1
|
Wang X, Gao Y, Zang P, Zhang G, Yang X, Liu Q. Decrease in beneficial bacteria and increase in harmful bacteria in Gastrodia seedlings and their surrounding soil are mainly responsible for degradation of Gastrodia asexual propagation. FRONTIERS IN PLANT SCIENCE 2024; 15:1334958. [PMID: 38379940 PMCID: PMC10877603 DOI: 10.3389/fpls.2024.1334958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/10/2024] [Indexed: 02/22/2024]
Abstract
Introduction Asexual reproduction of Gastrodia elata Bl. f. glauca S. chow (GeB) produces degeneration with increasing number of GeB. Therefore, we analyzed the microorganisms of GeB seedlings and surrounding soil by Illumina Miseq high-throughput sequencing technology. Methods In this study, Illumina Miseq high-throughput sequencing technology was applied to analyze the types and quantities of GeB seedlings and surrounding soil microorganisms in the first to third generations of asexual reproduction, isolated and identified the dominant strains of GeB in the first to third generations and screened the antagonistic bacteria of its pathogenic fungi, and evaluated the effects of beneficial bacteria on the production performance of seedlings planted with GeB. Results With an increase in the number of asexual reproductive generations, the number of pathogenic fungi and bacteria in GeB seedlings and the surrounding soil increased, and the number of beneficial fungi and bacteria decreased. Pseudomonas sp., Agrobacterium rhizomes, and Herbaspirillum hiltneri were isolated and identified in the first generation, and Trichoderma harzianum, Penicillium viridiatum, Fusarium oxysporum, and Novosphingobium sp. Were isolated and identified in the third generation. Antagonistic strains of the three pathogenic bacterial strains were screened. In conclusion, beneficial bacteria significantly improved the production performance of asexual reproductive seedlings planted with GeB. Discussion In conclusion, our findings suggested that the microorganisms of GeB seedlings and the surrounding soil change as the number of generations of GeB reproduction increases, disrupts the microecological balance of surrounding soil and endophytic microbiomes.This study provides a theoretical basis for the degradation of asexual reproduction in GeB.
Collapse
Affiliation(s)
- Xi Wang
- College of Chinese Medicinal Materials and Laboratory of Medicinal Plant Cultivation and Breeding, National Administration of Traditional Chinese Medicine, Jilin Agricultural University, Changchun, China
| | - Yugang Gao
- College of Chinese Medicinal Materials and Laboratory of Medicinal Plant Cultivation and Breeding, National Administration of Traditional Chinese Medicine, Jilin Agricultural University, Changchun, China
| | - Pu Zang
- College of Chinese Medicinal Materials and Laboratory of Medicinal Plant Cultivation and Breeding, National Administration of Traditional Chinese Medicine, Jilin Agricultural University, Changchun, China
| | - Ge Zhang
- College of Chinese Medicinal Materials and Laboratory of Medicinal Plant Cultivation and Breeding, National Administration of Traditional Chinese Medicine, Jilin Agricultural University, Changchun, China
| | - Xinyu Yang
- College of Chinese Medicinal Materials and Laboratory of Medicinal Plant Cultivation and Breeding, National Administration of Traditional Chinese Medicine, Jilin Agricultural University, Changchun, China
| | - Qun Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| |
Collapse
|
2
|
Siddiqi MZ, Rajivgandhi G, Faiq M, Im WT. Isolation and Characterization of Sphingomonas telluris, Sphingomonas caseinilyticus Isolated from Wet Land Soil. Curr Microbiol 2023; 80:264. [PMID: 37386175 DOI: 10.1007/s00284-023-03339-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 05/22/2023] [Indexed: 07/01/2023]
Abstract
Two novel bacterial strains, designated as SM33T and NSE70-1T, were isolated from wet soil in South Korea. To get the taxonomic positions, the strains were characterized. The genomic information (both 16S rRNA gene and draft genome sequence analysis) show that both novel isolates (SM33T and NSE70-1T) belong to the genus Sphingomonas. SM33T share the highest 16s rRNA gene similarity (98.2%) with Sphingomonas sediminicola Dae20T. In addition, NSE70-1T show 96.4% 16s rRNA gene similarity with Sphingomonas flava THG-MM5T. The draft genome of strains SM33T and NSE70-1T consist of a circular chromosome of 3,033,485 and 2,778,408 base pairs with DNA G+C content of 63.9, and 62.5%, respectively. Strains SM33T and NSE70-1T possessed the ubiquinone Q-10 as the major quinone, and a fatty acid profile with C16:0, C18:1 2-OH, C16:1 ω7c/C16:1 ω6c (summed feature 3) and C18:1 ω7c/C18:1 ω6c (summed feature 8) as major fatty acids. The major polar lipids of SM33T and NSE70-1T were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and phosphatidylcholine, respectively. Moreover, genomic, physiological, and biochemical results allowed the phenotypic and genotypic differentiation of strains SM33T and NSE70-1T from their closest and other species of the genus Sphingomonas with validly published names. Therefore, the SM33T and NSE70-1T represent novel species of the genus Sphingomonas, for which the name Sphingomonas telluris sp. nov. (type strain SM33T = KACC 22222T = LMG 32193T), and Sphingomonas caseinilyticus (type strain NSE70-1T = KACC 22411T = LMG 32495T).
Collapse
Affiliation(s)
- Muhammad Zubair Siddiqi
- Department of Biotechnology, Hankyong National University, 327 Jungang-ro, Anseong-si, Gyeonggi-do, 17579, Republic of Korea
- AceEMzyme Co., Ltd., Academic Industry Cooperation, Room 403, 327 Jungang-ro, Anseong-si, Gyeonggi-do, 17579, Republic of Korea
- HK Ginseng Research Center, 327 Jungang-no, Anseong-si, Gyeonggi-do, 17579, Republic of Korea
| | - Govindan Rajivgandhi
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat Sen University, Guangzhou, 510275, People's Republic of China
| | - Muhammad Faiq
- Department of Food Science and Technology, The University of Agriculture, Peshawar, 25130, Khyber Pakhtunkhwa, Pakistan
| | - Wan-Taek Im
- Department of Biotechnology, Hankyong National University, 327 Jungang-ro, Anseong-si, Gyeonggi-do, 17579, Republic of Korea.
- AceEMzyme Co., Ltd., Academic Industry Cooperation, Room 403, 327 Jungang-ro, Anseong-si, Gyeonggi-do, 17579, Republic of Korea.
- HK Ginseng Research Center, 327 Jungang-no, Anseong-si, Gyeonggi-do, 17579, Republic of Korea.
| |
Collapse
|
3
|
Siddiqi MZ, Rajivgandhi G, Lee SY, Im WT. Characterization of four novel bacterial species of the genus Sphingomonas, Sphingomonas anseongensis, Sphingomonas alba, Sphingomonas brevis and Sphingomonas hankyongi sp.nov., isolated from wet land. Int J Syst Evol Microbiol 2023; 73. [PMID: 37216283 DOI: 10.1099/ijsem.0.005884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023] Open
Abstract
Four novel bacterial strains, designated as RG327T, SE158T, RB56-2T and SE220T, were isolated from wet soil in the Republic of Korea. To determine their taxonomic positions, the strains were fully characterized. On the basis of genomic information (16S rRNA gene and draft genome sequences), all four isolates represent members of the genus Sphingomonas. The draft genomes of RG327T, SE158T, RB56-2T and SE220T consisted of circular chromosomes of 2 226 119, 2 507 338, 2 593 639 and 2 548 888 base pairs with DNA G+C contents of 64.6, 63.6, 63.0 and 63.1 %, respectively. All the isolates contained ubiquinone Q-10 as the predominant quinone compound and a fatty acid profile with C16 : 0, C17 : 1ω6c, C18 : 1 2-OH, summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c/C18 : 1ω6c) as the major fatty acids, supporting the affiliation of strains RG327T, SE158T, RB56-2T and SE220T to the genus Sphingomonas. The major identified polar lipids in all four novel isolates were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and phosphatidylcholine. Moreover, the physiological, biochemical results and low level of DNA-DNA relatedness and average nucleotide identity values allowed the phenotypic and genotypic differentiation of RG327T, SE158T, RB56-2T and SE220T from other species of the genus Sphingomonas with validly published names and indicated that they represented novel species of the genus Sphingomonas, for which the names Sphingomonas anseongensis sp. nov. (RG327T = KACC 22409T = LMG 32497T), Sphingomonas alba sp. nov. (SE158T = KACC 224408T = LMG 324498T), Sphingomonas brevis (RB56-2T = KACC 22410T = LMG 32496T) and Sphingomonas hankyongi sp. nov., (SE220T = KACC 22406T = LMG 32499T) are proposed.
Collapse
Affiliation(s)
- Muhammad Zubair Siddiqi
- Department of Biotechnology, Hankyong National University, 327 Jungang-ro Anseong-si, Gyeonggi-do 17579, Republic of Korea
- HK Ginseng Research Center, Hankyong National University, 327 Jungang-ro Anseong-si, Gyonggi-do, 13449, Republic of Korea
- AceEMzyme Co., Ltd., Room 733, 815 Daewangpangyo-ro, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13449, Republic of Korea
| | - Govindan Rajivgandhi
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun YatSen University, Guangzhou 510275, PR China
| | - Soon-Youl Lee
- Department of Biotechnology, Hankyong National University, 327 Jungang-ro Anseong-si, Gyeonggi-do 17579, Republic of Korea
- HK Ginseng Research Center, Hankyong National University, 327 Jungang-ro Anseong-si, Gyonggi-do, 13449, Republic of Korea
| | - Wan-Taek Im
- Department of Biotechnology, Hankyong National University, 327 Jungang-ro Anseong-si, Gyeonggi-do 17579, Republic of Korea
- HK Ginseng Research Center, Hankyong National University, 327 Jungang-ro Anseong-si, Gyonggi-do, 13449, Republic of Korea
- AceEMzyme Co., Ltd., Room 733, 815 Daewangpangyo-ro, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13449, Republic of Korea
| |
Collapse
|
4
|
Sphingomonas hominis sp. nov., isolated from hair of a 21-year-old girl. Antonie Van Leeuwenhoek 2020; 113:1523-1530. [DOI: 10.1007/s10482-020-01460-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/04/2020] [Indexed: 11/25/2022]
|
5
|
Zhang H, Xu L, Zhang JX, Sun JQ. Sphingomonas suaedae sp. nov., a chitin-degrading strain isolated from rhizosphere soil of Suaeda salsa. Int J Syst Evol Microbiol 2020; 70:3816-3823. [DOI: 10.1099/ijsem.0.004238] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, chitin-degrading, motile bacterial strain with a single polar flagellum, designated XS-10T, was isolated from saline soil sampled from the rhizosphere of Suaeda salsa, Tumd Right Banner, Inner Mongolia, PR China. Strain XS-10T grew at 10–40 °C (optimum, 35 °C), pH 5.0–9.0 (optimum, pH 8.0) and 0–12.5% NaCl (optimum 2.0 %). The phylogenetic analysis based on both the 16S rRNA gene and the phylogenomic tree revealed that strain XS-10T formed a clade with
Sphingomonas turrisvirgatae
MCT13T and
Sphingomonas koreensis
JSS-26T, sharing 98.4 and 97.5 % 16S rRNA gene similarities to
S. koreensis
JSS-26T and
S. turrisvirgatae
MCT13T, respectively. Spermidine and Q-10 were the major polyamine and the major respiratory quinone, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, two unidentified lipids and an unidentified aminophospholipid. The major fatty acids were summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c), C16 : 0 and C17 : 1
ω6c. The genome of strain XS-10T consisted of a 4 154 291 bp chromosome with a DNA G+C content of 65.5 mol%. The average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values of strain XS-10T with
S. turrisvirgatae
MCT13T and
S. koreensis
JSS-26T were 77.8 and 78.6 %, 75.9 and 76.3 %, and 22.0 and 22.9 %, respectively. Based on the phylogenetic, phenotypic, and genotypic characteristics, strain XS-10T is considered to represent a novel species of the genus
Sphingomonas
, for which the name Sphingomonas suaedae sp. nov. is proposed. The type strain is XS-10T (=CGMCC 1.17078T=JCM 33850T).
Collapse
Affiliation(s)
- Hui Zhang
- Inner Mongolia Key Laboratory of Environmental Pollution Prevention and Waste Resource Recycle & Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Lian Xu
- Inner Mongolia Key Laboratory of Environmental Pollution Prevention and Waste Resource Recycle & Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Jin-Xin Zhang
- Inner Mongolia Key Laboratory of Environmental Pollution Prevention and Waste Resource Recycle & Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Ji-Quan Sun
- Inner Mongolia Key Laboratory of Environmental Pollution Prevention and Waste Resource Recycle & Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| |
Collapse
|
6
|
Li YQ, Zhang H, Xiao M, Dong ZY, Zhang JY, Narsing Rao MP, Li WJ. Cellulomonas endophytica sp. nov., isolated from Gastrodia elata Blume. Int J Syst Evol Microbiol 2020; 70:3091-3095. [PMID: 32238231 DOI: 10.1099/ijsem.0.004133] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, facultatively anaerobic and non-motile strain, designated SYSUP0004T, was isolated from the tubers of Gastrodia elata Blume collected from Yunnan Province, PR China. The 16S rRNA gene sequence result showed that the strain SYSUP0004T shared low similarity (97.7 %) with the type strain of Cellulomonas marina. SYSUP0004T grew at pH 6.0-9.0 (optimum, pH 8.0), temperature 4-30 °C (optimum, 28 °C) and could tolerate NaCl up to 4 % w/v (optimum in the absence of NaCl). The cell-wall peptidoglycan type was A4β with an interpeptide bridge l-ornithine-d-glutamic acid. Cell-wall sugars were mannose, ribose, glucose, galactose and fucose. The menaquinone was MK-9(H4). The major fatty acids were anteiso-C15:0, anteiso-C15 : 1 A, C16 : 0 and anteiso-C17 : 0. The polar lipids of SYSUP0004T were diphosphatidylglycerol, unidentified phosphoglycolipid, phosphatidylinositol mannosides and unidentified glycolipid. The genomic DNA G+C content was 76.5 %. The average nucleotide identity values between SYSUP0004T and members of the genus Cellulomonas were below the cut-off level (95-96 %) recommended as the ANI criterion for interspecies identity. Thus, based on the above results strain SYSUP0004T represents a novel species of the genus Cellulomonas, for which the name Cellulomonas endophytica sp. nov. is proposed. The type strain, SYSUP0004T (=KCTC 49025T=CGMCC 1.16405T).
Collapse
Affiliation(s)
- Yan-Qiong Li
- Kunming Medical University Haiyuan College, Kunming, PR China
| | - Hui Zhang
- Kunming Medical University Haiyuan College, Kunming, PR China
| | - Min Xiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat- Sen University, Guangzhou, PR China
| | - Zhou-Yan Dong
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat- Sen University, Guangzhou, PR China
| | - Jing-Yi Zhang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat- Sen University, Guangzhou, PR China
| | - Manik Prabhu Narsing Rao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat- Sen University, Guangzhou, PR China.,Department of Biotechnology, Dayananda Sagar College of Engineering (Affiliated to Visvesvaraya Technological University, Belagavi), Bangalore, Karnataka, India
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat- Sen University, Guangzhou, PR China.,CAS Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Urumqi, Xinjiang, PR China
| |
Collapse
|
7
|
Amycolatopsis alkalitolerans sp. nov., isolated from Gastrodia elata Blume. J Antibiot (Tokyo) 2019; 73:35-39. [PMID: 31434994 DOI: 10.1038/s41429-019-0222-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 06/19/2019] [Accepted: 08/06/2019] [Indexed: 11/08/2022]
Abstract
A Gram-staining positive and nonmotile strain designated SYSUP0005T was isolated from tubers of Gastrodia elata Blume. The 16S rRNA gene sequence result showed that strain SYSUP0005T shared highest sequence similarity with the type strain of Amycolatopsis cappadoca (95.7%), Amycolatopsis taiwanensis (95.4%), Amycolatopsis pigmentata (95.4%), Amycolatopsis ruanii (95.1%), and Amycolatopsis helveola (94.8%). Growth occurs at 14-37 °C (optimum temperature, 28 °C), at pH 6-9 (optimum, pH 8) and in the presence of up to 6% (w/v) NaCl. Strain SYSUP0005T had meso-diaminopimelic acid in its peptidoglycan. The whole cell sugars were galactose, ribose, and xylose. The predominant menaquinone was MK-9(H4) and minor menaquinones were MK-9(H2) and MK-9(H8). The polar lipids were diphosphatidylglycerol (DPG); phosphatidylmonomethylethanolamine (PME), phosphatidylethanolamine (PE), phosphatidylinositol (PI), unidentified glycolipid (GL), and unidentified phospholipid (PL). The genomic DNA G + C content was 69.6 mol%. The major fatty acids were iso-C16:0, anteiso-C17:0, C16:0, iso-C14:0, C17:1 ω6c, C17:0, and Summed Feature 3 (C16:1 ω7c/C16:1 ω6c). On the basis of the phenotypic, phylogenetic, chemotaxonomic characters, and genomic comparison, SYSUP0005T represents a novel species of the genus Amycolatopsis, for which the name Amycolatopsis alkalitolerans sp. nov. is proposed. The type strain is SYSUP0005T (=KCTC 49024T = CGMCC4.7463T).
Collapse
|