, nucleic acid, and peptidoglycan degrading enzymes were found in long-term warmed soils. We conclude that an acceleration in microbial turnover under warming is coupled to higher investments in N acquisition enzymes, particularly those involved in the breakdown and recycling of microbial residues, in comparison with ambient conditions.

Site and Bioenergy Cropping System Similarly Affect Distinct Live and Total Soil Microbial Communities

Bioenergy crops are a promising energy alternative to fossil fuels. During bioenergy feedstock production, crop inputs shape the composition of soil microbial communities, which in turn influences nutrient cycling and plant productivity. In addition to cropping inputs, site characteristics (e.g., soil texture, climate) influence bacterial and fungal communities. We explored the response of soil microorganisms to bioenergy cropping system (switchgrass vs. maize) and site (sandy loam vs. silty loam) within two long-term experimental research stations. The live and total microbial community membership was investigated using 16S and ITS amplicon sequencing of soil RNA and DNA. For both nucleic acid types, we expected fungi and prokaryotes to be differentially impacted by crop and site due their dissimilar life strategies. We also expected live communities to be more strongly affected by site and crop than the total communities due to a sensitivity to recent stimuli. Instead, we found that prokaryotic and fungal community composition was primarily driven by site with a secondary crop effect, highlighting the importance of soil texture and fertility in shaping both communities. Specific highly abundant prokaryotic and fungal taxa within live communities were indicative of site and cropping systems, providing insight into treatment-specific, agriculturally relevant microbial taxa that were obscured within total community profiles. Within live prokaryote communities, predatory Myxobacteria spp. were largely indicative of silty and switchgrass communities. Within live fungal communities, Glomeromycota spp. were solely indicative of switchgrass soils, while a few very abundant Mortierellomycota spp. were indicative of silty soils. Site and cropping system had distinct effects on the live and total communities reflecting selection forces of plant inputs and environmental conditions over time. Comparisons between RNA and DNA communities uncovered live members obscured within the total community as well as members of the relic DNA pool. The associations between live communities and relic DNA are a product of the intimate relationship between the ephemeral responses of the live community and the accumulation of DNA within necromass that contributes to soil organic matter, and in turn shapes soil microbial dynamics.

The exposome paradigm to predict environmental health in terms of systemic homeostasis and resource balance based on NMR data science

The environment, from microbial ecosystems to recycled resources, fluctuates dynamically due to many physical, chemical and biological factors, the profile of which reflects changes in overall state, such as environmental illness caused by a collapse of homeostasis. To evaluate and predict environmental health in terms of systemic homeostasis and resource balance, a comprehensive understanding of these factors requires an approach based on the "exposome paradigm", namely the totality of exposure to all substances. Furthermore, in considering sustainable development to meet global population growth, it is important to gain an understanding of both the circulation of biological resources and waste recycling in human society. From this perspective, natural environment, agriculture, aquaculture, wastewater treatment in industry, biomass degradation and biodegradable materials design are at the forefront of current research. In this respect, nuclear magnetic resonance (NMR) offers tremendous advantages in the analysis of samples of molecular complexity, such as crude bio-extracts, intact cells and tissues, fibres, foods, feeds, fertilizers and environmental samples. Here we outline examples to promote an understanding of recent applications of solution-state, solid-state, time-domain NMR and magnetic resonance imaging (MRI) to the complex evaluation of organisms, materials and the environment. We also describe useful databases and informatics tools, as well as machine learning techniques for NMR analysis, demonstrating that NMR data science can be used to evaluate the exposome in both the natural environment and human society towards a sustainable future.

Decomposition of Microbial Necromass Is Divergent at the Individual Taxonomic Level in Soil

The turnover of microbial biomass plays an important part in providing a significant source of carbon (C) to soil organic C. However, whether the decomposition of microbial necromass (non-living microbial biomass) in the soil varies at the individual taxa level remains largely unknown. To fill up these gaps, we compared the necromass decomposition of bacterial and archaeal taxa by separating live microbial biomass with 18O-stable isotope probing from dead microbial biomass in soil. Our results showed that most of the microbial necromass at the operational taxonomic unit level (88.51%), which mainly belong to Acidobacteria, Actinobacteria, Gemmatimonadetes, and Proteobacteria, decomposed significantly after 30 days. In addition, there were great variations in necromass decomposition within each phylum, such as the decomposition of operational taxonomic units in Proteobacteria that ranged from 51% (Beijerinckia) to 92% (Nitrosospira). More importantly, the necromass decomposition was not related to the chemical composition of the cell wall but might positively correlate with the guanine-cytosine content of DNA and negatively correlated with genome size. This study provided a new insight that the decomposition of microbial necromass in soil was divergent at the individual taxonomic level and could not be fully explained by previously proposed mechanisms.

Contrasting pathways of carbon sequestration in paddy and upland soils

Paddy soils make up the largest anthropogenic wetlands on earth, and are characterized by a prominent potential for organic carbon (C) sequestration. By quantifying the plant- and microbial-derived C in soils across four climate zones, we identified that organic C accrual is achieved via contrasting pathways in paddy and upland soils. Paddies are 39%-127% more efficient in soil organic C (SOC) sequestration than their adjacent upland counterparts, with greater differences in warmer than cooler climates. Upland soils are more replenished by microbial-derived C, whereas paddy soils are enriched with a greater proportion of plant-derived C, because of the retarded microbial decomposition under anaerobic conditions induced by the flooding of paddies. Under both land-use types, the maximal contribution of plant residues to SOC is at intermediate mean annual temperature (15-20°C), neutral soil (pH~7.3), and low clay/sand ratio. By contrast, high temperature (~24°C), low soil pH (~5), and large clay/sand ratio are favorable for strengthening the contribution of microbial necromass. The greater contribution of microbial necromass to SOC in waterlogged paddies in warmer climates is likely due to the fast anabolism from bacteria, whereas fungi are unlikely to be involved as they are aerobic. In the scenario of land-use conversion from paddy to upland, a total of 504 Tg C may be lost as CO2 from paddy soils (0-15 cm) solely in eastern China, with 90% released from the less protected plant-derived C. Hence, preserving paddy systems and other anthropogenic wetlands and increasing their C storage through sustainable management are critical for maintaining global soil C stock and mitigating climate change.

Large-scale importance of microbial carbon use efficiency and necromass to soil organic carbon

Optimal methods for incorporating soil microbial mechanisms of carbon (C) cycling into Earth system models (ESMs) are still under debate. Specifically, whether soil microbial physiology parameters and residual materials are important to soil organic C (SOC) content is still unclear. Here, we explored the effects of biotic and abiotic factors on SOC content based on a survey of soils from 16 locations along a ~4000 km forest transect in eastern China, spanning a wide range of climate, soil conditions, and microbial communities. We found that SOC was highly correlated with soil microbial biomass C (MBC) and amino sugar (AS) concentration, an index of microbial necromass. Microbial C use efficiency (CUE) was significantly related to the variations in SOC along this national-scale transect. Furthermore, the effect of climatic and edaphic factors on SOC was mainly via their regulation on microbial physiological properties (CUE and MBC). We also found that regression models on explanation of SOC variations with microbial physiological parameters and AS performed better than the models without them. Our results provide the empirical linkages among climate, microbial characteristics, and SOC content at large scale and confirm the necessity of incorporating microbial biomass and necromass pools in ESMs under global change scenarios.

The role of interfacial reactions in controlling the distribution of Cd within goethite-humic acid-bacteria composites

Mineral-organic interfacial reactions strongly influence the adsorption, distribution and bioavailability of metal cations in soil systems. The molecular binding mechanisms and distribution of Cd onto goethite, humic acid, Pseudomonas putida cells, and their composites at different mass ratios were studied through the combination of bulk adsorption coupled with EXAFS, ITC and SCM. In binary and ternary composites, the energetics of the overall adsorption of Cd was dominated by the entropy of Cd adsorption onto the organic fraction. The formation of a type-B HA bridging complex >FeOH-HACOOCdOH enhanced Cd adsorption by 10-30% at low Cd concentrations, and more than 93.5% of the adsorbed Cd was bound onto HA fraction. In ternary systems, the component additivity over-estimated Cd adsorption onto bacteria by ~21.8%, likely due to site blocking effects. Models involving the masking of phosphoryl sites and HA bridging reactions can simulate the distribution of Cd in the composites. Our modelling suggests that HA is the main scavenger of Cd under a range of environmental conditions, and that bacteria become important in affecting the distribution of Cd under lower pH settings. This study demonstrates the impact of iron oxide-HA-bacteria interactions on the fate and distribution of Cd in soils and associated environments.

Nitrogen Deposition Reduces the Diversity and Abundance of cbbL Gene-Containing CO2-Fixing Microorganisms in the Soil of the Stipa baicalensis Steppe

CO₂ fixation by autotrophic microbes has a significant effect on the carbon cycle in temperate grasslands. Nitrogen (N) deposition in soil has been steadily increasing for decades, which has consequences for soil microorganisms. However, the impact of this deposition on the diversity and abundance of CO₂-fixing soil microorganisms remains unclear in temperate grasslands. In the present study, the cbbL gene, a key gene in the Calvin–Benson–Bassham cycle that encodes the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase, was used to study CO₂-fixing microbes under different rates of N addition (0, 15, 30, 50, 100, and 150 kg N ha^–1 yr^–1) in a 9-year field experiment in a temperate grassland. The results showed that N addition led to significant reductions in cbbL gene abundance and genetic diversity and altered cbbL gene community composition. High N addition enhanced the relative abundances of Acidiferrobacterales and Rhizobiales but reduced those of Burkholderiales and Rhodobacterales. Structural equation modeling further revealed that N addition primarily reduced cbbL genetic diversity by increasing the soil NO₃-N content and decreasing the soil pH. N addition indirectly reduced cbbL gene abundance, possibly by increasing the soil N/phosphorus (P) ratio and decreasing the soil pH. These findings suggest that N addition increases the soil available N and causes soil acidification, which may inhibit growth of CO₂-fixing microbes to some extent.

Application of Fourier transform ion cyclotron resonance mass spectrometry in deciphering molecular composition of soil organic matter: A review

Swiftly deciphering soil organic matter (SOM) composition is critical for research on soil degradation and restoration. Recent advances in analytical techniques (e.g., optical methods and mass spectrometry) have expanded our understanding of the composition, origin, and evolution of SOM. In particular, the use of Fourier transform ion cyclotron resonance mass spectrometers (FTICR-MS) makes it possible to interpret SOM compositions at the molecular level. In this review, we discuss extraction, enrichment, and purification methods for SOM using FTICR-MS analysis; summarize ionization techniques, FTICR-MS mechanisms, data analysis methods, and molecular compositions of SOM in different environments (providing new insights into its origin and evolution); and discuss factors affecting its molecular diversity. Our results show that digenesis, combustion, pyrolysis, and biological metabolisms jointly contribute to the molecular diversity of SOM molecules. The SOM thus formed can further undergo photodegradation during transportation from land to fresh water (and subsequently oceans), resulting in the formation of dissolved organic matter (DOM). Better understanding the molecular features of DOM therefore accelerates our understanding of SOM evolution. In addition, we assess the degradation potential of SOM in different environments to better inform soil remediation methods. Finally, we discuss the merits and drawbacks of applying FTICR-MS on the analysis of SOM molecules, along with existing gaps in knowledge, challenges, and new opportunities for research in FTICR-MS applications and SOM identification.

Intercropping Alters the Soil Microbial Diversity and Community to Facilitate Nitrogen Assimilation: A Potential Mechanism for Increasing Proso Millet Grain Yield

Intercropping of cereals and legumes has been used in modern agricultural systems, and the soil microorganisms associated with legumes play a vital role in organic matter decomposition and nitrogen (N) fixation. This study investigated the effect of intercropping on the rhizosphere soil microbial composition and structure and how this interaction affects N absorption and utilization by plants to improve crop productivity. Experiments were conducted to analyze the rhizosphere soil microbial diversity and the relationship between microbial composition and N assimilation by proso millet (Panicum miliaceum L.) and mung bean (Vigna radiata L.) from 2017 to 2019. Four different intercropping row arrangements were evaluated, and individual plantings of proso millet and mung bean were used as controls. Microbial diversity and community composition were determined through Illumina sequencing of 16S rRNA and internal transcribed spacer (ITS) genes. The results indicated that intercropping increased N levels in the soil-plant system and this alteration was strongly dependent on changes in the microbial (bacterial and fungal) diversities and communities. The increase in bacterial alpha diversity and changes in unique operational taxonomic unit (OTU) numbers increased the soil N availability and plant N accumulation. Certain bacterial taxa (such as Proteobacteria) and fungal taxa (such as Ascomycota) were significantly altered under intercropping and showed positive responses to increased N assimilation. The average grain yield of intercropped proso millet increased by 13.9-50.1% compared to that of monoculture proso millet. Our data clearly showed that intercropping proso millet with mung bean altered the rhizosphere soil microbial diversity and community composition; thus, this intercropping system represents a potential mechanism for promoting N assimilation and increasing grain yield.

PFAS and Dissolved Organic Carbon Enrichment in Surface Water Foams on a Northern U.S. Freshwater Lake

Information is needed on the concentration of per- and polyfluoroalkyl substances (PFAS) in foams on surface waters impacted by aqueous film-forming foam (AFFF). Nine pairs of foam and underlying bulk water were collected from a single freshwater lake impacted by PFAS and analyzed for PFAS by liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QToF) and for dissolved organic carbon (DOC). The DOC of two foam:bulk water pairs was characterized by ¹H NMR. Foams were comprised of 16 PFAS with concentrations as high as 97 000 ng/L (PFOS) along with longer-chain, more hydrophobic PFAS. Only five PFAS (PFOS and shorter chain lengths) were quantified in underlying bulk waters. Enrichment factors (foam:bulk water) ranged from 10 (PFHxA) up to 2830 (PFOS). Foams impacted by AFFF gave the greatest concentrations and number of PFAS classes with PFOS concentrations exceeding the EPA health advisory level (70 ng/L). PFAS concentrations were significantly below published critical micelle concentrations and constituted <0.1% of overall DOC concentrations in foam, indicating that PFAS are a minor fraction of DOC and that DOC likely plays a central role in foam formation. Estimates indicate that foam ingestion is a potentially important route of exposure for children and adults when they are in surface waters where foam is present.

Tracing bacterial and fungal necromass dynamics of municipal sludge in landfill bioreactors using biomarker amino sugars

The dynamics of microbial necromass of municipal solid waste over long-term landfill remain unknown. This study presents the first investigation on the dynamics of bacterial and fungal necromass of municipal sludge in non-aeration versus alternating aeration landfill bioreactors by using amino sugar biomarkers. Results showed that under non-aeration treatment, the decomposition rate of muramic acid derived from bacteria is higher than that of fungal-derived glucosamine. The relative change in glucosamine and muramic acid in the early period of landfills under the alternating aeration treatment is consistent with that under non-aeration treatment. However, with the increase in alternating aeration cycles, bacterial necromass muramic acid exerts a lower decomposition rate than fungal necromass glucosamine. Throughout the entire landfill period, galactosamine is the amino sugar with the slowest decomposition rate under non-aeration mode but the amino sugar with the fastest decomposition rate under alternating aeration mode. The present work fills the knowledge gap of microbial necromass dynamics of municipal solid waste in landfills.

Metagenomic and 14 C tracing evidence for autotrophic microbial CO2 fixation in paddy soils

Autotrophic carbon dioxide (CO₂ ) fixation by microbes is ubiquitous in the environment and potentially contributes to the soil organic carbon (SOC) pool. However, the multiple autotrophic pathways of microbial carbon assimilation and fixation in paddy soils remain poorly characterized. In this study, we combine metagenomic analysis with ¹⁴ C-labelling to investigate all known autotrophic pathways and CO₂ assimilation mechanisms in five typical paddy soils from southern China. Marker genes of six autotrophic pathways are detected in all soil samples, which are dominated by the cbbL genes (67%-82%) coding the ribulose-bisphosphate carboxylase large chain in the Calvin cycle. These marker genes are associated with a broad range of phototrophic and chemotrophic genera. Significant amounts of ¹⁴ C-CO₂ are assimilated into SOC (74.3-175.8 mg ¹⁴ C kg^-1 ) and microbial biomass (5.2-24.1 mg ¹⁴ C kg^-1 ) after 45 days incubation, where more than 70% of ¹⁴ C-SOC was concentrated in the relatively stable humin fractions. These results show that paddy soil microbes contain the genetic potential for autotrophic carbon fixation spreading over broad taxonomic ranges, and can incorporate atmospheric carbon into organic components, which ultimately contribute to the stable SOC pool.

Elevated temperature increases the accumulation of microbial necromass nitrogen in soil via increasing microbial turnover

Microbial-derived nitrogen (N) is now recognized as an important source of soil organic N. However, the mechanisms that govern the production of microbial necromass N, its turnover, and stabilization in soil remain poorly understood. To assess the effects of elevated temperature on bacterial and fungal necromass N production, turnover, and stabilization, we incubated ¹⁵ N-labeled bacterial and fungal necromass under optimum moisture conditions at 10°C, 15°C, and 25°C. We developed a new ¹⁵ N tracing model to calculate the production and mineralization rates of necromass N. Our results showed that bacterial and fungal necromass N had similar mineralization rates, despite their contrasting chemistry. Most bacterial and fungal necromass ¹⁵ N was recovered in the mineral-associated organic matter fraction through microbial anabolism, suggesting that mineral association plays an important role in stabilizing necromass N in soil, independently of necromass chemistry. Elevated temperature significantly increased the accumulation of necromass N in soil, due to the relatively higher microbial turnover and production of necromass N with increasing temperature than the increases in microbial necromass N mineralization. In conclusion, we found elevated temperature may increase the contribution of microbial necromass N to mineral-stabilized soil organic N.

Increasing the organic carbon stocks in mineral soils sequesters large amounts of phosphorus

Despite the fact that phosphorus (P) is critical for plant biomass production in many ecosystems, the implications of soil organic carbon (OC) sequestration for the P cycle have hardly been discussed yet. Thus, the aims of this study are, first, to synthesize results about the relationship between C and P in soil organic matter (SOM) and organic matter inputs to soils, second, to review processes that affect the C:P ratio of SOM, and third, to discuss implications of OC storage in terrestrial ecosystems for P sequestration. The study shows that the storage of OC in mineral soils leads to the sequestration of large amounts of organic phosphorus (OP) since SOM in mineral soils is very rich in P. The reasons for the strong enrichment of OP with respect to OC in soils are the mineralization of OC and the formation of microbial necromass that is P-rich as well as the strong sorption of OP to mineral surfaces that prevents OP mineralization. In particular, the formation of mineral-associated SOM that is favorable for storing OC in soil over decadal to centennial timescales sequesters large amounts of OP. Storage of 1,000 kg C in the clay size fraction in the topsoils of croplands sequesters 13.1 kg P. In contrast, the OC:OP ratios of wood and of peatlands are much larger than the ones in cropland soils. Thus, storage of C in wood in peatlands sequesters much less P than the storage of OC in mineral soils. In order to increase the C stocks in terrestrial ecosystems and to lock up as little P as possible, it would be more reasonable to protect and restore peatlands and to produce and preserve wood than to store OC in mineral soils.

A continental scale spatial investigation of lake sediment organic compositions using sedimentomics

Sedimentomics is a new method used to investigate carbon cycling in sediment organic matter. This untargeted method, based on metabolomics workflows, was used to investigate the molecular composition of sediment organic matter across northern Canada (Nunavut and Northwest Territories). Unique "lake districts" were defined using unsupervised clustering based on changes in sediment organic carbon compositions across space. Supervised machine learning analyses were used to compare the "lake districts" to commonly used regional classification systems like the treeline, ecozones, and/or georegions. Treeline was the best model to explain the compositional variance of sediment organic carbon from lakes across Canada, closely followed by the georegions model. A novel sediment metaphenomics analysis was also applied to determine how well environmental constraints explain the variation of sediment organic matter composition across a continent. We determined that sedimentomics is more informative than traditional measurements (such as total organic carbon) and can be integrated with other "omics" techniques.

Conversion behaviors of litter-derived organic carbon of two halophytes in soil and their influence on SOC stabilization of wetland in the Yangtze River Estuary

Soil organic carbon (SOC) is both a product and a cause of soil development. Previous studies found that less carbon (C) is fixed by Phragmites communis than Spartina alterniflora in the Jiuduansha wetland of the Yangtze River Estuary. However, the P. communis zone presented higher contents of SOC and humus, which was mainly related to lower soil respiration (SR). It is not well known how different plants affect turnover of original SOC in the Jiuduansha wetland, and thus soil development and tidal flat evolution. In this study, in-field surveys and microcosm experiments were conducted to trace turnover of plant C and evaluate dynamics of SOC using stable C isotopic techniques. Spartina alterniflora decayed faster than P. communis, and more of its derived OC was lost through SR and leaching. Although S. alterniflora-derived OC suppressed the degradation of original SOC, it was consumed to a greater extent, making less supplementation to SOC. Phragmites communis-derived OC showed less degradability and accelerated the degradation of original SOC, but was more incorporated into new SOC and finally caused higher increase in SOC, specifically in bare tidal flat soil with poor original SOC. Overall, compared with S. alterniflora, P. communis-derived OC more effectively replaced the unstable original SOC, thereby improving the content and stability of SOC, especially for soil in early-development stages of tidal flats.