1
|
Zhang P, Ding W, Zheng H. Composition and diversity of endophytic bacterial communities in the tubers of Pinellia ternata from different regions and their effects on succinate biosynthesis based on high-throughput sequencing. 3 Biotech 2024; 14:262. [PMID: 39381023 PMCID: PMC11456575 DOI: 10.1007/s13205-024-04108-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Accepted: 09/25/2024] [Indexed: 10/10/2024] Open
Abstract
In this study, high-throughput sequencing (HTS) technology was used to investigate the composition and diversity of endophytic bacteria and their effects on succinic acid biosynthesis in P. ternata tubers from three different geographical locations (MS, SL, and ZT). A total of 1777 amplicon sequence variants (ASVs) were annotated, and the diversity and composition of endophytic bacteria in P. ternata tubers were significantly different among different regions. The ZT samples presented the highest α diversity, and the Shannon diversity, richness, and Pielou evenness index were all ZT > MS > SL. Co-occurrence network analysis revealed that endophytic bacterial groups such as Stenotrophomonas, Pseudomonas, Mycobacterium, and Chryseomicrobium were key groups in the endophytic bacterial interaction network, indicating that they play a role in maintaining community stability. In addition, some endophytic bacteria were associated with the biosynthesis of succinic acid, a key bioactive compound in P. ternata. The succinate content was positively correlated with the genera Brevundimonas, Ensifer, Nocardioides, and Paenibacillus, while it was negatively correlated with the genera Lentimicrobium, Anaerovorax, and Pajaroellobacter. These findings highlight the key role of endophytic bacteria in regulating the efficacy of P. ternata. These findings provide key information for further elucidating the mechanism by which endophytic bacteria affect the synthesis of bioactive compounds.
Collapse
Affiliation(s)
- Peng Zhang
- Research Center for Ecology, College of Science, Tibet University, Lhasa, 850000 China
| | - Wei Ding
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, 430070 China
| | - Heng Zheng
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan, 430070 China
| |
Collapse
|
2
|
Hou W, Xing Y, Xue H, Huang Y, Huang Y, Men W, Yang Y, Kang T, Dou D, Zheng H, Xu L. Exploring the diversity and potential functional characteristics of microbiota associated with different compartments of Schisandra chinensis. Front Microbiol 2024; 15:1419943. [PMID: 38939187 PMCID: PMC11208631 DOI: 10.3389/fmicb.2024.1419943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 06/03/2024] [Indexed: 06/29/2024] Open
Abstract
Introduction Symbiotic microbial have a significant impact on the growth and metabolism of medicinal plants. Schisandra chinensis is a very functionally rich medicinal herb; however, its microbial composition and diversity have been poorly studied. Methods In the present study, the core microbiomes associated with the rhizospheric soil, roots, stems, leaves, and fruits of S. chinensis from six geographic locations were analyzed by a macro-genomics approach. Results Alpha and beta diversity analyses showed that the diversity of microbial composition of S. chinensis fruits did not differ significantly among the geographic locations as compared to that in different plant compartments. Principal coordinate analysis showed that the microbial communities of S. chinensis fruits from the different ecological locations were both similar and independent. In all S. chinensis samples, Proteobacteria was the most dominant bacterial phylum, and Ascomycota and Basidiomycota were the most dominant fungal phyla. Nitrospira, Bradyrhizobium, Sphingomonas, and Pseudomonas were the marker bacterial populations in rhizospheric soils, roots, stems and leaves, and fruits, respectively, and Penicillium, Golubevia, and Cladosporium were the marker fungal populations in the rhizospheric soil and roots, stems and leaves, and fruits, respectively. Functional analyses showed a high abundance of the microbiota mainly in biosynthesis. Discussion The present study determined the fungal structure of the symbiotic microbiome of S. chinensis, which is crucial for improving the yield and quality of S. chinensis.
Collapse
Affiliation(s)
- Wenjuan Hou
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Yanping Xing
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Hefei Xue
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Yanchang Huang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Yutong Huang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Wenxiao Men
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Yanyun Yang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
- State Key Laboratory of Dao-di Herbs, Beijng, China
| | - Tingguo Kang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Deqiang Dou
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Han Zheng
- State Key Laboratory of Dao-di Herbs, Beijng, China
| | - Liang Xu
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
- State Key Laboratory of Dao-di Herbs, Beijng, China
| |
Collapse
|
3
|
Kovalev MA, Gladysh NS, Bogdanova AS, Bolsheva NL, Popchenko MI, Kudryavtseva AV. Editing Metabolism, Sex, and Microbiome: How Can We Help Poplar Resist Pathogens? Int J Mol Sci 2024; 25:1308. [PMID: 38279306 PMCID: PMC10816636 DOI: 10.3390/ijms25021308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 01/14/2024] [Accepted: 01/19/2024] [Indexed: 01/28/2024] Open
Abstract
Poplar (Populus) is a genus of woody plants of great economic value. Due to the growing economic importance of poplar, there is a need to ensure its stable growth by increasing its resistance to pathogens. Genetic engineering can create organisms with improved traits faster than traditional methods, and with the development of CRISPR/Cas-based genome editing systems, scientists have a new highly effective tool for creating valuable genotypes. In this review, we summarize the latest research data on poplar diseases, the biology of their pathogens and how these plants resist pathogens. In the final section, we propose to plant male or mixed poplar populations; consider the genes of the MLO group, transcription factors of the WRKY and MYB families and defensive proteins BbChit1, LJAMP2, MsrA2 and PtDef as the most promising targets for genetic engineering; and also pay attention to the possibility of microbiome engineering.
Collapse
Affiliation(s)
- Maxim A. Kovalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
- Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Natalya S. Gladysh
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
| | - Alina S. Bogdanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
- Institute of Agrobiotechnology, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, 127434 Moscow, Russia
| | - Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
| | - Mikhail I. Popchenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
| | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
| |
Collapse
|
4
|
Liu J, Qiu S, Yang L, Yang C, Xue T, Yuan Y. Germination of pecan seeds changes the microbial community. PeerJ 2023; 11:e16619. [PMID: 38107585 PMCID: PMC10725176 DOI: 10.7717/peerj.16619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/16/2023] [Indexed: 12/19/2023] Open
Abstract
Endophytes are core of the plant-associated microbiome, and seed endophytes are closely related to the plant growth and development. Seed germination is an important part of pecan's life activities, but the composition and changes of microbes during different germination processes have not yet been revealed in pecan seeds. In order to deeply explore the characteristics of endophytes during the germination process of pecan, high-throughput sequencing was performed on seeds at four different germination stages. Findings of present study was found that the diversity and composition of microorganisms were different in different germination stages, and the microbial richness and diversity were highest in the seed endocarp break stage. It was speculated that the change of endophytes in pecan seeds was related to the germination stage. By evaluating the relationship between microbial communities, the core microbiota Cyanobacteria, Proteobacteria and Actinobacteria (bacterial) and Anthophyta and Ascomycota (fungal) core microbiota were identified in germinating pecan seeds. Finally, biomarkers in different germination processes of pecan seeds were identified by LEfSe analysis, among which Proteobacteria, Gamma proteobacteria and, Cyanobacteria and Ascomycota and Sordariomycetes were most abundant. Thus, this study will help to explore the interaction mechanism between pecan seeds and endophytes in different germination processes, and provide materials for the research and development of pecan seed endophytes.
Collapse
Affiliation(s)
- Jia Liu
- Department of Civil and Architecture and Engineering, Chuzhou University, Anhui, China
| | - Sumei Qiu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Liping Yang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Can Yang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Tingting Xue
- Department of Civil and Architecture and Engineering, Chuzhou University, Anhui, China
| | - Yingdan Yuan
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| |
Collapse
|
5
|
Liu J, Xu H, Wang Z, Liu J, Gong X. Core Endophytic Bacteria and Their Roles in the Coralloid Roots of Cultivated Cycas revoluta (Cycadaceae). Microorganisms 2023; 11:2364. [PMID: 37764208 PMCID: PMC10537169 DOI: 10.3390/microorganisms11092364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/10/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
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 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.
Collapse
Affiliation(s)
- Jiating Liu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (H.X.); (Z.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiyan Xu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (H.X.); (Z.W.)
| | - Zhaochun Wang
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (H.X.); (Z.W.)
| | - Jian Liu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (H.X.); (Z.W.)
| | - Xun Gong
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (H.X.); (Z.W.)
| |
Collapse
|
6
|
Wang X, Wu G, Han S, Yang J, He X, Li H. Differentiation and Identification of Endophytic Bacteria from Populus Based on Mass Fingerprints and Gene Sequences. Int J Mol Sci 2023; 24:13449. [PMID: 37686254 PMCID: PMC10487577 DOI: 10.3390/ijms241713449] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Plant endophytic bacteria play important roles in plants' growth and resistance to stress. It is important to characterize endophytic bacteria to be able to understand their benefits. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has become a powerful technique for bacterial identification due to its high throughput and simple procedures. In this study, the endophytic bacteria separated from Populus (the leaves, roots and stems of Populus tomentosa Carrière; stems of Populus nigra Linn. var. nigra; and stems of Populus canadensis Moench) were identified and classified based on MALDI-TOF MS data and 16S rRNA gene sequencing. The sampling and preparation of bacteria were optimized to obtain meaningful protein mass fingerprints. The composite correlation index (CCI) values of the inter-genera and inter-species protein mass fingerprints demonstrated sufficient differences between the strains. In the CCI value matrix for ten species in the same genus, all the CCI values were less than 0.5. Among the species, 95.6% of all the CCI values were less than 0.5. After data processing, the classification capacity of the protein mass fingerprints was verified using inter-specific and inter-generic PCoA. To compare different methods' potential for differentiation and phylogenetic analysis, a dendrogram of the MS profiles and a phylogenetic tree based on the 16S rRNA gene sequences were constructed using 61 endophytic bacteria found in Populus. The clustering and grouping results show that the phylogenetic analysis based on MALDI-TOF MS is similar to that based on 16S rRNA gene sequencing. This study provides a valuable reference for differentiating and identifying endophytic bacteria according to their protein mass fingerprints.
Collapse
Affiliation(s)
- Xia Wang
- College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (X.W.); (G.W.); (S.H.); (J.Y.)
- Department of Chemistry, MOE (Ministry of Education) Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Guanqi Wu
- College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (X.W.); (G.W.); (S.H.); (J.Y.)
- Department of Chemistry, MOE (Ministry of Education) Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Shuo Han
- College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (X.W.); (G.W.); (S.H.); (J.Y.)
| | - Jingjing Yang
- College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (X.W.); (G.W.); (S.H.); (J.Y.)
| | - Xiangwei He
- College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (X.W.); (G.W.); (S.H.); (J.Y.)
| | - Haifang Li
- Department of Chemistry, MOE (Ministry of Education) Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| |
Collapse
|
7
|
Fan D, Schwinghamer T, Liu S, Xia O, Ge C, Chen Q, Smith DL. Characterization of endophytic bacteriome diversity and associated beneficial bacteria inhabiting a macrophyte Eichhornia crassipes. FRONTIERS IN PLANT SCIENCE 2023; 14:1176648. [PMID: 37404529 PMCID: PMC10316030 DOI: 10.3389/fpls.2023.1176648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/24/2023] [Indexed: 07/06/2023]
Abstract
Introduction The endosphere of a plant is an interface containing a thriving community of endobacteria that can affect plant growth and potential for bioremediation. Eichhornia crassipes is an aquatic macrophyte, adapted to estuarine and freshwater ecosystems, which harbors a diverse bacterial community. Despite this, we currently lack a predictive understanding of how E. crassipes taxonomically structure the endobacterial community assemblies across distinct habitats (root, stem, and leaf). Methods In the present study, we assessed the endophytic bacteriome from different compartments using 16S rRNA gene sequencing analysis and verified the in vitro plant beneficial potential of isolated bacterial endophytes of E. crassipes. Results and discussion Plant compartments displayed a significant impact on the endobacterial community structures. Stem and leaf tissues were more selective, and the community exhibited a lower richness and diversity than root tissue. The taxonomic analysis of operational taxonomic units (OTUs) showed that the major phyla belonged to Proteobacteria and Actinobacteriota (> 80% in total). The most abundant genera in the sampled endosphere was Delftia in both stem and leaf samples. Members of the family Rhizobiaceae, such as in both stem and leaf samples. Members of the family Rhizobiaceae, such as Allorhizobium- Neorhizobium-Pararhizobium-Rhizobium were mainly associated with leaf tissue, whereas the genera Nannocystis and Nitrospira from the families Nannocystaceae and Nitrospiraceae, respectively, were statistically significantly associated with root tissue. Piscinibacter and Steroidobacter were putative keystone taxa of stem tissue. Most of the endophytic bacteria isolated from E. crassipes showed in vitro plant beneficial effects known to stimulate plant growth and induce plant resistance to stresses. This study provides new insights into the distribution and interaction of endobacteria across different compartments of E. crassipes Future study of endobacterial communities, using both culture-dependent and -independent techniques, will explore the mechanisms underlying the wide-spread adaptability of E. crassipesto various ecosystems and contribute to the development of efficient bacterial consortia for bioremediation and plant growth promotion.
Collapse
Affiliation(s)
- Di Fan
- School of Biology, Food and Environment, Hefei University, Hefei, China
| | - Timothy Schwinghamer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Shuaitong Liu
- School of Biology, Food and Environment, Hefei University, Hefei, China
| | - Ouyuan Xia
- School of Biology, Food and Environment, Hefei University, Hefei, China
| | - Chunmei Ge
- School of Biology, Food and Environment, Hefei University, Hefei, China
| | - Qun Chen
- School of Biology, Food and Environment, Hefei University, Hefei, China
| | - Donald L. Smith
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| |
Collapse
|
8
|
Zhan Y, Liu H, Cao Z, Chen W, Li Z, Bai L, Pan L. Comparative analysis of fungal communities between herbicide-resistant and -susceptible Alopecurus aequalis. Front Cell Infect Microbiol 2022; 12:1094853. [PMID: 36619755 PMCID: PMC9816403 DOI: 10.3389/fcimb.2022.1094853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction Alopecurus aequalis is a grass species invading Chinese canola and wheat fields. An A. aequalis KMN-R population surviving mesosulfuron-methyl treatment with recommended rates was acquired from wheatland. Here, we aimed to confirm the resistance profiles of KMN-R to acetolactate synthetase (ALS) inhibiting herbicides and explore the possible resistance mechanisms to mesosulfuron-methyl in this weed population. Methods The dose-response tests performed in our study were used to test the toxicity of A. aequalis to ALS-inhibiting herbicides. Sanger sequencing was used to analyze the ALS gene of mesosulfuron-methyl -resistant and -susceptible A. aequalis. RNA sequencing analysis was used to find candidate genes that may confer metabolic resistance to the mesosulfuron-methyl in resistant A. aequalis population. Mesosulfuron-methyl -resistant and -susceptible A. aequalis populations fungal composition was measured via Illumina MiSeq Sequencing. Results Dose-response results indicated that KMN-R population evolved resistance to mesosulfuron-methyl and other tested ALS-inhibiting herbicides. Known resistance-conferring Trp-574-Leu gene mutation in A. aequalis ALS was detected in the KMN-R population. Pretreatment with 4-chloro-7-nitrobenzoxadiazole reversed mesosulfuron-methyl resistance in KMN-R. Glutathione S-transferases (GST) gene GSTZ2 and GSTT3 were highly expressed in KMN-R population. In addition, we evaluated the alpha diversity in A. aequalis, centering on OTU abundance, equality, and multiplicity, and found that the fungal community composition had more unexplained variance between KMN-R and KMN-S A. aequalis. We also observed higher abundances of specific fungi in KMN-R A. aequalis. Discussion The results proved that resistance to mesosulfuron-methyl in A. aequalis KMN-R population is probably caused by target site- and non-target site-based relating GST and provided the basis for further research between fungal interaction and herbicide resistance.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Lang Pan
- *Correspondence: Lang Pan, ; Lianyang Bai,
| |
Collapse
|
9
|
Yang J, Masoudi A, Li H, Gu Y, Wang C, Wang M, Yu Z, Liu J. Microbial community structure and niche differentiation under different health statuses of Pinus bungeana in the Xiong'an New Area in China. Front Microbiol 2022; 13:913349. [PMID: 36118200 PMCID: PMC9481298 DOI: 10.3389/fmicb.2022.913349] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
Pinus bungeana is a native but endangered plant species in China, with high ornamental value and adaptability to drought and cold. The relationship between the soil community structure and endophytic microbes in the tissues of P. bungeana under different health statuses is poorly understood. In this study, the endophytic bacterial and fungal communities of P. bungeana under different health statuses were compared and analyzed in the Xiong'an New Area. Using high-throughput deep sequencing [16S and internal transcribed spacer (ITS) rRNA] techniques, the effect of the health status of P. bungeana on the microbial communities in bulk soil, rhizospheric soil, roots, stems, and leaves was determined in this study. We observed that the diversity of the bacterial and fungal communities of the aboveground parts (stems and leaves) of healthy P. bungeana plants was much higher than that of the unhealthy plants. However, the diversity of bacterial and fungal communities in the belowground parts (bulk soil, rhizospheric soil, and roots) showed almost no difference in microbial community richness, indicating that the possible cause of illness was transmitted in a "top-down" manner. Furthermore, there were significant differences in the microbial diversity and community structure in different ecological niches of P. bungeana (P < 0.01). Proteobacteria and Actinobacteria were the dominant bacterial phyla, while Ascomycota, Basidiomycota, and Mortierellomycota were the predominant fungal phyla. Redundancy analysis (RDA) revealed that soil organic matter (SOM), total phosphorous (TP), total potassium (TK), total nitrogen (TN), water content (WC), power of hydrogen (pH), total carbon (TC), and the ratio of carbon to nitrogen (C/N) were significantly correlated with the composition of the microbial communities. Altogether, these results provide a scientific basis for further studies on the mechanism underlying the "aboveground-underground" microbial interactions in plantation forests, which can aid in promoting the healthy and sustainable development of the Millennium Xiulin forest in the Xiong'an New Area.
Collapse
Affiliation(s)
- Jia Yang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Abolfazl Masoudi
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Hao Li
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Yifan Gu
- School of Geographic Sciences, Hebei Normal University, Shijiazhuang, China
| | - Can Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Min Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Zhijun Yu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Jingze Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| |
Collapse
|
10
|
Huang Y, Dong Y, Ren Y, Wang S, Li Y, Du K, Lin X, Yang M. Niches and Seasonal Changes, Rather Than Transgenic Events, Affect the Microbial Community of Populus × euramericana ‘Neva’. Front Microbiol 2022; 12:805261. [PMID: 35154035 PMCID: PMC8831546 DOI: 10.3389/fmicb.2021.805261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 12/27/2021] [Indexed: 01/05/2023] Open
Abstract
Exploring the complex spatiotemporal changes and colonization mechanism of microbial communities will enable microbial communities to be better used to serve agricultural and ecological operations. In addition, evaluating the impact of transgenic plants on endogenous microbial communities is necessary for their commercial application. In this study, microbial communities of Populus × euramericana ‘Neva’ carrying Cry1Ac-Cry3A-BADH genes (ECAA1 line), Populus × euramericana ‘Neva’ carrying Cry1Ac-Cry3A-NTHK1 genes (ECAB1 line), and non-transgenic Populus × euramericana ‘Neva’ from rhizosphere soil, roots, and phloem collected in different seasons were compared and analyzed. Our analyses indicate that the richness and diversity of bacterial communities were higher in the three Populus × euramericana ‘Neva’ habitats than in those of fungi. Bacterial and fungal genetic-distance-clustering results were similar; rhizosphere soil clustered in one category, with roots and phloem in another. The diversity and evenness values of the microbial community were: rhizosphere soil > phloem > root system. The bacterial communities in the three habitats were dominated by the Proteobacteria, and fungal communities were dominated by the Ascomycota. The community composition and abundance of each part were quite different; those of Populus × euramericana ‘Neva’ were similar among seasons, but community abundance fluctuated. Seasonal fluctuation in the bacterial community was greatest in rhizosphere soil, while that of the fungal community was greatest in phloem. The transgenic lines ECAA1 and ECAB1 had a bacterial and fungal community composition similar to that of the control samples, with no significant differences in community structure or diversity among the lines. The abundances of operational taxonomic units (OTUs) were low, and differed significantly among the lines. These differences did not affect the functioning of the whole specific community. Sampling time and location were the main driving factors of changes in the Populus × euramericana ‘Neva’ microbial community. Transgenic events did not affect the Populus × euramericana ‘Neva’ rhizosphere or endophytic microbial communities. This study provides a reference for the safety evaluation of transgenic plants and the internal colonization mechanism of microorganisms in plants.
Collapse
Affiliation(s)
- Yali Huang
- Institute of Forest Biotechnology, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - Yan Dong
- Institute of Forest Biotechnology, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - Yachao Ren
- Institute of Forest Biotechnology, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - Shijie Wang
- Institute of Forest Biotechnology, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - Yongtan Li
- Institute of Forest Biotechnology, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - Kejiu Du
- Institute of Forest Biotechnology, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - Xin Lin
- Institute of Forest Biotechnology, Forestry College, Hebei Agricultural University, Baoding, China
- Agricultural Office of Kenfeng Subdistrict Office, Tangshan, China
| | - Minsheng Yang
- Institute of Forest Biotechnology, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
- *Correspondence: Minsheng Yang,
| |
Collapse
|
11
|
Zhang H, Wei TP, Li LZ, Luo MY, Jia WY, Zeng Y, Jiang YL, Tao GC. Multigene Phylogeny, Diversity and Antimicrobial Potential of Endophytic Sordariomycetes From Rosa roxburghii. Front Microbiol 2021; 12:755919. [PMID: 34912312 PMCID: PMC8667620 DOI: 10.3389/fmicb.2021.755919] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/08/2021] [Indexed: 11/13/2022] Open
Abstract
Rosa roxburghii Tratt. is widely applied in food, cosmetics, and traditional medicine, and has been demonstrated to possess diverse bioactivities. Plant endophytic fungi are important microbial resources with great potential for application in many fields. They not only establish mutualistic symbiosis with host plants but also produce a variety of bioactive compounds. Therefore, in the present study, endophytic fungi were isolated from R. roxburghii, the diversity and antimicrobial activities were evaluated. As a result, 242 strains of endophytic Sordariomycetes were successfully isolated. Multigene phylogenetic analyses showed that these isolates included eight orders, 19 families, 33 genera. The dominant genera were Diaporthe (31.4%), Fusarium (14.4%), Chaetomium (7.9%), Dactylonectria (7.0%), Graphium (4.5%), Colletotrichum (4.1%), and Clonostachys (4.1%). For different tissues of R. roxburghii, alpha diversity analysis revealed that the diversity of fungal communities decreased in the order of root, fruit, stem, flower, leaf, and seed, and Clonostachys and Dactylonectria exhibited obvious tissue specificity. Meanwhile, functional annotation of 33 genera indicated that some fungi have multitrophic lifestyles combining endophytic, pathogenic, and saprophytic behavior. Additionally, antimicrobial activities of endophytic Sordariomycetes against Lasiodiplodia theobromae, Botryosphaeria dothidea, Colletotrichum capsici, Pyricularia oryzae, Rhizoctonia solani, Fusarium oxysporum, Pseudomonas syringae, Pantoea agglomerans, Staphylococcus aureus, Bacillus subtilis, Escherichia coli, and Pseudomonas aeruginosa were screened. Dual culture test assays showed that there were 40 different endophytic species with strong inhibition of at least one or moderate inhibition of two or more against the 12 tested strains. The results from the filter paper diffusion method suggested that extracellular metabolites may be more advantageous than intracellular metabolites in the development of antimicrobial agents. Eleven isolates with good activities were screened. In particular, Hypomontagnella monticulosa HGUP194009 and Nigrospora sphaerica HGUP191020 have shown promise in both broad-spectrum and intensity. Finally, some fungi that commonly cause disease have been observed to have beneficial biological activities as endophytic fungi. In conclusion, this study showed the species composition, alpha diversity, and lifestyle diversity of endophytic Sordariomycetes from R. roxburghii and demonstrated these isolates are potential sources for exploring antimicrobial agents.
Collapse
Affiliation(s)
- Hong Zhang
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China.,Guizhou Academy of Testing and Analysis, Guiyang, China
| | - Tian-Peng Wei
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China
| | - Lin-Zhu Li
- Guizhou Academy of Testing and Analysis, Guiyang, China
| | - Ming-Yan Luo
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China
| | - Wei-Yu Jia
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China
| | - Yan Zeng
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China
| | - Yu-Lan Jiang
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China
| | - Guang-Can Tao
- Guizhou Academy of Testing and Analysis, Guiyang, China.,Food Safety and Nutrition (Guizhou) Information Technology Co., Ltd., Guiyang National High-Tech Industrial Development Zone, Guiyang, China
| |
Collapse
|
12
|
Ujvári G, Turrini A, Avio L, Agnolucci M. Possible role of arbuscular mycorrhizal fungi and associated bacteria in the recruitment of endophytic bacterial communities by plant roots. MYCORRHIZA 2021; 31:527-544. [PMID: 34286366 PMCID: PMC8484141 DOI: 10.1007/s00572-021-01040-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/17/2021] [Indexed: 05/12/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) represent an important group of root symbionts, given the key role they play in the enhancement of plant nutrition, health, and product quality. The services provided by AMF often are facilitated by large and diverse beneficial bacterial communities, closely associated with spores, sporocarps, and extraradical mycelium, showing different functional activities, such as N2 fixation, nutrient mobilization, and plant hormone, antibiotic, and siderophore production and also mycorrhizal establishment promotion, leading to the enhancement of host plant performance. The potential functional complementarity of AMF and associated microbiota poses a key question as to whether members of AMF-associated bacterial communities can colonize the root system after establishment of mycorrhizas, thereby becoming endophytic. Root endophytic bacterial communities are currently studied for the benefits provided to host plants in the form of growth promotion, stress reduction, inhibition of plant pathogens, and plant hormone release. Their quantitative and qualitative composition is influenced by many factors, such as geographical location, soil type, host genotype, and cultivation practices. Recent data suggest that an additional factor affecting bacterial endophyte recruitment could be AMF and their associated bacteria, even though the mechanisms allowing members of AMF-associated bacterial communities to actually establish in the root system, becoming endophytic, remain to be determined. Given the diverse plant growth-promoting properties shown by AMF-associated bacteria, further studies are needed to understand whether AMF may represent suitable tools to introduce beneficial root endophytes in sustainable and organic agriculture where the functioning of such multipartite association may be crucial for crop production.
Collapse
Affiliation(s)
- Gergely Ujvári
- Department of Agriculture, Food and Environment, University of Pisa, 56124, Pisa, Italy
| | - Alessandra Turrini
- Department of Agriculture, Food and Environment, University of Pisa, 56124, Pisa, Italy
| | - Luciano Avio
- Department of Agriculture, Food and Environment, University of Pisa, 56124, Pisa, Italy
| | - Monica Agnolucci
- Department of Agriculture, Food and Environment, University of Pisa, 56124, Pisa, Italy.
| |
Collapse
|
13
|
Lei F, Liu X, Huang H, Fu S, Zou K, Zhang S, Zhou L, Zeng J, Liu H, Jiang L, Miao B, Liang Y. The Macleaya cordata Symbiont: Revealing the Effects of Plant Niches and Alkaloids on the Bacterial Community. Front Microbiol 2021; 12:681210. [PMID: 34177865 PMCID: PMC8219869 DOI: 10.3389/fmicb.2021.681210] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/07/2021] [Indexed: 11/13/2022] Open
Abstract
Endophytes are highly associated with plant growth and health. Exploring the variation of bacterial communities in different plant niches is essential for understanding microbe-plant interactions. In this study, high-throughput gene sequencing was used to analyze the composition and abundance of bacteria from the rhizospheric soil and different parts of the Macleaya cordata. The results indicated that the bacterial community structure varied widely among compartments. Bacterial diversity was observed to be the highest in the rhizospheric soil and the lowest in fruits. Proteobacteria, Actinobacteria, and Bacteroidetes were found as the dominant phyla. The genera Sphingomonas (∼47.77%) and Methylobacterium (∼45.25%) dominated in fruits and leaves, respectively. High-performance liquid chromatography (HPLC) was employed to measure the alkaloid content of different plant parts. Significant correlations were observed between endophytic bacteria and alkaloids. Especially, Sphingomonas showed a significant positive correlation with sanguinarine and chelerythrine. All four alkaloids were negatively correlated with the microbiota of stems. The predicted result of PICRUST2 revealed that the synthesis of plant alkaloids might lead to a higher abundance of endophytic microorganisms with genes related to alkaloid synthesis, further demonstrated the correlation between bacterial communities and alkaloids. This study provided the first insight into the bacterial community composition in different parts of Macleaya cordata and the correlation between the endophytic bacteria and alkaloids.
Collapse
Affiliation(s)
- Fangying Lei
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Haonan Huang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Shaodong Fu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Kai Zou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Shuangfei Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Li Zhou
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, China
| | - Jianguo Zeng
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, China
| | - Hongwei Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Luhua Jiang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Bo Miao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| |
Collapse
|
14
|
Zhou Z, Yu M, Ding G, Gao G, He Y. Diversity and structural differences of bacterial microbial communities in rhizocompartments of desert leguminous plants. PLoS One 2020; 15:e0241057. [PMID: 33351824 PMCID: PMC7755220 DOI: 10.1371/journal.pone.0241057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 10/07/2020] [Indexed: 11/18/2022] Open
Abstract
By assessing diversity variations of bacterial communities under different rhizocompartment types (i.e., roots, rhizosphere soil, root zone soil, and inter-shrub bulk soil), we explore the structural difference of bacterial communities in different root microenvironments under desert leguminous plant shrubs. Results will enable the influence of niche differentiation of plant roots and root soil on the structural stability of bacterial communities under three desert leguminous plant shrubs to be examined. High-throughput 16S rRNA genome sequencing was used to characterize diversity and structural differences of bacterial microbes in the rhizocompartments of three xeric leguminous plants. Results from this study confirm previous findings relating to niche differentiation in rhizocompartments under related shrubs, and they demonstrate that diversity and structural composition of bacterial communities have significant hierarchical differences across four rhizocompartment types under leguminous plant shrubs. Desert leguminous plants showed significant hierarchical filtration and enrichment of the specific bacterial microbiome across different rhizocompartments (P < 0.05). The dominant bacterial microbiome responsible for the differences in microbial community structure and composition across different niches of desert leguminous plants mainly consisted of Proteobacteria, Actinobacteria, and Bacteroidetes. All soil factors of rhizosphere and root zone soils, except for NO3-N and TP under C. microphylla and the two Hedysarum spp., recorded significant differences (P < 0.05). Moreover, soil physicochemical factors have a significant impact on driving the differentiation of bacterial communities under desert leguminous plant shrubs. By investigating the influence of niches on the structural difference of soil bacterial communities with the differentiation of rhizocompartments under desert leguminous plant shrubs, we provide data support for the identification of dominant bacteria and future preparation of inocula, and provide a foundation for further study of the host plants-microbial interactions.
Collapse
Affiliation(s)
- Ziyuan Zhou
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of State Forestry Administration on Soil and Water Conservation, Beijing Forestry University, Beijing, P. R. China
| | - Minghan Yu
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of State Forestry Administration on Soil and Water Conservation, Beijing Forestry University, Beijing, P. R. China
- * E-mail: (MY); (GD)
| | - Guodong Ding
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of State Forestry Administration on Soil and Water Conservation, Beijing Forestry University, Beijing, P. R. China
- * E-mail: (MY); (GD)
| | - Guanglei Gao
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of State Forestry Administration on Soil and Water Conservation, Beijing Forestry University, Beijing, P. R. China
| | - Yingying He
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of State Forestry Administration on Soil and Water Conservation, Beijing Forestry University, Beijing, P. R. China
| |
Collapse
|
15
|
Zhou Z, Yu M, Ding G, Gao G, He Y, Wang G. Effects of Hedysarum leguminous plants on soil bacterial communities in the Mu Us Desert, northwest China. Ecol Evol 2020; 10:11423-11439. [PMID: 33144975 PMCID: PMC7593153 DOI: 10.1002/ece3.6779] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 08/16/2020] [Accepted: 08/18/2020] [Indexed: 11/19/2022] Open
Abstract
This study assessed the influence of rhizocompartment types (i.e., root, rhizosphere soil, root-zone soil, and intershrub bulk soil) on the diversity of soil microbial communities under desert leguminous plant shrubs. Moreover, the influence and variations of soil physicochemical factors in interactions among leguminous plants, soil, and microbes were investigated. Both 16S rRNA high-throughput genome sequencing and conventional soil physicochemical index determination were used to characterize both the bacterial diversity and soil physicochemical properties in the rhizocompartments of two Hedysarum species (Hedysarum mongolicum and Hedysarum scoparium) in the Mu Us Desert of China. All nutrient indices (except total phosphorus and available phosphorus) in rhizosphere soil were uniformly higher than those in both root-zone soil and intershrub bulk soil (p < .05). The bacterial community diversity in the root, undershrub soil (i.e., rhizosphere and root zone), and intershrub bulk soil also showed significant differences (p < .05). The bacterial community in the root is mainly composed of Proteobacteria, Actinobacteria, Bacteroidetes, Tenericutes, and Chloroflexi, among which bacteria of the Proteobacteria genus are dominant. Root endophyte and rhizosphere soil microbiomes were mainly influenced by soil nutrients, while bacterial communities in root-zone soil and intershrub bulk soil were mainly influenced by soil pH and NH4 +-N. The rhizocompartment types of desert leguminous plants impose a significant influence on the diversity of soil microbial communities. According to these findings, nitrogen-fixing rhizobia can co-exist with nonsymbiotic endophytes in the roots of desert leguminous plants. Moreover, plants have a hierarchical filtering and enriching effect on beneficial microbes in soil via rhizocompartments. Soil physicochemical factors have a significant influence on both the structure and composition of microbial communities in various rhizocompartments, which is derived from the interactions among leguminous plants, soil, and microbes.
Collapse
Affiliation(s)
- Ziyuan Zhou
- Yanchi Research StationSchool of Soil and Water ConservationBeijing Forestry UniversityBeijingChina
- Key Laboratory of State Forestry Administration on Soil and Water ConservationBeijing Forestry UniversityBeijingChina
| | - Minghan Yu
- Yanchi Research StationSchool of Soil and Water ConservationBeijing Forestry UniversityBeijingChina
- Key Laboratory of State Forestry Administration on Soil and Water ConservationBeijing Forestry UniversityBeijingChina
| | - Guodong Ding
- Yanchi Research StationSchool of Soil and Water ConservationBeijing Forestry UniversityBeijingChina
- Key Laboratory of State Forestry Administration on Soil and Water ConservationBeijing Forestry UniversityBeijingChina
| | - Guanglei Gao
- Yanchi Research StationSchool of Soil and Water ConservationBeijing Forestry UniversityBeijingChina
- Key Laboratory of State Forestry Administration on Soil and Water ConservationBeijing Forestry UniversityBeijingChina
| | - Yingying He
- Yanchi Research StationSchool of Soil and Water ConservationBeijing Forestry UniversityBeijingChina
- Key Laboratory of State Forestry Administration on Soil and Water ConservationBeijing Forestry UniversityBeijingChina
| | - Genzhu Wang
- Key Laboratory of State Forestry Administration on Soil and Water ConservationBeijing Forestry UniversityBeijingChina
| |
Collapse
|
16
|
Barraza A, Vizuet-de-Rueda JC, Alvarez-Venegas R. Highly diverse root endophyte bacterial community is driven by growth substrate and is plant genotype-independent in common bean ( Phaseolus vulgaris L.). PeerJ 2020; 8:e9423. [PMID: 32617194 PMCID: PMC7323714 DOI: 10.7717/peerj.9423] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 06/04/2020] [Indexed: 11/25/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Aarón Barraza
- Programa de Agricultura en Zonas Áridas, CONACYT-CIBNOR, Centro de Investigaciones Biológicas del Noroeste, La Paz, Baja California Sur, México
| | - Juan Carlos Vizuet-de-Rueda
- Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, Mexico
| | - Raúl Alvarez-Venegas
- Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, Mexico
| |
Collapse
|
17
|
Hao G, Bakker MG, Kim HS. Enhanced Resistance to Fusarium graminearum in Transgenic Arabidopsis Plants Expressing a Modified Plant Thionin. PHYTOPATHOLOGY 2020; 110:1056-1066. [PMID: 32043419 DOI: 10.1094/phyto-12-19-0447-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The fungal pathogen Fusarium graminearum causes Fusarium head blight (FHB) on wheat, barley, and other grains. FHB results in yield reductions and contaminates grain with trichothecene mycotoxins, which threaten food safety and food security. Innovative mechanisms for controlling FHB are urgently needed. We have previously shown that transgenic tobacco and citrus plants expressing a modified thionin (Mthionin) exhibited enhanced resistance toward several bacterial pathogens. The aim of this study was to investigate whether overexpression of Mthionin could be similarly efficacious against F. graminearum, and whether transgenic expression of Mthionin impacts the plant microbiome. Transgenic Arabidopsis plants expressing Mthionin were generated and confirmed. When challenged with F. graminearum, Mthionin-expressing plants showed less disease and fungal biomass in both leaves and inflorescences compared with control plants. When infiltrated into leaves, macroconidia of F. graminearum germinated at lower rates and produced less hyphal growth in Arabidopsis leaves expressing Mthionin. Moreover, marker genes related to defense signaling pathways were expressed at significantly higher levels after F. graminearum infection in Mthionin transgenic Arabidopsis plants. However, Mthionin expression did not appreciably alter the overall microbiome associated with transgenic plants grown under controlled conditions; across leaves and roots of Mthionin-expressing and control transgenic plants, only a few bacterial and fungal taxa differed, and differences between Mthionin transformants were of similar magnitude compared with control plants. In sum, our data indicate that Mthionin is a promising candidate to produce transgenic crops for reducing FHB severity and ultimately mycotoxin contamination.
Collapse
Affiliation(s)
- Guixia Hao
- Mycotoxin Prevention and Applied Microbiology Research Unit, NCAUR, U.S. Department of Agriculture-Agricultural Research Service, Peoria, IL 61604
| | - Matthew G Bakker
- Mycotoxin Prevention and Applied Microbiology Research Unit, NCAUR, U.S. Department of Agriculture-Agricultural Research Service, Peoria, IL 61604
| | - Hye-Seon Kim
- Mycotoxin Prevention and Applied Microbiology Research Unit, NCAUR, U.S. Department of Agriculture-Agricultural Research Service, Peoria, IL 61604
| |
Collapse
|