Biofumigation is an effective, non-chemical method to control soil-borne pests and diseases and to maximize crop yield. We studied the responses of soil bacterial and fungal communities, the soil’s nutritional state and strawberry yield, when the soil was biofumigated each year for five consecutive years using fresh chicken manure (BioFum). BioFum significantly increased the soil’s NH4+-N, NO3−-N, available P and K and organic matter. Fusarium spp. and Phytophthora spp. which are known to cause plant disease, were significantly decreased after BioFum. In addition, Biofum increased the soil’s temperature, enhanced chlorophyll levels in the leaves of strawberry plants, and the soluble sugar and ascorbic acid content in strawberry fruit. We used high-throughput gene sequencing to monitor changes in the soil’s bacterial and fungal communities. Although BioFum significantly decreased the diversity of these communities, it increased the relative abundance of some biological control agents in the phylum Actinobacteria and the genera Pseudomonas, Bacillus and Chaetomium. An increase in these biological control agents would reduce the incidence of soil-borne pathogens and plant disease. Although strawberry marketable yield using BioFum was higher in the first three years, the decline in the final two years could be due to the accumulation of P and K which may have delayed flowering and fruiting. Methods to overcome yield losses using BioFum need to be developed in the future. Our research, however, showed that BioFum enhanced soil fertility, reduced the presence of soil pathogens, increased the relative abundance of beneficial bacteria and fungi and improved strawberry quality. Unlike chemical soil treatments that can cause pest and disease resistance when used continuously over many years, our multi-year research program on BioFum showed that this treatment provided significant benefits to the soil, plant and strawberry fruit.

Microbiota associated with airborne particulate matter (PM) is an important indicator of indoor pollution as they can be pathogenic and cause serious health threats to the exposed occupants. Present study aimed to investigate the level of culturable microbes associated with PM and their toxicological characterization in urban and rural houses of Pune city. Highest concentration of bacterial aerosols observed to be associated with PM₁₀ size fraction in urban site (2136 ± 285 CFU/m³) whereas maximum fungal concentration has been measured in rural houses (1521 ± 302 CFU/m³). Predominantly found bacterial species were Bacillus sp., S. aureus, and Pseudomonas aeruginosa and fungal species were Aspergillus sp., Cladosporium sp., and Penicillium sp. in both urban and rural residential premises. Concentration of endotoxin measured using the kinetic Limulus Amebocyte Lysate assay exhibited that the level of endotoxin in both urban and rural sites are associated with household characteristics and the activities performed in indoor as well as outdoor. Cell free DTT assay confirmed the ability of these airborne microbes to induce the production of reactive oxygen species (ROS) varying along with the types of microorganisms. On exposure of A549 cells to airborne microbes, a significant decrease in cell viability was observed in terms of both necrosis and apoptosis pathway. Elevated production of nitric oxide (NO) and proinflammatory cytokines in epithelial cells and macrophages clearly suggest the inflammatory nature of these airborne microbes. Results derived from the present study demonstrated that the indoor air of urban and rural houses of Pune is contaminated in terms of microbial load. Therefore, attention should be paid to control the factors favoring the microbial growth in order to safeguard the health of exposed inhabitants.

Mycotoxins are toxic fungal metabolites, contaminating cereal grains in field or during processing and storage periods. These environmental contaminants pose great threats to humans and animals’ health due to their toxic effects. Type A trichothecenes, fumonisins and fusaric acid (FA) are commonly detected mycotoxins produced by various Fusarium species. Trichoderma spp. are promising antagonists in agriculture for their activities against plant pathogens, and also regarded as potential candidates for bioremediation of environmental contaminants. Managing toxigenic fungi by antagonistic Trichoderma is regarded as a sustainable and eco-friendly strategy for mycotoxin control. However, the metabolic activities of Trichoderma on natural occurring mycotoxins were less investigated. Our current work comprehensively explored the activities of Trichoderma against type A trichothecenes, fumonisins and FA producing Fusarium species via co-culture competition and indirect volatile assays. Furthermore, we investigated metabolism of type A trichothecenes and FA in Trichoderma isolates. Results indicated that Trichoderma were capable of bio-transforming T-2 toxin, HT-2 toxin, diacetoxyscirpenol and neosolaniol into their glycosylated forms and one Trichoderma strain could bio transform FA into low toxic fusarinol. These findings proved that Trichoderma isolates could manage toxigenic Fusarium via direct competition and volatile-mediated indirect inhibition. In addition, these antagonists possess defensive systems against mycotoxins for self-protection, which enriches our understanding on the interaction mechanism of Trichoderma spp. on toxigenic fungus.

Fungi have an exceptional capability to flourish in presence of heavy metals and pesticide. However, the mechanism of bioremediation of pesticide (lindane) and multimetal [mixture of cadmium (Cd), chromium (Cr), copper (Cu), nickel (Ni), lead (Pb), zinc (Zn)] by a fungus is little understood. In the present study, Aspergillus fumigatus, a filamentous fungus was found to accumulate heavy metals in the order [Zn(98%)>Pb(95%)>Cd(63%)>Cr(62%)>Ni(46%)>Cu(37%)] from a cocktail of 30 mg L⁻¹ multimetal and lindane (30 mg L⁻¹) in a composite media amended with 1% glucose. Particularly, Pb and Zn uptake was enhanced in presence of lindane. Remarkably, lindane was degraded to 1.92 ± 0.01 mg L⁻¹ in 72 h which is below the permissible limit value (2.0 mg L⁻¹) for the discharge of lindane into the aquatic bodies as prescribed by European Community legislation. The utilization of lindane as a cometabolite from the complex environment was evident by the phenomenal growth of the fungal pellet biomass (5.89 ± 0.03 g L⁻¹) at 72 h with cube root growth constant of fungus (0.0211 g¹/³ L⁻¹/³ h⁻¹) compared to the biomasses obtained in case of the biotic control as well as in presence of multimetal complex without lindane. The different analytical techniques revealed the various stress coping strategies adopted by A. fumigatus for multimetal uptake in the simultaneous presence of multimetal and pesticide. From the Transmission electron microscope coupled energy dispersive X-ray analysis (TEM-EDAX) results, uptake of the metals Cd, Cu and Pb in the cytoplasmic membrane and the accumulation of the metals Cr, Ni and Zn in the cytoplasm of the fungus were deduced. Fourier-transform infrared spectroscopy (FTIR) revealed involvement of carboxyl/amide group of fungal cell wall in metal chelation. Thus A. fumigatus exhibited biosorption and bioaccumulation as the mechanisms involved in detoxification of multimetals.

Chinese dark tea is widely enjoyed for its multiple health-promoting effects and pleasant taste. However, its production involves fermentation by microbiota in raw tea, some of which are filamentous fungi and thus potential mycotoxin producers. Accordingly, whether mycotoxins pose health risk on dark tea consumption has become a public concern. In this study, a cleaning method of multi-functional column (MFC) and immunoaffinity column (IAC) in tandem combined to HPLC detection was developed and validated for determining ten mycotoxins of six groups (i.e., aflatoxins of B₁, B₂, G₁ and G₂, ochratoxin A, zearalenone, deoxynivalenol, fumonisins of B₁, B₂, and T-2) in dark teas. The interferences from secondary metabolites were effectively reduced, and the sensitivities and recoveries of the method were qualified for tea matrices. Six groups mycotoxins were determined in 108 samples representing the major Chinese dark teas by using the new method. Subsequently, the dietary exposure and health risks were evaluated for different age and gender groups in Kunming and Pu’er in China and Ulan Bator in Mongolia. The occurrence of zearalenone was 4.63% and that of ochratoxin A was 1.85%, with the other four groups mycotoxins were below the limits of quantification. The hazard index values for the five groups’ non-carcinogenic mycotoxins were far below 1.0. The deterministic risk assessment indicated no non-carcinogenic risks for dark tea consumption in the three areas. Probabilistic estimation showed that the maximum value of 95th percentile carcinogenic risk value for the aflatoxins was 2.12 × 10⁻⁸, which is far below the acceptable carcinogenic risk level (10⁻⁶). Hereby, six groups mycotoxins in Chinese dark tea showed no observed risk concern to consumers.

Volcanic eruptions are important components of natural disturbances that provide a model to explore the effects of volcanic eruption disturbances on soil microorganisms. Despite widespread research, to the best of our knowledge, no studies of volcanic eruption disturbances have investigated the effects on soil microbial communities in the montane meadow steppe. To address this gap, we meticulously investigated the characteristics of the soil microbial communities from the volcano and steppe sites using Illumina MiSeq high-throughput sequencing. Hierarchical clustering analysis and principal coordinate analysis (PCoA) showed that the soil microbial communities from the volcano and steppe sites differed. The diversity and richness of the soil microbial communities from the steppe sites were significantly higher than at the volcano sites (P < 0.05), and the soil microbial communities in the steppe sites had higher stability. The effects of volcanic eruption disturbances on the bacterial community development are greater than its effects on the fungal communities. The environmental filtering of volcanic eruptions selectively retained some special microorganisms (i.e., Conexibacter, Agaricales, and Gaiellales) with strong adaptability to the environmental disturbances, enhanced metabolic activity for sodium and calcium reabsorption, and increased relative abundances of the lichenized saprotrophs. The soil microbial communities from the volcano and steppe sites cooperate to form complex networks of species interactions, which are strongly influenced by the interaction of the soil and vegetation factors. Our findings provide new information on the effects of volcanic eruption disturbances on the soil microbial communities in the montane meadow steppe.

Phoxim, a broad-spectrum organophosphate pesticide, is widely used in agriculture to control insect pests in vegetable crops as well as in farm mammals. However, the indiscriminate use of phoxim has increased its release into the environment, leading to the contamination of plant-based foods such as vegetables. In this study, we investigated the effect of Trichoderma asperellum (TM, an opportunistic fungus) on phoxim residue in tomato roots and explored the mechanisms of phoxim metabolism through analysis of detoxification enzymes and gene expression. Degradation kinetics of phoxim showed that TM inoculation rapidly and significantly reduced phoxim residues in tomato roots. Phoxim concentrations at 5d, 10d and 15d post treatment were 75.12, 65.71 and 77.45% lower in TM + phoxim than only phoxim treatment, respectively. The TM inoculation significantly increased the glutathione (GSH) content, the activity of glutathione S-transferase (GST) and the transcript levels of GSH, GST1, GST2 and GST3 in phoxim-treated roots. In addition, the activity of peroxidase and polyphenol peroxidase involved in the xenobiotic conversion also increased in TM + phoxim treatment. The expression of detoxification genes, such as CYP724B2, GR, ABC2 and GPX increased by 3.82, 3.08, 7.89 and 2.46 fold, respectively in TM + phoxim compared with only phoxim. Similarly, the content of ascorbate (AsA) and the ratio of AsA to dehydroascorbate increased by 45.16% and 57.34%, respectively in TM + phoxim-treated roots. Our results suggest that TM stimulates plant detoxification potential in all three phases (conversion, conjugation and sequestration) of xenobiotc metabolism, leading to a reduced phoxim residue in tomato roots.

Microcystins (MCs) are toxins produced during cyanobacterial blooms. They reach soil and translocated to plants through irrigation of agricultural land with water from MC-impacted freshwater systems. To date we have good understanding of MC effects on plants, but not for their effects on plant-associated microbiota. We tested the hypothesis that MC-LR, either alone or with other stressors present in the water of the Karla reservoir (a low ecological quality and MC-impacted freshwater system), would affect radish plants and their rhizospheric and phyllospheric microbiome. In this context a pot experiment was employed where radish plants were irrigated with tap water without MC-LR (control) or with 2 or 12 μg L⁻¹ of pure MC-LR (MC2 and MC12), or water from the Karla reservoir amended (12 μg L⁻¹) or not with MC-LR. We measured MC levels in plants and rhizospheric soil and we determined effects on (i) plant growth and physiology (ii) the nitrifying microorganisms via q-PCR, (ii) the diversity of bacterial and fungal rhizospheric and epiphytic communities via amplicon sequencing. MC-LR and/or Karla water treatments resulted in the accumulation of MC in taproot at levels (480–700 ng g⁻¹) entailing possible health risks. MC did not affect plant growth or physiology and it did not impose a consistent inhibitory effect on soil nitrifiers. Karla water rather than MC-LR was the stronger determinant of the rhizospheric and epiphytic microbial communities, suggesting the presence of biotic or abiotic stressors, other than MC-LR, in the water of the Karla reservoir which affect microorganisms with a potential role (i.e. pathogens inhibition, methylotrophy) in the homeostasis of the plant-soil system. Overall, our findings suggest that MC-LR, when applied at environmentally relevant concentrations, is not expected to adversely affect the radish-microbiota system but might still pose risk for consumers’ health.

The conversion of natural forests to tea plantations largely affects soil nitrous oxide (N₂O) emissions and soil microbial communities. However, the impacts of this conversion on the contribution of fungi to N₂O emission and on fungal community structure remain unclear. In this study, we determined the soil N₂O emission rate, N₂O production by fungi, associated fungal community diversity, and related ecological factors in chronological changes of tea crop systems (3, 36 and 105 years old tea orchards named T3, T36 and T105, respectively), and in an adjacent soil from a natural forest. The results indicate that the tea plantations significantly enhanced soil N₂O production compared with the forest soil. Tea plantations significantly decreased soil pH and C/N ratio, but increased soil inorganic nitrogen (N). Furthermore, they increased the fungal contribution to the production of soil N₂O, but decreased the bacterial counterpart. We also observed that fungal community and functional composition differed distinctly between tea plantations and forest. Additionally, most of the fungal groups in high N₂O emission soils (T36 and T105) were identified as the genus Fusarium, which were positively correlated with soil N₂O emissions. The variation in N₂O emission response could be well explained by NO₃⁻-N, soil organic carbon (SOC), C/N, and Fusarium, which contributed to up to 97% of the observed variance. Altogether, these findings provide significant direct evidence that the increase of soil N₂O emissions and fungal communities be attributed to the conversion of natural forest to tea plantations.

For decades, a vast array of innovative biosorbents have been found out and used in the removal of heavy metals, including bacteria, algae and fungi, etc. Although extensive biological species have been tried as a biosorbent for heavy metals removal, for removal efficiency or economy efficiency limited, it has failed to make a substantial breakthrough in practical application. Thus, many improved methods based on biosorbents emerged. In this review, based on the literature and our research results, we highlight three types of novel methods for biosorbents removal of heavy metals: chemical modification of biosorbents; biomass and chemical materials combination; multiple biomass complex systems. We mainly focus on their configuration, biosorption performance, their creation method, regeneration/reuse, their application and development in the future. Through the comparative analysis of various methods, we think that intracellular autogenous nanomaterials may open up another window in biosorption of heavy metals area. At the same time, the combination of various treatment methods will be the development tendency of heavy metal pollution treatment in the future.