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Hnini M, Aurag J. Prevalence, diversity and applications potential of nodules endophytic bacteria: a systematic review. Front Microbiol 2024; 15:1386742. [PMID: 38812696 PMCID: PMC11133547 DOI: 10.3389/fmicb.2024.1386742] [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: 02/16/2024] [Accepted: 04/29/2024] [Indexed: 05/31/2024] Open
Abstract
Legumes are renowned for their distinctive biological characteristic of forming symbiotic associations with soil bacteria, mostly belonging to the Rhizobiaceae familiy, leading to the establishment of symbiotic root nodules. Within these nodules, rhizobia play a pivotal role in converting atmospheric nitrogen into a plant-assimilable form. However, it has been discerned that root nodules of legumes are not exclusively inhabited by rhizobia; non-rhizobial endophytic bacteria also reside within them, yet their functions remain incompletely elucidated. This comprehensive review synthesizes available data, revealing that Bacillus and Pseudomonas are the most prevalent genera of nodule endophytic bacteria, succeeded by Paenibacillus, Enterobacter, Pantoea, Agrobacterium, and Microbacterium. To date, the bibliographic data available show that Glycine max followed by Vigna radiata, Phaseolus vulgaris and Lens culinaris are the main hosts for nodule endophytic bacteria. Clustering analysis consistently supports the prevalence of Bacillus and Pseudomonas as the most abundant nodule endophytic bacteria, alongside Paenibacillus, Agrobacterium, and Enterobacter. Although non-rhizobial populations within nodules do not induce nodule formation, their presence is associated with various plant growth-promoting properties (PGPs). These properties are known to mediate important mechanisms such as phytostimulation, biofertilization, biocontrol, and stress tolerance, emphasizing the multifaceted roles of nodule endophytes. Importantly, interactions between non-rhizobia and rhizobia within nodules may exert influence on their leguminous host plants. This is particularly shown by co-inoculation of legumes with both types of bacteria, in which synergistic effects on plant growth, yield, and nodulation are often measured. Moreover these effects are pronounced under both stress and non-stress conditions, surpassing the impact of single inoculations with rhizobia alone.
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Affiliation(s)
| | - Jamal Aurag
- Microbiology and Molecular Biology Team, Center of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
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2
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Razmilic V, Nouioui I, Karlyshev A, Jawad R, Trujillo ME, Igual JM, Andrews BA, Asenjo JA, Carro L, Goodfellow M. Micromonospora parastrephiae sp. nov. and Micromonospora tarensis sp. nov., isolated from the rhizosphere of a Parastrephia quadrangularis plant growing in the Salar de Tara region of the Central Andes in Chile. Int J Syst Evol Microbiol 2023; 73. [PMID: 38059605 DOI: 10.1099/ijsem.0.006189] [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: 12/08/2023] Open
Abstract
Two novel Micromonospora strains, STR1-7T and STR1S-6T, were isolated from the rhizosphere of a Parastrephia quadrangularis plant growing in the Salar de Tara region of the Atacama Desert, Chile. Chemotaxonomic, cultural and phenotypic features confirmed that the isolates belonged to the genus Micromonospora. They grew from 20 to 37 °C, from pH7 to 8 and in the presence of up to 3 %, w/v NaCl. The isolates formed distinct branches in Micromonospora gene trees based on 16S rRNA gene sequences and on a multi-locus sequence analysis of conserved house-keeping genes. A phylogenomic tree generated from the draft genomes of the isolates and their closest phylogenetic neighbours showed that isolate STR1-7T is most closely related to Micromonospora orduensis S2509T, and isolate STR1S-6 T forms a distinct branch that is most closely related to 12 validly named Micromonospora species, including Micromonospora saelicesensis the earliest proposed member of the group. The isolates were separated from one another and from their closest phylogenomic neighbours using a combination of chemotaxonomic, genomic and phenotypic features, and by low average nucleotide index and digital DNA-DNA hybridization values. Consequently, it is proposed that isolates STR1-7T and STR1S-6T be recognized as representing new species in the genus Micromonospora, namely as Micromonospora parastrephiae sp. nov. and Micromonospora tarensis sp. nov.; the type strains are STR1-7T (=CECT 9665T=LMG 30768T) and STR1S-6T (=CECT 9666T=LMG 30770T), respectively. Genome mining showed that the isolates have the capacity to produce novel specialized metabolites, notably antibiotics and compounds that promote plant growth, as well as a broad-range of stress-related genes that provide an insight into how they cope with harsh abiotic conditions that prevail in high-altitude Atacama Desert soils.
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Affiliation(s)
- Valeria Razmilic
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago, Chile
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
- Department of Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124, Braunschweig, Germany
| | - Andrey Karlyshev
- Department of Biomolecular Sciences, School of Life Sciences, Pharmacy and Chemistry, Faculty of Health, Science, Social Care and Education, Kingston University London, Kingston upon Thames, KT1 2EE, UK
| | - Rana Jawad
- Department of Biomolecular Sciences, School of Life Sciences, Pharmacy and Chemistry, Faculty of Health, Science, Social Care and Education, Kingston University London, Kingston upon Thames, KT1 2EE, UK
| | - Martha E Trujillo
- Microbiology and Genetics Department, University of Salamanca, Salamanca, Spain
| | - Jose M Igual
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), c/Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Barbara A Andrews
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago, Chile
| | - Juan A Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago, Chile
| | - Lorena Carro
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
- Microbiology and Genetics Department, University of Salamanca, Salamanca, Spain
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
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3
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Riesco R, Ortúzar M, Román-Ponce B, Sánchez-Juanes F, Igual JM, Trujillo ME. Six novel Micromonospora species associated with the phyllosphere and roots of leguminous plants: Micromonospora alfalfae sp. nov., Micromonospora cabrerizensis sp. nov., Micromonospora foliorum sp. nov., Micromonospora hortensis sp. nov., Micromonospora salmantinae sp. nov., and Micromonospora trifolii sp. nov. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Six actinobacterial strains isolated from diverse legume tissues collected in various locations in Spain were characterized to determine their taxonomic status. Using 16S rRNA gene sequencing, the strains were primarily identified as members of the genus
Micromonospora
with more than 99 % similarity. Digital DNA–DNA hybridization values and average nucleotide identities between the six strains and the nearest type strains confirmed that each strain represented a novel species. Genome sequences were analysed to infer their metabolic profiles, their potential to produce secondary metabolites and plant growth promoting features. Chemotaxonomic and physiological studies were carried out to complete the phenotypic characterization and to distinguish the new
Micromonospora
species. The genomic and phenotypic characterization of the
Micromonospora
strains strongly support their classification as representatives of new species with the following names: Micromonospora alfalfae sp. nov., Micromonospora cabrerizensis sp. nov., Micromonospora foliorum sp. nov., Micromonospora hortensis sp. nov., Micromonospora salmantinae sp. nov. and Micromonospora trifolii sp. nov., with the type strains MED01T, LAH09T, PSH25T, NIE111T, PSH03T and NIE79T, respectively.
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Affiliation(s)
- Raúl Riesco
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain
| | - Maite Ortúzar
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain
| | - Brenda Román-Ponce
- Present address: Universidad Politécnica del Estado de Morelos, Morelos, Boulevard Cuauhnáhuac 556, Lomas del Texcal, 62550, Jiutepec, Mexico
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain
| | - Fernando Sánchez-Juanes
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, CSIC, Salamanca, Spain
- Department of Biochemistry and Molecular Biology, University of Salamanca, Salamanca, Spain
| | - José Mariano Igual
- Instituto de Recursos Naturales y Agrobiología de Salamanca (CSIC), Cordel de Merinas 40-52, 37008, Salamanca, Spain
| | - Martha E. Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain
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4
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Lee DH, Ra JS, Kim MJ, Kim SB. Micromonospora antibiotica sp. nov. and Micromonospora humidisoli sp. nov., two new actinobacterial species exhibiting antimicrobial potential. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two novel actinobacterial strains, designated MMS20-R2-23T and MMS20-R2-29T, were isolated from riverside soil and subjected to taxonomic characterization. Both strains were Gram-stain-positive, aerobic, non-motile and filamentous, and formed orange to strong orange-brown coloured colonies, which later turned black. Both strains grew optimally at mesophilic temperatures, neutral to slightly alkaline pH and in the absence of NaCl. Analysis of 16S rRNA gene sequences indicated that the two novel strains fell into phylogenetic clusters belonging to the genus
Micromonospora
. Strains MMS20-R2-23T and MMS20-R2-29T showed the highest 16S rRNA gene sequence similarity to
Micromonospora phytophila
SG15T (99.3 %) and
Micromonospora humida
MMS20-R1-14T (99.4 %), respectively. Based on the comparative genome analysis, strain MMS20-R2-23T had the highest orthologous average nucleotide identity (orthoANI) value of 92.70 % with
Micromonospora matsumotoense
DSM 44100T, and MMS20-R2-29T shared 94.99 % with
Micromonospora wenchangensis
CCTCC AA 2012002T. Besides, the digital DNA–DNA hybridization (dDDH) values of MMS20-R2-23T and MMS20-R2-29T with the same species were 47.6 and 59.2% respectively, which were also highest among the compared species, thus confirming the separation of each strain at species level from related species. The orthoANI and dDDH values between MMS20-R2-23T and MMS20-R2-29T were 92.18 and 44.9% respectively. The genomes of strains MMS20-R2-23T and MMS20-R2-29T were estimated as 7.56 Mbp and 7.13 Mbp in size, and the DNA G+C contents were 72.5 and 72.9 mol%, respectively. The chemotaxonomic properties of both strains were consistent with those of the genus. The novel strains showed antimicrobial activity against a broad range of microbes, in particular Gram-positive bacteria and yeasts. It is evident that each of the isolated strains merits recognition as representing novel species of
Micromonospora
, for which the names Micromonospora antibiotica sp. nov. (type strain=MMS20-R2-23T=KCTC 49542T=JCM 34495T) and Micromonospora humidisoli sp. nov. (type strain=MMS20-R2-29T=KCTC 49543T=JCM 34496T) are proposed.
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Affiliation(s)
- Dong Hyeon Lee
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99 Daehak-ro, Yuseong, Daejeon 34134, Republic of Korea
| | - Jun Sik Ra
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99 Daehak-ro, Yuseong, Daejeon 34134, Republic of Korea
| | - Min Ji Kim
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99 Daehak-ro, Yuseong, Daejeon 34134, Republic of Korea
| | - Seung Bum Kim
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99 Daehak-ro, Yuseong, Daejeon 34134, Republic of Korea
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5
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Hrbáčková M, Luptovčiak I, Hlaváčková K, Dvořák P, Tichá M, Šamajová O, Novák D, Bednarz H, Niehaus K, Ovečka M, Šamaj J. Overexpression of alfalfa SIMK promotes root hair growth, nodule clustering and shoot biomass production. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:767-784. [PMID: 33112469 PMCID: PMC8051612 DOI: 10.1111/pbi.13503] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 10/08/2020] [Accepted: 10/15/2020] [Indexed: 05/03/2023]
Abstract
Nitrogen-fixing rhizobia and legumes have developed complex mutualistic mechanism that allows to convert atmospheric nitrogen into ammonia. Signalling by mitogen-activated protein kinases (MAPKs) seems to be involved in this symbiotic interaction. Previously, we reported that stress-induced MAPK (SIMK) shows predominantly nuclear localization in alfalfa root epidermal cells. Nevertheless, SIMK is activated and relocalized to the tips of growing root hairs during their development. SIMK kinase (SIMKK) is a well-known upstream activator of SIMK. Here, we characterized production parameters of transgenic alfalfa plants with genetically manipulated SIMK after infection with Sinorhizobium meliloti. SIMKK RNAi lines, causing strong downregulation of both SIMKK and SIMK, showed reduced root hair growth and lower capacity to form infection threads and nodules. In contrast, constitutive overexpression of GFP-tagged SIMK promoted root hair growth as well as infection thread and nodule clustering. Moreover, SIMKK and SIMK downregulation led to decrease, while overexpression of GFP-tagged SIMK led to increase of biomass in above-ground part of plants. These data suggest that genetic manipulations causing downregulation or overexpression of SIMK affect root hair, nodule and shoot formation patterns in alfalfa, and point to the new biotechnological potential of this MAPK.
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Affiliation(s)
- Miroslava Hrbáčková
- Faculty of ScienceDepartment of Cell BiologyCentre of the Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
| | - Ivan Luptovčiak
- Faculty of ScienceDepartment of Cell BiologyCentre of the Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
| | - Kateřina Hlaváčková
- Faculty of ScienceDepartment of Cell BiologyCentre of the Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
| | - Petr Dvořák
- Faculty of ScienceDepartment of Cell BiologyCentre of the Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
| | - Michaela Tichá
- Faculty of ScienceDepartment of Cell BiologyCentre of the Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
| | - Olga Šamajová
- Faculty of ScienceDepartment of Cell BiologyCentre of the Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
| | - Dominik Novák
- Faculty of ScienceDepartment of Cell BiologyCentre of the Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
| | - Hanna Bednarz
- Faculty of BiologyCenter for Biotechnology – CeBiTecUniversität BielefeldBielefeldGermany
| | - Karsten Niehaus
- Faculty of BiologyCenter for Biotechnology – CeBiTecUniversität BielefeldBielefeldGermany
| | - Miroslav Ovečka
- Faculty of ScienceDepartment of Cell BiologyCentre of the Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
| | - Jozef Šamaj
- Faculty of ScienceDepartment of Cell BiologyCentre of the Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
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6
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Kaewkla O, Suriyachadkun C, Franco CMM. Micromonospora veneta sp. nov., an endophytic actinobacterium with potential for nitrogen fixation and for bioremediation. Arch Microbiol 2021; 203:2853-2861. [PMID: 33754164 DOI: 10.1007/s00203-021-02260-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 02/03/2021] [Accepted: 02/22/2021] [Indexed: 11/26/2022]
Abstract
Strain CAP181T, an endophytic actinobacterium, was isolated from a surface sterilized root sample of a native pine tree, Flinders University, Adelaide, South Australia. Chemotaxonomic data including cell wall components, major fatty acids, and major menaquinones confirmed the affiliation of strain CAP181T to the genus Micromonospora. This strain was Gram stain positive with well-developed substrate mycelia to form a single spore with hairy surface. The phylogenetic tree showed that M. coerulea NBRC 13504 T is the closest phylogenetic neighbour, sharing 99.2% 16S rRNA gene similarity and the next closest neighbor is M. chaiyaphumensis DSM 45246 T (98.7%). Genome mining of this strain revealed genes encoding to enzymes relating to nitrogen fixation and bioremediation. Based on genotypic and phenotypic studies including DNA-DNA hybridization data, strain CAP181T was different from any of the closely related species with valid names. The name proposed for the new species is Micromonospora veneta sp. nov. The type strain is CAP181T (= DSM 109713 T = NRRL B-65535 T).
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Affiliation(s)
- Onuma Kaewkla
- Department of Biology, Faculty of Science, Mahasarakham University, Kantaravichai, Maha Sarakham Province, 44150, Thailand.
- Department of Medical Biotechnology, College of Medicine and Public Health, Flinders University, Bedford park, Adelaide, 5042, Australia.
| | - Chanwit Suriyachadkun
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Klong Luang, Pathumthani, 12120, Thailand
| | - Christopher Milton Mathew Franco
- Department of Medical Biotechnology, College of Medicine and Public Health, Flinders University, Bedford park, Adelaide, 5042, Australia
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7
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Insuk C, Kuncharoen N, Cheeptham N, Tanasupawat S, Pathom-Aree W. Bryophytes Harbor Cultivable Actinobacteria With Plant Growth Promoting Potential. Front Microbiol 2020; 11:563047. [PMID: 33133038 PMCID: PMC7550540 DOI: 10.3389/fmicb.2020.563047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 08/24/2020] [Indexed: 11/23/2022] Open
Abstract
This study was designed to investigate the cultivable actinobacteria associated with bryophytes and their plant growth promoting ability. Thirteen actinobacteria were isolated and tested for their ability to promote growth of plant in vitro and in planta. All isolates were able to produce IAA and siderophores. Six isolates were identified as members of the genus Micromonospora. Five isolates belonged to the genus Streptomyces and one each of Microbispora and Mycobacterium. Micromonospora sp. CMU55-4 was inoculated to rare moss [Physcomitrium sphaericum (C. Ludw.) Fürnr.] and could increase the amount of carotenoid, fresh weight, and dry weight of this moss. In addition, this strain promoted capsule production, and rescued P. sphaericum’s gametophytes during acclimatization to land. Strain CMU55-4 was identified as Micromonospora chalcea based on whole genome sequence analysis. Its plant growth promoting potential was further characterized through genome mining. The draft genome size was 6.6 Mb (73% GC). The genome contained 5,933 coding sequences. Functional annotation predicted encoded genes essential for siderophore production, phosphate solubilization that enable bacteria to survive under nutrient limited environment. Glycine-betaine accumulation and trehalose biosynthesis also aid plants under drought stress. M. chalcea CMU55-4 also exhibited genes for various carbohydrate metabolic pathways indicating those for efficient utilization of carbohydrates inside plant cells. Additionally, predictive genes for heat shock proteins, cold shock proteins, and oxidative stress such as glutathione biosynthesis were identified. In conclusion, our results demonstrate that bryophytes harbor plant growth promoting actinobacteria. A representative isolate, M. chalcea CMU55-4 promotes the growth of P. sphaericum moss and contains protein coding sequences related to plant growth promoting activities in its genome.
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Affiliation(s)
- Chadabhorn Insuk
- Master of Science Program in Applied Microbiology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.,Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Nattakorn Kuncharoen
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Naowarat Cheeptham
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, Canada
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Wasu Pathom-Aree
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.,Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
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8
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Fu G, Wang R, Ding J, Qi H, Zhao Z, Chen C, Zhang H, Xue Z, Wang J, Wu M. Micromonospora zhangzhouensis sp. nov., a Novel Actinobacterium Isolated from Mangrove Soil, Exerts a Cytotoxic Activity in vitro. Sci Rep 2020; 10:3889. [PMID: 32127574 PMCID: PMC7054543 DOI: 10.1038/s41598-020-60677-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 02/13/2020] [Indexed: 11/21/2022] Open
Abstract
A new bacterial strain, designated HM134T, was isolated from a sample of soil collected from a Chinese mangrove Avicennia marina forest. Assessed by a polyphasic approach, the taxonomy of strain HM134T was found to be associated with a range of phylogenetic and chemotaxonomic properties consistent with the genus Micromonospora. Phylogenetic analysis based on the 16s rRNA gene sequence indicated that strain HM134T formed a distinct lineage with the most closely related species, including M. rifamycinica AM105T, M. wenchangensis CCTCC AA 2012002T and M. mangrovi 2803GPT1-18T. The ANI values between strain HM134T and the reference strains ranged from 82.6% to 95.2%, which was below the standard criteria for classifying strains as the same species (96.5%). Strain HM134T and related species shared in silico dDDH similarities values below the recommended 70% cut-off for the delineation of species (range from 25.7–62.6%). The DNA G+C content of strain HM134T was 73.2 mol%. Analysis of phylogenetic, genomic, phenotypic and chemotaxonomic characteristics revealed that strain HM134T is considered to represent a novel species of the genus Micromonospora, for which the name M. zhangzhouensis sp. nov. is proposed. The extract of strain HM134T was demonstrated to exhibit cytotoxic activity against the human cancer cell lines HepG2, HCT-116 and A549. Active substance presented in the fermentation broth of strain HM134T was isolated by bioassay-guided analysis and purified afterwards. A new derivative of diterpenoid was identified through electrospray ionizing mass spectrometry (MS) and nuclear magnetic resonance (NMR). The compound showed different cytotoxic activities against cancer cells, with the highest cytotoxicity against HCT-116, corresponding to IC50 value of 38.4 μg/mL.
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Affiliation(s)
- Geyi Fu
- Ocean College, Zhejiang University, Zhoushan, China
| | - Ruijun Wang
- Ocean College, Zhejiang University, Zhoushan, China
| | - Jinglin Ding
- Zhoushan Tourism & Health College, Zhoushan, China
| | - Huan Qi
- Zhejiang Key Laboratory of Antifungal Drugs, Zhejiang Hisun Pharmaceutical Co., Ltd., Taizhou, China
| | - Zhe Zhao
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Can Chen
- Ocean College, Zhejiang University, Zhoushan, China
| | - Hui Zhang
- Zhejiang Key Laboratory of Antifungal Drugs, Zhejiang Hisun Pharmaceutical Co., Ltd., Taizhou, China.,College of Biochemical Engineering, Anhui Polytechnic University, Wuhu, China
| | - Zhenglian Xue
- College of Biochemical Engineering, Anhui Polytechnic University, Wuhu, China
| | - Jidong Wang
- Zhejiang Key Laboratory of Antifungal Drugs, Zhejiang Hisun Pharmaceutical Co., Ltd., Taizhou, China. .,College of Biochemical Engineering, Anhui Polytechnic University, Wuhu, China.
| | - Min Wu
- Ocean College, Zhejiang University, Zhoushan, China. .,College of Life Sciences, Zhejiang University, Hangzhou, China.
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9
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Martínez-Hidalgo P, Flores-Félix JD, Velázquez E, Brau L, Trujillo ME, Martínez-Molina E. High taxonomic diversity of Micromonospora strains isolated from Medicago sativa nodules in Western Spain and Australia. Syst Appl Microbiol 2019; 43:126043. [PMID: 31796230 DOI: 10.1016/j.syapm.2019.126043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 11/08/2019] [Accepted: 11/15/2019] [Indexed: 10/25/2022]
Abstract
The genus Micromonospora has been found in nodules of several legumes and some new species of this genus were isolated from these plant organs. In this study we analysed the taxonomic diversity of Micromonospora strains isolated from alfalfa nodules in Spain and Australia on the basis of three phylogenetic markers, the rrs and gyrB genes and 16S-23S intergenic spacer (ITS). The genome analysis of selected strains representative of different clusters or lineages found after rrs, gyrB and ITS analyses confirmed the results obtained with these phylogenetic markers. They showed that the analysed strains belong to at least 18 Micromonospora species including previously described ones, such as Micromonospora noduli, Micromonospora ureilytica, Micromonospora taraxaci, Micromonospora zamorensis, Micromonospora aurantiaca and Micromonospora tulbaghiae. Most of these strains belong to undescribed species of Micromonospora showing the high taxonomic diversity of strains from this genus inhabiting alfalfa nodules. Although Micromonospora strains are not able to induce the formation of these nodules, and it seems that they do not contribute to fix atmospheric nitrogen, they could play a role related with the mechanisms of plant growth promotion and pathogen protection presented by Micromonospora strains isolated from legume nodules.
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Affiliation(s)
- Pilar Martínez-Hidalgo
- Departamento de Biología, Geología, Física y Química inorgánica. Universidad Rey Juan Carlos. Departamental II despacho 248. Av. Tulipán s/n, 28933 Móstoles, Madrid.
| | - José David Flores-Félix
- Departamento de Microbiología y Genética and Instituto Hispanoluso de Investigaciones Agrarias (CIALE). Universidad de Salamanca. Edificio Departamental de Biología. Lab 209. Av. Doctores de la Reina S/N. 37007 Salamanca
| | - Encarna Velázquez
- Departamento de Microbiología y Genética and Instituto Hispanoluso de Investigaciones Agrarias (CIALE). Universidad de Salamanca. Edificio Departamental de Biología. Lab 209. Av. Doctores de la Reina S/N. 37007 Salamanca; Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain
| | - Lambert Brau
- Deakin University, Geelong, Australia, Centre for Regional and Rural Futures, School of Life and Environmental Sciences
| | - Martha E Trujillo
- Departamento de Microbiología y Genética and Instituto Hispanoluso de Investigaciones Agrarias (CIALE). Universidad de Salamanca. Edificio Departamental de Biología. Lab 209. Av. Doctores de la Reina S/N. 37007 Salamanca
| | - Eustoquio Martínez-Molina
- Departamento de Microbiología y Genética and Instituto Hispanoluso de Investigaciones Agrarias (CIALE). Universidad de Salamanca. Edificio Departamental de Biología. Lab 209. Av. Doctores de la Reina S/N. 37007 Salamanca; Unidad Asociada Grupo de Interacción Planta-Microorganismo Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain
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10
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Carro L, Castro JF, Razmilic V, Nouioui I, Pan C, Igual JM, Jaspars M, Goodfellow M, Bull AT, Asenjo JA, Klenk HP. Uncovering the potential of novel micromonosporae isolated from an extreme hyper-arid Atacama Desert soil. Sci Rep 2019; 9:4678. [PMID: 30886188 PMCID: PMC6423291 DOI: 10.1038/s41598-019-38789-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 12/12/2018] [Indexed: 11/29/2022] Open
Abstract
The taxonomic status, biotechnological and ecological potential of several Micromonospora strains isolated from an extreme hyper arid Atacama Desert soil were determined. Initially, a polyphasic study was undertaken to clarify the taxonomic status of five micromonosporae, strains LB4, LB19, LB32T, LB39T and LB41, isolated from an extreme hyper-arid soil collected from one of the driest regions of the Atacama Desert. All of the isolates were found to have chemotaxonomic, cultural and morphological properties consistent with their classification in the genus Micromonospora. Isolates LB32T and LB39T were distinguished from their nearest phylogenetic neighbours and proposed as new species, namely as Micromonospora arida sp. nov. and Micromonospora inaquosa sp. nov., respectively. Eluted methanol extracts of all of the isolates showed activity against a panel of bacterial and fungal indicator strains, notably against multi-drug resistant Klebsiella pneumoniae ATCC 700603 while isolates LB4 and LB41 showed pronounced anti-tumour activity against HepG2 cells. Draft genomes generated for the isolates revealed a rich source of novel biosynthetic gene clusters, some of which were unique to individual strains thereby opening up the prospect of selecting especially gifted micromonosporae for natural product discovery. Key stress-related genes detected in the genomes of all of the isolates provided an insight into how micromonosporae adapt to the harsh environmental conditions that prevail in extreme hyper-arid Atacama Desert soils.
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Affiliation(s)
- Lorena Carro
- Microbiology and Genetics Department, University of Salamanca, Salamanca, Spain.
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK.
| | - Jean Franco Castro
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, Universidad de Chile, Beauchef 851, Santiago, Chile
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Scotland, UK
| | - Valeria Razmilic
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, Universidad de Chile, Beauchef 851, Santiago, Chile
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
| | - Che Pan
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
| | - José M Igual
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), Salamanca, Spain
- Grupo de Interacción Planta-Microorganismo, Universidad de Salamanca, Unidad Asociada al CSIC, Spain
| | - Marcel Jaspars
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Scotland, UK
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
| | - Alan T Bull
- School of Biosciences, University of Kent Canterbury, Canterbury, UK
| | - Juan A Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, Universidad de Chile, Beauchef 851, Santiago, Chile
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon Tyne, UK
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11
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Carro L, Razmilic V, Nouioui I, Richardson L, Pan C, Golinska P, Asenjo JA, Bull AT, Klenk HP, Goodfellow M. Hunting for cultivable Micromonospora strains in soils of the Atacama Desert. Antonie van Leeuwenhoek 2018; 111:1375-1387. [PMID: 29480426 DOI: 10.1007/s10482-018-1049-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 02/16/2018] [Indexed: 02/01/2023]
Abstract
Innovative procedures were used to selectively isolate small numbers of Micromonospora strains from extreme hyper-arid and high altitude Atacama Desert soils. Micromonosporae were recognised on isolation plates by their ability to produce filamentous microcolonies that were strongly attached to the agar. Most of the isolates formed characteristic orange colonies that lacked aerial hyphae and turned black on spore formation, whereas those from the high altitude soil were dry, blue-green and covered by white aerial hyphae. The isolates were assigned to seven multi- and eleven single-membered groups based on BOX-PCR profiles. Representatives of the groups were assigned to either multi-membered clades that also contained marker strains or formed distinct phyletic lines in the Micromonospora 16S rRNA gene tree; many of the isolates were considered to be putatively novel species of Micromonospora. Most of the isolates from the high altitude soils showed activity against wild type strains of Bacillus subtilis and Pseudomonas fluorescens while those from the rhizosphere of Parastrephia quadrangulares and from the Lomas Bayas hyper-arid soil showed resistance to UV radiation.
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Affiliation(s)
- Lorena Carro
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK.
| | - Valeria Razmilic
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK.,Department of Chemical Engineering and Biotechnology, Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Chile, Beauchef 850, Santiago, Chile
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Lee Richardson
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Che Pan
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Patrycja Golinska
- Department of Microbiology, Nicolaus Copernicus University, Torun, Poland
| | - Juan A Asenjo
- Department of Chemical Engineering and Biotechnology, Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Chile, Beauchef 850, Santiago, Chile
| | - Alan T Bull
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
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