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19 pages, 9320 KiB

Open AccessArticle

Isolation, Identification, and Biocontrol Mechanisms of Endophytic Burkholderia arboris DHR18 from Rubber Tree against Red Root Rot Disease

by Xiangjia Meng, Youhong Luo, Xinyang Zhao, Yongwei Fu, Lifang Zou, Haibin Cai, Yi Zhou and Min Tu

Microorganisms 2024, 12(9), 1793; https://doi.org/10.3390/microorganisms12091793 - 29 Aug 2024

Viewed by 754

Abstract

Red root rot disease is a devastating fungal disease of rubber trees caused by Ganoderma pseudoferreum (Wakef). Biocontrols using beneficial microorganisms are safe and sustainable. We isolated a DHR18 endophytic bacterium from a healthy rubber tree to obtain a new efficient antagonistic bacterium [...] Read more.

Red root rot disease is a devastating fungal disease of rubber trees caused by Ganoderma pseudoferreum (Wakef). Biocontrols using beneficial microorganisms are safe and sustainable. We isolated a DHR18 endophytic bacterium from a healthy rubber tree to obtain a new efficient antagonistic bacterium for red root rot disease affecting rubber trees and evaluated the mechanism of action involved using a double culture assay, genome annotation analysis, and the ethyl acetate extraction method. The results revealed that the DHR18 strain inhibits G. pseudoferreum growth and has broad-spectrum antifungal activity by secreting cell wall hydrolases (proteases and chitinases), indole-3-acetic acid, and siderophores. Furthermore, it fixes nitrogen and is involved in biofilm formation and phosphate solubilisation, improving disease resistance and tree growth. The results showed that the antifungal substances secreted by DHR18 are mainly lipopeptides. Simultaneously, DHR18 enhanced the rubber tree resistance to G. pseudoferreum by increasing the activities of defence enzymes superoxide dismutase, phenylalanine ammonia lyase, peroxidase, catalase, and polyphenol oxidase. The results indicate that B. arboris DHR18 has biocontrol potential and could be used as a candidate strain for the control of red root rot disease in rubber trees. Full article

(This article belongs to the Special Issue Plant-Microbe Interaction State-of-the-Art Research in China)

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12 pages, 3818 KiB

Open AccessArticle

Population Genomics analysis of Leptosphaeria biglobosa Associated with Brassica napus in China Reveals That Geographical Distribution Influences Its Genetic Polymorphism

by Yiji Shi, Zhiting Guo, Shunjun Bao, Jiali Xu, Keqi Li, Songbai Rong, Qiangsheng Li, Aixia Xu, Duojie Zhandui, Zhen Huang and Mingguang Chu

Microorganisms 2024, 12(7), 1347; https://doi.org/10.3390/microorganisms12071347 - 1 Jul 2024

Viewed by 889

Abstract

Blackleg disease, a major threat to Brassica crops worldwide, is primarily caused by the pathogen Leptosphaeria biglobosa. Investigating the genetic variation of L. biglobosa is crucial for managing and preventing the disease in Brassica napus. To date, there is scarce genomic [...] Read more.

Blackleg disease, a major threat to Brassica crops worldwide, is primarily caused by the pathogen Leptosphaeria biglobosa. Investigating the genetic variation of L. biglobosa is crucial for managing and preventing the disease in Brassica napus. To date, there is scarce genomic variation information available for populations of L. biglobosa in China. In this study, 73 L. biglobosa strains of canola stalks were collected from 12 provinces in China and subjected to re-sequencing. The 73 assemblies averaged 1340 contigs, 72,123 bp N50, and 30.17 Mb in size. In total, 9409 core orthogroups and 867 accessory orthogroups were identified. A total of 727,724 mutation loci were identified, including 695,230 SNPs and 32,494 indels. Principal component analysis (PCA) and population structure analysis showed that these strains could be divided into seven subgroups. The strains in most provinces were clustered into a single subgroup, suggesting a strong influence of the geographic environment on strain variation. The average nucleotide diversity (θπ) of all strains was 1.03 × 10⁻³, indicating important genetic diversity among strains from different regions of China. This study provides valuable resources for future comparative genomics, gives new insights into the population evolution of L. biglobosa, and supports the development of strategies for managing blackleg disease in canola. Full article

(This article belongs to the Special Issue Plant-Microbe Interaction State-of-the-Art Research in China)

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16 pages, 3966 KiB

Open AccessArticle

Leaf Health Status Regulates Endophytic Microbial Community Structure, Network Complexity, and Assembly Processes in the Leaves of the Rare and Endangered Plant Species Abies fanjingshanensis

by Long Li, Rong Zheng, Zuhua Wang, Haibo Li, Yongjia Shi, Zhongjie Pan and Min Liu

Microorganisms 2024, 12(7), 1254; https://doi.org/10.3390/microorganisms12071254 - 21 Jun 2024

Cited by 1 | Viewed by 860

Abstract

The rare and endangered plant species Abies fanjingshanensis, which has a limited habitat, a limited distribution area, and a small population, is under severe threat, particularly due to poor leaf health. The plant endophytic microbiome is an integral part of the host, [...] Read more.

The rare and endangered plant species Abies fanjingshanensis, which has a limited habitat, a limited distribution area, and a small population, is under severe threat, particularly due to poor leaf health. The plant endophytic microbiome is an integral part of the host, and increasing evidence indicates that the interplay between plants and endophytic microbes is a key determinant for sustaining plant fitness. However, little attention has been given to the differences in the endophytic microbial community structure, network complexity, and assembly processes in leaves with different leaf health statuses. Here, we investigated the endophytic bacterial and fungal communities in healthy leaves (HLs) and non-healthy leaves (NLs) of A. fanjingshanensis using 16S rRNA gene and internal transcribed spacer sequencing and evaluated how leaf health status affects the co-occurrence patterns and assembly processes of leaf endophytic microbial communities based on the co-occurrence networks, the niche breadth index, a neutral community model, and C-score metrics. HLs had significantly greater endophytic bacterial and fungal abundance and diversity than NLs, and there were significant differences in the endophytic microbial communities between HLs and NLs. Leaf-health-sensitive endophytic microbes were taxonomically diverse and were mainly grouped into four ecological clusters according to leaf health status. Poor leaf health reduced the complexity of the endophytic bacterial and fungal community networks, as reflected by a decrease in network nodes and edges and an increase in degrees of betweenness and assortativity. The stochastic processes of endophytic bacterial and fungal community assembly were weakened, and the deterministic processes became more important with declining leaf health. These results have important implications for understanding the ecological patterns and interactions of endophytic microbial communities in response to changing leaf health status and provide opportunities for further studies on exploiting plant endophytic microbes to conserve this endangered Abies species. Full article

(This article belongs to the Special Issue Plant-Microbe Interaction State-of-the-Art Research in China)

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22 pages, 5345 KiB

Open AccessArticle

Macrogenomics-Based Analysis of the Effects of Intercropped Soybean Photosynthetic Characteristics and Nitrogen-Assimilating Enzyme Activities on Yield at Different Nitrogen Levels

by Liqiang Zhang, Yudi Feng, Zehang Zhao, Bate Baoyin, Zhengguo Cui, Hongyu Wang, Qiuzhu Li and Jinhu Cui

Microorganisms 2024, 12(6), 1220; https://doi.org/10.3390/microorganisms12061220 - 18 Jun 2024

Viewed by 1044

Abstract

Currently, China’s soybean self-sufficiency rate is only 15%, highlighting the soybean crisis and the supply chain risks that pose a major threat to China’s food security. Thus, it has become imperative to step up efforts to boost soybean production capacity while promoting the [...] Read more.

Currently, China’s soybean self-sufficiency rate is only 15%, highlighting the soybean crisis and the supply chain risks that pose a major threat to China’s food security. Thus, it has become imperative to step up efforts to boost soybean production capacity while promoting the green and sustainable development of regional farmland ecosystems. In this context, the present study comprehensively investigated the effects of intercropping and nitrogen application rate on soybean yield, as well as the changes in gradients generated by different levels of nitrogen application. Based on six consecutive years of maize–soybean intercropping planting patterns, the inter-root soils of soybeans were collected at the flowering stage and evaluated for soil nitrogen content, nitrogen-assimilating enzyme activities, and microbial community composition of soybean, which were correlated with yield, to clarify the main pathways and modes of intercropping effects. The N₂ level (80 kg·ha⁻¹) was favourable for higher yield. In comparison to monocropping, the intercropping reduced yield by 9.65–13.01%, photosynthetic characteristics by 1.33–7.31%, and plant nitrogen-assimilating enzyme activities by 8.08–32.01% at the same level of N application. Likewise, soil urease and catalase activities were reduced by 9.22 and 1.80%, while soil nitrogen content declined by an average of 6.38%. Gemmatimonas and Bradyrhizobium enrichment significantly increased soil nitrogen content, photosynthetic characteristics, and soybean yield, while it was reduced by Candidatus_Udaeobacter and Candidatus_Solibacte enrichment. The results of this study provide a theoretical basis for further optimising maize–soybean intercropping, which is crucial for enhancing the agricultural production structure and improving the overall soybean production capacity. Full article

(This article belongs to the Special Issue Plant-Microbe Interaction State-of-the-Art Research in China)

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17 pages, 4845 KiB

Open AccessArticle

Maize/Soybean Intercropping with Straw Return Increases Crop Yield by Influencing the Biological Characteristics of Soil

by Jingjing Cui, Shuang Li, Bate Baoyin, Yudi Feng, Danyang Guo, Liqiang Zhang and Yan Gu

Microorganisms 2024, 12(6), 1108; https://doi.org/10.3390/microorganisms12061108 - 30 May 2024

Cited by 3 | Viewed by 1403

Abstract

With mounting demand for high-quality agricultural products and the relentless exploitation of arable land resources, finding sustainable ways to safely cultivate food crops is becoming ever more important. Here, we investigated the effects of the integrated cropping technique “straw return + intercropping” on [...] Read more.

With mounting demand for high-quality agricultural products and the relentless exploitation of arable land resources, finding sustainable ways to safely cultivate food crops is becoming ever more important. Here, we investigated the effects of the integrated cropping technique “straw return + intercropping” on the soil aggregates as well as the microbial biomass carbon (MBC) content, enzyme activities and microbial diversity in soils of maize and soybean crops. Our results show that in comparison to straw removal and monoculture, straw return and intercropping increase the rhizosphere’s MBC content (59.10%) of soil, along with urease (47.82%), sucrase (57.14%), catalase (16.14%) and acid phosphatase (40.66%) activities as well as the microbial diversity under maize and soybean. Under the same straw treatment, the yield of maize when intercropped surpassed that when grown in monoculture, with the land equivalent ratio of the intercropping treatment under straw return being highest. Overall, the intercropping of maize and soybean is beneficial for the healthy development of sustainable agriculture in the black soil region of northeast China, especially when combined with straw return to fields. Full article

(This article belongs to the Special Issue Plant-Microbe Interaction State-of-the-Art Research in China)

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17 pages, 9500 KiB

Open AccessArticle

The Growth-Promoting and Colonization of the Pine Endophytic Pseudomonas abietaniphila for Pine Wilt Disease Control

by Yueyuan Peng, Yuwei Tang, Da Li and Jianren Ye

Microorganisms 2024, 12(6), 1089; https://doi.org/10.3390/microorganisms12061089 - 27 May 2024

Viewed by 1143

Abstract

In this study, we focused on evaluating the impact of Pseudomonas abietaniphila BHJ04 on the growth of Pinus massoniana seedlings and its biocontrol efficacy against pine wilt disease (PWD). Additionally, the colonization dynamics of P. abietaniphila BHJ04 on P. massoniana were examined. The [...] Read more.

In this study, we focused on evaluating the impact of Pseudomonas abietaniphila BHJ04 on the growth of Pinus massoniana seedlings and its biocontrol efficacy against pine wilt disease (PWD). Additionally, the colonization dynamics of P. abietaniphila BHJ04 on P. massoniana were examined. The growth promotion experiment showed that P. abietaniphila BHJ04 significantly promoted the growth of the branches and roots of P. massoniana. Pot control experiments indicated that strain BHJ04 significantly inhibited the spread of PWD. There were significant changes in the expression of several genes related to pine wood nematode defense in P. massoniana, including chitinase, nicotinamide synthetase, and triangular tetrapeptide-like superfamily protein isoform 9. Furthermore, our results revealed significant upregulation of genes associated with the water stress response (dehydration-responsive proteins), genetic material replication (DNA/RNA polymerase superfamily proteins), cell wall hydrolase, and detoxification (cytochrome P450 and cytochrome P450 monooxygenase superfamily genes) in the self-regulation of P. massoniana. Colonization experiments demonstrated that strain BHJ04 can colonize the roots, shoots, and leaves of P. massoniana, and the colonization amount on the leaves was the greatest, reaching 160,000 on the 15th day. However, colonization of the stems lasted longer, with the highest level of colonization observed after 45 d. This study provides a preliminary exploration of the growth-promoting and disease-preventing mechanisms of P. abietaniphila BHJ04 and its ability to colonize pines, thus providing a new biocontrol microbial resource for the biological control of plant diseases. Full article

(This article belongs to the Special Issue Plant-Microbe Interaction State-of-the-Art Research in China)

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16 pages, 6140 KiB

Open AccessArticle

Bacterial Lipopeptides Are Effective against Pear Fire Blight

by Ihsan ud Din, Lina Hu, Yuan Jiang, Jie Wei, Muhammad Afzal and Li Sun

Microorganisms 2024, 12(5), 896; https://doi.org/10.3390/microorganisms12050896 - 29 Apr 2024

Viewed by 1216

Abstract

Fire blight, a devastating disease caused by Erwinia amylovora, poses a significant threat to pear and apple trees in Xinjiang province, China. In an effort to combat this pathogen, we isolated 10 bacteria from various components of apple and crabapple trees and [...] Read more.

Fire blight, a devastating disease caused by Erwinia amylovora, poses a significant threat to pear and apple trees in Xinjiang province, China. In an effort to combat this pathogen, we isolated 10 bacteria from various components of apple and crabapple trees and conducted screenings to assess their ability to inhibit E. amylovora in vitro. Through biochemical tests and partial 16S rRNA gene sequencing, we identified two promising strains, Priestia megaterium strain H1 and Bacillus subtilis strain I2. These strains were then evaluated for their efficacy in biocontrol under controlled laboratory conditions, focusing on immature fruits and leaves. Remarkably, all selected antagonists exhibited the capability to reduce the severity of the disease on both fruit and leaves. P. megaterium strain H1 and B. subtilis strain I2 exhibited significant reductions in disease incidence on both immature fruits and leaves compared to the control. Specifically, on immature fruits, they achieved reductions of 53.39% and 44.76%, respectively, while on leaves, they demonstrated reductions of 59.55% and 55.53%, respectively. Furthermore, during the study, we detected the presence of lipopeptides, including surfactin, iturins, bacillomycin D, and fengycins, in the methanol extract obtained from these two antagonistic bacteria using thin-layer chromatography (TLC). Based on the results obtained, B. subtilis strain I2 and P. megaterium strain H1 exhibit considerable potential for controlling fire blight. However, further evaluation of their efficacy under natural field conditions is essential to validate their practicality as a biocontrol method. Full article

(This article belongs to the Special Issue Plant-Microbe Interaction State-of-the-Art Research in China)

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18 pages, 2585 KiB

Open AccessArticle

Difference in the Effect of Applying Bacillus to Control Tomato Verticillium Wilt in Black and Red Soil

by Zhenhua Guo, Ziyu Lu, Zhongwang Liu, Wei Zhou, Shuangyu Yang, Jiayan Lv and Mi Wei

Microorganisms 2024, 12(4), 797; https://doi.org/10.3390/microorganisms12040797 - 15 Apr 2024

Viewed by 1070

Abstract

In practical applications, the effectiveness of biological control agents such as Bacillus is often unstable due to different soil environments. Herein, we aimed to explore the control effect and intrinsic mechanism of Bacillus in black soil and red soil in combination with tomato [...] Read more.

In practical applications, the effectiveness of biological control agents such as Bacillus is often unstable due to different soil environments. Herein, we aimed to explore the control effect and intrinsic mechanism of Bacillus in black soil and red soil in combination with tomato Verticillium wilt. Bacillus application effectively controlled the occurrence of Verticillium wilt in red soil, reducing the incidence by 19.83%, but played a limited role in black soil. Bacillus colonized red soil more efficiently. The Verticillium pathogen decreased by 71.13% and 76.09% after the application of Bacillus combinations in the rhizosphere and bulk of the red soil, respectively, while there was no significant difference in the black soil. Additionally, Bacillus application to red soil significantly promoted phosphorus absorption. Furthermore, it significantly altered the bacterial community in red soil and enriched genes related to pathogen antagonism and phosphorus activation, which jointly participated in soil nutrient activation and disease prevention, promoting tomato plant growth in red soil. This study revealed that the shaping of the bacterial community by native soil may be the key factor affecting the colonization and function of exogenous Bacillus. Full article

(This article belongs to the Special Issue Plant-Microbe Interaction State-of-the-Art Research in China)

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15 pages, 2897 KiB

Open AccessArticle

Multi-Omics Approaches Provide New Insights into the Identification of Putative Fungal Effectors from Valsa mali

by Gulnaz Kahar, Yakupjan Haxim, Abdul Waheed, Tohir A. Bozorov, Xiaojie Liu, Xuejing Wen, Mingqi Zhao and Daoyuan Zhang

Microorganisms 2024, 12(4), 655; https://doi.org/10.3390/microorganisms12040655 - 26 Mar 2024

Viewed by 1427

Abstract

Pathogenic fungi secrete numerous effectors into host cells to manipulate plants’ defense mechanisms. Valsa mali, a necrotrophic fungus, severely impacts apple production in China due to the occurrence of Valsa canker. Here, we predicted 210 candidate effector protein (CEP)-encoding genes from V. [...] Read more.

Pathogenic fungi secrete numerous effectors into host cells to manipulate plants’ defense mechanisms. Valsa mali, a necrotrophic fungus, severely impacts apple production in China due to the occurrence of Valsa canker. Here, we predicted 210 candidate effector protein (CEP)-encoding genes from V. mali. The transcriptome analysis revealed that 146 CEP-encoding genes were differentially expressed during the infection of the host, Malus sieversii. Proteome analysis showed that 27 CEPs were differentially regulated during the infection stages. Overall, 25 of the 146 differentially expressed CEP-encoding genes were randomly selected to be transiently expressed in Nicotiana benthamiana. Pathogenicity analysis showed that the transient expression of VM1G-05058 suppressed BAX-triggered cell death while the expression of VM1G-10148 and VM1G-00140 caused cell death in N. benthamiana. In conclusion, by using multi-omics analysis, we identified potential effector candidates for further evaluation in vivo. Our results will provide new insights into the investigation of virulent mechanisms of V. mali. Full article

(This article belongs to the Special Issue Plant-Microbe Interaction State-of-the-Art Research in China)

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13 pages, 3662 KiB

Open AccessArticle

Comparison of Rhizosphere Bacterial Communities of Pinus squamata, a Plant Species with Extremely Small Populations (PSESP) in Different Conservation Sites

by Fengrong Li, Shugang Lu and Weibang Sun

Microorganisms 2024, 12(4), 638; https://doi.org/10.3390/microorganisms12040638 - 22 Mar 2024

Viewed by 1042

Abstract

Pinus squamata is one of the most threatened conifer species in the world. It is endemic to northeastern Yunnan Province, China, and has been prioritized as a Plant Species with Extremely Small Populations (PSESP). The integrated study of soil properties and rhizosphere bacteria [...] Read more.

Pinus squamata is one of the most threatened conifer species in the world. It is endemic to northeastern Yunnan Province, China, and has been prioritized as a Plant Species with Extremely Small Populations (PSESP). The integrated study of soil properties and rhizosphere bacteria can assist conservation to understand the required conditions for the protection and survival of rare and endangered species. However, differences between the rhizospheric bacterial communities found in the soil surrounding P. squamata at different conservation sites remain unclear. In this study, Samples were collected from wild, ex situ, and reintroduced sites. Bacterial communities in different conservation sites of P. squamata rhizosphere soils were compared using Illumina sequencing. The soil physicochemical properties were determined, the relationships between the bacterial communities and soil physicochemical factors were analyzed, and the potential bacterial ecological functions were predicted. The reintroduced site Qiaojia (RQ) had the highest richness and diversity of bacterial community. Actinobacteria, Proteobacteria, and Acidobacteriota were the dominant phyla, and Bradyrhizobium, Mycobacterium, Acidothermus were the most abundant genera. Samples were scattered (R = 0.93, p = 0.001), indicating significant difference between the different conservation sites. The abundance of Mycobacterium differed between sites (0.01 < p ≤ 0.05), and the relative abundances of Bradyrhizobium and Acidothermus differed significantly among different sites (0.001 < p ≤ 0.01). Soil total potassium (TK) and available nitrogen (AN) were the main factors driving bacterial community at the phylum level (0.01 < p ≤ 0.05). This study generated the first insights into the diversity, compositions, and potential functions of bacterial communities associated with the rhizosphere soils of P. squamata in different conservation sites and provides a foundation to assess the effect of conservation based on bacterial diversity and plant growth-promoting rhizobacteria (PGPR) to guide future research into the conservation of P. squamata. Full article

(This article belongs to the Special Issue Plant-Microbe Interaction State-of-the-Art Research in China)

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19 pages, 5102 KiB

Open AccessArticle

A Novel Strain of Bacillus cereus with a Strong Antagonistic Effect Specific to Sclerotinia and Its Genomic and Transcriptomic Analysis

by Wanfu Ma, Jinhao Ding, Qingyun Jia, Qianru Li, Shanhai Jiao, Xupeng Guo, Chengming Fan, Yuhong Chen and Zanmin Hu

Microorganisms 2024, 12(3), 611; https://doi.org/10.3390/microorganisms12030611 - 19 Mar 2024

Cited by 1 | Viewed by 1469

Abstract

Sclerotinia, which is caused by Sclerotinia sclerotiorum, is a severe disease of oilseed rape, which is an important oil crop worldwide. In this study, we isolated a novel strain of Bacillus cereus, named B. cereus HF10, from the rhizosphere soil of [...] Read more.

Sclerotinia, which is caused by Sclerotinia sclerotiorum, is a severe disease of oilseed rape, which is an important oil crop worldwide. In this study, we isolated a novel strain of Bacillus cereus, named B. cereus HF10, from the rhizosphere soil of the reed on the seaside of Yagzhou Bay, Sanya city, Hainan Province, China. HF10 exhibited a significant antagonistic effect on Sclerotinia sclerotiorum, with an inhibition rate of 79%, and to other species in Sclerotinia, but no antagonistic effect was found on various other fungi or bacteria. HF10 had an 82.3% inhibitory effect on the S. sclerotiorum infection of oilseed rape leaves and a 71.7% control effect on Sclerotinia infection in oilseed rape based on in vitro and in vivo experiments, respectively. The genomics and transcriptomics of HF10 and its loss of the antifungal function mutant Y11 were analyzed, and the results provided insight into potential antifungal substances. Our work provides a novel strain, HF10, for developing a promising biological control agent against Sclerotinia, which infects oilseed rape and other plants. Full article

(This article belongs to the Special Issue Plant-Microbe Interaction State-of-the-Art Research in China)

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18 pages, 3903 KiB

Open AccessArticle

Isolation and Identification of Biocontrol Bacteria against Atractylodes Chinensis Root Rot and Their Effects

by Shouyang Luo, Chunjie Tian, Hengfei Zhang, Zongmu Yao, Zhihui Guan, Yingxin Li, Jianfeng Zhang and Yanyu Song

Microorganisms 2023, 11(10), 2384; https://doi.org/10.3390/microorganisms11102384 - 25 Sep 2023

Cited by 3 | Viewed by 1872

Abstract

Fusarium root rot (FRR) seriously affects the growth and productivity of A. chinensis. Therefore, protecting A. chinensis from FRR has become an important task, especially for increasing A. chinensis production. The purpose of this study was to screen FRR control strains from [...] Read more.

Fusarium root rot (FRR) seriously affects the growth and productivity of A. chinensis. Therefore, protecting A. chinensis from FRR has become an important task, especially for increasing A. chinensis production. The purpose of this study was to screen FRR control strains from the A. chinensis rhizosphere soil. Eighty-four bacterial strains and seven fungal strains were isolated, and five strains were identified with high inhibitory effects against Fusarium oxysporum (FO): Trichoderma harzianum (MH), Bacillus amyloliquefaciens (CJ5, CJ7, and CJ8), and Bacillus subtilis (CJ9). All five strains had high antagonistic effects in vitro. Results showed that MH and CJ5, as biological control agents, had high control potential, with antagonistic rates of 86.01% and 82.78%, respectively. In the pot experiment, the growth levels of roots and stems of A. chinensis seedlings treated with MH+CJ were significantly higher than those of control plants. The total nitrogen, total phosphorus, total potassium, indoleacetic acid, and chlorophyll contents in A. chinensis leaves were also significantly increased. In the biocontrol test, the combined MH + CJ application significantly decreased the malondialdehyde content in A. chinensis roots and significantly increased the polyphenol oxidase, phenylalanine ammonolyase, and peroxidase ability, indicating a high biocontrol effect. In addition, the application of Bacillus spp. and T. harzianum increased the abundance and diversity of the soil fungal population, improved the soil microbial community structure, and significantly increased the abundance of beneficial strains, such as Holtermanniella and Metarhizium. The abundance of Fusarium, Volutella, and other pathogenic strains was significantly reduced, and the biocontrol potential of A. chinensis root rot was increased. Thus, Bacillus spp. and T. harzianum complex bacteria can be considered potential future biocontrol agents for FRR. Full article

(This article belongs to the Special Issue Plant-Microbe Interaction State-of-the-Art Research in China)

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15 pages, 3123 KiB

Open AccessArticle

Core Endophytic Bacteria and Their Roles in the Coralloid Roots of Cultivated Cycas revoluta (Cycadaceae)

by Jiating Liu, Haiyan Xu, Zhaochun Wang, Jian Liu and Xun Gong

Microorganisms 2023, 11(9), 2364; https://doi.org/10.3390/microorganisms11092364 - 21 Sep 2023

Cited by 4 | Viewed by 1804

Abstract

As a gymnosperm group, cycads are known for their ancient origin and specialized coralloid root, which can be used as an ideal system to explore the interaction between host and associated microorganisms. Previous studies have revealed that some nitrogen-fixing cyanobacteria contribute greatly to [...] Read more.

As a gymnosperm group, cycads are known for their ancient origin and specialized coralloid root, which can be used as an ideal system to explore the interaction between host and associated microorganisms. Previous studies have revealed that some nitrogen-fixing cyanobacteria contribute greatly to the composition of the endophytic microorganisms in cycad coralloid roots. However, the roles of host and environment in shaping the composition of endophytic bacteria during the recruitment process remain unclear. Here, we determined the diversity, composition, and function prediction of endophytic bacteria from the coralloid roots of a widely cultivated cycad, Cycas revoluta Thunb. Using next-generation sequencing techniques, we comprehensively investigated the diversity and community structure of the bacteria in coralloid roots and bulk soils sampled from 11 sites in China, aiming to explore the variations in core endophytic bacteria and to predict their potential functions. We found a higher microbe diversity in bulk soils than in coralloid roots. Meanwhile, there was no significant difference in the diversity and composition of endophytic bacteria across different localities, and the same result was found after removing cyanobacteria. Desmonostoc was the most dominant in coralloid roots, followed by Nostoc, yet these two cyanobacteria were not shared by all samples. Rhodococcus, Edaphobacter, Niastella, Nordella, SH-PL14, and Virgisporangium were defined as the core microorganisms in coralloid roots. A function prediction analysis revealed that endophytic bacteria majorly participated in the plant uptake of phosphorus and metal ions and in disease resistance. These results indicate that the community composition of the bacteria in coralloid roots is affected by both the host and environment, in which the host is more decisive. Despite the very small proportion of core microbes, their interactions are significant and likely contribute to functions related to host survival. Our study contributes to an understanding of microbial diversity and composition in cycads, and it expands the knowledge on the association between hosts and symbiotic microbes. Full article

(This article belongs to the Special Issue Plant-Microbe Interaction State-of-the-Art Research in China)

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15 pages, 4223 KiB

Open AccessArticle

Diversity and Network Relationship Construction of Soil Fungal Communities in Lactarius hatsudake Tanaka Orchard during Harvest

by Airong Shen, Baoming Shen, Lina Liu, Yun Tan, Liangbin Zeng, Zhuming Tan and Jilie Li

Microorganisms 2023, 11(9), 2279; https://doi.org/10.3390/microorganisms11092279 - 11 Sep 2023

Cited by 3 | Viewed by 1546

Abstract

Lactarius hatsudake Tanaka is a mycorrhizal edible mushroom with rich economic and nutritional value. Although it is artificially planted, its yield is unstable. Soil fungi, including L. hatsudake, coexist with many other microorganisms and plants. Therefore, complex microbial communities have an influence [...] Read more.

Lactarius hatsudake Tanaka is a mycorrhizal edible mushroom with rich economic and nutritional value. Although it is artificially planted, its yield is unstable. Soil fungi, including L. hatsudake, coexist with many other microorganisms and plants. Therefore, complex microbial communities have an influence on the fruiting body formation of L. hatsudake. L. hatsudake and its interactions with the rest of the fungal community over time are not completely understood. In this study, we performed high-throughput sequencing of microorganisms in the basal soil of the fruiting body (JT), mycorrhizosphere soil (JG), and non-mushroom-producing soil (CK) in a 6-year-old L. hatsudake plantation at harvest. The results showed that the soil of the L. hatsudake plantation was rich in fungal communities and a total of 10 phyla, 19 classes, 53 orders, 90 families, 139 genera, and 149 species of fungi were detected. At the phylum level, the major groups were Basidiomycota and Ascomycota. At the genus level, the dominant groups were Lactarius, Trichoderma, Suillus, and Penicillium. Among them, L. hatsudake had an absolute dominant position in the soil fungal community of the plantation, and was the only group of Lactarius in the plantation soil. Penicillium cryptum and Penicillium adametzii were unique to the JT soil sample. Chaetopsphaeria, Myxocephala, Devriesia, and Psathyrella were positively correlated with L. hatsudake. In the constructed fungal network, the total number of nodes were ranked in descending order as JG (441) > CK (405) > JT (399), while the total number of edges were ranked in descending order as CK (1360) > JG (647) > JT (586). Analysis of the fungal assembly process revealed that groups CK and JG have determinative processes that dominated community building, while the JT group exhibited a dominant random process with a 0.60 probability. The results indicated that L. hatsudake was successfully colonized in the plantation soil. During harvest, the CK group exhibited the largest network size and the most complex fungal interactions, while the fungal community structure in the mushroom cultivation zone (JT and JG) was stable and less susceptible to external environmental interference. L. hatsudake affects the fungal community in the soil surrounding its fruiting body. Full article

(This article belongs to the Special Issue Plant-Microbe Interaction State-of-the-Art Research in China)

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15 pages, 2769 KiB

Open AccessArticle

Nigrospora oryzae Causing Leaf Spot Disease on Chrysanthemum × morifolium Ramat and Screening of Its Potential Antagonistic Bacteria

by Haodong Sha, Xinyi Liu, Xiaoe Xiao, Han Zhang, Xueting Gu, Weiliang Chen and Bizeng Mao

Microorganisms 2023, 11(9), 2224; https://doi.org/10.3390/microorganisms11092224 - 1 Sep 2023

Cited by 4 | Viewed by 2454

Abstract

Chrysanthemum × morifolium Ramat. is a famous perennial herb with medicinal, edible, and ornamental purposes, but the occurrence of plant diseases can reduce its value. A serious disease that caused leaf spots in C. morifolium appeared in 2022 in Tongxiang City, Zhejiang Province, [...] Read more.

Chrysanthemum × morifolium Ramat. is a famous perennial herb with medicinal, edible, and ornamental purposes, but the occurrence of plant diseases can reduce its value. A serious disease that caused leaf spots in C. morifolium appeared in 2022 in Tongxiang City, Zhejiang Province, China. The C. morifolium leaves with brown spots were collected and used for pathogen isolation. By completing Koch’s postulates, it was proven that the isolate had pathogenicity to infect C. morifolium. It was determined that the pathogen isolated from chrysanthemum leaves was Nigrospora oryzae, through morphology and a multilocus sequence analysis method using a combination of the internal transcribed spacer gene (ITS), beta-tubulin gene (TUB2), and translation elongation factor 1-alpha gene (TEF1-α). This is the first report of C. morifolium disease caused by N. oryzae in the world. Through dual culture assay on PDA plates, 12 strains of bacteria with antagonistic effects were selected from 231 strains from the C. morifolium phyllosphere, among which Bacillus siamensis D65 had the best inhibitory effect on N. oryzae growth. In addition, the components of a strain D65 fermentation broth were profiled by SPME-GC-Q-TOF analysis, providing a foundation for further application and research of biological control. Full article

(This article belongs to the Special Issue Plant-Microbe Interaction State-of-the-Art Research in China)

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16 pages, 4612 KiB

Open AccessArticle

Diversity and Abundance of Bacterial and Fungal Communities Inhabiting Camellia sinensis Leaf, Rhizospheric Soil, and Gut of Agriophara rhombata

by Hao Qu, Yaqin Long, Xuesong Wang, Kaibo Wang, Long Chen, Yunqiu Yang and Linbo Chen

Microorganisms 2023, 11(9), 2188; https://doi.org/10.3390/microorganisms11092188 - 30 Aug 2023

Cited by 2 | Viewed by 1417

Abstract

Agriophara rhombata is a tea leaf moth that is considered one of the most destructive pests of Camellia sinensis (tea plant). Several recent studies have shown that many insects acquire part of the microbiome from their host and soil, but the pattern and [...] Read more.

Agriophara rhombata is a tea leaf moth that is considered one of the most destructive pests of Camellia sinensis (tea plant). Several recent studies have shown that many insects acquire part of the microbiome from their host and soil, but the pattern and diversity of their microbiome have not been clearly demonstrated. The present study aimed to investigate the bacterial and fungal communities present in the rhizospheric soil and leaf of tea plant compared to the gut of tea moth at different developmental stages (larvae, pupae, adult female and male) using Illumina MiSeq technology. Alpha diversity (Shannon index) showed higher (p < 0.05) bacterial and fungal diversity in soil samples than in leaf and tea moth larvae, pupae, and adult gut samples. However, during different developmental stages of tea moth, bacterial and fungal diversity did not differ (p > 0.05) between larvae, pupae, female, and male guts. Beta diversity also revealed more distinct bacterial and fungal communities in soil and leaf samples compared with tea moth gut samples, which had a more similar microbiome. Furthermore, Proteobacteria, Firmicutes, and Tenericutes were detected as the dominant bacterial phyla, while Ascomycota, Basidiomycota, and Mortierellomycota were the most abundant fungal phyla among all groups, but their relative abundance was comparatively higher (p < 0.05) in soil and leaf samples compared to tea moth gut samples. Similarly, Klebsiella, Streptophyta, and Enterococcus were the top three bacterial genera, while Candida, Aureobasidium, and Strelitziana were the top three fungal genera, and their relative abundance varied significantly (p < 0.05) among all groups. The KEGG analysis also revealed significantly higher (p < 0.5) enrichment of the functional pathways of bacterial communities in soil and leaf samples than in tea moth gut samples. Our study concluded that the bacterial and fungal communities of soil and tea leaves were more diverse and were significantly different from the tea moth gut microbiome at different developmental stages. Our findings contribute to our understanding of the gut microbiota of the tea moth and its potential application in the development of pest management techniques. Full article

(This article belongs to the Special Issue Plant-Microbe Interaction State-of-the-Art Research in China)

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14 pages, 7669 KiB

Open AccessArticle

Phylogeny of Regulators of G-Protein Signaling Genes in Leptographium qinlingensis and Expression Levels of Three RGSs in Response to Different Terpenoids

by Tian Gan, Huanli An, Ming Tang and Hui Chen

Microorganisms 2022, 10(9), 1698; https://doi.org/10.3390/microorganisms10091698 - 24 Aug 2022

Cited by 2 | Viewed by 1612

Abstract

Leptographium qinlingensis is a bark beetle-vectored pine pathogen in the Chinese white pine beetle (Dendroctonus armandi) epidemic in Northwest China. L. qinlingensis colonizes pines despite the trees’ massive oleoresin terpenoid defenses. Regulators of G-protein signaling (RGS) proteins modulate heterotrimeric G-protein signaling [...] Read more.

Leptographium qinlingensis is a bark beetle-vectored pine pathogen in the Chinese white pine beetle (Dendroctonus armandi) epidemic in Northwest China. L. qinlingensis colonizes pines despite the trees’ massive oleoresin terpenoid defenses. Regulators of G-protein signaling (RGS) proteins modulate heterotrimeric G-protein signaling negatively and play multiple roles in the growth, asexual development, and pathogenicity of fungi. In this study, we have identified three L. qinlingensis RGS genes, and the phylogenetic analysis shows the highest homology with the regulators of G-protein signaling proteins sequence from Ophiostoma piceae and Grosmannia clavigera. The expression profiles of three RGSs in the mycelium of L. qinlingensis treated with six different terpenoids were detected, as well as their growth rates. Under six terpenoid treatments, the growth and reproduction in L. qinlingensis were significantly inhibited, and the growth inflection day was delayed from 8 days to 12–13 days. By analyzing the expression level of three RGS genes of L. qinlingensis with different treatments, results indicate that LqFlbA plays a crucial role in controlling fungal growth, and both LqRax1 and LqRgsA are involved in overcoming the host chemical resistances and successful colonization. Full article

(This article belongs to the Special Issue Plant-Microbe Interaction State-of-the-Art Research in China)

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Review

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19 pages, 2958 KiB

Open AccessReview

Alfalfa Spring Black Stem and Leaf Spot Disease Caused by Phoma medicaginis: Epidemic Occurrence and Impacts

by Yanru Lan, Wennan Zhou, Tingyu Duan, Yanzhong Li, Cory Matthew and Zhibiao Nan

Microorganisms 2024, 12(7), 1279; https://doi.org/10.3390/microorganisms12071279 - 24 Jun 2024

Viewed by 961

Abstract

Alfalfa spring black stem and leaf spot disease (ASBS) is a cosmopolitan soil-borne and seed-borne disease caused by Phoma medicaginis, which adversely affects the yield, and nutritive value and can stimulate production of phyto-oestrogenic compounds at levels that may adversely affect ovulation [...] Read more.

Alfalfa spring black stem and leaf spot disease (ASBS) is a cosmopolitan soil-borne and seed-borne disease caused by Phoma medicaginis, which adversely affects the yield, and nutritive value and can stimulate production of phyto-oestrogenic compounds at levels that may adversely affect ovulation rates in animals. This review summarizes the host range, damage, and symptoms of this disease, and general features of the infection cycle, epidemic occurrence, and disease management. ASBS has been reported from over 40 countries, and often causes severe yield loss. Under greenhouse conditions, reported yield loss was 31–82% for roots, 32–80% for leaves, 21% for stems and 26–28% for seedlings. In field conditions, the forage yield loss is up to 56%, indicating that a single-cut yield of 5302 kg/ha would be reduced to 2347 kg/ha. P. medicaginis can infect up to 50 species of plants, including the genera Medicago, Trifolium, Melilotus, and Vicia. ASBS is more severe during warm spring conditions before the first harvest than in hot summer and cooler winter conditions, and can infect alfalfa roots, stems, leaves, flowers, pods, and seeds, with leaf spot and/or black stem being the most typical symptoms. The primary infection is caused by the overwintering spores and mycelia in the soil, and on seeds and the cortex of dead and dry stems. The use of resistant cultivars is the most economical and effective strategy for the control of ASBS. Although biological control has been studied in the glasshouse and is promising, chemical control is the main control method in agriculture. Full article

(This article belongs to the Special Issue Plant-Microbe Interaction State-of-the-Art Research in China)

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