1
|
Draft Genome Sequence of the Drought-Tolerant Plant Growth-Promoting Rhizobacterium Bacillus altitudinis UKM RB11, Isolated from Upland Paddy Rhizosphere. Microbiol Resour Announc 2022; 11:e0061722. [PMID: 36106889 PMCID: PMC9584285 DOI: 10.1128/mra.00617-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Asia’s paddy areas endure tropical and equatorial monsoon climates and are prone to drought stress. The drought-tolerant plant growth-promoting rhizobacterium (PGPR) strain Bacillus altitudinis UKM RB11 was isolated from upland paddy soil in Malaysia. Its 3.7-Mb genome sequence contains numerous genes involved with tolerance to drought and high temperatures and plant growth promotion.
Collapse
|
2
|
Awad AAM, Ahmed AI, Elazem AHA, Sweed AAA. Mitigation of CaCO3 Influence on Ipomoea batatas Plants Using Bacillus megaterium DSM 2894. AGRONOMY 2022; 12:1571. [DOI: 10.3390/agronomy12071571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
The application of PGPB is considered a surrogate approach to reducing the amounts of phosphorus fertilizers applied in addition to its role in improving nutrient availability under stress conditions. The objective of this study was to evaluate five levels of calcium superphosphate (CSP); ultimately, CSP was applied in five levels: CSP20, CSP40, CSP60, CSP80, and CSP100 were applied at 69, 138, 207, 276, and 345 kg ha−1, respectively, and two treatments of Bacillus megaterium DSM 2894 (with and without) were applied on sweet potato (Beauregard cv.) plants grown in calcareous soils in the 2019 and 2020 seasons in Egypt. Some macro- and micronutrient (i.e., nitrogen (N), phosphorus (P), calcium (Ca), iron (Fe), manganese (Mn), zinc (Zn), and copper (Cu)) uptake, antiradical power (ARP), and protein and total root yields (TRYs) were determined. The plants inoculated with B. megaterium DSM 2894 had increased leaf N, P, and Mn contents in both seasons; in addition, Ca was increased in the second season. Furthermore, all of the root nutrient contents (except N) as well as the ARP and TRY were increased in both seasons as compared with those of the noninoculated plants. On the other hand, the maximum values of the leaf Ca, Fe, and Cu contents and the root Ca, Fe, and Zn contents were recorded with the CSP20 treatment in both seasons. CSP60 was the superior treatment for N (in the leaves), Mn (in the roots), ARP, protein contents, and TRY in both seasons and for the leaf Zn content in the 2019 season. The application of the CSP100 treatment gave the highest values for the leaf and root P contents and the root Cu contents in both seasons as well as for the leaf Mn content in the first season and the root N content in the 2020 growth season. Thus, it was concluded that the application of CSP20, CSP60, and CSP100 treatments with the B. megaterium DSM2894 mixture gave the best values compared to the use of CSP or DSM2894 individually to attenuate CaCO3-induced damage.
Collapse
|
3
|
Phazna TA, Ngashangva N, Yentrembam RBS, Maurya R, Mukherjee P, Sharma C, Verma PK, Sarangthem I. Draft genome sequence and functional analysis of Lysinibacillus xylanilyticus t26, a plant growth-promoting bacterium isolated from Capsicum chinense rhizosphere. J Biosci 2022. [DOI: 10.1007/s12038-022-00264-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
4
|
Fathi F, Saberi Riseh R, Khodaygan P, Hosseini S, Skorik YA. Microencapsulation of a Pseudomonas Strain (VUPF506) in Alginate-Whey Protein-Carbon Nanotubes and Next-Generation Sequencing Identification of This Strain. Polymers (Basel) 2021; 13:4269. [PMID: 34883770 PMCID: PMC8659823 DOI: 10.3390/polym13234269] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/24/2021] [Accepted: 12/03/2021] [Indexed: 12/11/2022] Open
Abstract
Alginate is a common agent used for microencapsulation; however, the formed capsule is easily damaged. Therefore, alginate requires blending with other biopolymers to reduce capsule vulnerability. Whey protein is one polymer that can be incorporated with alginate to improve microcapsule structure. In this study, three different encapsulation methods (extrusion, emulsification, and spray drying) were tested for their ability to stabilize microencapsulated Pseudomonas strain VUPF506. Extrusion and emulsification methods enhanced encapsulation efficiency by up to 80% and gave the best release patterns over two months. A greenhouse experiment using potato plants treated with alginate-whey protein microcapsules showed a decrease in Rhizoctonia disease intensity of up to 70%. This is because whey protein is rich in amino acids and can serve as a resistance induction agent for the plant. In this study, the use of CNT in the ALG-WP system increased the rooting and proliferation and reduced physiological complication. The results of this study showed that the technique used in encapsulation could have a significant effect on the efficiency and persistence of probiotic bacteria. Whole genome sequence analysis of strain VUPF506 identified it as Pseudomonas chlororaphis and revealed some genes that control pathogens.
Collapse
Affiliation(s)
- Fariba Fathi
- Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, Imam Khomeini Square, Rafsanjan 7718897111, Iran; (F.F.); (R.S.R.); (P.K.); (S.H.)
| | - Roohallah Saberi Riseh
- Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, Imam Khomeini Square, Rafsanjan 7718897111, Iran; (F.F.); (R.S.R.); (P.K.); (S.H.)
| | - Pejman Khodaygan
- Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, Imam Khomeini Square, Rafsanjan 7718897111, Iran; (F.F.); (R.S.R.); (P.K.); (S.H.)
| | - Samin Hosseini
- Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, Imam Khomeini Square, Rafsanjan 7718897111, Iran; (F.F.); (R.S.R.); (P.K.); (S.H.)
| | - Yury A. Skorik
- Institute of Macromolecular Compounds of the Russian Academy of Sciences, Bolshoi VO 31, 199004 St. Petersburg, Russia
| |
Collapse
|
5
|
Yang J, Zhu Q, Xu F, Yang M, Du H, Bian X, Lu Z, Lu Y, Lu F. Genome Mining, Heterologous Expression, Antibacterial and Antioxidant Activities of Lipoamides and Amicoumacins from Compost-Associated Bacillus subtilis fmb60. Molecules 2021; 26:molecules26071892. [PMID: 33810551 PMCID: PMC8036425 DOI: 10.3390/molecules26071892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 11/25/2022] Open
Abstract
Bacillus subtilis fmb60, which has broad-spectrum antimicrobial activities, was isolated from plant straw compost. A hybrid NRPS/PKS cluster was screened from the genome. Sixteen secondary metabolites produced by the gene cluster were isolated and identified using LC-HRMS and NMR. Three lipoamides D–F (1–3) and two amicoumacin derivatives, amicoumacins D, E (4, 5), were identified, and are reported here for the first time. Lipoamides D–F exhibited strong antibacterial activities against harmful foodborne bacteria, with the MIC ranging from 6.25 to 25 µg/mL. Amicoumacin E scavenged 38.8% of ABTS+ radicals at 1 mg/mL. Direct cloning and heterologous expression of the NRPS/PKS and ace gene cluster identified its importance for the biosynthesis of amicoumacins. This study demonstrated that there is a high potential for biocontrol utilization of B. subtilis fmb60, and genome mining for clusters of secondary metabolites of B. subtilis fmb60 has revealed a greater biosynthetic potential for the production of novel natural products than previously anticipated.
Collapse
Affiliation(s)
- Jie Yang
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; (J.Y.); (Q.Z.); (F.X.)
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
- Jiangsu Marine Resources Development Research Institute, Lianyungang 222000, China
| | - Qingzheng Zhu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; (J.Y.); (Q.Z.); (F.X.)
| | - Feng Xu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China; (J.Y.); (Q.Z.); (F.X.)
| | - Ming Yang
- Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (M.Y.); (X.B.)
| | - Hechao Du
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China; (H.D.); (Z.L.)
| | - Xiaoying Bian
- Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (M.Y.); (X.B.)
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China; (H.D.); (Z.L.)
| | - Yingjian Lu
- College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210003, China
- Correspondence: (Y.L.); (F.L.); Tel./Fax: +86-258-439-5155 (Y.L.); +86-258-439-5963 (F.L.)
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China; (H.D.); (Z.L.)
- Correspondence: (Y.L.); (F.L.); Tel./Fax: +86-258-439-5155 (Y.L.); +86-258-439-5963 (F.L.)
| |
Collapse
|
6
|
Chen Y, Liu T, Li Q, Ma Y, Cheng J, Xu L. Screening for Candidate Genes Associated with Biocontrol Mechanisms of Bacillus pumilus DX01 Using Tn5 Transposon Mutagenesis and a 2-DE-Based Comparative Proteomic Analysis. Curr Microbiol 2020; 77:3397-3408. [PMID: 32915287 DOI: 10.1007/s00284-020-02191-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 08/28/2020] [Indexed: 12/27/2022]
Abstract
A total of 1467 mutants of the biocontrol bacterium Bacillus pumilus DX01 were obtained by Tn5 insertional mutagenesis and subjected to the determination of antagonistic capabilities. Compared with the wild-type strain DX01, the mutant M25 was identified to have the most significant reduction in antagonistic capability against the phytopathogen Bipolaris maydis and extracellular proteinase activity. The integration site of the exogenous T-DNA in the genome of mutant M25 was revealed in the coding region of malony CoA-ACP transacylase (MCAT) gene (mcat), which belongs to a polyketide synthase (PKS) gene cluster, DX01pks of B. pumilus DX01. Furthermore, the whole DX01pks gene cluster was cloned using Illumina Solexa sequencing technology, and it has a modular framework different from the other two gene clusters involved in polyketide synthesis in B. amyloliquefaciens FZB42 (pks1) and B. subtilis 168 (pksX). Finally, in order to gain more insights into the molecular mechanisms of biocontrol of B. pumilus DX01, the changes in the relative level of expression of total proteins between the original strain DX01 and the mutant M25 were detected by 2-DE-based proteomic analysis. A total of twenty differentially expressed proteins were identified upon the mcat gene transposition mutagenesis. Of these proteins, seven proteins were up-regulated in expression level and the other proteins were down-regulated. Taken together, the results in this study showed that Tn5 transposon mutagenesis of B. pumilus DX01 can lead to a significant change of antiphytopathogen ability, and the DX01pks gene cluster possibly play a potential role in the biocontrol processes of this bacterium.
Collapse
Affiliation(s)
- Yunpeng Chen
- Department of Resources and Environment, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Tong Liu
- Department of Resources and Environment, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qiongjie Li
- Department of Resources and Environment, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yifei Ma
- Department of Resources and Environment, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiejie Cheng
- Department of Resources and Environment, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lurong Xu
- Department of Resources and Environment, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| |
Collapse
|
7
|
Leontidou K, Genitsaris S, Papadopoulou A, Kamou N, Bosmali I, Matsi T, Madesis P, Vokou D, Karamanoli K, Mellidou I. Plant growth promoting rhizobacteria isolated from halophytes and drought-tolerant plants: genomic characterisation and exploration of phyto-beneficial traits. Sci Rep 2020; 10:14857. [PMID: 32908201 PMCID: PMC7481233 DOI: 10.1038/s41598-020-71652-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 08/17/2020] [Indexed: 01/25/2023] Open
Abstract
Plant growth promoting rhizobacteria (PGPR) are able to provide cross-protection against multiple stress factors and facilitate growth of their plant symbionts in many ways. The aim of this study was to isolate and characterize rhizobacterial strains under natural conditions, associated with naturally occurring representatives of wild plant species and a local tomato cultivar, growing in differently stressed Mediterranean ecosystems. A total of 85 morphologically different rhizospheric strains were isolated; twenty-five exhibited multiple in vitro PGP-associated traits, including phosphate solubilization, indole-3-acetic acid production, and 1-aminocyclopropane-1-carboxylate deaminase activity. Whole genome analysis was applied to eight selected strains for their PGP potential and assigned seven strains to Gammaproteobacteria, and one to Bacteroidetes. The genomes harboured numerous genes involved in plant growth promotion and stress regulation. They also support the notion that the presence of gene clusters with potential PGP functions is affirmative but not necessary for a strain to promote plant growth under abiotic stress conditions. The selected strains were further tested for their ability to stimulate growth under stress. This initial screening led to the identification of some strains as potential PGPR for increasing crop production in a sustainable manner.
Collapse
Affiliation(s)
- Kleopatra Leontidou
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Savvas Genitsaris
- International Hellenic University, 57001, Thermi, Greece.,Department of Ecology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Anastasia Papadopoulou
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Nathalie Kamou
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Irene Bosmali
- Institute of Applied Biosciences, CERTH, 57001, Thessaloniki, Greece
| | - Theodora Matsi
- Soil Science Laboratory, School of Agriculture, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | | | - Despoina Vokou
- Department of Ecology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Katerina Karamanoli
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece.
| | - Ifigeneia Mellidou
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece. .,Institute of Plant Breeding and Genetic Resources, HAO, 57001, Thermi, Thessaloniki, Greece.
| |
Collapse
|
8
|
Draft Genome Sequence of the Plant Growth-Promoting Rhizobacterium Klebsiella sp. Strain KBG6.2, Imparting Salt Tolerance to Rice. Microbiol Resour Announc 2020; 9:9/35/e00491-20. [PMID: 32855243 PMCID: PMC7453279 DOI: 10.1128/mra.00491-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Klebsiella sp. strain KBG6.2 is a potential salt-tolerant, plant growth-promoting rhizobacterium isolated from a rice field in Konark, Odisha, India. Here, we report the whole-genome sequencing of Klebsiella sp. strain KBG6.2, which has a 5.038-Mb genome containing 4,867 predicted protein-coding sequences and 79 RNA genes. Klebsiella sp. strain KBG6.2 is a potential salt-tolerant, plant growth-promoting rhizobacterium isolated from a rice field in Konark, Odisha, India. Here, we report the whole-genome sequencing of Klebsiella sp. strain KBG6.2, which has a 5.038-Mb genome containing 4,867 predicted protein-coding sequences and 79 RNA genes.
Collapse
|
9
|
Ankati S, Rani TS, Podile AR. Partner-triggered proteome changes in the cell wall of Bacillus sonorensis and roots of groundnut benefit each other. Microbiol Res 2018; 217:91-100. [DOI: 10.1016/j.micres.2018.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 10/02/2018] [Accepted: 10/06/2018] [Indexed: 01/01/2023]
|
10
|
Barth C, Weiss MC, Roettger M, Martin WF, Unden G. Origin and phylogenetic relationships of [4Fe-4S]-containing O 2 sensors of bacteria. Environ Microbiol 2018; 20:4567-4586. [PMID: 30225854 DOI: 10.1111/1462-2920.14411] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/10/2018] [Indexed: 11/28/2022]
Abstract
The advent of environmental O2 about 2.5 billion years ago forced microbes to metabolically adapt and to develop mechanisms for O2 sensing. Sensing of O2 by [4Fe-4S]2+ to [2Fe-2S]2+ cluster conversion represents an ancient mechanism that is used by FNREc (Escherichia coli), FNRBs (Bacillus subtilis), NreBSa (Staphylococcus aureus) and WhiB3Mt (Mycobacterium tuberculosis). The phylogenetic relationship of these sensors was investigated. FNREc homologues are restricted to the proteobacteria and a few representatives from other phyla. Homologues of FNRBs and NreBSa are located within the bacilli, of WhiB3 within the actinobacteria. Archaea contain no homologues. The data reveal no similarity between the FNREc , FNRBs , NreBSa and WhiB3 sensor families on the sequence and structural levels. These O2 sensor families arose independently in phyla that were already present at the time O2 appeared, their members were subsequently distributed by lateral gene transfer. The chemistry of [4Fe-4S] and [2Fe-2S] cluster formation and interconversion appears to be shared by the sensor protein families. The type of signal output is, however, family specific. The homologues of FNREc and NreBSa vary with regard to the number of Cys residues that coordinate the cluster. It is suggested that the variants derive from lateral gene transfer and gained other functions.
Collapse
Affiliation(s)
- C Barth
- Microbiology and Wine Research, Institute for Molecular Physiology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - M C Weiss
- Institute for Molecular Evolution, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - M Roettger
- Institute for Molecular Evolution, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - W F Martin
- Institute for Molecular Evolution, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - G Unden
- Microbiology and Wine Research, Institute for Molecular Physiology, Johannes Gutenberg University Mainz, Mainz, Germany
| |
Collapse
|
11
|
Kim JS, Lee JE, Nie H, Lee YJ, Kim ST, Kim SH. Physiological and proteomic analysis of plant growth enhancement by the rhizobacteria Bacillus sp. JS. Genes Genomics 2018; 40:129-136. [PMID: 29892922 DOI: 10.1007/s13258-017-0615-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 09/27/2017] [Indexed: 10/18/2022]
Abstract
In this study, the effects of the plant growth-promoting rhizobacterium (PGPR), Bacillus sp. JS on the growth of tobacco (Nicotiana tabacum 'Xanthi') and lettuce (Lactuca sativa 'Crispa'), were evaluated by comparing various growth parameters between plants treated with the bacterium and those exposed to water or nutrient broth as control. In both tobacco and lettuce, fresh weight and length of shoots were increased upon exposure to Bacillus sp. JS. To explain the overall de novo expression of plant proteins by bacterial volatiles, two-dimensional gel electrophoresis was performed on samples from PGPR-treated tobacco plants. Our results showed that chlorophyll a/b binding proteins were significantly up-regulated, and total chlorophyll content was also increased. Our findings indicate the potential benefits of using Bacillus sp. JS as a growth-promoting factor in agricultural practice, and highlight the need for further research to explore these benefits.
Collapse
Affiliation(s)
- Ji Seong Kim
- Department of Environmental Horticulture, The University of Seoul, Seoulsiripdae-ro 163, Dongdaemun-gu, Seoul, 130-743, South Korea
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8572, Japan
| | - Jeong Eun Lee
- Department of Environmental Horticulture, The University of Seoul, Seoulsiripdae-ro 163, Dongdaemun-gu, Seoul, 130-743, South Korea
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8572, Japan
| | - Hualin Nie
- Department of Environmental Horticulture, The University of Seoul, Seoulsiripdae-ro 163, Dongdaemun-gu, Seoul, 130-743, South Korea
| | - Yong Jae Lee
- Department of Environmental Horticulture, The University of Seoul, Seoulsiripdae-ro 163, Dongdaemun-gu, Seoul, 130-743, South Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang, 627-706, South Korea
| | - Sun-Hyung Kim
- Department of Environmental Horticulture, The University of Seoul, Seoulsiripdae-ro 163, Dongdaemun-gu, Seoul, 130-743, South Korea.
| |
Collapse
|
12
|
Wanapaisan P, Laothamteep N, Vejarano F, Chakraborty J, Shintani M, Muangchinda C, Morita T, Suzuki-Minakuchi C, Inoue K, Nojiri H, Pinyakong O. Synergistic degradation of pyrene by five culturable bacteria in a mangrove sediment-derived bacterial consortium. JOURNAL OF HAZARDOUS MATERIALS 2018; 342:561-570. [PMID: 28886568 DOI: 10.1016/j.jhazmat.2017.08.062] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 08/17/2017] [Accepted: 08/23/2017] [Indexed: 05/22/2023]
Abstract
A pyrene-degrading microbial consortium was obtained after enrichment with mangrove sediment collected from Thailand. Five cultivable bacteria (Mycobacterium spp. PO1 and PO2, Novosphingobium pentaromativorans PY1, Ochrobactrum sp. PW1, and Bacillus sp. FW1) were successfully isolated from the consortium. Draft genomes of them showed that two different morphotypes of Mycobacterium (PO1 and PO2), possessed a complete gene set for pyrene degradation. PY1 contained genes for phthalate assimilation via protocatechuate, a central intermediate, by meta-cleavage pathway, and PW1 possessed genes for protocatechuate degradation via ortho-cleavage pathway. The occurrence of biosurfactant-producing genes in FW1 suggests the involvement in enhancing the pyrene bioavailability. Biotransformation experiments revealed that Mycobacterium completely degraded 100mgL-1 pyrene within six days, whereas no significant degradation was observed with the others. Notably, PY1 and PW1 exhibited higher activity for protocatechuate degradation than the others. The artificially reconstructed consortia containing Mycobacterium with the other three strains (PY1, PW1 and FW1) showed three-fold higher degradation rate for pyrene than the individual Mycobacterium. The enhanced pyrene biodegradation achieved in the consortium was due to the cooperative interaction of bacterial mixture. Our findings showing that synergistic degradation of pyrene in the consortium will facilitate the application of the defined bacterial consortium in bioremediation.
Collapse
Affiliation(s)
- Pagakrong Wanapaisan
- Department of Microbiology, Faculty of Science, Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Natthariga Laothamteep
- Department of Microbiology, Faculty of Science, Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Felipe Vejarano
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Joydeep Chakraborty
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Masaki Shintani
- Faculty of Engineering, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, Shizuoka 432-8561, Japan
| | - Chanokporn Muangchinda
- Department of Microbiology, Faculty of Science, Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Tomomi Morita
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; Department of Bioscience and Engineering, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama, Saitama 337-8570, Japan
| | - Chiho Suzuki-Minakuchi
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kengo Inoue
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki, Miyazaki 889-2192, Japan
| | - Hideaki Nojiri
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
| | - Onruthai Pinyakong
- Department of Microbiology, Faculty of Science, Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok 10330, Thailand; Research Program on Remediation Technologies for Petroleum Contamination, Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok 10330, Thailand; Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok 10330, Thailand.
| |
Collapse
|
13
|
Shariati J V, Malboobi MA, Tabrizi Z, Tavakol E, Owlia P, Safari M. Comprehensive genomic analysis of a plant growth-promoting rhizobacterium Pantoea agglomerans strain P5. Sci Rep 2017; 7:15610. [PMID: 29142289 PMCID: PMC5688152 DOI: 10.1038/s41598-017-15820-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 10/31/2017] [Indexed: 11/09/2022] Open
Abstract
In this study, we provide a comparative genomic analysis of Pantoea agglomerans strain P5 and 10 closely related strains based on phylogenetic analyses. A next-generation shotgun strategy was implemented using the Illumina HiSeq 2500 technology followed by core- and pan-genome analysis. The genome of P. agglomerans strain P5 contains an assembly size of 5082485 bp with 55.4% G + C content. P. agglomerans consists of 2981 core and 3159 accessory genes for Coding DNA Sequences (CDSs) based on the pan-genome analysis. Strain P5 can be grouped closely with strains PG734 and 299 R using pan and core genes, respectively. All the predicted and annotated gene sequences were allocated to KEGG pathways. Accordingly, genes involved in plant growth-promoting (PGP) ability, including phosphate solubilization, IAA and siderophore production, acetoin and 2,3-butanediol synthesis and bacterial secretion, were assigned. This study provides an in-depth view of the PGP characteristics of strain P5, highlighting its potential use in agriculture as a biofertilizer.
Collapse
Affiliation(s)
- Vahid Shariati J
- Plant Molecular Biotechnology Department, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.,NIGEB Genome Center, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Mohammad Ali Malboobi
- Plant Molecular Biotechnology Department, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran. .,R&D Department, Green Biotech Inc., Suite 10, 47 Bu-Ali-Sina St. W, Bistoun Ave, Fatemi Sq, Tehran, Iran.
| | - Zeinab Tabrizi
- Plant Molecular Biotechnology Department, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.,NIGEB Genome Center, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Elahe Tavakol
- Department of Crop Production and Plant Breeding, College of Agriculture Shiraz University, Shiraz, Iran
| | - Parviz Owlia
- Molecular Microbiology Research Center, Faculty of Medicine, Shahed University, Tehran, Iran
| | - Maryam Safari
- Energy and Environmental Biotechnology Department, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| |
Collapse
|
14
|
Adelskov J, Patel BKC. A molecular phylogenetic framework for Bacillus subtilis using genome sequences and its application to Bacillus subtilis subspecies stecoris strain D7XPN1, an isolate from a commercial food-waste degrading bioreactor. 3 Biotech 2016; 6:96. [PMID: 28330166 PMCID: PMC4809863 DOI: 10.1007/s13205-016-0408-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 02/28/2016] [Indexed: 11/25/2022] Open
Abstract
A thermophilic, heterotrophic and facultatively anaerobic bacterium designated strain D7XPN1 was isolated from Baku BakuKing™, a commercial food-waste degrading bioreactor (composter). The strain grew optimally at 45 °C (growth range between 24 and 50 °C) and pH 7 (growth pH range between pH 5 and 9) in Luria Broth supplemented with 0.3 % glucose. Strain D7XPN1 tolerated up to 7 % NaCl and showed amylolytic and xylanolytic activities. 16S rRNA gene analysis placed strain D7XPN1 in the cluster represented by Bacillus subtilis and the genome analysis of the 4.1 Mb genome sequence determined using RAST (Rapid Annotation using Subsystem Technology) indicated a total of 5116 genomic features were present of which 2320 features could be grouped into several subsystem categories. Of these, 615 features were related to carbohydrate metabolism which included a range of enzymes with potential in the biodegradation of food wastes, a property consistent with the ecological habitat of the isolate. ANIb (Average Nucleotide Identity based on BLAST) analysis with 49 Bacillus subtilis genomes indicated that it was distantly related to the three currently taxonomically validated B. subtilis subspecies namely B. subtilis subsp. subtilis (95.6 %), B. subtilis subsp. spizizenii (93 %) and B. subtilis subsp. inaquosorum (92 %) and based on our current knowledge warranted that it be included as a separate cluster together with strain JS which it was closely related (98.69 %). The close relationship of strains D7XPN1 and JS is also supported from our results from electronic DNA–DNA Hybridization (e-DDH) studies. Furthermore, our additional in-depth phylogenomic analyses using three different datasets unequivocally supported the creation of a fourth B. subtilis subspecies to include strains D7XPN1 and JS for which we propose strain D7XPN1T (=KCTC 33554T, JCM 30051T) as the type strain, and designate it as B. subtilis subsp. stecoris.
Collapse
Affiliation(s)
- Joseph Adelskov
- Microbial Gene Research and Resources Facility, School of Natural Sciences, Griffith University, Brisbane, QLD, 4111, Australia
| | - Bharat K C Patel
- Microbial Gene Research and Resources Facility, School of Natural Sciences, Griffith University, Brisbane, QLD, 4111, Australia.
| |
Collapse
|
15
|
Liu W, Wang Q, Hou J, Tu C, Luo Y, Christie P. Whole genome analysis of halotolerant and alkalotolerant plant growth-promoting rhizobacterium Klebsiella sp. D5A. Sci Rep 2016; 6:26710. [PMID: 27216548 PMCID: PMC4877636 DOI: 10.1038/srep26710] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 05/09/2016] [Indexed: 11/09/2022] Open
Abstract
This research undertook the systematic analysis of the Klebsiella sp. D5A genome and identification of genes that contribute to plant growth-promoting (PGP) traits, especially genes related to salt tolerance and wide pH adaptability. The genome sequence of isolate D5A was obtained using an Illumina HiSeq 2000 sequencing system with average coverages of 174.7× and 200.1× using the paired-end and mate-pair sequencing, respectively. Predicted and annotated gene sequences were analyzed for similarity with the Kyoto Encyclopedia of Genes and Genomes (KEGG) enzyme database followed by assignment of each gene into the KEGG pathway charts. The results show that the Klebsiella sp. D5A genome has a total of 5,540,009 bp with 57.15% G + C content. PGP conferring genes such as indole-3-acetic acid (IAA) biosynthesis, phosphate solubilization, siderophore production, acetoin and 2,3-butanediol synthesis, and N2 fixation were determined. Moreover, genes putatively responsible for resistance to high salinity including glycine-betaine synthesis, trehalose synthesis and a number of osmoregulation receptors and transport systems were also observed in the D5A genome together with numerous genes that contribute to pH homeostasis. These genes reveal the genetic adaptation of D5A to versatile environmental conditions and the effectiveness of the isolate to serve as a plant growth stimulator.
Collapse
Affiliation(s)
- Wuxing Liu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Qingling Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Jinyu Hou
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Chen Tu
- Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Yongming Luo
- Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Peter Christie
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| |
Collapse
|
16
|
Kim JS, Lee J, Lee CH, Woo SY, Kang H, Seo SG, Kim SH. Activation of Pathogenesis-related Genes by the Rhizobacterium, Bacillus sp. JS, Which Induces Systemic Resistance in Tobacco Plants. THE PLANT PATHOLOGY JOURNAL 2015; 31:195-201. [PMID: 26060440 PMCID: PMC4454002 DOI: 10.5423/ppj.nt.11.2014.0122] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 01/05/2015] [Accepted: 02/08/2015] [Indexed: 05/27/2023]
Abstract
Plant growth promoting rhizobacteria (PGPR) are known to confer disease resistance to plants. Bacillus sp. JS demonstrated antifungal activities against five fungal pathogens in in vitro assays. To verify whether the volatiles of Bacillus sp. JS confer disease resistance, tobacco leaves pre-treated with the volatiles were damaged by the fungal pathogen, Rhizoctonia solani and oomycete Phytophthora nicotianae. Pre-treated tobacco leaves had smaller lesion than the control plant leaves. In pathogenesis-related (PR) gene expression analysis, volatiles of Bacillus sp. JS caused the up-regulation of PR-2 encoding β-1,3-glucanase and acidic PR-3 encoding chitinase. Expression of acidic PR-4 encoding chitinase and acidic PR-9 encoding peroxidase increased gradually after exposure of the volatiles to Bacillus sp. JS. Basic PR-14 encoding lipid transfer protein was also increased. However, PR-1 genes, as markers of salicylic acid (SA) induced resistance, were not expressed. These results suggested that the volatiles of Bacillus sp. JS confer disease resistance against fungal and oomycete pathogens through PR genes expression.
Collapse
Affiliation(s)
- Ji-Seong Kim
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8572,
Japan
- Department of Environmental Horticulture, The University of Seoul, Seoul 130-743,
Korea
| | - Jeongeun Lee
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8572,
Japan
- Department of Environmental Horticulture, The University of Seoul, Seoul 130-743,
Korea
| | - Chan-hui Lee
- Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701,
Korea
| | - Su Young Woo
- Department of Environmental Horticulture, The University of Seoul, Seoul 130-743,
Korea
| | - Hoduck Kang
- Department of Biological and Environmental Science, Dongguk University, Seoul 100-715,
Korea
| | - Sang-Gyu Seo
- Department of Environmental Horticulture, The University of Seoul, Seoul 130-743,
Korea
| | - Sun-Hyung Kim
- Department of Environmental Horticulture, The University of Seoul, Seoul 130-743,
Korea
| |
Collapse
|
17
|
Gene expression profile affected by volatiles of new plant growth promoting rhizobacteria, Bacillus subtilis strain JS, in tobacco. Genes Genomics 2015. [DOI: 10.1007/s13258-015-0267-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
18
|
Draft Genome Sequence of Bacillus subtilis Strain D7XPN1, Isolated from Commercial Bioreactor-Degrading Food Waste. GENOME ANNOUNCEMENTS 2014; 2:2/5/e00989-14. [PMID: 25278534 PMCID: PMC4183878 DOI: 10.1128/genomea.00989-14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The analysis of the 4.1-Mb draft genome sequence of a moderately thermophilic, heterotrophic, and facultatively anaerobic bacterium, Bacillus subtilis strain D7XPN1, identified genes for a range of enzymes with potential in the biodegradation of food waste, a property consistent with the ecological habitat of the isolate.
Collapse
|
19
|
Gupta A, Gopal M, Thomas GV, Manikandan V, Gajewski J, Thomas G, Seshagiri S, Schuster SC, Rajesh P, Gupta R. Whole genome sequencing and analysis of plant growth promoting bacteria isolated from the rhizosphere of plantation crops coconut, cocoa and arecanut. PLoS One 2014; 9:e104259. [PMID: 25162593 PMCID: PMC4146471 DOI: 10.1371/journal.pone.0104259] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 07/09/2014] [Indexed: 12/17/2022] Open
Abstract
Coconut, cocoa and arecanut are commercial plantation crops that play a vital role in the Indian economy while sustaining the livelihood of more than 10 million Indians. According to 2012 Food and Agricultural organization's report, India is the third largest producer of coconut and it dominates the production of arecanut worldwide. In this study, three Plant Growth Promoting Rhizobacteria (PGPR) from coconut (CPCRI-1), cocoa (CPCRI-2) and arecanut (CPCRI-3) characterized for the PGP activities have been sequenced. The draft genome sizes were 4.7 Mb (56% GC), 5.9 Mb (63.6% GC) and 5.1 Mb (54.8% GB) for CPCRI-1, CPCRI-2, CPCRI-3, respectively. These genomes encoded 4056 (CPCRI-1), 4637 (CPCRI-2) and 4286 (CPCRI-3) protein-coding genes. Phylogenetic analysis revealed that both CPCRI-1 and CPCRI-3 belonged to Enterobacteriaceae family, while, CPCRI-2 was a Pseudomonadaceae family member. Functional annotation of the genes predicted that all three bacteria encoded genes needed for mineral phosphate solubilization, siderophores, acetoin, butanediol, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, chitinase, phenazine, 4-hydroxybenzoate, trehalose and quorum sensing molecules supportive of the plant growth promoting traits observed in the course of their isolation and characterization. Additionally, in all the three CPCRI PGPRs, we identified genes involved in synthesis of hydrogen sulfide (H2S), which recently has been proposed to aid plant growth. The PGPRs also carried genes for central carbohydrate metabolism indicating that the bacteria can efficiently utilize the root exudates and other organic materials as energy source. Genes for production of peroxidases, catalases and superoxide dismutases that confer resistance to oxidative stresses in plants were identified. Besides these, genes for heat shock tolerance, cold shock tolerance and glycine-betaine production that enable bacteria to survive abiotic stress were also identified.
Collapse
Affiliation(s)
- Alka Gupta
- Central Plantation Crops Research Institute, Kasaragod, Kerala, India
| | - Murali Gopal
- Central Plantation Crops Research Institute, Kasaragod, Kerala, India
| | - George V. Thomas
- Central Plantation Crops Research Institute, Kasaragod, Kerala, India
| | - Vinu Manikandan
- SciGenom Labs Pvt. Ltd., Plot 43A, SDF 3rd Floor CSEZ, Kakkanad, Cochin, Kerala, India
| | - John Gajewski
- Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, 310 Wartik Lab, University Park, Pennsylvania, United States of America
| | | | - Somasekar Seshagiri
- Department of Molecular Biology, Genentech Inc., South San Francisco, California, United States of America
| | - Stephan C. Schuster
- Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, 310 Wartik Lab, University Park, Pennsylvania, United States of America
- Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technical University, Singapore, Singapore
| | - Preeti Rajesh
- SciGenom Labs Pvt. Ltd., Plot 43A, SDF 3rd Floor CSEZ, Kakkanad, Cochin, Kerala, India
| | - Ravi Gupta
- SciGenom Labs Pvt. Ltd., Plot 43A, SDF 3rd Floor CSEZ, Kakkanad, Cochin, Kerala, India
| |
Collapse
|
20
|
Mining of a streptothricin gene cluster from Streptomyces sp. TP-A0356 genome via heterologous expression. SCIENCE CHINA-LIFE SCIENCES 2013; 56:619-27. [DOI: 10.1007/s11427-013-4504-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 05/28/2013] [Indexed: 12/29/2022]
|
21
|
Molecular signatures for
Bacillus
species: demarcation of the
Bacillus subtilis
and
Bacillus cereus
clades in molecular terms and proposal to limit the placement of new species into the genus
Bacillus. Int J Syst Evol Microbiol 2013; 63:2712-2726. [DOI: 10.1099/ijs.0.048488-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genus
Bacillus
is a phylogenetically incoherent taxon with members of the group lacking a common evolutionary history. Comprising aerobic and anaerobic spore-forming bacteria, no characteristics are known that can distinguish species of this genus from other similar endospore-forming genera. With the availability of complete genomic data from over 30 different species from this group, we have constructed detailed phylogenetic trees to determine the relationships among
Bacillus
and other closely related taxa. Additionally, we have performed comparative genomic analysis for the determination of molecular markers, in the form of conserved signature indels (CSIs), to assist in the understanding of relationships among species of the genus
Bacillus
in molecular terms. Based on the analysis, we report here the identification of 11 and 6 CSIs that clearly differentiate a ‘
Bacillus subtilis
clade’ and a ‘
Bacillus cereus
clade’, respectively, from all other species of the genus
Bacillus
. No molecular markers were identified that supported a larger clade within this genus. The subtilis and the cereus clades were also the largest observed monophyletic groupings among species from the genus
Bacillus
in the phylogenetic trees based on 16S rRNA gene sequences and those based upon concatenated sequences for 20 conserved proteins. Thus, the relationships observed among these groups of species through CSIs are independently well supported by phylogenetic analysis. The molecular markers identified in this study provide a reliable means for the reorganization of the currently polyphyletic genus
Bacillus
into a more evolutionarily consistent set of groups. It is recommended that the genus
Bacillus
sensu stricto should comprise only the monophyletic subtilis clade that is demarcated by the identified CSIs, with
B. subtilis
as its type species. Members of the adjoining cereus clade (referred to as the Cereus clade of bacilli), although they are distinct from the subtilis clade, will also retain the
Bacillus
genus name as they contain several clinically important species, and their transfer into a new genus could have serious consequences. However, all other species that are currently part of the genus
Bacillus
and not part of these two clades should be eventually transferred to other genera. We also propose that all novel species of the genus
Bacillus
must meet minimal requirements, foremost among which is that the branching of the prospective species with the
Bacillus
sensu stricto clade or the Cereus clade of bacilli should be strongly supported by 16S rRNA gene sequence trees or trees based upon concatenated protein sequences. Additionally, the presence of one or more of the CSIs that are specific for these clades may be used to confirm molecularly the placement of the species into these clades. The identified CSIs, in addition to their usefulness for taxonomic and diagnostic purposes, also provide novel probes for genetic and biochemical studies of these bacteria.
Collapse
|
22
|
Genome Sequencing of Bacillus subtilis Strain XF-1 with High Efficiency in the Suppression of Plasmodiophora brassicae. GENOME ANNOUNCEMENTS 2013; 1:e0006613. [PMID: 23558530 PMCID: PMC3622977 DOI: 10.1128/genomea.00066-13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The genome of the rhizobacterium Bacillus subtilis XF-1 is 4.06 Mb in size and harbors 3,853 coding sequences (CDS). Giant gene clusters were dedicated to the nonribosomal synthesis of antimicrobial lipopeptides and polyketides. Remarkably, XF-1 possesses a gene cluster involved in the synthesis of chitosanase that is related to the suppression of the pathogen Plasmodiophora brassicae.
Collapse
|
23
|
Twenty-one genome sequences from Pseudomonas species and 19 genome sequences from diverse bacteria isolated from the rhizosphere and endosphere of Populus deltoides. J Bacteriol 2013; 194:5991-3. [PMID: 23045501 DOI: 10.1128/jb.01243-12] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To aid in the investigation of the Populus deltoides microbiome, we generated draft genome sequences for 21 Pseudomonas strains and 19 other diverse bacteria isolated from Populus deltoides roots. Genome sequences for isolates similar to Acidovorax, Bradyrhizobium, Brevibacillus, Caulobacter, Chryseobacterium, Flavobacterium, Herbaspirillum, Novosphingobium, Pantoea, Phyllobacterium, Polaromonas, Rhizobium, Sphingobium, and Variovorax were generated.
Collapse
|
24
|
Genome sequences published outside of Standards in Genomic Sciences, May-June 2012. Stand Genomic Sci 2012. [PMCID: PMC3558956 DOI: 10.4056/sigs.3126494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.
Collapse
|