Microbial community composition is related to soil biological and chemical properties and bacterial wilt outbreak

Assessing the biodiversity of rhizosphere and endophytic fungi in Knoxia valerianoides under continuous cropping conditions

BACKGROUND

Rhizosphere and endophytic fungi play important roles in plant health and crop productivity. However, their community dynamics during the continuous cropping of Knoxia valerianoides have rarely been reported. K. valerianoides is a perennial herb of the family Rubiaceae and has been used in herbal medicines for ages. Here, we used high-throughput sequencing technology Illumina MiSeq to study the structural and functional dynamics of the rhizosphere and endophytic fungi of K. valerianoides.

RESULTS

The findings indicate that continuous planting has led to an increase in the richness and diversity of rhizosphere fungi, while concomitantly resulting in a decrease in the richness and diversity of root fungi. The diversity of endophytic fungal communities in roots was lower than that of the rhizosphere fungi. Ascomycota and Basidiomycota were the dominant phyla detected during the continuous cropping of K. valerianoides. In addition, we found that root rot directly affected the structure and diversity of fungal communities in the rhizosphere and the roots of K. valerianoides. Consequently, both the rhizosphere and endophyte fungal communities of root rot-infected plants showed higher richness than the healthy plants. The relative abundance of Fusarium in two and three years old root rot-infected plants was significantly higher than the control, indicating that continuous planting negatively affected the health of K. valerianoides plants. Decision Curve Analysis showed that soil pH, organic matter (OM), available K, total K, soil sucrase (S_SC), soil catalase (S_CAT), and soil cellulase (S_CL) were significantly related (p < 0.05) to the fungal community dynamics.

CONCLUSIONS

The diversity of fungal species in the rhizosphere and root of K. valerianoides was reported for the first time. The fungal diversity of rhizosphere soil was higher than that of root endophytic fungi. The fungal diversity of root rot plants was higher than that of healthy plants. Soil pH, OM, available K, total K, S_CAT, S_SC, and S_CL were significantly related to the fungal diversity. The occurrence of root rot had an effect on the community structure and diversity of rhizosphere and root endophytic fungi.

Screening, identification and evaluation of an acidophilic strain of Bacillus velezensis B4-7 for the biocontrol of tobacco bacterial wilt

Tobacco (Nicotiana tabacum L.) bacterial wilt, caused by Ralstonia solanacearum, is indeed a highly destructive plant disease, leading to substantial damage in tobacco production. While biological control is considered an effective measure for managing bacterial wilt, related research in this area has been relatively limited compared to other control methods. In order to discover new potential antagonistic bacteria with high biocontrol efficacy against tobacco bacterial wilt, we conducted an analysis of the microbial composition differences between disease-suppressive and disease-conducive soils using Illumina sequencing. As a result, we successfully isolated six strains from the disease-suppressive soil that exhibited antibacterial activity against Ralstonia solanacearum. Among these strains, B4-7 showed the strongest antibacterial activity, even at acidic conditions with a pH of 4.0. Based on genome analysis using Average Nucleotide Identity (ANI), B4-7 was identified as Bacillus velezensis. In greenhouse and field trials, strain B4-7 significantly reduced the disease index of tobacco bacterial wilt, with control efficiencies reaching 74.03% and 46.88% respectively. Additionally, B4-7 exhibited plant-promoting abilities that led to a 35.27% increase in tobacco production in field conditions. Quantitative real-time (qPCR) analysis demonstrated that strain B4-7 effectively reduced the abundance of R. solanacearum in the rhizosphere. Genome sequencing and Liquid Chromatography-Mass Spectrometry (LC-MS) analysis revealed that strain B4-7 potentially produces various lipopeptide metabolites, such as microlactin, bacillaene, difficidin, bacilysin, and surfactin. Furthermore, B4-7 influenced the structure of the rhizosphere soil microbial community, increasing bacterial abundance and fungal diversity, while also promoting the growth of different beneficial microorganisms. In addition, B4-7 enhanced tobacco's resistance to R. solanacearum by increasing the activities of defense enzymes, including superoxide dismutase (SOD), phenylalanine ammonia-lyase (PAL), peroxidase (POD), catalase (CAT), and polyphenol oxidase (PPO). Collectively, these findings suggest that B. velezensis B4-7 holds significant biocontrol potential and can be considered a promising candidate strain for eco-friendly management of tobacco bacterial wilt.

Effects of the invasion of Ralstonia solanacearum on soil microbial community structure in Wuhan, China

This study investigated the change in the microbiome of tomato rhizosphere soils after the invasion of Ralstonia solanacearum and analyzed the correlation between microbes and soil physicochemical properties. Diversity analyses of the bacteria in healthy and diseased rhizosphere soil samples (HRS and DRS) revealed that HRS had a higher species diversity and were compositionally different from DRS (P ≤ 0.05). Substantial differences in the relative abundance of Actinobacteria (37.52% vs 28.96%, P ≤ 0.05) and Proteobacteria (29.20% vs 35.59%, P ≤ 0.05) were identified in HRS and DRS, respectively. Taxonomic composition analysis showed ten differentially abundant genera, and seven of them (Gaiella, Roseisolibacter, Solirubrobacter, Kribbella, Acidibacter, Actinomarinicola, and Marmoricola) are more abundant in HRS. Soil pH and enzyme activities were negatively correlated with the abundance of R. solanacearum. The contents of total nitrogen (TN), total phosphorus (TP), total potassium (TK), alkaline nitrogen (alkaline N), available phosphorus (AP), available potassium (AK), NO3-N(NN), NH4+-N (AN), and organic matter (OM) were all significantly increased in DRS. The composition and richness of protozoa in the samples show significant differences. Cephalobus, Acrobeles, Heteromita, norank_Tylenchida, and Rotylenchulus were enriched in DRS. Microbial interaction networks revealed that the HRS networks were more complex than the DRS networks. Overall, the results of this study demonstrate that healthy soil has a more complex microbial community structure and higher enzyme activity, and the invasion of R. solanacearum damages the soil microbial system.IMPORTANCEHow does the invasion of Ralstonia solanacearum affect tomato rhizosphere bacteria and protozoa? Which microbial changes can affect the growth of R. solanacearum? To date, most research studies focus on bacteria, with little research on protozoa, and even less on the synergistic effects between protozoa and bacteria. Here, we analyzed the correlation between tomato rhizosphere bacterial and protozoan communities and soil physicochemical properties during the invasion of R. solanacearum. We found that the diversity and abundance of rhizosphere microorganisms in healthy rhizosphere soil samples (HRS) were significantly higher than those in diseased rhizosphere soil samples (DRS), and there were significant changes in soil pH and enzyme activity. Overall, in this study, the analysis of microbial changes during the invasion of R. solanacearum provides a theoretical basis for the prevention and control of bacterial wilt.

Metagenomic insights into the response of soil microbial communities to pathogenic Ralstonia solanacearum

Understanding the response of soil microbial communities to pathogenic Ralstonia solanacearum is crucial for preventing bacterial wilt outbreaks. In this study, we investigated the soil physicochemical and microbial community to assess their impact on the pathogenic R.solanacearum through metagenomics. Our results revealed that certain archaeal taxa were the main contributors influencing the health of plants. Additionally, the presence of the pathogen showed a strong negative correlation with soil phosphorus levels, while soil phosphorus was significantly correlated with bacterial and archaeal communities. We found that the network of microbial interactions in healthy plant rhizosphere soils was more complex compared to diseased soils. The diseased soil network had more linkages, particularly related to the pathogen occurrence. Within the network, the family Comamonadaceae, specifically Ramlibacter_tataouinensis, was enriched in healthy samples and showed a significantly negative correlation with the pathogen. In terms of archaea, Halorubrum, Halorussus_halophilus (family: Halobacteriaceae), and Natronomonas_pharaonis (family: Haloarculaceae) were enriched in healthy plant rhizosphere soils and showed negative correlations with R.solanacearum. These findings suggested that the presence of these archaea may potentially reduce the occurrence of bacterial wilt disease. On the other hand, Halostagnicola_larseniia and Haloterrigena_sp._BND6 (family: Natrialbaceae) had higher relative abundance in diseased plants and exhibited significantly positive correlations with R.solanacearum, indicating their potential contribution to the pathogen's occurrence. Moreover, we explored the possibility of functional gene sharing among the correlating bacterial pairs within the Molecular Ecological Network. Our analysis revealed 468 entries of horizontal gene transfer (HGT) events, emphasizing the significance of HGT in shaping the adaptive traits of plant-associated bacteria, particularly in relation to host colonization and pathogenicity. Overall, this work revealed key factors, patterns and response mechanisms underlying the rhizosphere soil microbial populations. The findings offer valuable guidance for effectively controlling soil-borne bacterial diseases and developing sustainable agriculture practices.

In Vitro Sensitivity Test of Fusarium Species from Weeds and Non-Gramineous Plants to Triazole Fungicides

Fusarium species are common plant pathogens that cause serious crop losses worldwide. Fusarium spp. colonize not only the main host plants, crops, but also alternative hosts. The effectiveness of fungicide use in disease management ranges from very successful to possibly promoting the growth of the pathogen. Triazole fungicides are widely used to control these pathogens due to their broad-spectrum activity and systemic nature. This paper reviews the sensitivity of 40 Fusarium strains isolated from weeds, non-gramineous plants, and spring wheat to metconazole, prothioconazole, and tebuconazole. The effect of fungicides was determined by the percentage inhibition of F. graminearum, F. culmorum, F. sporotrichioides, and F. avenaceum fungal mycelial growth. The 50% effective concentration (EC50) values of all isolates on metconazole were lower than 2.9 mg L-1, prothioconazole EC50 ranged from 0.12 to 23.6 mg L-1, and tebuconazole ranged from 0.09 to 15.6 mg L-1. At 0.00025-0.025 mg L-1, the fungicides were ineffective, except for the growth of the F. avenaceum species. It was observed that isolates from weeds were more sensitive to low concentrations of fungicide than isolates from crop plants. In general, information is scarce regarding the comparison of fungicide resistance in Fusarium isolates from weed and crop plants, making this study an additional contribution to the existing knowledge base.

A QTL of eggplant shapes the rhizosphere bacterial community, co-responsible for resistance to bacterial wilt

Resistant crop cultivars can recruit beneficial rhizobacteria to resist disease. However, whether this recruitment is regulated by quantitative trait loci (QTL) is unclear. The role of QTL in recruiting specific bacteria against bacterial wilt (BW) is an important question of practical significance to disease management. Here, to identify QTL controlling BW resistance, Super-BSA was performed in F2 plants derived from resistant eggplant cultivar R06112 × susceptible cultivar S55193. The QTL was narrowed down through BC1F1-BC3F1 individuals by wilting symptoms and KASP markers. Rhizosphere bacterial composition of R06112, S55193, and resistant individuals EB158 (with the QTL) and susceptible individuals EB327 (without QTL) from BC2F1 generation were assessed by Illumina sequencing-based analysis, and the activation of plant immunity by the bacterial isolates was analyzed. Evidence showed that BW-resistant is controlled by one QTL located at the 270 kb region on chromosome 10, namely EBWR10, and nsLTPs as candidate genes confirmed by RNA-Seq. EBWR10 has a significant effect on rhizobacteria composition and significantly recruits Bacillus. pp. A SynCom of three isolated Bacillus. pp trains significantly reduced the disease incidence, changed activities of CAT, PPO, and PAL and concentration of NO, H2O2, and O2-, activated SA and JA signaling-dependent ISR, and displayed immune activation against Ralstonia solanacearum in eggplant. Our findings demonstrate for the first time that the QTL can recruit beneficial rhizobacteria, which jointly promote the suppression of BW. This method charts a path to develop the QTL in resistant cultivar-driven probiotics to ameliorate plant diseases.

Deciphering Differences in Microbial Community Diversity between Clubroot-Diseased and Healthy Soils

Clubroot (Plasmodiophora brassicae) is an important soilborne disease that causes severe damage to cruciferous crops in China. This study aims to compare the differences in chemical properties and microbiomes between healthy and clubroot-diseased soils. To reveal the difference, we measured soil chemical properties and microbial communities by sequencing 18S and 16S rRNA amplicons. The available potassium in the diseased soils was higher than in the healthy soils. The fungal diversity in the healthy soils was significantly higher than in the diseased soils. Ascomycota and Proteobacteria were the most dominant fungal phylum and bacteria phylum in all soil samples, respectively. Plant-beneficial microorganisms, such as Chaetomium and Sphingomonas, were more abundant in the healthy soils than in the diseased soils. Co-occurrence network analysis found that the healthy soil networks were more complex and stable than the diseased soils. The link number, network density, and clustering coefficient of the healthy soil networks were higher than those of the diseased soil networks. Our results indicate that the microbial community diversity and network structure of the clubroot-diseased soils were different from those of the healthy soils. This study is of great significance in exploring the biological control strategies of clubroot disease.

The occurrence of clubroot in cruciferous crops correlates with the chemical and microbial characteristics of soils

Clubroot disease, caused by Plasmodiophora brassicae, is a serious soil-borne disease in Brassica crops worldwide. It seriously occurs in conducive soils of southern China, while never happens in some areas of northern China with suppressive soils. To understanding the differences, we measured the soil suppressiveness, chemical properties, and microbial communities in suppressive and conducive soils by bioassay and sequencing of 16S and 18S rRNA amplicons. The biological basis of clubroot suppressiveness was supported by the ability to remove it by pasteurization. The pH value and calcium content in the suppressive soils were higher than those in the conducive soils. Suppressive soils were associated with higher fungal diversity and bacterial abundance. The fungal phyla Chytridiomycota, Olpidiomycota, and Mucoromycota and the bacterial phyla Acidobacteriota and Gemmatimonadota were enriched in suppressive soils. More abundant beneficial microbes, including Chaetomium and Lysobacter, were found in the suppressive soils than in the conducive soils. Molecular ecological network analysis revealed that the fungal network of suppressive soils was more complex than that of conducive soils. Our results indicate that plant health is closely related to soil physicochemical and biological properties. This study is of great significance for developing strategies for clubtroot disease prevention and control.

Long-Term Field Application of a Plant Growth-Promoting Rhizobacterial Consortium Suppressed Root-Knot Disease by Shaping the Rhizosphere Microbiota

Root-knot nematodes (Meloidogyne spp.) are one of the most economically important plant parasitic nematodes, infecting almost all cultivated plants and resulting in severe yield losses every year. Plant growth-promoting rhizobacteria (PGPR) have been extensively used to prevent and control root-knot diseases and increase yield. In this study, the effect of a consortium of three PGPR strains (Bacillus cereus AR156, B. subtilis SM21, and Serratia sp. XY21; hereafter "BBS") on root-knot disease of cucumber was evaluated. The application of BBS significantly reduced the severity of root-knot disease by 56 to 72%, increased yield by 36 to 55%, and improved fruit quality by 14 to 90% and soil properties by 1 to 90% relative to the control in the cucumber fields of the Nanjing suburb, Jiangsu Province, from 2015 to 2018. BBS altered the rhizosphere bacterial community. Compared with the control group, it significantly (false discovery rate, P < 0.05) increased the abundance of 14 bacterial genera that were negatively correlated with disease severity. Additionally, the redundancy analysis suggested that BBS-treated rhizosphere soil samples were dominated by disease-suppressive bacteria, including the genera Iamia, Kutzneria, Salinibacterium, Mycobacterium, Kribbella, Pseudonocardia, Sporichthya, Sphaerisporangium, Actinomadura, Flavisolibacter, Phenylobacterium, Bosea, Hyphomicrobium, Agrobacterium, Sphingomonas, and Nannocystis, which were positively related to total organic carbon, total nitrogen, total organic matter, dissolved organic carbon, [Formula: see text]-N, and available phosphorus contents. This suggests that BBS suppresses root-knot nematodes and improves the soil chemical properties of cucumber by altering the rhizosphere microbial community.

Impact of Ecological Restoration on the Physicochemical Properties and Bacterial Communities in Alpine Mining Area Soils

Ecological restoration has notably impacted microbe and soil characteristics in abandoned open pit mines, especially in alpine regions. Yet, the adaptive responses of microbial communities in the initial years of mine site restoration remain largely unexplored. This study endeavors to offer a thorough comprehension of soil properties and microbial dynamics during the initial phases of alpine mining land reclamation. It places emphasis on physicochemical properties and microbial community composition and evaluates the feasibility of phytoremediation, along with proposing subsequent measures. Our study employs spatial sequence instead of time-sequenceal sequence to investigate early-stage changes in soil microbes and physicochemical properties in alpine mining land reclamation. We used high-throughput sequencing for the 16S rRNA amplicon study. Over time, soil physicochemical properties improved noticeably. Soil pH shifted from neutral to alkaline (7.04-8.0), while soil electrical conductivity (EC) decreased to 77 μS·cm-1 in R_6a. Cation exchange capacity (CEC) initially decreased from R_2a (12.30-27.98 cmol·kg-1) and then increased. Soil organic matter increased from 17.7 to 43.2 g·kg-1 over time during mine reclamation and restoration. The dominant bacterial community consisted of Proteobacteria (33.94% to 52.09%), Acidobacteriota (4.94% to 15.88%), Bacteroidota (6.52% to 11.15%), Actinobacteriota (7.18% to 9.61%), and Firmicutes (4.52% to 16.80%) with varying relative abundances. Gene annotation of sequences from various reclamation years revealed general function prediction, translation, ribosome structure, cell wall/membrane/envelope biogenesis, nucleotide translocation, and metabolism, along with other related functions. Mine reclamation improved soil fertility and properties, with the R_6a treatment being the most effective. Starting in the 2nd year of reclamation, the effective phosphorus content and the dominance of microbial bacteria, notably the Bacillus content, decreased. Firmicute fertilization promoted phosphorus and bacterial growth. In conclusion, employing a blend of sequencing and experimental approaches, our study unveils early-stage enhancements in soil microbial and physicochemical properties during the reclamation of alpine mining areas. The results underscore the beneficial impacts of vegetation restoration on key properties, including soil fertility, pore structure, and bacterial community composition. Special attention is given to assessing the effectiveness of the R_6a treatment and identifying deficiencies in the R_2a treatment. It serves as a reference for addressing the challenges associated with soil fertility and microbial community structure restoration in high-altitude mining areas in Qinghai-Tibet. This holds great significance for soil and water conservation as well as vegetation restoration in alpine mining regions. Furthermore, it supports the sustainable restoration of local ecosystems.

The Correlation between the Gut Microbiota of Endoclita signifer (Lepidoptera, Hepialidae) Larvae and Their Host Preferences

Insects' gut microbiota plays a crucial role in their host selection, adaptation, and plasticity. This study explored the impact of gut bacteria on the adaptation of host selection under different stresses (diverse feeding preferences and no feeding preferences). The seventh instar E. signifer larvae were artificially transferred from the most-selected host E. grandis × E. urophylla (Es) to more preferred hosts, M. apelta (Ma), as well as the non-preferred host, B. papyrifera (Bp). We then obtained the larval gut of three different feeding preference hosts. The gut bacterial DNA was sequenced and analyzed based on 16S rRNA. There were significant differences in the composition of dominant gut bacteria between Es with Ma and Bp, but without significant differences between Ma and Bp. In the process, Burkholderia and Microbacillus with degrading pesticides had significant changes, and Enterococcus with insect gut probiotics also had significant changes. The presence of enterococcus may be one of the main causes of intestinal microbiota changes before and after host transfer. Notably, when the feeding of E. signifer changes, the complex connections that exist between gut bacteria also change. Additionally, there was a negative correlation between the feeding preferences of E. signifer and the metabolic functions of their gut bacteria. This study provided a theoretical basis for the prediction and use of gut bacteria to interfere with the feeding of E. signifer.

Bacterial Microbiome Differences between the Roots of Diseased and Healthy Chinese Hickory (Carya cathayensis) Trees

Carya cathayensis is an important economic nut tree that is endemic to eastern China. As such, outbreaks of root rot disease in C. cathayensis result in reduced yields and serious economic losses. Moreover, while soil bacterial communities play a crucial role in plant health and are associated with plant disease outbreaks, their diversity and composition in C. cathayensis are not clearly understood. In this study, Proteobacteria, Acidobacteria, and Actinobacteria were found to be the most dominant bacterial communities (accounting for approximately 80.32% of the total) in the root tissue, rhizosphere soil, and bulk soil of healthy C. cathayensis specimens. Further analysis revealed the abundance of genera belonging to Proteobacteria, namely, Acidibacter, Bradyrhizobium, Paraburkholderia, Sphaerotilus, and Steroidobacter, was higher in the root tissues of healthy C. cathayensis specimens than in those of diseased and dead trees. In addition, the abundance of four genera belonging to Actinobacteria, namely, Actinoallomurus, Actinomadura, Actinocrinis, and Gaiella, was significantly higher in the root tissues of healthy C. cathayensis specimens than in those of diseased and dead trees. Altogether, these results suggest that disruption in the balance of these bacterial communities may be associated with the development of root rot in C. cathayensis, and further, our study provides theoretical guidance for the isolation and control of pathogens and diseases related to this important tree species.

Community ecological study on the reduction of soil antimony bioavailability by SRB-based remediation technologies

Sulfate-reducing bacteria (SRB) were effective in stabilizing Sb. However, the influence of electron donors and acceptors during SRB remediation, as well as the ecological principles involved, remained unclear. In this study, Desulfovibrio desulfuricans ATCC 7757 was utilized to stabilize soil Sb within microcosm. Humic acid (HA) or sodium sulfate (Na2SO4) were employed to enhance SRB capacity. The SRB+HA treatment exhibited the highest Sb stabilization rate, achieving 58.40%. Bacterial community analysis revealed that SRB altered soil bacterial diversity, community composition, and assembly processes, with homogeneous selection as the predominant assembly processes. When HA and Na2SO4 significantly modified the stimulated microbial community succession trajectories, shaped the taxonomic composition and interactions of the bacterial community, they showed converse effect in shaping bacterial community which were both helpful for promoting dissimilatory sulfate reduction. Na2SO4 facilitated SRB-mediated anaerobic reduction and promoted interactions between SRB and bacteria involved in nitrogen and sulfur cycling. The HA stimulated electron generation and storage, and enhanced the interactions between SRB and bacteria possessing heavy metal tolerance or carbohydrate degradation capabilities.

Rhizosphere Microbiome and Phenolic Acid Exudation of the Healthy and Diseased American Ginseng Were Modulated by the Cropping History

The infection of soil-borne diseases has the potential to modify root exudation and the rhizosphere microbiome. However, the extent to which these modifications occur in various monocropping histories remains inadequately explored. This study sampled healthy and diseased American ginseng (Panax quinquefolius L.) plants under 1-4 years of monocropping and analyzed the phenolic acids composition by HPLC, microbiome structure by high-throughput sequencing technique, and the abundance of pathogens by quantitative PCR. First, the fungal pathogens of Fusarium solani and Ilyonectria destructans in the rhizosphere soil were more abundant in the diseased plants than the healthy plants. The healthy American ginseng plants exudated more phenolic acid, especially p-coumaric acid, compared to the diseased plants after 1-2 years of monocropping, while this difference gradually diminished with the increase in monocropping years. The pathogen abundance was influenced by the exudation of phenolic acids, e.g., total phenolic acids (r = -0.455), p-coumaric acid (r = -0.465), and salicylic acid (r = -0.417), and the further in vitro test confirmed that increased concentration of p-coumaric acid inhibited the mycelial growth of the isolated pathogens for root rot. The healthy plants had a higher diversity of rhizosphere bacterial and fungal microbiome than the diseased plants only after a long period of monocropping. Our study has revealed that the cropping history of American ginseng has altered the effect of pathogens infection on rhizosphere microbiota and root exudation.

Plant and soil-associated microbiome dynamics determine the fate of bacterial wilt pathogen Ralstonia solanacearum

MAIN CONCLUSION

Plant and the soil-associated microbiome is important for imparting bacterial wilt disease tolerance in plants. Plants are versatile organisms that are endowed with the capacity to withstand various biotic and abiotic stresses despite having no locomotory abilities. Being the agent for bacterial wilt (BW) disease, Ralstonia solanacearum (RS) colonizes the xylem vessels and limits the water supply to various plant parts, thereby causing wilting. The havoc caused by RS leads to heavy losses in crop productivity around the world, for which a sustainable mitigation strategy is urgently needed. As several factors can influence plant-microbe interactions, comprehensive understanding of plant and soil-associated microbiome under the influence of RS and various environmental/edaphic conditions is important to control this pathogen. This review mainly focuses on microbiome dynamics associated with BW disease and also provide update on microbial/non-microbial approaches employed to control BW disease in crop plants.

Dynamics of rhizosphere bacterial communities and soil physiochemical properties in response to consecutive ratooning of sugarcane

Ratooning in sugarcane often leads to soil problems such as degradation, acidification, and soil-borne diseases that negatively impact agriculture output and sustainability. Understanding the alteration in bacterial communities, activities, and their diversity connected to the plant and soil under consecutive ratooning still needs to be clarified. To address this gap, multidisciplinary approaches such as Illumina sequencing and measurement of soil nutrients and enzymes were used in this study to analyze soil samples in a field with three consecutive ratooning sugarcane crops. The results revealed a decline in crop yield and significant changes (P < 0.05) in soil nutrients and bacterial diversity. Ratooning resulted in an acidic environment that potentially affected soil nutrients and enzyme activity responsible for the cycling of carbon, nitrogen, and phosphorous. Non-metric dimensional scaling (NMDS) confirmed the effect of ratooning on soil attributes. Moreover, a positive correlation between soil physiochemical properties and soil enzymes was observed. Alpha diversity indices indicated greater bacterial diversity in ratooning sugarcane. Bacterial diversity varied throughout the ratooning crop, and significant (P < 0.05) changes in the relative abundance of specific phyla were observed. For example, the relative abundance of Proteobacteria was decreased, and Acidobacteria was increased. Furthermore, the relative abundance of bacterial phyla was strongly correlated with soil attributes (enzymes and nutrients). Additionally, ratooning results in the depletion or enrichment of important agriculture microbial genera such as Sphingomonas, Burkholderia, and Acidothermus (P < 0.05), respectively. In conclusion, ratooning led to soil acidification, decreased fertility, and altered microbial structure and activity. Thus, restraining soil acidity by means of liming or biofertilizers to maintain soil nutrients, enzymatic activities, and microbial structure could benefit plants and soil to help create a long-term eco-friendly sugarcane cropping system.

Variation and stability of rhizosphere bacterial communities of Cucumis crops in association with root-knot nematodes infestation

Introduction

Root-knot nematodes (RKN) disease is a devastating disease in Cucumis crops production. Existing studies have shown that resistant and susceptible crops are enriched with different rhizosphere microorganisms, and microorganisms enriched in resistant crops can antagonize pathogenic bacteria. However, the characteristics of rhizosphere microbial communities of Cucumis crops after RKN infestation remain largely unknown.

Methods

In this study, we compared the changes in rhizosphere bacterial communities between highly RKN-resistant Cucumis metuliferus (cm3) and highly RKN-susceptible Cucumis sativus (cuc) after RKN infection through a pot experiment.

Results

The results showed that the strongest response of rhizosphere bacterial communities of Cucumis crops to RKN infestation occurred during early growth, as evidenced by changes in species diversity and community composition. However, the more stable structure of the rhizosphere bacterial community in cm3 was reflected in less changes in species diversity and community composition after RKN infestation, forming a more complex and positively co-occurrence network than cuc. Moreover, we observed that both cm3 and cuc recruited bacteria after RKN infestation, but the bacteria enriched in cm3 were more abundant including beneficial bacteria Acidobacteria, Nocardioidaceae and Sphingomonadales. In addition, the cuc was enriched with beneficial bacteria Actinobacteria, Bacilli and Cyanobacteria. We also found that more antagonistic bacteria than cuc were screened in cm3 after RKN infestation and most of them were Pseudomonas (Proteobacteria, Pseudomonadaceae), and Proteobacteria were also enriched in cm3 after RKN infestation. We hypothesized that the cooperation between Pseudomonas and the beneficial bacteria in cm3 could inhibit the infestation of RKN.

Discussion

Thus, our results provide valuable insights into the role of rhizosphere bacterial communities on RKN diseases of Cucumis crops, and further studies are needed to clarify the bacterial communities that suppress RKN in Cucumis crops rhizosphere.

Tobacco microbial screening and application in improving the quality of tobacco in different physical states

The first-cured tobacco contains macromolecular substances with negative impacts on tobacco products quality, and must be aged and fermented to mitigate their effects on the tobacco products quality. However, the natural fermentation takes a longer cycle with large coverage area and low economic efficiency. Microbial fermentation is a method to improve tobacco quality. The change of chemical composition of tobacco during the fermentation is often correlated with shapes of tobacco. This study aimed to investigate the effects of tobacco microorganisms on the quality of different shapes of tobacco. Specifically, Bacillus subtilis B1 and Cytobacillus oceanisediminis C4 with high protease, amylase, and cellulase were isolated from the first-cured tobacco, followed by using them for solid-state fermentation of tobacco powder (TP) and tobacco leaves (TL). Results showed that strains B1 and C4 could significantly improve the sensory quality of TP, enabling it to outperform TL in overall texture and skeleton of tobacco products during cigarette smoking. Compared with the control, microbial fermentation could increase reducing sugar; regulate protein, starch, and cellulose, reduce nicotine, improve total aroma substances, and enable the surface of fermented TP and TL to be more loose, wrinkled, and porous. Microbial community analysis indicated that strains B1 and C4 could change the native structure of microbial community in TP and TL. LEfSe analysis revealed that the potential key biomarkers in TP and TL were Bacilli, Pseudonocardia, Pantoea, and Jeotgalicoccus, which may have cooperative effects with other microbial taxa in improving tobacco quality. This study provides a theoretical basis for improving tobacco fermentation process for better cigarettes quality.

Different Response Mechanisms of Rhizosphere Microbial Communities in Two Species of Amorphophallus to Pectobacterium carotovorum subsp. carotovorum Infection

Soft rot is a widespread, catastrophic disease caused by Pectobacterium carotovorum subsp. carotovorum (Pcc) that severely damages the production of Amorphophallus spp. This study evaluated the rhizosphere bacterial and fungal communities in Pcc-infected and uninfected plants of two species of Amorphophallus, A. muelleri and A. konjac. Principal component analysis showed that the samples formed different clusters according to the Pcc infection status, indicating that Pcc infection can cause a large number of changes in the bacterial and fungal communities in the Amorphophallus spp. rhizosphere soil. However, the response mechanisms of A. muelleri and A. konjac are different. There was little difference in the overall microbial species composition among the four treatments, but the relative abundances of core microbiome members were significantly different. The relative abundances of Actinobacteria, Chloroflexi, Acidobacteria, Firmicutes, Bacillus, and Lysobacter were lower in infected A. konjac plants than in healthy plants; in contrast, those of infected A. muelleri plants were higher than those in healthy plants. For fungi, the relative abundances of Ascomycota and Fusarium in the rhizosphere of infected A. konjac plants were significantly higher than those of healthy plants, but those of infected A. muelleri plants were lower than those of healthy plants. The relative abundance of beneficial Penicillium fungi was lower in infected A. konjac plants than in healthy plants, and that of infected A. muelleri plants was higher than that of healthy plants. These findings can provide theoretical references for further functional research and utilization of Amorphophallus spp. rhizosphere microbial communities in the future.

Different changes of bacterial diversity and soil metabolites in tea plants-legume intercropping systems

As an essential agroforestry, intercropping legumes can improve the physical, chemical, and biological fertility of the soil in tea plantations. However, the effects of intercropping different legume species on soil properties, bacterial communities, and metabolites remain elusive. In this study, the 0-20 cm and 20-40 cm soils of three planting patterns (T1: tea plants/mung bean intercropping, T2: tea plants/adzuki bean intercropping, T3: tea plants/mung bean and adzuki bean intercropping) were sampled to explore the diversity of the bacterial community and soil metabolites. The findings showed that, as compared to monocropping, intercropping systems had greater concentrations of organic matter (OM) and dissolved organic carbon (DOC). Notably, pH values were significantly lower, and soil nutrients increased in intercropping systems compared with monoculture in 20-40 cm soils, especially in T3. In addition, intercropping resulted in an increased relative abundance of Proteobacteria but a decreased relative abundance of Actinobacteria. 4-methyl-Tetradecane, acetamide, and diethyl carbamic acid were key metabolites mediating the root-microbe interactions, especially in tea plants/adzuki intercropping and tea plants/mung bean, adzuki bean mixed intercropping soils. Co-occurrence network analysis showed that arabinofuranose, abundant in tea plants and adzuki bean intercropping soils, showed the most remarkable correlation with the soil bacterial taxa. Our findings demonstrate that intercropping with adzuki beans is better at enhancing the diversity of soil bacteria and soil metabolites and is more weed-suppressing than other tea plants/legume intercropping systems.

Rhizosphere Microbial Community and Metabolites of Susceptible and Resistant Tobacco Cultivars to Bacterial Wilt

Soil-borne diseases are closely related to rhizosphere microecosystem. While, plant species and genotypes are important factors affected rhizosphere microecosystem. In this study, the rhizosphere soil microbial community and metabolites of susceptible and resistant tobacco cultivars were investigated. The results showed that there were significant differences in the rhizosphere microbial community and metabolites between susceptible cultivar Yunyan87 and resistant cultivar Fandi3. Furthermore, the rhizosphere soil of Fandi3 showed a higher microbial diversity than that of Yunyan87. The abundance of R. solanacearum was much higher in the rhizosphere soil of Yunyan87 than in the rhizosphere soil of Fandi3, resulting in a higher disease incidence and index. While the abundance of beneficial bacteria in the rhizosphere soil of Fandi3 were higher than that of Yunyan87. Additionally, there were significant differences in metabolites between Yunyan87 and Fandi3 cultivars, and 4-hydroxybenzaldehyde, 3-hydroxy-4-methoxybenzoic acid, vamillic aldehyde, benzoic acid, 4-hydroxybenzyl alcohol, p-hydroxybenzoic acid and phthalic acid were notably high in Yunyan87. Redundancy analysis (RDA) indicated that the rhizosphere microbial community of Fandi3 and Yunyan87 were highly correlated with various environmental factors and metabolites. Overall, susceptible and resistant tobacco cultivars had different impact on rhizosphere microbial community and metabolites. The results expand our understanding of the roles of tobacco cultivars in plant-micro-ecosystem interactions, and provide a basis for the control of tobacco bacterial wilt.

Effects of different soil moisture on the growth, quality, and root rot disease of organic Panax notoginseng cultivated under pine forests

The under-forest economy in the agroforestry system can improve land use efficiency, protect ecological environment, and promote arable land sustainable development. However, the effects of soil moisture in the forest and irrigation strategies on the healthy growth of intercropping crops are still incomplete. Here, considering the organic Panax notoginseng cultivated under pine forests (PPF) as the research object, we explored the effects of different soil moisture on the physiological state, yield, quality and disease occurrence of PPF. Our results suggested that 80-85% and 95-100% field capacity (FC) treatments were more conducive to increased photosynthetic rate and biomass accumulation of PPF, but 50-55% and 65-70% FC treatments were more conducive to the accumulation of saponins in PPF leaves. Notably, the root rot index of PPF was highest under 95-100% FC (19.51) treatment, significantly higher than that under 65-70% FC (8.44) and 80-85% FC (10.21) treatments. Further, the rhizosphere microorganisms of PPF under different soil moisture treatments were sequenced, and the sequencing data analysis revealed that high soil moisture (95-100% FC) could destroy the microbial diversity balance and cause the accumulation of pathogens (Fusarium oxysporum and Ilyonectria radicicola), leading to a high incidence of root rot. The incidence of PPF root rot was negatively correlated with rhizosphere microbial diversity. Overall, our results highlight that the quantitative irrigation (80-85% FC) is conducive to maintaining the balance between yield, saponin content and disease occurrence of PPF, providing a practical basis for PPF irrigation strategy and promoting the sustainable development of PPF agroforestry system.

The use of selenium for controlling plant fungal diseases and insect pests

The selenium (Se) applications in biomedicine, agriculture, and environmental health have become great research interest in recent decades. As an essential nutrient for humans and animals, beneficial effects of Se on human health have been well documented. Although Se is not an essential element for plants, it does play important roles in improving plants' resistances to a broad of biotic and abiotic stresses. This review is focused on recent findings from studies on effects and mechanisms of Se on plant fungal diseases and insect pests. Se affects the plant resistance to fungal diseases by preventing the invasion of fungal pathogen through positively affecting plant defense to pathogens; and through negative effects on pathogen by destroying the cell membrane and cellular extensions of pathogen inside plant tissues after invasion; and changing the soil microbial community to safeguard plant cells against invading fungi. Plants, grown under Se enriched soils or treated with Se through foliar and soil applications, can metabolize Se into dimethyl selenide or dimethyl diselenide, which acts as an insect repellent compound to deter foraging and landing pests, thus providing plant mediated resistance to insect pests; moreover, Se can also lead to poisoning to some pests if toxic amounts of Se are fed, resulting in steady pest mortality, lower reproduction rate, negative effects on growth and development, thus shortening the life span of many insect pests. In present manuscript, reports are reviewed on Se-mediated plant resistance to fungal pathogens and insect pests. The future perspective of Se is also discussed on preventing the disease and pest control to protect plants from economic injuries and damages.

The Endophytic Root Microbiome Is Different in Healthy and Ralstonia solanacearum-Infected Plants and Is Regulated by a Consortium Containing Beneficial Endophytic Bacteria

Plant bacterial wilt disease caused by Ralstonia solanacearum leads to huge economic losses worldwide. Endophytes play vital roles in promoting plant growth and health. It is hypothesized that the endophytic root microbiome and network structure are different in healthy and diseased plants. Here, the endophytic root microbiomes and network structures of healthy and diseased tobacco plants were investigated. Composition and network structures of endophytic root microbiomes were distinct between healthy and diseased plants. Healthy plants were enriched with more beneficial bacteria and bacteria with antagonistic activity against R. solanacearum. R. solanacearum was most abundant in diseased plants. Microbial networks in diseased plants had fewer modules and edges, lower connectivity, and fewer keystone microorganisms than those in healthy plants. Almost half of the nodes were unique in the two networks. Ralstonia was identified as a key microorganism of the diseased-plant network. In healthy plants, abundant bacteria and biomarkers (Pseudomonas and Streptomyces) and keystone microorganisms (Bacillus, Lysobacter, and Paenibacillus) were plant-beneficial bacteria and showed antibacterial and plant growth-promoting activities. The endophytic strain Bacillus velezensis E9 produced bacillaene to inhibit R. solanacearum. Consortia containing keystone microorganisms and beneficial endophytic bacteria significantly regulated the endophytic microbiome and attenuated bacterial wilt by inducing systemic resistance and producing antibiotic. Overall, the endophytic root microbiome and network structure in diseased plants were different from those in healthy plants. The endophytic root microbiome of diseased plants had low abundances of beneficial bacteria and an unstable network and lacked beneficial keystone microorganisms, which favored infection. Synthetic microbial consortia were effective measures for preventing R. solanacearum infection. IMPORTANCE Bacterial wilt disease causes heavy yield losses in many crops. Endophytic microbiomes play important roles in control of plant diseases. However, the role of the endophytic root microbiome in controlling bacterial wilt disease is poorly understood. Here, differences in endophytic root microbiomes and network structures between healthy and diseased tobacco plants are reported. A synthetic microbial consortium containing beneficial endophytic bacteria was used to regulate the endophytic microbiome and attenuate bacterial wilt disease. The results could be generally used to guide control of bacterial wilt disease.

Construction, Characterization, and Application of an Ammonium Transporter (AmtB) Deletion Mutant of the Nitrogen-Fixing Bacterium Kosakonia radicincitans GXGL-4A in Cucumis sativus L. Seedlings

Nitrogen is an important factor affecting crop yield, but excessive use of chemical nitrogen fertilizer has caused decline in nitrogen utilization and soil and water pollution. Reducing the utilization of chemical nitrogen fertilizers by biological nitrogen fixation (BNF) is feasible for green production of crops. However, there are few reports on how to have more ammonium produced by nitrogen-fixing bacteria (NFB) flow outside the cell. In the present study, the amtB gene encoding an ammonium transporter (AmtB) in the genome of NFB strain Kosakonia radicincitans GXGL-4A was deleted and the △amtB mutant was characterized. The results showed that deletion of the amtB gene had no influence on the growth of bacterial cells. The extracellular ammonium nitrogen (NH₄⁺) content of the △amtB mutant under nitrogen-free culture conditions was significantly higher than that of the wild-type strain GXGL-4A (WT-GXGL-4A), suggesting disruption of NH₄⁺ transport. Meanwhile, the plant growth-promoting effect in cucumber seedlings was visualized after fertilization using cells of the △amtB mutant. NFB fertilization continuously increased the cucumber rhizosphere soil pH. The nitrate nitrogen (NO₃^-) content in soil in the △amtB treatment group was significantly higher than that in the WT-GXGL-4A treatment group in the short term but there was no difference in soil NH₄⁺ contents between groups. Soil enzymatic activities varied during a 45-day assessment period, indicating that △amtB fertilization influenced soil nitrogen cycling in the cucumber rhizosphere. The results will provide a solid foundation for developing the NFB GXGL-4A into an efficient biofertilizer agent.

Pseudomonas sivasensis 2RO45 inoculation alters the taxonomic structure and functioning of the canola rhizosphere microbial community

Inoculation with plant growth-promoting rhizobacteria (PGPR) is an eco-friendly sustainable strategy for improving crop productivity in diverse environments under different conditions. Our earlier study demonstrated that Pseudomonas sivasensis 2RO45 significantly stimulated canola (Brassica napus L. var. napus) growth. The aim of the present study was to investigate the structural and functional dynamics in the canola rhizosphere microbiome after inoculation with PGPR P. sivasensis 2RO45. The results based on alpha diversity metrics showed that P. sivasensis 2RO45 did not significantly alter the diversity of the native soil microbiota. However, the introduced strain modified the taxonomic structure of microbial communities, increasing the abundance of plant beneficial microorganisms, e.g., bacteria affiliated with families Comamonadaceae, Vicinamibacteraceae, genus Streptomyces, and fungi assigned to Nectriaceae, Didymellaceae, Exophiala, Cyphellophora vermispora, and Mortierella minutissima. The analysis of community level physiological profiling (CLPP) revealed that microbial communities in the P. sivasensis 2RO45 treated canola rhizospheres were more metabolically active than those in the non-treated canola rhizosphere. Four carbon sources (phenols, polymers, carboxylic acids, and amino acids) were better metabolized by the microbial communities from the rhizosphere of plants inoculated with the P. sivasensis 2RO45 than non-inoculated canola rhizospheres. Based on the community-level physiological profiles, the functional diversity of the rhizosphere microbiome was altered by the P. sivasensis 2RO45 inoculation. Substrate utilization Shannon diversity (H) index and evenness (E) index were significantly increased in the treated canola plants. The study provides new insight into PGPR-canola interactions for sustainable agriculture development.

Biogeochemical behavior and pollution control of arsenic in mining areas: A review

Arsenic (As) is one of the most toxic metalloids that possess many forms. As is constantly migrating from abandoned mining area to the surrounding environment in both oxidation and reducing conditions, threatening human health and ecological safety. The biogeochemical reaction of As included oxidation, reduction, methylation, and demethylation, which is closely associated with microbial metabolisms. The study of the geochemical behavior of arsenic in mining areas and the microbial remediation of arsenic pollution have great potential and are hot spots for the prevention and remediation of arsenic pollution. In this study, we review the distribution and migration of arsenic in the mining area, focus on the geochemical cycle of arsenic under the action of microorganisms, and summarize the factors influencing the biogeochemical cycle of arsenic, and strategies for arsenic pollution in mining areas are also discussed. Finally, the problems of the risk control strategies and the future development direction are prospected.

Microbiome analysis and biocontrol bacteria isolation from rhizosphere soils associated with different sugarcane root rot severity

To explore the causal pathogen and the correlated rhizosphere soil microecology of sugarcane root rot, we sampled the sugarcane root materials displaying different disease severity, and the corresponding rhizosphere soil, for systematic root phenotype and microbial population analyses. We found that with increased level of disease severity reflected by above-ground parts of sugarcane, the total root length, total root surface area and total volume were significantly reduced, accompanied with changes in the microbial population diversity and structure in rhizosphere soil. Fungal community richness was significantly lower in the rhizosphere soil samples from mildly diseased plant than that from either healthy plant, or severely diseased plant. Particularly, we noticed that a peculiar decrease of potential pathogenic fungi in rhizosphere soil, including genera Fusarium, Talaromyces and Neocosmospora, with increased level of disease severity. As for bacterial community, Firmicutes was found to be of the highest level, while Acidobacteria and Chloroflexi of the lowest level, in rhizosphere soil from healthy plant compared to that from diseased plant of different severity. FUNGuild prediction showed that the proportion of saprophytic fungi was higher in the rhizosphere soil of healthy plants, while the proportion of pathogenic fungi was higher in the rhizosphere soil of diseased plants. By co-occurrence network analysis we demonstrated the Bacillus and Burkholderia were in a strong interaction with Fusarium pathogen(s). Consistently, the biocontrol and/or growth-promoting bacteria isolated from the rhizosphere soil were mostly (6 out of 7) belonging to Bacillus and Burkholderia species. By confrontation culture and pot experiments, we verified the biocontrol and/or growth-promoting property of the isolated bacterial strains. Overall, we demonstrated a clear correlation between sugarcane root rot severity and rhizosphere soil microbiome composition and function, and identified several promising biocontrol bacteria strains with strong disease suppression effect and growth-promoting properties.

Metagenomic Analysis of Garden Soil-Derived Microbial Consortia and Unveiling Their Metabolic Potential in Mitigating Toxic Hexavalent Chromium

Soil microbial communities connect to the functional environment and play an important role in the biogeochemical cycle and waste degradation. The current study evaluated the distribution of the core microbial population of garden soil in the Varanasi region of Uttar Pradesh, India and their metabolic potential for mitigating toxic hexavalent chromium from wastewater. Metagenomes contain 0.2 million reads and 56.5% GC content. The metagenomic analysis provided insight into the relative abundance of soil microbial communities and revealed the domination of around 200 bacterial species belonging to different phyla and four archaeal phyla. The top 10 abundant genera in garden soil were Gemmata, Planctomyces, Steroidobacter, Pirellula, Pedomicrobium, Rhodoplanes, Nitrospira Mycobacterium, Pseudonocardia, and Acinetobacter. In this study, Gemmata was dominating bacterial genera. Euryarchaeota, Parvarchaeota, and Crenarchaeota archaeal species were present with low abundance in soil samples. X-ray photoelectric spectroscopy (XPS) analysis indicates the presence of carbon, nitrogen-oxygen, calcium, phosphorous, and silica in the soil. Soil-derived bacterial consortia showed high hexavalent chromium [Cr (VI)] removal efficiency (99.37%). The bacterial consortia isolated from garden soil had an important role in the hexavalent chromium bioremediation, and thus, this study could be beneficial for the design of a heavy-metal treatment system.

Differentially enriched fungal communities in root rot resistant and susceptible varieties of tobacco (Nicotiana tabacum L.) under continuous monoculture cropping

Root rot is a major disease of tobacco that causes crop losses of up to 15-20% of global tobacco production. The present study aimed to compare the fungal communities, and physicochemical properties of rhizosphere soil of root rot resistant (Yunyan 87; Y) and susceptible (Honghua Dajinyuan; H) tobacco varieties. Four treatments of each variety under continuous monocropping cultures included: control groups (HT0 and YT0); 2 years of continuous cropping (HT2 and YT2); 4 years of continuous cropping (HT4 and YT4); and 8 years of continuous cropping (YT8 and HT8). The soil physicochemical properties including available nitrogen (AN), available phosphorus (AP), available potassium (AK), and organic matter (OM) were increased (p < 0.05) from HT0 to HT8, whereas the resistant variety (Y) showed an inconsistent trend from YT0 to YT8. The pH was decreased (p < 0.05) from HT0 to HT8 and YT0 to YT8. Further, the disease incidence rate and disease index of the H variety also increased (p < 0.05) from HT0 to HT8. Alpha diversity analysis revealed that susceptible variety had higher fungal diversity from HT0 to HT8, while resistant variety exhibited lower diversity from YT0 to YT8. Ascomycota and Mortierellomycota were the dominant phyla in H and Y. Ascomycota abundance was increased (p < 0.05), whereas Mortierellomycota was decreased (p < 0.05) for continuous cropping years in H and Y. Penicillium, Fusarium, and Chrysosporium were the top three abundant genera in both varieties. The relative abundance of Penicillium spp. was increased (p < 0.05) in Y, whereas decreased (p < 0.05) in H variety. Specifically, Chrysosporium spp. was increased (p < 0.05) whereas Fusarium spp. was decreased (p < 0.05) in YT2. Redundancy analysis (RDA) revealed that fungal communities in H and Y rhizospheres were influenced by pH and carbon content, respectively. The top three highly enriched (p < 0.05) pathways in both varieties were fatty acid elongation, fatty acid β-oxidation I, and glyoxylate cycle. Our study concluded that resistant variety exhibited lower fungal diversity and functionally enriched metabolic pathways than susceptible variety that might be the result of molecular breeding practices, however, the relative abundance of Penicillium spp. were increased in resistant variety under long-term monoculture cropping.

The host niches of soybean rather than genetic modification or glyphosate application drive the assembly of root-associated microbial communities

Plant roots significantly influence soil microbial diversity, and soil microorganisms play significant roles in both natural and agricultural ecosystems. Although the genetically modified (GM) crops with enhanced insect and herbicide resistance are thought to have unmatched yield and stress resistance advantages, thorough and in-depth case studies still need to be carried out in a real-world setting due to the potential effects of GM plants on soil microbial communities. In this study, three treatments were used: a recipient soybean variety Jack, a triple transgenic soybean line JD321, and the glyphosate-treated JD321 (JD321G). Three sampling stages (flowering, seed filling and maturing), as well as three host niches of soybean rhizosphere [intact roots (RT), rhizospheric soil (RS) and surrounding soil (SS)] were established. In comparison to Jack, the rhizospheric soil of JD321G had higher urease activity and lower nitrite reductase at the flowering stage. Different treatments and different sampling stages existed no significant effects on the compositions of microbial communities at different taxonomic levels. However, at the genus level, the relative abundance of three plant growth-promoting fungal genera (i.e. Mortierella, Chaetomium and Pseudombrophila) increased while endophytic bacteria Chryseobacterium and pathogenic bacteria Streptomyces decreased from the inside to the outside of the roots (i.e. RT → RS → SS). Moreover, two bacterial genera, Bradyrhizobium and Ensifer were more abundant in RT than in RS and SS, as well as three species, Agrobacterium radiobacter, Ensifer fredii and Ensifer meliloti, which are closely related to nitrogen-fixation. Furthermore, five clusters of orthologous groups (COGs) associated to nitrogen-fixation genes were higher in RT than in RS, whereas only one COG annotated as dinitrogenase iron-molybdenum cofactor biosynthesis protein was lower. Overall, the results imply that the rhizosphere host niches throughout the soil-plant continuum largely control the composition and function of the root-associated microbiome of triple transgenic soybean.

Bacterial Community Structure and Function Shift in Rhizosphere Soil of Tobacco Plants Infected by Meloidogyne incognita

Root-knot nematode disease is a widespread and catastrophic disease of tobacco. However, little is known about the relationship between rhizosphere bacterial community and root-knot nematode disease. This study used 16S rRNA gene sequencing and PICRUSt to assess bacterial community structure and function changes in rhizosphere soil from Meloidogyne incognita-infected tobacco plants. We studied the rhizosphere bacterial community structure of M. incognita-infected and uninfected tobacco plants through a paired comparison design in two regions of tobacco planting area, Yuxi and Jiuxiang of Yunnan Province, southwest China. According to the findings, M. incognita infection can alter the bacterial population in the soil. Uninfested soil has more operational taxonomic unit numbers and richness than infested soil. Principal Coordinate Analysis revealed clear separations between bacterial communities from infested and uninfested soil, indicating that different infection conditions resulted in significantly different bacterial community structures in soils. Firmicutes was prevalent in infested soil, but Chloroflexi and Acidobacteria were prevalent in uninfested soil. Sphingomonas, Streptomyces, and Bradyrhizobium were the dominant bacteria genera, and their abundance were higher in infested soil. By PICRUSt analysis, some metabolism-related functions and signal transduction functions of the rhizosphere bacterial community in the M. incognita infection-tobacco plants had a higher relative abundance than those uninfected. As a result, rhizosphere soils from tobacco plants infected with M. incognita showed considerable bacterial community structure and function alterations.

Analysis of rhizosphere bacterial communities of tobacco resistant and non-resistant to bacterial wilt in different regions

Tobacco bacterial wilt has seriously affected tobacco production. Ethyl methanesulfonate (EMS) induced tobacco bacterial wilt resistant mutants are important for the control of tobacco bacterial wilt. High-throughput sequencing technology was used to study the rhizosphere bacterial community assemblages of bacterial wilt resistant mutant tobacco rhizosphere soil (namely KS), bacterial wilt susceptible tobacco rhizosphere soil (namely GS) and bulk soil (namely BS) in Xuancheng, Huanxi, Yibin and Luzhou. Alpha analysis showed that the bacterial community diversity and richness of KS and GS in the four regions were not significantly different. However, analysis of intergroup variation in the top 15 bacterial communities in terms of abundance showed that the bacterial communities of KS and GS were significantly different from BS, respectively. In addition, pH, alkali-hydrolysable nitrogen (AN) and soil organic carbon (SOC) were positively correlated with the bacterial community of KS and negatively correlated with GS in the other three regions except Huanxi. Network analysis showed that the three soils in the four regions did not show a consistent pattern of network complexity. PICRUSt functional prediction analysis showed that the COG functions were similar in all samples. All colonies were involved in RNA processing and modification, chromatin structure and dynamics, etc. In conclusion, our experiments showed that rhizosphere bacterial communities of tobacco in different regions have different compositional patterns, which are strongly related to soil factors.

Study of the effect of bacterial-mediated legume plant growth using bacterial strain Serratia marcescens N1.14 X-45

Soil microorganisms play an indispensable role in plant growth and are widely used to promote plant growth. However, poor microbial strains are homogeneous. The heavy application of chemical fertilizers and pesticides to agricultural soil has adversely affected the soil flora, necessitating the regulation of the soil flora to maintain soil health. In this study, X-45, a highly efficient and phosphorus-dissolving strain of the lysogenic bacterium Serratia marcescens N1.14 was isolated from bare rock slope soil samples from Yueyang Avenue, Hunan Province, China. We observed that microbial strain X-45 could release P from the rocks into solution when the sample rocks were used as the only phosphorus source. Furthermore, we observed that the P content in media increased by 3.08 X compared to the control. After applying X-45 as a bacterial fertilizer, the growth of potted Indigofera pseudotinctoria plants significantly increased, the soil physicochemical properties were significantly improved, and the relative abundance of Bradyrhizobium in the soil increased significantly from 1 to 42%. Besides, Bradyrhizobium became the most dominant genus in the soil. The indirect promotion of another beneficial microorganism by X-45 further revealed the intrinsic mechanism by which X-45 exerted its effect on plant promotion and soil improvement. Using this bacteria, the hypothesis of the superposition effect of legume plant promotion was also confirmed.

Specific metabolites drive the deterministic assembly of diseased rhizosphere microbiome through weakening microbial degradation of autotoxin

BACKGROUND

Process and function that underlie the assembly of a rhizosphere microbial community may be strongly linked to the maintenance of plant health. However, their assembly processes and functional changes in the deterioration of soilborne disease remain unclear. Here, we investigated features of rhizosphere microbiomes related to Fusarium wilt disease and assessed their assembly by comparison pair of diseased/healthy sequencing data. The untargeted metabolomics was employed to explore potential community assembly drivers, and shotgun metagenome sequencing was used to reveal the mechanisms of metabolite-mediated process after soil conditioning.

RESULTS

Results showed the deterministic assembly process associated with diseased rhizosphere microbiomes, and this process was significantly correlated to five metabolites (tocopherol acetate, citrulline, galactitol, octadecylglycerol, and behenic acid). Application of the metabolites resulted in a deterministic assembly of microbiome with the high morbidity of watermelon. Furthermore, metabolite conditioning was found to weaken the function of autotoxin degradation undertaken by specific bacterial group (Bradyrhizobium, Streptomyces, Variovorax, Pseudomonas, and Sphingomonas) while promoting the metabolism of small-molecule sugars and acids initiated from another bacterial group (Anaeromyxobacter, Bdellovibrio, Conexibacter, Flavobacterium, and Gemmatimonas). Video Abstract CONCLUSION: These findings strongly suggest that shifts in a metabolite-mediated microbial community assembly process underpin the deterministic establishment of soilborne Fusarium wilt disease and reveal avenues for future research focusing on ameliorating crop loss due to this pathogen.

Impact of arsenic on microbial community structure and their metabolic potential from rice soils of West Bengal, India

Paddy soil is a heterogenous ecosystem that harbours diverse microbial communities critical for maintaining ecosystem sustainability and crop yield. Considering the importance of soil in crop production and recent reports on its contamination with arsenic (As) across the South East Asia, its microbial community composition and biogeochemical functions remained inadequately studied. We have characterized the microbial communities of rice soil from eleven paddy fields of As-contaminated sites from West Bengal (India), through metagenomics and amplicon sequencing. 16S rRNA gene sequencing showed considerable bacterial diversity [over 0.2 million Operational Taxonomic Units (OTUs)] and abundance (upto 1.6 × 10⁷ gene copies/g soil). Existence of a core-microbiome (261 OTUs conserved out of a total 141,172 OTUs) across the samples was noted. Most of the core-microbiome members were also found to represent the abundant taxa of the soil. Statistical analyses suggested that the microbial communities were highly constrained by As, Fe K, N, PO₄^3-, SO₄^2- and organic carbon (OC). Members of Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Planctomycetes and Thaumarchaeota constituted the core-microbiome. Co-occurrence network analysis displayed significant interaction among diverse anaerobic, SO₄^2- and NO₃^- reducing, cellulose and other organic matter or C1 compound utilizing, fermentative and aerobic/facultative anaerobic bacteria and archaea. Correlation analysis suggested that taxa which were positively linked with soil parameters that maintain soil health and productivity (e.g., N, K, PO₄^3- and Fe) were adversely impacted by increasing As concentration. Shotgun metagenomics highlighted major metabolic pathways controlling the C (3-hydroxypropionate bicycle), N (Denitrification, dissimilatory NO₃^- reduction to ammonium), and S (assimilatory SO₄^2- reduction and sulfide oxidation) cycling, As homeostasis (methylation and reduction) and plant growth promotion (polyphosphate hydrolysis and auxin biosynthesis). All these major biogeochemical processes were found to be catalyzed by the members of most abundant/core-community.

The Structure and Function of Microbial Community in Rhizospheric Soil of American Ginseng (Panax quinquefolius L.) Changed with Planting Years

The changes of microbial communities of rhizospheric soil in different ages are speculated to cause soil-borne diseases and replanting problem in American ginseng (Panax quinquefolius L.) cultivation. This study analyzed the physicochemical properties and microbial communities of rhizospheric soil during the planting of American ginseng in the Wendeng area of Weihai, China. The water content and organic matter content of American ginseng rhizospheric soil decreased year by year. A decline in the diversity of bacteria and fungi was observed in the rhizospheric soils planting American ginseng compared with the traditional crop wheat in the control group. During the later planting stage, the abundances of Proteobacteria, Actinobacteria, and Basidiomycota were lower, whereas that of Acidobacteria, Firmicutes, and Mucoromycota were higher. Through the correlation analysis between environmental factors and microbial community, it was found that the content of soil phosphorus was significantly positively correlated with the root rot pathogen Fusarium. The results of functional prediction showed that the decrease of secondary metabolite synthesis of rhizospheric soil bacteria and the increase of plant pathogenic fungi may be the important reasons for the increase of diseases in the later stage of American ginseng planting. This study revealed the evolution of rhizosphere microbial community and function in the process of American ginseng planting, which is valuable for planting management.

Use of Metagenomic Whole Genome Shotgun Sequencing Data in Taxonomic Assignment of Dipterygium glaucum Rhizosphere and Surrounding Bulk Soil Microbiomes, and Their Response to Watering

The metagenomic whole genome shotgun sequencing (mWGS) approach was used to detect signatures of the rhizosphere microbiomes of Dipterygium glaucum and surrounding bulk soil microbiomes, and to detect differential microbial responses due to watering. Preliminary results reflect the reliability of the experiment and the rationality of grouping microbiomes. Based on the abundance of non-redundant genes, bacterial genomes showed the highest level, followed by Archaeal and Eukaryotic genomes, then, the least abundant viruses. Overall results indicate that most members of bacteria have a higher abundance/relative abundance (AB/RA) pattern in the rhizosphere towards plant growth promotion, while members of eukaryota have a higher pattern in bulk soil, most likely acting as pathogens. The results also indicate the contribution of mycorrhiza (genus Rhizophagus) in mediating complex mutualistic associations between soil microbes (either beneficial or harmful) and plant roots. Some of these symbiotic relationships involve microbes of different domains responding differentially to plant root exudates. Among these are included the bacterial genus Burkholderia and eukaryotic genus Trichoderma, which have antagonistic activities against the eukaryotic genus Fusarium. Another example involves Ochrobactrum phage POA1180, its bacterial host and plant roots. One of the major challenges in plant nutrition involves other microbes that manipulate nitrogen levels in the soil. Among these are the microbes that perform contraversal actions of nitrogen fixation (the methanogen Euryarchaeota) and ammonia oxidation (Crenarchaeota). The net nitrogen level in the soil is originally based on the AB/RA of these microbes and partially on the environmental condition. Watering seems to influence the AB/RA of a large number of soil microbes, where drought-sensitive microbes (members of phyla Acidobacteria and Gemmatimonadetes) showed an increased AB/RA pattern after watering, while others (Burkholderia and Trichoderma) seem to be among microbes assisting plants to withstand abiotic stresses. This study sheds light on the efficient use of mWGS in the taxonomic assignment of soil microbes and in their response to watering. It also provides new avenues for improving biotic and abiotic resistance in domestic plant germplasm via the manipulation of soil microbes.

Microbial Consortia: An Engineering Tool to Suppress Clubroot of Chinese Cabbage by Changing the Rhizosphere Bacterial Community Composition

Clubroot disease, caused by Plasmodiophora brassicae, is a serious threat to Chinese cabbage (Brassica rapa subsp. pekinensis) production, which results in extensive yield losses. At present, clubroot control mainly depends upon pesticides, which provoke food-safety concerns, and the application of sole biocontrol agents cannot successfully control the disease. In this study, we investigated the effect of Bacillus cereus BT-23, Lysobacter antibioticus 13-6, and Lysobacter capsici ZST1-2 as sole strains, intra-/inter-genus co-culture, and microbial consortia on clubroot disease, plant growth, and rhizosphere bacterial diversity in a field experiment. The microbial consortia efficiently controlled the incidence of clubroot disease, with a biocontrol effect of about 65.78%, by decreasing the soil acidity and enhancing the yield (17,662.49 kg/acre). The high-throughput sequencing results demonstrated that the phyla Proteobacteria and Bacteroidetes were present in high relative abundance in the rhizosphere soil of the Chinese cabbage. Furthermore, Firmicutes was found as a unique phylum in the rhizosphere soil of CK-H and T1-T7, except for CK-D. The application of microbial consortia recovers the imbalance in indigenous microbial communities. Therefore, we conclude that microbial consortia can reduce the clubroot incidence in Chinese cabbage by decreasing the soil acidity and altering the diversity and structure of rhizosphere bacterial communities. This study highlights the potential of microbial consortia as an engineering tool to control devastating soilborne diseases in commercial crops.

Microvirga roseola sp. nov. and Microvirga lenta sp. nov., isolated from Taklamakan Desert soil

Two Gram-negative, rod-shaped, non-spore-forming bacteria, designated SM9T and SM2T, were isolated from Taklamakan Desert soil samples. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strains SM9T and SM2T had the highest sequence similarity to the type strains Microvirga indica BCRC 80972T and Microvirga soli NBRC 112417T with similarity values of 98.2 and 97.7 %, respectively, and Microvirga was among the predominant genera in the desert soil. The draft genomes of these two strains were 4.56 Mbp (SM9T) and 5.08 Mbp (SM2T) long with 65.1 mol% (SM9T) and 63.5 mol% (SM2T) G+C content. To adapt to the desert environment, these two strains possessed pathways for the synthesis of stress metabolite trehalose. The major fatty acids (>5 %) included C18 : 1 ω9c in SM2T, but C16 : 0, C18 : 0 and C19 : 0 cyclo ω8c in SM9T, while the major menaquinone was ubiquinone 10 in both strains. The major polar lipids of SM9T and SM2T were phosphatidylglycerol, phosphatidylethanolamine and phospholipid. The average nucleotide identity and digital DNA–DNA hybridization results further indicated that strains SM9T and SM2T were distinguished from phylogenetically related species and represented two novel species within the genus Microvirga , for which the names Microvirga roseola sp. nov. (type strain SM2T=KCTC 72792T=CGMCC 1.17776T) and Microvirga lenta sp. nov. (type strain SM9T=KCTC 82729T=CCTCC AB 2021131T) are proposed.

Effect of Bacterial Wilt on Fungal Community Composition in Rhizosphere Soil of Tobaccos in Tropical Yunnan

Bacterial wilt, which is a major soil-borne disease with widespread occurrence, poses a severe danger in the field of tobacco production. However, there is very limited knowledge on bacterial wilt-induced microecological changes in the tobacco root system and on the interaction between Ralstonia solanacearum and fungal communities in the rhizosphere soil. Thus, in this study, changes in fungal communities in the rhizosphere soil of tobaccos with bacterial wilt were studied by 18S rRNA gene sequencing. The community composition of fungi in bacterial wilt-infected soil and healthy soil in two tobacco areas (Gengma and Boshang, Lincang City, Yunnan Province, China) was studied through the paired comparison method in July 2019. The results showed that there were significant differences in fungal community composition between the rhizosphere soil of diseased plants and healthy plants. The changes in the composition and diversity of fungal communities in the rhizosphere soil of tobaccos are vital characteristics of tobaccos with bacterial wilt, and the imbalance in the rhizosphere microecosystem of tobacco plants may further aggravate the disease.

Evaluation of nutrient characteristics and bacterial community in agricultural soil groups for sustainable land management

The soil bacterial community is critical for understanding biological processes in soils and is used for agricultural soil management. The understanding of microorganisms and ecology in different soil groups classified based on soil properties (e.g., minerals, soil texture, location, nitrogen, phosphorus, organic carbon and pH, among others), is limited. To suggest soil management strategies using bacterial data, we classified soils into four groups based on physical-chemical characteristics and elucidated their relationships with soil nutrient characteristics and the bacterial community in agricultural fields in Saraburi Province, Thailand. Results show that soil groups with high bacterial diversity had positive correlations with total Kjeldahl nitrogen and available phosphorus but were negatively affected by total organic carbon and pH levels. Dominant bacterial genera included Lactobacillus, Phascolarctobacterium, Prevotella, Clostridium, Gaiellales and Blautia. Significant key biomarkers were found (p < 0.05). Nutrient-rich soil groups (high available P, acidic pH) were found with genus Agromyces, while low nutrient soil groups (low available P, basic pH) were found with Hydrogenispora, Ignavibacterium and Bauldia. Based on co-occurrence networks, organic degrading bacteria functioned with other bacteria at high degrees of interconnections, suggesting organic amendment, biostimulation and biodegradation using nutrient-rich organic substrates could be used for agricultural soil improvements.

The Cropping Obstacle of Garlic Was Associated With Changes in Soil Physicochemical Properties, Enzymatic Activities and Bacterial and Fungal Communities

Aims

In garlic cultivation, long-time monoculture has resulted in continuous-cropping obstacles. However, the cause has not been studied to date.

Methods

We analyzed soils from garlic fields in Pengzhou, China, to determine continuous-cropping obstacle related changes in soil physicochemical properties and enzyme activities, and in the diversity and composition of bacterial and fungal communities. Furthermore, we examined the relationships between soil properties and the bacterial and fungal communities.

Results

The soil pH and the soil catalase, urease, invertase, and polyphenol oxidase activities were lower in the cropping obstacle soil than in the healthy control soil. The richness and diversity of the bacteria were lower in the cropping obstacle soil than in the control. The bacterial and fungal communities in the cropping obstacle soil were clearly different from those in the control soil. The differences in bacterial communities between the cropping obstacle soil and the control soil were associated with differences in pH and available potassium content. The taxa with higher relative abundances in the cropping obstacle soils included potential plant pathogens and the taxa with lower relative abundances included potential plant growth promoters.

Conclusion

The enrichment of plant pathogens and the depletion of plant growth promoting fungi may have contributed to the poor growth of garlic in the cropping obstacle soil. The enzyme activity and microbial community differences were associated with acidification that was likely an important factor in the deterioration of the soil ecological environment and the garlic cropping obstacle. The results provide information to guide agricultural practices in cultivating garlic.

Plant growth-promoting and antibacterial activities of cultivable bacteria alive in tobacco field against Ralstonia solanacearum

Bacterial wilt disease caused by Ralstonia solanacearum leads to decrease of crops yield. Investigation of cultivable bacteria diversity provides more microbial species for screening antagonistic bacteria. In the present study, a variety of cultivation methods were used to investigate the diversity of cultivable bacteria alive in tobacco field. A total of 441 bacterial strains were obtained that belonged to four phyla, 49 genera and 146 species. Actinobacteria and Proteobacteria were the dominant phyla. Agrobacterium, Arthrobacter, Bacillus, Klebsiella, Paenarthrobacter, Pseudomonas and Pseudarthrobacter were the dominant genera. Some rare genera were discovered including Bosea, Cedecea, Delftia and Dyella. Diversity, species and abundances of bacteria altered under different cultivation conditions. One hundred three bacterial strains showed plant growth-promoting attributes. Twenty Bacillus strains showed high antibacterial activity against R. solanacearum. In field experiments, individual strain and consortia of Bacillus subtilis, B. siamensis and B. vallismortis effectively inhibited bacterial wilt. The core genes that controlled synthesis of secondary metabolites were knocked out in B. vallismortis SSB-10. Difficidin, which was synthesized by dif operon and controlled by sfp gene, was the antibacterial substance produced by SSB-10. Difficidin destroyed cell wall and cell membrane of R. solanacearum and inhibited its motility, production of extracellular polysaccharides and cellulase activity.

Evolutions and Managements of Soil Microbial Community Structure Drove by Continuous Cropping

Continuous cropping obstacles have increasingly become an important phenomenon affecting crop yield and quality. Its harm includes the deterioration of soil basic physical and chemical properties, changes of soil microbial community structure, accumulation of autotoxins, weakness of plant growth, and aggravation of diseases and pests. In this review, the evolutionary trend of soil microbial structure driven by continuous cropping was generalized, while drivers of these changes summed up as destruction of soil microbial living environment and competition within the community. We introduced a microorganism proliferation and working model with three basics and a vector, and four corresponding effective measures to reshape the structure were comprehensively expounded. According to the model, we also put forward three optimization strategies of the existing measures. In which, synthetic microbiology provides a new solution for improving soil community structure. Meanwhile, to ensure the survival and reproduction of soil microorganisms, it is necessary to consider their living space and carbon sources in soil fully. This review provided a comprehensive perspective for understanding the evolutionary trend of the soil microbial community under continuous cropping conditions and a summary of reshaping measures and their optimization direction.

Colonization and Interaction of Bacteria Associated With Chinese Chives Affected by Ecological Compartments and Growth Conditions

Chinese chive has a long history of planting in China. At present, there are many studies on endophytic bacteria and rhizosphere microorganisms of Chinese chive, but the effects of ecological compartment and growth conditions on bacterial communities in Chinese chives are unclear. Here, we aimed to elucidate the differences in bacterial a-diversity, β-diversity, community structure, core species differences, interaction networks and predicted metabolic functions among bacterial communities in different ecological compartments (the phylloplane, leaf endosphere, stem endosphere, root endosphere, and rhizosphere) in Chinese chives in an open field, a solar greenhouse, an arched shed, and a hydroponic system. Sixty samples were collected from these five ecological compartments under four growth conditions, and we compared the bacterial profiles of these groups using 16S rRNA sequencing. We evaluated the differences in diversity and composition among bacterial communities in these ecological compartments, analyzed the bacterial interaction patterns under the different growth conditions, and predicted the bacterial metabolic pathways in these ecological compartments and growth conditions. The results showed that the effects of ecological compartments on bacterial diversity, community composition, interaction network pattern, and functional expression of Chinese chives were greater than those of growth condition. Ecological compartments (R² = 0.5292) could better explain bacterial community division than growth conditions (R² = 0.1056). The microbial interaction networks and indicator bacteria in different ecological compartments showed that most of the bacteria that played the role of key nodes (OTUs) in each ecological compartment were bacteria with high relative abundance in the compartment. However, the bacteria that played the role of key nodes (OTUs) in bulbs were not Proteobacteria with the highest relative abundance in the compartment, but Actinobacteria that were significantly enriched in the root endosphere and rhizosphere ecological compartments. In addition, interactions among bacteria were interrupted in the hydroponic system, and specific bacterial communities and interaction patterns in Chinese chives varied among growth conditions. Prediction of metabolic functions indicated that plant metabolic activity related to stress responses and induction of system resistance was greater in belowground ecological compartments.

Analysis of soil bacterial communities and physicochemical properties associated with Fusarium wilt disease of banana in Malaysia

Fusarium wilt (FW) caused by Fusarium oxysporum f. sp. cubense Tropical Race 4 (TR4) is a soil-borne disease that infects bananas, causing severe economic losses worldwide. To reveal the relationship between bacterial populations and FW, the bacterial communities of healthy and TR4-infected rhizosphere and bulk soils were compared using 16S rRNA gene sequencing. Soil physicochemical properties associated with FW were also analyzed. We found the community structure of bacteria in the healthy and TR4 infected rhizosphere was significantly different compared to bulk soil within the same farm. The rhizosphere soils of infected plants exhibited higher richness and diversity than healthy plant with significant abundance of Proteobacteria. In the healthy rhizosphere soil, beneficial bacteria such as Burkholderia and Streptomyces spp. were more abundant. Compared to the infected rhizosphere soil, healthy rhizosphere soil was associated with RNA metabolism and transporters pathways and a high level of magnesium and cation exchange capacity. Overall, we reported changes in the key taxa of rhizospheric bacterial communities and soil physicochemical properties of healthy and FW-infected plants, suggesting their potential role as indicators for plant health.

Rhizosphere analysis of field-grown Panax ginseng with different degrees of red skin provides the basis for preventing red skin syndrome

Background

Ginseng red skin root syndrome (GRS) is one of the most common ginseng (Panax ginseng Meyer) diseases. It leads to a severe decline in P. ginseng quality and seriously affects the P. ginseng industry in China. However, as a root disease, the characteristics of the GRS rhizosphere microbiome are still unclear.

Methods

The amplicon bacterial 16 S rRNA genes and fungal ITS (Internal Transcribed Spacer) regions Illumina sequencing technology, combined with microbial diversity and composition analysis based on R software, was used to explore the relationship between soil ecological environment and GRS.

Results

There were significant differences in the diversity and richness of soil microorganisms between the rhizosphere with different degrees of disease, especially between healthy P. ginseng (HG) and heavily diseased groups. The variation characteristics of microbial abundance in different taxa levels were analyzed. The interaction network of rhizosphere microorganisms of P. ginseng under GRS background was established. We also found that different P. ginseng rhizosphere microbial communities have multiple changes in stability and complexity through the established interaction network. Microbes closely related to potential pathogenic fungi were also identified according to the interaction network, which provided clues for looking for biological control agents. Finally, the Distance-based redundancy analysis (dbRDA) results indicated that total phosphorus (TP), available potassium (AK), available phosphorus (AP), catalase (CAT), invertase (INV) are the key factors that influence the microbial communities. Moreover, the content of these key factors in the rhizosphere was negatively correlated with disease degrees.

Conclusions

In this study, we comprehensively analyzed the rhizosphere characteristics of P. ginseng with different levels of disease, and explored the interaction relationship among microorganisms. These results provide a basis for soil improvement and biological control of field-grown in the future.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02430-9.

Bacterial community dynamics of tomato hydroponic greenhouses infested with hairy root disease

The rhizosphere is a complex ecosystem consisting of microbes in the interface between growth medium and plant roots, which affects plant productivity and health. This is one of the few studies analysing bacterial communities present in the rhizosphere of hydroponically grown plants. Tomato grown under hydroponic conditions is prone to hairy root disease (HRD) that is caused by rhizogenic Agrobacterium biovar 1 strains. In this study, using high-throughput amplicon sequencing of partial ribosomal RNA (rRNA) genes, we aimed to characterize bacterial communities in rockwool samples obtained from healthy or HRD-infested tomato during an entire growing season. Alpha diversity of rockwool increased in direct relation with time and samples obtained from healthy greenhouses presented a significantly lower alpha diversity than those from HRD-infested greenhouses. Beta diversity showed that bacterial community composition changed throughout the growing season. Amplicon Sequence Variants (ASVs) identified as rhizogenic Agrobacterium bv. 1 were more prevalent in HRD-infected greenhouses. Conversely, ASVs identified as Paenibacillus, previously identified as biocontrol organisms of rhizogenic agrobacteria, were more prevalent in healthy greenhouses. Altogether, our study greatly contributes to the knowledge of bacterial communities in rockwool hydroponics.

Pyrosequencing and phenotypic microarray to decipher bacterial community variation in Sorghum bicolor (L.) Moench rhizosphere

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Different cultivation practices and climatic conditions play an important role in governing and modulating soil microbial communities.

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This work, investigated the changes in bacterial community composition at taxonomic and functional level in rhizosphere soil of sweet sorghum under extensive cultivation practices at three different field sites of South Africa.

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16S rRNA amplicon sequencing data revealed that at the phylum level, the dominant group was Cyanobacteria with a relative abundance of 63.3%, 71.8% and 81.6% from ASHSOIL1, ASHSOIL2, and ASHSOIL3, respectively.

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Community-level physiological profiling (CLPP) analysis revealed that the metabolic activity of the bacterial community in ASHSOIL3 was the highest, followed by ASHSOIL1 and ASHSOIL2.

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Overall, this study showed that soil pH, nutrient availability and cultivation practices played significant roles in governing the bacterial community composition in sorghum rhizosphere.

Different cultivation practices and climatic conditions play an important role in governing and modulating soil microbial communities as well as soil health. This study investigated, for the first time, keystone microbial taxa inhabiting the rhizosphere of sweet sorghum (Sorghum bicolor) under extensive cultivation practices at three different field sites of South Africa (North West-South (ASHSOIL1); Mpumalanga-West – (ASHSOIL2); and Free State-North West – (ASHSOIL3)). Soil analysis of these sites revealed differences in P, K, Mg, and pH. 16S rRNA amplicon sequencing data revealed that the rhizosphere bacterial microbiome differed significantly both in the structure and composition across the samples. The sequencing data revealed that at the phylum level, the dominant group was Cyanobacteria with a relative abundance of 63.3%, 71.8%, and 81.6% from ASHSOIL1, ASHSOIL2, and ASHSOIL3, respectively. Putative metabolic requirements analyzed by METAGENassist software revealed the ASHSOIL1 sample as the prominent ammonia degrader (21.1%), followed by ASHSOIL3 (17.3%) and ASHSOIL2 (11.1%). The majority of core-microbiome taxa were found to be from Cyanobacteria, Bacteroidetes, and Proteobacteria. Functionally, community-level physiological profiling (CLPP) analysis revealed that the metabolic activity of the bacterial community in ASHSOIL3 was the highest, followed by ASHSOIL1 and ASHSOIL2. This study showed that soil pH and nutrient availability and cultivation practices played significant roles in governing the bacterial community composition in the sorghum rhizosphere across the different sites.