1
|
Guo K, Kunito T, Otsuka S. Complete genome sequence of Bacillus subtilis NA05 (=NBRC 116153), a phosphate-solubilizing bacterium isolated from crop field soil. Microbiol Resour Announc 2024; 13:e0015424. [PMID: 38767396 DOI: 10.1128/mra.00154-24] [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: 02/15/2024] [Accepted: 04/24/2024] [Indexed: 05/22/2024] Open
Abstract
We report the complete genome sequence of the phosphate-solubilizing bacterium Bacillus subtilis NA05 (=NBRC 116153), consisting of a circular chromosome of ~3.8 M bp and two circular plasmids. The data presented here provide further insight into the genetic and functional potential of B. subtilis and the mechanism of phosphate solubilization.
Collapse
Affiliation(s)
- Kerui Guo
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takashi Kunito
- Faculty of Science, Shinshu University, Matsumoto, Nagano, Japan
| | - Shigeto Otsuka
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
2
|
Peng D, Wang Z, Tian J, Wang W, Guo S, Dai X, Yin H, Li L. Phyllosphere bacterial community dynamics in response to bacterial wildfire disease: succession and interaction patterns. FRONTIERS IN PLANT SCIENCE 2024; 15:1331443. [PMID: 38533399 PMCID: PMC10963427 DOI: 10.3389/fpls.2024.1331443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/08/2024] [Indexed: 03/28/2024]
Abstract
Plants interact with complex microbial communities in which microorganisms play different roles in plant development and health. While certain microorganisms may cause disease, others promote nutrient uptake and resistance to stresses through a variety of mechanisms. Developing plant protection measures requires a deeper comprehension of the factors that influence multitrophic interactions and the organization of phyllospheric communities. High-throughput sequencing was used in this work to investigate the effects of climate variables and bacterial wildfire disease on the bacterial community's composition and assembly in the phyllosphere of tobacco (Nicotiana tabacum L.). The samples from June (M1), July (M2), August (M3), and September (M4) formed statistically separate clusters. The assembly of the whole bacterial population was mostly influenced by stochastic processes. PICRUSt2 predictions revealed genes enriched in the M3, a period when the plant wildfire disease index reached climax, were associated with the development of the wildfire disease (secretion of virulence factor), the enhanced metabolic capacity and environmental adaption. The M3 and M4 microbial communities have more intricate molecular ecological networks (MENs), bursting with interconnections within a densely networked bacterial population. The relative abundances of plant-beneficial and antagonistic microbes Clostridiales, Bacillales, Lactobacillales, and Sphingobacteriales, showed significant decrease in severally diseased sample (M3) compared to the pre-diseased samples (M1/M2). Following the results of MENs, we further test if the correlating bacterial pairs within the MEN have the possibility to share functional genes and we have unraveled 139 entries of such horizontal gene transfer (HGT) events, highlighting the significance of HGT in shaping the adaptive traits of plant-associated bacteria across the MENs, particularly in relation to host colonization and pathogenicity.
Collapse
Affiliation(s)
- Deyuan Peng
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Zhenhua Wang
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Jinyan Tian
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Wei Wang
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Shijie Guo
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Xi Dai
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Krstić Tomić T, Atanasković I, Nikolić I, Joković N, Stević T, Stanković S, Berić T, Lozo J. Culture-Dependent and Metabarcoding Characterization of the Sugar Beet ( Beta vulgaris L.) Microbiome for High-Yield Isolation of Bacteria with Plant Growth-Promoting Traits. Microorganisms 2023; 11:1538. [PMID: 37375040 DOI: 10.3390/microorganisms11061538] [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: 04/25/2023] [Revised: 05/22/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
The diversity of plant-associated bacteria is vast and can be determined by 16S rRNA gene metabarcoding. Fewer of them have plant-beneficial properties. To harness their benefits for plants, we must isolate them. This study aimed to check whether 16S rRNA gene metabarcoding has predictive power in identifying the majority of known bacteria with plant-beneficial traits that can be isolated from the sugar beet (Beta vulgaris L.) microbiome. Rhizosphere and phyllosphere samples collected during one season at different stages of plant development were analyzed. Bacteria were isolated on rich unselective media and plant-based media enriched with sugar beet leaves or rhizosphere extracts. The isolates were identified by sequencing the 16S rRNA gene and tested in vitro for their plant-beneficial properties (stimulation of germination; exopolysaccharide, siderophore, and HCN production; phosphate solubilization; and activity against sugar beet pathogens). The highest number of co-occurring beneficial traits was eight, found in isolates of five species: Acinetobacter calcoaceticus, Bacillus australimaris, B. pumilus, Enterobacter ludwiigi, and Pantoea ananatis. These species were not detected by metabarcoding and have not previously been described as plant-beneficial inhabitants of sugar beets. Thus, our findings point out the necessity of a culture-dependent microbiome analysis and advocate for low-nutrient plant-based media for high-yield isolation of plant-beneficial taxa with multiple beneficial traits. A culture-dependent and -independent approach is required for community diversity assessment. Still, isolation on plant-based media is the best approach to select isolates for potential use as biofertilizers and biopesticides in sugar beet cultivation.
Collapse
Affiliation(s)
| | - Iva Atanasković
- University of Belgrade, Faculty of Biology, 11000 Belgrade, Serbia
- University of Belgrade, Faculty of Biology, Centre for Biological Control and Plant, Growth Promotion, 11000 Belgrade, Serbia
| | - Ivan Nikolić
- University of Belgrade, Faculty of Biology, 11000 Belgrade, Serbia
- University of Belgrade, Faculty of Biology, Centre for Biological Control and Plant, Growth Promotion, 11000 Belgrade, Serbia
| | - Nataša Joković
- Faculty of Sciences and Mathematics, University of Niš, 18000 Niš, Serbia
| | - Tatjana Stević
- Institute for Medicinal Plants Research "Dr. Josif Pančić", 11000 Belgrade, Serbia
| | - Slaviša Stanković
- University of Belgrade, Faculty of Biology, 11000 Belgrade, Serbia
- University of Belgrade, Faculty of Biology, Centre for Biological Control and Plant, Growth Promotion, 11000 Belgrade, Serbia
| | - Tanja Berić
- University of Belgrade, Faculty of Biology, 11000 Belgrade, Serbia
- University of Belgrade, Faculty of Biology, Centre for Biological Control and Plant, Growth Promotion, 11000 Belgrade, Serbia
| | - Jelena Lozo
- University of Belgrade, Faculty of Biology, 11000 Belgrade, Serbia
- University of Belgrade, Faculty of Biology, Centre for Biological Control and Plant, Growth Promotion, 11000 Belgrade, Serbia
| |
Collapse
|
5
|
Wolfgang A, Temme N, Tilcher R, Berg G. Understanding the sugar beet holobiont for sustainable agriculture. Front Microbiol 2023; 14:1151052. [PMID: 37138624 PMCID: PMC10149816 DOI: 10.3389/fmicb.2023.1151052] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/31/2023] [Indexed: 05/05/2023] Open
Abstract
The importance of crop-associated microbiomes for the health and field performance of plants has been demonstrated in the last decades. Sugar beet is the most important source of sucrose in temperate climates, and-as a root crop-yield heavily depends on genetics as well as on the soil and rhizosphere microbiomes. Bacteria, fungi, and archaea are found in all organs and life stages of the plant, and research on sugar beet microbiomes contributed to our understanding of the plant microbiome in general, especially of microbiome-based control strategies against phytopathogens. Attempts to make sugar beet cultivation more sustainable are increasing, raising the interest in biocontrol of plant pathogens and pests, biofertilization and -stimulation as well as microbiome-assisted breeding. This review first summarizes already achieved results on sugar beet-associated microbiomes and their unique traits, correlating to their physical, chemical, and biological peculiarities. Temporal and spatial microbiome dynamics during sugar beet ontogenesis are discussed, emphasizing the rhizosphere formation and highlighting knowledge gaps. Secondly, potential or already tested biocontrol agents and application strategies are discussed, providing an overview of how microbiome-based sugar beet farming could be performed in the future. Thus, this review is intended as a reference and baseline for further sugar beet-microbiome research, aiming to promote investigations in rhizosphere modulation-based biocontrol options.
Collapse
Affiliation(s)
- Adrian Wolfgang
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Nora Temme
- KWS SAAT SE & Co. KGaA, Einbeck, Germany
| | | | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Microbiome Biotechnology Department, Leibniz-Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- *Correspondence: Gabriele Berg
| |
Collapse
|