Extracellular Enzyme Activities Research Articles

Phytoplankton-derived polysaccharides and microbial peptidoglycans are key nutrients for deep-sea microbes in the Mariana Trench

BackgroundThe 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.ResultsIn 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.ConclusionsTranscriptomic 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.6w3UcpMmGbcStWK5zJqVACVideo

Weed control, soil health, and yield tradeoffs of between-bed management strategies in organic plasticulture vegetable production

Planting a cover crop living mulch between plastic mulch beds in fresh market vegetable production can reduce soil erosion and runoff, and offers an opportunity to grow an income generating cash crop alongside a soil building cover crop. However, potential negative impacts on yield, variable weed control, unclear impacts on soil health, and limited management recommendations challenge adoption of this practice, despite grower interest. In a two-year study in southwest Michigan, living mulches were evaluated in the production of plasticulture organic summer squash (Cucurbita pepo cv. Lioness) and bell pepper (Capsicum annuum cv. Paladin). Strategies evaluated included three common grower practices (cultivation, dead straw mulch, mowing ambient weeds) and three mowed living mulch treatments (Italian ryegrass [Lolium multiflorum] monoculture, rye [Secale cereale] monoculture, and a Dutch white clover [Trifolium repens]/rye mixture). We determined the impact of these strategies on weed control, organic matter inputs, vegetable crop performance, nitrogen retention, and soil microbial communities. We found that cultivation and dead mulch provided superior in-season weed control, reducing weed biomass by an average of 86% compared to 18% among living mulch treatments, with associated reductions in the weed seedbank compared to living mulches and mowed weeds. In most cases, living mulch establishment was a challenge and weed biomass on average accounted for 99, 74, and 94% of organic matter inputs in rye, ryegrass, and clover/rye treatments, respectively. Squash performance was unaffected by our treatments, but pepper yield reductions ranged from 41 to 54% in all treatments relative to cultivation in one of two years. Living mulches and the weedy treatment showed the ability to reduce end-of-season potentially leachable nitrogen by 61% compared to cultivation and dead mulching. Soil microbial abundance and functional diversity were similar across treatments, but extracellular enzyme activity was higher in dead mulch, living mulch and weedy treatments compared to cultivation. Results from this study help quantify tradeoffs between common grower practices for managing weeds and soil between plastic mulch beds, highlight key challenges with living mulch alternatives, and identify areas for future research.

Microbial interactions with microplastics: Insights into the plastic carbon cycle in the ocean

The fate of microplastics (MPs) in the ocean is mostly driven by (i) photo-oxidation to smaller particles and dissolved constituents, which fuel the dissolved organic carbon pool (plastic-derived DOC, pDOC), and (ii) interactions with organic matter forming sinking aggregates (marine plastic snow). Two separate laboratory experiments were conducted to investigate the two pathways of MPs. In the first experiment, we measured potential rates of microbial pDOC utilization in bottle incubations over 15 days with microbial assemblages from coastal and offshore waters. Microbial utilization of pDOC was more efficient in the coastal (72% bioreactive pDOC) compared with the offshore experiment (32% bioreactive pDOC) 15 days. Changes in bacterial cell abundance and extracellular enzyme activities (glucosidase, peptidase, esterases) indicated that a fraction of pDOC was repackaged into microbial exopolymeric substances (EPS), stimulating growth of known EPS degrading bacteria within the phyla Verrucomicrobiota and Planctomycetota. Microbial EPS likely also played a key role in our second experiment that showed the formation of marine plastic snow in roller tanks with cultured cells of Emiliana huxleyi but not with cells of an Isocrysis sp. culture. Average sinking velocities of marine plastic snow were a factor of 1.2 lower compared with marine snow without MPs. Both aggregate types showed reduced sinking velocities in a density stratified sinking column. Our results from the two experiments on (i) microbial utilization of pDOC and (ii) the formation and sinking of marine plastic snow indicate potential effects of plastic-derived compounds on microbial elemental cycles (i.e., pDOC repackaged into EPS) with consequences for the efficiency of the biological carbon pump (i.e., marine plastic snow reduces carbon export) and the fate of plastic-derived compounds in the ocean.

Mixed Chinese Fir Plantations Alter the C, N, and P Resource Limitations Influencing Microbial Metabolism in Soil Aggregates

Assessing the limitations of microbial metabolic resources is crucial for understanding plantation soil quality and enhancing fertility management. However, the variation of microbial resource limitations at the aggregate level in response to changes in stands remains unclear. This research explores carbon (C), nitrogen (N), and phosphorus (P) limitations affecting microbial metabolism in bulk soils and aggregates in two mixed and one pure Chinese fir stands in subtropical China, analyzing resource limitations concerning soil carbon, nutrients, and microbial indicators. The results revealed that microbes in all aggregates of the pure stands and in the micro aggregates (<0.25 mm) of the three stands were relatively limited by C and P. In contrast, microbial metabolism was more N-limited in macroaggregates (>2 mm) and small aggregates (2–0.25 mm) in the mixed stands. Additionally, in the mixed stands the proportion of soil macroaggregates increased, and that of micro aggregates decreased, resulting in a shift from C and P limitation to N limitation for bulk soil microbial metabolism. Redundancy analysis identified soil aggregate organic carbon and nutrient content as the main factors affecting microbial resource limitation, rather than their stoichiometric ratios. Pathway analysis further confirmed that soil nutrients and their stoichiometric ratios indirectly influenced soil microbe resource limitation by regulating microbial biomass, microbial respiration, and extracellular enzyme activities. Thus, the impact of mixed plantations on soil nutrients and microbial activity at the aggregate level may be crucial for maintaining land fertility and achieving sustainability.

Straw return with fertilizer improves soil CO2 emissions by mitigating microbial nitrogen limitation during the winter wheat season

Straw return is the key measure of green agricultural production. Nitrogen (N) and phosphorus (P) play pivotal roles in crop growth and carbon (C) cycling in agroecosystems. However, the mechanism of soil CO2 emissions and enzyme stoichiometry regulation by straw return with N and P application remain unknown. Therefore, this study is aimed to use enzyme stoichiometry to investigate the effects of straw return with N and P fertilizer application on soil CO2 emissions, enzyme activity, and microbial nutrient limitation through a two-year field experiment. A split-plot experimental design was used (straw as the main plot and fertilizer as the sub plot). The results indicated that the addition of N, P (SNP) increased CO2 emissions by 25.54 %, and N application (SN) reduced CO2 emissions by 27.01 %, compared with straw return (SW). Enzyme stoichiometry indicated that straw return with N and P application exhibited significant C and N limitations. In soil nutrients and nutrient stoichiometry, compared with the S0W treatment, straw return with fertilizer (SNP, SN) significantly increased microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), dissolved organic carbon (DOC) and dissolved organic nitrogen (DON); SNP treatment increased β-1,4- n −acetylaminoglucosidase (NAG) enzyme activity by 53.72 %, increased l −leucine aminopeptidase (LAP) enzyme activity by 58.11 %, and increased one P-acquiring enzyme alkaline monoalkaline phosphatase (AKP) enzyme activity by 39.49 % (P < 0.05). Structural equation modeling suggested that straw return and fertilization can influence microbial biomass phosphorus (MBP) and vector length (VL) by affecting MBN, which, in turn, affects CO2 emissions. Soil microbes regulate CO2 emissions using stoichiometric flexibility to maintain a stoichiometric balance of nutrients and microbes. Therefore, straw return with N and P fertilizers to winter wheat soils can meet the requirements of microbial stoichiometry, modulate microbial and extracellular enzyme activities, and effectively regulate CO2 emissions and resource limitations.

Effects of Land-Use Type and Salinity on Soil Carbon Mineralization in Coastal Areas of Northern Jiangsu Province

Sea level rise due to glacier melting caused by climate warming is a major global challenge, but the mechanism of the effect of salinity on soil carbon (C) mineralization in different land types is not clear. The pathways by which salinity indirectly affects soil carbon mineralization rates need to be investigated. Whether or not the response mode is consistent among different land-use types, as well as the intrinsic links and interactions between soil microbial resource limitation, environmental stress, microbial extracellular enzyme activity, and soil carbon mineralization, remain to be demonstrated. In this paper, three typical land-use types (wetland, forest, and agroforestry) were selected, and different salinity levels (0‰, 3‰, 6‰, and 32‰) were designed to conduct a 125-day laboratory incubation experiment to determine the soil CO2 release rate, soil physicochemical properties, and soil enzyme activities, and to correlate C mineralization with biotic and abiotic factors. A correlation analysis of soil physical and chemical properties, extracellular enzyme activities, and carbon mineralization rates was conducted to investigate their intrinsic linkages, and a multiple linear regression of C mineralization at different sites was performed to explore the variability of mineralization among different site types. Structural equation models were established in the pre- and post-incubation stages to study the pathways of soil C mineralization at different incubation times, and the mechanism of mineralization was further verified by enzyme stoichiometry. The results showed that, at the end of 125 days of incubation, the 32‰ salinity addition reduced the cumulative mineralization of forest and agroforestry types by 28.41% and 34.35%, respectively, compared to the 0‰ salinity addition. Soil C mineralization in the three different land-use types was highly correlated with the active C fractions of readily oxidizable C (ROC), dissolved organic C, and microbial biomass C (MBC) in the soil, with the standardized coefficients of multivariate linear regression reaching 0.67 for MBC in the wetland and −0.843 for ROC in the forest. Under long-term salinity additions, increased salinity would reduce the microbial respiratory quotient value by inhibiting β-glucosidase activity, thus indirectly affecting the rate of CO2 release. With added salinity, the mineralization of non-saline soil was more susceptible to the inhibitory effect of salinity, whereas the mineralization of salinized soil was more controlled by soil C pools.

Heterogeneity of phosphorus sources invokes distinct niche partitioning pathways of ectomycorrhizal fungi in forest soils

Ectomycorrhizal (ECM) fungi are pivotal in acquiring phosphorus (P) in nutrient-deficient soils, especially beyond the rhizosphere. However, the extent to which ECM community structure and function affect the utilization of various P-containing substrates in forest soils is not fully understood. This study explored the influence of different P substrates — calcium orthophosphate, phosphate-saturated goethite, fluorapatite, and wheat bran—on the release of plant-available P and colonized fungal communities using hyphal in-growth mesh bags. Our results show that these substrates released comparable amounts of plant-available P to the Pinaceae hosts. A significant correlation was observed between the relative abundance of Tylospora (Atheliaceae) and Hourangia (Boletaceae), and their extracellular enzyme activities involved in P acquisition and trivalent iron reduction. This correlation was particularly evident in fungal taxa characterized by long/medium-distance hyphal exploration types. These findings underscore the ECM fungi's distinct preferences for different P-containing substrates, emphasizing the importance of recognizing these preferences to enhance forest management in low P environments.

Gastrointestinal response to the early administration of antimicrobial agents in growing turkeys infected with Escherichia coli

This study investigated the effects of the early administration of enrofloxacin (E) or doxycycline (D) for the first 5 consecutive days of life, or the continuous administration of the coccidiostat monensin (M) throughout the rearing period on gastrointestinal function in turkeys infected with avian pathogenic Escherichia coli (APEC) in an early or later stage of rearing. Experiment 1 lasted 21 d, and turkeys in groups E, D, and M were infected with APEC on d 15. Experiment 2 lasted 56 d, and it had a factorial arrangement of treatments where birds in groups E, D, and M were infected with APEC on d 15 or d 50. In both experiments, control groups (C) consisted of infected and uninfected birds without antibiotic or coccidiostat administration. On d 21 (Experiment 1) and d 56 (Experiment 2), 8 birds from each subgroup were killed, and the ileal and cecal digesta were sampled to analyze the activity of bacterial enzymes and the concentrations of short-chain fatty acids (SCFA). The experimental treatments did not affect the final body weight or body weight gain of birds. Both experiments demonstrated that APEC contributed to an increase in ammonia levels of the cecal digesta (means from 2 experiments: 0.311 vs. 0.225 mg/g in uninfected birds) and ileal pH (6.79 vs. 6.00) and viscosity (2.43 vs. 1.83 mPa⋅s). Moreover, the E. coli challenge enhanced the extracellular activity of several cecal bacterial enzymes, especially in older turkeys infected with APEC in a later stage of life. The continuous administration of monensin throughout the rearing period resulted in a weaker gastrointestinal response in older birds, compared with the other 2 antibiotics administered for the first 5 d of life. The results of the study are inconclusive as both desirable and undesirable effects of preventive early short-term antibiotic therapy were observed in turkeys, including normalization of ileal viscosity and cecal ammonia concentration (positive effect), and disruption in cecal SCFA production (negative effect).

Long‐term straw mulching alleviates microbial nutrient limitations and increases carbon‐use efficiency within aggregates

AbstractLong‐term straw mulching was known to change soil nutrient content, aggregate distribution and extracellular enzyme activities. However, the impact of long‐term straw mulching on microbial nutrient limitations and carbon‐use efficiency (CUEst) within aggregates remains unclear. To fill the gap, we conducted a 10‐year field experiment in a semi‐arid region and used an ecoenzymatic stoichiometry model to quantify microbial resource limitations in soil aggregates under long‐term mulching. We studied the effects of two mulching measures (plastic film mulching [FM] and straw mulching [SM], with no mulching as the control [CK]) on the nutrient content and limitations within aggregates. The results show that compared with FM, SM increased the proportion of aggregates to larger &gt;2 mm and decreased the proportion of aggregates in the 2–0.25 mm classes. Additionally, FM resulted in carbon (C) and phosphorus (P) limitations in the soil, particularly in the &gt;2 mm class, while SM alleviated these constraints. This effect was primarily attributed to the increase in soil organic carbon (SOC) and microbial biomass carbon content (Cm), especially the enhanced carbon content associated with larger aggregates (&gt;2 mm) and the increased activities of carbon–nitrogen (C–N)‐acquiring enzymes. SM also resulted in high CUEst by influencing microbial P limitation. Random forest analysis indicates that soil abiotic factors, particularly SOC and total nitrogen (TN), were the main drivers of microbial resource limitations within the aggregates. These findings suggest that the mulching material determines the development of soil aggregates and resource allocation within these aggregates. Thus, the study provides valuable insights for formulating effective carbon management strategies in semi‐arid regions.

Extracellular Enzymatic Activity of Malassezia spp.Isolated from Pityriasis Versicolor Patients and Healthy Individuals

Extracellular Enzymatic Activity of Malassezia spp.Isolated from Pityriasis Versicolor Patients and Healthy Individuals

Enzymatic Bioregeneration of Activated Carbon by Laccase

Activated carbon is widely used in combination with biological treatment systems for the treatment of organic compounds, which are refractory or toxic in conventional biological treatment systems. In these systems, compounds adsorbed on activated carbon may desorb within time due to a concentration gradient between adsorbent and the bulk liquid caused by the biodegradation of substrates in the liquid phase by microorganisms. The desorbed compounds are further biodegraded by microorganisms. This mechanism is called bioregeneration of activated carbon. Previous studies showed that bioregeneration percentages could be higher than the concentration gradient-driven desorbability. This was attributed to exoenzymatic bioregeneration occurring due to the activity of extracellular enzymes secreted by microorganisms in these systems. These extracellular enzymes can diffuse into the activated carbon pores where they can react with the previously adsorbed compounds resulting in their desorption from the carbon surface and degradation. However, the effect of extracellular enzymes on bioregeneration was not conclusively proven in any of the literature studies on bioregeneration because extracellular enzymes were not directly used for the purpose of bioregeneration. In this study, enzymatic bioregeneration of activated carbon was investigated by directly using an extracellular enzyme, laccase, which is known from the literature to catalyze the oxidation reactions of phenolic substances and is commercially available in its pure form. Therefore phenol, 2-nitrophenol, and bisphenol-A were used as the target compounds. For this purpose, batch adsorption, abiotic desorption, enzymatic degradation and enzymatic bioregeneration experiments were performed using two different activated carbon types; thermally and chemically activated ones. The results showed that there was a significant difference between the total enzymatic bioregeneration efficiencies and abiotic desorption efficiencies for each phenolic compound depending on the activated carbon type. Thereby, exoenzymatic bioregeneration has been quantitatively shown for the first time in the literature.

Thinning enhances forest soil C storage by shifting the soil toward an oligotrophic condition

Forests are significant carbon reservoirs, with approximately one-third of this carbon stored in the soil. Forest thinning, a prevalent management technique, is designed to enhance timber production, preserve biodiversity, and maintain ecosystem functions. Through its influence on biotic and abiotic factors, thinning can profoundly alter soil carbon storage. Yet, the full implications of thinning on forest soil carbon reservoirs and the mechanisms underpinning these changes remain elusive. In this study, we undertook a two-year monitoring initiative, tracking changes in soil extracellular enzyme activities (EEAs), microbial communities, and other abiotic parameters across four thinning intensities within a temperate pine forest. Our results show a marked increase in soil carbon stock following thinning. However, thinning also led to decreased dissolved organic carbon (DOC) content and a reduced DOC to soil organic carbon (SOC) ratio, pointing toward a decline in soil carbon lability. Additionally, fourier transform infrared spectroscopy (FTIR) analysis revealed an augmented relative abundance of aromatic compounds after thinning. There was also a pronounced increase in absolute EEAs (per gram of dry soil) post-thinning, implying nutrient limitations for soil microbes. Concurrently, the composition of bacterial and fungal communities shifted toward oligotrophic dominance post thinning. Specific EEAs (per gram of soil organic matter) exhibit a significant reduction following thinning, indicating a deceleration in organic matter decomposition rates. In essence, our findings reveal that thinning transitions soil toward an oligotrophic state, dampening organic matter decomposition, and thus bolstering the soil carbon storage potential of forest. This study provides enhanced insights into the nuanced relationship between thinning practices and forest soil carbon dynamics, serving as a robust foundation for enlightened forest management strategies.

Short-term responses of soil enzyme activities and stoichiometry to litter input in Castanopsis carlesii and Cunninghamia lanceolata plantations.

Litter input triggers the secretion of soil extracellular enzymes and facilitates the release of carbon (C), nitrogen (N), and phosphorus (P) from decomposing litter. However, how soil extracellular enzyme activities were controlled by litter input with various substrates is not fully understood. We examined the activities and stoichiometry of five enzymes including β-1,4-glucosidase, β-D-cellobiosidase, β-1,4-N-acetyl-glucosaminidase, leucine aminopeptidase and acidic phosphatase (AP) with and without litter input in 10-year-old Castanopsis carlesii and Cunninghamia lanceolata plantations monthly during April to August, in October, and in December 2021 by using an in situ microcosm experiment. The results showed that: 1) There was no significant effect of short-term litter input on soil enzyme activity, stoichiometry, and vector properties in C. carlesii plantation. In contrast, short-term litter input significantly increased the AP activity by 1.7% in May and decreased the enzymatic C/N ratio by 3.8% in August, and decreased enzymatic C/P and N/P ratios by 11.7% and 10.3%, respectively, in October in C. lanceolata plantation. Meanwhile, litter input increased the soil enzymatic vector angle to 53.8° in October in C. lanceolata plantations, suggesting a significant P limitation for soil microorganisms. 2) Results from partial least squares regression analyses showed that soil dissolved organic matter and microbial biomass C and N were the primary factors in explaining the responses of soil enzymatic activity to short-term litter input in both plantations. Overall, input of low-quality (high C/N) litter stimulates the secretion of soil extracellular enzymes and accelerates litter decomposition. There is a P limitation for soil microorganisms in the study area.

Crop Conversion from Annual to Perennials: An Effective Strategy to Affect Soil Multifunctionality

Although crop conversion from annual to perennial crops has been considered as one path towards climate-smart and resource-efficient agriculture, the effects of this conversion on soil multifunctionality and biomass yields remain unclear. The objective of the study is to enhance soil multifunctionality while exerting a marginal influence on farmer income. Here, we investigated the effects of annual winter wheat (Triticum aestivum L.) and two perennial crops (a grass (Lolium perenne L.), a legume (Medicago sativa L.), and their mixture) on soil multifunctionality and biomass yield on the Yellow River floodplain. Soil multifunctionality was assessed by the capacity of water regulation and the multifunctionality of carbon (C), nitrogen (N), and phosphorus (P) cycles. C cycle multifunctionality index is the average of β-xylosidase, β-cellobiosidase, and β-1, 4-glucosidase. N cycle multifunctionality index is the average of L-leucine aminopeptidase and β-1, 4-N-acetyl-glucosaminidase, and acid phosphatase represented (and dominated) P cycle functions. The results showed that perennial crops enhanced soil multifunctionality by 207% for L. perenne, 311% for M. sativa, and 438% for L. perenne + M. sativa, compared with annual winter wheat (T. aestivum). The effect of perennial crops on soil multifunctionality increased with infiltration rate, dissolved organic C, microbial biomass C, and extracellular enzymatic activities for both C and N acquisition. However, we observed that perennial crops had a lower biomass yield than annual crop. Therefore, the transition of agricultural landscapes to perennials needs to take into account the balance between environmental protection and food security, as well as environmental heterogeneity, to promote sustainable agricultural development.

Plant-associated bacteria and enzymes support Canavalia rosea growth in coastal hypersaline soils

Canavalia rosea is an extremophilic legume that grows in hypersaline and nutrient-deficient ecosystems. The extremophilic nature of C. rosea may be attributed to its ability to establish symbiotic associations with nutrient mineralizing and plant growth promoting (PGP) bacteria housed in the nodules. This study examined legume-microbe symbiosis and plant nutrition of C. rosea growing in subtropical coastal zone in KwaZulu-Natal province, South Africa. Canavalia rosea adult plants of the same age from Westbrook, Scottburgh and Durban were collected for plant biomass and plant nutrition and root nodules were used for bacterial extraction and identification. Rhizosphere soils sampled from the three localities were used for bacterial extraction and identification, extracellular enzyme assays and soil characteristics (pH, nutrient concentrations, total cation, and exchange acidity). Westbrook, Scottburgh and Durban soils were nutrient-deficient with varying total cations, acid saturation and a pH range of 7.3–7.6. Soil nutrient mineralizing extracellular enzyme activities varied across study sites. The culturable bacterial strains isolated from the sampled soils belonged to the Pseudomonas, Pantoea and Flavobacterium genera. Canavalia rosea root nodules were nodulated by Pseudomonas guariconensis, Pseudomonas fulva, Pseudomonas fluorescens, Pseudomonas chlororaphis and Pseudomonas chlororaphis subsp. aurantiaca. Plants growing in Westbrook soils had a significantly higher total plant biomass compared to Scottburgh and Durban plants. Plant P concentration did not vary significantly between sites while plant N and C concentrations varied significantly. Plant-associated and soil bacteria with phosphorus (P) solubilising, nitrogen (N) cycling, and N fixing functions and associated enzymes seem to facilitate the mobilization of nutrients enabling C. rosea to thrive in hypersaline and low-nutrient environments.

Identification, characterization and complete genome analysis of a Vibrio anguillarum isolated from Sebastes schlegelii

Vibrio anguillarum is an important fish pathogen in mariculture, which can infect fish with great economic losses. In this study, a Vibrio anguillarum isolated from Sebastes schlegelii was named VA1 and was identified and characterized from aspects of morphology, physiological and biochemical characteristics, 16SRNA, virulence genes, drug sensitivity, and extracellular enzyme activity. At the same time, The VA1 was investigated at the genomic level. The results showed that a Gram-negative was isolated from the diseased fish. The VA1 was characterized with uneven surface and visible flagella wrapped in a sheath and microbubble structures. The VA1 was identified as Vibrio anguillarum based on the 16S RNA sequence and physiological and biochemical characteristics. The VA1 carried most of the virulence genes (24/29) and was resistant to penicillin, oxacillin, ampicillin, cefradine, neomycin, pipemidic acid, ofloxacin, and norfloxacin. The pathogenicity of the isolated strain was confirmed by an experimental analysis, and its LD50 was 6.43 × 106 CFU/ml. The VA1 had the ability to secrete gelatinase, protease, and amylase, and it had α-hemolysis. The whole genome size of the VA1 was 4232328bp and the G + C content was 44.95 %, consisting of two circular chromosomes, Chromosome1 and Chromosome2, with no plasmid. There were 1006 predicted protein coding sequences (CDSs). A total of 526 genes were predicted as virulence-related genes which could be classified as type IV pili, flagella, hemolysin, siderophore, and type VI secretion system. Virulence genes and correlation data were supported with the histopathological examination of the affected organs and tissues. 194 genes were predicted as antibiotic resistance genes, including fluoroquinolone antibiotic, aminoglycoside antibiotic, and beta-lactam resistant genes, which agreed with the results of the above drug sensitivity, indicating VA1 to be a multidrug-resistant bacterium. This study provided a theoretical basis for a better understanding of pathogenicity and antibiotic resistance, which might contribute to the prevention of V. anguillarum in the future.

Animal manures increased maize yield by promoting microbial activities and inorganic phosphorus transformation in reclaimed soil aggregates

Animal manures positively affect soil microbial activity and inorganic phosphorus (Pi) accumulation. However, how different types of manures affect microbial-driven Pi transformation at the aggregate scale is largely unclear. Here, we conducted a field experiment focused on maize cultivation in a reclamation site. Five fertilization treatments included no fertilizer (CK), chemical fertilizer (CF), chicken manure (CHM), pig manure (PM), and cow manure (CM). We examined microbial biomass, soil extracellular enzyme activities associated with carbon and phosphorus cycling, and Pi fractions (Labile-P, Moderately labile-P, and Stable-P) in three aggregate sizes (> 2 mm large macro-aggregates, 0.25–2 mm small macro-aggregates, and < 0.25 mm micro-aggregates), as well as grain yield. The results showed that manures addition significantly increased the proportion of large macro-aggregates and aggregate stability compared to chemical fertilizer. Stable-P constituted the largest proportion among the Pi fractions, accounting for 63 %–72 %. However, manures reduced Stable-P (5.4 %–10.7 %) and increased Labile-P (111 %–190 %) in Pi, especially in micro-aggregates. Both chemical fertilizer and manures increased microbial biomass and enzyme activities in aggregates, with manures causing a greater enhancement of soil microbial biomass carbon (SMBC) and C-cycling enzymes, especially under pig manure, and improving soil microbial biomass phosphorus (SMBP) and P-cycling enzymes, especially under chicken manure. Phytase, phosphatase and SMBP accounted for 81.4 %, 81.2 % and 87 % of the differences in large macro-aggregates, small macro-aggregates, and micro-aggregates, respectively. The structural equation model (SEM) demonstrated that manures facilitated the transformation of Stable-P to Labile-P by regulating aggregates and microbial activity, which consequently increased yield. In summary, manures addition, particularly chicken manure, can enhance inorganic phosphate (Pi) accumulation and transformation, thereby mitigating phosphorus (P) limitation in calcareous reclamation soils.

Unveiling hidden interactions: Microorganisms, enzymes, and mangroves at different stages of succession in the Shankou Mangrove Nature Reserve, China

Understanding the interactions between microorganisms, soil extracellular enzymes, and mangroves is crucial for conserving and restoring mangrove ecosystems. However, the unique environments associated with mangroves have resulted in a lack of pertinent data regarding the interactions between these components. Root, stem, leaf, and soil samples were collected at three distinct stages of mangrove succession. Stoichiometry was employed to analyze the carbon, nitrogen, and phosphorus contents of these samples and to quantify extracellular enzyme activities, microbial biomass, and various physicochemical factors in the soil. The results showed that the trends of C, N, and P in the mangrove plants were consistent. Microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), and microbial biomass phosphorus (MBP) were the highest in the Kandelia obovate community. Catalase (CAT) and β-D-G showed the highest content in K. obovate and Bruguiera gymnorrhiza, whereas cellulase showed the opposite trend. Urease was least abundant in the K. obovate community, whereas neutral protease (NPR) and acid phosphatase (ACP) were most abundant. The overall soil environment in mangroves exhibited a state of N limitation, with varying degrees of limitation observed across different succession stages. The demand for P became more intense in the later stages of succession, particularly in the K. obovate and B. gymnorrhiza communities. In conjunction with correlation analysis, it indicated that the input of mangrove plant litter had a significant regulatory influence on the C, N, and P contents in the soil. There was a significant positive correlation between MBC, MBN, and MBP, indicating synergistic effects of C, N, and P on soil microorganisms. Therefore, evaluating the nutrient ratios and sufficiency of mangroves allowed us to comprehensively understand the present environmental conditions. This study aims to develop sustainable management strategies for the conservation and restoration of mangroves.

Microbes alter substrate from mineral‐associated carbon to litterfall with nitrogen additions and warming

AbstractNitrogen (N) additions often decrease soil respiration and increase soil organic carbon (C) stock. However, it is unclear how microbial substrates may shift with N additions and increasing temperature. Leveraging 12 years of N fertilization experiments and the associated shift in the dominant vegetation from C4 to C3, we explored the δ13C‐CO2 and temperature sensitivities of respired CO2 and extracellular enzyme activities in control and fertilized soils. N additions increased cellulose‐decaying extracellular enzyme activity while respiration remained similar between the control and fertilized soils. Temperature sensitivity of cellulose‐decaying extracellular enzyme activity decreased with the N additions. The δ13C‐CO2 data reveal that, as temperature increased, microbes in fertilized soils changed their dominant substrate from bulk soil organic C to plant litterfall. Our results suggest that long‐term N fertilization imposed C limitation on microbes, leading to enhanced microbial efforts to acquire C. This study highlights how long‐term N additions can promote the relative preservation of organic C in mineral soil while litterfall, the precursor to mineral‐associated C, is increasingly decayed as temperatures increase.

Global emergent responses of stream microbial metabolism to glacier shrinkage

Most cryospheric ecosystems are energy limited. How their energetics will respond to climate change remains largely unknown. This is particularly true for glacier-fed streams, which interface with the cryosphere and initiate some of Earth’s largest river systems. Here, by studying resource stoichiometry and microbial energetics in 154 glacier-fed streams sampled by the Vanishing Glaciers project across Earth’s major mountain ranges, we show that these ecosystems and their benthic microbiome are overall carbon and phosphorus limited. Threshold elemental ratios and low carbon use efficiencies (median: 0.15) modelled from extracellular enzymatic activities corroborate resource limitation in agreement with maintenance metabolism of benthic microorganisms. Space-for-time substitution analyses suggest that glacier shrinkage will stimulate benthic primary production in glacier-fed streams, thereby relieving microbial metabolism from carbon limitation. Concomitantly, we find that increasing streamwater temperature will probably stimulate microbial growth (temperature sensitivity: 0.62 eV). Consequently, elevated microbial demands for phosphorus, but diminishing inputs from subglacial sources, may intensify phosphorus limitation as glaciers shrink. Our study thus unveils a ‘green transition’ towards autotrophy in the world’s glacier-fed streams, entailing shifts in the energetics of their microorganisms.