Enzymatic Strategies and Carbon Use Efficiency of a Litter-Decomposing Fungus Grown on Maize Leaves, Stems, and Roots

Challenges of accounting nitrous oxide emissions from agricultural crop residues

Crop residues are important inputs of carbon (C) and nitrogen (N) to soils and thus directly and indirectly affect nitrous oxide (N2 O) emissions. As the current inventory methodology considers N inputs by crop residues as the sole determining factor for N2 O emissions, it fails to consider other underlying factors and processes. There is compelling evidence that emissions vary greatly between residues with different biochemical and physical characteristics, with the concentrations of mineralizable N and decomposable C in the residue biomass both enhancing the soil N2 O production potential. High concentrations of these components are associated with immature residues (e.g., cover crops, grass, legumes, and vegetables) as opposed to mature residues (e.g., straw). A more accurate estimation of the short-term (months) effects of the crop residues on N2 O could involve distinguishing mature and immature crop residues with distinctly different emission factors. The medium-term (years) and long-term (decades) effects relate to the effects of residue management on soil N fertility and soil physical and chemical properties, considering that these are affected by local climatic and soil conditions as well as land use and management. More targeted mitigation efforts for N2 O emissions, after addition of crop residues to the soil, are urgently needed and require an improved methodology for emission accounting. This work needs to be underpinned by research to (1) develop and validate N2 O emission factors for mature and immature crop residues, (2) assess emissions from belowground residues of terminated crops, (3) improve activity data on management of different residue types, in particular immature residues, and (4) evaluate long-term effects of residue addition on N2 O emissions.

Elucidating the role of media nitrogen in augmenting the production of lignin-depolymerizing enzymes by white-rot fungi

Indigenous white-rot fungal isolates Schizophyllum commune, Phanerochaete chrysosporium, Ganoderma racenaceum, and Lentinus squarrosulus, demonstrating the ability to depolymerize lignin of the crop residues, were studied for their potential to produce ligninolytic enzymes using modified production media under conditions of limiting and excess nitrogen for higher enzymatic expressions. Secretome-rich media on the investigation confirmed the successful production of lignin-depolymerizing enzymes, viz. laccase, lignin peroxidase, manganese peroxidase, and versatile peroxidase. Production of laccases and peroxidases was statistically significant in nitrogen-limiting media with and without the substrate, across all white-rot fungal cultures at 95% confidence interval. Nitrogen-limiting media with the substrate on analysis extracellularly expressed 99.27 U of laccase and 68.48 U of manganese peroxidase in Schizophyllum commune, while 195.14 U of lignin peroxidase was produced by Phanerochaete chrysosporium. Lentinus squarrosulus expressed 455.34 U of laccase and 357.13 U of versatile peroxidase with 250.09 U of laccase and 206.95 U of manganese peroxidase produced by Ganoderma racenaceum for every milliliter of the media used. Nitrogen-limiting media triggered the production of laccase during the initial stages of growth while the expression of peroxidases was predominant at a later stage. Also, this media evinced increased enzymatic yields with low biomass content compared to nitrogen-excess conditions. The extant study confirmed the positive influence of nitrogen-limiting media in the efficient production of ligninolytic enzymes and their suggestive degradation potential for environmental pollutants, making these enzymes a safe, clean alternative to the use of chemicals and the media to be effective for large-scale production of ligninolytic enzymes. IMPORTANCE Lignin on account of its high abundance, complex polymeric structure, and biochemical properties is identified as a promising candidate in renewable energy and bioproduct manufacturing. However, depolymerization of lignin remains a major challenge in lignin utilization, entailing the employment of harsh treatments representing not only an environmental concern but also a waste of economic potential. Developing an alternative green technology to minimize this impact is imperative. Methods using enzymes to depolymerize lignin are the focus of recent studies. Current research work emphasized the efficient expression of the major lignin-depolymerizing enzymes: laccases, lignin peroxidases, manganese peroxidases, and versatile peroxidases from native isolates of white-rot fungus for several biotechnological applications as well as treatment of crop residues for use as ruminant feed in improving productivity. The importance of nitrogen in augmenting the expression of lignin-depolymerizing enzymes and providing a media recipe for the cost-effective production of ligninolytic enzymes is highlighted.

Current controversies on mechanisms controlling soil carbon storage: implications for interactions with practitioners and policy-makers. A review

There is currently an intense debate about the potential for additional organic carbon storage in soil, the strategies by which it may be accomplished and what the actual benefits might be for agriculture and the climate. Controversy forms an essential part of the scientific process, but on the topic of soil carbon storage, it may confuse the agricultural community and the general public and may delay actions to fight climate change. In an attempt to shed light on this topic, the originality of this article lies in its intention to provide a balanced description of contradictory scientific opinions on soil carbon storage and to examine how the scientific community can support decision-making despite the controversy. In the first part, we review and attempt to reconcile conflicting views on the mechanisms controlling organic carbon dynamics in soil. We discuss the divergent opinions about chemical recalcitrance, the microbial or plant origin of persistent soil organic matter, the contribution of particulate organic matter to additional organic carbon storage in soil, and the spatial and energetic inaccessibility of soil organic matter to decomposers. In the second part, we examine the advantages and limitations of big data management and modeling, which are essential tools to link the latest scientific theories with the actions taken by stakeholders. Finally, we show how the analysis and discussion of controversies can guide scientists in supporting stakeholders for the design of (i) appropriate trade-offs for biomass use in agriculture and forestry and (ii) climate-smart management practices, keeping in mind their still unresolved effects on soil carbon storage.

Effects of defoliation and nitrogen on carbon dioxide (CO2) emissions and microbial communities in soils of cherry tree orchards

Background

In farmland, microbes in soils are affected by exogenous carbon, nitrogen, and soil depth and are responsible for soil organic carbon (SOC) mineralization. The cherry industry has been evolving rapidly in northwest China and emerged as a new source of income for local farmers to overcome poverty. Accordingly, it is highly imperative to probe the effect of defoliation and nitrogen addition on carbon dioxide (CO₂) emissions and microbial communities in soils of dryland cherry orchards.

Methods

CO₂ emissions and microbial communities were determined in soil samples at three depths, including 0-10 cm, 10-30 cm, and 30-60 cm, from a 15-year-old rain-fed cherry orchard. The samples were respectively incubated with or without 1% defoliation under three input levels of nitrogen (0 mg kg^-1, 90 mg kg^-1, and 135 mg kg^-1) at 25°C in the dark for 80 days.

Results

Defoliation and nitrogen addition affected CO₂ emissions and microbial communities and increased microbial biomass carbon (MBC), the activity of soil catalase, alkaline phosphatase, and cellulase in soils of the dryland cherry orchard. The culture with defoliation significantly promoted CO₂ emissions in soils at the three depths mainly by increasing the MBC, catalase, alkaline phosphatase, and cellulase activities, resulted in positive priming index. Nitrogen addition elevated the MBC and changed soil enzymes and reduced CO₂ emissions in soils at the three depths. Moreover, the priming index was higher in deep soils than in top and middle soils under the condition of defoliation and nitrogen addition. No significant differences were observed in the soil bacterial diversity (Chao1, Shannon, and Simpson) among all treatments. Meanwhile, the relative abundance of Proteobacteria was markedly increased and that of Acidobacteria was substantially diminished in soils at the three depths by defoliation and nitrogen addition. The results sustained that defoliation and nitrogen can regulate SOC dynamics by directly and indirectly affecting soil microbial activities and communities. As a result, the combination of defoliation return and nitrogen fertilization management is a promising strategy to increase SOC and promote soil quality in dryland cherry orchards.

Contrasting effects of maize litter and litter-derived biochar on the temperature sensitivity of paddy soil organic matter decomposition

Organic matter input regulates the rate and temperature sensitivity (expressed as Q10) of soil organic matter (SOM) decomposition by changing microbial composition and activities. It remains unclear how the incorporation of litter-made biochar instead of litter affects the Q10 of SOM decomposition. Using a unique combination of two-and three-source partitioning methods (isotopic discrimination between C3/C4 pathways and 14C labeling), we investigated: (1) how maize litter versus litter-made biochar (of C4 origin) addition influenced the Q10 of SOM (C3 origin) under 10°C warming, and (2) how the litter or biochar amendments affected the Q10 of 14C-labeled fresh organic matter (FOM) after long-term incubation. Compared with biochar addition, litter increased the rates and Q10 of mass-specific respiration, SOM and FOM decomposition, as well as the contents of SOM-derived dissolved organic C (DOC) and total phospholipid fatty acids (PLFA). Litter-amended soils have much higher activities (Vmax) of β-glucosidase, N-acetyl-β-glucosaminidase, and leucine aminopeptidase, suggesting larger enzyme pools than in soils with biochar. The Q10 of enzyme Vmax (1.6–2.0) and Km (1.2–1.4) were similar between litter-and biochar-amended soils, and remained stable with warming. However, warming reduced microbial biomass (PLFA) and enzyme activity (Vmax), suggesting decreased enzyme production associated with smaller microbial biomass or faster enzyme turnover at higher temperatures. Reductions in PLFA content and enzyme Vmax due to warming were larger in litter-amended soils (by 31%) than in the control and biochar-amended soils (by 4–11%), implying the active litter-feeding microorganisms have a smaller degree of heat tolerance than the inactive microorganisms under biochar amendments. The reduction in enzyme activity (Vmax) by warming was lower in soils with biochar than in the control soil. Our modeling suggested that the higher Q10 in litter-amended soils was mainly caused by faster C loss under warming, linked to reductions in microbial biomass and growth efficiency, rather than the slightly increased SOM-originated substrate availability (DOC). Overall, using straw-made biochar instead of straw per se as a soil amendment lowers the Q10 of SOM and FOM by making microbial communities and enzyme pools more temperature-tolerant, and consequently reduces SOM losses under warming.

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

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

Increased soil organic matter after 28 years of nitrogen fertilization only with plastic film mulching is controlled by maize root biomass

Nitrogen (N) fertilization and plastic film mulching (PFM) are two widely applied management practices for crop production. Both of them impact soil organic matter individually, but their interactive effects as well as the underlying mechanisms are unknown. Soils from a 28-year field experiment with maize monoculture under three levels of N fertilization (0, 135, and 270 kg N ha^-1 yr^-1) and with or without PFM were analyzed for soil organic C (SOC) content, total soil nitrogen (N), root biomass, enzyme activities, and SOC mineralization rates. After 28 years, N fertilization increased root biomass and consequently, SOC by 26% (averaged across the two fertilizer application rates) and total soil N by 25%. These increases, however, were only in soil with PFM, as PFM reduced N leaching and loss, as a result of a diurnal internal water cycle under the mulch. The SOC mineralization was slower with N fertilization, regardless of the PFM treatment. This trend was attributed to the 43% decrease of β-glucosidase activity (C cycle enzyme) and 51% drop of leucine aminopeptidase (N cycle) with N fertilization, as a result of a strong decrease in soil pH. In conclusion, root biomass acting as the main source of soil C, resulted in an increase of soil organic matter after 28 year of N fertilization only with PFM.

Microbial storage and its implications for soil ecology

Organisms throughout the tree of life accumulate chemical resources, in particular forms or compartments, to secure their availability for future use. Here we review microbial storage and its ecological significance by assembling several rich but disconnected lines of research in microbiology, biogeochemistry, and the ecology of macroscopic organisms. Evidence is drawn from various systems, but we pay particular attention to soils, where microorganisms play crucial roles in global element cycles. An assembly of genus-level data demonstrates the likely prevalence of storage traits in soil. We provide a theoretical basis for microbial storage ecology by distinguishing a spectrum of storage strategies ranging from surplus storage (storage of abundant resources that are not immediately required) to reserve storage (storage of limited resources at the cost of other metabolic functions). This distinction highlights that microorganisms can invest in storage at times of surplus and under conditions of scarcity. We then align storage with trait-based microbial life-history strategies, leading to the hypothesis that ruderal species, which are adapted to disturbance, rely less on storage than microorganisms adapted to stress or high competition. We explore the implications of storage for soil biogeochemistry, microbial biomass, and element transformations and present a process-based model of intracellular carbon storage. Our model indicates that storage can mitigate against stoichiometric imbalances, thereby enhancing biomass growth and resource-use efficiency in the face of unbalanced resources. Given the central roles of microbes in biogeochemical cycles, we propose that microbial storage may be influential on macroscopic scales, from carbon cycling to ecosystem stability.

N2O emissions from decomposing crop residues are strongly linked to their initial soluble fraction and early C mineralization

The emission of nitrous oxide (N₂O), a strong greenhouse gas, during crop residue decomposition in the soil can offset the benefits of residue recycling. The IPCC inventory considers agricultural N₂O emissions proportional to the amount of nitrogen (N) added by residues to soils. However, N₂O involves several emission pathways driven directly by the form of N returned and indirectly by changes in the soil induced by decomposition. We investigated the decomposition factors related to N₂O emissions under controlled conditions. Residues of sugar beet (SUB), wheat (WHT), rape seed (RAS), potato (POT), pea (PEA), mustard (MUS), red clover (RC), alfalfa (ALF), and miscanthus (MIS), varying by maturity at the time of collection, were incubated in two soils (GRI and SLU) at 15 °C with a water-filled pore space of 60%. The residues contained a wide proportion range of water-soluble components, components soluble in neutral detergent (SOL-NDS), hemicellulose, cellulose, and lignin. Their composition drastically influenced the dynamics of C mineralization and soil ammonium and nitrate and was correlated with N₂O flux dynamics. The net cumulative N₂O emitted after 60 days originated mostly from MUS (4828 ± 892 g N-N₂O ha^-1), SUB (2818 ± 314 g N-N₂O ha^-1) and RC (2567 ± 1245 g N-N₂O ha^-1); the other residue treatments had much lower emissions (<200 g N-N₂O ha^-1). For the first time N₂O emissions could be explained only by the residue content in the SOL-NDS, according to an exponential relationship. Residues with a high SOL-NDS (>25% DM) were also non-senescent and promoted high N₂O emissions (representing 1-5% of applied N), likely directly by nitrification and indirectly by denitrification in microbial hotspots. Crop residue quality appears to be valuable information for accurately predicting N₂O emissions and objectively weighing their other potential benefits to agriculture and the environment.

Back to the Future: Decomposability of a Biobased and Biodegradable Plastic in Field Soil Environments and Its Microbiome under Ambient and Future Climates

Decomposition by microorganisms of plastics in soils is almost unexplored despite the fact that the majority of plastics released into the environment end up in soils. Here, we investigate the decomposition process and microbiome of one of the most promising biobased and biodegradable plastics, poly(butylene succinate-co-adipate) (PBSA), under field soil conditions under both ambient and future predicted climates (for the time between 2070 and 2100). We show that the gravimetric and molar mass of PBSA is already largely reduced (28-33%) after 328 days under both climates. We provide novel information on the PBSA microbiome encompassing the three domains of life: Archaea, Bacteria, and Eukarya (fungi). We show that PBSA begins to decompose after the increase in relative abundances of aquatic fungi (Tetracladium spp.) and nitrogen-fixing bacteria. The PBSA microbiome is distinct from that of surrounding soils, suggesting that PBSA serves as a new ecological habitat. We conclude that the microbial decomposition process of PBSA in soil is more complex than previously thought by involving interkingdom relationships, especially between bacteria and fungi.

Phylogenetic and metabolic diversity have contrasting effects on the ecological functioning of bacterial communities

Quantifying the relative contributions of microbial species to ecosystem functioning is challenging, because of the distinct mechanisms associated with microbial phylogenetic and metabolic diversity. We constructed bacterial communities with different diversity traits and employed exoenzyme activities (EEAs) and carbon acquisition potential (CAP) from substrates as proxies of bacterial functioning to test the independent effects of these two aspects of biodiversity. We expected that metabolic diversity, but not phylogenetic diversity would be associated with greater ecological function. Phylogenetically relatedness should intensify species interactions and coexistence, therefore amplifying the influence of metabolic diversity. We examined the effects of each diversity treatment using linear models, while controlling for the other, and found that phylogenetic diversity strongly influenced community functioning, positively and negatively. Metabolic diversity, however, exhibited negative or non-significant relationships with community functioning. When controlling for different substrates, EEAs increased along with phylogenetic diversity but decreased with metabolic diversity. The strength of diversity effects was related to substrate chemistry and the molecular mechanisms associated with each substrate's degradation. EEAs of phylogenetically similar groups were strongly affected by within-genus interactions. These results highlight the unique flexibility of microbial metabolic functions that must be considered in further ecological theory development.

C-STABILITY an innovative modeling framework to leverage the continuous representation of organic matter

The understanding of soil organic matter (SOM) dynamics has considerably advanced in recent years. It was previously assumed that most SOM consisted of recalcitrant compounds, whereas the emerging view considers SOM as a range of polymers continuously processed into smaller molecules by decomposer enzymes. Mainstreaming this new paradigm in current models is challenging because of their ill-adapted framework. We propose the C-STABILITY model to resolve this issue. Its innovative framework combines compartmental and continuous modeling approaches to accurately reproduce SOM cycling processes. C-STABILITY emphasizes the influence of substrate accessibility on SOM turnover and makes enzymatic and microbial biotransformations of substrate explicit. Theoretical simulations provide new insights on how depolymerization and decomposers ecology impact organic matter chemistry and amount during decomposition and at steady state. The flexible mathematical structure of C-STABILITY offers a promising foundation for exploring new mechanistic hypotheses and supporting the design of future experiments.

Growing Medium Type Affects Organic Fertilizer Mineralization and CNPS Microbial Enzyme Activities

Managing plant fertilization is a major concern of greenhouse growers to achieve sustainable production with growing media (GM). Organic fertilization is popular but is more difficult to control, since organic compounds need first to be mineralized by microbes. After 7, 14, 28, and 56 days of incubation, we investigated the response of microbial activities and nutrient releases from three frequently used organic fertilizers (horn and two plant-based fertilizers) in three frequently employed GM types (peat, coir, and bark). We measured pH, electrical conductivity, nutrient contents (NH4+-N, NO3−-N, PO43−-P, SO42−-S), and enzyme activities (β-1.4-glucosidase, urease, acid phosphatase, arylsulfatase). After fertilization, microbes in coir expressed all the C, N, P, and S functions studied, making related nutrients available. In peat and bark, some C, N, P, and S-related pathways were locked. Peat presented high NH4+-N and PO43−-P releases linked to high acid phosphatase and β-glucosidase activities, while bark showed high nitrification rates but weak enzyme activities. Fertilizer types modulated these responses with lower activities and nutrient releases with horn. Our results contributed to better understanding mineralization processes in GM, showing different microbial responses to fertilization. This study pointed out the necessity to look deeper into microbial functions in GM optimizing biological and physicochemical properties.

Enzyme stoichiometry indicates the variation of microbial nutrient requirements at different soil depths in subtropical forests

Soil extracellular enzyme activities and associated enzymatic stoichiometry are considered sensitive indicators of nutrient availability and microbial substrate limitation. However, many of previous studies have been focusing on uppermost soil layer with a single enzyme as representative of the whole nutrient acquisition, leading to critical uncertainties in understanding soil nutrient availability and its relationship with microbial activities in deeper soils. In the current study, we investigated C-, N- and P-acquiring enzyme activities across a range of soil layers (0–10, 10–20, 20–40 and 40–60 cm), and examined the microbial C, N and P limitation in natural secondary forests (NSF) and Chinese fir (Cunninghamia lanceolata) plantation forests (CPF) in subtropical China. The results showed that microbial C and P co-limitation was detected in the two typical subtropical forests at all soil depths, rather than microbial N limitation. Microbial C and P limitation fluctuated along soil depth, but higher N was demanded by microbes in soil under 20 cm in both forests. The present results highlight the asymmetrical patterns of microbial nutrient limitation along the whole soil profile, and provide essential information in understanding nutrient limitations in deeper soils. These vertical and asymmetrical nutrient limitation patterns should be incorporated into future research studies priority.

Flexible Carbon-Use Efficiency across Litter Types and during Decomposition Partly Compensates Nutrient Imbalances-Results from Analytical Stoichiometric Models

Mathematical models involving explicit representations of microbial processes have been developed to infer microbial community properties from laboratory and field measurements. While this approach has been used to estimate the kinetic constants related to microbial activity, it has not been fully exploited for inference of stoichiometric traits, such as carbon-use efficiency (CUE). Here, a hierarchy of analytically-solvable mass-balance models of litter carbon (C) and nitrogen (N) dynamics is developed, to infer decomposer CUE from measured C and N contents during litter decomposition. The models are solved in the phase space—expressing litter remaining N as a function of remaining C—rather than in time, thus focusing on the stoichiometric relations during decomposition rather than the kinetics of degradation. This approach leads to explicit formulas that depend on CUE and other microbial properties, which can then be treated as model parameters and retrieved via nonlinear regression. CUE is either assumed time-invariant or as a function of the fraction of remaining litter C as a substitute for time. In all models, CUE tends to increase with increasing litter N availability across a range of litter types. When temporal trends in CUE are considered, CUE increases during decomposition of N-poor litter cohorts, in which decomposers are initially N-limited, but decreases in N-rich litter possibly due to C-limitation. These patterns of flexible CUE that partly compensate stoichiometric imbalances are robust to moderate shifts in decomposer C:N ratio and hold across wide climatic gradients.

Degradation and Microbial Uptake of C60 Fullerols in Contrasting Agricultural Soils

The environmental fate of functionalized carbon nanomaterials (CNM) remains poorly understood. Using ¹³C-labeled nanomaterial we present the results of a study investigating the mineralization and microbial uptake of surface-functionalized C₆₀ (fullerols) in agricultural soils with contrasting properties. Soil microcosms rapidly mineralized fullerol C, as determined by ¹³C-content in the respired CO₂, with higher fullerol mineralization in an organic, clay-rich soil versus a silty, low C soil (∼56.3% vs ∼30.9% fullerol C mineralized over 65 days). By tracking the enriched ¹³C from fullerol into microbial phospholipid fatty acids (PLFA) we also report, for the first time, the incorporation of nanomaterial-derived C into soil microbial biomass, primarily by fungi and Gram-negative bacteria. While more fullerol C was incorporated into PLFA in the organic C-rich soil (0.77% vs 0.19% of PLFA C), this soil incorporated fullerol C into biomass less efficiently than the silty, low C soil (0.13% and 0.84% of assimilated fullerol C, respectively). These results demonstrate that, in contrast to pristine C₆₀, surface functionalized C₆₀ are unlikely to accumulate in surface soils and are readily mineralized by a range of soil microorganisms.