Potential Enzyme Activities Research Articles

Soil aggregate size distribution mediates microbial responses to prolonged acid deposition in a subtropical forest in south China

Extended exposure to acid rain has vastly limited soil microbial activity with the consequences for soil carbon (C) storage, but less is known about the microbial responses within soil aggregates that to some extent determine soil C stabilization. Here, we investigated the main microbial group compositions and the relevant potential enzyme activities within different soil aggregates sizes (microaggregates (<250 μm), small macroaggregates (250–2000 μm), and microaggregates (>2000 μm)) in a subtropical forest with decade-long simulated acid rain (SAR) treatments. Four SAR treatments were set by irrigating plots with water of different pH values (i.e., 3.0, 3.5, 4.0, and 4.5 as a control). Results showed that the SAR treatment significantly inhibited microbial activities, specifically decreasing both bacterial and fungal abundances, leading to declines in C-degrading potential enzyme activities. Conversely, potential enzyme activities related to phosphorus (P) and nitrogen (N) mineralization as well as the enzyme stoichiometry for P/N ratio significantly increased under the SAR treatment. The SAR treatment showed no significant differences in microbial abundance across the three soil aggregate sizes. However, it had a more pronounced effect on potential enzyme activities in their optimal aggregate sizes, such as hydrolytic enzymes like β-glucosidase in macroaggregates and oxidases like phenol oxidase and peroxidase in microaggregates. Overall, C-degrading potential enzyme activities were more strongly decreased in the microaggregates than in macroaggregates, and the distribution in aggregates was significantly altered, transforming from large to small sizes under the SAR treatment, which together may boost SOC stabilization and accumulation. Additionally, our findings indicate that prolonged acid rain also caused soil nutrient limitation and imbalance, particularly for P, in subtropical forests. This study highlights the importance of soil aggregate size in regulating microbial responses to acid rain, which should be integrated into ecosystem models to predict soil biogeochemical cycles under future climate conditions.

Migrating ripples create streambed heterogeneity altering microbial diversity and metabolic activity

AbstractSandy sediments of lowland streams are typically transported at low flow in the form of migrating ripples. In these bedforms, microbial communities spanning all trophic guilds (heterotrophic bacteria, fungi, photoautotrophic and phagotrophic protists) are exposed to highly frequent moving–resting cycles of sediment grains. Up to date, it is unknown to what extent ripple migration impacts community metabolism and composition as well as the vertical zonation of sediment‐associated multitrophic microbial communities compared to stationary sediments. We hypothesize that, as a result of mechanical abrasion and limited light supply, migrating ripple sediments have lower microbial abundance, diversity, metabolism and resource acquisition and no vertical zonation compared to stationary sediments. We collected samples from five lowland streams in north‐eastern Germany between May and June 2020. The coarser and better sorted sediments of migrating ripples had a higher oxygen concentration and less organic matter than stationary sediments. Photosynthetic pigments, potential extracellular enzyme activities, bacterial cell counts, and fungal gene copies were lower in migrating ripples than in stationary sediments. In contrast, cell‐specific bacterial production was higher in migrating ripples. Metabarcoding revealed that bedform migration was important in shaping the community structure of bacteria, fungi, and phagotrophic protists. Dry mass‐related net community production, respiration, and bacterial production were higher in superficial compared to underlying layers irrespective of sediment transport. By modulating the abundance, diversity, and structure of different trophic guilds of microbial communities and their resource acquisition, migrating bedforms create streambed heterogeneity, shaping regional biodiversity and the flow of matter through the benthic food web.

Shelf life determination of two palm wine varieties and its effect on biochemical properties and enzyme production.

In palm wine, the available complex microbiota plays very vital roles in the general attributes of the beverage as well as the significance of the various metabolites generated. This research focused on evaluating the biochemical properties of the palm wine obtained from two different varieties of oil palm (Elaeis guineensis) and its potential enzyme activity, as well as assessing the effect of the changes that occur during the keeping time. The biochemical contents (alcohol, total titratable acid, reducing sugar, and pH) were evaluated every 2 h over a period of 144 h. The palm wine varieties were also analyzed for cellulase and amylase production. There was an increase in ethanol for both varieties from 7.29±0.02% (1 h) to 14.82±0.02 (144 h) for variety 1, and from 8.35±0.01% (1 h) to 16.32±0.03% (144 h) for variety 2; the TTA increased with keeping time from 2.25±0.03% (1 h) to 4.42±0.03% (144 h) for variety 1, and from 2.35±0.02% (1h) to 5.01±0.04 (144 h) for variety 2. Reducing sugar decreased from 476.58±0.04 mg/L (1 h) to 42.84±0.75 mg/L (144 h) for variety 1, while variety 2 decreased from 238.18±0.05 mg/L (1 h) to 43.73±0.63 mg/L (144 h). The pH of the palm wine also experienced a decrease for variety 1 from 5.2±0.06 at 1 h to 2.8±0.17 at 144 h, while the variety 2 decreased from 4.8±0.17 at 1 h to 2.8±0.1 at 144 h. There was a reduction in the sugar content with the accumulation of alcohol, which occurred in both varieties, and a drop in the pH due to an increase in organic acids. The palm wine varieties were screened for cellulase and amylase activity, with the highest amylase yield for varieties 1 and 2 at 0.62 U/ml and 0.21 U/ml, respectively on the first day, while that of cellulase was observed at 48 h (0.34 U/ml) for V1 and at 1 h (0.2 U/ml) for V2. The result of this current study proves the importance of the microbial consortium in fresh palm wine as well as its potential as a source of enzyme production, and also shows that these parameters are affected by the keeping time.

Contour prairie strips alter microbial communities and functioning both below and in adjacent cropland soils

Prairie strips are narrow strips of native, perennial vegetation (10–40 m width) integrated within cropped fields to provide benefits for water quality and biodiversity. However, the impact of prairie strips on soil microbial communities and function, both underneath the prairie strips and in the adjacent cropland, is not known. We assessed the effect of restoring native perennial vegetation on soil C and N, potential enzyme activities (PEA), and microbial community composition in the soil directly underneath and cropland adjacent (0.1 to 9 m) to 12-year-old prairie strips integrated within row crop fields. We found that prairie strips consistently increased soil microbial biomass carbon (>56 %) and altered PEA in complex ways. Generally, prairie strips increased hydrolase and decreased oxidoreductase PEA. Prairie strips also changed the soil microbial community directly under prairie vegetation, and, contrary to the expectation that greater plant diversity leads to greater soil microbial diversity, prairie strips reduced bacterial and fungal diversity. The prairie strip's effect on adjacent cropland soils depended on year, but it was strong when it occurred and was typically independent of distance from the prairie strip. Prairie strips increased PEA in adjacent soils (<9 m) by as much as 38 % and shifted bacterial and fungal beta diversity, but neither showed patterns with distance from the prairie strip, indicating that prairie strips cause field-scale shifts in soil biota and functioning, and these effects are not mediated by proximity to the prairie strip. Understanding the mechanisms underlying prairie strips' impact on soil biota, both underneath and adjacent to the prairie, is key to optimize their agroecosystem benefits.

Coating seeds with biopolymers extracted from waste-activated sludge

Seeds can be coated with biopolymers extracted from waste-activated sludge, and the seeds of lettuce and spinach can be coated. When coated with the biopolymers, these seeds exhibited largely improved resistance to high temperature and humidity. The seeds coated or not coated with the biopolymers were aged, and the germination potential, germination ratio, and antioxidant enzyme activity of the coated seeds exhibited markedly greater differences than did those of the uncoated seeds. Moreover, the CAT, POD, and APX activities in the coated lettuce and spinach seeds increased by 56%, 2%, and 17%, respectively (lettuce), as did the activity of 8%, 3%, and 31%, respectively (spinach). In the pot trials, the contents of soluble protein and soluble sugar and the activities of antioxidant enzymes were also enhanced—42% and 56% (lettuce) as well as 34% and 23% (spinach). Thus, biopolymers can contribute to protecting against the aging of some rare seeds.

Seed bio-priming with ACC deaminase-producing bacterial strains alleviates impact of drought stress in Soybean (Glycine max (L.) Merr.)

This study investigated the efficacy of 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase-producing rhizobacterial strains isolated from soybean rhizosphere to alleviate the negative impact of drought stress in soybean. Twenty rhizobacterial strains were isolated from disease-resistant soybeans, and only four isolates displayed ACC deaminase activity (more than 500 nmol of ketobutyrate mg protein−1 h−1). These strains also exhibited a variety of plant growth-promoting (PGP) traits, such as ammonia production, indole acetic acid concentration (>35 g mL−1), hydrogen cyanide (HCN) production, and solubilization of inorganic calcium orthophosphate (>70 μg mL−1). Based on 16S rDNA gene sequencing, the bacterial isolates (AKAD 1-2, AKAD 1-3, AKAD 3-1, and AKAD 3-7) were identified as Pantoea agglomerans (MH304295), Bacillus subtilis (MH304311), Bacillus cereus (MH333217), and Bacillus licheniformis (MH304284), respectively. .Seed bio-priming with these rhizobacteria improvedin vivodrought tolerance, mitigated drought stress and increased shoot length (16–68.6%), root length (40–108%), proline content (14.87–42.69%), sugar content (11.36–67.3%), and protein content (11.77–45%). The potential enzymatic activities of catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD) also increased by 35.87%, 26.63%, and 15.15%, respectively, in drought-stressed plants. The results support the efficacy of these isolates as effective bio-stimulants for improving crop performance in drought-affected agricultural fields. Thus, the present work opens new avenues for harnessing the potential of rhizobacterial bio-stimulants to address the challenges posed by drought stress in soybean cultivation, thereby advancing sustainable agricultural strategies for future food security.

H2O2 promotes trimming-induced tillering by regulating energy supply and redox status in bermudagrass.

Tillering/branching pattern plays a significant role in determining the structure and diversity of grass, and trimming has been found to induce tillering in turfgrass. Recently, it has been reported that hydrogen peroxide (H2O2) regulates axillary bud development. However, the role of H2O2 in trimming-induced tillering in bermudagrass, a kind of turfgrass, remains unclear. Our study unveils the significant impact of trimming on promoting the sprouting and growth of tiller buds in stolon nodes, along with an increase in the number of tillers in the main stem. This effect is accompanied by spatial-temporal changes in cytokinin and sucrose content, as well as relevant gene expression in axillary buds. In addition, the partial trimming of new-born tillers results in an increase in sucrose and starch reserves in their leaves, which can be attributed to the enhanced photosynthesis capacity. Importantly, trimming promotes a rapid H2O2 burst in the leaves of new-born tillers and axillary stolon buds. Furthermore, exogenous application of H2O2 significantly increases the number of tillers after trimming by affecting the expression of cytokinin-related genes, bolstering photosynthesis potential, energy reserves and antioxidant enzyme activity. Taken together, these results indicate that both endogenous production and exogenous addition of H2O2 enhance the inductive effects of trimming on the tillering process in bermudagrass, thus helping boost energy supply and maintain the redox state in newly formed tillers.

Ectomycorrhizal fungi are more sensitive to high soil nitrogen levels in forests exposed to nitrogen deposition.

Ectomycorrhizal fungi are essential for nitrogen (N) cycling in many temperate forests and responsive to anthropogenic N addition, which generally decreases host carbon (C) allocation to the fungi. In the boreal region, however, ectomycorrhizal fungal biomass has been found to correlate positively with soil N availability. Still, responses to anthropogenic N input, for instance through atmospheric deposition, are commonly negative. To elucidate whether variation in N supply affects ectomycorrhizal fungi differently depending on geographical context, we investigated ectomycorrhizal fungal communities along fertility gradients located in two nemo-boreal forest regions with similar ranges in soil N : C ratios and inorganic N availability but contrasting rates of N deposition. Ectomycorrhizal biomass and community composition remained relatively stable across the N gradient with low atmospheric N deposition, but biomass decreased and the community changed more drastically with increasing N availability in the gradient subjected to higher rates of N deposition. Moreover, potential activities of enzymes involved in ectomycorrhizal mobilisation of organic N decreased as N availability increased. In forests with low external input, we propose that stabilising feedbacks in tree-fungal interactions maintain ectomycorrhizal fungal biomass and communities even in N-richsoils. By contrast, anthropogenic N input seems to impair ectomycorrhizal functions.

Composts of diverse green wastes improve the soil biological quality, but do not alleviate drought impact on lettuce (Lactuca sativa L.) growth

AbstractIntense soil cultivation and climate change have detrimental effects on soils. Solutions are needed to improve the biological quality and water holding capacity of agricultural soils. A greenhouse experiment was conducted to investigate the interactive effect of compost application and drought stress on a soil/plant system in order to determine the improvement of soil quality and plant growth and the alleviation of drought stress. Lettuce (Lactuca sativa L.) was grown under greenhouse conditions in a sandy soil with sufficient mineral fertilizer application to test the effect of five compost types (three made from municipal garden and park wastes with differing nutrient contents, one from municipal household waste, and one from farm plant residues) applied at 30 Mg ha−1 dry weight, with which we compared soil quality and plant growth to soil without compost application. Treatment pots were irrigated or subjected to drought conditions during the last 14 days of lettuce growth. Assays of potential N mineralization during 28 days, dehydrogenase and β‐glucosidase activities, and a phospholipid fatty acid (PLFA) analysis were performed to assess effects on soil biological quality. Gas exchange, leaf relative water content, biomass, nitrogen accumulation, and root tip growth of lettuce were measured to investigate compost and drought stress effects on lettuce physiology. All composts improved indices of soil biological quality significantly, except for fungal abundance, relative to soil without compost. The greatest increase was obtained from farm compost, which significantly increased potential nitrogen (N) mineralization and soil enzyme activities of β‐glucosidase and dehydrogenase by factors of 4, 2, and 43, respectively. Furthermore, soil with farm compost generally showed a higher abundance of soil microbial organisms compared with soil without compost, which could be related to its high cellulose and hemicellulose contents. The lowest abundance of microbial organisms was generally found in soil with garden and park waste compost with a medium nutrient content, which could be related to its low organic matter content. The beneficial effect of compost on soil biological quality did not lead to improved lettuce growth, which suggests that soil biological quality (ameliorated by compost application) is not important for a fast‐growing crop, such as lettuce, that is sufficiently fertilized. Drought stress reduced aboveground lettuce biomass, root tip growth, and the abundance of most soil microbial groups significantly, but compost in soil did not alleviate these negative effects. In conclusion, the farm compost made from grass–clover, straw, and vegetable residues is superior to garden and park waste and household waste composts in terms of beneficial effects on soil biological quality. Compost clearly improved soil biological quality, but did not influence lettuce's response to drought stress. The knowledge gained in this study is useful for producing tailor‐made compost with desired effects of improved soil biological quality.

Land management of formerly subtropical Atlantic Forest reduces soil carbon stocks and alters microbial community structure and function

Soil carbon (C) sequestration has been proposed as one means to mitigate the effects of climate change and to guarantee food safety. However, forest conversion to managed land uses can deplete soil C stocks and affect soil microbial communities, potentially impacting a wide range of ecosystem services. Our objective was to investigate the effect of forest conversion to intensive land uses on soil C dynamics and soil microbial community structure and function in the subtropical portion of the Atlantic Forest biome. We evaluated four land uses - forest fragment, grassland, and agriculture with five or fifty years of cultivation. We analyzed soil C pools, edaphic variables, and soil bacterial/archaeal (16S) and fungal (ITS) communities. Forest conversion to managed land uses reduced soil C stocks and altered soil microbial community structure, with implications for soil C dynamics. Bacterial/archaeal and fungal community composition were strongly correlated with pH, base saturation, and calcium (Ca) and magnesium (Mg) content. However, soil C pools were not associated with potential extracellular enzyme activity or microbial diversity. Finally, the fungal species Mortierella minutissima ASV_1 and several bacterial groups were positively correlated with soil C stocks, potentially representing indicators of soil C storage. Our study indicates that land use change affects the interplay between soil microbial communities and soil C pools, with consequences to soil C storage. Our findings may support the development of soil C enhancement programs within the Atlantic Forest biome.

Soil biomass-related enzyme activity indicates minimal functional changes after 16 years of persistent drought treatment in a Mediterranean holm oak forest

Long-term drought impacts soil microbial responses and enzymatic activity, affecting carbon budget and nutrient cycling in terrestrial ecosystems. We examined a Mediterranean holm oak forest subjected to 16 years of drought treatment to understand the effects on soil organic matter decomposition, nutrient cycling, and enzymatic activity. We compared potential and biomass-related (normalized to microbial biomass) soil enzyme activity with measurements taken 10 years earlier. Relationships between potential enzyme activity, soil moisture, temperature, nutrient availability, and plant/microbial activity were explored. The prolonged drought led to decreased potential activities of all enzymes, especially acid phosphatase, protease, and urease. However, biomass-related activities of protease, urease, and phosphatase were unaffected. Interestingly, biomass-related beta-glucosidase activity increased during dry seasons, indicating a functional adaptation for carbon acquisition during extreme dry conditions. The negative impact of drought on potential enzyme activity intensified over time, particularly during summer when drought intensity increased. Soil water availability, microbial biomass, and nutrient availability strongly influenced potential enzyme activity. Long-term drought and summer aridity led to increased substrate accumulation in the soil. However, no significant changes were observed in biomass-related activities of nitrogen and phosphorus-acquiring enzymes. This lack of change is likely attributed to a decrease in the absolute potential enzyme activity capacity, caused by a reduction in microbial biomass in drought-affected plots, thereby favoring substrate accumulation. Specific functional adaptations were observed, including increased carbon acquisition by soil microbes during extreme summer drought. Long-term water scarcity in water-limited ecosystems diminishes the system's capacity to acquire resources through enzyme production, impacting mineralization and nutrient dynamics. Future climate scenarios may entail reduced ecosystem-level mineralization, carbon and nitrogen shifts from plants to soil, compromising plant control over nutrients, and increasing the risk of resource loss through leaching and erosion.

Altered rainfall greatly affects enzyme activity but has limited effect on microbial biomass in Australian dryland soils

Drylands support a substantial proportion of the worlds biodiversity and are important to food production but are sensitive to changes in rainfall regimes. Altered rainfall has been shown to impact plant growth and soil microbial activity in drylands but the longer-term effect on belowground communities and biogeochemical cycles remains uncertain. We explored how four years of reduced and increased rainfall influenced soil total and available carbon (C), nitrogen (N) and phosphorus (P) content, microbial biomass and potential extracellular enzyme activity under field conditions at six dryland sites in eastern Australia. The study coincided with a severe 3-year drought that resulted in low standing plant biomass and soil C content at all sites. Microbial biomass attributes varied considerably across sites, with rainfall treatment effects limited to decreased fungal biomass and lower fungal:bacterial ratios in semi-arid Nyngan and reduced fungal:bacterial ratios and microbial biomass C in semi-arid Quilpie in reduced treatments compared with increased rainfall plots. Similarly, available soil C, N and P varied considerably among sites, with more available N and P at four and all sites, respectively, in reduced rainfall treatments particularly when compared with increased rainfall treatments. Rainfall treatments consistently influenced enzyme activity across all sites, with higher rates in increased rainfall plots indicative of greater microbial activity and enhanced nutrient cycling. Enzymatic activity associated with N cycling showed a negative relationship with available N while enzymes associated with P cycling related positively to available C and negatively to available P. This indicates that microbes invested more in production of enzymes associated with less available nutrients. Enzyme activity was not related to microbial biomass suggesting a disconnect between biomass and enzyme production and that rainfall treatments altered the ecosystem's specific enzyme activity (activity per unit of microbial biomass). Our results suggest that altered rainfall consistently impacted dryland ecosystem function, but that microbial biomass is a poor proxy for rainfall-induced changes in soil processes.

Direct and indirect effects of Basta®, a glufosinate-based herbicide, on banana plantation soil microbial diversity and function

Herbicide applications have doubled over the past 30 years to control weeds, but their use may influence soil microbial communities, which mediate important ecosystem services. Here, we characterised the direct effects of a single application of Basta® (glufosinate), at 1× and 2× the recommended rate (5 and 10 kg product ha−1), as well as the indirect effects of vegetation loss on the diversity and function of soil microbial communities within a banana plantation. A 10-month pre-experimental period using Basta® to remove additional vegetation from half of the experimental area created conditions for assessing the indirect herbicide effects. Direct assessments on soil microbial communities began when the Basta® herbicide treatments were applied to the areas with and without vegetation and continued over multiple time-points, for 56 days. Herbicide treatment had no significant direct impacts on basal, and substrate induced respiration rates, or the potential activities of microbial enzymes as inferred from fluorescein diacetate hydrolysis (FDA) and β-glucosidase assays. Similarly, phylogenetic marker gene sequencing indicated that Basta® application did not significantly influence the diversity of soil bacterial or fungal communities. Indirectly, Basta® had a greater influence on the soil microbial activity and functions by removing understory vegetation cover around banana plants. This suggested that continual use of herbicides to reduce soil vegetation cover under bananas had a greater impact on soil microbial communities than a single application of the herbicide. Furthermore, the presence or absence of vegetation cover, significantly altered the abundance of Fusarium oxysporum, plus an additional eight bacterial and ten fungal taxa. Our results indicated that a single application of glufosinate as Basta® at the recommended or double the recommended rate, did not adversely affect soil microbial communities or their activities in banana plantations directly. However, application of herbicides, such as Basta® in crops like banana, indirectly alters soil microbial communities and their activities through loss of vegetation cover and should only be used as a component of an integrated weed management system.

Sevoflurane alleviates oxygen-glucose deprivation/reoxygenation-induced damage in HT22 cells by activating the Keap1/Nrf2/ARE pathway to inhibit oxidative stress

Objective: This study aimed to investigate the impact of sevoflurane on oxygen-glucose deprivation/reoxygenation-induced damage in HT22 cells and its associated mechanisms. Methods: HT22 cells were treated with sevoflurane, and an oxygen-glucose deprivation/reoxygenation injury model was established. The HT22 cells were randomly divided into the control group, oxygen-glucose deprivation/reoxygenation group, sevoflurane low-dose group, sevoflurane medium-dose group, and sevoflurane high-dose group. The proliferation of HT22 cells was assessed using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The apoptosis rate and mitochondrial membrane potential of HT22 cells were determined by flow cytometry. Protein expression levels of B-cell lymphoma-2-associated X protein (Bax), B-cell lymphoma-2 (Bcl-2), nuclear factor erythroid 2-related factor 2 (Nrf2), Kelch-like ECH-associated protein 1 (Keap1), and heme oxygenase-1 (HO-1) in HT22 cells were examined using Western blot. Reactive oxygen species (ROS) levels were measured with 2',7'-dichlorofluorescin diacetate (DCFH-DA). Malondialdehyde (MDA), glutathione peroxidase (GSH-Px) levels, and superoxide dismutase (SOD) enzyme activity in HT22 cells were determined using assay kits. Results: Compared to controls, OGD/R group had reduced cell viability, mitochondrial potential, Bcl-2, nuclear Nrf2, HO-1, GSH-Px levels, and SOD enzyme activity (p < 0.05), with increased apoptosis, Bax, cytoplasmic Nrf2, ROS, and MDA levels. Sevoflurane groups showed opposite trends (p < 0.05). Conclusion: Sevoflurane can mitigate oxygen-glucose deprivation/reoxygenation-induced damage in HT22 cells, and its mechanism may be related to the activation of the Keap1/Nrf2/ARE pathway to inhibit oxidative stress.

Linking the rhizosphere effects of 12 woody species on soil microbial activities with soil and root nitrogen status

The rhizosphere effect depicts the changes in soil physical, chemical, and biological properties due to altered microbial activity in response to root activity, which has important implications for soil carbon and nutrient cycling. However, how the plant-induced changes in rhizosphere soil microbial activity correlate with root and soil nutrient status remains uncertain. Here we targeted 12 woody species of distinct growth forms, i.e., tree vs. shrub, in an urban park on a university campus in Beijing, China. We measured root carbon and nitrogen concentrations and soil properties of paired rhizosphere and bulk soils for each plant. We investigated how the rhizosphere effects on microbial properties, as indicated by microbial biomass and potential activity of soil extracellular hydrolases, varied among the 12 woody species and between trees and shrubs, as well as how they were regulated by bulk soil and root nitrogen status. In general, across the 12 species, root nitrogen content, which is a potential indicator of plant life span and nutrient acquisition strategy, was positively correlated with the rhizosphere effect on potential enzyme activity, while the inverse was true for root carbon: nitrogen ratio, which further verified the role of root functional traits in controlling soil nutrient cycling through the rhizosphere effect. Moreover, soil organic carbon, total nitrogen, and available nitrogen concentrations were all found to be negatively correlated with the rhizosphere effect on microbial properties, which highlighted the stimulation of rhizosphere microbial activity for nitrogen acquisition (the nitrogen-mining hypothesis). Trees and shrubs exhibited no significant differences in their rhizosphere effects, and there was a potential difference in the role of rhizosphere effect in regulating soil nitrogen cycling between legumes and non-legumes. Overall, our study highlights the role of plant nutrient acquisition strategy and soil nutrient status in regulating the rhizosphere effect of woody species on microbial-driven soil processes, which is essential for a better understanding of mechanisms by which plants sustain their nutrient supply.

Earthworm activities change phosphorus mobilization and uptake strategies in deep soil layers

The drilosphere is described as a microbial hotspot in soil, which is rich in labile nutrients. However, phosphorus (P) quality and availability change along the drilosphere from labile organically-bound P in upper layers to immobilized Ca-phosphate with increasing depth. In this study, we postulated (1) that microbial P turnover is generally accelerated in the drilosphere compared to bulk soil as a result of an increase in labile nutrients, and (2) that P mineralization is dominant in upper layers of the drilosphere and P solubilization in deeper layers of the drilosphere, respectively. Furthermore, we hypothesized (3) that the enhanced P mobilization in the drilosphere favors copiotrophic and earthworm gut derived bacteria like Pseudomonadaceae, which distinguishes the community composition from that of the bulk soil. We investigated the effect of earthworm activities on potential phosphatase activities, abundance and diversity of bacterial communities involved in P mobilization (gcd, phoD, appA, phnX, phoN) and uptake (pstS, pitA) along a soil depth gradient in a short rotation coppice in Northeast Germany. Potential phosphatase activities and gene abundances revealed increasing potentials for organic P mineralization and high-affinity P uptake via the Pst system in the drilosphere below 50 cm depth. Conversely, in the upper soil layers potential for bacterial P mobilization were similar between drilosphere and bulk soil. We also observed drilosphere-related changes in the composition of bacterial communities involved in P solubilization and low-affinity P uptake via the Pit system below 60 cm depth. In the drilosphere compared to bulk soil, Pseudomonadaceae were enriched and played a major role in solubilization and low-affinity uptake of P, while bacteria potentially involved in N turnover like Bradyrhizobiaceae and Phyllobacteriaceae were less abundant. Our study suggested that earthworms increased the potential enzyme activity and abundance of bacteria carrying the Pho-regulon genes in the drilosphere of the deeper soil layers. Furthermore, earthworm-derived bacteria were enriched in the drilosphere at the same soil depth, especially those involved in P solubilization and carrying the Pit system.

The First Evidence of Potential Antibacterial Activity of Laccase Enzyme from Indonesian White Rot Fungi against Pathogenic Bacteria

The antibacterial agent can be extracted from plants, animals, and microorganisms such as fungi. The potential antibacterial activity of laccase derived from fungi remains limited in current reports. This study aimed to investigate the characteristics of laccase from Indonesian white rot fungi (WRF) and explore its potential as an antibacterial agent. The laccases were produced by Trametes hirsuta D7, Trametes hirsuta EDN 082, Leiotrametes menziesii BRB 73, and Lentinus sajor-caju BRB 12 using oil palm empty fruit bunch as a substrate. The results showed that the Indonesian WRF tested produced brownish-yellow laccase. FTIR analysis demonstrated similar peak patterns but distinct absorption intensities among the laccases. Trametes hirsuta D7 gained 0.044 U/ml of the greatest laccase activity. Laccase, with minimal activity of 0.001 U/ml–0.026 U/ml, suppressed the propagation of Propionibacterium acnes and Staphylococcus aureus. Escherichia coli and Pseudomonas aeruginosa could be inhibited by the laccase with a minimum activity of 0.002 U/ml–0.044 U/ml. However, S. aureus and E. coli showed the Minimum Bactericidal Concentration in the laccase activity range of 0.018 U/ml–0.308 U/ml. Gram-positive and Gram-negative bacteria grow more slowly when the laccase is present, supposed the laccase as a potential antibacterial agent.

Ecosystem‐level decoupling in response to reduced precipitation frequency and degradation in steppe grassland

Abstract Grasslands across arid and semi‐arid regions are predicted to experience reductions in precipitation frequency. Besides, grassland degradation has become a serious problem in many of these areas. Despite increasing evidence suggesting compound effects of these synchronous alterations on biotic and abiotic ecosystem constituents, we still do not know how they will impact the coupling among ecosystem constituents and its consequences on ecosystem functioning. Here, we assessed the effects of decreased precipitation frequency and grassland degradation on ecosystem coupling, quantified based on the mean strength of pairwise correlations among multispecies communities and their physicochemical environment, individual functions and ecosystem multifunctionality, and reported their relationships within a mechanistic plant–nematode–micro‐organism–soil interactions framework. Decreased precipitation frequency led to poorly coupled ecosystems, and reduced aboveground plant biomass, soil water content, soil nutrient levels, soil biota abundance and multifunctionality. By contrast, belowground plant biomass and soil potential enzyme activities increased under decreased precipitation frequency treatment. Severe degradation resulted in decoupled ecosystems and suppressed most of individual functions and multifunctionality. Using structural equation modelling, we showed that coupling had a strong direct positive effect on multifunctionality (standardized total effect: 0.74), while multifunctionality was weakened by greater soil water variation (−0.54) and higher soil pH (−0.53). The great sensitivity of ecosystem coupling to altered precipitation regimes and degradation highlights the importance of considering interactions among biotic and abiotic components when predicting early ecological impacts under changing environments. Moreover, the positive relationship between ecosystem coupling and functioning suggests that restoration of degraded grasslands may be achieved by intensifying ecological interactions. Read the free Plain Language Summary for this article on the Journal blog.

Expression, Purification, and Characterization of Plasmodium vivax Lactate Dehydrogenase from Bacteria without Codon Optimization.

Plasmodium vivax is the most widespread cause of malaria, especially in subtropical and temperate regions such as Asia-Pacific and America. P. vivax lactate dehydrogenase (PvLDH), an essential enzyme in the glycolytic pathway, is required for the development and reproduction of the parasite. Thus, LDH from these parasites has garnered attention as a diagnostic biomarker for malaria and as a potential molecular target for developing antimalarial drugs. In this study, we prepared a transformed Escherichia coli strain for the overexpression of PvLDH without codon optimization. We introduced this recombinant plasmid DNA prepared by insertion of the PvLDH gene in the pET-21a(+) expression vector, into the Rosetta(DE3), an E. coli strain suitable for eukaryotic protein expression. The time, temperature, and inducer concentration for PvLDH expression from this E. coli Rosetta(DE3), containing the original PvLDH gene, were optimized. We obtained PvLDH with a 31.0 mg/L yield and high purity (>95%) from this Rosetta(DE3) strain. The purified protein was characterized structurally and functionally. The PvLDH expressed and purified from transformed bacteria without codon optimization was successfully demonstrated to exhibit its potential tetramer structure and enzyme activity. These findings are expected to provide valuable insights for research on infectious diseases, metabolism, diagnostics, and therapeutics for malaria caused by P. vivax.

Rank-ordering of known enzymes as starting points for re-engineering novel substrate activity using a convolutional neural network

Retro-biosynthetic approaches have made significant advances in predicting synthesis routes of target biofuel, bio-renewable or bio-active molecules. The use of only cataloged enzymatic activities limits the discovery of new production routes. Recent retro-biosynthetic algorithms increasingly use novel conversions that require altering the substrate or cofactor specificities of existing enzymes while connecting pathways leading to a target metabolite. However, identifying and re-engineering enzymes for desired novel conversions are currently the bottlenecks in implementing such designed pathways. Herein, we present EnzRank, a convolutional neural network (CNN) based approach, to rank-order existing enzymes in terms of their suitability to undergo successful protein engineering through directed evolution or de novo design towards a desired specific substrate activity. We train the CNN model on 11,800 known active enzyme-substrate pairs from the BRENDA database as positive samples and data generated by scrambling these pairs as negative samples using substrate dissimilarity between an enzyme's native substrate and all other molecules present in the dataset using Tanimoto similarity score. EnzRank achieves an average recovery rate of 80.72% and 73.08% for positive and negative pairs on test data after using a 10-fold holdout method for training and cross-validation. We further developed a web-based user interface (available at https://huggingface.co/spaces/vuu10/EnzRank) to predict enzyme-substrate activity using SMILES strings of substrates and enzyme sequence as input to allow convenient and easy-to-use access to EnzRank. In summary, this effort can aid de novo pathway design tools to prioritize starting enzyme re-engineering candidates for novel reactions as well as in predicting the potential secondary activity of enzymes in cell metabolism.