Synergy between fungi and bacteria promotes polycyclic aromatic hydrocarbon cometabolism in lignin-amended soil

Enhancing bacterial biodegradation of n-hexane by utilizing the adsorption capacity of non-degrading fungi

Biodegradation of hydrophobic volatile organic compounds (VOCs) such as n-hexane is limited by their poor accessibility. Constructing fungal-bacterial degradation alliances is an effective approach, but the role of those fungi without the capability to degrade VOCs may have been overlooked. In this study, a non-n-hexane-degrading fungus, Fusarium keratoplasticum FK, was utilized to enhance n-hexane degradation by the bacterium Mycobacterium neworleansense WCJ. It was shown that strain WCJ removed 64.84% of n-hexane (at a concentration of 648.20 mg L-1) over 3 d, and 84.04% after introducing strain FK. Microbial growth kinetic studies revealed that the growth of strain WCJ was also promoted. Through a stepwise adsorption-degradation experiment combined with qPCR technology, it was found that the strain WCJ could utilize the n-hexane pre-adsorbed by strain FK, with an increase in copy number from 108.2662 to 108.7731. Therefore, the non-degrading fungi can improved the accessibility of n-hexane by providing n-hexane adsorbed by the mycelium to the degrading bacteria. In addition, the adsorption tests and characterization of the fungal samples before and after Soxhlet extraction indicated that the adsorption of n-hexane on strain FK conformed to Lagergren's pseudo-second-order kinetics and Freundlich adsorption isotherms, and was correlated with the presence of lipids and nonpolar groups. This study emphasizes the potential role of non-degrading fungi in bioremediation and proposes a viable strategy to enhance the bacterial degradation of hydrophobic VOCs.

Characterization of manganese(II)-coupled functional microorganisms in driving lignin degradation during straw composting

The intricate structure of lignin in straw makes it challenging to hydrolyze, making it a key focus of current research. However, there has been limited study on the effect of enzyme inducer (MnSO4) combined with functional microorganisms on lignin degradation during straw composting. Based on this, four composting treatment groups were set up in this study. Control (CK), functional microorganism addition treatment (F), Mn2+ enzyme inducer (Mn), and Mn2+ enzyme inducer coupled with functional microorganism addition treatment (FMn) were tested for composting. Manganese(II)-coupled microorganisms improved lignin degradation: FMn > Mn > F > CK. They increased the lignin loss rate from 25.54 % to 42.61 %. Laccase activity increased from 3.45 to 43.74 U/g and manganese peroxidase activity increased from 145.52 to 264.91 U/g. And gene abundance was increased. Microbial community structure and dominant genera changed. Structural equations support the idea that functional microorganisms coupled with manganese can modify physicochemical indices, thereby regulating gene expression and enhancing enzyme activity. Furthermore, the stimulation of fungal growth and increased extracellular laccase and manganese peroxidase activities can affect the degradation of lignin. This study provides new insights and theoretical support for efficient lignin degradation and efficient resource utilization of compost products.

The role of cattle manure-driven polysaccharide precursors in humus formation during composting of spent mushroom substrate

The study examined the impact of adding cattle manure to the composting process of Agaricus bisporus mushroom substrate on compost humification. A control group CK comprised entirely of Agaricus bisporus mushroom substrate, while the experimental group CD (70 percent Agaricus bisporus mushroom substrate and 30 percent cattle manure) comprised the two composting treatments that were established. The study determined that the addition of cow dung has promoted the formation of humus components. Particularly, humic substance (HS-C) and humic acid (HA) increased by 41.3 and 74.7%, respectively, and the ratio of humic acid to fulvic acid (HA/FA) also increased by 2.78. It showed that the addition of cow dung accelerated the synthesis and decomposition of precursors, such as polysaccharides, polyphenols, and reducing sugars. Thereby promoting the formation of humic acid. Network analysis revealed that adding cow dung promoted microbial interactions increased the complexity and stability of the bacterial and fungal symbiotic network, enhanced cooperation and reciprocity among microbes, and assisted in transforming fulvic acid (FA) components. Structural equation modeling (SEM) is a multivariate data analysis method for analyzing complex relationships among constructs and core indicators. SEM illustrated that introducing cattle manure into the composting process resulted in alterations to the correlation between physicochemical parameters and the microbial community, in addition to humus formation. Polysaccharides are the primary precursors for polymerization to form HA, which is an essential prerequisite for the conversion of fulvic acid to humic acid. Additionally, microbes affected the formation of humus, with bacteria substantially more influential than fungi. These findings provide new ideas for regulating the degree of humification in the composting process and have important practical implications for optimizing mushroom cultivation and composting techniques today.

Bioremediation of petroleum hydrocarbons polluted soil by spent mushroom substrates: Microbiological structure and functionality

Spent mushroom substrate (SMS) holds valuable microbiota that can be useful in remediating polluted soils with hydrocarbons. However, the microorganisms behind the bioremediation process remain uncertain. In this work, a bioremediation assay of total petroleum hydrocarbons (TPHs) polluted soil by SMS application was performed to elucidate the microorganisms and consortia involved in biodegradation by a metabarcoding analysis. Untreated polluted soil was compared to seven bioremediation treatments by adding SMS of Agaricus bisporus, Pleurotus eryngii, Pleurotus ostreatus, and combinations. Soil microbial activity, TPH biodegradation, taxonomic classification, and predictive functional analysis were evaluated in the microbiopiles at 60 days. Different metagenomics approaches were performed to understand the impact of each SMS on native soil microbiota and TPHs biodegradation. All SMSs enhanced the degradation of aliphatic and aromatic hydrocarbons, being A. bisporus the most effective, promoting an efficient consortium constituted by the bacterial families Alcanivoraceae, Alcaligenaceae, and Dietziaceae along with the fungal genera Scedosporium and Aspergillus. The predictive 16 S rRNA gene study partially explained the decontamination efficacy by observing changes in the taxonomic structure of bacteria and fungi, and changes in the potential profiles of estimated degradative genes across the different treatments. This work provides new insights into TPHs bioremediation.

Determination of soil phenanthrene degradation through a fungal-bacterial consortium

Fungal-bacterial consortia enhance organic pollutant removal, but the underlying mechanisms are unclear. We used stable isotope probing (SIP) to explore the mechanism of bioaugmentation involved in polycyclic aromatic hydrocarbon (PAH) biodegradation in petroleum-contaminated soil by introducing the indigenous fungal strain Aspergillus sp. LJD-29 and the bacterial strain Pseudomonas XH-1. While each strain alone increased phenanthrene (PHE) degradation, the simultaneous addition of both strains showed no significant enhancement compared to treatment with XH-1 alone. Nonetheless, the assimilation effect of microorganisms on PHE was significantly enhanced. SIP revealed a role of XH-1 in PHE degradation, while the absence of LJD-29 in 13C-DNA indicated a supporting role. The correlations between fungal abundance, degradation efficiency, and soil extracellular enzyme activity indicated that LJD-29, while not directly involved in PHE assimilation, played a crucial role in the breakdown of PHE through extracellular enzymes, facilitating the assimilation of metabolites by bacteria. This observation was substantiated by the results of metabolite analysis. Furthermore, the combination of fungus and bacterium significantly influenced the diversity of PHE degraders. Taken together, this study highlighted the synergistic effects of fungi and bacteria in PAH degradation, revealed a new fungal-bacterial bioaugmentation mechanism and diversity of PAH-degrading microorganisms, and provided insights for in situ bioremediation of PAH-contaminated soil.IMPORTANCEThis study was performed to explore the mechanism of bioaugmentation by a fungal-bacterial consortium for phenanthrene (PHE) degradation in petroleum-contaminated soil. Using the indigenous fungal strain Aspergillus sp. LJD-29 and bacterial strain Pseudomonas XH-1, we performed stable isotope probing (SIP) to trace active PHE-degrading microorganisms. While inoculation of either organism alone significantly enhanced PHE degradation, the simultaneous addition of both strains revealed complex interactions. The efficiency plateaued, highlighting the nuanced microbial interactions. SIP identified XH-1 as the primary contributor to in situ PHE degradation, in contrast to the limited role of LJD-29. Correlations between fungal abundance, degradation efficiency, and extracellular enzyme activity underscored the pivotal role of LJD-29 in enzymatically facilitating PHE breakdown and enriching bacterial assimilation. Metabolite analysis validated this synergy, unveiling distinct biodegradation mechanisms. Furthermore, this fungal-bacterial alliance significantly impacted PHE-degrading microorganism diversity. These findings advance our understanding of fungal-bacterial bioaugmentation and microorganism diversity in polycyclic aromatic hydrocarbon (PAH) degradation as well as providing insights for theoretical guidance in the in situ bioremediation of PAH-contaminated soil.

Synergistic analysis of lignin degrading bacterial consortium and its application in rice straw fiber film

Fiber film have received widespread attention due to its green friendliness. We can use microorganisms to degrade lignin in straw to obtain cellulose and make fiber films. Herein, a group of high-temperature (50 °C) lignin degrading bacterial consortium (LDH) was enriched and culture conditions for lignin degradation were optimized. Combined with high-throughput sequencing technology, the synergistic effect of LDH-composited bacteria was analyzed. Then LDH was used to treat rice straw for the bio-pulping experiment. The results showed that the lignin of rice straw was degraded 32.4 % by LDH at 50 °C for 10 d, and after the optimization of culture conditions, lignin degradation rate increased by 9.05 % (P < 0.001). The bacteria that compose in LDH can synergistically degrade lignin. Paenibacillus can encode all lignin-degrading enzymes present in the LDH. Preliminary tests of LDH in the pulping industry have been completed. This study is the first to use high temperature lignin degrading bacteria to fabricate fiber film.

Enhancing soil health and nutrient cycling through soil amendments: Improving the synergy of bacteria and fungi

The synergy between bacteria and fungi is a key determinant of soil health and have a positive effect on plant development under drought conditions, with the potentially enhancing the sustainability of amending soil with natural materials. However, identifying how soil amendments influence plant growth is often difficult due to the complexity of microorganisms and their links with different soil amendment types and environmental factors. To address this, we conducted a field experiment to examine the impact of soil amendments (biochar, Bacillus mucilaginosus, Bacillus subtilis and super absorbent polymer) on plant growth. We also assessed variations in microbial community, links between fungi and bacteria, and soil available nutrients, while exploring how the synergistic effects between fungus and bacteria influenced the response of soil amendments to plant growth. This study revealed that soil amendments reduced soil bacterial diversity but increased the proportion of the family Enterobacteriaceae, Nitrosomonadaceae, and also increased soil fungal diversity and the proportion of the sum of the family Lasiosphaeriaceae, Chaetomiaceae, Pleosporaceae. Changes in soil microbial communities lead to increase the complexity of microbial co-occurrence networks. Furthermore, this heightened network complexity enhanced the synergy of soil bacteria and fungi, supporting bacterial functions related to soil nutrient cycling, such as metabolic functions and genetic, environmental, and cellular processes. Hence, the BC and BS had 3.0-fold and 0.5-fold greater root length densities than CK and apple tree shoot growth were increased by 62.14 %,50.53 % relative to CK, respectively. In sum, our results suggest that the synergistic effect of bacteria and fungi impacted apple tree growth indirectly by modulating soil nutrient cycling. These findings offer a new strategy for enhancing the quality of arable land in arid and semi-arid regions.

Effects of short and long-term thermal exposure on microbial compositions in soils contaminated with mixed benzene and benzo[a]pyrene: A short communication

Polycyclic aromatic hydrocarbons (PAHs) and benzene, toluene, ethylbenzene, and xylene (BTEX) are the most persistent and toxic organic contaminants often found co-contaminated in anthropogenic and petrochemical industrial sites. Therefore, an experiment was performed for the safe biodegradation of benzene and benzo[a]pyrene (BaP) through thermally-enhanced biodegradation, and to explore the influence of elevated thermal treatments on microbial diversity and composition. The results revealed that elevated thermal treatments (15 to 45 °C) significantly enhanced the diversity of both bacteria and fungi. The composition analysis revealed that short-term and long-term elevated temperature conditions can directly enhance the specificity of microorganisms that play a crucial role in the biodegradation of benzene and BaP co-contaminated soil. Moreover, the indirect role of elevated temperature conditions on microbial compositions was through the fluctuations of soil properties, especially soil pH, moisture, TOC, potassium, phosphorous, total Fe, Fe(II), and Fe(III). In addition, the correlation analyses revealed that thermal exposure enhances the synergistic association (fungal-fungal, fungal-bacterial, bacterial-bacterial) of microbes to degrade the toxic contaminants and to cope with harsh environmental conditions. These results concluded that the biodegradation of benzene and BaP co-contamination was efficiently enhanced under the thermally-enhanced biodegradation approach and the elevation of temperature can affect the microbial compositions directly via microbial specificity or indirectly by influencing the soil properties.

Soil properties and organochlorine compounds co-shape the microbial community structure: A case study of an obsolete site

Organochlorine compounds (OCs) such as chlorobenzenes (CB) are persistent organic pollutants that are ubiquitous in soils at organochlorine pesticides (OCP) production sites. Long-term contamination with OCs might alter the soil microbial structure and further affect soil functions. However, the effects of OCs regarding the shaping of microbial community structures in the soils of OCs-contaminated sites remain obscure, especially in the vertical soil profile where pollutants are highly concealed. Hence this paper explored the status and causes of OCs pollution (CB, hexachlorocyclohexane (HCH), and dichlorodiphenyltrichloroethane (DDT)) in an obsolete site, and its combined effects with soil properties (pH, available phosphorus (AP), dissolved organic carbon (DOC), etc) on microbial community structure. The mean total concentration of OCs in the subsoils was up to 996 times higher than that in the topsoils, with CB constituting over 90% of OCs in the subsoil. Historical causes, anthropogenic effects, soil texture, and the nature of OCs contributed to the differences in the spatial distribution of OCs. Redundancy analysis revealed that both the soil properties and OCs were important factors in shaping microbial composition and diversity. Variation partitioning analysis further indicated that soil properties had a greater impact on microbial community structure than OCs. Significant differences in microbial composition between topsoils and subsoils were observed through linear discriminant analysis effect size (LEfSe) analysis, primarily driven by different pollutant conditions. Additionally, co-occurrence network analysis indicated that heavily contaminated subsoils exhibited closer and more intricate bacterial community interactions compared to lightly contaminated topsoils. This work reveals the impact of environmental factors in co-shaping the structure of soil microbial communities. These findings advance our understanding of the intricate interplay among organochlorine pollutants, soil properties, and microbial communities, and provides valuable insights into devising effective management strategies in OCs-contaminated soils.

Microbes and microbial strategies in carcinogenic polycyclic aromatic hydrocarbons remediation: a systematic review

Degradation, detoxification, or removal of the omnipresent polycyclic aromatic hydrocarbons (PAHs) from the ecosphere as well as their prevention from entering into food chain has never appeared simple. In this context, cost-effective, eco-friendly, and sustainable solutions like microbe-mediated strategies have been adopted worldwide. With this connection, measures have been taken by multifarious modes of microbial remedial strategies, i.e., enzymatic degradation, biofilm and biosurfactant production, application of biochar-immobilized microbes, lactic acid bacteria, rhizospheric-phyllospheric-endophytic microorganisms, genetically engineered microorganisms, and bioelectrochemical techniques like microbial fuel cell. In this review, a nine-way directional approach which is based on the microbial resources reported over the last couple of decades has been described. Fungi were found to be the most dominant taxa among the CPAH-degrading microbial community constituting 52.2%, while bacteria, algae, and yeasts occupied 37.4%, 9.1%, and 1.3%, respectively. In addition to these, category-wise CPAH degrading efficiencies of each microbial taxon, consortium-based applications, CPAH degradation-related molecular tools, and factors affecting CPAH degradation are the other important aspects of this review in light of their appropriate selection and application in the PAH-contaminated environment for better human-health management in order to achieve a sustainable ecosystem.

Aerobic denitrifying bacterial-fungal consortium mediating nitrate removal: Dynamics, network patterns and interactions

In recent years, nitrogen removal by mixed microbial cultures has received increasing attention owing to cooperative metabolism. A natural bacterial-fungal consortium was isolated from mariculture, which exhibited an excellent aerobic denitrification capacity. Under aerobic conditions, nitrate removal and denitrification efficiencies were up to 100% and 44.27%, respectively. High-throughput sequencing and network analysis suggested that aerobic denitrification was potentially driven by the co-occurrence of the following bacterial and fungal genera: Vibrio, Fusarium, Gibberella, Meyerozyma, Exophiala and Pseudoalteromonas, with the dominance of Vibrio and Fusarium in bacterial and fungal communities, respectively. In addition, the isolated consortium had a high steady aerobic denitrification performance in our sub-culturing experiments. Our results provide new insights on the dynamics, network patterns and interactions of aerobic denitrifying microbial consortia with a high potential for new biotechnology applications.

Artificial mixed microbial system for polycyclic aromatic hydrocarbons degradation

Polycyclic aromatic hydrocarbons (PAHs) are environmental pollutants with major risks to human health. Biological degradation is environmentally friendly and the most appealing remediation method for a wide range of persistent pollutants. Meanwhile, due to the large microbial strain collection and multiple metabolic pathways, PAH degradation via an artificial mixed microbial system (MMS) has emerged and is regarded as a promising bioremediation approach. The artificial MMS construction by simplifying the community structure, clarifying the labor division, and streamlining the metabolic flux has shown tremendous efficiency. This review describes the construction principles, influencing factors, and enhancement strategies of artificial MMS for PAH degradation. In addition, we identify the challenges and future opportunities for the development of MMS toward new or upgraded high-performance applications.

The effects of pectin on the gut microbiota and serum metabolites in mice fed with a high fat diet and exposed to low-dose antibiotics

A sedentary lifestyle, unhealthy diet, and antibiotic use among other environmental factors have been associated with an increased incidence of metabolic disorders and inflammation, as well as gut dysbiosis. Pectin is an edible polysaccharide that exists widely in the cell wall of plants. Our previous study has shown that pectin with various degrees of esterification displayed different effects on preventing acute colitis and regulating the gut microbiome and serum metabolome. This study aimed to further explore the differential effects of pectin with various degrees of esterification on mice simultaneously treated with a high-fat diet and low-dose antibiotics. The results showed that low-esterified pectin L102 improved the biomarkers of metabolic disorders including blood glucose and body weight. The high-esterified pectin H121 and the low-esterified pectin L13 ameliorated inflammatory markers such as superoxide dismutase (SOD). The enrichment of probiotic bacteria such as Lactobacillus by pectin L102, reduction of conditional pathogens such as Klebsiella by pectin L13, and changes in circulating metabolites like L-tryptophan and 3-indoleacrylate by all three types of pectins were detected. These data provide evidence for a differential effect of different types of pectin on the gut microbiota and metabolic health.

Dissolved Organic Matter and Lignin Modulate Aquatic Toxicity and Oxidative Stress Response Activated by Layered Double Hydroxides Nanomaterials

Advanced nanomaterials can be released into the environment and can coexist with natural organic matter (NOM). However, evidence on the impacts of NOM on the environmental behavior and toxicity of advanced nanomaterials is still scarce. Here, we investigated the behavior and toxic effects of two layered double hydroxides (LDHs) nanomaterials with different metallic constituents (Mg-Al-LDH and Zn-Al-LDH) at relatively low exposure concentrations on a freshwater green alga (Chlorella pyrenoidosa) in the absence and presence of two types of NOM, namely dissolved organic matter (DOM) and dealkaline lignin (DL). The DOM or DL interaction with the LDHs at different mixture levels was shown to be an antagonistic effect on the growth inhibition toxicity to C. pyrenoidosa mainly. The estimation of the index of Integrated Biological Responses version 2 indicated that the joint interaction of the LDHs with DOM or DL occurred in the following order of frequency synergism > antagonism > additivity. Furthermore, the physicochemical characteristics of LDHs were crucial for illuminating the mechanism by which the DOM or DL modified the LDH-induced oxidative stress response. These findings highlighted the important role of NOM in the behavior and effect of LDHs as a representative of a new class of multifunctional nanomaterials in the freshwater environment.

Arbuscular mycorrhizal fungi alter rhizosphere bacterial community characteristics to improve Cr tolerance of Acorus calamus

Arbuscular mycorrhizal fungi (AMF) can improve plant tolerance to heavy metal stress in terrestrial ecosystems. However, in wetland ecosystems, AMF can improve the tolerance of wetland plants to heavy metals by changing the structure and composition of rhizosphere bacterial communities, which is still rarely studied. In this study, we investigated the effects of AMF on the structure and composition of bacterial communities in the rhizosphere of plants under different chromium concentrations. The results showed that Cr(Ⅵ) concentration in Acorus calamus. rhizosphere soil decreased by 12.6 % (5.6-21.7 %) on average after AMF inoculation, At the same time, it promoted the uptake of nutrients by A. calamus and increased soil carbon input. In addition, Cr stress decreased the bacterial community diversity and abundance index by 9.8 % (1.6-18.1 %) and 24.5 % (17.3-27.6 %) on average. On the contrary, the rhizosphere soil bacterial diversity and abundance index increased by 7.3 % (2.2-19.1 %) and 13.9 % (6.0-20.9 %) on average after AMF inoculation. Moreover, compared with the non-inoculated AMF group, the bacterial community structure of A. calamus rhizosphere changed by 24.6 % under Cr stress, The common number of species increased by 6.4 %. In addition, after inoculation of AMF significantly promote the growth of a large number of bacteria related to organic degradation, plant growth, and oxidative stress, increased soil carbon input improved the soil microenvironment. Meanwhile, After AMF inoculation, the Number of edges, Number of Nodes, Average degree, and Average Path length in the symbiotic network of rhizosphere soil bacterial community increased by 34.6 %, 10 %, 44.3 %, and 26.4 %, respectively. Therefore, it offers a possibility that AMF can enhance the tolerance of wetland plants to soil Cr pollution by improving the structure and composition of bacterial communities in the rhizosphere soils of wetland plants, which provide a basis for wetland plants to repair soil Cr pollution.

Fungal bioproducts for petroleum hydrocarbons and toxic metals remediation: recent advances and emerging technologies

Petroleum hydrocarbons and toxic metals are sources of environmental contamination and are harmful to all ecosystems. Fungi have metabolic and morphological plasticity that turn them into potential prototypes for technological development in biological remediation of these contaminants due to their ability to interact with a specific contaminant and/or produced metabolites. Although fungal bioinoculants producing enzymes, biosurfactants, polymers, pigments and organic acids have potential to be protagonists in mycoremediation of hydrocarbons and toxic metals, they can still be only adjuvants together with bacteria, microalgae, plants or animals in such processes. However, the sudden accelerated development of emerging technologies related to the use of potential fungal bioproducts such as bioinoculants, enzymes and biosurfactants in the remediation of these contaminants, has boosted fungal bioprocesses to achieve higher performance and possible real application. In this review, we explore scientific and technological advances in bioprocesses related to the production and/or application of these potential fungal bioproducts when used in remediation of hydrocarbons and toxic metals from an integral perspective of biotechnological process development. In turn, it sheds light to overcome existing technological limitations or enable new experimental designs in the remediation of these and other emerging contaminants.

Fungal Assisted Valorisation of Polymeric Lignin: Mechanism, Enzymes and Perspectives

Lignocellulose is considered one of the significant recalcitrant materials and also is difficult to break down because of its complex structure. Different microbes such as bacteria and fungi are responsible for breaking down these complex lignin structures. This article discussed briefly the lignin-degrading bacteria and their critical steps involved in lignin depolymerization. In addition, fungi are regarded as the ideal microorganism for the degradation of lignin because of their highly effective hydrolytic and oxidative enzyme systems for the breakdown of lignocellulosic materials. The white rot fungi, mainly belonging to basidiomycetes, is the main degrader of lignin among various microorganisms. This could be achieved because of the presence of lignolytic enzymes such as laccases, lignin peroxidases, and manganese peroxidases. The significance of the fungi and lignolytic enzyme’s role in lignin depolymerization, along with its mechanism and chemical pathways, are emphasized in this article.

Contributions of Beneficial Microorganisms in Soil Remediation and Quality Improvement of Medicinal Plants

Medicinal plants (MPs) are important resources widely used in the treatment and prevention of diseases and have attracted much attention owing to their significant antiviral, anti-inflammatory, antioxidant and other activities. However, soil degradation, caused by continuous cropping, excessive chemical fertilizers and pesticide residues and heavy metal contamination, seriously restricts the growth and quality formation of MPs. Microorganisms, as the major biota in soil, play a critical role in the restoration of the land ecosystem. Rhizosphere microecology directly or indirectly affects the growth and development, metabolic regulation and active ingredient accumulation of MPs. Microbial resources, with the advantages of economic efficiency, harmless to environment and non-toxic to organisms, have been recommended as a promising alternative to conventional fertilizers and pesticides. The introduction of beneficial microbes promotes the adaptability of MPs to adversity stress by enhancing soil fertility, inhibiting pathogens and inducing systemic resistance. On the other hand, it can improve the medicinal quality by removing soil pollutants, reducing the absorption and accumulation of harmful substances and regulating the synthesis of secondary metabolites. The ecological and economic benefits of the soil microbiome in agricultural practices are increasingly recognized, but the current understanding of the interaction between soil conditions, root exudates and microbial communities and the mechanism of rhizosphere microecology affecting the secondary metabolism of MPs is still quite limited. More research is needed to investigate the effects of the microbiome on the growth and quality of different medicinal species. Therefore, the present review summarizes the main soil issues in medicinal plant cultivation, the functions of microbes in soil remediation and plant growth promotion and the potential mechanism to further guide the use of microbial resources to promote the ecological cultivation and sustainable development of MPs.

Resistance and resilience of soil bacterial community to zero-valent iron disposal of lindane contamination

Zero-valent iron (ZVI, Fe⁰) enables chemical reduction of environmental pollutants coupled with reactivity loss due to surface oxidation. During ZVI treatment process, however, microbial community stability in terms of resistance and resilience remains largely unclear. Here, we monitored bacterial community succession over a 4 weeks period in soil microcosms with or without 2% (w/w) Fe⁰ amendment. To simulate soil pollution, 100 μg g^-1 chlorinated pesticide lindane (γ-hexachlorocyclohexane) was added to the microcosms as a model contaminant. In addition to microbial activity as measured by soil organic carbon mineralization, bacterial abundance, diversity and composition were determined using qPCR and high-throughput sequencing of 16 S rRNA genes. Co-occurrence analysis was performed to reveal the interaction patterns within the bacterial communities. The results indicated that ZVI caused near-complete transformation of lindane, while in the microcosms without Fe⁰ amendment the pesticide was recalcitrant. ZVI strongly inhibited CO₂-efflux at the early stage of incubation, but the bacterial community appeared to be less sensitive to Fe⁰ amendment. The ratios of negative to positive correlations between network nodes suggested that Fe⁰ had marginal influence on community stability compared to the lindane treatments, which destabilized the bacterial community. Community succession occurred in the presence of ZVI, as exemplified by a dominancy transition from anaerobic to aerobic taxa. Yet, ZVI alleviated the stress of lindane on soil bacteria by improving community structure and increasing network complexity. Taken together, these findings demonstrate the stability of soil bacterial community under Fe⁰ stress, which might be conducive to functional recovery of soil microorganisms following ZVI remediation.

The neglected effects of polysaccharide transformation on sludge humification during anaerobic digestion with thermal hydrolysis pretreatment

Humus accumulation during sludge stabilization is attracting increasing attention because of its land use potential. This study investigated the effects of thermal hydrolysis pretreatment (THP) on sludge humification and the related regulatory mechanisms during anaerobic digestion (AD). The sludge subjected to AD with THP at 160 °C (AnD-160) exhibited 7.3% and 8.5% higher total extractable carbon (TEC) and humic acid carbon (HAC) concentrations than the unpretreated sludge, respectively, while the sludge subjected to AD with THP at 180 °C (AnD-180) exhibited 1.4% and 7.0% lower concentrations. Humification of AnD-160 and AnD-180 were enhanced and inhibited, respectively. THP influenced sludge humification during AD through both intracellular polyphenol synthesis and extracellular humus condensation pathways related to polysaccharide metabolism. The 160 °C-pretreated sludge exhibited higher polysaccharide availability (more soluble polysaccharides and reducing sugars) than the other samples and thus had more active intracellular polyphenol metabolism during AD. The polyphenol accumulation stimulated the synthesis of related condensation enzymes (polyphenol oxidase and quinone oxidoreductases), facilitating extracellular HA production during AD. However, THP at 180 °C resulted in the highest production of melanoidins with CO-C heterocycles through C = O and CH sites of polysaccharides (778.46 vs. 193.87 R.U. nm²-mL/g for the unpretreated sample). This heterocyclization decreased the polysaccharide availability and inhibited intracellular polyphenol synthesis, consequently inhibiting condensation enzymes supply and extracellular HA production during AD. Overall, this study highlights the crucial but neglected role of polysaccharides in sludge humification during AD: the availability of polysaccharides affected by their occurrence state and molecular structure could determine the humification, which can be regulated by THP at different temperature.

Potential and mechanism for bioremediation of papermaking black liquor by a psychrotrophic lignin-degrading bacterium, Arthrobacter sp. C2

To meet the challenge of bioremediation of black liquor in pulp and paper mills at low temperatures, a psychrotrophic lignin-degrading bacterium was employed in black liquor treatment for the first time. In this study, Arthrobacter sp. C2 exhibited excellent cold adaptability and lignin degradation ability, with a lignin degradation rate of 65.5% and a mineralization rate of 43.9% for 3 g/L lignin at 15 °C. Bioinformatics analysis and multiple experiments confirmed that cold shock protein 1 (Csp1) was the dominant cold regulator of strain C2, and dye-decolorizing peroxidase (DyP) played a crucial role in lignin degradation. Moreover, structural equation modeling (SEM), mRNA monitoring, and phenotypic variation analysis demonstrated that Csp1 not only mediated cold adaptation but also modulated DyP activity by controlling dyp gene expression, thus driving lignin depolymerization for strain C2 at low temperatures. Furthermore, 96.4% of color, 64.2% of chemical oxygen demand (COD), and 100% of nitrate nitrogen (NO₃^--N) were removed from papermaking black liquor by strain C2 within 15 days at 15 °C. This study provides insights into the association between the cold regulator and catalytic enzyme of psychrotrophic bacteria and offers a feasible alternative strategy for the bioremediation of papermaking black liquor in cold regions.

Fungal-bacterial network in PAH-contaminated coastal marine sediment

Fungal microbiome interacts with the other biotic components in coastal sediment playing a key role in the overall coordination of the whole microbial community. These interactions are affected by human activities, such as the constant affluence of polycyclic aromatic hydrocarbons (PAHs). Although fungi and bacteria interactions have been found to play a key role in PAH bioremediation in soil, the effect of PAHs on fungal diversity and their specific interactions with bacteria in coastal sediments are yet to be investigated. The understanding of fungal bacterial interactions under PAH contamination is critical for further bioremediation regarding the important fungal diversity observed in coastal sediment. Here, we investigated the fungal bacterial co-occurrence in PAH-contaminated sediments. The co-occurrence network, constructed with sequencing data (bacterial 16S and fungal 18S rRNA genes barcoding) from 51 PAH-contaminated samples, revealed modules dominated by either fungi or bacteria, reflecting probably the different types of interaction possible between fungi and bacteria. Then, a network constructed from non-contaminated sample data was compared with a network built from the corresponding PAH-contaminated samples issued from a mesocosm experiment. The comparison revealed the effect of PAHs in fungi and bacteria interactions, characterized by a PAH-contaminated network exhibiting less abundant and diverse fungal and bacterial ASVs than the non-contaminated network. However, the links between the remaining ASVs in the PAH-contaminated network showed stronger correlations. Noteworthy, an ASV affiliated to Chrytridiomycota phylum was identified as a keystone fungal ASV forming a module in association with facultative anaerobic and anaerobic bacteria affiliated to the families Prolixibacteraceae, Fusobacteriaceae, and Desulfobulbaceae. These results suggest that fungi promote bacterial anaerobic metabolisms, which are important to cope with the presence of PAHs in sediments. Our study reveals the importance of fungal bacterial interactions in coastal sediments paving the way for future studies to fully understand fungal role in coastal sediment.