Unearthing microbial diversity of Taxus rhizosphere via MiSeq high-throughput amplicon sequencing and isolate characterization

Fungal bioaugmentation enhanced herbicide removal via soil microbial fuel cell: Taking Myrothecium verrucaria and haloxyfop-P as an example

Microbial fuel cell (MFC), which produces electricity while removing pollutants, is a green approach of ecological restoration. Whether fungal bioaugmentation could enhance the herbicide removal in MFC has not been fully investigated. This study aims to construct the fungal-augmented MFC device, compare the effects of different types of remediation against soil haloxyfop-P, and explore the mechanisms of xeno-fungusphere MFC in alleviating organic pollution. The Myrothecium verrucaria addition achieved the current density of 15.27 μA/cm2 and power density (PD) of 1.174 μW/cm2, which were much higher than those with indigenous microbes and MFC alone. On day 60, the haloxyfop removal efficiency of 93.7 % was achieved with the M. verrucaria bioaugmentation, and double herbicide further increased the removal efficiency to 97.9 %, along with PD of 9.3 μW/cm2. The M. verrucaria addition significantly changed the correlation pattern between bacterial genera, as well as between dominant genera and herbicide degradation, electrogenesis, edaphic factors and functional abundance. Facing herbicide challenge, the biogeochemical processes of C/N/Fe/Mn/S were reorganized in MFC microbiota, which were also profoundly impacted by bioelectric field and xeno-fungusphere. The MFC degradation of haloxyfop-P followed the second-order kinetics; the fungal addition reduced the gap between the highest occupied molecular orbitals and lowest unoccupied molecular orbitals of herbicide molecules, and reduced the energy barrier for the herbicide transformation. Compared with MFC alone, xeno-fungusphere MFC had a better effect, which can remediate the soil without additional power supply, making it a cost-effective self-sustaining remediation strategy.

Fungal endophytes of Taxus species and regulatory effect of two strains on taxol synthesis

BACKGROUND

Taxol, derived from Taxus trees, is a valuable natural resource for the development of anticancer drugs. Endophytic fungi from Taxus trees are a promising alternative source of Taxol. However, the impact of plant-endophytic microbial interaction on the host's Taxol biosynthesis is largely unknown.

RESULTS

In the current study, the diversity of endophytic fungi in three different Taxus species was analyzed using Internal Transcribed Spacer sequencing. A total of 271 Operational Taxonomic Units (OTUs) were identified, grouping into 2 phyla, 8 classes, 16 orders, 19 families, and 19 genera. Alpha and beta diversity analysis indicated significant differences in endophytic fungal communities among the various Taxus trees. At the genus level, Alternaria and Davidiella were predominantly found in T. mairei and T. media, respectively. By utilizing a previously published dataset, a Pearson correlation analysis was conducted to predict the taxol biosynthesis-related fungal genera. Following screening, two isolates of Alternaria (L7 and M14) were obtained. Effect of inoculation with Alternaria isolates on the gene expression and metabolite accumulation of T. mairei was determined by transcriptomic and untargeted metabolomic studies. The co-inoculation assay suggests that the two Alternaria isolates may have a negative regulatory effect on taxol biosynthesis by influencing hormone signaling pathways.

CONCLUSION

Our findings will serve as a foundation for advancing the production and utilization of Taxus and will also aid in screening endophytic fungi related to taxol production.

Effects of error, chimera, bias, and GC content on the accuracy of amplicon sequencing

IMPORTANCE

Amplicon sequencing of targeted genes is the predominant approach to estimate the membership and structure of microbial communities. However, accurate reconstruction of community composition is difficult due to sequencing errors, and other methodological biases and effective approaches to overcome these challenges are essential. Using a mock community of 33 phylogenetically diverse strains, this study evaluated the effect of GC content on sequencing results and tested different approaches to improve overall sequencing accuracy while characterizing the pros and cons of popular amplicon sequence data processing approaches. The sequencing results from this study can serve as a benchmarking data set for future algorithmic improvements. Furthermore, the new insights on sequencing error, chimera formation, and GC bias from this study will help enhance the quality of amplicon sequencing studies and support the development of new data analysis approaches.

Effects of tillage patterns and stover mulching on N2O production, nitrogen cycling genes and microbial dynamics in black soil

Stover-covered no-tillage (NT) is of great significance to the rational utilization of stover resources and improvement of cultivated land quality, and also has a profound impact on ensuring groundwater, food and ecosystem security. However, the effects of tillage patterns and stover mulching on soil nitrogen turnover remain elusive. Based on the long-term conservation tillage field experiment in the mollisol area of Northeast China since 2007, the shotgun metagenomic sequencing of soils and microcosm incubation were combined with physical and chemical analyses, alkyne inhibition analysis to elucidate the regulatory mechanisms of NT and stover mulching on the farmland soil nitrogen emissions and microbial nitrogen cycling genes. Compared with conventional tillage (CT), NT stover mulching significantly reduced the emission of N2O instead of CO2, especially when 33% mulching was adopted, and correspondingly the nitrate nitrogen of NT33 was higher than that of other mulching amounts. The stover mulching was associated with higher total nitrogen, soil organic carbon and pH. The abundance of AOB (ammonia-oxidizing bacteria)-amoA (ammonia monooxygenase subunit A) was substantially increased by stover mulching, while the abundance of denitrification genes was reduced in most cases. Under alkyne inhibition, the tillage mode, treatment time, gas condition and interactions between them noticeably influenced the N2O emission and nitrogen transformation. In CT, NT0 (no mulching) and NT100 (full mulching), the relative contribution of AOB to N2O production was markedly higher than that of ammonia oxidizing archaea. Different tillage modes were associated with distinct microbial community composition, albeit NT100 was closer to CT than to NT0. Compared with CT, the co-occurrence network of microbial communities was more complex in NT0 and NT100. Our findings suggest that maintaining a low-quantity stover mulching could regulate soil nitrogen turnover toward proficiently enhancing soil health and regenerative agriculture, and coping with global climate change.

Revealing the relative importance among plant species, slope positions, and soil types on rhizosphere microbial communities in northern tropical karst and non-karst seasonal rainforests of China

Rhizosphere microbes have an extremely close relationship with plants and the study on the relationship between rhizosphere microorganisms and their influencing factors is conducive to the protection of vegetation and the maintenance of biodiversity. Here we investigated how plant species, slope positions and soil types affect the rhizosphere microbial community. Slope positions and soil types were collected from northern tropical karst and non-karst seasonal rainforests. The results indicated that soil types played a predominant role in the development of rhizosphere microbial communities (28.3% of separate contribution rate), more than plant species identity (10.9% of separate contribution rate) and slope position (3.5% of separate contribution rate). Notably, environmental factors closely related to soil properties were the major influence factors that controlling the rhizosphere bacterial community structure in the northern tropical seasonal rainforest, especially pH. Additionally, plant species also influenced the rhizosphere bacterial community. In low nitrogen content soil environments, rhizosphere biomarkers of dominant plant species were often nitrogen-fixing strains. It suggested that plants might have a selective adaptation mechanism to rhizosphere microorganisms to obtain the advantages of nutrient supply. Overall, soil types exerted the biggest influence on rhizosphere microbial community structure, followed by plant species and finally slope positions.

Rhizobacterial compositions and their relationships with soil properties and medicinal bioactive ingredients in Cinnamomum migao

Introduction

Rhizobacterial communities and their metabolites can affect plant growth, development, and stress resistance, as well as the biosynthesis and accumulation of bioactive compounds in medicinal plants. This relationship has been well-characterized in many medicinal herbs, although much less commonly in medicinal trees.

Methods

Here, we analyzed the composition and structure of Cinnamomum migao rhizobacterial communities across nine growing regions in Yunnan, Guizhou and Guangxi, China, as well as differences in soil properties and fruit bioactive compounds.

Results

Results showed that the C. migao rhizobacterial communities exhibited high species richness, but location-specific differences in structure. Site-specific differences in soil properties and bioactive compounds were also observed. Furthermore, rhizobacterial community compositions were correlated with both soil properties and fruit bioactive compounds, metabolism-related functions were most common in C. migao rhizobacteria.

Discussion

Several bacterial genera, including Acidothermus, Acidibacter, Bryobacter, Candidatus_Solibacter, and Acidimicrobiales, potentially promote the biosynthesis and accumulation of 1,8-cineole, cypressene, limonene, and α-terpineol, Nitrospira and Alphaproteobacteria may play an inhibitory role. Finally, our results emphasized the critical role that soil pH and nitrogen levels play in driving rhizobacterial community structure, and specific functional bacteria can also counteract with soil properties, Acidibacter and Nitrospira can affect soil pH and nitrogen effectiveness. Overall, this study provides additional insight into the complex correlation of rhizosphere microorganisms with bioactive ingredients and soil properties of medicinal plants.

Variations of Phyllosphere and Rhizosphere Microbial Communities of Pinus koraiensis Infected by Bursaphelenchus xylophilus

Pine wood nematode, Bursaphelenchus xylophilus, as one of the greatest threats to pine trees, is spreading all over the world. Plant microorganisms play an important role in the pathogenesis of nematodes. The phyllosphere and rhizosphere bacterial and fungal communities associated with healthy Pinus koraiensis (PKa) and P. koraiensis infected by B. xylophilus at the early (PKb) and last (PKc) stages were analyzed. Our results demonstrated that pine wood nematode (PWD) could increase the phyllosphere bacterial Pielou_e, Shannon, and Simpson index; phyllosphere fungal Chao 1 index, as well as rhizosphere bacterial Pielou_e, Shannon, and Simpson index; and rhizosphere fungal Pielou_e, Shannon, and Simpson index. What's more, slight shifts of the microbial diversity were observed at the early stage of infection, and the microbial diversity increased significantly as the symptoms of infection worsened. With the infection of B. xylophilus in P. koraiensis, Bradyrhizobium (rhizosphere bacteria), Massilia (phyllosphere bacteria), and Phaeosphaeriaceae (phyllosphere fungi) were the major contributors to the differences in community compositions among different treatments. With the infection of PWD, most of the bacterial groups tended to be co-excluding rather than co-occurring. These changes would correlate with microbial ability to suppress plant pathogen, enhancing the understanding of disease development and providing guidelines to pave the way for its possible management.

A Snapshot of Microbial Succession and Volatile Compound Dynamics in Flat Peach Wine During Spontaneous Fermentation

Flat peaches possess characteristic flavors and are rich in nutrients. The fermentation of flat peaches to produce wine through complex biochemical reactions is an effective method to overcome their seasonal defects. Spontaneously fermented flat peach wine has plentiful and strong flavors, but the microbiota of fermentation are still unknown. In this study, the microbial succession and volatile compound dynamics of spontaneous fermentation in Xinjiang flat peach wine were investigated using high-throughput sequencing (HTS) and headspace solid phase microextraction (HS-SPME) coupled with gas chromatography-mass spectrometry (GC-MS) technology, respectively, to better understand the microbiota involved. Multivariate data analysis was used to predict the relationship between microorganisms and volatile chemicals. The results showed that Kazachstania, Pichia, Aspergillus, Fructobacillus, Leuconostoc, and Lactobacillus were the dominant genera during the spontaneous fermentation of flat peach wine. Furthermore, ethyl hexanoate, 3-hexen-1-yl acetate, ethyl caprate, ethyl caprylate, phenethyl acetate, ethanol, γ-decalactone, decanal, 1-hexanoic acid, and octanoic acid endued flat peach wine with a strong fruity and fatty aroma. The core functional microbiota (primarily consisting of 11 bacterial and 14 fungal taxa) was strongly associated with the production of 27 volatile compounds in the spontaneously fermented flat peach wine, according to multivariate data analysis. Some alcohols and esters were positively linked with the presence of Kazachstania and Pichia. Meanwhile, the presence of Fructobacillus, Leuconostoc, Lactobacillus, and Weissella was significantly correlated with 2-non-anol, ethanol, 3-methyl-1-butanol, octyl formate, isoamyl lactate, and ethyl lactate. This snapshot of microbial succession and volatile compound dynamics provides insights into the microorganisms involved in flat peach wine fermentation and could guide the production of flat peach wine with desirable characteristics.

Biotransformation ability of endophytic fungi: from species evolution to industrial applications

Increased understanding of the interactions between endophytic fungi and plants has led to the discovery of a new generation of chemical compounds and processes between endophytic fungi and plants. Due to the long-term co-evolution between fungal endophytes and host plants, endophytes have evolved special biotransformation abilities, which can have critical consequences on plant metabolic processes and their composition. Biotransformation or bioconversion can impact the synthesis and decomposition of hormones, sugars, amino acids, vitamins, lipids, proteins, and various secondary metabolites, including flavonoids, polysaccharides, and terpenes. Endophytic fungi produce enzymes and various bioactive secondary metabolites with industrial value and can degrade or sequester inorganic and organic small molecules and macromolecules (e.g., toxins, pollutants, heavy metals). These fungi also have the ability to cause highly selective catalytic conversion of high-value compounds in an environmentally friendly manner, which can be important for the production/innovation of bioactive molecules, food and nutrition, agriculture, and environment. This work mainly summarized recent research progress in this field, providing a reference for further research and application of fungal endophytes. KEY POINTS: •The industrial value of degradation of endophytes was summarized. • The commercial value for the pharmaceutical industry is reviewed.

Hydrogen peroxide plus ascorbic acid enhanced organic matter deconstructions and composting performances via changing microbial communities

This work aims to investigate the influence of hydrogen peroxide (H₂O₂) and ascorbic acid (ASCA) on the physicochemical characteristics, organic matter (OM) deconstructions, humification degree and succession of bacterial communities for co-composting of bagasse pith and dairy manure. The results indicated that H₂O₂ and ASCA accelerated the degradation of lignocellulose, improved the transformation of dissolved organic matter (DOM), and enhanced the content of humic substance (HS) and the degree of its aromatization. The bacterial communities were significantly changed in the presence of additives, in which the relative abundances of Firmicutes and Actinobacteria significantly increased. Redundancy analysis (RDA) indicated that the degradation of OM and lignocellulose more influenced the bacterial community compositions. Conclusively, adding H₂O₂ and ASCA accelerated lignocellulose degradation efficiency, and improved the composting process, which provided an optimized method to dispose of lignocellulose wastes and livestock manure.

Safety and efficiency of sewage sludge and garden waste compost as a soil amendment based on the field application in woodland

Sewage sludge (SS) and garden waste (GW) compost can be used as soil amendments to improve the soil environment. Studies done till date have been focused on the changes of harmful substances during sludge composting, but the safety and efficacy of SS and GW composting on woodland soil environment are still unclear. In the study, a field experiment was performed using to investigate the safety and efficacy of SS and GW compost as a soil amendment on woodland soil. Soil nutrients (such as nitrogen, phosphorus and potassium), organic matter and electrical conductivity were significantly increased after the addition of the SS and GW compost, while there were no significant changes in soil heavy metals content and soil enzyme activities. From these soil properties, it was found that SS and GW compost was safe and efficacious in improving the soil environment. The application of SS and GW compost had no significant effect on microbial diversity. Co-occurrence network analysis revealed that SS and GW compost efficaciously enhanced the interaction between bacterial communities, which proved that it was safe and efficacious. Furthermore, SS and GW compost enhanced ABC transporters and carbohydrate metabolism of bacterial community, while reduced the pathotroph action (such as the plant pathogen) and wood saprotrophs. Overall, these results proved the safety and efficacy of SS and GW compost as soil amendments after being added to the soil. This study contributes to the use of harmless treatments and reutilization processes of SS and GW.

Exploring dynamics and associations of dominant lignocellulose degraders in tomato stalk composting

The plant residues of tomato bring pressures to the environment and composting provides a feasible method to treat such agricultural waste. However, little is known about the succession and associations of the dominant lignocellulose degraders in the compost system. To further accelerate the process by inoculating key functional microorganisms, a compost pile composed of tomato stalk with maize straw addition was constructed, and the whole community structure and functions of the dominant were investigated by applying the integrated mata-omics. Results showed that Actinobacteria, Firmicutes, and Ascomycota dominated and drove the assembly of the co-occurrence network. In the thermophilic stage, Thermobifida was the exclusive degrader of cellulose, and Thermobifida fusca was the most important cellulolytic actinomycete. Saccharomonospora viridis, Planifilum fulgidum, Thermobacillus sp. and the dominant ascomycota of Aspergillus sclerotialis participated in hemicellulose decomposing. In the cooling phase, functional microorganisms became more diverse, with Nocardiopsis flavescens, Glycomyces artemisiae, Glycomyces sambucus, Streptomyces rubrolavendulae and Streptomyces vietnamensis joining the cellulose-degrading rank, and Chaetomium thermophilum emerging as the main hemicellulose degrader. More than two thirds of the bacteria-bacteria interactions and all the fungi-fungi associations were positive, while, both competition (for the same substrate of hemicellulose) and synergy (preference for cellulose and hemicellulose) coexisted in the bacteria-fungi interactions. In conclusion, these findings provide useful information for understanding the biodegradation of tomato plant residues better, and effects of the functional agents identified on composting process should be further studied.

Increased Organic Fertilizer and Reduced Chemical Fertilizer Increased Fungal Diversity and the Abundance of Beneficial Fungi on the Grape Berry Surface in Arid Areas

Fertilizer practices can significantly impact the fruit quality and microbial diversity of the orchards. The fungi on the surface of fruits are essential for fruit storability and safety. However, it is not clear whether fertilization affects the fungal diversity and community structure on the surface of grape berries. Here, grape quality and the fungal diversity on the surface of grapes harvested from three fertilizer treatments were analyzed shortly after grape picking (T0) and following 8 days of storage (T1). The study involved three treatments: (1) common chemical fertilizer for 2 years (CH); (2) increased organic fertilizer and reduced chemical fertilizer for 1 year (A.O); and (3) increased organic fertilizer and reduced chemical fertilizer for 2 years (B.O). The application of increased organic fertilizer and reduced chemical fertilizer increased the soluble solids content (SSC) of the grape berries and decreased the pH of the grape juice. A total of 827,947 high-quality fungal sequences were recovered and assigned to 527 operational taxonomic units. Members of the Ascomycota phylum were dominant in all samples and accounted for 94.41% of the total number of detected sequences, followed by the Basidiomycota (5.05%), and unidentified fungi (0.54%). Alpha and beta diversity analyses revealed significantly different fungal populations in the three fertilizer treatments over the two time periods. The fungal diversity and richness on the grape berry surface in the B.O and A.O treatments were higher than those in the CH treatment. Among the detected fungi, the B.O treatments were mainly Pichia, Aureobasidium, and Candida genera, while the CH treatments were Botrytis, Aspergillus, and Penicillium. Moreover, significant differences were revealed between the two assessment times (T0 and T1). The samples from the T0 timepoint had higher fungal richness and diversity than the samples from T1 timepoint. Increasing organic fertilizer usage in grape management could improve grape quality and went on to increase the fungal diversity, as well as the relative abundance (RA) of beneficial fungi on grape berry surfaces. The correlation analysis suggested that the pH of the grape juice was significantly negatively correlated with fungal diversity parameters.

A Degeneration Gradient of Poplar Trees Contributes to the Taxonomic, Functional, and Resistome Diversity of Bacterial Communities in Rhizosphere Soils

Bacterial communities associated with roots influence the health and nutrition of the host plant. However, the microbiome discrepancy are not well understood under different healthy conditions. Here, we tested the hypothesis that rhizosphere soil microbial diversity and function varies along a degeneration gradient of poplar, with a focus on plant growth promoting bacteria (PGPB) and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG (antibiotics resistance genes) annotation revealed that available potassium (AK) was correlated with microbial diversity and function. We proposed several microbes, Bradyrhizobium, Sphingomonas, Mesorhizobium, Nocardioides, Variovorax, Gemmatimonadetes, Rhizobacter, Pedosphaera, Candidatus Solibacter, Acidobacterium, and Phenylobacterium, as candidates to reflect the soil fertility and the plant health. The highest abundance of multidrug resistance genes and the four mainly microbial resistance mechanisms (antibiotic efflux, antibiotic target protection, antibiotic target alteration, and antibiotic target replacement) in healthy poplar rhizosphere, corroborated the relationship between soil fertility and microbial activity. This result suggested that healthy rhizosphere soil harbored microbes with a higher capacity and had more complex microbial interaction network to promote plant growing and reduce intracellular levels of antibiotics. Our findings suggested a correlation between the plant degeneration gradient and bacterial communities, and provided insight into the role of high-turnover microbial communities as well as potential PGPB as real-time indicators of forestry soil quality, and demonstrated the inner interaction contributed by the bacterial communities.

The Utility of Electrochemical Systems in Microbial Degradation of Polycyclic Aromatic Hydrocarbons: Discourse, Diversity and Design

Polycyclic aromatic hydrocarbons (PAHs), especially high molecular weight PAHs, are carcinogenic and mutagenic organic compounds that are difficult to degrade. Microbial remediation is a popular method for the PAH removal in diverse environments and yet it is limited by the lack of electron acceptors. An emerging solution is to use the microbial electrochemical system, in which the solid anode is used as an inexhaustible electron acceptor and the microbial activity is stimulated by biocurrent in situ to ensure the PAH removal and avoid the defects of bioremediation. Based on the extensive investigation of recent literatures, this paper summarizes and comments on the research progress of PAH removal by the microbial electrochemical system of diversified design, enhanced measures and functional microorganisms. First, the bioelectrochemical degradation of PAHs is reviewed in separate and mixed PAH degradation, and the removal performance of PAHs in different system configurations is compared with the anode modification, the enhancement of substrate and electron transfer, the addition of chemical reagents, and the combination with phytoremediation. Second, the key functional microbiota including PAH degrading microbes and exoelectrogens are overviewed as well as the reduced microbes without competitive advantage. Finally, the typical representations of electrochemical activity especially the internal resistance, power density and current density of systems and influence factors are reviewed with the correlation analysis between PAH removal and energy generation. Presently, most studies focused on the anode modification in the bioelectrochemical degradation of PAHs and actually more attentions need to be paid to enhance the mass transfer and thus larger remediation radius, and other smart designs are also proposed, especially that the combined use of phytoremediation could be an eco-friendly and sustainable approach. Additionally, exoelectrogens and PAH degraders are partially overlapping, but the exact functional mechanisms of interaction network are still elusive, which could be revealed with the aid of advanced bioinformatics technology. In order to optimize the efficacy of functional community, more advanced techniques such as omics technology, photoelectrocatalysis and nanotechnology should be considered in the future research to improve the energy generation and PAH biodegradation rate simultaneously.

Effects of Plant and Soil Characteristics on Phyllosphere and Rhizosphere Fungal Communities During Plant Development in a Copper Tailings Dam

Interactions between plants and microbes can affect ecosystem functions, and many studies have demonstrated that plant properties influence mutualistic microorganisms. Here, high-throughput sequencing was used to investigate rhizosphere and phyllosphere fungal communities during different plant development stages. Results demonstrated that phyllosphere and rhizosphere fungal community structures were distinct during all developmental stages while they were mediated separately by plant carbon and soil sulfur. Comparatively, the effect of root properties on phyllosphere fungal diversity was greater than soil properties. Moreover, rhizosphere fungal networks of Bothriochloa ischaemum were more complex than phyllosphere fungal networks. This study demonstrated that the effect of plant and soil traits on phyllosphere and rhizosphere fungal communities could potentially be significant, depending on the applicable environmental condition and plant development stage. Although links between phyllosphere and rhizosphere communities have been established, further studies on functional fungal groups during phytoremediation processes are necessary. This study comprehensively analyzed dynamic relationships between phyllosphere and rhizosphere fungal communities during different plant development stages in a polluted environment. These fungal communities were determined to be expedient to the development and utilization of beneficial microbial communities during different development stages, which could more effectively help to stabilize and reclaim contaminated copper tailings soil.

Characterization of bacterial community structure in the rhizosphere of Triticum aestivum L

The plant microbiome influence plant health, yield and vigor and has attained a considerable attention in the present era. In the current study, native bacterial community composition and diversity colonizing Triticum aestivum L. rhizosphere at two distant geographical locations including Mirpur Azad Kashmir and Islamabad was elucidated. Based on IonS5™XL platform sequencing of respective samples targeting 16S rRNA gene that harbor V3-V4 conserved region revealed 1364 and 1254 microbial operational taxonomic units (OTUs) at ≥97% similarity and were classified into 23, 20 phyla; 70, 65 classes; 101, 87 orders; 189,180 families; 275, 271 genera and 94, 95 species. Respective predominant phyla accounting for 97.90% and 98.60% of bacterial community were Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidetes, Firmicutes, Chloroflexi and Gemmatimonadetes. Diversity indices revealed variations in relative abundance of bacterial taxa owing to distant geographical locations however predominant bacterial taxa at both locations were similar. These findings paved a way to dissect consequence of associated microbiota on future wheat production system.

Rhizosphere microbiome: Engineering bacterial competitiveness for enhancing crop production

Plants in nature are constantly exposed to a variety of abiotic and biotic stresses which limits their growth and production. Enhancing crop yield and production to feed exponentially growing global population in a sustainable manner by reduced chemical fertilization and agrochemicals will be a big challenge. Recently, the targeted application of beneficial plant microbiome and their cocktails to counteract abiotic and biotic stress is gaining momentum and becomes an exciting frontier of research. Advances in next generation sequencing (NGS) platform, gene editing technologies, metagenomics and bioinformatics approaches allows us to unravel the entangled webs of interactions of holobionts and core microbiomes for efficiently deploying the microbiome to increase crops nutrient acquisition and resistance to abiotic and biotic stress. In this review, we focused on shaping rhizosphere microbiome of susceptible host plant from resistant plant which comprises of specific type of microbial community with multiple potential benefits and targeted CRISPR/Cas9 based strategies for the manipulation of susceptibility genes in crop plants for improving plant health. This review is significant in providing first-hand information to improve fundamental understanding of the process which helps in shaping rhizosphere microbiome.

Metabolic function, trophic mode, organics degradation ability and influence factor of bacterial and fungal communities in chicken manure composting

The metabolic function and organic degradation behavior of bacterial and fungal communities were detected in 60 days composting of chicken manure and pumice by using Biolog tools, PICRUSt and FUNGuild. Fungal diversity increased from 57 OTUs in fresh chicken manure to 109 OTUs in high temperature stage, while bacterial diversity decreased from 86 OTUs to 44 OTUs after composting treatment. The carbohydrates degradation ability of bacterial community was enhanced in the high temperature stage. Fungal community had relatively higher degradation rates of carboxylic acids and amino acids in the maturation stage. Saprotroph was the main trophic mode of fungal community during the incubation process. The fungal animal pathogen decreased from 12.5% to 1.2% after composting treatment. Bacterial community composition and substrates degradation rate were mainly influenced by redox potential, pH and moisture, while temperature was the main environmental factor influencing on organic degradation of fungal community.

Pharmaceutical resource discovery from traditional medicinal plants: Pharmacophylogeny and pharmacophylogenomics

The worldwide botanical and medicinal culture diversity are astonishing and constitute a Pierian spring for innovative drug R&D. Here, the latest awareness and the perspectives of pharmacophylogeny and pharmacophylogenomics, as well as their expanding utility in botanical drug R&D, are systematically summarized and highlighted. Chemotaxonomy is based on the fact that closely related plants contain the same or similar chemical profiles. Correspondingly, it is better to combine morphological characters, DNA markers and chemical markers in the inference of medicinal plant phylogeny. Medicinal plants within the same phylogenetic groups may have the same or similar therapeutic effects, thus forming the core of pharmacophylogeny. Here we systematically review and comment on the versatile applications of pharmacophylogeny in (1) looking for domestic resources of imported drugs, (2) expanding medicinal plant resources, (3) quality control, identification and expansion of herbal medicines, (4) predicting the chemical constituents or active ingredients of herbal medicine and assisting in the identification and determination of chemical constituents, (5) the search for new drugs sorting out, and (6) summarizing and improving herbal medicine experiences, etc. Such studies should be enhanced within the context of deeper investigations of molecular biology and genomics of traditional medicinal plants, phytometabolites and metabolomics, and ethnomedicine-based pharmacological activity, thus enabling the sustainable conservation and utilization of traditional medicinal resources.

Impact of Drug Metabolism/Pharmacokinetics and their Relevance Upon Traditional Medicine-based Cardiovascular Drug Research

BACKGROUND

The representative cardiovascular herbs, i.e. Panax, Ligusticum, Carthamus, and Pueraria plants, are traditionally and globally used in the prevention and treatment of various cardiovascular diseases. Modern phytochemical studies have found many medicinal compounds from these plants, and their unique pharmacological activities are being revealed. However, there are few reviews that systematically summarize the current trends of Drug Metabolism/Pharmacokinetic (DMPK) investigations of cardiovascular herbs.

METHODS

Here, the latest understanding, as well as the knowledge gaps of the DMPK issues in drug development and clinical usage of cardiovascular herbal compounds, was highlighted.

RESULTS

The complicated herb-herb interactions of cardiovascular Traditional Chinese Medicine (TCM) herb pair/formula significantly impact the PK/pharmacodynamic performance of compounds thereof, which may inspire researchers to develop a novel herbal formula for the optimized outcome of different cardiovascular diseases. While the Absorption, Distribution, Metabolism, Excretion and Toxicity (ADME/T) of some compounds has been deciphered, DMPK studies should be extended to more cardiovascular compounds of different medicinal parts, species (including animals), and formulations, and could be streamlined by versatile omics platforms and computational analyses.

CONCLUSION

In the context of systems pharmacology, the DMPK knowledge base is expected to translate bench findings to clinical applications, as well as foster cardiovascular drug discovery and development.

Seasonal dynamics of microbial diversity in the rhizosphere of Ulmus pumila L. var. sabulosa in a steppe desert area of Northern China

The seasonal dynamics of microbial diversity within the rhizosphere of Ulmus pumila L. var. sabulosa in the hinterland of the Otindag Sandy Land of China were investigated using high-throughput sequencing of bacterial 16S rRNA genes and fungal ITS region sequences. A significant level of bacterial and fungal diversity was observed overall, with detection of 7,676 bacterial Operational Taxonomic Units (OTUs) belonging to 40 bacteria phyla and 3,582 fungal OTUs belonging to six phyla. Proteobacteria, Actinobacteria, and Firmicutes were the dominant bacterial phyla among communities, while Ascomycota, Basidiomycota, and Zygomycota were the dominant phyla of fungal communities. Seasonal changes influenced the α-diversity and β-diversity of bacterial communities within elm rhizospheres more than for fungal communities. Inferred functional analysis of the bacterial communities identified evidence for 41 level two KEGG (Kyoto Encyclopedia of Genes and Genomes) orthology groups, while guild-based analysis of the fungal communities identified eight ecological guilds. Metabolism was the most prevalent bacterial functional group, while saprotrophs prevailed among the identified fungal ecological guilds. Soil moisture and soil nutrient content were important factors that affected the microbial community structures of elm rhizospheres across seasons. The present pilot study provides an important baseline investigation of elm rhizosphere microbial communities.

Functional and Transcriptomic Characterization of a Dye-decolorizing Fungus from Taxus Rhizosphere

We isolated three laccase-producing fungus strains from Taxus rhizosphere. Myrotheium verrucaria strain DJTU-sh7 had the highest laccase activity of 216.2 U/ml, which was increased to above 300 U/ml after optimization. DJTU-sh7 had the best decolorizing effect for three classes of reactive dyes. The DJTU-sh7-containing fungal consortium displayed the robust decolorizing ability. Both color removal efficiency and chemical oxygen demand were increased in the consortium mediated biotransformation. Transcriptome changes of M. verrucaria elicited by azo dye and phenolic were quantified by the high throughput transcriptome sequencing, and the activities of the selected oxidases and reductases were determined. The possible involvement of oxidases and reductases, especially laccase, aryl alcohol oxidase, and ferric reductase in the biotransformation of dye and phenolic compounds was revealed at both transcriptomic and phenotypic levels. Revealing the transcriptomic mechanisms of fungi in dealing with organic pollutants facilitates the fine-tuned manipulation of strains in developing novel bioremediation and biodegradation strategies.

We isolated three laccase-producing fungus strains from Taxus rhizosphere. Myrotheium verrucaria strain DJTU-sh7 had the highest laccase activity of 216.2 U/ml, which was increased to above 300 U/ml after optimization. DJTU-sh7 had the best decolorizing effect for three classes of reactive dyes. The DJTU-sh7-containing fungal consortium displayed the robust decolorizing ability. Both color removal efficiency and chemical oxygen demand were increased in the consortium mediated biotransformation. Transcriptome changes of M. verrucaria elicited by azo dye and phenolic were quantified by the high throughput transcriptome sequencing, and the activities of the selected oxidases and reductases were determined. The possible involvement of oxidases and reductases, especially laccase, aryl alcohol oxidase, and ferric reductase in the biotransformation of dye and phenolic compounds was revealed at both transcriptomic and phenotypic levels. Revealing the transcriptomic mechanisms of fungi in dealing with organic pollutants facilitates the fine-tuned manipulation of strains in developing novel bioremediation and biodegradation strategies.

Difference in microbial community and taste compounds between Mucor-type and Aspergillus-type Douchi during koji-making

Douchi has attracted people's attention because of its unique taste and rich health function. The microbes participated in the koji-making process contribute to taste compounds of Douchi. However, the majority of studies on Douchi focused on their functional components and the microbial community in single type of Douchi during koji-making so far. In the present study, the taste components of Mucor-type and Aspergillus-type Douchi were measured initially and the results showed that the amino acid and organic acid levels as well as the percentage of unsaturated fatty acids in Mucor-type Douchi were significantly higher than those in Aspergillus-type. The investigation of the microbial composition in two types of Douchi showed that Aspergillus, Candida, Meyerozyma and Lecanicillium were shared by >50% of samples during koji-making. Comparison of the microbial community between the two types of Douchi revealed that Meyerozyma and Lecanicillium were the main microbial community with significant difference during the initial stage of koji-making, while Candida was significantly different during the later stage of koji-making. When supplemented with Meyerozyma and Candida in Aspergillus-type Douchi, the level of all amino acid and organic acids as well as the percentage of unsaturated fatty acid was significant improved, which further validated the importance roles of the two microorganisms in enhancing the taste components of Douchi during koji-making. The results provide useful information on optimizing the microbial community structure of Douchi during the process of koji-making and improving the product quality.

Succession of organics metabolic function of bacterial community in swine manure composting

Organics metabolic function of bacterial communities was evaluated in 60 days composting of swine manure and pumice by using MiSeq sequencing, PICRUSt and Biolog tools. The diversity of bacterial communities significantly decreased during the first 10 days, and gradually increased in the cooling and curing phase. The PICRUSt and Biolog analysis indicated that carbohydrate, lipid and amino acids metabolisms were relatively higher in the thermophilic phases. Xenobiotics biodegradation and metabolism, lipid metabolism, terpenoids and polyketides and biosynthesis of other secondary metabolites were mainly detected in the curing phases. Canonical correspondence analysis (CCA) indicated that the succession of bacterial community and organics utilization characteristics were highly affected by the temperature, moisture and oxidation reduction potential (ORP) in the swine composting system.

Changes in structure and function of fungal community in cow manure composting

In this study, dynamic changes in fungal communities, trophic modes and effect factors in 60 days composting of cow manure were analyzed by using high throughput sequencing, FUNGuild and Biolog FF MicroPlate, respectively. Orpinomyces (relative abundance >10.85%) predominated in feedstock, and Mycothermus became the dominating genus (relative abundance >75%) during the active phase. Aerobic composting treatment had a significant effect on fungal trophic modes with pathogenic fungi fading away and wood saprotrophs increasing over composting time. Fungal communities had the higher carbon sources utilization capabilities at the thermophilic phase and mature phase than those in the other periods. Oxidation reduction potential (ORP) significantly increased from -180 to 180 mV during the treatment. Redundancy analysis showed that the succession of fungal community during composting had a significant association with ORP (p < .05). This indicated that aerobic composting treatment not only influenced fungal community structure, but also changed fungal trophic modes and metabolic characteristics.

The first Taxus rhizosphere microbiome revealed by shotgun metagenomic sequencing

In the present study, the shotgun high throughput metagenomic sequencing was implemented to globally capture the features of Taxus rhizosphere microbiome. Total reads could be assigned to 6925 species belonging to 113 bacteria phyla and 301 species of nine fungi phyla. For archaea and virus, 263 and 134 species were for the first time identified, respectively. More than 720,000 Unigenes were identified by clean reads assembly. The top five assigned phyla were Actinobacteria (363,941 Unigenes), Proteobacteria (182,053), Acidobacteria (44,527), Ascomycota (fungi; 18,267), and Chloroflexi (15,539). KEGG analysis predicted numerous functional genes; 7101 Unigenes belong to "Xenobiotics biodegradation and metabolism." A total of 12,040 Unigenes involved in defense mechanisms (e.g., xenobiotic metabolism) were annotated by eggNOG. Talaromyces addition could influence not only the diversity and structure of microbial communities of Taxus rhizosphere, but also the relative abundance of functional genes, including metabolic genes, antibiotic resistant genes, and genes involved in pathogen-host interaction, bacterial virulence, and bacterial secretion system. The structure and function of rhizosphere microbiome could be sensitive to non-native microbe addition, which could impact on the pollutant degradation. This study, complementary to the amplicon sequencing, more objectively reflects the native microbiome of Taxus rhizosphere and its response to environmental pressure, and lays a foundation for potential combination of phytoremediation and bioaugmentation.

Functional characteristics and influence factors of microbial community in sewage sludge composting with inorganic bulking agent

The metabolic function of microbial community dominated organics and nutrients transformation in aerobic composting process. In this study, the metabolic characteristics of bacterial and fungal communities were evaluated in 60 days composting of sludge and pumice by using FUNGuild and PICRUSt, respectively. The results showed that microbial community structure and metabolic characteristics were distinctively different at four composting periods. Bacterial genes related to carbohydrate metabolisms decreased during the first 30 days, but bacterial sequences associated with oxidative phosphorylation and fatty acids synthesis were enhanced in curing phase. Most of fungal animal pathogen and plant pathogen disappeared after treatment, and the abundance of saprotroph fungi increased from 44.3% to 97.8%. Oxidation reduction potential (ORP) significantly increased from -28 to 175 mV through incubation. RDA analysis showed that ORP was a crucial factor on the succession of both bacterial and fungal communities in sludge composting system.

Rhizospheric microbial communities associated with wild and cultivated frankincense producing Boswellia sacra tree

Boswellia sacra, a frankincense producing endemic tree, has been well known for its cultural, religious and economic values. However, the tree has been least explored for the associated microsymbiota in the rhizosphere. The current study elucidates the fungal and bacterial communities of the rhizospheric regions of the wild and cultivated B. sacra tree populations through next generation sequencing. The sequence analysis showed the existence of 1006±8.9 and 60.6±3.1 operational taxonomic unit (OTUs) for bacterial and fungal communities respectively. In fungal communities, five major phyla were found with significantly higher abundance of Ascomycota (60.3%) in wild population and Basidiomycota (52%) in cultivated tree rhizospheres. Among bacterial communities, 31 major phyla were found, with significant distribution of Actinobacteria in wild tree rhizospheres, whereas Proteobacteria and Acidobacteria were highly abundant in cultivated trees. The diversity and abundance of microbiome varied significantly depending upon soil characteristics of the three different populations. In addition, significantly higher glucosidases, cellulases and indole-3-acetic acid were found in cultivated tree’s rhizospheres as compared to wild tree populations. for these plants to survive the harsh arid-land environmental conditions. The current study is a first comprehensive work and advances our knowledge about the core fungal and bacterial microbial microbiome associated with this economically important tree.

Metabolite profiling of non-sterile rhizosphere soil

Rhizosphere chemistry is the sum of root exudation chemicals, their breakdown products and the microbial products of soil-derived chemicals. To date, most studies about root exudation chemistry are based on sterile cultivation systems, which limits the discovery of microbial breakdown products that act as semiochemicals and shape microbial rhizosphere communities. Here, we present a method for untargeted metabolic profiling of non-sterile rhizosphere soil. We have developed an experimental growth system that enables the collection and analysis of rhizosphere chemicals from different plant species. High-throughput sequencing of 16SrRNA genes demonstrated that plants in the growth system support a microbial rhizosphere effect. To collect a range of (a)polar chemicals from the system, we developed extraction methods that do not cause detectable damage to root cells or soil-inhabiting microbes, thus preventing contamination with cellular metabolites. Untargeted metabolite profiling by UPLC-Q-TOF mass spectrometry, followed by uni- and multivariate statistical analyses, identified a wide range of secondary metabolites that are enriched in plant-containing soil, compared with control soil without roots. We show that the method is suitable for profiling the rhizosphere chemistry of Zea mays (maize) in agricultural soil, thereby demonstrating the applicability to different plant-soil combinations. Our study provides a robust method for the comprehensive metabolite profiling of non-sterile rhizosphere soil, which represents a technical advance towards the establishment of causal relationships between the chemistry and microbial composition of the rhizosphere.

Impact of tillage practices on soil bacterial diversity and composition under the tobacco-rice rotation in China

Tobacco-rice rotation is a common farming system in south China, and many tillage practices such as straw mulching, dolomite dust, and quicklime application have been adopted to improve crop production. These agricultural management practices alter soil physical and chemical properties and affect microbial life environment and community composition. In this research, six tillage practices including no tobacco and rice straw mulching (CK), tobacco and rice straw mulching (TrSr), rice straw returning fire (TrSc), tobacco and rice straw mulching with dolomite dust (TSD), rice straw returning fire and quicklime (TSQ), and rice straw returning fire, quicklime and reduced fertilizer (TSQf) were conducted to detect changes in soil bacterial diversity and composition using Illumina sequencing. The results showed that the total number of operational taxonomic units (OTUs) from the six treatments was 2030, and the number of mutual OTUs among all samples was 550. The TrSc treatment had the highest diversity and richness, while TSQf had the lowest. Soil physio-chemical properties and microbial diversity can influence each other. Proteobacteria and Actinobacteria had the greatest proportion in all treatments. The abundance of Nitrospirae was the highest in the TrSc treatment. The TSQf treatment had the highest abundance of Firmicutes. The abundance of Nitrospira in the TrSc treatment was 2.29-fold over CK. Streptomyces affiliated with Firmicutes improved by 37.33% in TSQf compared to TSQ. TSQf treatment was considered to be the most important factor in determining the relative abundance at the genus level.

The metabolic pathway of metamifop degradation by consortium ME-1 and its bacterial community structure

Metamifop is universally used in agriculture as a post-emergence aryloxyphenoxy propionate herbicide (AOPP), however its microbial degradation mechanism remains unclear. Consortium ME-1 isolated from AOPP-contaminated soil can degrade metamifop completely after 6 days and utilize it as the carbon source for bacterial growth. Meanwhile, consortium ME-1 possessed the ability to degrade metamifop stably under a wide range of pH (6.0-10.0) or temperature (20-42 °C). HPLC-MS analysis shows that N-(2-fluorophenyl)-2-(4-hydroxyphenoxy)-N-methyl propionamide, 2-(4-hydroxyphenoxy)-propionic acid, 6-chloro-2-benzoxazolinone and N-methyl-2-fluoroaniline, were detected and identified as four intermediate metabolites. Based on the metabolites identified, a putative metabolic pathway of metamifop was proposed for the first time. In addition, the consortium ME-1 was also able to transform or degrade other AOPP such as fenoxaprop-p-ethyl, clodinafop-propargyl, quizalofop-p-ethyl and cyhalofop-butyl. Moreover, the community structure of ME-1 with lower microbial diversity compared with the initial soil sample was investigated by high throughput sequencing. β-Proteobacteria and Sphingobacteria were the largest class with sequence percentages of 46.6% and 27.55% at the class level. In addition, 50 genera were classified in consortium ME-1, of which Methylobacillus, Sphingobacterium, Bordetella and Flavobacterium were the dominant genera with sequence percentages of 25.79, 25.61, 14.68 and 9.55%, respectively.