Extracellular Enzyme Activities Research Articles

Effects of degradable and non-degradable microplastics and oxytetracycline co-exposure on soil N2O and CO2 emissions

Microplastics and antibiotics are emerging contaminants that can elicit considerable adverse effects on carbon and nitrogen cycles and greenhouse gas emissions. The effect of the combined occurrence of antibiotics and different types of microplastics on soil ecosystem is poorly understood. We investigated the effects of oxytetracycline (OTC), polylactic acid (PLA) microplastics, and polyethylene (PE) microplastics alone and in combination on plant root growth traits, soil extracellular enzymatic activity, and nitrous oxide (N2O) and carbon dioxide (CO2) emissions from the soil. Plant root growth traits including root area, root surface area, root volume and root branches were negatively affected by all treatments; soil extracellular enzymatic activity was also negatively affected by all treatments expect for the cellobiohydrolase. The results showed that CO2 emission increased in all treatments, with a maximum increase of 505 % in the PLA treatment; however, N2O emissions increased in the OTC treatment by 44 % but decreased in all other treatments as compared to the control. Furthermore, partial least squares path modeling analysis suggested that soil extracellular enzymes significantly influenced soil N2O and CO2 emissions (P < 0.05) and had a strong correlation with root growth traits (P < 0.05). We thus concluded that changes in soil extracellular enzymatic activities and plant root growth traits, which were affected by different microplastic and antibiotic treatments, influenced soil CO2 and N2O gas emissions.

Microbiome structure variation and soybean's defense responses during flooding stress and elevated CO2.

With current trends in global climate change, both flooding episodes and higher levels of CO2 have been key factors to impact plant growth and stress tolerance. Very little is known about how both factors can influence the microbiome diversity and function, especially in tolerant soybean cultivars. This work aims to (i) elucidate the impact of flooding stress and increased levels of CO2 on the plant defenses and (ii) understand the microbiome diversity during flooding stress and elevated CO2 (eCO2). We used next-generation sequencing and bioinformatic methods to show the impact of natural flooding and eCO2 on the microbiome architecture of soybean plants' below- (soil) and above-ground organs (root and shoot). We used high throughput rhizospheric extra-cellular enzymes and molecular analysis of plant defense-related genes to understand microbial diversity in plant responses during eCO2 and flooding. Results revealed that bacterial and fungal diversity was substantially higher in combined flooding and eCO2 treatments than in non-flooding control. Microbial diversity was soil>root>shoot in response to flooding and eCO2. We found that sole treatment of eCO2 and flooding had significant abundances of Chitinophaga, Clostridium, and Bacillus. Whereas the combination of flooding and eCO2 conditions showed a significant abundance of Trichoderma and Gibberella. Rhizospheric extra-cellular enzyme activities were significantly higher in eCO2 than flooding or its combination with eCO2. Plant defense responses were significantly regulated by the oxidative stress enzyme activities and gene expression of Elongation factor 1 and Alcohol dehydrogenase 2 in floodings and eCO2 treatments in soybean plant root or shoot parts. This work suggests that climatic-induced changes in eCO2 and submergence can reshape microbiome structure and host defenses, essential in plant breeding and developing stress-tolerant crops. This work can help in identifying core-microbiome species that are unique to flooding stress environments and increasing eCO2.

Shifts in microbial community composition and metabolism correspond with rapid soil carbon accumulation in response to 20 years of simulated nitrogen deposition

Anthropogenic nitrogen (N) deposition and fertilization in boreal forests frequently reduces decomposition and soil respiration and enhances C storage in the topsoil. This enhancement of the C sink can be as strong as the aboveground biomass response to N additions and has implications for the global C cycle, but the mechanisms remain elusive. We hypothesized that this effect would be associated with a shift in the microbial community and its activity, and particularly by fungal taxa reported to be capable of lignin degradation and organic N acquisition. We sampled the organic layer below the intact litter of a Norway spruce (Picea abies (L.) Karst) forest in northern Sweden after 20 years of annual N additions at low (12.5 kg N ha−1 yr−1) and high (50 kg N ha−1 yr−1) rates. We measured microbial biomass using phospholipid fatty-acid analysis (PLFA) and ergosterol measurements and used ITS metagenomics to profile the fungal community of soil and fine-roots. We probed the metabolic activity of the soil community by measuring the activity of extracellular enzymes and evaluated its relationships with the most N responsive soil fungal species. Nitrogen addition decreased the abundance of fungal PLFA markers and changed the fungal community in humus and fine-roots. Specifically, the humus community changed in part due to a shift from Oidiodendron pilicola, Cenococcum geophilum, and Cortinarius caperatus to Tylospora fibrillosa and Russula griseascens. These microbial community changes were associated with decreased activity of Mn-peroxidase and peptidase, and an increase in the activity of C acquiring enzymes. Our results show that the rapid accumulation of C in the humus layer frequently observed in areas with high N deposition is consistent with a shift in microbial metabolism, where decomposition associated with organic N acquisition is downregulated when inorganic N forms are readily available.

Land Use Change from Natural Tropical Forests to Managed Ecosystems Reduces Gross Nitrogen Production Rates and Increases the Soil Microbial Nitrogen Limitation.

Understanding the underlying mechanisms of soil microbial nitrogen (N) utilization under land use change is critical to evaluating soil N availability or limitation and its environmental consequences. A combination of soil gross N production and ecoenzymatic stoichiometry provides a promising avenue for nutrient limitation assessment in soil microbial metabolism. Gross N production via 15N tracing and ecoenzymatic stoichiometry through the vector and threshold element ratio (Vector-TER) model were quantified to evaluate the soil microbial N limitation in response to land use changes. We used tropical soil samples from a natural forest ecosystem and three managed ecosystems (paddy, rubber, and eucalyptus sites). Soil extracellular enzyme activities were significantly lower in managed ecosystems than in a natural forest. The Vector-TER model results indicated microbial carbon (C) and N limitations in the natural forest soil, and land use change from the natural forest to managed ecosystems increased the soil microbial N limitation. The soil microbial N limitation was positively related to gross N mineralization (GNM) and nitrification (GN) rates. The decrease in microbial biomass C and N as well as hydrolyzable ammonium N in managed ecosystems led to the decrease in N-acquiring enzymes, inhibiting GNM and GN rates and ultimately increasing the microbial N limitation. Soil GNM was also positively correlated with leucine aminopeptidase and β-N-acetylglucosaminidase. The results highlight that converting tropical natural forests to managed ecosystems can increase the soil microbial N limitation through reducing the soil microbial biomass and gross N production.

Exploration capacity versus specific enzymatic activity of ectomycorrhizas in response to primary productivity and soil phosphorus availability in Bornean tropical rainforests.

Ectomycorrhizal (ECM) fungi are functionally important in biogeochemical cycles in tropical ecosystems. Extracellular enzymatic activity of ECM on a ground-area basis is the product of two attributes; exploration capacity (ECM surface-area) and specific enzymatic activity. Here, we elucidated which attribute better explained the ECM enzymatic activity in response to different levels of soil phosphorus (P) and Nitrogen (N) availability in five Bornean tropical rainforests. We determined the surface area of ECM root tips as well as the enzymatic activities per ECM surface area for carbon (C), N and P degrading enzymes in each site. We evaluated the relationship of ECM enzyme activities with the resource availabilities of C (Above-ground net primary production; ANPP), N, and P of ECM by a generalized linear mixed model. The ECM enzymatic activities on a ground-area basis were more significantly determined by specific enzymatic activity than by the exploration capacity. Specific enzymatic activities were generally negatively affected by C (ANPP) and soil P availability. ECM fungi enhance the specific enzyme activity rather than the exploration capacity to maintain the capacity of nutrient acquisition. The less dependence of ECM fungi on the exploration capacity in these forests may be related to the limitation of C supply from host trees. We highlighted the adaptive mechanisms of ECM fungi on nutrient acquisition in tropical ecosystems through the response of enzymatic activity to nutrient availability across the elements.

Extracellular enzymatic activity of endophytic fungi isolated from spines of rattan palm (Calamus castaneus Griff.)

Extracellular enzymatic activity of endophytic fungi isolated from spines of rattan palm (Calamus castaneus Griff.)

Exploring the Influence of Ecological Niches and Hologenome Dynamics on the Growth of Encephalartos villosus in Scarp Forests

Information on how bacteria in plants and soil, along with extracellular enzymes, affect nutrient cycling in Encephalartos villosus growing in phosphorus deficient and acidic scarp forests is lacking. Bacteria in coralloid roots, rhizosphere, and non-rhizosphere soils were isolated to determine the potential role of soil bacterial communities and their associated enzyme activities in nutrient contributions in rhizosphere and non-rhizosphere soils. The role of soil characteristics and associated bacteria on E. villosus nutrition and nitrogen source reliance was investigated. Encephalartos villosus leaves, coralloid roots, rhizosphere, and non-rhizosphere soils were collected at two scarp forests. Leaf nutrition, nitrogen source reliance, soil nutrition, and extracellular enzyme activities were assayed. A phylogenetic approach was used to determine the evolutionary relationship between identified bacterial nucleotide sequences. The clustering pattern of isolated bacterial strains was primarily dictated by the ecological niches from which they originated (rhizosphere soil, non-rhizosphere soil, and coralloid roots), thus indicating that host-microbe interactions may be a key driver of this pattern, in line with the hologenome theory. There were insignificant differences in the phosphorus and nitrogen cycling enzyme activities in E. villosus rhizosphere and non-rhizosphere soils in both localities. Significantly positive correlations were recorded between nitrogen and phosphorus cycling enzymes and phosphorus and nitrogen concentrations in rhizosphere and non-rhizosphere soils. Additionally, more than 70% of the leaf nitrogen was derived from the atmosphere. This study challenged the conventional expectation that environmental filters alone dictate microbial community composition in similar habitats and revealed that host-microbe interactions, as proposed by the hologenome theory, are significant drivers of microbial community structuring. The isolated bacteria and their plant growth promoting traits play a role in E. villosus nutrition and nitrogen source reliance and secrete nutrient cycling enzymes that promote nutrient availability in rhizosphere and non-rhizosphere soils.

Microbial diversity and their extracellular enzyme activities among different soil particle sizes in mossy biocrust under N limitation in the southeastern Tengger Desert, China.

Mossy biocrust represents a stable stage in the succession of biological soil crust in arid and semi-arid areas, providing a microhabitat that maintains microbial diversity. However, the impact of mossy biocrust rhizoid soil and different particle sizes within the mossy biocrust layer and sublayer on microbial diversity and soil enzyme activities remains unclear. This study utilized Illumina MiSeq sequencing and high-throughput fluorometric technique to assess the differences in microbial diversity and soil extracellular enzymes between mossy biocrust rhizoid soil and different particle sizes within the mossy biocrust sifting and sublayer soil. The results revealed that the total organic carbon (TOC), total nitrogen (TN), ammonium (NH4+) and nitrate (NO3-) in mossy biocrust rhizoid soil were the highest, with significantly higher TOC, TN, and total phosphorus (TP) in mossy biocrust sifting soil than those in mossy biocrust sublayer soil. Extracellular enzyme activities (EAAs) exhibited different responses to various soil particle sizes in mossy biocrust. Biocrust rhizoid soil (BRS) showed higher C-degrading enzyme activity and lower P-degrading enzyme activity, leading to a significant increase in enzyme C: P and N: P ratios. Mossy biocrust soils were all limited by microbial relative nitrogen while pronounced relative nitrogen limitation and microbial maximum relative carbon limitation in BRS. The diversity and richness of the bacterial community in the 0.2 mm mossy biocrust soil (BSS0.2) were notably lower than those in mossy biocrust sublayer, whereas the diversity and richness of the fungal community in the rhizoid soil were significantly higher than those in mossy biocrust sublayer. The predominant bacterial phyla in mossy biocrust were Actinobacteriota, Protebacteria, Chloroflexi, and Acidobacteriota, whereas in BSS0.2, the predominant bacterial phyla were Actinobacteriota, Protebacteria, and Cyanobacteria. Ascomycota and Basidiomycota were dominant phyla in mossy biocrust. The bacterial and fungal community species composition exhibited significant differences. The mean proportions of Actinobacteriota, Protebacteria, Chloroflexi, Acidobacteriota, Acidobacteria, Cyanobacteria, and Bacteroidota varied significantly between mossy biocrust rhizoid and different particle sizes of mossy biocrust sifting and sublayer soil (p < 0.05). Similarly, significant differences (p < 0.05) were observed in the mean proportions of Ascomycota, Basidiomycota, and Glomeromycota between mossy biocrust rhizoid and different particle sizes within the mossy biocrust sifting and sublayer soil. The complexity and connectivity of bacterial and fungal networks were higher in mossy biocrust rhizoid soil compared with different particle sizes within the mossy biocrust sifting and sublayer soil. These results offer valuable insights to enhance our understanding of the involvement of mossy biocrust in the biogeochemical cycle of desert ecosystems.

Understanding phosphorus mobilization mechanisms in acidic soil amended with calcium-silicon-magnesium-potassium fertilizer

Calcium-silicon-magnesium-potassium fertilizer (CSMP) is usually used as an amendment to counteract soil acidification caused by historical excessive nitrogen (N) applications. However, the impact of CSMP addition on phosphorus (P) mobilization in acidic soils and the related mechanisms are not fully understood. Specifically, a knowledge gap exists with regards to changes in soil extracellular enzymes that contribute to P release. Such a knowledge gap was investigated by an incubation study with four treatments: i) initial soil (Control), ii) urea (60 mg kg−1) addition (U); iii) CSMP (1%) addition (CSMP) and iv) urea (60 mg kg−1) and CSMP (1%) additions (U + CSMP). Phosphorus mobilization induced by different processes was distinguished by biologically based P extraction. The Langmuir equation, K edge X-ray absorption near-edge structure spectroscopy, and ecoenzyme vector analysis according to the extracellular enzyme activity stoichiometry were deployed to investigate soil P sorption intensity, precipitation species, and microbial-driven turnover of organophosphorus. Results showed that CaCl2 extractable P (or citric acid extractable P) content increased by 63.4% (or 39.2%) in the soil with CSMP addition, compared with the study control. The accelerated mobilization of aluminum (Al)/iron (Fe)-bound P after CSMP addition, indicated by the reduction of the sum of FePO4·2H2O and AlPO4 proportion, contributed to this increase. The decrease of P sorption capacity can also be responsible for it. The CSMP addition increased enzyme extractable P in the soil nearly 7-fold and mitigated the limitations of carbon (C) and P for soil microorganisms (indicated by the enzyme stoichiometry and ecoenzyme vector analysis), suggesting that microbial turnover processes also contribute to P mobilization in amended acidic soil. These findings indicate that the P mobilization in CSMP amended acidic soil not only attributed to both decreasing P sorption capacity and dissolving phosphate precipitation, but also to the increase of the microbial turnover of the organophosphorus pool.

Pulsed inputs of high molecular weight organic matter shift the mechanisms of substrate utilisation in marine bacterial communities.

Heterotrophic bacteria hydrolyze high molecular weight (HMW) organic matter extracellularly prior to uptake, resulting in diffusive loss of hydrolysis products. An alternative 'selfish' uptake mechanism that minimises this loss has recently been found to be common in the ocean. We investigated how HMW organic matter addition affects these two processing mechanisms in surface and bottom waters at three stations in the North Atlantic Ocean. A pulse of HMW organic matter increased cell numbers, as well as the rate and spectrum of extracellular enzymatic activities at both depths. The effects on selfish uptake were more differentiated: in Gulf Stream surface waters and productive surface waters south of Newfoundland, selfish uptake of structurally simple polysaccharides increased upon HMW organic matter addition. The number of selfish bacteria taking up structurally complex polysaccharides, however, was largely unchanged. In contrast, in the oligotrophic North Atlantic gyre, despite high external hydrolysis rates, the number of selfish bacteria was unchanged, irrespective of polysaccharide structure. In deep bottom waters (> 4000 m), structurally complex substrates were processed only by selfish bacteria. Mechanisms of substrate processing-and the extent to which hydrolysis products are released to the external environment-depend on substrate structural complexity and the resident bacterial community.

Role of an arbuscular mycorrhizal fungus in vegetation restoration as indicated by bacterial diversity and microbial metabolic limitation in soil underlying moss biocrusts

Arbuscular mycorrhizal (AM) fungi contribute to the revegetation of degraded ecosystems such as coal mining areas and may indirectly affect the development of biological soil crusts (biocrusts). However, bacterial diversity and microbial nutrient cycling in the soil underlying biocrusts are seldom considered when assessing ecological restoration effects. Bacterial community composition was quantified and compared using 16S rRNA gene sequencing, metabolic limitation of microbes via extracellular enzymatic stoichiometry and their association with carbon use efficiency (CUE) in soil underlying moss biocrusts in vegetated areas inoculated with an AM fungus or uninoculated and in uninoculated unvegetated areas. The AM fungal inoculum significantly influenced bacterial community composition and diversity, extracellular enzyme activities and CUE in soil underlying moss biocrusts mainly by affecting soil nutrients. Correlation analysis revealed that Actinobacteria, Armatimonadetes, Bacteroidetes, Chlorobi, Cyanobacteria, Saccharibacteria, and Verrucomicrobia were positively correlated with soil nutrients carbon (C), nitrogen (N) and phosphorus (P). A vector analysis of extracellular enzyme activity indicates that soil microbial communities underlying moss biocrusts were limited by P but microbial communities in areas inoculated with the AM fungus had the lowest relative P limitation. The alleviation of microbial P limitation increased the microbial CUE and bacterial phylum community and alpha diversity, leading to an increase in subsoil C content underlying moss biocrusts. This indicates that microbial communities in soil underlying moss biocrusts under in restoration areas containing the AM fungus were more stable under environmental stress, and the inclusion of AM fungal inoculation may be recommended as the preferred option for ecosystem restoration in arid and semi-arid coal mining areas.

Evaluation of farmland soil health and optimization of evaluation system under different green manure applications in a semi‐arid irrigation area

AbstractHealthy soil is essential for maintaining food security and enhancing ecosystem functions. Green manure application improves soil fertility and is an alternative to chemical fertilizers; however, research on optimizing soil health assessment systems and providing comprehensive and accurate information for local farmland green manure management models remains limited. In this study, we used maize and potato intercropped with green manure farmland in the main crop production area of a semi‐arid irrigation area in Northwest China as the research object, integrated the regional soil environment characteristics, and used principal component analysis and other methods to establish a minimum index data set including physicochemical, biological, and yield indices. A soil health assessment system applicable to the study region was constructed and optimized by drawing the scoring curve. The results showed that green manure treatment exerted a positive effect on the soil bulk density, nutrient content, extracellular enzyme activity, and the yield of maize and potato fields. This evaluation method showed that both green manure treatments could improve the soil health index of two major crop fields, with scores of 6.9 (3.7–8.6) and 6.2 (4.5–7.0) for maize and potato farmland, respectively, with a greater positive effect caused on maize. This evaluation system can not only reflect the soil conditions of farmland accurately given the application of green manure in the semi‐arid irrigation areas of northwest China but also provide reference for the promotion of organic fertilizers such as green manure and the resolution of regional soil health differences.

Stochastic processes dominated the soil bacterial community assemblages along an altitudinal gradient in boreal forests

Soil bacteria, as integral components of the soil microbial community, play pivotal roles in biogeochemical cycles and ecosystem functions in boreal forests. The altitudinal patterns of soil bacteria have been widely reported, but their community assembly is uncertain. Here, we investigated the soil bacterial community attributes (diversity, taxonomic and functional composition, and bacterial interactions) and ecological processes associated with community assembly on Mt. Oakley in the northern Greater Khingan Mountains via Illumina MiSeq sequencing and functional annotation tools. The alpha diversity indices of the soil bacteria exhibited a progressively decreasing trend with increasing altitude across seasons. The relative abundance of the dominant bacterial taxa was more sensitive to altitude than to season. More complex (more nodes and links) bacterial interactions were detected at the lowest and highest altitudinal sites, as well as in September. The variations in the taxonomic and functional compositions of the soil bacteria induced by altitude were mainly driven by the variations in soil pH and extracellular enzyme activities. Stochastic (dispersal limitation and drift) processes largely controlled the soil bacterial community assemblages across spatiotemporal scales. The community assemblages of soil bacteria were affected by altitude-induced changes in the taxonomic composition and functional groups. Collectively, our results have significant implications for understanding bacterial biogeography and community assembly mechanisms along altitudinal gradients in boreal forest ecosystems.

Alterations in the composition and metabolite profiles of the saline-alkali soil microbial community through biochar application

Saline-alkali soil poses significant chanllenges to sustainable development of agriculture. Although biochar is commonly used as a soil organic amendment, its microbial remediation mechanism on saline-alkali soil requires further confirmation. To address this, we conducted a pot experiment using cotton seedlings to explore the potential remediation mechanism of rice straw biochar (BC) at three different levels on saline-alkaline soil. The results showed that adding of 2% biochar greatly improved the quality of saline-alkaline soil by reducing pH levels, electrical conductivity (EC), and water-soluble ions. Moreover, biochar increased the soil organic matter (SOM), nutrient availability and extracellular enzyme activity. Interestingly, it also reduced soil salinity and salt content in various cotton plant tissues. Additionally, biochar had a notable impact on the composition of the microbial community, causing changes in soil metabolic pathways. Notably, the addition of biochar promoted the growth and metabolism of dominant salt-tolerant bacteria, such as Proteobacteria, Bacteroidota, Acidobacteriota, and Actinobacteriota. By enhancing the positive correlation between microorganisms and metabolites, biochar alleviated the inhibitory effect of salt ions on microorganisms. In conclusion, the incorporation of biochar significantly improves the soil microenvironment, reduces soil salinity, and shows promise in ameliorating saline-alkaline soil conditions.

The silicon regulates microbiome diversity and plant defenses during cold stress in Glycine max L.

With climate change, frequent exposure of bioenergy and food crops, specifically soybean (Glycine max L.), to low-temperature episodes is a major obstacle in maintaining sustainable plant growth at early growth stages. Silicon (Si) is a quasi-essential nutrient that can help to improve stress tolerance; however, how Si and a combination of cold stress episodes influence plant growth, plant physiology, and microbiome diversity has yet to be fully discovered. The soybean plants were exposed to cold stress (8-10°C) with or without applying Si, and the different plant organs (shoot and root) and rhizospheric soil were subjected to microbiome analysis. The plant growth, physiology, and gene expression analysis of plant defenses during stress and Si were investigated. We showed that cold stress significantly retarded soybean plants' growth and biomass, whereas, Si-treated plants showed ameliorated negative impacts on plant growth at early seedling stages. The beneficial effects of Si were also evident from significantly reduced antioxidant activities - suggesting lower cold-induced oxidative stress. Interestingly, Si also downregulated critical genes of the abscisic acid pathway and osmotic regulation (9-cis-epoxy carotenoid dioxygenase and dehydration-responsive element binding protein) during cold stress. Si positively influenced alpha and beta diversities of bacterial and fungal microbiomes with or without cold stress. Results showed significant variation in microbiome composition in the rhizosphere (root and soil) and phyllosphere (shoot) in Si-treated plants with or without cold stress exposures. Among microbiome phyla, Proteobacteria, Bacteroidota, and Ascomycota were significantly more abundant in Si treatments in cold stress than in control conditions. For the core microbiome, we identified 179 taxa, including 88 unique bacterial genera in which Edaphobacter, Haliangium, and Streptomyces were highly abundant. Enhanced extracellular enzyme activities in the cold and Si+cold treatments, specifically phosphatase and glucosidases, also reflected the microbiome abundance. In conclusion, this work elucidates cold-mediated changes in microbiome diversity and plant growth, including the positive impact Si can have on cold tolerance at early soybean growth stages - a step toward understanding crop productivity and stress tolerance.

Analyzing soil enzymes to assess soil quality parameters in long-term copper accumulation through a machine learning approach

Soil contamination by agrochemicals is a big concern for soil health and ecosystem functioning. This is especially true for non-degradable substances like heavy metals (HM) that, because of their long-term use, are reaching significant values today due to soil accumulation. Among agrochemicals, copper (Cu) has been important in fighting fungal diseases on perennial crops for centuries.Laboratory experiments can be useful to understand the highest potential toxic effect of Cu but need to reflect what happens with long-term application in a dynamic and living agroecosystem. This study uses multivariate data analysis and machine learning to investigate long-term Cu accumulation on soil quality parameters, especially soil extracellular enzymatic activities. We collected soil samples from 21 apple orchards in South Tyrol, Italy. The orchards had different concentrations of Cu. We took 315 samples in total and analyzed them for various soil properties. We also measured the concentrations of elements in apple leaves and the activities of soil extracellular enzymes. We depicted the effect of Cu on several enzymatic activities, shedding light on the effect of Cu on the soil microbial communities functionality. Our results show that Cu concentrations in the study area affect only phosphatase activity, showing effects above 60 mg kg−1 of available Cu. Protease activity was positively correlated with Cu, while soil organic matter and management mainly influenced the carbon (C) cycle enzymes. Phosphatase decrease could be of concern for the potential disruption of the Phosphorus (P) cycle in the soil and plays a role in plant nutrition, as seen by P concentration in apple trees' leaves.We demonstrated how machine learning can help interpret complex and multivariate environmental data and overcome some downsides of traditional statistical models.

Engineering the Tat-secretion pathway of Bacillus licheniformis for the secretion of cytoplasmic enzyme arginase.

The industrial bacterium Bacillus licheniformis has long been used as a microbial factory for the production of enzymes due to its ability to secrete copious amounts of native extracellular proteins and its generally regarded as safe (GRAS) status. However, most attempts to use B. licheniformis to produce heterologous and cytoplasmic enzymes primarily via the general secretory (Sec) pathway have had limited success. The twin-arginine transport (Tat) pathway offers a promising alternative for the extracellular export of Sec-incompatible proteins because it transports full, correctly folded proteins. However, compared to the Sec pathway, the yields of the Tat pathway have historically been too low for commercial use. To improve the export efficiency of the Tat pathway, we identified the optimal Tat-dependent signal peptides and increased the abundance of the Tat translocases, the signal peptidase (SPase), and the intracellular chaperones. These strategic modifications significantly improved the Tat-dependent secretion of the cytoplasmic enzyme arginase into the culture medium using B. licheniformis. The extracellular enzymatic activity of arginase showed a 5.2-fold increase after these modifications. Moreover, compared to the start strain B. licheniformis 0F3, the production of extracellular GFP was improved by 3.8 times using the strategic modified strain B. licheniformis 0F13, and the extracellular enzymatic activity of SOX had a 1.3-fold increase using the strain B. licheniformis 0F14. This Tat-based production chassis has the potential for enhanced production of Sec-incompatible enzymes, therefore expanding the capability of B. licheniformis as an efficient cellular factory for the production of high-value proteins. KEY POINTS: • Systematic genetic modification of Tat-pathway in B. licheniformis. • Significant enhancement of the secretion capacity of Tat pathway for delivery the cytoplasmic enzyme arginase. • A new platform for efficient extracellular production of Sec-incompatible enzymes.

Exploring the hidden treasures: Deep-sea bacterial community structure in the Bay of Bengal and their metabolic profile

Deep sea bacterial communities demonstrate remarkable adaptability to high-pressure environments coupled with low temperatures which has sparked curiosity about their diversity and exceptional metabolic pathways. Additionally, bacteria in the deep sea exert a substantial influence over various biogeochemical processes. To date, we have relatively very little information about the deep-sea bacterial communities and, they remain largely unexplored. We investigated the variability in the physicochemical conditions, heavy metals and their influence on deep-sea bacterial community structure across three different depths in the Bay of Bengal. The structural and metabolic diversity of deep-sea sediment microbial communities were examined through culture-based sequencing of 16S rRNA genes, ecto-enzymatic studies, and community-level physiological profiling. Bacillota was the most dominant phylum representing 61% of the cultured bacterial isolates, while the remaining belonged to Actinomycetota and Pseudomonodata. Five potential novel species belonging to the genera Fictibacillus, Lysinibacillus, Salinicola, Robertmurraya and Blastococcus were identified. The extracellular enzymatic activity was positive for &amp;gt;50% of the bacterial isolates, wherein the genera Bacillus and Micromonospora exhibited versatile profiles. High metabolic diversity was recorded through the carbon substrate utilization profiles indicating that microbial communities are active participants in biogeochemical cycles in the deep sea. The most prominently utilized carbon substrates were α-cyclodextrin, glucose-1-phosphate, D-xylose, glycogen, and 2-hydroxy benzoic acid which serve as organic substrates for microbial metabolism, facilitating the decomposition of organic matter and, recycling carbon in deep-sea ecosystems. Multivariate statistical analyses confirmed that the environmental variables had a profound influence on the bacterial community. The findings shed light on spatial variability in the bacterial community structure, enzyme activity and metabolic profiles, and enhance our understanding of Bay of Bengal deep-sea sedimentary microbial ecology.

Soil extracellular enzyme stoichiometry reveals the nutrient limitations in soil microbial metabolism under different carbon input manipulations

Changes in the quality and quantity of litter and root inputs due to climate change and human activities can influence below-ground biogeochemical processes in forest ecosystems. However, it is unclear whether and how much aboveground litter and root inputs affect soil microbial metabolism and nutrient limitation mechanisms. In this study, according to a 4-years field manipulation experiment, litter and root manipulations (control (CK), double litter input (DL), no litter (NL), no root (NR), and no inputs (NI)) were set up to analyze the extracellular enzyme activities and stoichiometric ratios characteristics of 0–10 cm and 10–20 cm soils, explore the metabolic limitations of microorganisms, and clarify the main driving factors restricting nutrient limitation. The results showed that the enzyme activities associated with the C cycling (β-1,4-glucosidase (BG), cellulose disaccharide hydrolase (CBH)) and N cycling (β-1,4-N-acetylglucosaminidase (NAG), leucine aminopeptidase (LAP)) in DL treatment were significantly higher than those in NR treatment. Moreover, enzyme activities related to P cycling are significantly higher in comparison to other treatments. The acid phosphatase (AP), which is related to the P cycle, showed the highest activity under NR treatment. In addition, there was no significant difference in soil microbial metabolic limitation by the different carbon inputs, which did not change the original nutrient limitation pattern. The main drivers of microbial nutrient metabolic limitation included soil physicochemical properties, soil total nutrients, and available nutrients, among which soil SWC and pH presented the greatest influence on microbial C limitation and soil total nutrients showed the greatest influence on microbial N limitation. Changes in soil carbon input altered soil extracellular enzyme activities and their stoichiometric ratios by affecting soil physicochemical properties, total nutrients. This study provides data for the understanding of material cycling in forest ecosystems under environmental change.

Crop residue heterogeneity: Decomposition by potential indigenous ligno-cellulolytic microbes and enzymatic profiling

The continuous depletion of fossil resources, energy-crisis and environmental pollution has gained popularity for careful selection of suitable microbial consortium to efficiently decompose crop residue and facilitate nutrient cycling. While crop residue is commonly incorporated into soil, the impact of the heterogeneity of residue on decomposition and biological mechanisms involved in extracellular carbon (C) cycle related enzyme activities remain not fully understood. To address this problem, an incubation study was conducted on chemical heterogeneity of straw and root residue with indigenous ligno-cellulolytic microbial consortium on extracellular enzymes as their activity is crucial for making in-situ residue management decisions under field condition. The activity of extracellular enzymes in different substrates showed differential variation with the type of enzyme and ranged from 16.9 to 77.6 µg mL−1, 135.7 to 410.8 µg mL−1, 66.9 to 177.1 µg mL−1 and 42.1 to 160.9 µg mL−1 for cellulase, xylanase, laccase and lignin peroxidase, respectively. Extracellular enzyme activities were sensitive to heterogeneity of biochemical constituent's present in straw and root residues and enhanced the decomposition processes with indigenous ligno-cellulolytic microbial consortium (Bacillus altitudinis, Streptomyces flavomacrosporus and Aspergillus terreus). Correlation matrix elucidated A. terreus and B. altitudinis as potential indigenous ligno-cellulolytic microbial inoculant influencing soil enzymatic activity (p < 0.001). This research work demonstrates a substantial impact of chemically diverse crop residues on the decomposition of both straw and root. It also highlights the pivotal role played by key indigenous decomposers and interactions between different microorganisms in governing the decomposition of straw and root primarily through release of extracellular enzymes. Consequently, it is novel bio-emerging strategy suggested that incorporation of the crop residues under field conditions should be carried out in conjunction with the potential indigenous ligno-cellulolytic microbial consortium for efficient decomposition in a short period of time under sustainable agriculture system.