Illumina-based analysis of the rhizosphere microbial communities associated with healthy and wilted Lanzhou lily (Lilium davidii var. unicolor) plants grown in the field

Investigation of the biocontrol mechanism of a novel Pseudomonas species against phytopathogenic Fusarium graminearum revealed by multi-omics integration analysis

Phytopathogenic Fusarium graminearum poses significant threats to crop health and soil quality. Although our laboratory-cultivated Pseudomonas sp. P13 exhibited potential biocontrol capacities, its effectiveness against F. graminearum and underlying antifungal mechanisms are still unclear. In light of this, our study investigated a significant inhibitory effect of P13 on F. graminearum T1, both in vitro and in a soil environment. Conducting genomic, metabolomic, and transcriptomic analyses of P13, we sought to identify evidence supporting its antagonistic effects on T1. The results revealed the potential of P13, a novel Pseudomonas species, to produce active antifungal components, including phenazine-1-carboxylate (PCA), hydrogen cyanide (HCN), and siderophores [pyoverdine (Pvd) and histicorrugatin (Hcs)], as well as the dynamic adaptive changes in the metabolic pathways of P13 related to these active ingredients. During the logarithmic growth stage, T1-exposed P13 strategically upregulated PCA and HCN biosynthesis, along with transient inhibition of the tricarboxylic acid (TCA) cycle. However, with growth stabilization, upregulation of PCA and HCN synthesis ceased, whereas the TCA cycle was enhanced, increasing siderophores secretion (Pvd and Hcs), suggesting that this mechanism might have caused continuous inhibition of T1. These findings improved our comprehension of the biocontrol mechanisms of P13 and provided the foundation for potential application of Pseudomonas strains in the biocontrol of phytopathogenic F. graminearum.

IMPORTANCE

Pseudomonas spp. produces various antifungal substances, making it an effective natural biocontrol agent against pathogenic fungi. However, the inhibitory effects and the associated antagonistic mechanisms of Pseudomonas spp. against Fusarium spp. are unclear. Multi-omics integration analyses of the in vitro antifungal effects of novel Pseudomonas species, P13, against F. graminearum T1 revealed the ability of P13 to produce antifungal components (PCA, HCN, Pvd, and Hcs), strategically upregulate PCA and HCN biosynthesis during logarithmic growth phase, and enhance the TCA cycle during stationary growth phase. These findings improved our understanding of the biocontrol mechanisms of P13 and its potential application against pathogenic fungi.

Influence of Bacillus subtilis strain Z-14 on microbial ecology of cucumber rhizospheric vermiculite infested with fusarium oxysporum f. sp. cucumerinum

Fusarium oxysporum (FO) is a typical soil-borne pathogenic fungus, and the cucumber wilt disease caused by F. oxysporum f. sp. cucumerinum (FOC) seriously affects crop yield and quality. Vermiculite is increasingly being used as a culture substrate; nevertheless, studies exploring the effectiveness and mechanisms of biocontrol bacteria in this substrate are limited. In this study, vermiculite was used as a culture substrate to investigate the control effect of Bacillus subtilis strain Z-14 on cucumber wilt and the rhizospheric microecology, focusing on colonization ability, soil microbial diversity, and rhizosphere metabolome. Pot experiments showed that Z-14 effectively colonized the cucumber roots, achieving a controlled efficacy of 61.32% for wilt disease. It significantly increased the abundance of Bacillus and the expression of NRPS and PKS genes, while reducing the abundance of FO in the rhizosphere. Microbial diversity sequencing showed that Z-14 reduced the richness and diversity of the rhizosphere bacterial community, increased the richness and diversity of the fungal community, and alleviated the effect of FO on the community structure of the cucumber rhizosphere. The metabolomics analysis revealed that Z-14 affected ABC transporters, amino acid synthesis, and the biosynthesis of plant secondary metabolites. Additionally, Z-14 increased the contents of phenylacetic acid, capsidol, and quinolinic acid, all of which were related to the antagonistic activity in the rhizosphere. Z-14 exhibited a significant control effect on cucumber wilt and influenced the microflora and metabolites in rhizospheric vermiculite, providing a theoretical basis for further understanding the control effect and mechanism of cucumber wilt in different culture substrates.

Rhizosphere microbial markers (micro-markers): A new physical examination indicator for traditional Chinese medicines

Rhizosphere microorganisms, as one of the most important components of the soil microbiota and plant holobiont, play a key role in the medicinal plant-soil ecosystem, which are closely related to the growth, adaptability, nutrient absorption, stress tolerance and pathogen resistance of host plants. In recent years, with the wide application of molecular biology and omics technologies, the outcomes of rhizosphere microorganisms on the health, biomass production and secondary metabolite biosynthesis of medicinal plants have received extensive attention. However, whether or to what extent rhizosphere microorganisms can contribute to the construction of the quality evaluation system of Chinese medicinal materials is still elusive. Based on the significant role of rhizosphere microbes in the survival and quality formation of medicinal plants, this paper proposed a new concept of rhizosphere microbial markers (micro-markers), expounded the relevant research methods and ideas of applying the new concept, highlighted the importance of micro-markers in the quality evaluation and control system of traditional Chinese medicines (TCMs), and introduced the potential value in soil environmental assessment, plant pest control and quality assessment of TCMs. It provides reference for developing ecological planting of TCMs and ensuring the production of high quality TCMs by regulating rhizosphere microbial communities.

Association of soil fungal community composition with incidence of Fusarium wilt of banana in Malaysia

Banana (Musa spp.), an important food crop in many parts of the world, is threatened by a deadly wilt disease caused by Fusarium oxysporum f. sp. cubense Tropical Race 4 (TR4). Increasing evidence indicates that plant actively recruits beneficial microbes in the rhizosphere to suppress soil-borne pathogens. Hence, studies on the composition and diversity of the root-associated microbial communities are important for banana health. Research on beneficial microbial communities has focused on bacteria, although fungi can also influence soil-borne disease. Here, high-throughput sequencing targeting the fungal internal transcribed spacer (ITS) was employed to systematically characterize the difference in the soil fungal community associated with Fusarium wilt (FW) of banana. The community structure of fungi in the healthy and TR4-infected rhizospheres was significantly different compared with that of bulk soil within the same farm. The rhizosphere soils of infected plants exhibited higher richness and diversity compared with healthy plants, with significant abundance of Fusarium genus at 14%. In the healthy rhizosphere soil, Penicillium spp. were more abundant at 7% and positively correlated with magnesium. This study produced a detailed description of fungal community structure in healthy and TR4-infected banana soils in Malaysia and identified candidate biomarker taxa that may be associated with FW disease promotion and suppression. The findings also expand the global inventory of fungal communities associated with the components of asymptomatic and symptomatic banana plants infected by TR4.

Rhizospheric microbial consortium of Lilium lancifolium Thunb. causes lily root rot under continuous cropping system

Tiger lily (Lilium lancifolium Thunb.) is a cash crop with a long history of cultivation in China. Its roots have long been used as a valuable component of Chinese medicine. Continuous cropping, the conventional planting approach for tiger lily, often leads to severe root rot disease, but it is not yet clear how this planting method leads to root rot. In this study, we analyzed the rhizosphere microbiome and predicted microbial protein function in tiger lily planted with the continuous cropping method in three different geological types of soil. In order to explore the specific rhizosphere microbiota triggering root rot disease, tiger lily was compared to maize grown in a similar system, which showed no disease development. An analysis of the chemical elements in the soil revealed that the Pseudomonas and Streptomyces genera, with pathogenic functions, were dominant in the tiger lily rhizosphere. The lower soil pH of tiger lily compared to maize supports the accumulation of pathogenic bacteria in the tiger lily rhizosphere. Meanwhile, we discovered that bacteria of the Flavobacterium genus, with their predicted phosphate transport function, specifically accumulated in the maize rhizosphere. Our findings suggest that Pseudomonas and Streptomyces bacteria may result in continuous cropping-induced root rot disease in tiger lily and that Flavobacterium could serve to protect maize from pathogenic bacteria.

Characterization of an Endophytic Antagonistic Bacterial Strain Bacillus halotolerans LBG-1-13 with Multiple Plant Growth-Promoting Traits, Stress Tolerance, and Its Effects on Lily Growth

Microbial inoculants are an important tool for increasing arable land productivity and decreasing mineral fertilizer application. This study was aimed at isolating and identifying endophytic antagonistic bacteria from lily (Lilium davidii var. unicolor) roots grown in Northwestern China and at evaluating their antifungal activity and plant growth-promoting characteristics. For this purpose, endophytic bacteria were isolated from plant roots, and plant growth-promoting strains were identified. One bacterial strain, isolated from the root part, was identified as Bacillus halotolerans based on 16S rRNA gene sequence analysis and was designated as LBG-1-13. The strain showed antagonistic activities against important plant pathogens of lily including Botrytis cinerea, Botryosphaeria dothidea, and Fusarium oxysporum. The highest percentage of growth inhibition, i.e., 71.65 ± 2.39%, was observed for LBG-1-13 against Botryosphaeria dothidea followed by 68.33 ± 4.70% and 48.22 ± 4.11% against Botrytis cinerea and Fusarium oxysporum, respectively. Meanwhile, the isolated strain also showed plant growth-promoting traits such as the production of indole-3-acetic acid (IAA), siderophore, ACC deaminase, and phosphate solubilization activity. The strain showed ACC deaminase activity and was able to cleave 58.41 ± 2.62 nmol α-ketobutyrate (mg protein)⁻¹ min⁻¹. The strain exhibited tolerance to salt and drought stress in an in vitro experiment. The strain LBG-1-13 was able to grow in the presence of 10% NaCl and 20% polyethylene glycol (PEG) in the growth medium. Inoculation of Lilium varieties, Tresor and Bright Diamond, with LBG-1-13 enhanced plant growth under greenhouse and field conditions, respectively. All these results demonstrated that Bacillus halotolerans LBG-1-13 could be utilized as a good candidate in the biocontrol of lily disease and plant growth promotion in sustainable agriculture.

Distribution, pathogenicity and disease control of Fusarium tricinctum

Plant pathogenic fungi such as Fusarium tricinctum cause various plant diseases worldwide, especially in temperate regions. In cereals, F. tricinctum is one of the most common species causing Fusarium head blight (FHB) and root rot. Infection with F. tricinctum results in high yield losses and reduction in quality, mainly due to mycotoxin contamination of grain. Mycotoxins produced by F. tricinctum, such as enniatins (ENs) and moniliformin (MON), which are the most studied mycotoxins, have been reported to have multiple toxic effects on humans and animals. Although chemical control of Fusarium infection has been applied to grains, it is not always effective in controlling disease or reducing the level of mycotoxins in wheat grains. To the contrary, chemical control may significantly increase infection of F. tricinctum in fungicide-treated plots after treatment. Our studies show that the bacterium Bacillus amyloliquefaciens, has good control effects against F. tricinctum. Therefore, its use as a biological control agent against various plant pathogens may be an effective strategy to control the spread of Fusarium pathogens. Here, we conduct a review of the literature involving this plant pathogen, its diversity, virulence, and methods to control.

Impacts of the Biocontrol Strain Pseudomonas simiae PICF7 on the Banana Holobiont: Alteration of Root Microbial Co-occurrence Networks and Effect on Host Defense Responses

The impact of the versatile biocontrol and plant-growth-promoting rhizobacteria Pseudomonas simiae PICF7 on the banana holobiont under controlled conditions was investigated. We examine the fate of this biological control agent (BCA) upon introduction in the soil, the effect on the banana root microbiota, and the influence on specific host genetic defense responses. While the presence of strain PICF7 significantly altered neither the composition nor the structure of the root microbiota, a significant shift in microbial community interactions through co-occurrence network analysis was observed. Despite the fact that PICF7 did not constitute a keystone, the topology of this network was significantly modified-the BCA being identified as a constituent of one of the main network modules in bacterized plants. Gene expression analysis showed the early suppression of several systemic acquired resistance and induced systemic resistance (ISR) markers. This outcome occurred at the time in which the highest relative abundance of PICF7 was detected. The absence of major and permanent changes on the banana holobiont upon PICF7 introduction poses advantages regarding the use of this beneficial rhizobacteria under field conditions. Indeed a BCA able to control the target pathogen while altering as little as possible the natural host-associated microbiome should be a requisite when developing effective bio-inoculants.

An Endophytic Strain of Bacillus amyloliquefaciens Suppresses Fusarium oxysporum Infection of Chinese Wolfberry by Altering Its Rhizosphere Bacterial Community

Root rot disease is a serious infection leading to production loss of Chinese wolfberry (Lycium barbarum). This study tested the potential for two bacterial biological control agents, Bacillus amyloliquefaciens HSB1 and FZB42, against five fungal pathogens that frequently cause root rot in Chinese wolfberry. Both HSB1 and FZB42 were found to inhibit fungal mycelial growth, in vitro and in planta, as well as to promote the growth of wolfberry seedlings. In fact, a biocontrol experiment showed efficiency of 100% with at least one treatment involving each biocontrol strain against Fusarium oxysporum. Metagenomic sequencing was used to assess bacterial community shifts in the wolfberry rhizosphere upon introduction of each biocontrol strain. Results showed that HSB1 and FZB42 differentially altered the abundances of different taxa present and positively influenced various functions of inherent wolfberry rhizosphere bacteria. This study highlights the application of biocontrol method in the suppression of fungal pathogens that cause root rot disease in wolfberry, which is useful for agricultural extension agents and commercial growers.

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.

Impact of biocontrol microbes on soil microbial diversity in ginger (Zingiber officinale Roscoe)

BACKGROUND

Bacteria are the most diverse and abundant group of soil organisms that influence plant growth and health. Bacillus and Trichoderma are commonly used as biological control agents (BCA) that directly or indirectly act on soil bacteria. Therefore, it is essential to understand how the applied microbes impact the indigenous microbial community before exploring their activity in the control of soilborne diseases.

RESULTS

MiSeq sequencing of the 16S rRNA gene was used to decipher the shift of rhizosphere bacterial community in ginger (Zingiber officinale Roscoe) treated with Bacillus subtilus and Trichoderma harzianum at different concentrations. The dominant phyla in treated and nontreated samples were Proteobacteria, Actinobacteria, Acidobacteria and comprised up to 54.7% of the total sequences. There were significant differences between BCA treated and nontreated samples in the bacteria community. BCA treated plants presented higher bacterial diversity than nontreated and higher dosage of BCA had a larger impact on rhizosphere microbiota, but the 'dose-response relationship' varied in different bacterial groups. Potential biomarkers at genus level were found, such as RB41, Pseudomonas, Nitrospira, Candidatus_Udaeobacter.

CONCLUSION

The combined use of Bacillus subtilus and Trichoderma harzianum could alter bacterial community structure and diversity in rhizosphere soil. BCA-microbes interactions as well as soil microbial ecology should be noticed in plant disease management. © 2021 Society of Chemical Industry.

Phyllospheric Microbial Composition and Diversity of the Tobacco Leaves Infected by Didymella segeticola

A Myriad of biotic and abiotic factors inevitably affects the growth and production of tobacco (Nicotiana tabacum L.), which is a model crop and sought-after worldwide for its foliage. Among the various impacts the level of disease severity poses on plants, the influence on the dynamics of phyllospheric microbial diversity is of utmost importance. In China, recurring reports of a phyto-pathogen, Didymella segeticola, a causal agent of tobacco leaf spot, accentuate the need for its in-depth investigation. Here, a high-throughput sequencing technique, IonS5^TMXL was employed to analyze tobacco leaves infected by D. segeticola at different disease severity levels, ranging from T1G (least disease index) to T4G (highest disease index), in an attempt to explore the composition and diversity of phyllospheric microbiota. In all healthy and diseased tobacco leaves, the most dominant fungal phylum was Ascomycota with a high prevalence of genus Didymella, followed by Boeremia, Meyerozyma and Alternaria, whereas in the case of bacterial phyla, Proteobacteria was prominent with Pseudomonas being a predominant genus, followed by Pantoea. The relative abundance of fungi, i.e., Didymella and Boeremia (Ascomycota) and bacteria, i.e., Pseudomonas and Pantoea (Proteobacteria) were higher in diseased groups compared to healthy groups. Healthy tissues exhibited relatively rich and diverse fungal communities in contrast with diseased groups. The infection of D. segeticola had a complex and significant effect on fungal as well as bacterial alpha diversity. FUNGuild analysis indicated that the relative abundance of pathotrophs and saprotrophs in diseased tissues proportionally increased with disease severity. PICRUSt analysis of diseased tissues indicated that the relative abundance of bacterial cell motility and membrane transport-related gene sequences elevated with an increase in disease severity from T1G to T3G and then tended to decrease at T4G. Conclusively, the current study shows the typical characteristics of the tobacco leaf microbiome and provides insights into the distinct microbiome shifts on tobacco leaves infected by D. segeticola.

Diversity and structural characteristics of soil microbial communities in different habitats of wild Lilium regale Wilson in Wenchuan area

Lilium regale Wilson (L.regale), originated in the Minjiang River basin in Sichuan, China, has different phenotypic characteristics in different environments. To analyze the correlation between the phenotypes of L.regale and its soil micro-ecological environment, wild habitat soil of L.regale at the two altitudes were selected to analyze the diversity and community structure of microorganisms in soil, and measure the soil physicochemical factors and enzyme activities. The structural composition and diversity of fungal and bacterial communities in hillside and valley soils were significantly different (p < 0.01). Soil available potassium (AK) and soil enzyme activities such as urease (S_UE), sucrase (S_SC), and catalase (S_CAT) differed significantly different between hillsides and valleys (p < 0.01), while organic matter (OM), total phosphorus (TP), and polyphenol oxidase (S_PPO) had no great variances. Correlation analysis was conducted between the common and differential microorganisms and the morphological characteristics, soil physicochemical factors and soil enzyme activities of L.regale in both hillside and valley. The results showed that both of the fungal and bacterial could be clustered into two distinct groups by positive and negative correlations, suggesting that the representative microorganism may have structural characteristics that are directly related to soil physicochemical properties and enzyme activities, which conversely affect the phenotype of Lily. Therefore, the study on the native species of horticultural plants and the local soil microhabitat environment will benefit the conservation of wild Lily and provide theoretical guidance for the domestication and breeding of horticultural plants.

Earthworm activity optimized the rhizosphere bacterial community structure and further alleviated the yield loss in continuous cropping lily (Lilium lancifolium Thunb.)

The soil microbial community plays a vital role in the biogeochemical cycles of bioelements and maintaining healthy soil conditions in agricultural ecosystems. However, how the soil microbial community responds to mitigation measures for continuous cropping obstacles remains largely unknown. Here we examined the impact of quicklime (QL), chemical fungicide (CF), inoculation with earthworm (IE), and a biocontrol agent (BA) on the soil microbial community structure, and the effects toward alleviating crop yield decline in lily. High-throughput sequencing of the 16S rRNA gene from the lily rhizosphere after 3 years of continuous cropping was performed using the Illumina MiSeq platform. The results showed that Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Chloroflexi and Gemmatimonadetes were the dominant bacterial phyla, with a total relative abundance of 86.15-91.59%. On the other hand, Betaproteobacteriales, Rhizobiales, Myxococcales, Gemmatimonadales, Xanthomonadales, and Micropepsales were the dominant orders with a relative abundance of 28.23-37.89%. The hydrogen ion concentration (pH) and available phosphorus (AP) were the key factors affecting the structure and diversity of the bacterial community. The yield of continuous cropping lily with using similar treatments decreased yearly for the leaf blight, but that of IE was significantly (p < 0.05) higher than with the other treatments in the same year, which were 17.9%, 18.54%, and 15.69% higher than that of blank control (CK) over 3 years. In addition, IE significantly (p < 0.05) increased organic matter (OM), available nitrogen (AN), AP, and available potassium (AK) content in the lily rhizosphere soil, optimized the structure and diversity of the rhizosphere bacterial community, and increased the abundance of several beneficial bacterial taxa, including Rhizobiales, Myxococcales, Streptomycetales and Pseudomonadales. Therefore, enriching the number of earthworms in fields could effectively optimize the bacterial community structure of the lily rhizosphere soil, promote the circulation and release in soil nutrients and consequently alleviate the loss of continuous cropping lily yield.

Genomics as a potential tool to unravel the rhizosphere microbiome interactions on plant health

Intense agricultural practices to meet rising food demands have caused ecosystem perturbations. For sustainable crop production, biological agents are gaining attention, but exploring their functional potential on a multi-layered complex ecosystem like the rhizosphere is challenging. This review explains the significance of genomics as a culture-independent molecular tool to understand the diversity and functional significance of the rhizosphere microbiome for sustainable agriculture. It discusses the recent significant studies in the rhizosphere environment carried out using evolving techniques like metagenomics, metatranscriptomics, and metaproteomics, their challenges, constraints infield application, and prospective solutions. The recent advances in techniques such as nanotechnology for the development of bioformulations and visualization techniques contemplating environmental safety were also discussed. The need for development of metagenomic data sets of regionally important crops, their plant microbial interactions and agricultural practices for narrowing down significant data from huge databases have been suggested. The role of taxonomical and functional diversity of soil microbiota in understanding soil suppression and part played by the microbial metabolites in the process have been analyzed and discussed in the context of 'omics' approach. 'Omics' studies have revealed important information about microbial diversity, their responses to various biotic and abiotic stimuli, and the physiology of disease suppression. This can be translated to crop sustainability and combinational approaches with advancing visualization and analysis methodologies fix the existing knowledge gap to a huge extend. With improved data processing and standardization of the methods, details of plant-microbe interactions can be successfully decoded to develop sustainable agricultural practices.

Effects of continuous cropping of sweet potatoes on the bacterial community structure in rhizospheric soil

BACKGROUND

Continuous cropping obstacles from sweet potatoes are widespread, which seriously reduce the yield and quality, causing certain economic losses. Bacteria of rhizospheric soil are the richest and are associated with obstacles to continuous cropping. However, few studies have examined how continuous sweet potato cropping affects the rhizospheric soil bacterial community structure.

RESULTS

In the study, the Illumina MiSeq method was used to explore the variations in rhizospheric soil bacterial community structure of different sweet potato varieties after continuous cropping, as well as the correlation between soil characteristics and the bacterial community. The results showed that (1) the dominant bacterial phyla in rhizospheric soils from both Xushu 18 and Yizi 138 were Proteobacteria, Acidobacteria, and Actinobacteria. The most dominant genus was Subgroup 6_norank. The relative abundance of rhizospheric soil bacteria varied significantly between the two sweet potato varieties. (2) The richness and diversity indexes of bacteria were higher in Xushu 18 rhizospheric soil than in Yizi 138 soil after continuous cropping. Moreover, beneficial Lysobacter and Bacillus were more prevalent in Xushu 18, while Yizi 138 contained more harmful Gemmatimonadetes. (3) Soil pH decreased after continuous cropping, and redundancy analysis indicated that soil pH was significantly correlated with the bacterial community. Spearman's rank correlation coefficient analysis demonstrated that pH was positively associated with Planctomycetes and Acidobacteria, but negatively associated with Actinobacteria and Firmicutes.

CONCLUSIONS

After continuous cropping, the bacterial community structure and physicochemical properties of sweet potato rhizospheric soil were changed, and the changes from different sweet potato varieties were different. The contents of Lysobacter and Bacillus were higher in the sweet potato variety resistant to continuous cropping. It provides a basis for developing new microbial fertilizers for sweet potatoes to alleviate the continuous cropping obstacle.

Composition and diversity of bacterial communities in the rhizosphere of the Chinese medicinal herb Dendrobium

BACKGROUND

Dendrobium is a precious herbal that belongs to Orchidaceae and is widely used as health care traditional Chinese medicine in Asia. Although orchids are mycorrhizal plants, most research still focuses on endophytes, and there is still large amount unknown about rhizosphere microorganisms. To investigate the rhizosphere microbial community of different Dendrobium species during the maturity stage, we used high-throughput sequencing to analyze microbial community in rhizosphere soil during the maturity stage of three kinds of Dendrobium species.

RESULTS

In our study, a total of 240,320 sequences and 11,179 OTUs were obtained from these three Dendrobium species. According to the analysis of OTU annotation results, different Dendrobium rhizosphere soil bacteria include 2 kingdoms, 63 phyla, 72 classes, 159 orders, 309 families, 850 genera and 663 species. Among all sequences, the dominant bacterial phyla (relative abundance > 1%) were Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, Firmicutes, Verrucomicrobia, Planctomycetes, Chloroflexi, and Gemmatimonadetes. And through WGCNA analysis, we found the hub flora was also belong to Acidobacteria, Actinobacteria and Proteobacteria.

CONCLUSIONS

We found that the rhizosphere bacterial communities of the three kinds of Dendrobium have significant differences, and that the main species of rhizosphere microorganisms of Dendrobium are concentrated in the Proteobacteria, Actinobacteria, and Bacteroidetes. Moreover, the smaller the bacterial level, the greater the difference among Dendrobium species. These results fill knowledge gaps in the rhizosphere microbial community of Dendrobium and provide a theoretical basis for the subsequent mining of microbial functions and the study of biological fertilizers.

Predicting disease occurrence with high accuracy based on soil macroecological patterns of Fusarium wilt

Soil-borne plant diseases are increasingly causing devastating losses in agricultural production. The development of a more refined model for disease prediction can aid in reducing crop losses through the use of preventative control measures or soil fallowing for a planting season. The emergence of high-throughput DNA sequencing technology has provided unprecedented insight into the microbial composition of diseased versus healthy soils. However, a single independent case study rarely yields a general conclusion predictive of the disease in a particular soil. Here, we attempt to account for the differences among various studies and plant varieties using a machine-learning approach based on 24 independent bacterial data sets comprising 758 samples and 22 independent fungal data sets comprising 279 samples of healthy or Fusarium wilt-diseased soils from eight different countries. We found that soil bacterial and fungal communities were both clearly separated between diseased and healthy soil samples that originated from six crops across nine countries or regions. Alpha diversity was consistently greater in the fungal community of healthy soils. While diseased soil microbiomes harbored higher abundances of Xanthomonadaceae, Bacillaceae, Gibberella, and Fusarium oxysporum, the healthy soil microbiome contained more Streptomyces Mirabilis, Bradyrhizobiaceae, Comamonadaceae, Mortierella, and nonpathogenic fungi of Fusarium. Furthermore, a random forest method identified 45 bacterial OTUs and 40 fungal OTUs that categorized the health status of the soil with an accuracy >80%. We conclude that these models can be applied to predict the potential for occurrence of F. oxysporum wilt by revealing key biological indicators and features common to the wilt-diseased soil microbiome.

A preliminary examination of the bacterial, archaeal, and fungal rhizosphere microbiome in healthy and Phellinus noxius-infected trees

Phellinus noxius is a pathogenic fungus that causes brown root rot disease, resulting in a widespread tree and crop mortality in the tropics and subtropics. Early stages of this disease are largely asymptomatic, hindering early diagnosis and effective treatment. We hypothesized that P. noxius infection would alter the rhizosphere microbiome of infected trees, based on which diagnostic biomarkers could be developed. Here, we examined for the first time the bacterial, archaeal, and fungal rhizosphere microbiome in four species of healthy and P. noxius‐infected trees (Ficus microcarpa, Celtis sinensis, Mallotus paniculatus, and Cinnamomum camphora) using high‐throughput amplicon sequencing. Results revealed the dominance of Proteobacteria and Actinobacteria in bacteria, Crenarchaeota and Euryarchaeota in archaea, and Ascomycota and Basidiomycota in fungi. Phellinus noxius infection did not affect the alpha diversity of the bacterial rhizosphere microbiome in all four tree species but affected that of archaea and fungi in a tree species‐dependent manner. Infection with P. noxius only affected the bacterial rhizosphere composition in M. paniculatus but not the other three tree species. By contrast, P. noxius infection affected the composition of the archaeal and fungal rhizosphere microbiome in all four tree species. Collectively, these results suggest that potential diagnostic biomarkers for brown root rot disease are tree species‐specific and should be developed based on different taxonomic groups. Our study has provided insights into the rhizosphere microbiome in healthy and P. noxius‐infected trees and laid a solid foundation for future comprehensive studies.

Highly diverse root endophyte bacterial community is driven by growth substrate and is plant genotype-independent in common bean (Phaseolus vulgaris L.)

The common bean (Phaseolus vulgaris L.) is the most important grain legume in the human diet with an essential role in sustainable agriculture mostly based on the symbiotic relationship established between this legume and rhizobia, a group of bacteria capable of fixing atmospheric nitrogen in the roots nodules. Moreover, root-associated bacteria play an important role in crop growth, yield, and quality of crop products. This is particularly true for legume crops forming symbiotic relationships with rhizobia, for fixation of atmospheric N₂. The main objective of this work is to assess the substrate and genotype effect in the common bean (Phaseolus vulgaris L.) root bacterial community structure. To achieve this goal, we applied next-generation sequencing coupled with bacterial diversity analysis. The analysis of the bacterial community structures between common bean roots showed marked differences between substrate types regardless of the genotype. Also, we were able to find several phyla conforming to the bacterial community structure of the common bean roots, mainly composed by Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, and Firmicutes. Therefore, we determined that the substrate type was the main factor that influenced the bacterial community structure of the common bean roots, regardless of the genotype, following a substrate-dependent pattern. These guide us to develop efficient and sustainable strategies for crop field management based on the soil characteristics and the bacterial community that it harbors.

Improvement of the aroma of lily rice wine by using aroma-producing yeast strain Wickerhamomyces anomalus HN006

A fruity aroma-producing yeast strain was isolated with the aim of improving the aroma of fermented lily rice wine, and identified as Wickerhamomyces anomalus HN006. In addition, the effects of adding solid residues of previous fermentation cycles, and of fungus α-amylase and W. anomalus HN006 supplementation on the biochemical parameters of lily rice wine were evaluated. The optimum quality of the wine, in terms of ethanol and residual sugar content, acidity levels and aroma, was obtained with 5% (w/v) solid residue addition, and supplementation with 10 U/g fungal α-amylase and 2% (v/v) W. anomalus inoculum on the 4th day of fermentation. Volatile compound profiles, the total amount of amino acids and the sensory characteristics of the lily rice wines produced by the two fermentation processes were also evaluated and compared. The lily rice wine obtained from our optimized experimental technology produced higher amounts of some esters, free fatty acids, alcohols, aldehydes, ketones, alkenes, volatile phenol and thiazole, in addition to higher total amino acid content and sensory scores compared to the traditionally brewed wine. Our process resulted in an intensification and improvement of lily rice wine aroma.

Rotations with Indian Mustard and Wild Rocket Suppressed Cucumber Fusarium Wilt Disease and Changed Rhizosphere Bacterial Communities

Crop monocropping usually results in an enrichment of soil-borne pathogens in soil. Crop rotation is an environmentally friendly method for controlling soil-borne diseases. Plant rhizosphere microorganisms, especially plant-beneficial microorganisms, play a major role in protecting plants from pathogens, but responses of these microorganisms to crop rotation remain unclear. Here, we evaluated the effects of rotations with Indian mustard (Brassica juncea) and wild rocket (Diplotaxis tenuifolia (L.) DC.) on cucumber Fusarium wilt disease caused by Fusarium oxysporum f.sp. cucumerinum (FOC). Cucumber rhizosphere bacterial community composition was analyzed by high-throughput amplicon sequencing. Bacteria, Pseudomonas spp., 2,4-diacetylphloroglucinol (an antifungal secondary metabolite) producer and FOC abundances were estimated by real-time PCR. Rotations with Indian mustard and wild rocket suppressed cucumber Fusarium wilt disease and cucumber rhizosphere FOC abundance. Crop rotations increased cucumber rhizosphere bacteria, Pseudomonas spp. and 2,4-diacetylphloroglucinol producer abundances. Moreover, crop rotations changed cucumber rhizosphere bacterial community composition and increased bacterial community diversity. However, crop rotations decreased soil inorganic nitrogen content and inhibited cucumber seedling growth. Overall, rotations with Indian mustard and wild rocket suppressed cucumber Fusarium wilt disease, which might be linked to the increased rhizosphere bacterial diversity and abundances of potential plant-beneficial microorganisms (such as Pseudomonas spp. and 2,4-diacetylphloroglucinol producer).

Rhizosphere Bacterial Communities Differ According to Fertilizer Regimes and Cabbage (Brassica oleracea var. capitata L.) Harvest Time, but Not Aphid Herbivory

Rhizosphere microbial communities are known to be highly diverse and strongly dependent on various attributes of the host plant, such as species, nutritional status, and growth stage. High-throughput 16S rRNA gene amplicon sequencing has been used to characterize the rhizosphere bacterial community of many important crop species, but this is the first study to date to characterize the bacterial and archaeal community of Brassica oleracea var. capitata. The study also tested the response of the bacterial community to fertilizer type (organic or synthetic) and N dosage (high or low), in addition to plant age (9 or 12 weeks) and aphid (Myzus persicae) herbivory (present/absent). The impact of aboveground herbivory on belowground microbial communities has received little attention in the literature, and since the type (organic or mineral) and amount of fertilizer applications are known to affect M. percicae populations, these treatments were applied at agricultural rates to test for synergistic effects on the soil bacterial community. Fertilizer type and plant growth were found to result in significantly different rhizosphere bacterial communities, while there was no effect of aphid herbivory. Several operational taxonomic units were identified as varying significantly in abundance between the treatment groups and age cohorts. These included members of the S-oxidizing genus Thiobacillus, which was significantly more abundant in organically fertilized 12-week-old cabbages, and the N-fixing cyanobacteria Phormidium, which appeared to decline in synthetically fertilized soils relative to controls. These responses may be an effect of accumulating root-derived glucosinolates in the B. oleracea rhizosphere and increased N-availability, respectively.

Changes in rhizosphere microbial communities in potted cucumber seedlings treated with syringic acid

Phytotoxic effects of phenolic compounds have been extensively studied, but less attention has been given to the effects of these compounds on soil microbial communities, which are crucial to the productivity of agricultural systems. Responses of cucumber rhizosphere bacterial and fungal communities to syringic acid (SA), a phenolic compound with autotoxicity to cucumber, were analyzed by high-throughput sequencing of 16S rRNA gene and internal transcribed spacer amplicons. SA at the concentration of 0.1 μmol g-1 soil changed rhizosphere bacterial and fungal community compositions, decreased bacterial community diversity but increased fungal community richness and diversity (P<0.05). Moreover, SA increased the relative abundances of bacterial phylum Proteobacteria and fungal classes Leotiomycetes, Pezizomycetes, Tremellomycetes and Eurotiomycetes, but decreased the relative abundances of bacterial phylum Firmicutes and fungal class Sordariomycetes (P<0.05). At the genus level, SA decreased the relative abundances of microbial taxa with pathogen-antagonistic and/or plant growth promoting potentials, such as Pseudomonas spp. (P<0.05). Real-time PCR validated that SA decreased cucumber rhizosphere Pseudomonas spp. abundance (P<0.05). In vitro study showed that SA (0.01 to 10 mM) inhibited the growth of a strain of Pseudomonas spp. with pathogen-antagonistic activities to cucumber pathogen Fusarium oxysporum f.sp. cucumerinum Owen (P<0.05). Overall, SA changed cucumber rhizosphere bacterial and fungal community compositions, which may exert negative effects on cucumber seedling growth through inhibiting plant-beneficial microorganisms.

Potential use of high-throughput sequencing of soil microbial communities for estimating the adverse effects of continuous cropping on ramie (Boehmeria nivea L. Gaud)

Ramie (Boehmeria nivea L. Gaud) fiber, one of the most important natural fibers, is extracted from stem bark. Continuous cropping is the main obstacle to ramie stem growth and a major cause of reduced yields. Root-associated microbes play crucial roles in plant growth and health. In this study, we investigated differences between microbial communities in the soil of healthy and continuously cropped ramie plants, and sought to identify potential mechanisms whereby these communities could counteract the problems posed by continuous cropping. Paired-end Illumina MiSeq analysis of 16S rRNA and ITS gene amplicons was employed to study bacterial and fungal communities. Long-term monoculture of ramie significantly decreased fiber yields and altered soil microbial communities. Our findings revealed how microbial communities and functional diversity varied according to the planting year and plant health status. Soil bacterial diversity increased with the period of ramie monoculture, whereas no significant differences were observed for fungi. Sequence analyses revealed that Firmicutes, Proteobacteria, and Acidobacteria were the most abundant bacterial phyla. Firmicutes abundance decreased with the period of ramie monoculture and correlated positively with the stem length, stem diameter, and fiber yield. The Actinobacteria, Chloroflexi, and Zygomycota phyla exhibited a significant (P < 0.05) negative correlation with yields during continuous cultivation. Some Actinobacteria members showed reduced microbial diversity, which prevented continuous ramie cropping. Ascomycota, Zygomycota, and Basidiomycota were the main fungal phyla. The relatively high abundance of Bacillus observed in healthy ramie may contribute to disease suppression, thereby promoting ramie growth. In summary, soil weakness and increased disease in ramie plants after long-term continuous cropping can be attributed to changes in soil microbes, a reduction in beneficial microbes, and an accumulation of harmful microbes.

Microbial communities in peatlands along a chronosequence on the Sanjiang Plain, China

Microbial communities play crucial roles in the global carbon cycle, particularly in peatland ecosystems under climate change. The peatlands of the Sanjiang Plain could be highly vulnerable to global warming because they are mainly located at the southern limit of northern peatlands. In this study, the alpha diversity and composition of bacterial communities in three different minerotrophic fens along a chronosequence were investigated. We captured a rich microbial community that included many rare operational taxonomic units (OTUs) but was dominated by a few bacterial classes that have frequently been detected in other peatland ecosystems. Notably, a large diversity of methanotrophs affiliated with Alpha- and Gammaproteobacteria was also detected. Bacterial alpha diversity and composition varied as a function of peat depth and its associated physical-chemical properties, such as total carbon, total nitrogen, pH and bulk density. We also found that bacterial community turnover (beta diversity) to be significantly correlated with soil age, whereas bacterial alpha diversity was not.

Symptom Development in Response to Combined Infection of In Vitro-grown Lilium longiflorum with Pratylenchus penetrans and Soilborne Fungi Collected from Diseased Roots of Field-grown Lilies

Eight fungal isolates (ELRF 1 to 8) were recovered from necrotic roots of Easter lilies, Lilium longiflorum cv. Nellie White, grown in a field in the U.S. Pacific Northwest. The eight fungal isolates were identified by sequencing and molecular phylogenetic analyses based on their ITS rDNA region. Five isolates were identified as Fusarium oxysporum, two as F. tricinctum, and one as Rhizoctonia sp. AG-I. This constitutes the first report of Rhizoctonia sp. AG-I infecting lilies worldwide and the first report of F. tricinctum infecting lilies in the United States. To study and validate their pathogenicity, pure cultures of each isolate were used to infect the roots of Easter lily plants growing in vitro. In addition, Easter lily plants growing in vitro were infected either with or without Pratylenchus penetrans, the root lesion nematode, prior to placing a culture plug of fungus 1 cm from a lily root. Pratylenchus penetrans is a nematode species commonly found in the sampled fields. The presence of both nematode and Rhizoctonia sp. AG-I isolate ELRF 3 in infected lilies was evaluated by molecular analyses, confirming the infection of roots 3 days after inoculation, prior to development of disease symptoms. Necrosis and root rot developed more rapidly with all eight fungal isolates when there had been prior infection with P. penetrans, the major nematode parasitizing Easter lily roots in the field in Oregon.