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Wang F, Zhao Z, Han Y, Li S, Bi X, Ren S, Pan Y, Wang D, Liu X. The Bacterial and Fungal Compositions in the Rhizosphere of Asarum heterotropoides Fr. Schmidt var. mandshuricum (Maxim.) Kitag. in a Typical Planting Region. Microorganisms 2024; 12:692. [PMID: 38674636 PMCID: PMC11051765 DOI: 10.3390/microorganisms12040692] [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: 02/29/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Asarum is a traditional Chinese medicinal plant, and its dried roots are commonly used as medicinal materials. Research into the traits of the bacteria and fungus in the Asarum rhizosphere and how they relate to the potency of medicinal plants is important. During four cropping years and collecting months, we used ITS rRNA gene amplicon and sequencing to assess the population, diversity, and predominant kinds of bacteria and fungus in the rhizosphere of Asarum. HPLC was used to determine the three bioactive ingredients, namely asarinin, aristolochic acid I, and volatile oil. The mainly secondary metabolites of Asarum, relationships between microbial communities, soil physicochemical parameters, and possible influences on microbial communities owing to various cropping years and collecting months were all statistically examined. The cropping years and collecting months affected the abundance and diversity of rhizosphere bacteria and fungi, but the cropping year had a significant impact on the structures and compositions of the bacterial communities. The rhizosphere microorganisms were influenced by both the soil physicochemical properties and enzyme activities. Additionally, this study revealed that Trichoderma was positively correlated with the three bioactive ingredients of Asarum, while Tausonia showed entirely opposite results. Gibberella and Leptosphaeria demonstrated a significantly negative correlation with asarinin and violate oil, but they were weakly correlated with the aristolochic acid I content. This study revealed variations in the Asarum rhizosphere microorganism population, diversity, and dominant types across four cropping years and collecting months. The relationship between Asarum secondary metabolites, the soil physicochemical properties, enzyme activities, and rhizosphere microorganisms was discussed. Our results will guide the exploration of the soil characteristics and rhizosphere microorganisms' structures by regulating the microbial community to enhance Asarum quality.
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Affiliation(s)
- Fuqi Wang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, China; (F.W.); (Z.Z.)
| | - Zilu Zhao
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, China; (F.W.); (Z.Z.)
| | - Yangyang Han
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, China; (F.W.); (Z.Z.)
| | - Shiying Li
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xinhua Bi
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Shumeng Ren
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, China; (F.W.); (Z.Z.)
| | - Yingni Pan
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, China; (F.W.); (Z.Z.)
| | - Dongmei Wang
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xiaoqiu Liu
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, China; (F.W.); (Z.Z.)
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Hou X, Yang J, Xie J, Zhu S, Zhang Z. Diversity and Antibiotic Resistance of Triticale Seed-Borne Bacteria on the Tibetan Plateau. Microorganisms 2024; 12:650. [PMID: 38674594 PMCID: PMC11052201 DOI: 10.3390/microorganisms12040650] [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: 02/17/2024] [Revised: 03/16/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
The Tibetan Plateau is located in southwestern China. It has many important ecological functions, such as biodiversity protection, and is an important grassland agroecosystem in China. With the development of modern agriculture and animal husbandry, antibiotics are widely used to treat humans and livestock, and antibiotics cannot be fully metabolised by both. Antibiotics eventually find their way into the environment, affecting other parts of grassland agroecosystems. Triticale (Triticosecale wittmack) is an artificial hybrid forage that can be used for both grain and forage. This study revealed the diversity of seedborne bacteria in triticale on the Tibetan Plateau and the resistance of the bacteria to nine antibiotics. It identified 37 representative strains and successfully obtained the spliced sequences of 36 strains of the bacteria, which were clustered into 5 phyla and 16 genera. Among them, 18 strains showed resistance to at least one of the 9 antibiotics, and the colony-forming unit (CFU) abundance of antibiotic-resistant bacteria (ARB) accounted for 45.38% of the total samples. Finally, the bacterial motility and biofilm formation ability were measured, and their correlation with bacterial resistance was analysed. The results showed that the bacterial resistance did not have an absolute positive correlation with the motility or biofilm formation ability.
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Affiliation(s)
| | | | | | | | - Zhenfen Zhang
- Key Laboratory of Grassland Ecosystem, Ministry of Education, Pratacultural College, Gansu Agricultural University, Lanzhou 730070, China; (X.H.); (J.Y.); (J.X.); (S.Z.)
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Pathak D, Suman A, Sharma P, Aswini K, Govindasamy V, Gond S, Anshika R. Community-forming traits play role in effective colonization of plant-growth-promoting bacteria and improved plant growth. FRONTIERS IN PLANT SCIENCE 2024; 15:1332745. [PMID: 38533409 PMCID: PMC10963436 DOI: 10.3389/fpls.2024.1332745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/21/2024] [Indexed: 03/28/2024]
Abstract
Community-forming traits (CFts) play an important role in the effective colonization of plant-growth-promoting bacterial communities that influence host plants positively by modulating their adaptive functions. In this study, by considering plant-growth-promoting traits (PGPts) and community-forming traits (CFts), three communities were constructed, viz., SM1 (PGPts), SM2 (CFts), and SM3 (PGPts+CFts). Each category isolates were picked up on the basis of their catabolic diversity of different carbon sources. Results revealed a distinctive pattern in the colonization of the communities possessed with CF traits. It was observed that the community with CFts colonized inside the plant in groups or in large aggregations, whereas the community with only PGPts colonized as separate individual and small colonies inside the plant root and leaf. The effect of SM3 in the microcosm experiment was more significant than the uninoculated control by 22.12%, 27.19%, and 9.11% improvement in germination percentage, chlorophyll content, and plant biomass, respectively. The significant difference shown by the microbial community SM3 clearly demonstrates the integrated effect of CFts and PGPts on effective colonization vis-à-vis positive influence on the host plant. Further detailed characterization of the interaction will take this technology ahead in sustainable agriculture.
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Affiliation(s)
| | - Archna Suman
- Division of Microbiology, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
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Wu C, Zhang X, Fan Y, Ye J, Dong L, Wang Y, Ren Y, Yong H, Liu R, Wang A. Vertical transfer and functional characterization of cotton seed core microbiome. Front Microbiol 2024; 14:1323342. [PMID: 38264479 PMCID: PMC10803423 DOI: 10.3389/fmicb.2023.1323342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/22/2023] [Indexed: 01/25/2024] Open
Abstract
Introduction Microbiome within plant tissues is pivotal for co-evolution with host plants. This microbiome can colonize the plant, with potential transmission via seeds between parents and offspring, affecting seedling growth and host plant adaptability to the environment. Methods We employed 16S rRNA gene amplicon analysis to investigate the vertical distribution of core microbiome in cotton seeds across ecological niches [rhizosphere, root, stem, leaf, seed and seed-P (parental seed)] of the three cotton genotypes. Results The findings demonstrated a significant decrease in microbiome diversity and network complexity from roots, stems, and leaves to seeds. The microenvironment exerted a more substantial influence on the microbiome structure of cotton than the genotypes. The core endophytic microorganisms in cotton seeds comprised 29 amplicon sequence variants (ASVs) affiliated with Acidimicrobiia, Alphaproteobacteria, Bacilli, Bacteroidia, Clostridia, Gammaproteobacteria, and unclassified_Proteobacteria. These vertically transmitted taxa are widely distributed in cotton plants. Through 16S rRNA gene-based function prediction analysis of the cotton microbiome, we preliminarily understood that there are potential differences in metabolic capabilities and phenotypic traits among microbiomes in different microhabitats. Discussion In conclusion, this study demonstrated the crucial role of the microenvironment in influencing the cotton microbiome and offered insights into the structures and functions of the cotton seed microbiome, facilitating future crop yield enhancement through core seed microbiome regulation.
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Affiliation(s)
- Chongdie Wu
- College of Life Sciences, Shihezi University, Shihezi, China
- Xinjiang Production and Construction Corps, Key Laboratory of Oasis Town and Mountain-basin System Ecology, Shihezi, China
| | - Xin Zhang
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Yongbin Fan
- College of Life Sciences, Shihezi University, Shihezi, China
- Xinjiang Production and Construction Corps, Key Laboratory of Oasis Town and Mountain-basin System Ecology, Shihezi, China
| | - Jingyi Ye
- College of Life Sciences, Shihezi University, Shihezi, China
- Xinjiang Production and Construction Corps, Key Laboratory of Oasis Town and Mountain-basin System Ecology, Shihezi, China
| | - Lingjun Dong
- College of Life Sciences, Shihezi University, Shihezi, China
| | - YuXiang Wang
- College of Life Sciences, Shihezi University, Shihezi, China
| | - YinZheng Ren
- College of Life Sciences, Shihezi University, Shihezi, China
| | - HongHong Yong
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Ruina Liu
- College of Life Sciences, Shihezi University, Shihezi, China
- Xinjiang Production and Construction Corps, Key Laboratory of Oasis Town and Mountain-basin System Ecology, Shihezi, China
| | - Aiying Wang
- College of Life Sciences, Shihezi University, Shihezi, China
- Xinjiang Production and Construction Corps, Key Laboratory of Oasis Town and Mountain-basin System Ecology, Shihezi, China
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Sun Z, Adeleke BS, Shi Y, Li C. The seed microbiomes of staple food crops. Microb Biotechnol 2023; 16:2236-2249. [PMID: 37815330 PMCID: PMC10686132 DOI: 10.1111/1751-7915.14352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/11/2023] Open
Abstract
The scientific community increasingly recognized that seed microbiomes are important for plant growth and nutrition. The versatile roles and modulating properties that microbiomes hold in the context of seeds seem to be an inherited approach to avert adverse conditions. These discoveries attracted extensive interest, especially in staple food crops (SFCs) where grain was consumed as food. Along with the rapid expansion of population and industrialization that posed a severe challenge to the yield of SFCs, microbiologists and botanists began to explore and engineer seed microbiomes, for safer and more fruitful grain production. To utilize seed microbiomes, we present an overall review of the most updated scientific literature on three representative SFCs (wheat, rice and maize) using the 5W1H (Which, Where, What, Why, When and How) method that provides a comprehensive understanding of the issue. These include which factors determine the composition of seed microbiomes? Where do seed microbiomes come from? What are these seed microbes? Why do these microbes choose seeds as their destination and when do microbes settle down and become seed communists? In addition, how do seed microbiomes work and can be manipulated effectively? Therefore, answering the aforementioned questions regarding SFCs seed microbiomes remain fundamental in bridging endophytic research gaps and harnessing their ecological services.
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Affiliation(s)
- Zhongke Sun
- School of Biological EngineeringHenan University of TechnologyZhengzhouChina
- Food Laboratory of ZhongyuanLuoheChina
| | - Bartholomew Saanu Adeleke
- School of Biological EngineeringHenan University of TechnologyZhengzhouChina
- Department of Biological Sciences, School of ScienceOlusegun Agagu University of Science and TechnologyOkitipupaNigeria
| | - Yini Shi
- School of Biological EngineeringHenan University of TechnologyZhengzhouChina
| | - Chengwei Li
- School of Biological EngineeringHenan University of TechnologyZhengzhouChina
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Hernández Flores JL, Martínez YJ, Ramos López MÁ, Saldaña Gutierrez C, Reyes AA, Armendariz Rosales MM, Cortés Pérez MJ, Mendoza MF, Ramírez Ramírez J, Zavala GR, Tovar Becerra PL, Valdez Santoyo L, Villasana Rodríguez K, Rodríguez Morales JA, Campos Guillén J. Volatile Organic Compounds Produced by Kosakonia cowanii Cp1 Isolated from the Seeds of Capsicum pubescens R & P Possess Antifungal Activity. Microorganisms 2023; 11:2491. [PMID: 37894149 PMCID: PMC10609226 DOI: 10.3390/microorganisms11102491] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 10/01/2023] [Indexed: 10/29/2023] Open
Abstract
The Kosakonia cowanii Cp1 strain was isolated from seeds of Capsicum pubescens R. & P. cultivated in Michoacan, Mexico. Genetic and ecological role analyses were conducted for better characterization. The results show that genome has a length of 4.7 Mbp with 56.22% G + C and an IncF plasmid of 128 Kbp with 52.51% G + C. Furthermore, pathogenicity test revealed nonpathogenic traits confirmed by the absence of specific virulence-related genes. Interestingly, when fungal inhibitory essays were carried out, the bacterial synthesis of volatile organic compounds (VOCs) with antifungal activity showed that Sclerotinia sp. and Rhizoctonia solani were inhibited by 87.45% and 77.24%, respectively. Meanwhile, Sclerotium rolfsii, Alternaria alternata, and Colletotrichum gloeosporioides demonstrated a mean radial growth inhibition of 52.79%, 40.82%, and 55.40%, respectively. The lowest inhibition was by Fusarium oxysporum, with 10.64%. The VOCs' characterization by headspace solid-phase microextraction combined with gas chromatography-mass spectrometry (HS-SPME-GC-MS) revealed 65 potential compounds. Some of the compounds identified with high relative abundance were ketones (22.47%), represented by 2-butanone, 3-hydroxy (13.52%), and alcohols (23.5%), represented by ethanol (5.56%) and 1-butanol-3-methyl (4.83%). Our findings revealed, for the first time, that K. cowanii Cp1 associated with C. pubescens seeds possesses potential traits indicating that it could serve as an effective biocontrol.
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Affiliation(s)
| | - Yomaiko Javier Martínez
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro 76010, Mexico; (Y.J.M.); (M.Á.R.L.); (A.A.R.); (M.M.A.R.); (M.J.C.P.); (M.F.M.); (J.R.R.); (G.R.Z.); (P.L.T.B.); (L.V.S.); (K.V.R.)
| | - Miguel Ángel Ramos López
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro 76010, Mexico; (Y.J.M.); (M.Á.R.L.); (A.A.R.); (M.M.A.R.); (M.J.C.P.); (M.F.M.); (J.R.R.); (G.R.Z.); (P.L.T.B.); (L.V.S.); (K.V.R.)
| | - Carlos Saldaña Gutierrez
- Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Av. de las Ciencias S/N, Querétaro 76220, Mexico;
| | - Aldo Amaro Reyes
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro 76010, Mexico; (Y.J.M.); (M.Á.R.L.); (A.A.R.); (M.M.A.R.); (M.J.C.P.); (M.F.M.); (J.R.R.); (G.R.Z.); (P.L.T.B.); (L.V.S.); (K.V.R.)
| | - Mariem Monserrat Armendariz Rosales
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro 76010, Mexico; (Y.J.M.); (M.Á.R.L.); (A.A.R.); (M.M.A.R.); (M.J.C.P.); (M.F.M.); (J.R.R.); (G.R.Z.); (P.L.T.B.); (L.V.S.); (K.V.R.)
| | - Maraly Jazmin Cortés Pérez
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro 76010, Mexico; (Y.J.M.); (M.Á.R.L.); (A.A.R.); (M.M.A.R.); (M.J.C.P.); (M.F.M.); (J.R.R.); (G.R.Z.); (P.L.T.B.); (L.V.S.); (K.V.R.)
| | - Mayela Fosado Mendoza
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro 76010, Mexico; (Y.J.M.); (M.Á.R.L.); (A.A.R.); (M.M.A.R.); (M.J.C.P.); (M.F.M.); (J.R.R.); (G.R.Z.); (P.L.T.B.); (L.V.S.); (K.V.R.)
| | - Joanna Ramírez Ramírez
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro 76010, Mexico; (Y.J.M.); (M.Á.R.L.); (A.A.R.); (M.M.A.R.); (M.J.C.P.); (M.F.M.); (J.R.R.); (G.R.Z.); (P.L.T.B.); (L.V.S.); (K.V.R.)
| | - Grecia Ramírez Zavala
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro 76010, Mexico; (Y.J.M.); (M.Á.R.L.); (A.A.R.); (M.M.A.R.); (M.J.C.P.); (M.F.M.); (J.R.R.); (G.R.Z.); (P.L.T.B.); (L.V.S.); (K.V.R.)
| | - Paola Lizeth Tovar Becerra
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro 76010, Mexico; (Y.J.M.); (M.Á.R.L.); (A.A.R.); (M.M.A.R.); (M.J.C.P.); (M.F.M.); (J.R.R.); (G.R.Z.); (P.L.T.B.); (L.V.S.); (K.V.R.)
| | - Laila Valdez Santoyo
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro 76010, Mexico; (Y.J.M.); (M.Á.R.L.); (A.A.R.); (M.M.A.R.); (M.J.C.P.); (M.F.M.); (J.R.R.); (G.R.Z.); (P.L.T.B.); (L.V.S.); (K.V.R.)
| | - Karen Villasana Rodríguez
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro 76010, Mexico; (Y.J.M.); (M.Á.R.L.); (A.A.R.); (M.M.A.R.); (M.J.C.P.); (M.F.M.); (J.R.R.); (G.R.Z.); (P.L.T.B.); (L.V.S.); (K.V.R.)
| | | | - Juan Campos Guillén
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro 76010, Mexico; (Y.J.M.); (M.Á.R.L.); (A.A.R.); (M.M.A.R.); (M.J.C.P.); (M.F.M.); (J.R.R.); (G.R.Z.); (P.L.T.B.); (L.V.S.); (K.V.R.)
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Establishment and Validation of a New Analysis Strategy for the Study of Plant Endophytic Microorganisms. Int J Mol Sci 2022; 23:ijms232214223. [PMID: 36430699 PMCID: PMC9697482 DOI: 10.3390/ijms232214223] [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: 10/17/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022] Open
Abstract
Amplicon sequencing of bacterial or fungal marker sequences is currently the main method for the study of endophytic microorganisms in plants. However, it cannot obtain all types of microorganisms, including bacteria, fungi, protozoa, etc., in samples, nor compare the relative content between endophytic microorganisms and plants and between different types of endophytes. Therefore, it is necessary to develop a better analysis strategy for endophytic microorganism investigation. In this study, a new analysis strategy was developed to obtain endophytic microbiome information from plant transcriptome data. Results showed that the new strategy can obtain the composition of microbial communities and the relative content between plants and endophytic microorganisms, and between different types of endophytic microorganisms from the plant transcriptome data. Compared with the amplicon sequencing method, more endophytic microorganisms and relative content information can be obtained with the new strategy, which can greatly broaden the research scope and save the experimental cost. Furthermore, the advantages and effectiveness of the new strategy were verified with different analysis of the microbial composition, correlation analysis, inoculant content test, and repeatability test.
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