Significant release and microbial utilization of amino sugars and D-amino acid enantiomers from microbial cell wall decomposition in soils

Microbial degradation and pollutant control in aerobic composting and anaerobic digestion of organic wastes: A review

Aerobic composting (AC) and anaerobic digestion (AD) are promising technologies for organic waste treatment, but their efficiency and safety are influenced by complex waste composition and persistent contaminants. This review identifies the advances in understanding microbial community dynamics, enzymatic degradation pathways, and the fate of contaminants during AC and AD processes. The findings indicate that substrate composition shapes dominant microbial populations and their degradative enzymes, with this correlation potentially useful for predicting functional microbial communities. Additionally, AC shows advantages in antibiotic elimination while AD excels in heavy metal immobilization, with both contributing to removing certain antibiotic resistance genes (ARGs). The strategic manipulation of environmental conditions, particularly temperature and oxygen levels, can drive microbial succession to optimize organic matter decomposition while minimizing ARG proliferation. Economic analyses reveal that AC offers lower operational costs and AD generates valuable by-products with potential energy recovery from organic waste. Case studies indicate that integrating both technologies can overcome individual limitations and enhance degradation efficiency compared to conventional single-technology approaches. This work proposes a comprehensive framework for developing coupled AC-AD systems to achieve more efficient and safer organic waste valorization than conventional single-technology approaches. This review has important implications for advancing sustainable waste management practices and mitigating the spread of antibiotic resistance in the environment.

A review on amino acids as proxies for organic matter degradation in aquatic ecosystems: implications for nutrient cycling, climate change, and ecosystem management

The fate and degradation of organic matter in aquatic systems is a vital link in nutrient cycling and sedimentation processes influenced by exogenous and endogenous factors, such as inputs from upstream sources, sediment suspension, and the decomposition of aquatic organisms. The interplay of organic carbon, microbes, and environmental factors shapes the distribution and degradation of organic matter. Characterizing the source distribution of sedimentary organic matter in aquatic systems using novel proxies can unravel new insights into the mechanisms that control its dispersal, preservation and fate, which is essential to understanding the global carbon and nitrogen cycles. Therefore, the present review critically investigated amino acids as crucial markers for assessing the degradation status in lacustrine and marine sediments and highlighted the pivotal function of biotic and abiotic determinants that influence the mineralization of organic matter. The review thoroughly discussed studies on the spatio-temporal distribution patterns of amino acids and their bio-refractory nature to overcome the challenges in evaluating sediment organic matter degradation in aquatic systems. Recognizing the paramount impact of climate change on aquatic ecosystems, the review further elucidated how integrating amino acid-based data into climate models is essential for predicting complex interplay between degradation processes and evolving environmental dynamics. Finally, the specific needs for further research and recommendations for developing efficient and sustainable strategies to study organic matter degradation were highlighted. The present review will deliver fresh inferences to researchers, ecologists, and policymakers for a better understanding of source distribution and degradation status of organic matter for evidence-based conservation and management strategies.

Unraveling the influence of microbial necromass on subsurface microbiomes: metabolite utilization and community dynamics

The role of microbial necromass (nonliving microbial biomass), a significant component of belowground organic carbon, in nutrient cycling and its impact on the dynamics of microbial communities in subsurface systems remains poorly understood. It is currently unclear whether necromass metabolites from various microbes are different, whether certain groups of metabolites are preferentially utilized over others, or whether different microbial species respond to various necromass metabolites. In this study, we aimed to fill these knowledge gaps by designing enrichments with necromass as the sole nutrient source for subsurface microbial communities. We used the soluble fraction of necromass from bacterial isolates belonging to Arthrobacter, Agrobacterium, and Pseudomonas genera, and our results indicate that metabolite composition of necromass varied slightly across different strains but generally included amino acids, organic acids, and nucleic acid constituents. Arthrobacter-derived necromass appeared more recalcitrant. Necromass metabolites enriched diverse microbial genera, particularly Massilia sp. responded quickly regardless of the necromass source. Despite differences in necromass utilization, microbial community composition converged rapidly over time across the three different necromass amendments. Uracil, xanthine, valine, and phosphate-containing isomers were generally depleted over time, indicating microbial assimilation for maintenance and growth. However, numerous easily assimilable metabolites were not significantly depleted, suggesting efficient necromass recycling and the potential for necromass stabilization in systems. This study highlights the dynamic interactions between microbial necromass metabolites and subsurface microbial communities, revealing both selective utilization and rapid community and necromass convergence regardless of the necromass source.

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.

Bioenergetic mapping of 'healthy microbiomes' via compound processing potential imprinted in gut and soil metagenomes

Despite mounting evidence of their importance in human health and ecosystem functioning, the definition and measurement of 'healthy microbiomes' remain unclear. More advanced knowledge exists on health associations for compounds used or produced by microbes. Environmental microbiome exposures (especially via soils) also help shape, and may supplement, the functional capacity of human microbiomes. Given the synchronous interaction between microbes, their feedstocks, and micro-environments, with functional genes facilitating chemical transformations, our objective was to examine microbiomes in terms of their capacity to process compounds relevant to human health. Here we integrate functional genomics and biochemistry frameworks to derive new quantitative measures of in silico potential for human gut and environmental soil metagenomes to process a panel of major compound classes (e.g., lipids, carbohydrates) and selected biomolecules (e.g., vitamins, short-chain fatty acids) linked to human health. Metagenome functional potential profile data were translated into a universal compound mapping 'landscape' based on bioenergetic van Krevelen mapping of function-level meta-compounds and corresponding functional relative abundances, reflecting imprinted genetic capacity of microbiomes to metabolize an array of different compounds. We show that measures of 'compound processing potential' associated with human health and disease (examining atherosclerotic cardiovascular disease, colorectal cancer, type 2 diabetes and anxious-depressive behavior case studies), and displayed seemingly predictable shifts along gradients of ecological disturbance in plant-soil ecosystems (three case studies). Ecosystem quality explained 60-92 % of variation in soil metagenome compound processing potential measures in a post-mining restoration case study dataset. With growing knowledge of the varying proficiency of environmental microbiota to process human health associated compounds, we might design environmental interventions or nature prescriptions to modulate our exposures, thereby advancing microbiota-oriented approaches to human health. Compound processing potential offers a simplified, integrative approach for applying metagenomics in ongoing efforts to understand and quantify the role of microbiota in environmental- and human-health.

Reevaluation and novel insights into amino sugar and neutral sugar necromass biomarkers in archaea, bacteria, fungi, and plants

Soil microbial necromass is an important contributor to soil organic matter (>50%) and it is largely composed of microbial residues. In soils, fragmented cell wall residues are mostly found in their polysaccharide forms of fungal chitin and bacterial peptidoglycan. Microbial necromass biomarkers, particularly amino sugars (AS) such as glucosamine (GlcN) and muramic acid (MurA) have been used to trace fungal and bacterial residues in soils, and to distinguish carbon (C) found in microbial residues from non-microbial organic C. Neutral sugars (NS), particularly the hexose/pentose ratio, have also been proposed as tracers of plant polysaccharides in soils. In our study, we extended the range of biomarkers to include AS and NS compounds in the biomass of 120 species belonging to archaea, bacteria, fungi, or plants. GlcN was the most common AS found in all taxa, contributing 42-91% to total AS content, while glucose was the most common NS found, contributing 56-79% to total NS. We identified talosaminuronic acid, found in archaeal pseudopeptidoglycan, as a new potential biomarker specific for Euryarchaeota. We compared the variability of these compounds between the different taxonomic groups using multivariate approaches, such as non-metric multidimensional scaling (NMDS) and partial least squares discriminant analysis (PLS-DA) and statistically evaluated their biomarker potential via indicator species analysis. Both NMDS and PLS-DA showcased the variability in the AS and NS contents between the different taxonomic groups, highlighting their potential as necromass residue biomarkers and allowing their extension from separating bacterial and fungal necromass to separating microbes from plants. Finally, we estimated new conversion factors where fungal GlcN is converted to fungal C by multiplying by 10 and MurA is converted to bacterial C by multiplying by 54. Conversion factors for talosaminuronic acid and galactosamine are also proposed to allow estimation of archaeal or all-microbial necromass residue C, respectively.

Cooperative microbial interactions drive spatial segregation in porous environments

The role of microbial interactions and the underlying mechanisms that shape complex biofilm communities are poorly understood. Here we employ a microfluidic chip to represent porous subsurface environments and show that cooperative microbial interactions between free-living and biofilm-forming bacteria trigger active spatial segregation to promote their respective dominance in segregated microhabitats. During initial colonization, free-living and biofilm-forming microbes are segregated from the mixed planktonic inoculum to occupy the ambient fluid and grain surface. Contrary to spatial exclusion through competition, the active spatial segregation is induced by cooperative interactions which improves the fitness of both biofilm and planktonic populations. We further show that free-living Arthrobacter induces the surface colonization by scavenging the biofilm inhibitor, D-amino acids and receives benefits from the public goods secreted by the biofilm-forming strains. Collectively, our results reveal how cooperative microbial interactions may contribute to microbial coexistence in segregated microhabitats and drive subsurface biofilm community succession.

Long-term nitrogen fertilization-induced enhancements of acid hydrolyzable nitrogen are mainly regulated by the most vital microbial taxa of keystone species and enzyme activities

It is well known that nitrogen (N) fertilizer input is required to improve crop productivity, but we lack a comprehensive understanding of how elevated N input changes the formation of soil acid hydrolyzable nitrogen (AHN) by adjusting the most vital microbial taxa of keystone species of microbial communities and enzyme activities. A 15-year field experiment comprising four levels of inorganic N fertilization was conducted to identify the most important bacterial and fungal taxa of the keystone species derived from cooccurrence networks as well as the vital enzyme activities at the bell mouth and maturity stages. Long-term N fertilization significantly increased the levels of AHN along with its four fractions, including amino acid N (AAN), ammonium N (AN), amino sugar N (ASN), and hydrolysable unidentified N (HUN), by 30.1-118.6 %, regardless of growth stage. Some most vital microbial taxa of keystone species and enzyme activities, which changed in response to N fertilization, mainly regulated each ANH fraction, that is, AHN and AN were mainly controlled by the enrichment of Nocardioides and β-1,4-N-acetyl-glucosaminidase (NAG), as well as by the reduction of Anaerolinea and urease (UR), AAN was determined by the enrichment of Hannaella and depletion of Penicillium, ASN was regulated by the enrichment of Hannaella and Arthrobacter, and HUN was influenced by the reduction of Penicillium and enrichment of Nitrosospira. These microbial genera have been found to be involved in dissimilatory nitrate reduction to ammonium (DNRA) and nitrification/denitrification processes and the two enzyme activities involved in organic N degradation and N-releasing processes, suggesting that the formation of AHN fractions was closely associated with specific functional microbial taxa and enzyme activities induced by N fertilization. Our results provide new insights into the associations among increased N input, altered formation of soil organic N, and shifts in microbial communities and enzyme activities.

Microbial Exopolysaccharide Composites in Biomedicine and Healthcare: Trends and Advances

Microbial exopolysaccharides (EPSs), e.g., xanthan, dextran, gellan, curdlan, etc., have significant applications in several industries (pharma, food, textiles, petroleum, etc.) due to their biocompatibility, nontoxicity, and functional characteristics. However, biodegradability, poor cell adhesion, mineralization, and lower enzyme activity are some other factors that might hinder commercial applications in healthcare practices. Some EPSs lack biological activities that make them prone to degradation in ex vivo, as well as in vivo environments. The blending of EPSs with other natural and synthetic polymers can improve the structural, functional, and physiological characteristics, and make the composites suitable for a diverse range of applications. In comparison to EPS, composites have more mechanical strength, porosity, and stress-bearing capacity, along with a higher cell adhesion rate, and mineralization that is required for tissue engineering. Composites have a better possibility for biomedical and healthcare applications and are used for 2D and 3D scaffold fabrication, drug carrying and delivery, wound healing, tissue regeneration, and engineering. However, the commercialization of these products still needs in-depth research, considering commercial aspects such as stability within ex vivo and in vivo environments, the presence of biological fluids and enzymes, degradation profile, and interaction within living systems. The opportunities and potential applications are diverse, but more elaborative research is needed to address the challenges. In the current article, efforts have been made to summarize the recent advancements in applications of exopolysaccharide composites with natural and synthetic components, with special consideration of pharma and healthcare applications.

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.

Rapid, sensitive analysis method for determining the nitrogen stable isotope ratio of total free amino acids in soil

RATIONALE

The amino acid-nitrogen (AA-N) isotope analysis of naturally abundant or isotope-labeled samples is indispensable for tracing nitrogen transfer in soil nitrogen biogeochemical cycling processes. Despite the usefulness of AA-N isotope analysis, the preparation methods are complex and time-consuming, and necessitate the use of toxic reagents.

METHODS

We present an improved, rapid method for AA-N isotope analysis with high precision. At a high pH, AA-N was released and oxidized to N₂ O using ClO^- under vacuum. Additionally, purge-and-trap isotope ratio mass spectrometry was used to analyze N₂ O. Moreover, we investigated the effect of various factors on the N₂ O conversion process with glycine and applied the results to seven representative single-N AAs (alanine, serine, cysteine, aspartic acid, glutamic acid, leucine, and phenylalanine) and five poly-N AAs (lysine, arginine, histidine, tryptophan, and asparagine), as well as side-chain analogs, blank reagent, and other N forms.

RESULTS

The concentration of ClO^- and the pH were determined to be crucial factors for achieving desirable AA-N to N₂ O conversion efficiencies. Glycine-N had the highest N₂ O yield of 70%, with isotopic results consistent with those of the reference values at a high precision (within 0.5‰ for natural abundance and 0.01 atom% for ¹⁵ N-enrichment) at the nanomolar N level. Additionally, the α-NH₂ AAs were labile, and the single-N AAs were more easily converted to N₂ O than poly-N AAs. With the exception of γ-aminobutyric acid, the N₂ O conversion efficiencies of the side-chain N analogs were very low (below 5%). This method was also applicable to the ¹⁵ N analysis of the total free AAs in complex soil samples without interference from analytical blanks and other forms of N.

CONCLUSIONS

Our method is highly selective for the α-NH₂ groups of an amino acid, and the oxidation of the side chain is difficult. In addition, the method is sensitive, rapid, and convenient, and does not require toxic reagents.

Living and Dead Microorganisms in Mediating Soil Carbon Stocks Under Long-Term Fertilization in a Rice-Wheat Rotation

Although soil microorganism is an active area of research, we are still in the early stages of understanding how living microorganisms influence the accumulations of soil microbial residues under different agricultural practices. Based on a 39-year fertilization experiment, we characterized the soil microbiota and correlated their compositions to soil microbial residues, which are indicated by amino sugars under a rice-wheat rotation. In the present study, fertilization regimes and crop season all exerted significant impacts on the compositions of soil microbial communities and their residues, although no significant difference in the microbial residues was found between soil depth (0-10 cm vs. 10-20 cm). Compared within fertilization regimes, the long-term fertilization, especially the application of organic manure, stimulated the accumulations of carbon (C) and nitrogen in soils and microbial residues. Upland soils in wheat season accumulated more microbial residues, particularly in fungal residues, than paddy soils in rice season. Our results suggested that the long-term application of organic manure favored the growth of soil microbial communities, and then increased the contents of microbial residues, particularly in fungal residues, leading to an enlargement of soil C pools. The keystone taxa Pseudaleuria identified by network analysis showed a significantly positive potential in soil C sequestration by increasing the accumulation of fungal residues. Thus, this study revealed the strong and close connections between microbial communities and their residues, and provided evidence about the critical role of keystone taxa in regulating C sequestration.

Chirality in Organic and Mineral Systems: A Review of Reactivity and Alteration Processes Relevant to Prebiotic Chemistry and Life Detection Missions

Chirality is a central feature in the evolution of biological systems, but the reason for biology’s strong preference for specific chiralities of amino acids, sugars, and other molecules remains a controversial and unanswered question in origins of life research. Biological polymers tend toward homochiral systems, which favor the incorporation of a single enantiomer (molecules with a specific chiral configuration) over the other. There have been numerous investigations into the processes that preferentially enrich one enantiomer to understand the evolution of an early, racemic, prebiotic organic world. Chirality can also be a property of minerals; their interaction with chiral organics is important for assessing how post-depositional alteration processes could affect the stereochemical configuration of simple and complex organic molecules. In this paper, we review the properties of organic compounds and minerals as well as the physical, chemical, and geological processes that affect organic and mineral chirality during the preservation and detection of organic compounds. We provide perspectives and discussions on the reactions and analytical techniques that can be performed in the laboratory, and comment on the state of knowledge of flight-capable technologies in current and future planetary missions, with a focus on organics analysis and life detection.

Organic N compounds in plant nutrition: have methodologies based on stable isotopes provided unequivocal evidence of direct N uptake?

During the past two decades, interest has developed in regard to the possibility that plant roots can take up organic N compounds directly, a concept which challenges the conventional wisdom that soil inorganic N forms (NH4+ and NO3-) are the sole primary sources of N absorbed by plant roots. We reviewed the literature based on single or dual (¹⁵N, ¹³C) stable isotope labelling techniques to test the hypothesis of direct uptake. Both isotopically enriched and natural abundance approaches were reviewed. Of the methods examined, the dual enrichment technique, when combined with compound specific and position-specific stable isotope analysis, provided incontrovertible evidence for direct uptake of simple amino acids. We demonstrate that dual labelling lacks overall sensitivity due to the high C concentration in plant tissue relative to N, and the higher natural abundance of ¹³C cf. ¹⁵N, which limits the period of measurement due to isotope dilution, and hence an assessment of the long-term contribution of direct uptake to the N economy of plant communities.

A holistic framework integrating plant-microbe-mineral regulation of soil bioavailable nitrogen

Soil organic nitrogen (N) is a critical resource for plants and microbes, but the processes that govern its cycle are not well-described. To promote a holistic understanding of soil N dynamics, we need an integrated model that links soil organic matter (SOM) cycling to bioavailable N in both unmanaged and managed landscapes, including agroecosystems. We present a framework that unifies recent conceptual advances in our understanding of three critical steps in bioavailable N cycling: organic N (ON) depolymerization and solubilization; bioavailable N sorption and desorption on mineral surfaces; and microbial ON turnover including assimilation, mineralization, and the recycling of microbial products. Consideration of the balance between these processes provides insight into the sources, sinks, and flux rates of bioavailable N. By accounting for interactions among the biological, physical, and chemical controls over ON and its availability to plants and microbes, our conceptual model unifies complex mechanisms of ON transformation in a concrete conceptual framework that is amenable to experimental testing and translates into ideas for new management practices. This framework will allow researchers and practitioners to use common measurements of particulate organic matter (POM) and mineral-associated organic matter (MAOM) to design strategic organic N-cycle interventions that optimize ecosystem productivity and minimize environmental N loss.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10533-021-00793-9.

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.

Phosphorus addition decreases microbial residual contribution to soil organic carbon pool in a tropical coastal forest

The soil nitrogen (N) and phosphorus (P) availability often constrains soil carbon (C) pool, and elevated N deposition could further intensify soil P limitation, which may affect soil C cycling in these N-rich and P-poor ecosystems. Soil microbial residues may not only affect soil organic carbon (SOC) pool but also impact SOC stability through soil aggregation. However, how soil nutrient availability and aggregate fractions affect microbial residues and the microbial residue contribution to SOC is still not well understood. We took advantage of a 10-year field fertilization experiment to investigate the effects of nutrient additions, soil aggregate fractions, and their interactions on the concentrations of soil microbial residues and their contribution to SOC accumulation in a tropical coastal forest. We found that continuous P addition greatly decreased the concentrations of microbial residues and their contribution to SOC, whereas N addition had no significant effect. The P-stimulated decreases in microbial residues and their contribution to SOC were presumably due to enhanced recycling of microbial residues via increased activity of residue-decomposing enzymes. The interactive effects between soil aggregate fraction and nutrient addition were not significant, suggesting a weak role of physical protection by soil aggregates in mediating microbial responses to altered soil nutrient availability. Our data suggest that the mechanisms driving microbial residue responses to increased N and P availability might be different, and the P-induced decrease in the contribution of microbial residues might be unfavorable for the stability of SOC in N-rich and P-poor tropical forests. Such information is critical for understanding the role of tropical forests in the global carbon cycle.

Quantitative assessment of microbial necromass contribution to soil organic matter

Soil carbon transformation and sequestration have received significant interest in recent years due to a growing need for quantitating its role in mitigating climate change. Even though our understanding of the nature of soil organic matter has recently been substantially revised, fundamental uncertainty remains about the quantitative importance of microbial necromass as part of persistent organic matter. Addressing this uncertainty has been hampered by the absence of quantitative assessments whether microbial matter makes up the majority of the persistent carbon in soil. Direct quantitation of microbial necromass in soil is very challenging because of an overlapping molecular signature with nonmicrobial organic carbon. Here, we use a comprehensive analysis of existing biomarker amino sugar data published between 1996 and 2018, combined with novel appropriation using an ecological systems approach, elemental carbon-nitrogen stoichiometry, and biomarker scaling, to demonstrate a suit of strategies for quantitating the contribution of microbe-derived carbon to the topsoil organic carbon reservoir in global temperate agricultural, grassland, and forest ecosystems. We show that microbial necromass can make up more than half of soil organic carbon. Hence, we suggest that next-generation field management requires promoting microbial biomass formation and necromass preservation to maintain healthy soils, ecosystems, and climate. Our analyses have important implications for improving current climate and carbon models, and helping develop management practices and policies.

Soil multifunctionality is affected by the soil environment and by microbial community composition and diversity

Microorganisms are critical in mediating carbon (C) and nitrogen (N) cycling processes in soils. Yet, it has long been debated whether the processes underlying biogeochemical cycles are affected by the composition and diversity of the soil microbial community or not. The composition and diversity of soil microbial communities can be influenced by various environmental factors, which in turn are known to impact biogeochemical processes. The objectives of this study were to test effects of multiple edaphic drivers individually and represented as the multivariate soil environment interacting with microbial community composition and diversity, and concomitantly on multiple soil functions (i.e. soil enzyme activities, soil C and N processes). We employed high-throughput sequencing (Illumina MiSeq) to analyze bacterial/archaeal and fungal community composition by targeting the 16S rRNA gene and the ITS1 region of soils collected from three land uses (cropland, grassland and forest) deriving from two bedrock forms (silicate and limestone). Based on this data set we explored single and combined effects of edaphic variables on soil microbial community structure and diversity, as well as on soil enzyme activities and several soil C and N processes. We found that both bacterial/archaeal and fungal communities were shaped by the same edaphic factors, with most single edaphic variables and the combined soil environment representation exerting stronger effects on bacterial/archaeal communities than on fungal communities, as demonstrated by (partial) Mantel tests. We also found similar edaphic controls on the bacterial/archaeal/fungal richness and diversity. Soil C processes were only directly affected by the soil environment but not affected by microbial community composition. In contrast, soil N processes were significantly related to bacterial/archaeal community composition and bacterial/archaeal/fungal richness/diversity but not directly affected by the soil environment. This indicates direct control of the soil environment on soil C processes and indirect control of the soil environment on soil N processes by structuring the microbial communities. The study further highlights the importance of edaphic drivers and microbial communities (i.e. composition and diversity) on important soil C and N processes.

Environmental effects on soil microbial nitrogen use efficiency are controlled by allocation of organic nitrogen to microbial growth and regulate gross N mineralization

Microbial nitrogen use efficiency (NUE) is the efficiency by which microbes allocate organic N acquired to biomass formation relative to the N in excess of microbial demand released through N mineralization. Microbial NUE thus is critical to estimate the capacity of soil microbes to retain N in soils and thereby affects inorganic N availability to plants and ecosystem N losses. However, how soil temperature and soil moisture/O2 affect microbial NUE to date is not clear. Therefore, two independent incubation experiments were conducted with soils from three land uses (cropland, grassland and forest) on two bedrocks (silicate and limestone). Soils were exposed to 5, 15 and 25 °C overnight at 60% water holding capacity (WHC) or acclimated to 30 and 60% WHC at 21% O2 and to 90% WHC at 1% O2 over one week at 20 °C. Microbial NUE was measured as microbial growth over microbial organic N uptake (the sum of growth N demand and gross N mineralization). Microbial NUE responded positively to temperature increases with Q10 values ranging from 1.30 ± 0.11 to 2.48 ± 0.67. This was due to exponentially increasing microbial growth rates with incubation temperature while gross N mineralization rates were relatively insensitive to temperature increases (Q10 values 0.66 ± 0.30 to 1.63 ± 0.15). Under oxic conditions (21% O2), microbial NUE as well as gross N mineralization were not stimulated by the increase in soil moisture from 30 to 60% WHC. Under suboxic conditions (90% WHC and 1% O2), microbial NUE markedly declined as microbial growth rates were strongly negatively affected due to increasing microbial energy limitation. In contrast, gross N mineralization rates increased strongly as organic N uptake became in excess of microbial growth N demand. Therefore, in the moisture/O2 experiment microbial NUE was mainly regulated by the shift in O2 status (to suboxic conditions) and less affected by increasing water availability per se. These temperature and moisture/O2 effects on microbial organic N metabolism were consistent across the soils differing in bedrock and land use. Overall it has been demonstrated that microbial NUE was controlled by microbial growth, and that NUE controlled gross N mineralization as an overflow metabolism when energy (C) became limiting or N in excess in soils. This study thereby greatly contributes to the understanding of short-term environmental responses of microbial community N metabolism and the regulation of microbial organic-inorganic N transformations in soils.

Dynamic of inorganic nitrogen and amino sugar to glucosamine addition in forest soils

Amino sugars (AS) are routinely used as microbial biomarkers to investigate the dynamics of soil carbon (C) and nitrogen (N) under different environments. However, the effect of any AS on soil C and N, or other AS, is not well-defined. In this study, acid soils from Dongbei (D) and Fujian (F) and alkaline soil from Henan (H) were selected to perform an incubation experiment under glucosamine addition for 36 days. In the present study, the dynamics of soil soluble organic C (SOC), NH₄⁺-N, NO₃^--N, soluble organic N (SON), and four AS: glucosamine (GluN), mannosamine (ManN), galactosamine (GalN), and muramic acid (MurN), were investigated. The results showed that AS was different among the three soils, but had similar dynamics in the same soil. The higher total C and inorganic N in the D and F relative to the H soil were related to the greater AS in two soils. With incubation, AS decreased in D soil and increased in F soil before 1 week, while after 1 week, the inverse dynamics were observed, which suggest that SOC or SOC combined with inorganic N may be a mechanism to adjust the dynamics of C from AS. Overall, glucosamine addition did not significantly affect AS in D, while the reverse was true for F and H soils. Glucosamine addition decreased AS at day 0 for D soil and at day 3 for F and H soils, and increased SOC. The lowered NH₄⁺-N and AS in D soil, but the higher values of these, were observed in F soil after 1 week of incubation. The increase of SON in D soil with glucosamine addition might be due to the depolymerization of soil organic matter (SOM) into SON. However, the decrease of SON in F soil could be attributed to the mineralization of SON.

Wide-spread limitation of soil organic nitrogen transformations by substrate availability and not by extracellular enzyme content

Proteins constitute the single largest soil organic nitrogen (SON) reservoir and its decomposition drives terrestrial N availability. Protein cleavage by extracellular enzymes is the rate limiting step in the soil organic N cycle and can be controlled by extracellular enzyme production or protein availability/stabilization in soil. Both controls can be affected by geology and land use, as well as be vulnerable to changes in soil temperature and moisture/O2. To explore major controls of soil gross protein depolymerization we sampled six soils from two soil parent materials (calcareous and silicate), where each soil type included three land uses (cropland, pasture and forest). Soil samples were subjected to three temperature treatments (5, 15, 25 °C at 60% water-holding capacity (WHC) and aerobic conditions) or three soil moisture/O2 treatments (30 and 60% WHC at 21% O2, 90% WHC at 1% O2, at 20 °C) in short-term experiments. Samples were incubated for one day in the temperature experiment and for one week in the moisture/O2 experiment. Gross protein depolymerization rates were measured by a novel 15N isotope pool dilution approach. The low temperature sensitivity of gross protein depolymerization, the lack of relationship with protease activity and strong effects of soil texture and pH demonstrate that this process is constrained by organo-mineral associations and not by soil enzyme content. This also became apparent from the inverse effects in calcareous and silicate soils caused by water saturation/O2 limitation. We highlight that the specific soil mineralogy influenced the response of gross depolymerization rates to water saturation/O2 limitation, causing (I) increasing gross depolymerization rates due to release of adsorbed proteins by reductive dissolution of Fe- and Mn-oxyhydroxides in calcareous soils and (II) decreasing gross depolymerization rates due to mobilization of coagulating and toxic Al3+ compounds in silicate soils.

Novel high-throughput approach to determine key processes of soil organic nitrogen cycling: Gross protein depolymerization and microbial amino acid uptake

Proteins comprise the largest soil N reservoir but cannot be taken up directly by microorganisms and plants due to size constraints and stabilization of proteins in organo-mineral associations. Therefore the cleavage of this high molecular weight organic N to smaller soluble compounds as amino acids is a key step in the terrestrial N cycle. In the last years two isotope pool dilution approaches have been successfully established to measure gross rates of protein depolymerization and microbial amino acid uptake in soils. However, both require laborious sample preparation and analyses, which limits sample throughput. Therefore, we here present a novel isotope pool dilution approach based on the addition of 15N-labeled amino acids to soils and subsequent concentration and 15N analysis by the oxidation of α-amino groups to NO2 - and further reduction to N2O, followed by purge-and-trap isotope ratio mass spectrometry (PT-IRMS). We applied this method in mesocosm experiments with forest and meadow soils as well as with a cropland soil amended with either organic C (cellulose) or organic N (bovine serum albumin). To measure direct organic N mineralization to NH4 +, the latter was captured in acid traps and analyzed by an elemental analyzer coupled to an isotope ratio mass spectrometer (EA-IRMS). Our results demonstrate that the proposed method provides fast and precise measurements of at%15N even at low amino acid concentrations, allows high sample throughput and enables parallel estimations of instantaneous organic N mineralization rates.

Growth explains microbial carbon use efficiency across soils differing in land use and geology

The ratio of carbon (C) that is invested into microbial growth to organic C taken up is known as microbial carbon use efficiency (CUE), which is influenced by environmental factors such as soil temperature and soil moisture. How microbes will physiologically react to short-term environmental changes is not well understood, primarily due to methodological restrictions. Here we report on two independent laboratory experiments to explore short-term temperature and soil moisture effects on soil microbial physiology (i.e. respiration, growth, CUE, and microbial biomass turnover): (i) a temperature experiment with 1-day pre-incubation at 5, 15 and 25 °C at 60% water holding capacity (WHC), and (ii) a soil moisture/oxygen (O2) experiment with 7-day pre-incubation at 20 °C at 30%, 60% WHC (both at 21% O2) and 90% WHC at 1% O2. Experiments were conducted with soils from arable, pasture and forest sites derived from both silicate and limestone bedrocks. We found that microbial CUE responded heterogeneously though overall positively to short-term temperature changes, and decreased significantly under high moisture level (90% WHC)/suboxic conditions due to strong decreases in microbial growth. Microbial biomass turnover time decreased dramatically with increasing temperature, and increased significantly at high moisture level (90% WHC)/suboxic conditions. Our findings reveal that the responses of microbial CUE and microbial biomass turnover to short-term temperature and moisture/O2 changes depended mainly on microbial growth responses and less on respiration responses to the environmental cues, which were consistent across soils differing in land use and geology.