ABTS assay of phenol oxidase activity in soil

Water Supply via Pedicel Reduces Postharvest Pericarp Browning of Litchi (Litchi chinensis) Fruit

Pericarp browning is the key factor for the extension of shelf life and the maintenance of the commercial value of harvested litchi fruit. Water loss is considered a leading factor of pericarp browning in litchi fruit. In this study, based on the distinct structure of litchi fruit, which is a special type of dry fruit with the aril as the edible part, the effects of water supply via pedicel (WSP) treatment on pericarp browning and the fruit quality of litchi were investigated. Compared with the packaging of the control fruit at 25 °C or 4 °C, the WSP treatment was found to significantly reduce pericarp browning and the decay of litchi fruit. The WSP-treated fruit had a higher L* value, total anthocyanin content, and pericarp water content, and the pericarp was thicker. The WSP treatment significantly suppressed the increase in the electrolyte leakage of the pericarp and maintained higher ascorbic acid (AA) contents in the aril. In addition, the WSP treatment was effective in reducing the activity and gene expression of browning-related genes Laccase (ADE/LAC) and Peroxidase (POD) during the storage period. In conclusion, the WSP treatment could be an effective method to delay pericarp browning and maintain the quality of harvested litchi fruit, and this further supports that litchi fruit has dry fruit characteristics.

Anaerobic growth and drug susceptibility of versatile fungal pathogen Scedosporium apiospermum

Although severe cases of invasive mycoses of different hypoxic and anoxic body parts have been reported, growth and drug susceptibility of fungal pathogens under anaerobic conditions remains understudied. The current study evaluated anaerobic growth potential and drug susceptibility of environmental Scedosporium apiospermum isolates under aerobic and anaerobic conditions. All tested strains showed equivalent growth and higher sensitivity to tested antifungal drugs under anaerobic conditions with lower minimum inhibitory concentration (MIC) as compared to aerobic conditions. Antifungal azoles were effective against isolates under both aerobic and anaerobic conditions. Most strains were resistant to antifungal echinocandins and polyenes under aerobic conditions but exhibited sensitivity under anaerobic conditions. This study provides evidence that resistance of S. apiospermum to antifungal drugs varies with oxygen concentration and availability and suggests re-evaluating clinical breakpoints for antifungal compounds to treat invasive fungal infections more effectively.

The potential roles of carotenoids in enhancing phytoremediation of bisphenol A contaminated soil by promoting plant physiology and modulating rhizobacterial community of tobacco

The widespread occurrence of bisphenol A (BPA), a typical endocrine-disrupting compound, poses potential threat to ecosystem and public health. Carotenoids are essential natural pigments, playing important roles in photosynthesis and antioxidant defense of plants. This study aimed to verify the value of carotenoids in enhancing plant tolerance to BPA stress and improving phytoremediation efficiency of tobacco (Nicotiana tabacum L.), through exogenous application of β-carotene (a typical carotenoid) and endogenous upregulation of carotenoids by overexpression of β-carotene hydroxylase (chyb) gene in tobacco. The results demonstrated that exogenous applied β-carotene alleviated the toxic effects of BPA exposure (100 mg kg^-1) on wild-type (WT) tobacco plants after being cultivated for 40 d, reflecting by the increase of biomass (201.2%), chlorophyll content (27.5%) and the decrease of malondialdehyde (MDA) content (70.7%). Similar with the results of exogenous application of β-carotene, chyb gene overexpressing tobacco showed less phytotoxicity exposed to BPA, through enhancing photosynthetic efficiency (42.1%) and reducing reactive oxygen species (ROS) production (18%). Notably, about 94.8% BPA in contaminated soil was removed under the cultivation of transgenic tobacco for 40 d, however, only 82.7% was removed in that of WT tobacco. Moreover, transgenic tobacco is beneficial for the growth of plant roots, thus upregulating the abundance of bacteria contributing to BPA degradation or soil nutrient cycling (e.g., Proteobacteria, Acidobacteria, Actinobacteria, Sphingomonas and MND1), which might further help to enhance plant growth and improve BPA removal efficiency in soil. This study extended our understanding of the possible mechanisms of carotenoids-involved alleviation of BPA stress in tobacco, providing a novel strategy to improve phytoremediation efficiency of plants in BPA contaminated soil.

Exploration of bacterial community-induced polycyclic aromatic hydrocarbons degradation and humus formation during co-composting of cow manure waste combined with contaminated soil

To solve polycyclic aromatic hydrocarbons (PAHs) pollution, composting was chosen as a remediation method. During composting, the dissipation of PAHs was carried out by resource utilization of organic solid waste and its degradation by bacteria. This study was conducted by co-composting with contaminated soil and cow manure. The results showed that the degradation rates of naphthalene (Nap), phenanthrene (Phe), and benzo[α]pyrene (BaP) could reach 82.2%, 79.4%, and 59.6% respectively during composting. Cluster analysis indicated that polyphenol oxidase (PPO), laccase, and protease were important drivers of PAHs transformation. The content of humic substances (HS) was 106.67 g/kg in PAH treatment, which was significantly higher than that in the control group at 65 days. The phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) and network analysis was used to infer the degradation mechanism of PAHs by microorganisms. The degradation of PAHs by PPO was found to have a significant contribution to the formation of HS. It was shown that PAHs and metabolic intermediates were more inclined to be oxidized and decomposed by PPO to form quinone, which in turn condensed with amino acids to form HS. Composting could promote the degradation of PAHs while improving the quality of compost, achieving a win-win situation.

Effects of planting of two common crops, Allium fistulosum and Brassica napus, on soil properties and microbial communities of ginseng cultivation in northeast China

Background

Long-term cultivation of ginseng can cause severe crop disorders and soil sickness. Crop rotation is an effective agricultural management measure to improve soil sustainability and decrease pathogens. However, the suitable ginseng rotation system and the changes in soil microbial community and soil characteristics under the rotation system need to be further explored.

Methods

To explore suitable ginseng crop rotation systems and improve soil utilization, Allium fistulosum and Brassica napus were planted on ginseng cultivation soil for one year. The effects of the two crops on the chemical properties and enzyme activities of the ginseng cultivation soil were evaluated by chemical analysis. In addition, amplicon sequencing targeting 16 s rDNA genes of bacteria and ITS of fungi has been used to characterize the functional and compositional diversity of microbial communities.

Results

The results elucidated that the levels of available phosphorus (AP) and available potassium (AK) in the soil increased significantly after one year of cultivation for both crops and Allium fistulosum cultivation may also have reduced soil salinity. In addition, the effects of the two crops on the activities of key soil enzymes were different. Catalase (CAT), urease (URE), and acid phosphatase (A-PHO) activities were significantly reduced and sucrase (SUC), and laccase (LAC) activities were significantly increased after Allium fistulosum planting. While A-PHO activity was significantly increased and LAC activity was significantly decreased after Brassica napus planting. Allium fistulosum significantly reduced the abundance of soil fungal communities. The cultivation of Allium fistulosum and Brassica napus significantly altered the composition of soil bacterial and fungal communities, where changes in the abundance of dominant microorganisms, such as Ascomycota, and Mortierellomycota, etc., were closely related to soil chemistry and enzyme activity. Moreover, both significantly reduced the abundance of the pathogenic fungus Ilyonectria.

Conclusions

Our study clarified the effects of Allium fistulosum and Brassica napus on the microbial community and physicochemical properties of ginseng cultivated soil and provides a basis for the sustainable application of ginseng cultivation soil and the development of ginseng crop rotation systems.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02592-0.

Phytoremediation potential, antioxidant response, photosynthetic behavior and rhizosphere bacterial community adaptation of tobacco (Nicotiana tabacum L.) in a bisphenol A-contaminated soil

Bisphenol A (BPA) is an emerging organic pollutant, widely distributed and frequently detected in soil in recent years. BPA toxicity is a problem that needs to be solved in terms of both human health and agricultural production. Up to now, the toxic effect of BPA and its mechanism of action on plants, as well as the possibility of using plants to remediate BPA-contaminated soil, remain to be explored. In this study, six treatment groups were set up to evaluate the effects of different concentrations of BPA on the germination and growth of tobacco (Nicotiana tabacum L.) by medium experiments. Furthermore, the representative indexes of photosynthetic and antioxidant system were determined. Meanwhile, tobacco seedlings were cultivated in soil to further explore the effects of BPA on rhizosphere soil enzyme activity and bacterial community structure with or without 100 mg/kg BPA exposure. The enhancement of BPA removal efficiency from soil by phytoremediation using tobacco plants would also be estimated. Our results showed that high doses of BPA in solid medium remarkably inhibited tobacco seedling growth, and its toxicology effect was positively correlated with BPA concentration, while lower BPA exposure (< 20 mg/L) had little limitation on tobacco growth and induced hormesis effect, which was reflected mainly in the increase of root length. In pot experiments, the reducing of chlorophyll content (36.4%) and net photosynthetic rate (41.2%) meant the inhibition of tobacco photosynthetic process due to high concentration of BPA exposure (100 mg/kg) in soil. The increase of H2O2 and O2- content suggested that BPA could destroy the balance of reactive oxygen species (ROS) in plants. However, tobacco plants still presented a high removal efficiency of BPA at the concentration of 100 mg/kg in soil, which could reach to 80% within 30 days. Furthermore, it was indicated that tobacco cultivation changed the structure of rhizosphere soil bacterial communities and the relative abundance of some valuable strains, including Proteobacteria, Acidobacteria and other strains, which might be participated in the BPA removal process. In addition, the tobacco-soil microbial system had the potential to reverse the negative effects caused by BPA through stimulating microorganism associated with soil nutrient cycling. In summary, tobacco is a competitive plant in phytoremediation of BPA-contaminated soil, though the growth of tobacco could be inhibited at high concentration of BPA. Moreover, tobacco might promote the removal efficiency of BPA by regulating the rhizosphere bacteria communities.

Assessing Impacts of Transgenic Plants on Soil Using Functional Indicators: Twenty Years of Research and Perspectives

Assessment of the effects of transgenic plants on microbiota and soil fertility is an important part of the overall assessment of their biosafety. However, the environmental risk assessment of genetically modified plants has long been focused on the aboveground effects. In this review, we discuss the results of two decades of research on the impact of transgenic plants on the physicochemical properties of soil, its enzyme activities and microbial biomass. These indicators allow us to assess both the short-term effects and long-term effects of cultivating transgenic plants. Most studies have shown that the effect of transgenic plants on the soil is temporary and inconsistent. Moreover, many other factors, such as the site location, weather conditions, varietal differences and management system, have a greater impact on soil quality than the transgenic status of the plants. In addition to the effects of transgenic crop cultivation, the review also considers the effects of transgenic plant residues on soil processes, and discusses the future prospects for studying the impact of genetically modified plants on soil ecosystems.

Anaerobic biodegradation of polycyclic aromatic hydrocarbons (PAHs) by fungi isolated from anaerobic coal-associated sediments at 2.5 km below the seafloor

Fungi represent the dominant eukaryotic group in the deep biosphere and well-populated in the anaerobic coal-bearing sediments up to ∼2.5 km below seafloor (kmbsf). But whether fungi are able to degrade and utilize coal to sustain growth in the anaerobic sub-seafloor environment remains unknown. Based on biodegradation investigation, we found that fungi isolated from sub-seafloor sediments at depths of ∼1.3-∼2.5 kmbsf showed a broad range of polycyclic aromatic hydrocarbons (PAHs) anaerobic degradation rates (3-25%). Among them, the white-rot fungus Schizophyllium commune 20R-7-F01 exhibited the highest degradation, 25%, 18% and 13%, of phenanthrene (Phe), pyrene (Pyr) and benzo[a]pyrene (BaP); respectively, after 10 days of anaerobic incubation. Phe was utilized well and about 40.4% was degraded by the fungus, after 20 days of anaerobic incubation. Moreover, the ability of fungi to degrade PAHs was positively correlated with the anaerobic growth of fungi, indicating that fungi can use PAHs as a sole carbon source under anoxic conditions. In addition, fungal degradation of PAHs was found to be related to the activity of carboxylases, but little or nothing to do with the activity of lignin modifying enzymes such as laccase (Lac), manganese peroxidase (MnP) and lignin peroxidase (LiP). These results suggest that sub-seafloor fungi possess a special mechanism to degrade and utilize PAHs as a carbon and energy source under anaerobic conditions. Furthermore, fungi living in sub-seafloor sediments may not only play an important role in carbon cycle in the anaerobic environments of the deep biosphere, but also be able to persist in deep sediment below seafloor for millions of years by using PAHs or related compounds as carbon and energy source. This anaerobic biodegradation ability could make these fungi suitable candidates for bioremediation of toxic pollutants such as PAHs from anoxic environments.

Activation effect of catechol on biotic and abiotic factors of humus formation during chicken manure composting

In this present study, catechol was added to promote humus formation in chicken manure composting using 12.5-L working volume lab-scale reactors. Chicken manure composting were carried out on two treatments, control (CK) and 0.5% (w/w) catechol treated group. Results showed that catechol addition reduced organic matter loss and improved the content of recalcitrant components. Humus and humic acid (HA) contents were, respectively, 69.2% and 82.3% higher in catechol treated-compost than in the control. With the addition of catechol, the bacterial community composition and richness was changed, e.g., the relative percentage of Bacillus and Sinibacillus were increased, which might contribute to humus and HA formation. Additionally, the activities of polyphenol oxidase and laccase (related to humus formation) were increased by the addition of catechol. Importantly, the catechol addition reduced the polyphenol content by 39.6% compared to control. Overall, the addition of catechol enhanced the biotic and abiotic factors to promote the humification process during composting, which might be a promising approach for accelerating the humification process and reducing contamination of phenolic compounds.

Tobacco-associated with Methylophilus sp. FP-6 enhances phytoremediation of benzophenone-3 through regulating soil microbial community, increasing photosynthetic capacity and maintaining redox homeostasis of plant

Benzophenone-3 (BP-3) has attracted widespread attention due to its large accumulation in the environment and its potential toxicity effects to human. This study aimed to investigate the effects of the combined application of tobacco and Methylophilus sp. strain FP-6 with both plant growth promoting (PGP) traits and BP-3 degradation function on BP-3 remediation in soil. The results showed that about 79.18% of BP-3 was removed from the soil after 30 days of plant culture inoculated with the FP-6 strain, which was significantly higher than the plant-alone treatment. Simultaneously, inoculation with strain FP-6 significantly improved growth performance, biomass production, antioxidant levels, osmoregulation substance, photosynthetic capacity and chlorophyll accumulation in tobacco. Moreover, the application of FP-6 shifted the bacterial community, and enhanced the abundance of BP-3-degrading or soil nutrient cycling-affecting bacteria (e.g., Chloroflexi, Bryobacter, MND1 and Myxococcales), which might be valuable for the promotion of plant growth and degradation of BP-3 in the soil. The results from this study gave first insights into the enhancement of BP-3 removal efficiency from soil by phytoremediation assisted with bacteria possessing both PGP properties and BP-3 degradation function. The role of soil bacterial community in this remediation process was also discussed.

Soil Enzyme Activity Regulates the Response of Soil C Fluxes to N Fertilization in a Temperate Cultivated Grassland

Exogenous nitrogen (N) inputs greatly change the emission and uptake of carbon dioxide (CO2) and methane (CH4) from temperate grassland soils, thereby affecting the carbon (C) budget of regional terrestrial ecosystems. Relevant research focused on natural grassland, but the effects of N fertilization on C exchange fluxes from different forage soils and the driving mechanisms were poorly understood. Here, a three-year N addition experiment was conducted on cultivated grassland planted with alfalfa (Medicago sativa) and bromegrass (Bromus inermis) in Inner Mongolia. The fluxes of soil-atmospheric CO2 and CH4; the content of the total dissolved N (TDN); the dissolved organic N (DON); the dissolved organic C (DOC); NH4+–N and NO3−–N in soil; enzyme activity; and auxiliary variables (soil temperature and moisture) were simultaneously measured. The results showed that N fertilization (>75 kg N ha−1 year−1) caused more serious soil acidification for alfalfa planting than for brome planting. N fertilization stimulated P-acquiring hydrolase (AP) in soil for growing Bromus inermis but did not affect C- and N-acquiring hydrolases (AG, BG, CBH, BX, LAP, and NAG). The oxidase activities (PHO and PER) of soil for planting Bromus inermis were higher than soil for planting Medicago sativa, regardless of N, whether fertilization was applied or not. Forage species and N fertilization did not affect soil CO2 flux, whereas a high rate of N fertilization (150 kg N ha−1 year−1) significantly inhibited CH4 uptake in soil for planting Medicago sativa. A synergistic effect between CO2 emission and CH4 uptake in soil was found over the short term. Our findings highlight that forage species affect soil enzyme activity in response to N fertilization. Soil enzyme activity may be an important regulatory factor for C exchange from temperate artificial grassland soil in response to N fertilization.

Elevated temperatures drive abiotic and biotic degradation of organic matter in a peat bog under oxic conditions

Understanding the effects of elevated temperatures on soil organic matter (SOM) decomposition pathways in northern peatlands is central to predicting their fate under future warming. Peatlands role as carbon (C) sink is dependent on both anoxic conditions and low temperatures that limit SOM decomposition. Previous studies have shown that elevated temperatures due to climate change can disrupt peatland's C balance by enhancing SOM decomposition and increasing CO₂ emissions. However, little is known about how SOM decomposition pathways change at higher temperatures. Here, we used an integrated research approach to investigate the mechanisms behind enhanced CO₂ emissions and SOM decomposition under elevated temperatures of surface peat soil collected from a raised and Sphagnum dominated mid-continental bog (S1 bog) peatland at the Marcel Experimental Forest in Minnesota, USA, incubated under oxic conditions at three different temperatures (4, 21, and 35 °C). Our results indicated that elevated temperatures could destabilize peatland's C pool via a combination of abiotic and biotic processes. In particular, temperature-driven changes in redox conditions can lead to abiotic destabilization of Fe-organic matter (phenol) complexes, previously an underestimated decomposition pathway in peatlands, leading to increased CO₂ production and accumulation of polyphenol-like compounds that could further inhibit extracellular enzyme activities and/or fuel the microbial communities with labile compounds. Further, increased temperatures can alter strategies of microbial communities for nutrient acquisition via changes in the activities of extracellular enzymes by priming SOM decomposition, leading to enhanced CO₂ emission from peatlands. Therefore, coupled biotic and abiotic processes need to be incorporated into process-based climate models to predict the fate of SOM under elevated temperatures and to project the likely impacts of environmental change on northern peatlands and CO₂ emissions.

Response of soil enzyme activity and soil bacterial community to PCB dissipation across different soils

Soils are a repository for polychlorinated biphenyls (PCBs). A pot incubation experiment was performed with four soils (black soil, paddy soil, oasis soil, and fluvo-aquic soil) treated with Aroclor 1242 to achieve PCB concentrations of 5 mg kg^-1. The soil enzyme activities of protease, phosphatase, catalase, dehydrogenase, and laccase were determined by spectrophotometry. The soil bacterial communities were investigated using Illumina sequencing analysis. The results showed that the characteristics of the test soils varied among the soil types. The fluvo-aquic soil had the greatest PCB dissipation rate (86.41%), followed by the oasis (79.31%), paddy (56.09%), and black (50.65%) soils. The soil pH, cation exchange capacity, soil organic matter content, and particle diameter played significant roles in PCB dissipation from soils. The soil type had a greater influence than PCB contamination on the soil enzyme activities and bacterial communities (alpha diversity, community structure, and composition). Among the four soils, the bacterial communities of the fluvo-aquic soil were the most susceptible to PCB contamination. However, the bacterial communities of the black soil were not changed by PCB contamination.

Phenoloxidase activity and organic carbon dynamics in historic Anthrosols in Scotland, UK

Phenolic compounds are chemical precursor building blocks of soil organic matter. Their occurrence can be inhibitory to certain enzymes present in soil, thereby influencing the rate of decomposition of soil organic matter. Microbe-derived phenoloxidases (laccases) are extracellular enzymes capable of degrading recalcitrant polyphenolic compounds. In this study, our aim was to investigate the relationships between phenoloxidase enzyme activity, organic carbon content and microbial abundance in the context of long-term anthropogenically amended soils. To achieve this, we used a series of complementary biochemical analytical methods including gas chromatography, enzyme assays and solid-state Carbon-13 Cross Polarisation Magic-Angle Spinning Nuclear Magnetic Resonance Spectroscopy (¹³C CPMAS NMR). Using several anthrosols found in St Andrews (Scotland, UK) that had been subjected to intense anthropogenic modification since the medieval period (11^th century AD) to present-day, we were able to scope the impact of past waste disposal on soils. The long-term anthropogenic impact led to organic matter-rich soils. Overall, phenoloxidase activity increased by up to 2-fold with soil depth (up to 100 cm) and was inversely correlated with microbial biomass. Solid-state ¹³C NMR characterisation of carbon species revealed that the observed decline in soil organic matter with depth corresponded to decreases in the labile organic carbon fractions as evidenced by changes in the O/N-alkyl C region of the spectra. The increase in phenoloxidase activity with depth would appear to be a compensatory mechanism for the reduced quantities of organic carbon and lower overall nutrient environment in subsoils. By enzymatically targeting phenolic compounds, microbes can better utilise recalcitrant carbon when other labile soil carbon sources become limited, thereby maintaining metabolic processes.

Fruit extract of red pitaya (Hylocereus undatus) prevents and reverses stress-induced impairments in the cholinergic and antioxidant systems of Caenorhabditis elegans

The addition of fruit to the diet is very important, and we can use nutraceutical and functional foods for this supplement. A little-known fruit is a red pitaya (Hylocereus undatus) that has been widely reported to have a high antioxidant potential. In this study, we analyzed the in vitro and in vivo antioxidant capacity of microencapsulated pitaya extract on the behavior, antioxidant, and nervous system of the nematode Caenorhabditis elegans. The worms were treated with fruit extract before and after juglone-induced stress, to determine the protective or curative effects of pitaya. We have been evaluated cholinergic, antioxidant, and behavioral biomarkers. We have evidenced that the pulp of pitaya contains antioxidant compounds and can serve as a potential nutraceutical product. In addition, the fruit extract was effective in preventing and/or reverse the stress-induced damages, even at high levels of chemical stress at all evaluated parameters. PRACTICAL APPLICATIONS: The potential applications and uses aimed by this research are related to the supplementation of foods given the antioxidant effect. Our data suggested that the effect of the pitaya fruit microencapsulated pulp extract was effective to prevent and repair the damage caused by oxidative stress. Besides the use of this microencapsulated extract can be an auxiliary in the treatment of diseases related to oxidative damage as well as promoting senescent aging. Another important use is the application of this extract as a dietary supplement to fortify the antioxidant system.

Biodiversity and biocatalyst activity of culturable hydrocarbonoclastic fungi isolated from Marac-Moruga mud volcano in South Trinidad

Mud volcanoes (MVs) are visible signs of oil and gas reserves present deep beneath land and sea. The Marac MV in Trinidad is the only MV associated with natural hydrocarbon seeps. Petrogenic polyaromatic hydrocarbons (PAHs) in its sediments must undergo biogeochemical cycles of detoxification as they can enter the water table and aquifers threatening ecosystems and biota. Recurrent hydrocarbon seep activity of MVs consolidates the growth of hydrocarbonoclastic fungal communities. Fungi possess advantageous metabolic and ecophysiological features for remediation but are underexplored compared to bacteria. Additionally, indigenous fungi are more efficient at PAH detoxification than commercial/foreign counterparts and remediation strategies remain site-specific. Few studies have focused on hydrocarbonoclastic fungal incidence and potential in MVs, an aspect that has not been explored in Trinidad. This study determined the unique biodiversity of culturable fungi from the Marac MV capable of metabolizing PAHs in vitro and investigated their extracellular peroxidase activity to utilize different substrates ergo their extracellular oxidoreductase activity (> 50% of the strains decolourized of methylene blue dye). Dothideomycetes and Eurotiomycetes (89% combined incidence) were predominantly isolated. ITS rDNA sequence cluster analysis confirmed strain identities. 18 indigenous hydrocarbonoclastic strains not previously reported in the literature and some of which were biosurfactant-producing, were identified. Intra-strain variability was apparent for PAH utilization, oil-tolerance and hydroxylase substrate specificity. Comparatively high levels of extracellular protein were detected for strains that demonstrated low substrate specificity. Halotolerant strains were also recovered which indicated marine-mixed substrata of the MV as a result of deep sea conduits. This work highlighted novel MV fungal strains as potential bioremediators and biocatalysts with a broad industrial applications.

Growth Response of Ginger (Zingiber officinale), Its Physiological Properties and Soil Enzyme Activities after Biochar Application under Greenhouse Conditions

This study aimed to investigate the effects of biochar (1%, 2%, and 3%) on seed germination, plant growth, root morphological characteristics, and physiological properties of ginger (Zingiber officinale) and soil enzymatic activities. Pot experiments under greenhouse conditions at 24 °C (day) and 16 °C (night) showed after six weeks that biochar additions of 2% and 3% significantly increased seed germination, plant height, leaf length, leaf number, as well as shoot and root dry weights compared to the control. Total root length significantly increased by 30%, 47%, and 74%, with increasing biochar contents (1%, 2%, and 3%) compared to the control. Root surface area, projected area, root diameter, and root volume reached a maximum at the 3% biochar treatment. The treatment with 2% biochar significantly increased fluorescein diacetate hydrolase and phenoloxidase activities by 33% and 59% compared to the control; so did the addition of 3% biochar, which significantly increased fluorescein diacetate hydrolases, phenoloxidase, and acid and alkaline phosphomonoesterase activity in soil compared to the control. Treatment with 3% biochar increased relative water content by 8%, chlorophyll content by 35%, and carotenoid content by 43% compared to the control. These results suggest that biochar can improve the performance of the rhizome of ginger and increase the activity of soil enzymes, thereby improving soil nutrient supply.

Terricolous mosses impact soil microbial biomass carbon and enzymatic activity under temperate forest types of the Garhwal Himalayas

Estimates of enzymatic activity are used as indices for soil quality, microbial nutrient demand, microbial growth, and activity. Mosses trap soil moisture, influence soil temperature, and create a microenvironment promoting an overall higher level of microbial activity, thus making the decomposition of organic matter more favorable. This study determines the role of mosses in influencing soil biochemical properties in three temperate forest types of the Garhwal Himalayas, Uttarakhand, viz., moist temperate deciduous forest, Ban oak forest, and moist deodar forest. Activities of major soil enzymes (dehydrogenase, β-glucosidase, acid phosphatase, aryl sulfatase, phenol oxidase, and urease) and soil microbial biomass carbon (SMBC) were determined under two different substrates, i.e., with and without moss cover in two different seasons, viz., monsoon and winter. The Pearson correlation of enzymes with specific soil nutrients they act upon has also been shown. The SMBC and on average activities of all the enzymes were predominantly higher in soil with moss cover during monsoon season and without moss cover in the winter season. SMBC in the three study sites ranged from 280.55 to 1707.64 µg C/g. Statistically significant differences (p < 0.01) were observed for all the properties within the substrates among all the three sites and across the two seasons. Our results suggest that mosses play a significant role in positively influencing soil biochemical properties in both seasons by creating a microscale mosaic that offers a high degree of heterogeneity in soil function. Our study emphasizes that mosses strongly affect soil enzyme activities and microbial biomass, thus improving soil health.

Soil organic carbon is significantly associated with the pore geometry, microbial diversity and enzyme activity of the macro-aggregates under different land uses

Microbial activity strongly influences the stabilization of soil organic matter (SOM), and is affected by the abiotic properties within soil aggregates, which tend to differ between land uses. Here, we assessed the effects of SOM and pore geometry on the diversity and activity of microbial communities within aggregates formed under different land uses (undisturbed, plantation, pasture, and cropping). X-ray micro-computed tomography (μCT) revealed that macro-aggregates (2-8 mm) of undisturbed soils were porous, highly-connected, and had 200% more macro-pores compared with those from pasture and cropping soils. While the macro-aggregates of undisturbed soils had greater soil organic carbon (SOC) contents and N-acetyl β-glucosaminidase, β-glucosidase, and phosphatase activities, those of cropped soils harboured more diverse bacterial communities. Organic carbon was positively associated with the porosity of the macro-aggregates, which was negatively associated with microbial diversity and positively associated with enzyme activity. Thus, the biophysical processes in macro-aggregates may be important for SOC stabilization within the macro-aggregates.

Carbohydrate depletion in roots impedes phosphorus nutrition in young forest trees

Nutrient imbalances cause the deterioration of tree health in European forests, but the underlying physiological mechanisms are unknown. Here, we investigated the consequences of decreasing root carbohydrate reserves for phosphorus (P) mobilisation and uptake by forest trees. In P-rich and P-poor beech (Fagus sylvatica) forests, naturally grown, young trees were girdled and used to determine root, ectomycorrhizal and microbial activities related to P mobilisation in the organic layer and mineral topsoil in comparison with those in nongirdled trees. After girdling, root carbohydrate reserves decreased. Root phosphoenolpyruvate carboxylase activities linking carbon and P metabolism increased. Root and ectomycorrhizal phosphatase activities and the abundances of bacterial genes catalysing major steps in P turnover increased, but soil enzymes involved in P mobilisation were unaffected. The physiological responses to girdling were stronger in P-poor than in P-rich forests. P uptake was decreased after girdling. The soluble and total P concentrations in roots were stable, but fine root biomass declined after girdling. Our results support that carbohydrate depletion results in reduced P uptake, enhanced internal P remobilisation and root biomass trade-off to compensate for the P shortage. As reductions in root biomass render trees more susceptible to drought, our results link tree deterioration with disturbances in the P supply as a consequence of decreased belowground carbohydrate allocation.

Acute effects of PAH contamination on microbial community of different forest soils

Polycyclic aromatic hydrocarbons (PAHs) are hazardous organic compounds with mutagenic, genotoxic and carcinogenic properties. Although PAHs in soil can cause toxicity to microorganisms, the microbial community is able to degrade these compounds. For this reason, it is important to study acute and short-term effects of PAH contamination on soil microbial community, also to shed light on its possible exploitation in soil restoration. The effects of acute PAH contamination on the structure and metabolic activity of microbial communities in three forest (beech, holm oak, black pine) soils were studied. The soils were spiked with phenanthrene, pyrene or benzo[a]pyrene and incubated in experimental mesocosms, under controlled conditions. Enzymatic activities (laccase, total peroxidase and hydrolase), as well as microbial biomass and community structure (through phospholipid fatty acid and ergosterol analyses), were evaluated in the three soil systems 4 days after contamination and compared to no-spiked soils. In soil under holm oak, there was a stimulation of Gram+ bacteria after contamination with all the 3 PAHs, whereas in soil under pine, pyrene and phenanthrene additions mainly stimulated fungi and actinomycetes.

Soil multifunctionality is affected by the soil environment and by microbial community composition and diversity

Microorganisms are critical in mediating carbon (C) and nitrogen (N) cycling processes in soils. Yet, it has long been debated whether the processes underlying biogeochemical cycles are affected by the composition and diversity of the soil microbial community or not. The composition and diversity of soil microbial communities can be influenced by various environmental factors, which in turn are known to impact biogeochemical processes. The objectives of this study were to test effects of multiple edaphic drivers individually and represented as the multivariate soil environment interacting with microbial community composition and diversity, and concomitantly on multiple soil functions (i.e. soil enzyme activities, soil C and N processes). We employed high-throughput sequencing (Illumina MiSeq) to analyze bacterial/archaeal and fungal community composition by targeting the 16S rRNA gene and the ITS1 region of soils collected from three land uses (cropland, grassland and forest) deriving from two bedrock forms (silicate and limestone). Based on this data set we explored single and combined effects of edaphic variables on soil microbial community structure and diversity, as well as on soil enzyme activities and several soil C and N processes. We found that both bacterial/archaeal and fungal communities were shaped by the same edaphic factors, with most single edaphic variables and the combined soil environment representation exerting stronger effects on bacterial/archaeal communities than on fungal communities, as demonstrated by (partial) Mantel tests. We also found similar edaphic controls on the bacterial/archaeal/fungal richness and diversity. Soil C processes were only directly affected by the soil environment but not affected by microbial community composition. In contrast, soil N processes were significantly related to bacterial/archaeal community composition and bacterial/archaeal/fungal richness/diversity but not directly affected by the soil environment. This indicates direct control of the soil environment on soil C processes and indirect control of the soil environment on soil N processes by structuring the microbial communities. The study further highlights the importance of edaphic drivers and microbial communities (i.e. composition and diversity) on important soil C and N processes.

First demonstration that ascomycetous halophilic fungi (Aspergillus sydowii and Aspergillus destruens) are useful in xenobiotic mycoremediation under high salinity conditions

Polycyclic aromatic hydrocarbons (PAH) and pharmaceutical compounds (PhC) are xenobiotics present in many saline wastewaters. Although fungi are known for their ability to remove xenobiotics, the potential of halophilic fungi to degrade highly persistent pollutants was not yet investigated. The use of two halophilic fungi, Aspergillus sydowii and Aspergillus destruens, for the elimination of PAH and PhC at saline conditions was studied. In saline synthetic medium both fungi used benzo-α-pyrene and phenanthrene as sole carbon source and removed over 90% of both PAH, A. sydowii due to biodegradation and A. destruens to bioadsorption. They removed 100% of a mixture of fifteen PAH in saline biorefinery wastewater. Test using Cucumis sativus demonstrated that wastewater treated with the two fungi lowered considerably the phytotoxicity. This study is the first demonstration that ascomycetous halophilic fungi, in contrast to other fungi (and in particular basidiomycetes) can be used for mycotreatments under salinity conditions.

A far-red fluorescent probe for sensing laccase in fungi and its application in developing an effective biocatalyst for the biosynthesis of antituberculous dicoumarin

A far-red fluorescent probe for sensing laccase in fungi and its application in developing an effective biocatalyst for the biosynthesis of antituberculous dicoumarin.

Growth explains microbial carbon use efficiency across soils differing in land use and geology

The ratio of carbon (C) that is invested into microbial growth to organic C taken up is known as microbial carbon use efficiency (CUE), which is influenced by environmental factors such as soil temperature and soil moisture. How microbes will physiologically react to short-term environmental changes is not well understood, primarily due to methodological restrictions. Here we report on two independent laboratory experiments to explore short-term temperature and soil moisture effects on soil microbial physiology (i.e. respiration, growth, CUE, and microbial biomass turnover): (i) a temperature experiment with 1-day pre-incubation at 5, 15 and 25 °C at 60% water holding capacity (WHC), and (ii) a soil moisture/oxygen (O2) experiment with 7-day pre-incubation at 20 °C at 30%, 60% WHC (both at 21% O2) and 90% WHC at 1% O2. Experiments were conducted with soils from arable, pasture and forest sites derived from both silicate and limestone bedrocks. We found that microbial CUE responded heterogeneously though overall positively to short-term temperature changes, and decreased significantly under high moisture level (90% WHC)/suboxic conditions due to strong decreases in microbial growth. Microbial biomass turnover time decreased dramatically with increasing temperature, and increased significantly at high moisture level (90% WHC)/suboxic conditions. Our findings reveal that the responses of microbial CUE and microbial biomass turnover to short-term temperature and moisture/O2 changes depended mainly on microbial growth responses and less on respiration responses to the environmental cues, which were consistent across soils differing in land use and geology.

A comparative structural analysis of the surface properties of asco-laccases

Laccases of different biological origins have been widely investigated and these studies have elucidated fundamentals of the generic catalytic mechanism. However, other features such as surface properties and residues located away from the catalytic centres may also have impact on enzyme function. Here we present the crystal structure of laccase from Myceliophthora thermophila (MtL) to a resolution of 1.62 Å together with a thorough structural comparison with other members of the CAZy family AA1_3 that comprises fungal laccases from ascomycetes. The recombinant protein produced in A. oryzae has a molecular mass of 75 kDa, a pI of 4.2 and carries 13.5 kDa N-linked glycans. In the crystal, MtL forms a dimer with the phenolic substrate binding pocket blocked, suggesting that the active form of the enzyme is monomeric. Overall, the MtL structure conforms with the canonical fold of fungal laccases as well as the features specific for the asco-laccases. However, the structural comparisons also reveal significant variations within this taxonomic subgroup. Notable differences in the T1-Cu active site topology and polar motifs imply molecular evolution to serve different functional roles. Very few surface residues are conserved and it is noticeable that they encompass residues that interact with the N-glycans and/or are located at domain interfaces. The N-glycosylation sites are surprisingly conserved among asco-laccases and in most cases the glycan displays extensive interactions with the protein. In particular, the glycans at Asn88 and Asn210 appear to have evolved as an integral part of the asco-laccase structure. An uneven distribution of the carbohydrates around the enzyme give unique properties to a distinct part of the surface of the asco-laccases which may have implication for laccase function–in particular towards large substrates.

Anthracene and benzo(a)pyrene degradation in soil is favoured by compost amendment: Perspectives for a bioremediation approach

In order to validate the use of compost in soil PAH bioremediation, the degradation of anthracene and benzo(a)pyrene was monitored in soils artificially contaminated and incubated in mesocosms under controlled conditions. The dynamics observed in compost amended soil were compared to those observed in soil added with a fungal consortium and untreated soil. At the same time, three microbial enzyme activities usually involved in PAH degradation (laccase, o-diphenol oxidase and peroxidase activities) were monitored. Both PAHs decreased along the time in the three mesocosms, with anthracene, with lower molecular weight, degrading with a higher rate and reaching lower residual values than benzo(a)pyrene. Although at the end of incubation, the residual values of investigated PAHs are similar in the three mesocosm types, PAH dynamics showed a higher degradation rate in the early stage in mesocosms added with the fungal mycelium and amended with compost. Among the three enzyme activities, only peroxidase showed higher values in treated than untreated mesocosms. Considering the ameliorating effects of compost on degraded soils, its use can be suggested in PAH bioremediation.

Microbial extracellular enzymes in biogeochemical cycling of ecosystems

Extracellular enzymes, primarily produced by microorganisms, affect ecosystem processes because of their essential roles in degradation, transformation and mineralization of organic matter. Extracellular enzymes involved in the cycling of carbon (C), nitrogen (N) and phosphorus (P) have been widely investigated in many different ecosystems, and several enzymes have been recognized as key components in regulating C storage and nutrient cycling. In this review, it was the first time to summarize the specific extracellular enzymes related to C storage and nutrient cycling for better understanding the important role of microbial extracellular enzymes in biogeochemical cycling of ecosystems. Subsequently, ecoenzymatic stoichiometry - the relative ratio of extracellular enzyme, has been reviewed and further provided a new perspective for understanding biogeochemical cycling of ecosystems. Finally, the new insights of using microbial extracellular enzyme in indicating biogeochemical cycling and then protecting ecosystems have been suggested.

Bio-prospecting Bacterial Diversity of Hot Springs in Northern Himalayan Region of India for Laccases

Bacterial diversity of hot springs of northern Himalayan region of India was studied and explored for laccases, the multicopper enzymes applicable in a large number of industries due to their ability to utilize a wide range of substrates. 220 operational taxonomic units (OTUs) out of 5551 sequence reads for bacterial diversity and 3 OTUs out of 19 sequence reads for Laccase like multicopper oxidases (LMCOs) diversity were generated. Bacteroidetes (74.28%) was the most abundant phylum including genus Paludibacter (66.96%), followed by phylum Proteobacteria (24.53%) including genera Chitinilyticum (7.55%) and Cellvibrio (6.14%). In case of laccase diversity, three LMCO sequences showed affiliation with proteobacteria and one with two domain laccase from uncultivable bacteroidetes. LMCO sequences belonged to H and N families.

Characterization of lignocellulolytic activities from fungi isolated from the deep-sea sponge Stelletta normani

Extreme habitats have usually been regarded as a source of microorganisms that possess robust proteins that help enable them to survive in such harsh conditions. The deep sea can be considered an extreme habitat due to low temperatures (<5°C) and high pressure, however marine sponges survive in these habitats. While bacteria derived from deep-sea marine sponges have been studied, much less information is available on fungal biodiversity associated with these sponges. Following screening of fourteen fungi isolated from the deep-sea sponge Stelletta normani sampled at a depth of 751 metres, three halotolerant strains (TS2, TS11 and TS12) were identified which displayed high CMCase and xylanase activities. Molecular based taxonomic approaches identified these strains as Cadophora sp. TS2, Emericellopsis sp. TS11 and Pseudogymnoascus sp. TS 12. These three fungi displayed psychrotolerance and halotolerant growth on CMC and xylan as sole carbon sources, with optimal growth rates at 20°C. They produced CMCase and xylanase activities, which displayed optimal temperature and pH values of between 50-70°C and pH 5-8 respectively, together with good thermostability and halotolerance. In solid-state fermentations TS2, TS11 and TS12 produced CMCases, xylanases and peroxidase/phenol oxidases when grown on corn stover and wheat straw. This is the first time that CMCase, xylanase and peroxidase/phenol oxidase activities have been reported in these three fungal genera isolated from a marine sponge. Given the biochemical characteristics of these ligninolytic enzymes it is likely that they may prove useful in future biomass conversion strategies involving lignocellulosic materials.

Stability of peatland carbon to rising temperatures

Peatlands contain one-third of soil carbon (C), mostly buried in deep, saturated anoxic zones (catotelm). The response of catotelm C to climate forcing is uncertain, because prior experiments have focused on surface warming. We show that deep peat heating of a 2 m-thick peat column results in an exponential increase in CH4 emissions. However, this response is due solely to surface processes and not degradation of catotelm peat. Incubations show that only the top 20-30 cm of peat from experimental plots have higher CH4 production rates at elevated temperatures. Radiocarbon analyses demonstrate that CH4 and CO2 are produced primarily from decomposition of surface-derived modern photosynthate, not catotelm C. There are no differences in microbial abundances, dissolved organic matter concentrations or degradative enzyme activities among treatments. These results suggest that although surface peat will respond to increasing temperature, the large reservoir of catotelm C is stable under current anoxic conditions.

Diversity and Distribution of Phenol Oxidase Producing Fungi from Soda Lake and Description of Curvularia lonarensis sp. nov

Soda lake is hyper alkaline and saline habitat located in closed craters with high evaporation rate. In current study fungal diversity from water and sediment samples of a soda lake (Lonar lake) located in Buldhana district of Maharashtra, India was investigated using extensive culturomics approach and mimicking the natural conditions of Lonar lake in culture media. A total of 104 diverse isolates of extremophilic fungi were recovered from this study and phylogenetically characterized by internal transcribed spacer (ITS) region sequencing. In addition, due to important role of phenol oxidase, and peroxidase in degradation of toxic phenol, lignin, etc., all isolated pure cultures were also screened for extracellular phenol oxidase and peroxidase production potential. Diversity analysis indicated that different groups of extremophilic fungi are present in the water and sediment samples of Lonar lake. A total of 38 species of fungi belonging to 18-different genera were recovered. Out of 104 isolates 32 showed ≤97% sequences similarity, which were morphologically different and could be potential novel isolates of extremophilic fungi. However, out of 104 isolates only 14 showed the extracellular phenol oxidase production potentials at alkaline pH. Curvularia sp. strain MEF018 showed highest phenol oxidase production at alkaline condition and had low sequence similarity with previously characterized species (96% with Curvularia pseudorobusta). Taxonomic characterization (morphological and physiological) and multi locus sequence analysis (MLSA) using combined alignment of ITS-LSU-gpd of strain MEF018 showed that it is a novel species of the genus Curvularia and hence proposed as Curvularia lonarensis sp. nov.

A novel fluorimetric method for laccase activities measurement using Amplex Red as substrate

In this paper, a novel fluorescence-based method for laccase assay was presented. The method was based on the transformation of Amplex Red into a highly fluorescent and colored resorufin catalyzed by laccase in the presence of O₂. The catalysis and transformation mechanism were investigated in detail. The kinetic parameters of the Amplex Red catalysis by laccase were determined using the Lineweaver-Burk equation. V_max and K_m were estimated to be 15.63μmolmin^-1 and 76.88μmolL^-1, respectively. Under optimal conditions, a good linear correlation was found between fluorescence intensity and laccase activities within 5.62-702UL^-1 (r=0.9992), with a detection limit of 1.76UL^-1 (S/N=3). A series of repeatability measurements (351UL^-1 laccase) gave reproducible results with a relative standard deviation (RSD) of 1.9% (n=11). The recoveries ranged from 93.7% to 100.0% after standard additions. Common existing species such as Mg²⁺, Zn²⁺, Ni²⁺, Al³⁺, Co²⁺, Cd²⁺, K⁺, Ca²⁺, Na⁺, Fe³⁺, Li⁺, Cu²⁺, Mn²⁺, Fe²⁺, l-lysine, glycine, glucose, phenol, humic acid, lignin peroxidase, manganese peroxidase alkaline phosphatase, cellulose, glucose oxidase, urease, catalase, invertase, and horseradish peroxidase did not significantly exhibit interference. The test solution (i.e., Amplex Red stock solution) could stabilize at least three months via storage in dark at 4±0.1°C. These results confirmed that the laccase-Amplex Red system was stable and reproducible with strong anti-interference ability and good selectivity, suggesting that this method can has great potential in practical applications for the assay of laccase activity. The proposed method was further successfully used to detect laccase activities in 38 soil samples. We noticed that the laccase activity significantly correlated with total nitrogen content (r=0.559; p<0.01) of soil, indicating laccase activity assay holds great promise as an index of soil analysis. These findings indicate that this presented method has great perspective in ecological investigation and fundamental research of soil environment.

Bio-Prospecting Laccases in the Bacterial Diversity of Activated Sludge From Pulp and Paper Industry

Activated sludge is an artificial ecosystem known to harbor complex microbial communities. Bacterial diversity in activated sludge from pulp and paper industry was studied to bioprospect for laccase, the multicopper oxidase applicable in a large number of industries due to its ability to utilize a wide range of substrates. Bacterial diversity using 454 pyrosequencing and laccase diversity using degenerate primers specific to conserved copper binding domain of laccase like multicopper oxidase (LMCO) genes were investigated. 1231 OTUs out of 11,425 sequence reads for bacterial diversity and 11 OTUs out of 15 reads for LMCO diversity were formed. Phylum Proteobacteria (64.95 %) with genus Thauera (13.65 %) was most abundant followed by phylum Bacteriodetes (11.46 %) that included the dominant genera Paludibacter (1.93 %) and Lacibacter (1.32 %). In case of LMCOs, 40 % sequences showed affiliation with Proteobacteria and 46.6 % with unculturable bacteria, indicating considerable novelty, and 13.3 % with Bacteroidetes. LMCOs belonged to H and J families.

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

Soil microorganisms can control the soil cycles of carbon (C), and depending on their C-use efficiency (CUE), these microorganisms either contribute to C stabilization in soil or produce CO₂ when decomposing organic matter. However, little is known regarding the enzyme investment of microbial decomposers and the effects on their CUE. Our objective was to elucidate the strategies of litter-decomposing fungi as a function of litter quality. Fungal biosynthesis and respiration were accounted for by quantifying the investment in enzyme synthesis and enzyme efficiency. The basidiomycete Phanerochaete chrysosporium was grown on the leaves, stems, and roots of maize over 126 days in controlled conditions. We periodically measured the fungal biomass, enzyme activity, and chemical composition of the remaining litter and continuously measured the evolved C–CO₂. The CUE observed for the maize litter was highest in the leaves (0.63), intermediate in the roots (0.40), and lowest in the stems (0.38). However, the enzyme efficiency and investment in enzyme synthesis did not follow the same pattern. The amount of litter C decomposed per mole of C-acquiring hydrolase activity was 354 μg C in the leaves, 246 μg C in the roots, and 1541 μg C in the stems (enzyme efficiency: stems > leaves > roots). The fungus exhibited the highest investment in C-acquiring enzyme when grown on the roots and produced 40–80% less enzyme activity when grown on the stems and leaves (investment in enzymes: roots > leaves > stems). The CUE was dependent on the initial availability and replenishment of the soluble substrate fraction with the degradation products. The production of these compounds was either limited because of the low enzyme efficiency, which occurred in the roots, or because of the low investments in enzyme synthesis, which occurred in the stems. Fungal biosynthesis relied on the ability of the fungus to invest in enzyme synthesis and the efficient interactions between the enzymes and the substrate. The investment decreased when N was limited, whereas the efficiency of the C-acquiring enzymes was primarily explained by the hemicellulose content and its embedment in recalcitrant lignin linkages. Our results are crucial for modeling microbial allocation strategies.

Oxidoreductases provide a more generic response to metallic stressors (Cu and Cd) than hydrolases in soil fungi: new ecotoxicological insights

The present study investigates the effect of metals on the secretion of enzymes from 12 fungal strains maintained in liquid cultures. Hydrolases (acid phosphatase, β-glucosidase, β-galactosidase, and N-acetyl-β-glucosaminidase) and ligninolytic oxidoreductases (laccase, Mn, and lignin peroxidases) activities, as well as biomass production, were measured in culture fluids from fungi exposed to Cu or Cd. Our results showed that all fungi secreted most of the selected hydrolases and that about 50% of them produced a partial oxidative system in the absence of metals. Then, exposure of fungi to metals led to the decrease in biomass production. At the enzymatic level, Cu and Cd modified the secretion profiles of soil fungi. The response of hydrolases to metals was contrasted and complex and depended on metal, enzyme, and fungal strain considered. By contrast, the metals always stimulated the activity of ligninolytic oxidoreductases in fungal strains. In some of them, oxidoreductases were specifically produced following metal exposure. Fungal oxidoreductases provide a more generic response than hydrolases, constituting thus a physiological basis for their use as biomarkers of metal exposure in soils.

Hydrodynamic voltammetry as a rapid and simple method for evaluating soil enzyme activities

Soil enzymes play essential roles in catalyzing reactions necessary for nutrient cycling in the biosphere. They are also sensitive indicators of ecosystem stress, therefore their evaluation is very important in assessing soil health and quality. The standard soil enzyme assay method based on spectroscopic detection is a complicated operation that requires the removal of soil particles. The purpose of this study was to develop a new soil enzyme assay based on hydrodynamic electrochemical detection using a rotating disk electrode in a microliter droplet. The activities of enzymes were determined by measuring the electrochemical oxidation of p-aminophenol (PAP), following the enzymatic conversion of substrate-conjugated PAP. The calibration curves of β-galactosidase (β-gal), β-glucosidase (β-glu) and acid phosphatase (AcP) showed good linear correlation after being spiked in soils using chronoamperometry. We also performed electrochemical detection using real soils. Hydrodynamic chronoamperometry can be used to assess the AcP in soils, with a detection time of only 90 s. Linear sweep voltammetry was used to measure the amount of PAP released from β-gal and β-glu by enzymatic reaction after 60 min. For the assessment of soil enzymes, the results of hydrodynamic voltammetry assay compared favorably to those using a standard assay procedure, but this new procedure is more user-friendly, rapid and simple.

Diversity of two-domain laccase-like multicopper oxidase genes in Streptomyces spp.: identification of genes potentially involved in extracellular activities and lignocellulose degradation during composting of agricultural waste

Traditional three-domain fungal and bacterial laccases have been extensively studied for their significance in various biotechnological applications. Growing molecular evidence points to a wide occurrence of more recently recognized two-domain laccase-like multicopper oxidase (LMCO) genes in Streptomyces spp. However, the current knowledge about their ecological role and distribution in natural or artificial ecosystems is insufficient. The aim of this study was to investigate the diversity and composition of Streptomyces two-domain LMCO genes in agricultural waste composting, which will contribute to the understanding of the ecological function of Streptomyces two-domain LMCOs with potential extracellular activity and ligninolytic capacity. A new specific PCR primer pair was designed to target the two conserved copper binding regions of Streptomyces two-domain LMCO genes. The obtained sequences mainly clustered with Streptomyces coelicolor, Streptomyces violaceusniger, and Streptomyces griseus. Gene libraries retrieved from six composting samples revealed high diversity and a rapid succession of Streptomyces two-domain LMCO genes during composting. The obtained sequence types cluster in 8 distinct clades, most of which are homologous with Streptomyces two-domain LMCO genes, but the sequences of clades III and VIII do not match with any reference sequence of known streptomycetes. Both lignocellulose degradation rates and phenol oxidase activity at pH 8.0 in the composting process were found to be positively associated with the abundance of Streptomyces two-domain LMCO genes. These observations provide important clues that Streptomyces two-domain LMCOs are potentially involved in bacterial extracellular phenol oxidase activities and lignocellulose breakdown during agricultural waste composting.

Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1

Lignocellulosic biofuels are promising as sustainable alternative fuels, but lignin inhibits access of enzymes to cellulose, and by-products of lignin degradation can be toxic to cells. The fast growth, high efficiency and specificity of enzymes employed in the anaerobic litter deconstruction carried out by tropical soil bacteria make these organisms useful templates for improving biofuel production. The facultative anaerobe Enterobacter lignolyticus SCF1 was initially cultivated from Cloud Forest soils in the Luquillo Experimental Forest in Puerto Rico, based on anaerobic growth on lignin as sole carbon source. The source of the isolate was tropical forest soils that decompose litter rapidly with low and fluctuating redox potentials, where bacteria using oxygen-independent enzymes likely play an important role in decomposition. We have used transcriptomics and proteomics to examine the observed increased growth of SCF1 grown on media amended with lignin compared to unamended growth. Proteomics suggested accelerated xylose uptake and metabolism under lignin-amended growth, with up-regulation of proteins involved in lignin degradation via the 4-hydroxyphenylacetate degradation pathway, catalase/peroxidase enzymes, and the glutathione biosynthesis and glutathione S-transferase (GST) proteins. We also observed increased production of NADH-quinone oxidoreductase, other electron transport chain proteins, and ATP synthase and ATP-binding cassette (ABC) transporters. This suggested the use of lignin as terminal electron acceptor. We detected significant lignin degradation over time by absorbance, and also used metabolomics to demonstrate moderately significant decreased xylose concentrations as well as increased metabolic products acetate and formate in stationary phase in lignin-amended compared to unamended growth conditions. Our data show the advantages of a multi-omics approach toward providing insights as to how lignin may be used in nature by microorganisms coping with poor carbon availability.

Field and lab conditions alter microbial enzyme and biomass dynamics driving decomposition of the same leaf litter

Fluctuations in climate and edaphic factors influence field decomposition rates and preclude a complete understanding of how microbial communities respond to plant litter quality. In contrast, laboratory microcosms isolate the intrinsic effects of litter chemistry and microbial community from extrinsic effects of environmental variation. Used together, these paired approaches provide mechanistic insights to decomposition processes. In order to elucidate the microbial mechanisms underlying how environmental conditions alter the trajectory of decay, we characterized microbial biomass, respiration, enzyme activities, and nutrient dynamics during early (<10% mass loss), mid- (10-40% mass loss), and late (>40% mass loss) decay in parallel field and laboratory litter bag incubations for deciduous tree litters with varying recalcitrance (dogwood < maple < maple-oak mixture < oak). In the field, mass loss was minimal (<10%) over the first 50 days (January-February), even for labile litter types, despite above-freezing soil temperatures and adequate moisture during these winter months. In contrast, microcosms displayed high C mineralization rates in the first week. During mid-decay, the labile dogwood and maple litters in the field had higher mass loss per unit enzyme activity than the lab, possibly due to leaching of soluble compounds. Microbial biomass to litter mass (B:C) ratios peaked in the field during late decay, but B:C ratios declined between mid- and late decay in the lab. Thus, microbial biomass did not have a consistent relationship with litter quality between studies. Higher oxidative enzyme activities in oak litters in the field, and higher nitrogen (N) accumulation in the lab microcosms occurred in late decay. We speculate that elevated N suppressed fungal activity and/or biomass in microcosms. Our results suggest that differences in microbial biomass and enzyme dynamics alter the decay trajectory of the same leaf litter under field and lab conditions.

Laccase-catalyzed oxidation of iodide and formation of organically bound iodine in soils

Laccase oxidizes iodide to molecular iodine or hypoiodous acid, both of which are easily incorporated into natural soil organic matter. In this study, iodide sorption and laccase activity in 2 types of Japanese soil were determined under various experimental conditions to evaluate possible involvement of this enzyme in the sorption of iodide. Batch sorption experiment using radioactive iodide tracer ((125)I(-)) revealed that the sorption was significantly inhibited by autoclaving (121 °C, 40 min), heat treatment (80 and 100 °C, 10 min), γ-irradiation (30 kGy), N(2) gas flushing, and addition of reducing agents and general laccase inhibitors (KCN and NaN(3)). Interestingly, very similar tendency of inhibition was observed in soil laccase activity, which was determined using 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonate) (ABTS) as a substrate. The partition coefficient (K(d): mL g(-1)) for iodide and specific activity of laccase in soils (Unit g(-1)) showed significant positive correlation in both soil samples. Addition of a bacterial laccase with an iodide-oxidizing activity to the soils strongly enhanced the sorption of iodide. Furthermore, the enzyme addition partially restored iodide sorption capacity of the autoclaved soil samples. These results suggest that microbial laccase is involved in iodide sorption on soils through the oxidation of iodide.

Microbial community structure and activity linked to contrasting biogeochemical gradients in bog and fen environments of the Glacial Lake Agassiz Peatland

The abundances, compositions, and activities of microbial communities were investigated at bog and fen sites in the Glacial Lake Agassiz Peatland of northwestern Minnesota. These sites contrast in the reactivity of dissolved organic matter (DOM) and the presence or absence of groundwater inputs. Microbial community composition was characterized using pyrosequencing and clone library construction of phylogenetic marker genes. Microbial distribution patterns were linked to pH, concentrations of dissolved organic carbon and nitrogen, C/N ratios, optical properties of DOM, and activities of laccase and peroxidase enzymes. Both bacterial and archaeal richness and rRNA gene abundance were >2 times higher on average in the fen than in the bog, in agreement with a higher pH, labile DOM content, and enhanced enzyme activities in the fen. Fungi were equivalent to an average of 1.4% of total prokaryotes in gene abundance assayed by quantitative PCR. Results revealed statistically distinct spatial patterns between bacterial and fungal communities. Fungal distribution did not covary with pH and DOM optical properties and was vertically stratified, with a prevalence of Ascomycota and Basidiomycota near the surface and much higher representation of Zygomycota in the subsurface. In contrast, bacterial community composition largely varied between environments, with the bog dominated by Acidobacteria (61% of total sequences), while the Firmicutes (52%) dominated in the fen. Acetoclastic Methanosarcinales showed a much higher relative abundance in the bog, in contrast to the dominance of diverse hydrogenotrophic methanogens in the fen. This is the first quantitative and compositional analysis of three microbial domains in peatlands and demonstrates that the microbial abundance, diversity, and activity parallel with the pronounced differences in environmental variables between bog and fen sites.

Laccase activity in soils: considerations for the measurement of enzyme activity

Laccases (benzenediol: oxygen oxidoreductases, EC 1.10.3.2) are copper-containing enzymes that catalyze the oxidative conversion of a variety of chemicals, such as mono-, oligo-, and polyphenols and aromatic amines. Laccases have been proposed to participate in the transformation of organic matter and xenobiotics as well as microbial interactions. Several laccase assays have been proposed and used in soils. Here, we show that the optimal pH conditions for the laccase substrates 2,2'-azinobis-3-ethylbenzothiazoline-6-sulfonic acid (ABTS, pH 3-5), 2,6-dimethoxyphenol (4-5.5), L-3,4-dihydroxyphenylalanine (DOPA; 4-6), guaiacol (3.5-5), 4-methylcatechol (3.5-5), and syringaldazine (5.5-7.0) are similar between purified laccases from Trametes versicolor and Pyricularia sp. and soil extracts; the substrate affinities of purified enzymes (K(M)) and soil extracts were also similar. The laccase assays showed specificity overlap with tyrosinase and ligninolytic peroxidases when hydrogen peroxide is present. The ABTS oxidation assay is able to reliably detect the presence of 13.5 pg mL(-1) or 0.199×10(-12) mol mL(-1) of T. versicolor laccase, which is three times more sensitive than the 2,6-dimethoxyphenol-based assay and more than 40 times more sensitive than any of the other assays. The low molecular mass soil-derived compounds and the isolated fulvic and humic acids influence the laccase assays and should be removed from the soil extracts before measurements of the enzyme activity are performed.

ISTA 14--impact of antibiotics from pig slurry on soil microbial communities, including the basidiomycete Trametes versicolor

Livestock slurry containing antibiotics is a source of contamination of agricultural soils, with possible effects on soil function and micro-organisms. Extracellular oxido-reductases and hydrolases from the fungus T. versicolor and fungal growth were monitored in liquid cultures in the presence of tetracycline, lincomycine, sulfadiazine and ciprofloxacin for 10 days, in order to assess the suitability of these enzymes as biomarkers. Among the conditions of treatment, statistical analysis demonstrated an increase in manganese-dependent peroxidase after exposure to sulfadiazine at 1 mg/L when compared with the control. Acid phosphatase activity was decreased by lincomycine at 1 or 10 mg/L. Conversely, β-glucosidase activity increased in the presence of this antibiotic at 10 mg/L. In Terrestrial Model Ecosystems spiked with contaminated pig slurry, lincomycine at the concentration of 8 or 80 μg/kg dry soil, and ciprofloxacin at 250 ng/kg dry soil decreased the activity of soil dehydrogenase, when compared with a green slurry treatment, over 28-day incubations. Laccase activity was similarly decreased in the presence of the highest concentration of antibiotics. We determined bacterial and fungal biomasses using Q-PCR. Bacterial biomass was increased in the presence of lincomycine at 80 μg/kg whatever the time of exposure, and to a lesser extent in the presence of ciprofloxacin at 250 ng/kg, but only at day 28. In contrast, both antibiotics, whatever their concentrations, did not modify fungal biomass in soil. In conclusion, we were unable to demonstrate important effects of antibiotics at concentrations found in the agricultural environment.

Impact of epiphytic and endogenous enzyme activities of senescent maize leaves and roots on the soil biodegradation process

This study was focused on investigating the role of the initial residue community, i.e. microorganisms and enzymes from the epiphytic and endophytic compartments, in soil decomposition processes. Aerial and underground parts (leaves and roots) of maize (Zea mays L.) plants were γ-irradiated, surface-sterilized with sodium hypochlorite (NaOCl)/ethanol or non-sterilized (controls), while the outer surface morphology of maize leaves and roots was examined by scanning electron microscopy (SEM). Non-sterilized and sterilized maize leaves and roots were incubated in soil to study carbon (C) mineralization kinetics and enzyme dynamics (L-leucine aminopeptidase, CBH-1, xylanase, cellulase and laccase). SEM results showed that initial microbial colonization was more pronounced on non-sterilized leaf and root surfaces than on sterilized samples. The hypochlorite treatment removed a part of the soluble components of leaves by washing and no specific effect of any type of colonizing microorganisms was observed on C mineralization. In contrast, γ irradiation and hypochlorite treatments did not affect root chemical characteristics and the quantitative effect of initial residue-colonizing microorganisms on C mineralization was demonstrated. The variations in C mineralization and enzyme dynamics between non-sterilized and sterilized roots suggested that activities of epiphytic and endogenic microorganisms were of the same order of magnitude.

Response of recalcitrant soil substances to reduced N deposition in a spruce forest soil: integrating laccase-encoding genes and lignin decomposition

A long-term field experiment conducted in a Norway spruce forest at Solling, Central Germany, was used to verify and compare the response of lignin-decomposing fungal communities in soils receiving current and preindustrial atmospheric nitrogen (N) input for 14.5 years. Therefore, we investigated the decomposition of lignin compounds in relation to phenol oxidase activity and the diversity of basidiomycetes containing laccase genes in organic and mineral horizons. Lignin-derived CuO oxidation products and enzyme activity decreased with soil depth, while the degree of oxidative transformation of lignin increased. These patterns did not change with reduced atmospheric N input, likely reflecting a lasting saturation in available N. The laccase gene diversity decreased with soil depth in spring. In autumn, this pattern was only found in the control plot, receiving current N input. Principal component analysis confirmed the depth profile and distinguished a response of the fungal community to reduced N deposition for most organic layers in spring and a roof effect for the Oe layer in autumn. These responses of the fungal community did not translate into changes in enzyme activity and lignin content and decomposition, suggesting that transformation processes in soils are well buffered despite the rapid response of the microbial community to environmental factors.