1
|
Nguyen NL, Van Dung V, Van Tung N, Nguyen TKL, Quan ND, Giang TTH, Ngan NTT, Hien NT, Nguyen HH. Draft genome sequencing of halotolerant bacterium Salinicola sp. DM10 unravels plant growth-promoting potentials. 3 Biotech 2023; 13:416. [PMID: 38009164 PMCID: PMC10667196 DOI: 10.1007/s13205-023-03833-3] [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: 09/30/2022] [Accepted: 10/24/2023] [Indexed: 11/28/2023] Open
Abstract
In this study, strain DM10 was isolated from mangrove roots and characterized as a halotolerant plant growth-promoting bacterium. Strain DM10 exhibited the ability to solubilize phosphate, produce siderophore, show 1-aminocyclopropane-1-carboxylic acid deaminase activity, and hydrolyze starch. The rice plants subjected to a treatment of NaCl (200 mM) and inoculated with strain DM10 showed an improvement in the shoot length, root length, and dried weight, when compared to those exposed solely to saline treatment. The comprehensive genome sequencing of strain DM10 revealed a genome spanning of 4,171,745 bp, harboring 3626 protein coding sequences. Within its genome, strain DM10 possesses genes responsible for both salt-in and salt-out strategies, indicative of a robust genetic adaptation aimed at fostering salt tolerance. Additionally, the genome encodes genes involved in phosphate solubilization, such as the synthesis of gluconic acid, high-affinity phosphate transport systems, and alkaline phosphatase. In the genome of DM10, we identified the acdS gene, responsible for encoding 1-aminocyclopropane-1-carboxylate deaminase, as well as the amy1A gene, which encodes α-amylase. Furthermore, the genome of DM10 contains sequences associated with the iron (3+)-hydroxamate and iron uptake clusters, responsible for siderophore production. Such data provide a deep understanding of the mechanism employed by strain DM10 to combat osmotic and salinity stress, facilitate plant growth, and elucidate its molecular-level behaviors.
Collapse
Affiliation(s)
- Ngoc-Lan Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
- Graduate of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
| | - Vu Van Dung
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
- Graduate of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
| | - Nguyen Van Tung
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
- Graduate of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
| | - Thi Kim Lien Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
| | - Nguyen Duc Quan
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
| | - Tran Thi Huong Giang
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
| | - Nguyen Thi Thanh Ngan
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
- Graduate of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
| | - Nguyen Thanh Hien
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
| | - Huy-Hoang Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
- Graduate of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi Vietnam
| |
Collapse
|
2
|
Li H, Li C, Song X, Li J, Zhang P, Sun F, Geng Z, Liu X. Isolation and identification of antagonistic Bacillus amyloliquefaciens HSE-12 and its effects on peanut growth and rhizosphere microbial community. Front Microbiol 2023; 14:1274346. [PMID: 37901825 PMCID: PMC10601714 DOI: 10.3389/fmicb.2023.1274346] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/02/2023] [Indexed: 10/31/2023] Open
Abstract
The HSE-12 strain isolated from peanut rhizosphere soil was identified as Bacillus amyloliquefaciens by observation of phenotypic characteristics, physiological and biochemical tests, 16S rDNA and gyrB gene sequencing. In vitro experiments showed that the strain possessed biocontrol activity against a variety of pathogens including Sclerotium rolfsii. The strain has the ability to produce hydrolytic enzymes, as well as volatile organic compounds with antagonistic and probiotic effects such as ethyleneglycol and 2,3-butanediol. In addition, HSE-12 showed potassium solubilizing (10.54 ± 0.19 mg/L), phosphorus solubilization (168.34 ± 8.06 mg/L) and nitrogen fixation (17.35 ± 2.34 mg/g) abilities, and was able to secrete siderophores [(Ar-A)/Ar × 100%: 56%] which promoted plant growth. After inoculating peanut with HSE-12, the available phosphorus content in rhizosphere soil increased by 27%, urease activity increased by 43%, catalase activity increased by 70% and sucrase activity increased by 50% (p < 0.05). The dry weight, fresh weight and the height of the first pair of lateral branches of peanuts increased by 24.7, 41.9, and 36.4%, respectively, compared with uninoculated peanuts. In addition, compared with the blank control, it increased the diversity and richness of peanut rhizosphere bacteria and changed the community structure of bacteria and fungi. The relative abundance of beneficial microorganisms such as Sphingomonas, Arthrobacter, RB41, and Micromonospora in rhizosphere soil was increased, while the relative abundance of pathogenic microorganisms such as Aspergillus, Neocosmospora, and Rhizoctonia was decreased.
Collapse
Affiliation(s)
- Huying Li
- College of Forestry, Shandong Agricultural University, Taian, China
- School of Nursing, Zibo Vocational Institute, Zibo, China
| | - Chaohui Li
- College of Forestry, Shandong Agricultural University, Taian, China
| | - Xin Song
- College of Forestry, Shandong Agricultural University, Taian, China
| | - Jintai Li
- College of Forestry, Shandong Agricultural University, Taian, China
| | - Pengcheng Zhang
- College of Forestry, Shandong Agricultural University, Taian, China
| | - Fengxia Sun
- College of Forestry, Shandong Agricultural University, Taian, China
- Key Laboratory of National Forestry and Grassland Administration on Silviculture of the Lower Yellow River, Shandong Agricultural University, Taian, China
| | - Zhigang Geng
- Ministry of Agriculture Key Laboratory of Seaweed Fertilizers, Qingdao, China
| | - Xunli Liu
- College of Forestry, Shandong Agricultural University, Taian, China
- Key Laboratory of National Forestry and Grassland Administration on Silviculture of the Lower Yellow River, Shandong Agricultural University, Taian, China
| |
Collapse
|
3
|
Zhang H, Xia Y, Cui JL, Ji X, Miao SM, Zhang G, Li YM. The composition characteristics of endophytic communities and their relationship with metabolites profile in Ephedra sinica under wild and cultivated conditions. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:95648-95659. [PMID: 37556062 DOI: 10.1007/s11356-023-29145-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 07/31/2023] [Indexed: 08/10/2023]
Abstract
Ephedra sinica is one of the most famous Chinese medicinal plants. The insufficient supply of wild resources has led to the increased use of cultivated products. However, the related medicinal quality differs significantly. Although the influence of external environment on the quality of E. sinica has been studied, the impact of endophytic microbes on it remains vague. This study characterized differential metabolites and microbial community compositions in wild and cultivated E. sinica by combining metabolomics with microbiomics, and explored the effect of endophytes on the formation of differential metabolites further. The results showed that the difference in quality between wild and cultivated E. sinica was mainly in the productions of alkaloids, flavonoids, and terpenoids. The associated endophytes had special compositional characteristics. For instance, the distribution and abundance of dominant endophytes varied between wild and cultivated E. sinica. Several endophytes had significant or highly significant correlations with the formations of ephedrine, pseudoephedrine, D-cathinone, methcathinone, coumarin, kaempferol, rhamnetin, or phenylacetic acid. This study will deepen our understanding of the plant-endophyte interactions and provide a strategy for the quality control of E. sinica products.
Collapse
Affiliation(s)
- Hui Zhang
- Institute of Applied Chemistry, Shanxi University, Taiyuan, 030006, Shanxi, China
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - Ye Xia
- Department of Food Science and Technology, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Jin-Long Cui
- Institute of Applied Chemistry, Shanxi University, Taiyuan, 030006, Shanxi, China.
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Beijing, 100700, China.
| | - Xin Ji
- Institute of Applied Chemistry, Shanxi University, Taiyuan, 030006, Shanxi, China
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - Shuang-Man Miao
- Institute of Applied Chemistry, Shanxi University, Taiyuan, 030006, Shanxi, China
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - Gang Zhang
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, 712046, China
| | - Yi-Min Li
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, 712046, China
| |
Collapse
|
4
|
Mazoyon C, Catterou M, Alahmad A, Mongelard G, Guénin S, Sarazin V, Dubois F, Duclercq J. Sphingomonas sediminicola Dae20 Is a Highly Promising Beneficial Bacteria for Crop Biostimulation Due to Its Positive Effects on Plant Growth and Development. Microorganisms 2023; 11:2061. [PMID: 37630621 PMCID: PMC10459697 DOI: 10.3390/microorganisms11082061] [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: 07/19/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Current agricultural practices rely heavily on synthetic fertilizers, which not only consume a lot of energy but also disrupt the ecological balance. The overuse of synthetic fertilizers has led to soil degradation. In a more sustainable approach, alternative methods based on biological interactions, such as plant growth-promoting bacteria (PGPRs), are being explored. PGPRs, which include both symbiotic and free-living bacteria, form mutualistic relationships with plants by enhancing nutrient availability, producing growth regulators, and regulating stress responses. This study investigated the potential of Sphingomonas sediminicola Dae20, an α-Proteobacteria species commonly found in the rhizosphere, as a beneficial PGPR. We observed that S. sediminicola Dae20 stimulated the root system and growth of three different plant species in the Brassicaceae family, including Arabidopsis thaliana, mustard, and rapeseed. The bacterium produced auxin, nitric oxide, siderophores and showed ACC deaminase activity. In addition to activating an auxin response in the plant, S. sediminicola Dae20 exhibited the ability to modulate other plant hormones, such as abscisic acid, jasmonic acid and salicylic acid, which are critical for plant development and defense responses. This study highlights the multifunctional properties of S. sediminicola Dae20 as a promising PGPR and underscores the importance of identifying effective and versatile beneficial bacteria to improve plant nutrition and promote sustainable agricultural practices.
Collapse
Affiliation(s)
- Candice Mazoyon
- Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR7058 CNRS), Université de Picardie Jules Verne (UPJV), 80000 Amiens, France; (C.M.); (M.C.); (A.A.); (F.D.)
| | - Manuella Catterou
- Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR7058 CNRS), Université de Picardie Jules Verne (UPJV), 80000 Amiens, France; (C.M.); (M.C.); (A.A.); (F.D.)
| | - Abdelrahman Alahmad
- Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR7058 CNRS), Université de Picardie Jules Verne (UPJV), 80000 Amiens, France; (C.M.); (M.C.); (A.A.); (F.D.)
- Agroécologie, Hydrogéochimie, Milieux et Ressources (AGHYLE, UP2018.C101) UniLaSalle Rouen, SFR NORVEGE FED 4277, 76130 Mont-Saint Aignan, France
| | - Gaëlle Mongelard
- Centre de Ressources Régionales en Biologie Moléculaire (CRRBM), Université de Picardie Jules Verne (UPJV), 80000 Amiens, France; (G.M.); (S.G.)
| | - Stéphanie Guénin
- Centre de Ressources Régionales en Biologie Moléculaire (CRRBM), Université de Picardie Jules Verne (UPJV), 80000 Amiens, France; (G.M.); (S.G.)
| | | | - Fréderic Dubois
- Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR7058 CNRS), Université de Picardie Jules Verne (UPJV), 80000 Amiens, France; (C.M.); (M.C.); (A.A.); (F.D.)
| | - Jérôme Duclercq
- Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR7058 CNRS), Université de Picardie Jules Verne (UPJV), 80000 Amiens, France; (C.M.); (M.C.); (A.A.); (F.D.)
| |
Collapse
|
5
|
Liu C, Siri M, Li H, Ren C, Huang J, Feng C, Liu K. Drought is threatening plant growth and soil nutrients of grassland ecosystems: A meta-analysis. Ecol Evol 2023; 13:e10092. [PMID: 37250445 PMCID: PMC10208897 DOI: 10.1002/ece3.10092] [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: 02/28/2023] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 05/31/2023] Open
Abstract
As a widespread direct effect of global warming, drought is currently wreaking havoc on terrestrial ecosystems' structure and function, however, the synthesized analysis is lacked to explore the general rules between drought changes and main functional factors of grassland ecosystems. In this work, meta-analysis was used to examine the impacts of drought on grassland ecosystems in recent decades. According to the results, drought greatly reduced aboveground biomass (AGB), aboveground net primary production (ANPP), height, belowground biomass (BGB), belowground net primary production (BNPP), microbial biomass nitrogen (MBN), microbial biomass carbon (MBC) and soil respiration (SR), and increased dissolved organic carbon (DOC), total nitrogen (TN), total phosphorus (TP), nitrate nitrogen (NO3--N), and the ratio of microbial biomass carbon and nitrogen (MBC/MBN). The drought-related environmental factor mean annual temperature (MAT) was negatively correlated with AGB, height, ANPP, BNPP, MBC, and MBN, however, mean annual precipitation (MAP) had positive effect on these variables. These findings indicate that drought is threatening the biotic environment of grassland ecosystem, and the positive steps should be taken to address the negative effects of drought on grassland ecosystems due to climate change.
Collapse
Affiliation(s)
- Cheng Liu
- College of Grassland Science and TechnologyChina Agricultural UniversityBeijingChina
| | - Muji Siri
- College of Grassland Science and TechnologyChina Agricultural UniversityBeijingChina
| | - Hui Li
- College of Grassland Science and TechnologyChina Agricultural UniversityBeijingChina
| | - Cheng Ren
- College of Grassland Science and TechnologyChina Agricultural UniversityBeijingChina
| | - Jing Huang
- College of Grassland Science and TechnologyChina Agricultural UniversityBeijingChina
| | - Changliang Feng
- College of Grassland Science and TechnologyChina Agricultural UniversityBeijingChina
| | - Kesi Liu
- College of Grassland Science and TechnologyChina Agricultural UniversityBeijingChina
- National Field Station of Grassland Ecosystem in GuyuanGuyuanChina
- Key Laboratory of Restoration Ecology of Cold Area in Qinghai Province, Northwest Institute of Plateau BiologyChinese Academy of SciencesXiningChina
| |
Collapse
|
6
|
Bourne ME, Gloder G, Weldegergis BT, Slingerland M, Ceribelli A, Crauwels S, Lievens B, Jacquemyn H, Dicke M, Poelman EH. Parasitism causes changes in caterpillar odours and associated bacterial communities with consequences for host-location by a hyperparasitoid. PLoS Pathog 2023; 19:e1011262. [PMID: 36947551 PMCID: PMC10069771 DOI: 10.1371/journal.ppat.1011262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 04/03/2023] [Accepted: 03/02/2023] [Indexed: 03/23/2023] Open
Abstract
Microorganisms living in and on macroorganisms may produce microbial volatile compounds (mVOCs) that characterise organismal odours. The mVOCs might thereby provide a reliable cue to carnivorous enemies in locating their host or prey. Parasitism by parasitoid wasps might alter the microbiome of their caterpillar host, affecting organismal odours and interactions with insects of higher trophic levels such as hyperparasitoids. Hyperparasitoids parasitise larvae or pupae of parasitoids, which are often concealed or inconspicuous. Odours of parasitised caterpillars aid them to locate their host, but the origin of these odours and its relationship to the caterpillar microbiome are unknown. Here, we analysed the odours and microbiome of the large cabbage white caterpillar Pieris brassicae in relation to parasitism by its endoparasitoid Cotesia glomerata. We identified how bacterial presence in and on the caterpillars is correlated with caterpillar odours and tested the attractiveness of parasitised and unparasitised caterpillars to the hyperparasitoid Baryscapus galactopus. We manipulated the presence of the external microbiome and the transient internal microbiome of caterpillars to identify the microbial origin of odours. We found that parasitism by C. glomerata led to the production of five characteristic volatile products and significantly affected the internal and external microbiome of the caterpillar, which were both found to have a significant correlation with caterpillar odours. The preference of the hyperparasitoid was correlated with the presence of the external microbiome. Likely, the changes in external microbiome and body odour after parasitism were driven by the resident internal microbiome of caterpillars, where the bacterium Wolbachia sp. was only present after parasitism. Micro-injection of Wolbachia in unparasitised caterpillars increased hyperparasitoid attraction to the caterpillars compared to untreated caterpillars, while no differences were found compared to parasitised caterpillars. In conclusion, our results indicate that host-parasite interactions can affect multi-trophic interactions and hyperparasitoid olfaction through alterations of the microbiome.
Collapse
Affiliation(s)
- Mitchel E Bourne
- Laboratory of Entomology, Wageningen University & Research, Wageningen, The Netherlands
| | - Gabriele Gloder
- CMPG Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department M2S, KU Leuven, Leuven, Belgium
- Leuven Plant Institute (LPI), KU Leuven, Leuven, Belgium
| | - Berhane T Weldegergis
- Laboratory of Entomology, Wageningen University & Research, Wageningen, The Netherlands
| | - Marijn Slingerland
- Laboratory of Entomology, Wageningen University & Research, Wageningen, The Netherlands
| | - Andrea Ceribelli
- Laboratory of Entomology, Wageningen University & Research, Wageningen, The Netherlands
| | - Sam Crauwels
- CMPG Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department M2S, KU Leuven, Leuven, Belgium
- Leuven Plant Institute (LPI), KU Leuven, Leuven, Belgium
| | - Bart Lievens
- CMPG Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department M2S, KU Leuven, Leuven, Belgium
- Leuven Plant Institute (LPI), KU Leuven, Leuven, Belgium
| | - Hans Jacquemyn
- Leuven Plant Institute (LPI), KU Leuven, Leuven, Belgium
- Laboratory of Plant Conservation and Population Biology, Biology Department, KU Leuven, Leuven, Belgium
| | - Marcel Dicke
- Laboratory of Entomology, Wageningen University & Research, Wageningen, The Netherlands
| | - Erik H Poelman
- Laboratory of Entomology, Wageningen University & Research, Wageningen, The Netherlands
| |
Collapse
|
7
|
Jiang L, Seo J, Peng Y, Jeon D, Lee JH, Kim CY, Lee J. A nostoxanthin-producing bacterium, Sphingomonas nostoxanthinifaciens sp. nov., alleviates the salt stress of Arabidopsis seedlings by scavenging of reactive oxygen species. Front Microbiol 2023; 14:1101150. [PMID: 36846770 PMCID: PMC9950776 DOI: 10.3389/fmicb.2023.1101150] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/18/2023] [Indexed: 02/12/2023] Open
Abstract
A novel, nostoxanthin-producing, endophytic bacterium, designated as AK-PDB1-5T, was isolated from the needle-like leaves of the Korean fir (Abies koreana Wilson) collected from Mt. Halla in Jeju, South Korea. A 16S rRNA sequence comparison indicated that the closest phylogenetic neighbors were Sphingomonas crusticola MIMD3T (95.6%) and Sphingomonas jatrophae S5-249T (95.3%) of the family Sphingomonadaceae. Strain AK-PDB1-5T had a genome size of 4,298,284 bp with a 67.8% G + C content, and digital DNA-DNA hybridization and OrthoANI values with the most closely related species of only 19.5-21% and 75.1-76.8%, respectively. Cells of the strain AK-PDB1-5T were Gram-negative, short rods, oxidase- and catalase-positive. Growth occurred at pH 5.0-9.0 (optimum pH 8.0) in the absence of NaCl at 4-37°C (optimum 25-30°C). Strain AK-PDB1-5T contained C14:0 2OH, C16:0 and summed feature 8 as the major cellular fatty acids (> 10%), while sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, phospholipids and lipids were found to be the major polar lipids. The strain produces a yellow carotenoid pigment; natural products prediction via AntiSMASH tool found zeaxanthin biosynthesis clusters in the entire genome. Biophysical characterization by ultraviolet-visible absorption spectroscopy and ESI-MS studies confirmed the yellow pigment was nostoxanthin. In addition, strain AK-PDB1-5T was found significantly promote Arabidopsis seedling growth under salt conditions by reducing reactive oxygen species (ROS). Based on the polyphasic taxonomic analysis results, strain AK-PDB1-5T was determined to be a novel species in the genus Sphingomonas with the proposed name Sphingomonas nostoxanthinifaciens sp. nov. The type strain is AK-PDB1-5T (= KCTC 82822T = CCTCC AB 2021150T).
Collapse
Affiliation(s)
- Lingmin Jiang
- Biological Resource Center, Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Republic of Korea
| | - Jiyoon Seo
- Biological Resource Center, Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Republic of Korea
| | - Yuxin Peng
- Biological Resource Center, Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Republic of Korea
| | - Doeun Jeon
- Biological Resource Center, Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Republic of Korea
| | - Ju Huck Lee
- Biological Resource Center, Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Republic of Korea
| | - Cha Young Kim
- Biological Resource Center, Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Republic of Korea
| | | |
Collapse
|
8
|
Mazoyon C, Hirel B, Pecourt A, Catterou M, Gutierrez L, Sarazin V, Dubois F, Duclercq J. Sphingomonas sediminicola Is an Endosymbiotic Bacterium Able to Induce the Formation of Root Nodules in Pea ( Pisum sativum L.) and to Enhance Plant Biomass Production. Microorganisms 2023; 11:microorganisms11010199. [PMID: 36677491 PMCID: PMC9861922 DOI: 10.3390/microorganisms11010199] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/13/2023] Open
Abstract
The application of bacterial bio-inputs is a very attractive alternative to the use of mineral fertilisers. In ploughed soils including a crop rotation pea, we observed an enrichment of bacterial communities with Sphingomonas (S.) sediminicola. Inoculation experiments, cytological studies, and de novo sequencing were used to investigate the beneficial role of S. sediminicola in pea. S. sediminicola is able to colonise pea plants and establish a symbiotic association that promotes plant biomass production. Sequencing of the S. sediminicola genome revealed the existence of genes involved in secretion systems, Nod factor synthesis, and nitrogenase activity. Light and electron microscopic observations allowed us to refine the different steps involved in the establishment of the symbiotic association, including the formation of infection threads, the entry of the bacteria into the root cells, and the development of differentiated bacteroids in root nodules. These results, together with phylogenetic analysis, demonstrated that S. sediminicola is a non-rhizobia that has the potential to develop a beneficial symbiotic association with a legume. Such a symbiotic association could be a promising alternative for the development of more sustainable agricultural practices, especially under reduced N fertilisation conditions.
Collapse
Affiliation(s)
- Candice Mazoyon
- Unité Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR7058 CNRS), Université de Picardie Jules Verne (UPJV), 80000 Amiens, France
| | - Bertrand Hirel
- Unité Mixte de Recherche 1318 INRA-AgroParisTech, Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique et de l'Environnement (INRAE), 78026 Versailles, France
| | - Audrey Pecourt
- Unité Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR7058 CNRS), Université de Picardie Jules Verne (UPJV), 80000 Amiens, France
| | - Manuella Catterou
- Unité Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR7058 CNRS), Université de Picardie Jules Verne (UPJV), 80000 Amiens, France
| | - Laurent Gutierrez
- Centre de Ressources Régionales en Biologie Moléculaire (CRRBM), Université de Picardie Jules Verne (UPJV), 80000 Amiens, France
| | | | - Fréderic Dubois
- Unité Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR7058 CNRS), Université de Picardie Jules Verne (UPJV), 80000 Amiens, France
| | - Jérôme Duclercq
- Unité Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR7058 CNRS), Université de Picardie Jules Verne (UPJV), 80000 Amiens, France
- Correspondence: ; Tel.: +33-3-22827612
| |
Collapse
|
9
|
Jiang X, Guo Y, Li H, Li X, Liu J. Ecological evolution during the three-year restoration using rhizosphere soil cover method at a Lead-Zinc tailing pond in Karst areas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 853:158291. [PMID: 36030848 DOI: 10.1016/j.scitotenv.2022.158291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 08/21/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
A major challenge for the restoration of the Lead-Zinc tailing pond in Karst areas lies in how to establish vegetation with less soil and restore the ecological functions of the substrate. In this study, a novel method, rhizosphere soil cover method (RSC), was applied to recover the vegetation at a Pb-Zn tailing pond in Karst areas. Two local tolerate plants, Miscanthus sinensis and Pueraria phaseoloides, were planted as pioneer species. Although 68 % of the tailing pond was not covered with soil, the vegetation coverage has reached over 90 % after restoration for three years. Compared with the natural revegetation process (vegetation coverage was <5 % after 20 years of natural succession), the revegetation in the tailing pond was accelerated by RSC and planting pioneer species. Both the plant's diversity and richness have significantly increased in the tailings pond during the restoration (p < 0.05). The important value indicators of M. sinensis and P. phaseoloides were the highest in the plant community, indicating the dominant role of these two plants in revegetation. Moreover, the total organic carbon, total nitrogen, total phosphorus, and total potassium in the tailings increased annually (p < 0.05), which demonstrated that the revegetation has improved the chemical properties in the substrate. In addition, the Shannon diversity index of bacteria in the tailings increased significantly from 4.11 to 5.51. The relative abundance of microbial genes related to carbon fixation and nitrogen fixation in the tailings increased by 17 % and 43 %, respectively. Meanwhile, the physicochemical properties, microbial community structure, and nutrient cycling function in the tailings without topsoil were improved more obviously than those in soils. It is thereby concluded that RSC is an efficient means for ecological restoration of the tailing ponds in Karst areas to improve the ecosystem structure and function of Pb-Zn tailings.
Collapse
Affiliation(s)
- Xusheng Jiang
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin 541004, China
| | - Yu Guo
- Technical Innovation Center of Mine Geological Environmental Restoration Engineering in Southern Karst Area, MNR, Guilin 541004, China
| | - Haixiang Li
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin 541004, China
| | - Xiangmin Li
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin 541004, China
| | - Jie Liu
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin 541004, China; Technical Innovation Center of Mine Geological Environmental Restoration Engineering in Southern Karst Area, MNR, Guilin 541004, China.
| |
Collapse
|
10
|
Lin Y, Mei L, Wei Q, Li B, Zhang P, Sun S, Cui G. Leymus chinensis resists degraded soil stress by modulating root exudate components to attract beneficial microorganisms. Front Microbiol 2022; 13:951838. [PMID: 36569063 PMCID: PMC9780673 DOI: 10.3389/fmicb.2022.951838] [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: 05/26/2022] [Accepted: 11/11/2022] [Indexed: 12/14/2022] Open
Abstract
Phytoremediation is an effective means to improve degraded soil nutrients and soil structure. Here, we investigated the remediation effects of Leymus chinensis on the physicochemical properties and structure of degraded soil after 3 years of cultivation and explored the bacterial and fungal drivers in root exudates by metabolomics and high-throughput sequencing. The results showed that root exudates increased soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP) and soil aggregates, and organic acids in root exudates reduced pH and activated insoluble nutrients into forms that are available to plants, such as available nitrogen (NH4 +-N), nitrate nitrogen (NO3 --N), and available phosphorus (AP). The cultivation of L. chinensis restored the diversity and richness of soil microorganisms and recruited potential beneficial bacteria and fungi to resist degraded soil stress, and L. chinensis also regulated the abundances of organic acids, amino acids and fatty acids in root exudates to remediate degraded soils. Spearman correlation analysis indicated that glutaric acid, 3-hydroxybutyric acid and 4-methylcatechol in root exudates attracted Haliangium, Nitrospira and Mortierella to the rhizosphere and dispersed the relative abundance of the harmful microorganisms Fusicolla and Fusarium. Our results demonstrate that L. chinensis enhances soil fertility, improves soil structure, promotes microbial diversity and abundance, and recruits potentially beneficial microorganisms by modulating root exudate components.
Collapse
|
11
|
Shi H, Xu P, Wu S, Yu W, Cheng Y, Chen Z, Yang X, Yu X, Li B, Ding A, Wang W, Sun Y. Analysis of rhizosphere bacterial communities of tobacco resistant and non-resistant to bacterial wilt in different regions. Sci Rep 2022; 12:18309. [PMID: 36316337 PMCID: PMC9622857 DOI: 10.1038/s41598-022-20293-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 09/12/2022] [Indexed: 11/06/2022] Open
Abstract
Tobacco bacterial wilt has seriously affected tobacco production. Ethyl methanesulfonate (EMS) induced tobacco bacterial wilt resistant mutants are important for the control of tobacco bacterial wilt. High-throughput sequencing technology was used to study the rhizosphere bacterial community assemblages of bacterial wilt resistant mutant tobacco rhizosphere soil (namely KS), bacterial wilt susceptible tobacco rhizosphere soil (namely GS) and bulk soil (namely BS) in Xuancheng, Huanxi, Yibin and Luzhou. Alpha analysis showed that the bacterial community diversity and richness of KS and GS in the four regions were not significantly different. However, analysis of intergroup variation in the top 15 bacterial communities in terms of abundance showed that the bacterial communities of KS and GS were significantly different from BS, respectively. In addition, pH, alkali-hydrolysable nitrogen (AN) and soil organic carbon (SOC) were positively correlated with the bacterial community of KS and negatively correlated with GS in the other three regions except Huanxi. Network analysis showed that the three soils in the four regions did not show a consistent pattern of network complexity. PICRUSt functional prediction analysis showed that the COG functions were similar in all samples. All colonies were involved in RNA processing and modification, chromatin structure and dynamics, etc. In conclusion, our experiments showed that rhizosphere bacterial communities of tobacco in different regions have different compositional patterns, which are strongly related to soil factors.
Collapse
Affiliation(s)
- Haoqi Shi
- grid.464493.80000 0004 1773 8570Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101 China ,grid.410727.70000 0001 0526 1937Graduate School of Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Peiwen Xu
- grid.464493.80000 0004 1773 8570Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101 China ,grid.410727.70000 0001 0526 1937Graduate School of Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Shengxin Wu
- Fujian Institute of Tobacco Agricultural Sciences, Fuzhou, 350003 China
| | - Wen Yu
- Fujian Institute of Tobacco Agricultural Sciences, Fuzhou, 350003 China
| | - Yazhi Cheng
- Fujian Institute of Tobacco Agricultural Sciences, Fuzhou, 350003 China
| | - Zhihua Chen
- Sichuan Tobacco Science Institute, Sichuan Branch of China National Tobacco Corporation, Chengdu, 615000 China
| | - Xingyou Yang
- Sichuan Tobacco Science Institute, Sichuan Branch of China National Tobacco Corporation, Chengdu, 615000 China
| | - Xiangwen Yu
- Sichuan Tobacco Science Institute, Sichuan Branch of China National Tobacco Corporation, Chengdu, 615000 China
| | - Bingjie Li
- grid.464493.80000 0004 1773 8570Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101 China ,grid.410727.70000 0001 0526 1937Graduate School of Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Anming Ding
- grid.464493.80000 0004 1773 8570Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101 China
| | - Weifeng Wang
- grid.464493.80000 0004 1773 8570Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101 China
| | - Yuhe Sun
- grid.464493.80000 0004 1773 8570Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101 China
| |
Collapse
|
12
|
Kong WL, Wang YH, Lu LX, Li PS, Zhang Y, Wu XQ. Rahnella aquatilis JZ-GX1 alleviates iron deficiency chlorosis in Cinnamomum camphora by secreting desferrioxamine and reshaping the soil fungal community. FRONTIERS IN PLANT SCIENCE 2022; 13:960750. [PMID: 36186024 PMCID: PMC9520127 DOI: 10.3389/fpls.2022.960750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/19/2022] [Indexed: 06/16/2023]
Abstract
Plant growth-promoting rhizobacteria are important for improving plant iron nutrition, but the interactions among inoculants, host plants and soil microorganisms have not been greatly explored. Rahnella aquatilis JZ-GX1 was applied to treat the increasingly serious iron deficiency chlorosis in Cinnamomum camphora, and the resulting improvement in chlorosis was determined by assessing the contents of chlorophyll, active iron, Fe2+ and antioxidant enzymes in leaves, the effects on the soil microbial community and the metabolism in the rhizosphere by high-throughput sequencing techniques and liquid chromatography-mass spectrometry (LC-MS). The results showed that inoculation with JZ-GX1 significantly increased the chlorophyll content of C. camphora, which promoted the redistribution of active iron in roots and leaves, increased the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and ascorbate peroxidase (APX), and thus reduced membrane damage in iron-deficient C. camphora caused by reactive oxygen species. According to genome prediction and ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) analysis, the JZ-GX1 strain could secrete desferrioxamine (DFO), and the concentration of DFO in C. camphora rhizosphere was 21-fold higher than that in uninoculated soil. The exogenous application of DFO increased the SPAD and Fe2+ contents in leaves. In addition, the inoculant affected the fungal community structure and composition in the C. camphora rhizosphere soil and increased the abundances of specific taxa, such as Glomus, Mortierella, Trichoderma, and Penicillium. Therefore, R. aquatilis JZ-GX1 application promoted iron absorption in C. camphora trees by secreting DFO and alleviated iron deficiency chlorosis through interactions with the local fungal community.
Collapse
Affiliation(s)
- Wei-Liang Kong
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Ya-Hui Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Lan-Xiang Lu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Pu-Sheng Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Yu Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Xiao-Qin Wu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, Jiangsu, China
| |
Collapse
|
13
|
Kour D, Yadav AN. Bacterial Mitigation of Drought Stress in Plants: Current Perspectives and Future Challenges. Curr Microbiol 2022; 79:248. [PMID: 35834053 DOI: 10.1007/s00284-022-02939-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 06/17/2022] [Indexed: 11/28/2022]
Abstract
Climate change is emerging as a crucial issue with global attention and leading to abiotic stress conditions. There are different abiotic stress which affects the crop production among which drought is known to be most destructive stress affecting crop productivity and world's food security. Different approaches are under consideration to increase adaptability of the plants under drought stress with plant-microbe interactions being a greater area of focus. Stress-adaptive microbes either from the rhizosphere, internal tissue, or aerial parts of plants have been reported which through different mechanisms help the plants to cope up with drought and also promote their growth. These mechanisms include the accumulation of osmolytes, decrease in the inhibitory levels of ethylene by aminocyclopropane-1-carboxylate (ACC) deaminase enzyme, and furnishing the unavailable nutrients to plants. Microbial genera including Azotobacter, Bacillus, Ochrobactrum, Pseudomonas, and Serratia are known to be self-adaptive and growth promoters under drought stressed conditions. Stress-adaptive plant growth promoting (PGP) microbes thus are excellent candidates for stress alleviation in drought environment to provide maximum benefits to the plants. The present review deals with the effect of the drought stress on plants, biodiversity of the drought-adaptive microbes, mechanisms of the drought stress alleviation through enhancement of stress alleviators, reduction of the stress aggravators, and modification of the molecular pathways as well as the multiple PGP attributes of the drought-adaptive microbes.
Collapse
Affiliation(s)
- Divjot Kour
- Department of Microbiology, Akal College of Basic Sciences, Eternal University, Baru Sahib, Sirmour, 173101, India
| | - Ajar Nath Yadav
- Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, 173101, India.
| |
Collapse
|
14
|
Effect of the Mineral-Microbial Complexes on the Quality, Soil Nutrients, and Microbial Community of Tailing Substrates for Growing Potted Rorippa. Microbiol Res 2022; 262:127084. [DOI: 10.1016/j.micres.2022.127084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/16/2022] [Accepted: 05/29/2022] [Indexed: 11/18/2022]
|
15
|
Luo Y, Zhou M, Wang F, Sheng H. Sphingomonas psychrotolerans sp. nov., isolated from root surface of Leontopodium leontopodioides in the Tianshan Mountains, Xinjiang, China. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005396] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel rod-shaped, Gram-stain-negative, aerobic bacterial strain, designated Cra20T, was isolated from the root surface of Leontopodium leontopodioides collected in the Tianshan Mountains, Xinjiang, PR China. Phylogenetic analysis based on 16S rRNA gene sequences, indicated that strain Cra20T was affiliated with the genus
Sphingomonas
, and was most closely related to
Sphingomonas gei
ZFGT-11T (99.0 %),
Sphingomonas naasensis
KIS18-15T (97.8%) and
Sphingomonas kyeonggiensis
THG-DT81T (97.2 %). The average nucleotide identity values between strain Cra20T,
S. gei
ZFGT-11T,
S. naasensis
KIS18-15T and
S. kyeonggiensis
THG-DT81T were 86.2, 84.2 and 78.2 %, respectively. The genomic DNA G+C content of strain Cra20T was 65.6 mol% (whole genome sequence), and Q-10 was the predominant ubiquinone. The major cellular fatty acids of strain Cra20T were summed feature 8 (comprising C18 : 1
ω6c and/or C18 : 1
ω7c, 67.3 %) and C14 : 0 2-OH (6.4 %). On the basis of genotypic, phenotypic and biochemical data, strain Cra20T is considered to represent a novel species of the genus
Sphingomonas
, for which the name Sphingomonas psychrotolerans sp. nov. is proposed. The type strain is Cra20T (=CGMCC 1.15510T=NBRC 112697T).
Collapse
Affiliation(s)
- Yang Luo
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China
- School of Life Sciences, Shangrao Normal University, Shangrao Agricultural Technology Innovation Research Institute, Shangrao 334000, PR China
| | - Meng Zhou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China
- School of Life Sciences, Shangrao Normal University, Shangrao Agricultural Technology Innovation Research Institute, Shangrao 334000, PR China
| | - Fang Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China
| | - Hongmei Sheng
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China
| |
Collapse
|
16
|
Yang X, Bao Y, Shao T, Wang W, Ma P, Wang W, Gallo A, Yuan X. Altitudinal Distribution Patterns of Phyllosphere Microbial Communities and Their Contribution to Silage Fermentation of Kobresia pygmaea Along the Elevation Gradient on the Tibetan Plateau. Front Microbiol 2022; 13:874582. [PMID: 35685941 PMCID: PMC9173736 DOI: 10.3389/fmicb.2022.874582] [Citation(s) in RCA: 3] [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: 02/24/2022] [Accepted: 04/08/2022] [Indexed: 11/21/2022] Open
Abstract
The study aimed to reveal altitudinal distribution patterns of phyllosphere microbial communities and silage fermentation of Kobresia pygmaea along the elevation gradient on the Tibetan Plateau. The K. pygmaea was individually collected from 2,500, 3,000, 4,000, 4,500, and 5,000 m above sea level (a.s.l.) on the Tibetan Plateau and ensiled for 60 days, respectively. The phyllosphere bacterial diversity increased while fungal diversity decreased along the elevation gradient, and bacterial and fungal richness showed a unimodal distribution with peak abundance at 4,000 and 3,000 m a.s.l., respectively. After 60 days of ensiling, the bacterial and fungal community composition changed but did not exhibit clear altitudinal distribution patterns. All K. pygmaea underwent a weak fermentation indicated by pH above 5.0 and low ratio of lactic/acetic acid (LA/AA). The S5000 and S3000 showed the highest and lowest pH, respectively. Although Lactobacillus dominated S4000 after 60 days of ensiling, S4000 still exhibited poor fermentation quality as well as silages from the other four regions. The higher ammonia N concentrations in S3000 and S4000 than the other silages were consistent with the detectable butyric acid in S3000 and S4000. The silage fermentation of K. pygmaea collected from five regions exhibited poor fermentation quality, thereby inoculating lactic acid bacteria to K. pygmaea before ensiling is highly recommended to improve fermentation quality on the Tibetan Plateau.
Collapse
Affiliation(s)
- Xin Yang
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Yuhong Bao
- State Key Laboratory of Germplasm Resources and Genetic Improvement of Tibetan Barley and Yak, Lhasa, China
- Institute of Grass Science, TAR Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Tao Shao
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Wenkang Wang
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Pengfei Ma
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Wenbo Wang
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Antonio Gallo
- Department of Animal Science, Food and Nutrition (DIANA), Faculty of Agricultural, Food and Environmental Sciences, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Xianjun Yuan
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| |
Collapse
|
17
|
Yang R, Zhang B, Xu Y, Zhang G, Liu Y, Zhang D, Zhang W, Chen T, Liu G. Genomic insights revealed the environmental adaptability of Planococcus halotolerans Y50 isolated from petroleum-contaminated soil on the Qinghai-Tibet Plateau. Gene 2022; 823:146368. [PMID: 35240255 DOI: 10.1016/j.gene.2022.146368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 11/28/2022]
Abstract
The Tibetan Plateau niche provides unprecedented opportunities to find microbes that are functional and commercial significance. The present study investigated the physiological and genomic characteristics of Planococcus halotolerans Y50 that was isolated from a petroleum-contaminated soil sample from the Qinghai-Tibet Plateau, and it displayed psychrotolerant, antiradiation, and oil-degraded characteristics. Whole genome sequencing indicated that strain Y50 has a 3.52 Mb genome and 44.7% G + C content, and it possesses 3377 CDSs. The presence of a wide range of UV damage repair genes uvrX and uvsE, DNA repair genes radA and recN, superoxide dismutase, peroxiredoxin and dioxygenase genes provided the genomic basis for the adaptation of the plateau environment polluted by petroleum. Related experiments also verified that the Y50 strain could degrade n-alkanes from C11-C23, and approximately 30% of the total petroleum at 25 °C within 7 days. Meanwhile, strain Y50 could withstand 5 × 103 J/m2 UVC and 10 KGy gamma ray radiation, and it had strong antioxidant and high radical scavengers for superoxide anion, hydroxyl radical and DPPH. In addition, pan-genome analysis and horizontal gene transfers revealed that strains with different niches have obtained various genes through horizontal gene transfer in the process of evolution, and the more similar their geographical locations, the more similar their members are genetically and ecologically. In conclusion, P. halotolerans Y50 possesses high potential of applications in the bioremediation of alpine hydrocarbons contaminated environment.
Collapse
Affiliation(s)
- Ruiqi Yang
- College of Urban Environment, Lanzhou City University, Lanzhou 730070, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, 730000, China
| | - Binglin Zhang
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy Sciences, Lanzhou 730000, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, 730000, China.
| | - Yeteng Xu
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy Sciences, Lanzhou 730000, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, 730000, China
| | - Gaosen Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, 730000, China; Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Yang Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, 730000, China; Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Dongming Zhang
- School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), KTH Royal Institute of Technology, Stockholm, Sweden
| | - Wei Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, 730000, China; Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy Sciences, Lanzhou 730000, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, 730000, China
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, 730000, China; Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| |
Collapse
|
18
|
Li Q, Xiang P, Zhang T, Wu Q, Bao Z, Tu W, Li L, Zhao C. The effect of phosphate mining activities on rhizosphere bacterial communities of surrounding vegetables and crops. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 821:153479. [PMID: 35092784 DOI: 10.1016/j.scitotenv.2022.153479] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/24/2022] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
The effects of phosphate mining on rhizosphere bacteria in surrounding vegetables and crops, including Lactuca sativa, Glycine max, and Triticum aestivum, are assessed in this study. As results, phosphate mining significantly increased the contents of some large elements, trace elements, and heavy metals in the surrounding agricultural soil, including phosphorus, magnesium, boron, cadmium, lead, arsenic, zinc, and chromium (P < 0.05). The community richness and diversity of bacteria in rhizosphere of the three crops were significantly reduced by phosphate mining (P < 0.05). Abundances of Sphingomonas and RB41 in the rhizosphere soil of phosphate mining area improved compared with the baseline in the non-phosphate mining area. Beta diversity analysis indicated that phosphate mining led to the differentiation of bacterial community structure in plant rhizospheres. Bacterial metabolic analysis indicated that different plant rhizosphere microbial flora developed various metabolic strategies in response to phosphate mining stress, including enriching unsaturated fatty acids, antibiological transport systems, cold shock proteins, etc. This study reveals the interaction between crops, rhizosphere bacteria, and soil pollutants. Select differentiated microbial strains suitable for specific plant rhizosphere environments are necessary for agricultural soil remediation. Additionally, the problem of destruction of agricultural soil and microecology caused by phosphate mining must be solved.
Collapse
Affiliation(s)
- Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Peng Xiang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Ting Zhang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Qian Wu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Zhijie Bao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Wenying Tu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Lijiao Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Changsong Zhao
- School of Public Health, Chengdu Medical College, Chengdu, Sichuan, China.
| |
Collapse
|
19
|
Fungal and Bacterial Communities in Tuber melanosporum Plantations from Northern Spain. FORESTS 2022. [DOI: 10.3390/f13030385] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Tuber melanosporum (Ascomycota, Pezizales) is an ectomycorrhizal fungus that produces highly appreciated hypogeous fruiting bodies called black truffles. The aim of this paper was to research the composition of ectomycorrhiza-associated fungal and bacterial communities in T. melanosporum oak plantations. Results of this paper showed the competitive effect of T. melanosporum on other fungal species, especially other mycorrhizal and pathogenic species. T. melanosporum was shown to be associated mainly with bacteria, some of them important for their properties as mycorrhizal helper bacteria. A dendrogram analysis of co-occurrence showed that T. melanosporum tended to co-occur with the following bacteria species: Singulisphaera limicola, Nannocistis excedens and Sporosarcina globispora. In addition, it was linked to fungal species such as Mortierella elongata, M. minutissima, Cryptococcus uzbekistanensis, C. chernovii and C. aerius. This study provides an exhaustive analysis of the diversity, structure and composition of fungal and bacterial communities associated with T. melanosporum to enhance understanding of the biology, composition and role of these communities in truffle plantations.
Collapse
|
20
|
Yang H, Wang C, Chen F, Yue L, Cao X, Li J, Zhao X, Wu F, Wang Z, Xing B. Foliar carbon dot amendment modulates carbohydrate metabolism, rhizospheric properties and drought tolerance in maize seedling. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 809:151105. [PMID: 34688768 DOI: 10.1016/j.scitotenv.2021.151105] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/16/2021] [Accepted: 10/16/2021] [Indexed: 06/13/2023]
Abstract
Improving maize drought tolerance is of great importance for scaling up production due to food security and population growth. Carbon dots (CDs) were synthesized by hydrothermal method with citric acid and ethylenediamine as carbon sources. Then, CDs (5 ml, 5 mg‧L-1) were sprayed on 25th day-old maize (Zea mays L., drought-stress, 35% soil moisture) for seven consecutive days (spraying ultra-pure water as control), after which the physiological parameters and rhizospheric properties of maize under drought were evaluated. Foliar sprayed CDs (5 mg‧L-1) could increase root exudates (e.g., succinic acid (14.5 folds), pyruvic acid (10.0 folds), and betaine (11.8 folds)), and modify microbial community. Particularly, the relative abundance of Pseudomonas, Sphingomonas, Nitrospira, and Conocybe were significantly increased by 344.4%, 233.3%, 126.2%, and 122.6%, respectively. The altered microbial abundance could improve soil available nitrogen and phosphorus by 33.5% and 16.8%, respectively, and increase plant water uptake by 37.2%. The change of exudate synthesis and microbial abundance could be driven by the significantly increased in net photosynthesis rate by 122.9%, and carbohydrate content by 35.4% in shoots and 113.6% in roots, respectively upon foliar application of CDs. Meanwhile, fresh weight of shoots and roots were increased by 62.1% and 50.6%, and dry weight of shoots and roots were increased by 29.2% and 37.5%, respectively. These results demonstrated that foliar application of CDs could improve the rhizosphere environment to enhance maize drought tolerance and even growth. Therefore, foliar application of CDs would be a promising strategy for sustainable nano-agriculture in response to drought stress.
Collapse
Affiliation(s)
- Hanyue Yang
- Institute of Environmental Processes and Pollution Control, School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Chuanxi Wang
- Institute of Environmental Processes and Pollution Control, School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Feiran Chen
- Institute of Environmental Processes and Pollution Control, School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Le Yue
- Institute of Environmental Processes and Pollution Control, School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xuesong Cao
- Institute of Environmental Processes and Pollution Control, School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jing Li
- Institute of Environmental Processes and Pollution Control, School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xiaoli Zhao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Fengchang Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Zhenyu Wang
- Institute of Environmental Processes and Pollution Control, School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Baoshan Xing
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003, USA
| |
Collapse
|
21
|
Li HP, Gan YN, Yue LJ, Han QQ, Chen J, Liu QM, Zhao Q, Zhang JL. Newly Isolated Paenibacillus monticola sp. nov., a Novel Plant Growth-Promoting Rhizobacteria Strain From High-Altitude Spruce Forests in the Qilian Mountains, China. Front Microbiol 2022; 13:833313. [PMID: 35250949 PMCID: PMC8895201 DOI: 10.3389/fmicb.2022.833313] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 01/11/2022] [Indexed: 11/25/2022] Open
Abstract
Species in the genus Paenibacillus from special habitats have attracted great attention due to their plant growth-promoting traits. A novel plant growth-promoting rhizobacteria (PGPR) species in the genus Paenibacillus was isolated from spruce forest at the height of 3,150 m in the Qilian Mountains, Gansu province, China. The phylogenetic analysis based on 16S rRNA, rpoB, and nifH gene sequences demonstrated that strain LC-T2T was affiliated in the genus Paenibacillus and exhibited the highest sequence similarity with Paenibacillus donghaensis KCTC 13049T (97.4%). Average nucleotide identity (ANIb and ANIm) and digital DNA–DNA hybridization (dDDH) between strain LC-T2T and P. donghaensis KCTC 13049T were 72.6, 83.3, and 21.2%, respectively, indicating their genetic differences at the species level. These differences were further verified by polar lipids profiles, major fatty acid contents, and several distinct physiological characteristics. Meanwhile, the draft genome analysis provided insight into the genetic features to support its plant-associated lifestyle and habitat adaptation. Subsequently, the effects of volatile organic compound (VOC) emitted from strain LC-T2T on the growth of Arabidopsis were evaluated. Application of strain LC-T2T significantly improved root surface area, root projection area, and root fork numbers by 158.3, 158.3, and 241.2%, respectively, compared to control. Also, the effects of LC-T2T on the growth of white clover (Trifolium repens L.) were further assessed by pot experiment. Application of LC-T2T also significantly improved the growth of white clover with root fresh weight increased over three-folds compared to control. Furthermore, the viable bacterial genera of rhizosphere soil were detected in each treatment. The number of genera from LC-T2T-inoculated rhizosphere soil was 1.7-fold higher than that of control, and some isolates were similar to strain LC-T2T, indicating that LC-T2T inoculation was effective in the rhizosphere soil of white clover. Overall, strain LC-T2T should be attributed to a novel PGPR species within the genus Paenibacillus based on phylogenetic relatedness, genotypic features, and phenotypic and inoculation experiment, for which the name Paenibacillus monticola sp. nov. is proposed.
Collapse
Affiliation(s)
- Hui-Ping Li
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
- Center for Grassland Microbiome, State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, China
| | - Ya-Nan Gan
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
- Center for Grassland Microbiome, State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, China
| | - Li-Jun Yue
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
- Center for Grassland Microbiome, State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, China
| | - Qing-Qing Han
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
- Center for Grassland Microbiome, State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, China
| | - Jia Chen
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
- Center for Grassland Microbiome, State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, China
| | - Qiong-Mei Liu
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
- Center for Grassland Microbiome, State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, China
| | - Qi Zhao
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
- Center for Grassland Microbiome, State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, China
- *Correspondence: Qi Zhao,
| | - Jin-Lin Zhang
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
- Center for Grassland Microbiome, State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, China
- Jin-Lin Zhang,
| |
Collapse
|
22
|
Shen Y, Zhang J, Nie J, Zhang H, Bacha SAS. Apple microbial communities and differences between two main Chinese producing regions. FOOD QUALITY AND SAFETY 2022. [DOI: 10.1093/fqsafe/fyab033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Microbes on fresh apples are closely associated with fruit disease, preservation and quality control. Investigation into the microbial communities on apples from different producing regions could reveal the microbial specificity and help disease prevention and quality control. In this paper, the apple surface microbes of forty-four samples from two main Chinese apple-producing regions, Bohai Bay (BHB) and the Loess Plateau (LP), were investigated by sequencing fungal internal transcribed spacer (ITS) and bacterial 16S rRNA hypervariable sequences. BHB and LP apples contained significantly different bacterial and fungal communities. BHB apples had a higher fungal diversity than LP apples. A total of 102 different fungal and bacterial taxonomies were obtained between apples from the two regions, in which 24 genera were predominant. BHB apples had higher phytopathogenic fungal genera, such as Tilletiopsis, Acremonium, Candida and Phoma, indicating the higher phytopathogenic risks of apples from the humid climate of the BHB region. LP apples contained more bacterial genera identified as gut microbes, indicating the potential risks of contaminating apples with foodborne pathogens in the arid environment of the LP. This study highlighted the environment-oriented microbial specificity on apples from two main apple-producing regions, and provided a basis for further investigation.
Collapse
Affiliation(s)
| | | | | | | | - Syed Asim Shah Bacha
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, China
| |
Collapse
|
23
|
Sahu KP, Patel A, Kumar M, Sheoran N, Mehta S, Reddy B, Eke P, Prabhakaran N, Kumar A. Integrated Metabarcoding and Culturomic-Based Microbiome Profiling of Rice Phyllosphere Reveal Diverse and Functional Bacterial Communities for Blast Disease Suppression. Front Microbiol 2021; 12:780458. [PMID: 34917058 PMCID: PMC8669949 DOI: 10.3389/fmicb.2021.780458] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 10/20/2021] [Indexed: 11/13/2022] Open
Abstract
Phyllosphere-the harsh foliar plant part exposed to vagaries of environmental and climatic variables is a unique habitat for microbial communities. In the present work, we profiled the phyllosphere microbiome of the rice plants using 16S rRNA gene amplicon sequencing (hereafter termed metabarcoding) and the conventional microbiological methods (culturomics) to decipher the microbiome assemblage, composition, and their functions such as antibiosis and defense induction against rice blast disease. The blast susceptible rice genotype (PRR78) harbored far more diverse bacterial species (294 species) than the resistant genotype (Pusa1602) that showed 193 species. Our metabarcoding of bacterial communities in phyllomicrobiome revealed the predominance of the phylum, Proteobacteria, and its members Pantoea, Enterobacter, Pseudomonas, and Erwinia on the phyllosphere of both rice genotypes. The microbiological culturomic validation of metabarcoding-taxonomic annotation further confirmed the prevalence of 31 bacterial isolates representing 11 genera and 16 species with the maximum abundance of Pantoea. The phyllomicrobiome-associated bacterial members displayed antifungal activity on rice blast fungus, Magnaporthe oryzae, by volatile and non-volatile metabolites. Upon phyllobacterization of rice cultivar PB1, the bacterial species such as Enterobacter sacchari, Microbacterium testaceum, Pantoea ananatis, Pantoea dispersa, Pantoea vagans, Pseudomonas oryzihabitans, Rhizobium sp., and Sphingomonas sp. elicited a defense response and contributed to the suppression of blast disease. qRT-PCR-based gene expression analysis indicated over expression of defense-associated genes such as OsCEBiP, OsCERK1, and phytohormone-associated genes such as OsPAD4, OsEDS1, OsPR1.1, OsNPR1, OsPDF2.2, and OsFMO in phyllobacterized rice seedlings. The phyllosphere bacterial species showing blast suppressive activity on rice were found non-plant pathogenic in tobacco infiltration assay. Our comparative microbiome interrogation of the rice phyllosphere culminated in the isolation and identification of agriculturally significant bacterial communities for blast disease management in rice farming through phyllomicrobiome engineering in the future.
Collapse
Affiliation(s)
- Kuleshwar Prasad Sahu
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Asharani Patel
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Mukesh Kumar
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Neelam Sheoran
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Sahil Mehta
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Bhaskar Reddy
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Pierre Eke
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Aundy Kumar
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| |
Collapse
|
24
|
Guo J, Chen Y, Lu P, Liu M, Sun P, Zhang Z. Roles of endophytic bacteria in Suaeda salsa grown in coastal wetlands: Plant growth characteristics and salt tolerance mechanisms. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 287:117641. [PMID: 34426384 DOI: 10.1016/j.envpol.2021.117641] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 05/24/2021] [Accepted: 06/20/2021] [Indexed: 05/11/2023]
Abstract
Salinity is a limiting factor in the growth of plants in coastal wetlands. The interaction of halophytes with salt-tolerant endophytes has been one of the major concerns in this area. However, the mechanism by which endophytes promote halophyte growth remains unclear. The growth and physiological responses of Suaeda salsa inoculated with endophytic bacteria (Sphingomonas prati and Sphingomonas zeicaulis) at 0 ‰ and 20 ‰ NaCl were studied. The results showed that Sphingomonas zeicaulis had stronger positive effects on the growth of Suaeda salsa under 0 ‰ NaCl, and Sphingomonas prati performed better under 20 ‰ NaCl. Sphingomonas prati inoculation increased the mean height, root length, fresh weight and dry weight by 45.43%, 9.91%, 82.00% and 102.25%, respectively, compared with the uninoculated treatment at 20 ‰ NaCl. Sphingomonas prati inoculation decreased MDA content by 23.78%, while the soluble sugar and soluble protein contents increased by 15.08% and 12.57%, respectively, compared to the control, at 20 ‰ NaCl. Increases in SOD and CAT in the Sphingomonas prati inoculation were 1.03 and 1.47-fold greater, respectively, than in the Sphingomonas zeicaulis inoculation, under 20 ‰ NaCl. Moreover, Sphingomonas prati and Sphingomonas zeicaulis had antagonistic interactions in Suaeda salsa according to the results of the "interaction equation" (most G values were negative). PCA, clustering analysis and the PLS model revealed two mechanisms for regulating plant salt tolerance by which Sphingomonas prati enhanced Suaeda salsa growth: (1) Sphingomonas prati improved intracellular osmotic metabolism and (2) Sphingomonas prati promoted the production of CAT in the antioxidant enzyme system and retained permeability. This study provides new insight into the comprehensive understanding and evaluation of endophytic bacteria as biological inoculants in plants under salt stress.
Collapse
Affiliation(s)
- Jiameng Guo
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
| | - Youyuan Chen
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China; Key Laboratory of Marine Environment and Ecology, Ministry of Education of China, Ocean University of China, Qingdao, China; Shandong Provincial Key Laboratory of Marine Environment and Geological Engineering, Ocean University of China, Qingdao, China.
| | - Pengzhan Lu
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
| | - Ming Liu
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
| | - Ping Sun
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
| | - Zhiming Zhang
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China; Key Laboratory of Marine Environment and Ecology, Ministry of Education of China, Ocean University of China, Qingdao, China; Shandong Provincial Key Laboratory of Marine Environment and Geological Engineering, Ocean University of China, Qingdao, China
| |
Collapse
|
25
|
Liang D, Xiao C, Song F, Li H, Liu R, Gao J. Complete Genome Sequence and Function Gene Identify of Prometryne-Degrading Strain Pseudomonas sp. DY-1. Microorganisms 2021; 9:microorganisms9061261. [PMID: 34200754 PMCID: PMC8230428 DOI: 10.3390/microorganisms9061261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 05/30/2021] [Accepted: 06/08/2021] [Indexed: 12/02/2022] Open
Abstract
The genus Pseudomonas is widely recognized for its potential for environmental remediation and plant growth promotion. Pseudomonas sp. DY-1 was isolated from the agricultural soil contaminated five years by prometryne, it manifested an outstanding prometryne degradation efficiency and an untapped potential for plant resistance improvement. Thus, it is meaningful to comprehend the genetic background for strain DY-1. The whole genome sequence of this strain revealed a series of environment adaptive and plant beneficial genes which involved in environmental stress response, heavy metal or metalloid resistance, nitrate dissimilatory reduction, riboflavin synthesis, and iron acquisition. Detailed analyses presented the potential of strain DY-1 for degrading various organic compounds via a homogenized pathway or the protocatechuate and catechol branches of the β-ketoadipate pathway. In addition, heterologous expression, and high efficiency liquid chromatography (HPLC) confirmed that prometryne could be oxidized by a Baeyer-Villiger monooxygenase (BVMO) encoded by a gene in the chromosome of strain DY-1. The result of gene knock-out suggested that the sulfate starvation-induced (SSI) genes in this strain might also involve in the process of prometryne degradation. These results would provide the molecular basis for the application of strain DY-1 in various fields and would contribute to the study of prometryne biodegradation mechanism as well.
Collapse
Affiliation(s)
- Dong Liang
- College of Life Science, Northeast Agricultural University, Harbin 150038, China; (D.L.); (C.X.); (H.L.)
| | - Changyixin Xiao
- College of Life Science, Northeast Agricultural University, Harbin 150038, China; (D.L.); (C.X.); (H.L.)
| | - Fuping Song
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
| | - Haitao Li
- College of Life Science, Northeast Agricultural University, Harbin 150038, China; (D.L.); (C.X.); (H.L.)
| | - Rongmei Liu
- College of Life Science, Northeast Agricultural University, Harbin 150038, China; (D.L.); (C.X.); (H.L.)
- Correspondence: (R.L.); (J.G.); Tel.: +86-133-5999-0992 (J.G.)
| | - Jiguo Gao
- College of Life Science, Northeast Agricultural University, Harbin 150038, China; (D.L.); (C.X.); (H.L.)
- Correspondence: (R.L.); (J.G.); Tel.: +86-133-5999-0992 (J.G.)
| |
Collapse
|
26
|
Borker SS, Thakur A, Kumar S, Kumari S, Kumar R, Kumar S. Comparative genomics and physiological investigation supported safety, cold adaptation, efficient hydrolytic and plant growth-promoting potential of psychrotrophic Glutamicibacter arilaitensis LJH19, isolated from night-soil compost. BMC Genomics 2021; 22:307. [PMID: 33910515 PMCID: PMC8082909 DOI: 10.1186/s12864-021-07632-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 04/20/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Night-soil compost (NSC) has traditionally been conserving water and a source of organic manure in northwestern Himalaya. Lately, this traditional method is declining due to modernization, its unhygienic conditions, and social apprehensions. Reduction in the age-old traditional practice has led to excessive chemical fertilizers and water shortage in the eco-sensitive region. In the current study, a bacterium has been analyzed for its safety, cold-adaptation, efficient degradation, and plant growth-promoting (PGP) attributes for its possible application as a safe bioinoculant in psychrotrophic bacterial consortia for improved night-soil composting. RESULTS Glutamicibacter arilaitensis LJH19, a psychrotrophic bacterium, was isolated from the NSC of Lahaul valley in northwestern Himalaya. The strain exhibited amylase (186.76 ± 19.28 U/mg), cellulase (21.85 ± 0.7 U/mg), and xylanase (11.31 ± 0.51 U/mg) activities at 10 °C. Possessing efficient hydrolytic activities at low-temperature garners the capability of efficient composting to LJH19. Additionally, the strain possessed multiple PGP traits such as indole acetic acid production (166.11 ± 5.7 μg/ml), siderophore production (85.72 ± 1.06% psu), and phosphate solubilization (44.76 ± 1.5 μg/ml). Enhanced germination index and germination rate of pea seeds under the LJH19 inoculation further supported the bacterium's PGP potential. Whole-genome sequencing (3,602,821 bps) and genome mining endorsed the cold adaptation, degradation of polysaccharides, and PGP traits of LJH19. Biosynthetic gene clusters for type III polyketide synthase (PKS), terpene, and siderophore supplemented the endorsement of LJH19 as a potential PGP bacterium. Comparative genomics within the genus revealed 217 unique genes specific to hydrolytic and PGP activity. CONCLUSION The physiological and genomic evidence promotes LJH19 as a potentially safe bio-inoculant to formulate psychrotrophic bacterial consortia for accelerated degradation and improved night-soil compost.
Collapse
Affiliation(s)
- Shruti Sinai Borker
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology Palampur, Palampur, Himachal Pradesh, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR- Human Resource Development Centre, Ghaziabad, Uttar Pradesh, 201 002, India
| | - Aman Thakur
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology Palampur, Palampur, Himachal Pradesh, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR- Human Resource Development Centre, Ghaziabad, Uttar Pradesh, 201 002, India
| | - Sanjeet Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology Palampur, Palampur, Himachal Pradesh, 176061, India
| | - Sareeka Kumari
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology Palampur, Palampur, Himachal Pradesh, 176061, India
| | - Rakshak Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology Palampur, Palampur, Himachal Pradesh, 176061, India.
| | - Sanjay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology Palampur, Palampur, Himachal Pradesh, 176061, India
| |
Collapse
|
27
|
Pirttilä AM, Mohammad Parast Tabas H, Baruah N, Koskimäki JJ. Biofertilizers and Biocontrol Agents for Agriculture: How to Identify and Develop New Potent Microbial Strains and Traits. Microorganisms 2021; 9:817. [PMID: 33924411 PMCID: PMC8069042 DOI: 10.3390/microorganisms9040817] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/09/2021] [Accepted: 04/11/2021] [Indexed: 12/02/2022] Open
Abstract
Microbiological tools, biofertilizers, and biocontrol agents, which are bacteria and fungi capable of providing beneficial outcomes in crop plant growth and health, have been developed for several decades. Currently we have a selection of strains available as products for agriculture, predominantly based on plant-growth-promoting rhizobacteria (PGPR), soil, epiphytic, and mycorrhizal fungi, each having specific challenges in their production and use, with the main one being inconsistency of field performance. With the growing global concern about pollution, greenhouse gas accumulation, and increased need for plant-based foods, the demand for biofertilizers and biocontrol agents is expected to grow. What are the prospects of finding solutions to the challenges on existing tools? The inconsistent field performance could be overcome by using combinations of several different types of microbial strains, consisting various members of the full plant microbiome. However, a thorough understanding of each microbiological tool, microbial communities, and their mechanisms of action must precede the product development. In this review, we offer a brief overview of the available tools and consider various techniques and approaches that can produce information on new beneficial traits in biofertilizer and biocontrol strains. We also discuss innovative ideas on how and where to identify efficient new members for the biofertilizer and biocontrol strain family.
Collapse
Affiliation(s)
- Anna Maria Pirttilä
- Ecology and Genetics, University of Oulu, FIN-90014 Oulu, Finland; (H.M.P.T.); (N.B.); (J.J.K.)
| | | | | | | |
Collapse
|
28
|
Kumar R, Borker SS, Thakur A, Thapa P, Kumar S, Mukhia S, Anu K, Bhattacharya A, Kumar S. Physiological and genomic evidence supports the role of Serratia quinivorans PKL:12 as a biopriming agent for the biohardening of micropropagated Picrorhiza kurroa plantlets in cold regions. Genomics 2021; 113:1448-1457. [PMID: 33744342 DOI: 10.1016/j.ygeno.2021.03.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/26/2021] [Accepted: 03/14/2021] [Indexed: 11/29/2022]
Abstract
The medicinal herb, Picrorhiza kurroa Royle ex Benth has become endangered because of indiscriminate over-harvesting. Although micropropagation has been attempted for mass propagation of the plant, survival of in vitro plantlets under green house/open field poses a major challenge. Biopriming of micropropagated plantlets with plant growth-promoting rhizobacteria (PGPR) are among the successful methods to combat this problem. Serratia quinivorans PKL:12 was the best-characterized PGPR from rhizospheric soil of P. kurroa as it increased the vegetative growth and survival of the micropropagated plantlets most effectively. Complete genome (5.29 Mb) predicted genes encoding proteins for cold adaptation and plant growth-promoting traits in PKL:12. Antibiotic and biosynthetic gene cluster prediction supported PKL:12 as a potential biocontrol agent. Comparative genomics revealed 226 unique genes with few genes associated with plant growth-promoting potential. Physiological and genomic evidence supports S. quinivorans PKL:12 as a potential agent for bio-hardening of micropropagated P. kurroa plantlets in cold regions.
Collapse
Affiliation(s)
- Rakshak Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India; Academy of Scientific and Innovative Research (AcSIR), CSIR- Human Resource Development Centre, Ghaziabad, Uttar Pradesh 201 002, India..
| | - Shruti Sinai Borker
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India; Academy of Scientific and Innovative Research (AcSIR), CSIR- Human Resource Development Centre, Ghaziabad, Uttar Pradesh 201 002, India
| | - Aman Thakur
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India; Academy of Scientific and Innovative Research (AcSIR), CSIR- Human Resource Development Centre, Ghaziabad, Uttar Pradesh 201 002, India
| | - Pooja Thapa
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
| | - Sanjeet Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
| | - Srijana Mukhia
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India; Department of Microbiology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Kumari Anu
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
| | - Amita Bhattacharya
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
| | - Sanjay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
| |
Collapse
|