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Leaf litter microbes collectively degrade plant polysaccharides, influencing land-atmosphere carbon exchange. An open question is how substrate complexity-defined as the structure of the saccharide and the amount of external processing by extracellular enzymes-influences species interactions. We tested the hypothesis that monosaccharides (i.e. xylose) promote negative interactions through resource competition, and polysaccharides (i.e. xylan) promote neutral or positive interactions through resource partitioning or synergism among extracellular enzymes. We assembled a three-species community of leaf litter-degrading bacteria isolated from a grassland site in Southern California. In the polysaccharide xylan, pairs of species stably coexisted and grew equally in coculture and in monoculture. Conversely, in the monosaccharide xylose, competitive exclusion and negative interactions prevailed. These pairwise dynamics remained consistent in a three-species community: all three species coexisted in xylan, while only two species coexisted in xylose, with one species capable of using peptone. A mathematical model showed that in xylose these dynamics could be explained by resource competition. Instead, the model could not predict the coexistence patterns in xylan, suggesting other interactions exist during biopolymer degradation. Overall, our study shows that substrate complexity influences species interactions and patterns of coexistence in a synthetic microbial community of leaf litter degraders.

Understanding the interactions of carbon and metal pollutants in anthropogenically impacted rivers is a prerequisite for determining the relative fates of these stressors. Here, through two sets of studies, we report carbon–metal pollutant interactions choosing the CO2 emission and sediment microbial extracellular enzyme activities as major determinants. The study, conducted along a 520-km main river and along a point source trajectory, showed a TOC-dependent but metal pollution-constrained CO2 emission. We found significant relationships (p < 0.05–0.001) between CO2 emission flux and its determinants: TOC, Cmic, FDAase and β-D-glucosidase. In the point source trajectory, CO2 emission flux was closely synchronous to these determinants. These relationships, however, were significantly constrained at the sites such as Knuj, Jjmu and Rjht where the concentrations of total heavy metal (∑THM) in the sediment exceed 347.44 µg g−1 indicating that the heavy metal pollution counteracted the C processing and consequently the CO2 emission flux. The study suggests that the excessive load of metal pollutants will eventually interrupt the C-cycling in the Ganga River inviting caution in C budgeting and C transport to coastal ocean. [ABSTRACT FROM AUTHOR]

Corn cobs consist primarily of a lignocellulosic material comprising hemicellulose, cellulose, and lignin in a crystalline state, which is resistant to microbial saccharification. Bioethanol production from corn cobs has rarely been attempted, especially using chemical pretreatment methods. The present study deals with the production and purification of fungal (Phanerochaete chrysosporium MTCC 787 and Pleurotus florida PAU 22‐01) extracellular ligninolytic enzymes – lignin peroxidase (LiP), manganese peroxidase (MnP), and laccase (Lac) – followed by their utilization for the biological pretreatment of corn cobs along with saccharification using commercial cellulase. Crude LiP, MnP, and Lac demonstrated specific activity of 2.23, 2.1, and 2.63 U/mg, respectively. The one‐step purification of crude enzyme using diethyl amino ethyl (DEAE) cellulose ion exchange chromatography resulted in 11.3, 10.1 and 8.62‐fold purification of LiP, MnP and Lac activity, respectively, with corresponding specific activity of 25.1 U/mg (LiP), 21.2 U/mg (MnP) and 22.7 U/mg (Lac) in the partially purified ligninozymes. Using the latter, biological pretreatment of 2.5 g corn cobs in a reaction volume of 30 mL containing approximately 200 units of Lac, Lip and MnP enzymes (in phosphate buffer, pH 6) resulted in a maximum of 78.4% delignification with a saccharification efficiency of 97.1% using commercial cellulases. [ABSTRACT FROM AUTHOR]

Purpose: The influence of organic amendments on the interplay among soil extracellular enzyme activities (EEAs) and their stoichiometry (EES) and nutrient availabilities, key indicators of resource limitations for soil microbes, is poorly understood. This study aims to investigate how manure compost (hereafter "manure") and its biochar derivative affect EEAs, EES and soil fertility. Materials and methods: We studied EEAs (BG, β-glucosidase; CBH, cellobiohydrolase; LAP, Leucine aminopeptidase; NAG, β-1,4-N-acetylglucosaminidase and AP, acid phosphatase), EES and soil fertility two years post-application of manure and biochar in central Alberta, Canada. Results and discussion: Applying manure and its biochar did not affect soil permanganate oxidable carbon (C), total phosphorus (P), and available P and nitroegn (N). Manure application increased NAG activity by 13.9% (75.9 nmol h−1 g−1 soil) relative to the control (66.6 nmol h−1 g−1 soil), whereas biochar application increased LAP activity by 22.1% (64.6 nmol h−1 g−1 soil) compared to the manure treatment (52.9 nmol h−1 g−1 soil), suggesting that manure addition caused microbial C limitation, while biochar addition led to microbial N limitation. However, both manure and biochar treatments did not affect soil NAG, CBH and AP, and enzymatic C:N, C:P, and N:P stoichiometry. Manure and biochar and their interactions with the soil ultimately affect soil physicochemical properties. Conclusions: Manure and its biochar differentially altered some soil N-cycling EEAs and C and N limitations two years after their applications. [ABSTRACT FROM AUTHOR]

The color of textile wastewater is still a main problem in wastewater treatment by biological processes. The colored effluents from textile factories usually exceed effluent standards. Therefore, various innovations were developed to treat textile wastewater for decolorization in the effluents. This research aims to decolorize textile wastewater by immobilizing white rot fungi degradation. At first, the 11 fungal stains were tested to find the decolorized efficiency then the high decolorized efficiency fungal stains were immobilized on four material media, namely water hyacinth stalks, coconut husk, corn cob, and loofah. After that, the immobilized fungi were cultivated in the culture media at 30, 60, and 120 C/N ratios, respectively. The results showed that Trametes sanguinea and Perenniporia tephropora were two stains with a high decolorized efficiency of 68.8% and 67.5% respectively, and the decolorized efficiency was increased when immobilized on loofahs and fed with 120 C/N ratio medium. In a comparison of two fungal stains, P. tephropora was found more suitable for the decolorization of textile wastewater than T. sanguinea because T. sanguinea could produce red-orange pigments that induced the colored enhancement in wastewater over time. Finally, immobilized P. tephropora was cultivated in a 120 C/N ratio medium within a 10 L continuous stirred tank reactor (8 L working volume) to investigate the decolorized efficiency, enzymatic activity, and repeated batch. It was found that three repeated cycles were carried out by reusing the immobilized P. tephropora and the highest decolorized efficiency was 63.4%. The enzymatic activity of laccase, manganese peroxidase, and lignin peroxidase was 15.5 U/L, 85.9 U/L, and 0 U/L, respectively [ABSTRACT FROM AUTHOR]

Soil microbial extracellular enzymes play crucial roles in soil carbon and nutrient cycling by catalyzing soil biochemical processes. However, the activity and stoichiometry of enzymes involved in the carbon, nitrogen, and phosphorus cycles in the environment with the highest density of wild giant pandas on the southern slopes of the Qinling Mountains is unknown. We have established eight research areas at an elevation of 1090–2621 m. The β‐1,4‐glucosidase (BG), β‐1,4‐N‐acetylglucosaminidase (NAG), and acid phosphatase (APase) in soil samples were measured. We used redundancy analysis and structural equation model to evaluate the driving factors of metabolic restriction of soil microorganisms along the elevational gradient, and four models were used to cross‐evaluate the nutrient restriction status of soil microorganisms. The results showed that most soil physiochemical properties, soil microbial biomass, and microbial extracellular enzymes exhibited a hump‐shaped trend with increasing elevation. Elevation indirectly affected soil enzyme activity and stoichiometry by C, N, and P status. Microorganisms are limited by C at lower and higher elevations but limited by N at medium elevations. These results could help strengthen the conservation and management of the wild panda's natural habitat. [ABSTRACT FROM AUTHOR]

Wildfire is a disturbance expected to increase in frequency and severity, changes that may impact carbon (C) dynamics in the soil ecosystem. Fire changes the types of C sources available to soil microbes, increasing pyrogenic C and coarse downed wood, and if there is substantial tree mortality, decreasing C from root exudates and leaf litter. To investigate the impact of this shift in the composition of C resources on microbial processes driving C cycling, we examined microbial activity in soil sampled from an Oregon burn 1 year after fire from sites spanning a range in soil burn severity from unburned to highly burned. We found evidence that postfire rhizosphere priming loss may reduce soil C loss after fire. We measured the potential activity of C‐acquiring and nitrogen (N)‐acquiring extracellular enzymes and contextualized the microbial resource demand using measurements of mineralizable C and N. Subsurface mineralizable C and N were unaltered by fire and negatively correlated with hydrolytic extracellular enzyme activity (EEA) in unburned, but not burned sites. EEA was lower in burned sites by up to 46%, but only at depths below 5 cm, and with greater decreases in sites with high soil burn severity. These results are consistent with a subsurface mechanism driven by tree mortality. We infer that in sites with high tree mortality, subsurface EEAs decreased due to loss of rhizosphere priming and that inputs of dead roots contributed to mineralizable C stabilization. [ABSTRACT FROM AUTHOR]

Biological soil crusts (biocrusts) are crucial elements of desert ecosystems, exhibiting patchy distribution patterns across the soil surface and significantly impacting surface soil nutrient dynamics. However, the influence of biocrust patch units, serving as fundamental functional entities, on microbial nutrient restriction remains underexplored. This study conducted measurements on moss crust patches of varying sizes and subcrust soils. Stoichiometric analysis of extracellular enzyme activities (EEAs) related to carbon, nitrogen, and phosphorus was performed, along with vector and redundancy analyses to evaluate microbial nutrient limitation and key influencing factors. The findings reveal that both patch size and soil layer of biocrusts collectively influence soil nutrients and enzyme dynamics, with heightened enzyme activity observed in the crust layer. Vector analysis based on EEA stoichiometry indicates that moss crust patch size insignificantly impacts microbial nutrient restriction within the crust layer. However, microbial nitrogen restriction in the subcrust layer demonstrates a “single‐peak” trend, initially increasing before gradually declining. This suggests that microorganisms in medium‐sized crust patches exhibit peak activity, intensifying nutrient competition. This research underscores the pivotal role of biocrust patch units as fundamental functional entities, offering comprehensive insights into microbial metabolic constraints under crust cover. The findings underscore the significant implications of enzyme stoichiometric characteristics for desert land management and conservation. [ABSTRACT FROM AUTHOR]

Introduction: Rhizosphere effects (REs) have recently been identified as important regulators of root and microbial nutrient acquisition and are positively involved in nutrient cycling of belowground carbon (C), nitrogen (N), and phosphorus (P). Nutrient conditions of the fine roots and soil N are likely to influence REs. Still, it is unclear how REs of soil nutrients themselves variably impact the supply of nutrients to plants in terms of the responses to soil N due to succession. Methods: In this study, we applied both fine roots and extracellular enzymes for vector analysis and stoichiometry of N:P to explore the metabolic limitations of roots and rhizospheric soil microbes and their relationships with REs across five levels of soil N (0, 5, 10, 15, and 20 kg N m-2 year-1) along successional age classes of 42, 55, and 65 years in a Pinus tabuliformis forest. Results: Overall, the metabolism of root and rhizospheric soil microbes was mediated by soil N. N limitation of roots initially decreased before increasing, whereas that of microbes demonstrated opposite trends to the N levels owing to competition for inorganic N between them by REs of NO3--N. However, N limitations of both roots and microbes were alleviated in young stands and increased with succession after the application of N. In addition, root N limitations were manipulated by REs of three different soil N-related indicators, i.e., total N, NH4 +-N, and NO3 --N. Rhizospheric soil microbial N limitation was almost unaffected by REs due to their strong homeostasis but was an important driver in the regulation of root N limitation. Discussion: Our results indicated that successional age was the most critical driver that directly and indirectly affected root N metabolism. However, the level of N application had a slight effect on root N limitation. Microbial N limitation and variations in the REs of N indicators regulated root N limitation in the rhizosphere. As a result, roots utilized REs to sequester N to alleviate N limitations. These findings contribute to novel mechanistic perspectives on the sustainability of N nutrition by regulating N cycling in a system of plant-soil-microbes in the rhizosphere to adapt to global N deposition or the heterogeneous distribution of bioavailable soil N with succession. [ABSTRACT FROM AUTHOR]

Although depolymerization of complex carbohydrates is a growth-limiting bottleneck for microbial decomposers, we still lack understanding about how the production of different types of extracellular enzymes affect individual microbes and in turn the performance of whole decomposer communities. In this work we use a theoretical model to evaluate the potential trade-offs faced by microorganisms in biopolymer decomposition which arise due to the varied biochemistry of different depolymerizing enzyme classes. We specifically consider two broad classes of depolymerizing extracellular enzymes, which are widespread across microbial taxa: exo-enzymes that cleave small units from the ends of polymer chains and endo-enzymes that act at random positions generating degradation products of varied sizes. Our results demonstrate a fundamental trade-off in the production of these enzymes, which is independent of system's complexity and which appears solely from the intrinsically different temporal depolymerization dynamics. As a consequence, specialists that produce either exo- or only endo-enzymes limit their growth to high or low substrate conditions, respectively. Conversely, generalists that produce both enzymes in an optimal ratio expand their niche and benefit from the synergy between the two enzymes. Finally, our results show that, in spatially-explicit environments, consortia composed of endo- and exo-specialists can only exist under oligotrophic conditions. In summary, our analysis demonstrates that the (evolutionary or ecological) selection of a depolymerization pathway will affect microbial fitness under low- or high substrate conditions, with impacts on the ecological dynamics of microbial communities. It provides a possible explanation why many polysaccharide degraders in nature show the genetic potential to produce both of these enzyme classes. Author summary: The decomposition of polysaccharides by microbes is a key process in the global carbon cycle. It requires the joint action of a variety of microbially-produced extracellular enzymes. They can be broadly classified into endo-enzymes, that act in the middle of polymers, and exo-enzymes, that cleave units from polymer ends. Little is known about the benefits for microbes producing a certain enzyme type and the interplay between enzyme producing strategies in mixed communities. This hampers our comprehensive understanding of decomposition in terrestrial and marine ecosystems and thus limits the prediction of decomposition processes, for example in a changing climate. Based on theoretical modelling, we revealed a fundamental trade-off in the action of these enzymes. While exo-enzymes are more efficient at high substrate conditions, endo-enzymes perform better when substrate is low. Generalists producing both enzymes expand their ecological niche of substrate availability compared to specialists only producing one of the two types. Complementary specialists only co-exist in oligotrophic conditions. We conclude that producing enzymes for specific steps within polymer degradation represents relevant ecological strategies for microbes in decomposer communities. [ABSTRACT FROM AUTHOR]

Plant parasitic nematodes (PPNs) pose a significant threat to global crop productivity, causing an estimated annual loss of US $157 billion in the agriculture industry. While synthetic chemical nematicides can effectively control PPNs, their overuse has detrimental effects on human health and the environment. Biocontrol agents (BCAs), such as bacteria and fungi in the rhizosphere, are safe and promising alternatives for PPNs control. These BCAs interact with plant roots and produce extracellular enzymes, secondary metabolites, toxins, and volatile organic compounds (VOCs) to suppress nematodes. Plant root exudates also play a crucial role in attracting beneficial microbes toward infested roots. The complex interaction between plants and microbes in the rhizosphere against PPNs is mostly untapped which opens new avenues for discovering novel nematicides through multi-omics techniques. Advanced omics approaches, including metagenomics, transcriptomics, proteomics, and metabolomics, have led to the discovery of nematicidal compounds. This review summarizes the status of bacterial and fungal biocontrol strategies and their mechanisms for PPNs control. The importance of omics-based approaches for the exploration of novel nematicides and future directions in the biocontrol of PPNs are also addressed. The review highlighted the potential significance of multi-omics techniques in biocontrol of PPNs to ensure sustainable agriculture. [ABSTRACT FROM AUTHOR]

Microflora of reptiles and amphibians pose a serious threat to the environment and humans, as these bacteria are more resistant to antimicrobials or have more virulence factors. In this study, we focused on the characterization of Gram-negative bacterial isolates obtained from Mauremys rivulata (Western Caspian turtle), Natrix natrix (Grass snake), Natrix tessellata (Dice snake) and Pelophylax bedriagae (Levantine frog) using cultural methods and determine some virulence factors (antibiotic resistance, VanA and TetM resistant genes, biofilm, siderophore and some enzymatic activities etc.). Multiple antibiotic resistance (MAR) and virulence index (VI) of each strain were also calculated. A total of 85 Gram-negative isolates exhibited varying levels of antibiotic resistance and the ability to produce one or more extracellular enzymes such as amylase, lecithinase, protease, lipase, hemolysis, siderophore, amino acid decarboxylase and DNase. Although the TetM has been identified in all 7 isolates, none of the isolates have shown the presence of the VanA gene. According to MAR and VI results, most of the isolates were found to be in the high threat group and these indexes were correlated with antibiotic resistance. The study data revealed that chemicals used in industry and agriculture both trigger environmental pollution and pose risk factors for wildlife. [ABSTRACT FROM AUTHOR]

The entomopathogenic fungus (EPF) Metarhizium acridum is a typical filamentous fungus and has been used to control migratory locusts (Locusta migratoria manilensis). This study examines the impact of the Zn(II)2Cys6 transcription factor, MaAzaR, in the virulence of M. acridum. Disruption of MaAzaR (ΔMaAzaR) diminished the fungus's ability to penetrate the insect cuticle, thereby decreasing its virulence. The median lethal time (LT50) for the ΔMaAzaR strain increased by approximately 1.5 d compared to the wild-type (WT) strain when topically inoculated, simulating natural infection conditions. ΔMaAzaR compromises the formation, turgor pressure, and secretion of extracellular hydrolytic enzymes in appressoria. However, the growth ability of ΔMaAzaR within the hemolymph is not impaired; in fact, it grows better than the WT strain. Moreover, RNA-sequencing (RNA-Seq) analysis of ΔMaAzaR and WT strains grown for 20 h on locust hindwings revealed 87 upregulated and 37 downregulated differentially expressed genes (DEGs) in the mutant strain. Pathogen–host interaction database (PHI) analysis showed that about 40% of the total DEGs were associated with virulence, suggesting that MaAzaR is a crucial transcription factor that directly regulates the expression of downstream genes. This study identifies a new transcription factor involved in EPF cuticle penetration, providing theoretical support and genetic resources for the developing highly virulent strains. [ABSTRACT FROM AUTHOR]

The culturable yeast communities in temperate forest soils under the ornithogenic influence were studied in a seasonal dynamic. To investigate the intense ornithogenic influence, conventional and "live" feeders were used, which were attached to trees in the forest and constantly replenished throughout the year. It was found that the yeast abundance in the soil under strong ornithogenic influence reached the highest values in winter compared to the other seasons and amounted to 4.8 lg (cfu/g). This was almost an order of magnitude higher than the minimum value of yeast abundance in ornithogenic soils determined for summer. A total of 44 yeast species, 21 ascomycetes and 23 basidiomycetes, were detected in ornithogenic soil samples during the year. These included soil-related species (Barnettozyma californica, Cyberlindnera misumaiensis, Cutaneotrichosporon moniliiforme, Goffeauzyma gastrica, Holtermanniella festucosa, Leucosporidium creatinivorum, L. yakuticum, Naganishia adeliensis, N. albidosimilis, N. globosa, Tausonia pullulans, and Vanrija albida), eurybionts (yeast-like fungus Aureobasidium pullulans, Debaryomyces hansenii, and Rhodotorula mucilaginosa), inhabitants of plant substrates and litter (Cystofilobasidium capitatum, Cys. infirmominiatum, Cys. macerans, Filobasidium magnum, Hanseniaspora uvarum, Metschnikowia pulcherrima, and Rh. babjevae) as well as a group of pathogenic and opportunistic yeast species (Arxiozyma bovina, Candida albicans, C. parapsilosis, C. tropicalis, Clavispora lusitaniae, and Nakaseomyces glabratus). Under an ornithogenic influence, the diversity of soil yeasts was higher compared to the control, confirming the uneven distribution of yeasts in temperate forest soils and their dependence on natural hosts and vectors. Interestingly, the absolute dominant species in ornithogenic soils in winter (when the topsoil temperature was below zero) was the basidiomycetous psychrotolerant yeast T. pullulans. It is regularly observed in various soils in different geographical regions. Screening of the hydrolytic activity of 50 strains of this species at different temperatures (2, 4, 10, 15 and 20 °C) showed that the activity of esterases, lipases and proteases was significantly higher at the cultivation temperature. Ornithogenic soils could be a source for the relatively easy isolation of a large number of strains of the psychrotolerant yeast T. pullulans to test, study and optimize their potential for the production of cold-adapted enzymes for industry. [ABSTRACT FROM AUTHOR]

The goal of this study was to isolate endophytic fungi from Ocimum sanctum L. and to evaluate their biological potential, including antibacterial, antioxidant, and enzymatic activities and further characterization of the bioactive compounds. Nine endophytic fungi were isolated from the leaves and stem tissues of O. sanctum collected from the botanical garden of Banaras Hindu University, Varanasi, India. All isolates were identified based on their microscopic structures and molecular sequencing of the ITS rDNA. Aspergillus clavatonanicus (SS7) and Cochliobolus hawaiiensis (SL3) showed the highest colonization frequencies in the stem and leaves (16 and 14%, respectively). All fungal isolates were tested for extracellular enzymatic activities of amylase, cellulase, and pectinase. Of the nine fungal isolates, 60% tested positive for amylase and cellulase, whereas 50% showed pectinase activity. Using a disc diffusion assay, the extracted secondary metabolites were checked for antibacterial activity against three human pathogenic bacteria. Two isolates, SL2 and SS7, exhibited the highest antibacterial activity against all pathogens, including Enterococcus faecalis, Klebsiella pneumoniae, and methicillin-resistant Staphylococcus aureus (MRSA). Crude extracts of the six fungal isolates showed positive antioxidant activity. The crude extract of Aspergillus allahabadii (isolate SL2) showed strong antibacterial and antioxidant activities and crystallized during purification. X-ray crystallography confirmed the identity of the crystal as citrinin, which also exhibited strong anticancer activity against Dalton's lymphoma cells. The results of this study suggest that endophytic fungi isolated from the leaf and stem tissues of Ocimum sanctum are potential sources of antibacterial, antioxidant, and anticancer compounds. [ABSTRACT FROM AUTHOR]

The phosphorus (P) concentration is increasing in parts of the Baltic Sea following the spring bloom. The fate of this excess P-pool is an open question, and here we investigate the role of microbial degradation processes in the excess P assimilation phase. During a 17-day-long mesocosm experiment in the southwest Finnish archipelago, we examined nitrogen, phosphorus, and carbon acquiring extracellular enzyme activities in three size fractions (<0.2, 0.2–3, and >3 µm), bacterial abundance, production, community composition, and its predicted metabolic functions. The mesocosms received carbon (C) and nitrogen (N) amendments individually and in combination (NC) to distinguish between heterotrophic and autotrophic processes. Alkaline phosphatase activity occurred mainly in the dissolved form and likely contributed to the excess phosphate conditions together with grazing. At the beginning of the experiment, peptidolytic and glycolytic enzymes were mostly produced by free-living bacteria. However, by the end of the experiment, the NC-treatment induced a shift in peptidolytic and glycolytic activities and degradation of phosphomonoesters toward the particle-associated fraction, likely as a consequence of higher substrate availability. This would potentially promote retention of nutrients in the surface as opposed to sedimentation, but direct sedimentation measurements are needed to verify this hypothesis. [ABSTRACT FROM AUTHOR]

Soil microbial traits and functions play a central role in soil organic carbon (SOC) dynamics. However, at the macroscale (regional to global) it is still unresolved whether (i) specific environmental attributes (e.g., climate, geology, soil types) or (ii) microbial community composition drive key microbial traits and functions directly. To address this knowledge gap, we used 33 grassland topsoils (0–10 cm) from a geoclimatic gradient in Chile. First, we incubated the soils for 1 week in favorable standardized conditions and quantified a wide range of soil microbial traits and functions such as microbial biomass carbon (MBC), enzyme kinetics, microbial respiration, growth rates as well as carbon use efficiency (CUE). Second, we characterized climatic and physicochemical properties as well as bacterial and fungal community composition of the soils. We then applied regression analysis to investigate how strongly the measured microbial traits and functions were linked with the environmental setting versus microbial community composition. We show that environmental attributes (predominantly the amount of soil organic matter) determined patterns of MBC along the gradient, which in turn explained microbial respiration and growth rates. However, respiration and growth normalized for MBC (i.e., specific respiration and growth) were more linked to microbial community composition than environmental attributes. Notably, both specific respiration and growth followed distinct trends and were related to different parts of the microbial community, which in turn resulted in strong effects on microbial CUE. We conclude that even at the macroscale, CUE is the result of physiologically decoupled aspects of microbial metabolism, which in turn is partially determined by microbial community composition. The environmental setting and microbial community composition affect different microbial traits and functions, and therefore both factors need to be considered in the context of macroscale SOC dynamics. [ABSTRACT FROM AUTHOR]

Dye is a substance that imparts colour onto textiles, fabrics, paper, leather, etc. and is not altered by washing, heating, and light. Dyes were extracted from plants, animals, and minerals until synthetic dyes came to the market, as synthetic dyes were more stable, readily available, and inexpensive. Despite being extremely important to the economy, they have been among the most significant global polluters. Textile dye industries have become the chief source of water pollution, with their effluents increasing the turbidity of water and reducing photosynthesis and dissolved oxygen levels. This leads to significant damage to aquatic biodiversity, threatening the survival of many species. Synthetic dyes have carcinogenic, mutagenic, and genotoxic effects on animals and human beings, posing a severe health risk. The degradation of dyes is essential for ensuring the sustainability of the environment for future generations. The traditional physicochemical means of dye treatment are not convenient because of the high solubility in water, cost of method utilisation and other disadvantages related to these techniques. To overcome the disadvantages of physicochemical treatment, biological methods or bioremediation can be used as an alternative. The objective of this review article is to study the mechanisms involved in the degradation of textile dyes by bacteria to obtain sustainable, economically and ecologically sound solutions for dye treatment. This paper will explain the various types of natural and synthetic dyes utilised in the textile industry, their chemistry, and how they affect water and soil ecosystems. The treatment of textile dye by various physicochemical methods and their advantages and disadvantages are also discussed. In bioremediation, the microorganisms utilize organic pollutants as a source of food or energy. Bioremediation uses biosorption and enzymatic activity for dye degradation, which does not disturb natural processes and is thus sustainable. The microorganisms secrete crucial extracellular and intracellular enzymes that carry out decolourisation and degradation through a series of events, which include hydrolysis, acidogenesis, and methanogenesis. We will discuss how aerobic and anaerobic microorganisms degrade these textile dyes through the process of biodegradation and bioaugmentation and how this technology provides a clean and eco-friendly method for removing textile dyes. [ABSTRACT FROM AUTHOR]

The extent to which soil enzyme activity in assessing soil nutrient availability is useful has been controversial. In this review, we discuss the utility of ecoenzymatic stoichiometry (i.e. the ratio of nutrient- to carbon (C)-acquiring enzyme activities) on the basis of the resource allocation model for ecoenzyme synthesis. Both the selection of appropriate enzymes and the balance between relative amounts of substrates and enzymes in the soil are decisive factors in utilizing the ecoenzymatic stoichiometry. Ecoenzymatic stoichiometry can evaluate the availability of nitrogen (N), phosphorus, and sulfur in many soils in which the enzyme catalytic reactions are substrate-limited but not enzyme-limited. However, the ecoenzymatic stoichiometry approach does not seem to be applicable in soils where microbes are limited by factors other than nutrient availability, such as low temperature, where the enzyme catalytic reactions are enzyme-limited. Certain enzymes, such as N-acetyl-β-glucosaminidase and protease, appear to be insensitive to soil N availability, because they release compounds containing both N and C which serve as sources for both N and C/energy. We propose the use of enzymes such as L-asparaginase and urease as N-acquiring enzymes that release a compound containing N but not C (i.e. NH4+) as the hydrolysis product. Ecoenzymatic stoichiometry can be considered as an indicator of long-term (weeks) temporally integrated soil nutrient availability, rather than instantaneous availability, for plants as well as microbes, because of (i) the long-term persistence of extracellular enzymes in soils; (ii) a significant correlation between ecoenzymatic stoichiometry and the measurements reflecting the quantity of long-term available nutrients in soil; and (iii) a significant correlation between ecoenzymatic stoichiometry and plant nutrient uptake. This review also identifies challenges in assessing microbial nutrient limitation using ecoenzymatic stoichiometry. With a comprehensive understanding of underlying mechanisms and limitations, ecoenzymatic stoichiometry can be used as a biologically relevant indicator of nutrient availability in combination with other approaches such as conventional chemical extraction methods and the nutrient addition approach. [ABSTRACT FROM AUTHOR]

Increasing nitrogen (N) deposition alters the availability of soil nutrients and is likely to intensify phosphorus (P) limitations, especially in P-limited tropical and subtropical forests. Soil microorganisms play vital roles in carbon (C) and nutrient cycling, but it is unclear whether and how much N and P imbalances affect the soil's microbial metabolism and mechanisms of nutrient limitations. In this study, a 3-year field experiment of N and P addition (control (CK), 100 kg N ha−1 yr−1 (N), 50 kg P ha−1 yr−1 (P), and NP) was set up to analyze the extracellular enzyme activities and stoichiometry characteristics of the top mineral soils in Chinese fir plantations with different stand ages (7, 20, and 33 years old). The results showed that the enzyme activities associated with the acquisition of C (β-1,4-glucosidase (BG) and β-d-cellobiohydrolase (CBH)) and P (acid phosphatases (APs)) in the N treatment were significantly higher than those in the CK treatment. Moreover, vector analysis revealed that both the vector's length and angle increased in stands of all ages, which indicated that N addition aggravated microbial C and P limitations. The P and NP treatments both significantly decreased the activity of AP and the enzymes' N:P ratio, thereby alleviating microbial P limitations, as revealed by the reduction in the vector's angle. Stand age was found to promote all enzymatic activities but had no obvious effects on the limitation of microbial metabolism with or without added nutrients in the soils under Chinese fir. Available N, Olsen-P, and pH were the main drivers of microbial metabolic limitations related to C nutrients. These results provide useful data for understanding the change in soil microbial activity in response to environmental changes, and suggest that P fertilization should be considered for management to improve productivity and C sequestration in Chinese fir plantation in the context of increased deposition of N. [ABSTRACT FROM AUTHOR]

Among 79 Bacillus spp. isolated from Miang, a fermented tea in north Thailand, 17 Bacillus strains were selected with probiotic potential in Nile tilapia culture based on the capabilities of bacteriocin production and associated antimicrobial activities against fish pathogens, Aeromonas hydrophila and Streptococcus agalactiae. However, only six isolates were selected for further extensive studies based on the strength of their antimicrobial activities and their tolerance against simulated gastrointestinal conditions. The molecular identification by 16S rRNA gene sequence analysis revealed that five isolates, K2.1, K6.1, K7.1, K15.4, and K22.6, were Bacillus tequilensis, and the isolate K29.2 was Bacillus siamensis. B. siamensis K29.2 showed complete susceptibility to antibiotics tested in this study, while B. tequilensis K 15.4 showed moderate resistance to some antibiotics; therefore, both strains were selected as potential probiotic bacteria. B. tequilensis K15.4 and B. siamensis K29.2 were capable of the production and secretion of extracellular protease and polysaccharide degrading enzymes, including cellulase, xylanase, and β-mannanase. The tannin tolerant test also demonstrated their ability to grow on selective agar plates and secrete cellulase and β-mannanase in the presence of hydrolyzable tannin. In addition, in vitro digestion of commercial fish substrate revealed that the extracellular enzymes produced by both strains efficiently reacted with feed protein and polysaccharides. Based on the results from this study, B. siamensis K29.2 was deemed to have the highest potential multifunctional probiotic qualities for application in Nile tilapia culture, while the antibiotic-resistant gene in B. tequilensis K15.4 must be clarified before field application. [ABSTRACT FROM AUTHOR]

The natural soil environment of Streptomyces is characterized by variations in the availability of nitrogen, carbon, phosphate and sulfur, leading to complex primary and secondary metabolisms. Their remarkable ability to adapt to fluctuating nutrient conditions is possible through the utilization of a large amount of substrates by diverse intracellular and extracellular enzymes. Thus, Streptomyces fulfill an important ecological role in soil environments, metabolizing the remains of other organisms. In order to survive under changing conditions in their natural habitats, they have the possibility to fall back on specialized enzymes to utilize diverse nutrients and supply compounds from primary metabolism as precursors for secondary metabolite production. We aimed to summarize the knowledge on the C-, N-, P- and S-metabolisms in the genus Streptomyces as a source of building blocks for the production of antibiotics and other relevant compounds. [ABSTRACT FROM AUTHOR]

Litter's chemical complexity influences carbon (C) cycling during its decomposition. However, the chemical and microbial mechanisms underlying the divergence or convergence of chemical complexity under UV radiation remain poorly understood. Here, we conducted a 397-day field experiment using 13C cross-polarization magic-angle spinning nuclear magnetic resonance (13C-CPMAS NMR) to investigate the interactions among the initial chemistry, microbial communities, and UV radiation during decomposition. Our study found that the initial concentrations of O-substituted aromatic C, di-O-alkyl C, and O-alkyl C in Deschampsia caespitosa were higher than those in Kobresia tibetica. Litter's chemical composition exhibited divergent patterns based on the initial chemistry, UV radiation, and decay time. Specifically, D. caespitosa consistently displayed higher concentrations of di-O-alkyl C and O-alkyl C compared to K. tibetica, regardless of the UV exposure and decay time. Additionally, litter's chemical complexity was positively correlated with changes in the extracellular enzyme activities, particularly those involved in lignin, cellulose, and hemicellulose degradation, which accounted for 9%, 20%, and 4% of the variation in litter's chemical complexity, respectively. These findings highlighted the role of distinct microbial communities in decomposing different C components through catabolism, leading to chemical divergence in litter. During the early decomposition stages, oligotrophic Planctomycetes and Acidobacteria metabolized O-alkyl C and di-O-alkyl C under UV-blocking conditions. In contrast, copiotrophic Actinobacteria and Chytridiomycota utilized these components under UV radiation exposure, reflecting their ability to thrive under UV stress conditions due to their rapid growth strategies in environments rich in labile C. Our study revealed that the inherent differences in the initial O-alkyl C and di-O-alkyl C contributed to the chemical divergence, while UV radiation further influenced this divergence by shifting the microbial community composition from oligotrophic to copiotrophic species. Thus, differences in the initial litter chemistry, microbial community, and UV radiation affected the quantity and quality of plant-derived C during decomposition. [ABSTRACT FROM AUTHOR]

The bio-depolymerization of coal is a promising technology for converting coal into low-molecular-weight industrial chemicals. In this study, we investigated the characteristics of biodepolymerized coal (BDC) and the associated depolymerization pathway. We analyzed the extracellular enzyme activities of Hypocrea lixii AH in the biodepolymerization system, performed Fourier transform infrared spectroscopy (FTIR) and 13C nuclear magnetic resonance spectroscopy (NMR) of BDC, and performed gas chromatography and mass spectrometry (GC/MS) of the BDC methanol extract. Results showed that the activities of peroxidase (POD), polyphenol oxidase (PPO), laccase (Lac), and lignin peroxidase (LiP) were 1377, 162, 10, and 1.919 U, respectively. Following biodepolymerization by Hypocrea lixii AH, 20 organic compounds were identified. Benzaldehyde 4-hydroxy-3,5-dimethoxy was the most dominant at 33.16%, followed by (Z)-9-octadecenamide, accounting for 14.73%. The aromaticity (fa) decreased from 54.3% to 23.7%, suggesting ring-opening reactions catalyzed by LiP and Lac. The ratio of carbonyl carbon (faC) increased from 8.3% to 16.2%, suggesting oxidation reactions catalyzed by POD. By comparing the structure of the Fushun oxidized coal model and BDC, a biodepolymerization pathway was elucidated. Biodepolymerization of Fushun oxidized coal is an oxidation–depolymerization process catalyzed by a series of enzymes, which breaks the aromatic rings and oxidizes side chains. Altogether, our findings provide a theoretical support for the chemical application of BDC. [ABSTRACT FROM AUTHOR]

Microbial communities are crucial for water quality and biogeochemical cycling in freshwaters. Microbes secrete extracellular enzymes to decompose organic matter for their needs of nutrients and scarce elements. Yet, there is a lack of knowledge on microbial metabolic limitations in freshwaters, especially in lake sediments. Here, we examined the carbon, nitrogen, and phosphorus-acquiring extracellular enzyme activities and the bacterial and fungal communities of 30 sediments across Xingkai Lake, the largest freshwater lake in Northeast Asia. We further analyzed the microbial metabolic limitations via extracellular enzyme stoichiometry and explored the direct and indirect effects of abiotic and biotic factors on the limitations. We found that microbial metabolisms were primarily limited by phosphorus in Xingkai Lake. For instance, microbial carbon and phosphorus limitations were closely correlated to abiotic factors like water depth, total dissolved solids, sediment total carbon, and conductivity. The metabolic limitations were also affected by biotic factors, such as showing positive relationships with the alpha and beta diversity of bacteria, and with the beta diversity of fungi. In addition, community compositions of bacteria and fungi were mainly correlated to abiotic factors such as total carbon and dissolved organic carbon, respectively. Collectively, microbial metabolic limitations were affected directly or indirectly by abiotic factors and microbial communities. Our findings indicate that microbial metabolic limitations are not only driven by bacteria and fungi but also by abiotic factors such as water depth and total nitrogen, and thus provide empirical evidence for effective management of freshwater lakes under climate warming and intensified human activities. [ABSTRACT FROM AUTHOR]

Heterotrophic bacteria in the ocean initiate biopolymer degradation using extracellular enzymes that yield low molecular weight hydrolysis products in the environment, or by using a selfish uptake mechanism that retains the hydrolysate for the enzyme‐producing cell. The mechanism used affects the availability of hydrolysis products to other bacteria, and thus also potentially the composition and activity of the community. In marine systems, these two mechanisms of substrate processing have been studied in the water column, but to date, have not been investigated in sediments. In surface sediments from an Arctic fjord of Svalbard, we investigated mechanisms of biopolymer hydrolysis using four polysaccharides and mucin, a glycoprotein. Extracellular hydrolysis of all biopolymers was rapid. Moreover, rapid degradation of mucin suggests that it may be a key substrate for benthic microbes. Although selfish uptake is common in ocean waters, only a small fraction (0.5%–2%) of microbes adhering to sediments used this mechanism. Selfish uptake was carried out primarily by Planctomycetota and Verrucomicrobiota. The overall dominance of extracellular hydrolysis in sediments, however, suggests that the bulk of biopolymer processing is carried out by a benthic community relying on the sharing of enzymatic capabilities and scavenging of public goods. [ABSTRACT FROM AUTHOR]

Over-dose pesticide application disrupts plant physiological processes and soil biological functions; however, the toxicity mechanisms of pesticides and the effectiveness of mitigation measures are still unclear. Our review shows that over-dose of pesticide can cause plant phytotoxicity by enhancing reactive oxygen species and cellular membrane electrolyte leakage, which subsequently decrease chlorophyll biosynthesis, vegetative growth and yield. However, the optimum use of pesticides (insecticides at 0.21 kg a.i. ha-1; herbicides at 1.44 kg a.i. ha-1 and fungicides at =0.4 kg a.i. ha-1) may not interfere with plant physiological functions, while indirectly improving plant nutrients absorption, translocation and yield. In the soil system, pesticide application decreases microbial population by disrupting the microbial metabolism and cellular protein denaturation. Moreover, pesticide application can restrict (by adsorption, etc.) glucose release from organic matter by decreasing the hydrolysis of extracellular enzymes, thereby reducing the labile C source for microbes and resulting in lower soil organic carbon cycling. The pesticide residue can decrease biological nitrogen fixation and nitrogen mineralization by decreasing diazotrophs and saprophytic bacterial population due to cellular hyperkinesis and misfunctions, respectively. Organo-phosphate pesticides can induce oxidative stress to microbes which can affect phosphorus (P) mineralization, but may also enhance P-solubilizing bacterial activities and P availability. The use of biosurfactants, exogenously induced microbes, and soil amendments (e.g., biochar) can effectively remediate pesticide toxicity through solubilization, microbial catabolism and sorption of pesticides by 70%, 78% and 69%, respectively. However, field application of biosurfactants and optimization of biochar characteristics remain challenging for effective pesticide sorption and remediation. [ABSTRACT FROM AUTHOR]

The second messenger cyclic diguanylate monophosphate (c‐di‐GMP) regulates a wide range of bacterial behaviours through diverse mechanisms and binding receptors. Single‐domain PilZ proteins, the most widespread and abundant known c‐di‐GMP receptors in bacteria, act as trans‐acting adaptor proteins that enable c‐di‐GMP to control signalling pathways with high specificity. This study identifies a single‐domain PilZ protein, XAC3402 (renamed N5MapZ), from the phytopathogen Xanthomonas citri subsp. citri (Xcc), which modulates Xcc virulence by directly interacting with the methyltransferase HemK. Through yeast two‐hybrid, co‐immunoprecipitation and immunofluorescent staining, we demonstrated that N5MapZ and HemK interact directly under both in vitro and in vivo conditions, with the strength of the protein–protein interaction decreasing at high c‐di‐GMP concentrations. This finding distinguishes N5MapZ from other characterized single‐domain PilZ proteins, as it was previously known that c‐di‐GMP enhances the interaction between those single‐domain PilZs and their protein partners. This observation is further supported by the fact that the c‐di‐GMP binding‐defective mutant N5MapZR10A can interact with HemK to inhibit the methylation of the class 1 translation termination release factor PrfA. Additionally, we found that HemK plays an important role in Xcc pathogenesis, as the deletion of hemK leads to extensive phenotypic changes, including reduced virulence in citrus plants, decreased motility, production of extracellular enzymes and stress tolerance. Gene expression analysis has revealed that c‐di‐GMP and the HemK‐mediated pathway regulate the expression of multiple virulence effector proteins, uncovering a novel regulatory mechanism through which c‐di‐GMP regulates Xcc virulence by mediating PrfA methylation via the single‐domain PilZ adaptor protein N5MapZ. [ABSTRACT FROM AUTHOR]

Background and aims: Vegetation restoration by altering soil properties has far-reaching impacts on soil extracellular enzyme activities (EEAs) and stoichiometry (EES). However, the response of EEAs and EES to changes in various soil properties along long-term vegetation restoration chronosequences in metal mining areas is still unrevealed. Methods: Soil organic carbon (SOC), nutrients such as total nitrogen (TN) and total phosphorus (TP), microbial biomass, physicochemical properties, heavy metals (Cd, Cr, Cu, Ni, V, and Zn), EEAs, and EES are appropriately analyzed along the chronosequence. Results: The EEAs exhibited an increasing trend at the early stage (0–15 years), which continued at high levels or increased thereafter at the late stage (16–49 years). The results also indicate that the enzyme C:P ratio increased linearly with time, whereas the enzyme C:N ratio lessened at the early stage and then grew at the late stage. Soil organic carbon, TN, and microbial biomass primarily controlled the variations in EEAs, and heavy metal contamination and SOC dominated the enzyme C:P ratio. Soil organic carbon and TN substantially regulated the variations in the enzyme C:N ratio at the early stage, and heavy metal contamination modulated the changes in the enzyme C:N ratio at the late stage. Conclusions: The present study suggests the potential N and P co-limitations in soils, which were essentially caused by the low P and N availabilities at the early stage of restoration. Meanwhile, we also highlight the significance of treating soil heavy metal contaminations to reduce the limitation of microbial C metabolism at the late stage. [ABSTRACT FROM AUTHOR]

Foxtail millet is typically dehulled before consumption or processing. However, foxtail millet bran also contains abundant phenolic compounds and other nutrients. Edible fungi have rich extracellular enzyme systems; are environmentally friendly and safe for consumption; and have been shown to effectively degrade lignin and cellulose. This study aimed to screen edible fungi that can effectively ferment undehusked foxtail millet, improving its nutritional value and antioxidant properties through solid‐state fermentation (SSF). The results demonstrated that fermentation utilizing Pleurotus geesteranus exhibited significant improvements in both the phenolic compound content and antioxidant properties of foxtail millet, with the optimal fermentation period determined to be 30 days. The physical and functional properties of fermented undehusked foxtail millet (FFM) flour were effectively improved, increasing crude protein, vitamin C, and crude polysaccharide contents by 11.46%, 27.78%, and 54.17%, respectively. In vitro scavenging activities of FFM were 73.19%, 93.86%, and 63.75% for 2,2‐diphenyl‐1‐picrylhydrazyl (DPPH), 2,2′‐azino‐bis(3‐ethylbenzothiazoline‐6‐sulfonic acid) (ABTS·+), and superoxide anion radicals (O2−), respectively. The total antioxidant capability (T‐AOC) and superoxide dismutase (SOD) activity of FFM were 1.01 mM Trolox equivalents (TE)/g and 89.05 U/g, respectively. Additionally, T‐AOC, SOD, and glutathione peroxidase (GSH‐Px) activities increased, whereas malondialdehyde (MDA) levels decreased in the heart, liver, and kidneys of mice treated with FFM flour, indicating enhanced antioxidant capacity. Therefore, fermentation with edible fungi is suitable for improving the nutritional composition and antioxidant properties of foxtail millet. [ABSTRACT FROM AUTHOR]

In the context of rheumatoid arthritis (RA) treatment, Methotrexate (MTX) plays a crucial role in preventing joint damage and bone erosion (BE). RA is characterized by elevated levels of matrix metalloproteinase 2 (MMP2), an enzyme responsible for extracellular matrix degradation, which contributes to joint damage and inflammation. Tissue inhibitor of metalloproteinase 2 (TIMP2) counteracts MMP2, and an imbalance between the two can exacerbate BE. Inosine triphosphatase (ITPA) is an enzyme involved in regulating inosine triphosphate levels, potentially linked to RA susceptibility. Genetic variations in ITPA, MMP2, and TIMP2 genes can influence MTX's efficacy. A study of 122 RA patients on MTX monotherapy assessed its effectiveness using Disease Activity Score (DAS28) changes over 6 months following EULAR response criteria. Genotyping, including MMP2 (rs243866, rs2285053), TIMP2 (rs2277698), and ITPA (rs1127354) polymorphisms, was performed. Among the patients, 87.7% were responders, 63.9% experienced BE, and 24.6% encountered adverse events. Notably, patients with the MMP2 (rs243866) GG genotype were the only ones reporting nausea (p=0.025). Patients with both the MMP2 (rs2285053) CC and TIMP2 (rs2277698) CT genotypes had a lower incidence of BE compared to those lacking this combination (p=0.048). The TIMP2 (rs2277698) CC genotype was associated with a higher baseline DAS28 score (p=0.035). In summary, this study suggests that specific MMP2/TIMP2 genotype combinations may serve as predictors for BE development in RA patients undergoing MTX monotherapy. [ABSTRACT FROM AUTHOR]

Clostridium perfringens (C. perfringens), a Gram-positive bacterium, produces a variety of toxins and extracellular enzymes that can lead to disease in both humans and animals. Common symptoms include abdominal swelling, diarrhea, and intestinal inflammation. Severe cases can result in complications like intestinal hemorrhage, edema, and even death. The primary toxins contributing to morbidity in C. perfringens-infected intestines are CPA, CPB, CPB2, CPE, and PFO. Amongst these, CPB, CPB2, and CPE are implicated in apoptosis development, while CPA is associated with cell death, increased intracellular ROS levels, and the release of the inflammatory factor IL-18. However, the exact mechanism by which PFO toxins exert their effects in the infected gut is still unidentified. This study demonstrates that a C. perfringens PFO toxin infection disrupts the intestinal epithelial barrier function through in vitro and in vivo models. This study emphasizes the notable influence of PFO toxins on intestinal barrier integrity in the context of C. perfringens infections. It reveals that PFO toxins increase ROS production by causing mitochondrial damage, triggering pyroptosis in IPEC-J2 cells, and consequently resulting in compromised intestinal barrier function. These results offer a scientific foundation for developing preventive and therapeutic approaches against C. perfringens infections. [ABSTRACT FROM AUTHOR]

Nematophagous fungi have been widely evaluated in the biological control of parasitic helminths in animals, both through their direct use and the use of their derived products. Fungal bioproducts can include extracellular enzymes, silver nanoparticles (AgNPs), as well as secondary metabolites. The aim of this study was to conduct a systematic review covering the evaluation of products derived from nematophagous fungi in the biological control of parasitic helminths in animals. In total, 33 studies met the inclusion criteria and were included in this review. The majority of the studies were conducted in Brazil (72.7%, 24/33), and bioproducts derived from the fungus Duddingtonia flagrans were the most commonly evaluated (36.3%, 12/33). The studies involved the production of extracellular enzymes (48.4%, 16/33), followed by crude enzymatic extract (27.2%, 9/33), secondary metabolites (15.1%, 5/33) and biosynthesis of AgNPs (9.1%, 3/33). The most researched extracellular enzymes were serine proteases (37.5%, 6/16), with efficacies ranging from 23.9 to 85%; proteases (31.2%, 5/16), with efficacies from 41.4 to 95.4%; proteases + chitinases (18.7%, 3/16), with efficacies from 20.5 to 43.4%; and chitinases (12.5%, 2/16), with efficacies ranging from 12 to 100%. In conclusion, extracellular enzymes are the most investigated derivatives of nematophagous fungi, with proteases being promising strategies in the biological control of animal helminths. Further studies under in vivo and field conditions are needed to explore the applicability of these bioproducts as tools for biological control. [ABSTRACT FROM AUTHOR]

The large molecular weight and high viscosity of natural konjac glucomannan (KGM) limit its industrial application. Microbial degradation of low-molecular-weight KGM has health benefits and various biological functions; however, the available KGM strains used in the industry have microbial contamination and low degradation efficiencies. Therefore, exploring novelly adaptable strains is critical for industrial processes. Here, the Bacillus licheniformis Z7-1 strain isolated from decaying konjac showed high efficiency for KGM degradation. The monosaccharide composition of the degradation products had a reduced molar ratio of mannose to glucose, indicating that Z7-1 preferentially degraded glucose in KGM. The degraded component was further characterized by ESI-MS, Fourier-transform infrared spectroscopy (FT-IR), and scanning electron microscopy (SEM), and it also exhibited good antibacterial activity against various food-spoilage bacteria. Genome sequencing and zymolytic analysis revealed that abundant carbohydrate-active enzymes exist in the Z7-1 genome, with at least five types of extracellular enzymes responsible for KGM degradation, manifesting multi-enzyme synergetic action. The extracellular enzymes had significant thermal stability, indicating their potential application in industry. This study provides an alternative method for obtaining low-molecular-weight KGM with antibacterial functions and supports foundational knowledge for its development as a biocatalyst for the direct conversion of biomass polysaccharides into functional components. [ABSTRACT FROM AUTHOR]

Recently, there has been a worldwide call to explore nature-friendly compounds, which could enhance plant growth and substitute for chemically synthesized products. Endophytes are a group of microorganisms that lives in the plants and algae symbiotically. In this research, endophytes were isolated from leaves of the halophyte, Limonium axillare. A total of 280 bacterial isolates were obtained from the leaves of L. axillare. Strains displaying similarities in terms of morphology and biochemical reactions were categorized into 48 groups. One representative from each group was identified and subjected to enzymatic and plant growth-promoting tests. Forty-eight isolates were identified using a sequence similarity-based method based on the 16S rDNA gene. The identified strains were categorized into two genera: Bacillus and Staphylococcus. Our investigation uncovered 44 isolates from the Bacillus genus, representing 10 different species, including Bacillus sp., B. pseudomycoides, B. cereus, B. paramycoides, B. velezensis, B. subtilis, B. thuringiensis, B. wiedmannii, B. anthracis, and B. bacterium. Furthermore, we observed that only 4 isolates belonged to the Staphylococcus genus, encompassing 3 distinct species: S. bacterium, S. succinus, and S. saprophyticus. The isolated bacteria were screened for extracellular enzymes, plant growth promoting traits, antifungal activity, and salinity tolerance. From the previous screening, diverse responses were obtained. Most of the isolates were secreted at least one of the hydrolysis enzymes (protease, lipase and amylase). (93.8%) of the strains showed phosphate solubilization activity. (33.3%) produce (IAA). Siderophore production potential was present in 91.7% of isolates, while ACC deaminase and HCN production activities were identified in 52.1 and 41.7% of strains, respectively. Additionally, DNase activity was evident in 27.1%, and ammonia production was observed in 31.3% of the isolates. The isolates Bacillus velezensis (AL4QUA) strain showed positive effect in the greenhouse experiment in terms of plant growth promoter agent and biocontrol agent against Fusarium oxysporum pathogen of tomato seedling. Thus, endophytes have the potential to reduce chemical inputs in conventional agricultural practices, increase nutrient uptake and improve plant stress resilience. [ABSTRACT FROM AUTHOR]

Endophytic microbial communities colonize plants growing under various abiotic stress conditions. Candelilla (Euphorbia antisyphilitica Zucc.) is a shrub that develops functionally in arid and semi‐arid zones of Mexico; these conditions generate an association between the plant and the microorganisms, contributing to the production of enzymes as a defense mechanism for resistance to abiotic stress. The objective of this research was to isolate and identify endophyte fungi of candelilla and bioprospection of these endophytic fungi for enzyme production using candelilla by‐products. Fungi were isolated and identified using ITS1/ITS4 sequencing. Their potency index (PI) was evaluated in producing endoglucanase, xylanase, amylase, and laccase. Fermentation was carried out at 30°C for 8 days at 200 rpm, with measurements every 2 days, using candelilla by‐products as substrate. All fungi exhibited higher cellulase, amylase, and laccase activities on the 2nd, 6th, and 8th day of fermentation, respectively, of fermentation. The fungus Aspergillus niger ITD‐IN4.1 showed the highest amylase activity (246.84 U/mg), the genus Neurospora showed the highest cellulase activity, reaching up to 13.45 FPU/mg, and the strain Neurospora sp. ITD‐IN5.2 showed the highest laccase activity (3.46 U/mg). This work provides the first report on the endophytic diversity of E. antisyphilitica and its potential role in enzyme production. [ABSTRACT FROM AUTHOR]

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• The isolated strain Providencia rettgeri was capable of degrading TCPP efficiently. • The degradation of TCPP was mainly via phosphoester bond hydrolysis. • BCPP (C6H13Cl2PO4) and MCPP (C3H8ClPO4) were the main degradation intermediates. • Both intracellular and extracellular enzymes could degrade TCPP. • The presence of Cu2+ had a promoting effect on TCPP degradation by enzyme. Tri (2-chloropropyl) phosphate (TCPP) was an emerging contaminant of global concern because of its frequent occurrence, potential toxic effects, and persistence in the environment. Microbial degradation might be an efficient and safe removal method, but limited information was available. In this study, Providencia rettgeri was isolated from contaminated sediment and showed it could use TCPP as unique phosphorus source to promote growth, and decompose 34.7% of TCPP (1 mg/L) within 5 days. The microbial inoculation and the initial concentration of TCPP could affect the biodegradation efficient. Further study results indicated that TCPP decomposition by Providencia rettgeri was mainly via phosphoester bond hydrolysis, evidenced by the production of bis (2-chloropropyl) phosphate (C 6 H 13 Cl 2 PO 4) and mono-chloropropyl phosphate (C 3 H 8 ClPO 4). Both intracellular and extracellular enzymes could degrade TCPP, but intracellular degradation was dominant in the later reaction stage, and the presence of Cu2+ ions had a promoting effect. These findings developed novel insights into the potential mechanism of TCPP microbial degradation. [Display omitted] [ABSTRACT FROM AUTHOR]

Abstract Background The deep sea represents the largest marine ecosystem, driving global-scale biogeochemical cycles. Microorganisms are the most abundant biological entities and play a vital role in the cycling of organic matter in such ecosystems. The primary food source for abyssal biota is the sedimentation of particulate organic polymers. However, our knowledge of the specific biopolymers available to deep-sea microbes remains largely incomplete. One crucial rate-limiting step in organic matter cycling is the depolymerization of particulate organic polymers facilitated by extracellular enzymes (EEs). Therefore, the investigation of active EEs and the microbes responsible for their production is a top priority to better understand the key nutrient sources for deep-sea microbes. Results In this study, we conducted analyses of extracellular enzymatic activities (EEAs), metagenomics, and metatranscriptomics from seawater samples of 50–9305 m from the Mariana Trench. While a diverse array of microbial groups was identified throughout the water column, only a few exhibited high levels of transcriptional activities. Notably, microbial populations actively transcribing EE genes involved in biopolymer processing in the abyssopelagic (4700 m) and hadopelagic zones (9305 m) were primarily associated with the class Actinobacteria. These microbes actively transcribed genes coding for enzymes such as cutinase, laccase, and xyloglucanase which are capable of degrading phytoplankton polysaccharides as well as GH23 peptidoglycan lyases and M23 peptidases which have the capacity to break down peptidoglycan. Consequently, corresponding enzyme activities including glycosidases, esterase, and peptidases can be detected in the deep ocean. Furthermore, cell-specific EEAs increased at 9305 m compared to 4700 m, indicating extracellular enzymes play a more significant role in nutrient cycling in the deeper regions of the Mariana Trench. Conclusions Transcriptomic analyses have shed light on the predominant microbial population actively participating in organic matter cycling in the deep-sea environment of the Mariana Trench. The categories of active EEs suggest that the complex phytoplankton polysaccharides (e.g., cutin, lignin, and hemicellulose) and microbial peptidoglycans serve as the primary nutrient sources available to deep-sea microbes. The high cell-specific EEA observed in the hadal zone underscores the robust polymer-degrading capacities of hadal microbes even in the face of the challenging conditions they encounter in this extreme environment. These findings provide valuable new insights into the sources of nutrition, the key microbes, and the EEs crucial for biopolymer degradation in the deep seawater of the Mariana Trench. Video Abstract

Fusarium head blight (FHB) is a destructive disease caused by several species of Fusarium, such as Fusarium graminearum and F. asiaticum. FHB affects cereal crops, including wheat, barley, and rice, worldwide. Fusarium-infected kernels not only cause reduced yields but also cause quality loss by producing mycotoxins, such as trichothecenes and zearalenone, which are toxic to animals and humans. For decades, chemical fungicides have been used to control FHB because of their convenience and high control efficacy. However, the prolonged use of chemical fungicides has caused adverse effects, including the emergence of drug resistance to pathogens and environmental pollution. Biological control is considered one of the most promising alternatives to chemicals and can be used for integrated management of FHB due to the rare possibility of environment pollution and reduced health risks. In this study, Bacillus velezensis JCK-7158 isolated from rice was selected as an ecofriendly alternative to chemical fungicides for the management of FHB. JCK-7158 produced the extracellular enzymes protease, chitinase, gelatinase, and cellulase; the plant growth hormone indole-3-acetic acid; and the 2,3-butanediol precursor acetoin. Moreover, JCK-7158 exhibited broad antagonistic activity against various phytopathogenic fungi and produced iturin A, surfactin, and volatile substances as active antifungal compounds. It also enhanced the expression of PR1, a known induced resistance marker gene, in transgenic Arabidopsis plants expressing ß-glucuronidase (GUS) fused with the PR1 promoter. Under greenhouse conditions, treatments with the culture broth and suspension concentrate formulation of JCK-7158 at a 1,000-fold dilution inhibited the development of FHB by 50 and 66%, respectively. In a field experiment, treatment with the suspension concentrate formulation of JCK-7158 at a 1,000-fold dilution effectively controlled the development of FHB with a control value of 55% and reduced the production of the mycotoxin nivalenol by 40%. Interestingly, treatment with JCK-7158 enhanced the expression of plant defense-related genes in salicylic acid, jasmonic acid, ethylene, and reactive oxygen species (ROS) signaling pathways before and after FHB pathogen inoculation. Taken together, our findings support that JCK-7158 has the potential to serve as a new biocontrol agent for the management of FHB. [ABSTRACT FROM AUTHOR]

Tetraspanins regulate signal transduction by interacting with partner proteins belonging to remarkably different protein families, including extracellular enzymes, integrins, members of the immunoglobulin superfamily, and intracellular signaling proteins. Structures of full-length tetraspanins have revealed a common overall architecture, with a cone-shaped transmembrane (TM) domain containing an intramembrane binding pocket. This pocket can bind lipids, which appear to modulate tetraspanin function. Many tetraspanins are conformationally dynamic, existing in at least two states with distinct TM conformations and ectodomain orientations. The molecular association of a tetraspanin with its partner can be mediated through the large extracellular loop (EC2 domain) and/or the TM domain. The dependency for each region differs based on the bound partner. Tetraspanins are a large, highly conserved family of four-pass transmembrane (TM) proteins that play critical roles in a variety of essential cellular functions, including cell migration, protein trafficking, maintenance of membrane integrity, and regulation of signal transduction. Tetraspanins carry out these biological functions primarily by interacting with partner proteins. Here, we summarize significant advances that have revealed fundamental principles underpinning structure–function relationships in tetraspanins. We first review the structural features of tetraspanin ectodomains and full-length apoproteins, and then discuss how recent structural studies of tetraspanin complexes have revealed plasticity in partner-protein recognition that enables tetraspanins to bind to remarkably different protein families, viral proteins, and antibody fragments. Finally, we discuss major questions and challenges that remain in studying tetraspanin complexes. [ABSTRACT FROM AUTHOR]

This study investigates the thermotolerant fungal biodiversity in caves and hot springs, focusing on their potential for extracellular enzyme production, specifically proteases. Samples were collected from the Cardonal region in Hidalgo, Mexico, using three different isolation methods. The study characterizes the morphological diversity of the isolated fungi and identifies various genera, including Aspergillus, Penicillium, Trichoderma, Cladosporium, and Fusarium, based on morphology. The isolated fungi were screened for their ability to produce extracellular enzymes on solid media, with a particular emphasis on proteases due to their industrial significance. Among the 35 isolated fungi, 20 exhibited proteolytic activity, and 12 strains were identified as good protease producers based on enzymatic index values. The study also evaluated the formation of fungal pellets by proteolytic fungi and found certain strains to display significant pellet formation. Additionally, protease production was examined by fungal pellets in submerged cultures, with isolate 6 demonstrating the highest protease activity. The findings highlight the diverse thermotolerant fungal biodiversity in extreme environments, and emphasize their potential for enzymatic production. This research contributes to our understanding of fungal ecology and provides insights into the biotechnological applications of these enzymes. The study recommends further molecular investigations to enhance biodiversity studies in such extreme environments. [ABSTRACT FROM AUTHOR]

Plant pathogenic Streptomyces species (PPSs) are capable of infecting plant tissues and inducing common scab (CS) in root and tuber crops, with potato common scab (PCS) being the fourth most widespread and damaging disease affecting potato production worldwide. In recent years, with increasing market demand for potato quality, PPSs have garnered significant attention. A thorough understanding of the pathogenic factors of PPSs is a prerequisite for the prevention and control of PCS and can provide targets for the development of PCS control agents. This article primarily summarises the types and damage caused by PPSs, as well as the biosynthesis and molecular regulation of key pathogenic factors, aimed at enhancing our understanding of the molecular pathogenic mechanisms of PPSs and at providing theoretical guidance for the future development of novel PCS control agents. The pathogenicity of PPSs depends predominantly on the phytotoxins, secreted proteins, and phytohormones produced by themselves. Thaxtomins, a group of cyclic dipeptide phytotoxins, are the major pathogenic factors for inhibiting cellulose synthesis in plant tissues and promoting pathogen invasion. Coronafacoyl phytotoxins (CORs) are mainly involved in suppressing plant defence responses, whilst concanamycins (CONs) affect the severity of necrosis in plant pathological tissues. The secreted proteins Nec1 and a homologue of tomatinase TomA inhibit host defence responses, and scabin from the mART family targets guanine in potato DNA, leading to cell apoptosis. Various extracellular enzymes, including glycosyl hydrolases and esterases, are also involved in the pathogenic process of PCS. To put it succinctly, the article mainly takes the pathogenic factors of PPSs as a breakthrough point, so as to fully understand the pathogenic mechanism of PPS molecules, in order to provide a theoretical basis for the future research and control strategies of scab disease. [ABSTRACT FROM AUTHOR]

In polar regions, global warming has accelerated the melting of glacial and buried ice, resulting in meltwater run-off and the mobilization of surface nutrients. Yet, the short-term effects of altered nutrient regimes on the diversity and function of soil microbiota in polyextreme environments such as Antarctica, remains poorly understood. We studied these effects by constructing soil microcosms simulating augmented carbon, nitrogen, and moisture. Addition of nitrogen significantly decreased the diversity of Antarctic soil microbial assemblages, compared with other treatments. Other treatments led to a shift in the relative abundances of these microbial assemblages although the distributional patterns were random. Only nitrogen treatment appeared to lead to distinct community structural patterns, with increases in abundance of Proteobacteria (Gammaproteobateria) and a decrease in Verrucomicrobiota (Chlamydiae and Verrucomicrobiae).The effects of extracellular enzyme activities and soil parameters on changes in microbial taxa were also significant following nitrogen addition. Structural equation modeling revealed that nutrient source and extracellular enzyme activities were positive predictors of microbial diversity. Our study highlights the effect of nitrogen addition on Antarctic soil microorganisms, supporting evidence of microbial resilience to nutrient increases. In contrast with studies suggesting that these communities may be resistant to change, Antarctic soil microbiota responded rapidly to augmented nutrient regimes. [ABSTRACT FROM AUTHOR]

'Weismann's barrier' has restricted theories of heredity to the transmission of genomic variation for the better part of a century. However, the discovery and elucidation of epigenetic mechanisms of gene regulation such as DNA methylation and histone modifications has renewed interest in studies on the inheritance of acquired traits and given them mechanistic plausibility. Although it is now clear that these mechanisms allow many environmentally acquired traits to be transmitted to the offspring, how phenotypic information is communicated from the body to its gametes has remained a mystery. Here, we discuss recent evidence that such communication is mediated by somatic RNAs that travel inside extracellular vesicles to the gametes where they reprogram the offspring epigenome and phenotype. How gametes learn about bodily changes has implications not only for the clinic, but also for evolutionary theory by bringing together intra‐ and intergenerational mechanisms of phenotypic plasticity and adaptation. [ABSTRACT FROM AUTHOR]

Background: A host‐plant and its associated microbiota are interdependent, with the enduring root zone microbial communities evolving over an extended period for a specific plant species. However, the long‐term stability and functioning of host‐associated microbiota, and their potential to be influenced by introduced plants, remain poorly understood. Aims: Our objective was to ascertain the relative contributions of core and rare microbiota in maintaining community stability and soil nutrient cycling in the presence of introduced plants. Methods: We executed a pot experiment where four plant species at varying successional stages were planted in soil collected from the root area of Pyracantha fortuneana. Soil samples were collected 2 years post‐planting. The soil nutrients, enzyme activities, and microbial networks under different introduced plants were analyzed. Results: The growth of Betula luminifera significantly enhanced soil enzyme activity, multi‐nutrient cycling level, and microbial community diversity, compared to soils cultivated with Imperata cylindrica and Zanthoxylum simulans. Furthermore, the treatment involving B. luminifera planting exhibited a lower clustering coefficient and higher average path length than other treatments. Core taxa demonstrated higher node degree and betweenness centrality than rare taxa, favoring the stability of the microbial network. Importantly, the core taxa, particularly their co‐occurrence network properties, were the primary drivers for multi‐nutrient cycles of P. fortuneana root zone soils. Among the core taxa, Mortierellomycetes, Dothideomycetes, Thermoleophili, and Rubrobacteria were abundant in the treatment involving B. luminifera and were significantly positively correlated with most soil nutrient extracellular enzymes, thereby contributing to soil multi‐nutrient cycling. Conclusion: Core taxa significantly influence the microbial stability in the root zone soil of P. fortuneana. The introduction of B. luminifera can enhance the stability of the microbial community structure within this soil, thereby promoting soil nutrient cycles. [ABSTRACT FROM AUTHOR]

Endophytic microbes of medicinal plants are known to involve the synthesis of several bioactive compounds, which promote plant growth and resistance to diseases. In order to investigate endophytes in the important medicinal plant Catharanthus roseus, 16 endophytic microorganism strains were isolated from root samples of C. roseus var. roseus and C. roseus var. ocellatus naturally growing in coastal areas of Nha Trang, Vietnam. Based on morphological characteristics and 16S rDNA gene marker sequences, four actinomycetes of Streptomyces and Microbiospora genera and twelve bacterial strains belonging to Bacillus, Enterobacter, Pseudomonas, Panenibacillus and Rhizobium genera were identified. Analysis of the extracellular enzyme activities of actinomycetes strains indicated that Streptomyces strains produced proteases, cellulases, xylanases and amylases and Microbiospora strains exhibited protease and cellulase activities. The results demonstrated the diversity of endophytes in the roots of C. roseus plants and their potential extracellular enzyme activities for further application. [ABSTRACT FROM AUTHOR]

This document is a correction notice for an article titled "Seasonal fluctuations of extracellular enzyme activities are related to the biogeochemical cycling of C, N and P in a tropical terra-firme forest." The original article contained errors in the calculated enzyme activities and equations used for the calculation of proportional activities. The corrected equations and figures have been provided. The corrected text and figures provide information on the average enzyme activities and their fluctuations in different soil depths throughout the year. The correction notice is authored by Karst J. Schaap, Lucia Fuchslueger, Carlos Alberto Quesada, Florian Hofhansl, Oscar Valverde-Barrantes, Plínio B. Camargo, and Marcel R. Hoosbeek. [Extracted from the article]