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Wentzien NM, Fernández-González AJ, Valverde-Corredor A, Lasa AV, Villadas PJ, Wicaksono WA, Cernava T, Berg G, Fernández-López M, Mercado-Blanco J. Pitting the olive seed microbiome. ENVIRONMENTAL MICROBIOME 2024; 19:17. [PMID: 38491515 PMCID: PMC10943921 DOI: 10.1186/s40793-024-00560-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/10/2024] [Indexed: 03/18/2024]
Abstract
BACKGROUND The complex and co-evolved interplay between plants and their microbiota is crucial for the health and fitness of the plant holobiont. However, the microbiota of the seeds is still relatively unexplored and no studies have been conducted with olive trees so far. In this study, we aimed to characterize the bacterial, fungal and archaeal communities present in seeds of ten olive genotypes growing in the same orchard through amplicon sequencing to test whether the olive genotype is a major driver in shaping the seed microbial community, and to identify the origin of the latter. Therefore, we have developed a methodology for obtaining samples from the olive seed's endosphere under sterile conditions. RESULTS A diverse microbiota was uncovered in olive seeds, the plant genotype being an important factor influencing the structure and composition of the microbial communities. The most abundant bacterial phylum was Actinobacteria, accounting for an average relative abundance of 41%. At genus level, Streptomyces stood out because of its potential influence on community structure. Within the fungal community, Basidiomycota and Ascomycota were the most abundant phyla, including the genera Malassezia, Cladosporium, and Mycosphaerella. The shared microbiome was composed of four bacterial (Stenotrophomonas, Streptomyces, Promicromonospora and Acidipropionibacterium) and three fungal (Malassezia, Cladosporium and Mycosphaerella) genera. Furthermore, a comparison between findings obtained here and earlier results from the root endosphere of the same trees indicated that genera such as Streptomyces and Malassezia were present in both olive compartments. CONCLUSIONS This study provides the first insights into the composition of the olive seed microbiota. The highly abundant fungal genus Malassezia and the bacterial genus Streptomyces reflect a unique signature of the olive seed microbiota. The genotype clearly shaped the composition of the seed's microbial community, although a shared microbiome was found. We identified genera that may translocate from the roots to the seeds, as they were present in both organs of the same trees. These findings set the stage for future research into potential vertical transmission of olive endophytes and the role of specific microbial taxa in seed germination, development, and seedling survival.
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Affiliation(s)
- Nuria M Wentzien
- Departamento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Antonio J Fernández-González
- Departamento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | | | - Ana V Lasa
- Departamento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Pablo J Villadas
- Departamento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, 8010, Graz, Austria
| | - Tomislav Cernava
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, SO17 1BJ, Southampton, UK
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, 8010, Graz, Austria
| | - Manuel Fernández-López
- Departamento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Jesús Mercado-Blanco
- Departamento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain.
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Khilyas IV, Markelova MI, Valeeva LR, Ivoilova TM, Shagimardanova E, Laikov AV, Elistratova AA, Berkutova ES, Lochnit G, Sharipova MR. Genomic insights and anti-phytopathogenic potential of siderophore metabolome of endolithic Nocardia mangyaensis NH1. Sci Rep 2024; 14:5676. [PMID: 38453942 PMCID: PMC10920908 DOI: 10.1038/s41598-024-54095-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/08/2024] [Indexed: 03/09/2024] Open
Abstract
Actinobacteria are one of the predominant groups that successfully colonize and survive in various aquatic, terrestrial and rhizhospheric ecosystems. Among actinobacteria, Nocardia is one of the most important agricultural and industrial bacteria. Screening and isolation of Nocardia related bacteria from extreme habitats such as endolithic environments are beneficial for practical applications in agricultural and environmental biotechnology. In this work, bioinformatics analysis revealed that a novel strain Nocardia mangyaensis NH1 has the capacity to produce structurally varied bioactive compounds, which encoded by non-ribosomal peptide synthases (NRPS), polyketide synthase (PKS), and post-translationally modified peptides (RiPPs). Among NRPS, five gene clusters have a sequence homology with clusters encoding for siderophore synthesis. We also show that N. mangyaensis NH1 accumulates both catechol- and hydroxamate-type siderophores simultaneously under iron-deficient conditions. Untargeted LC-MS/MS analysis revealed a variety of metabolites, including siderophores, lipopeptides, cyclic peptides, and indole-3-acetic acid (IAA) in the culture medium of N. mangyaensis NH1 grown under iron deficiency. We demonstrate that four CAS (chrome azurol S)-positive fractions display variable affinity to metals, with a high Fe3+ chelating capability. Additionally, three of these fractions exhibit antioxidant activity. A combination of iron scavenging metabolites produced by N. mangyaensis NH1 showed antifungal activity against several plant pathogenic fungi. We have shown that the pure culture of N. mangyaensis NH1 and its metabolites have no adverse impact on Arabidopsis seedlings. The ability of N. mangyaensis NH1 to produce siderophores with antifungal, metal-chelating, and antioxidant properties, when supplemented with phytohormones, has the potential to improve the release of macro- and micronutrients, increase soil fertility, promote plant growth and development, and enable the production of biofertilizers across diverse soil systems.
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Affiliation(s)
- Irina V Khilyas
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation.
| | - Maria I Markelova
- Laboratory of Multiomics Technologies of Living Systems, Institute Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Liia R Valeeva
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Tatiana M Ivoilova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Elena Shagimardanova
- Skolkovo Institute of Science and Technology, Moscow, Russian Federation
- Life Improvement by Future Technologies (LIFT) Center, Moscow, Russian Federation
| | - Alexander V Laikov
- Laboratory of Multiomics Technologies of Living Systems, Institute Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Anna A Elistratova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Ekaterina S Berkutova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Guenter Lochnit
- Protein Analytics, Institute of Biochemistry, Faculty of Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Margarita R Sharipova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
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Oren A, Göker M. Validation List no. 209. Valid publication of new names and new combinations effectively published outside the IJSEM. Int J Syst Evol Microbiol 2023; 73. [PMID: 36724088 DOI: 10.1099/ijsem.0.005709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
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Cai Q, Huang Y, Zhou L, Hu N, Liu Y, Guo F, Liu Q, Huang X, Zhang Y, Zeng L. A Complete Genome of Nocardia terpenica NC_YFY_NT001 and Pan-Genomic Analysis Based on Different Sources of Nocardia spp. Isolates Reveal Possibly Host-Related Virulence Factors. Infect Drug Resist 2022; 15:7259-7270. [PMID: 36536862 PMCID: PMC9758982 DOI: 10.2147/idr.s384673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/29/2022] [Indexed: 04/22/2024] Open
Abstract
OBJECTIVE We aimed to identify the possible virulence genes associated with Nocardia NC_YFY_NT001 isolated by ourselves and other Nocardia spp. METHODS The genome of Nocardia terpenica NC_YFY_NT001 was completed by using PacBio and Illumina platforms. A pan-genomic analysis was applied to selected complete Nocardia genomes. RESULTS Nocardia terpenica NC_YFY_NT001 can cause healthy mice death by tail intravenous injection. The genome of NT001 has one circular chromosome 8,850,000 bp and one circular plasmid 70,000 bp with ~68% GC content. The chromosome and plasmid encode 7914 and 80 proteins, respectively. Furthermore, a pan-genomic analysis showed a total of 45,825 gene clusters, then 304 core, 21,045 shell and 24,476 cloud gene clusters were classified using specific parameters. In addition, we found that catalases were more abundant in human isolates. Furthermore, we also found no significant differences in the MCE proteins between different strains from different sources. The pan-genomic analysis also showed that 67 genes could only be found in humoral isolates. ReX3 and DUF853 domain protein were found in all eight human isolates. The composition of unique genes in humoral isolate genomes indicated that the transcriptional regulators may be important when Nocardia invades the host, which allows them to survive in the new ecological system. CONCLUSION In this study, we confirmed that NT001 could cause infected animal death, and identified many possible virulence factors for our future studies. This study also provides new insight for our further study on Nocardia virulence mechanisms.
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Affiliation(s)
- Qinming Cai
- The First Affiliated Hospital of Nanchang University, School of Public Health, Nanchang University, Nanchang, People’s Republic of China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, People’s Republic of China
| | - Yongcheng Huang
- The First Affiliated Hospital of Nanchang University, School of Public Health, Nanchang University, Nanchang, People’s Republic of China
| | - Li Zhou
- The First Affiliated Hospital of Nanchang University, School of Public Health, Nanchang University, Nanchang, People’s Republic of China
| | - Niya Hu
- The First Affiliated Hospital of Nanchang University, School of Public Health, Nanchang University, Nanchang, People’s Republic of China
| | - Yanling Liu
- The First Affiliated Hospital of Nanchang University, School of Public Health, Nanchang University, Nanchang, People’s Republic of China
| | - Fujia Guo
- The First Affiliated Hospital of Nanchang University, School of Public Health, Nanchang University, Nanchang, People’s Republic of China
| | - Qiong Liu
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, People’s Republic of China
| | - Xiaotian Huang
- The First Affiliated Hospital of Nanchang University, School of Public Health, Nanchang University, Nanchang, People’s Republic of China
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, People’s Republic of China
| | - Yunyi Zhang
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, People’s Republic of China
| | - Lingbing Zeng
- The First Affiliated Hospital of Nanchang University, School of Public Health, Nanchang University, Nanchang, People’s Republic of China
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Gueddou A, Sbissi I, Louati M, Ghodhbane-Gtari F, Cherif-Silini H, Gtari M. Root Nodule Microsymbionts of Native Coriaria myrtifolia in Algeria. Microbiol Insights 2022; 15:11786361221133794. [PMID: 36325108 PMCID: PMC9619857 DOI: 10.1177/11786361221133794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 10/01/2022] [Indexed: 11/06/2022] Open
Abstract
Coriaria myrtifolia occurs as natural flora of warm temperate
climates of northern Algeria which commonly found in hedges, forest and ravine
edges. This actinorhizal species was known to establish a mutualistic symbiosis
with members of phylogenetic cluster 2 (including strains associated to
Coriaria spp., Ceanothus,
Datiscaceae, and Dryadoideae) within the
genus Frankia. Attempts to isolate C.
myrtifolia microsymbionts from native plants growing in 4 locations
in Algeria permitted to only recover asymbiotic Frankia strains
(unable to reestablish nodulation and to fix nitrogen) from phylogenetic cluster
4 and several non-Frankia actinobacteria including members of
Micrococcus, Micromonospora, Nocardia, Plantactinospora,
and Streptomyces genera. The biodiversity of
Frankia microsymbionts of C. myrtifolia
root nodules was assessed using PCR-amplification followed by partial nucleotide
sequencing of glnA1 (glutamine synthetase type 1) gene. On the
12 different glnA1 gene sequences obtained in this study, 9
were detected for the first time, and were mainly closelyrelated to
Mediterranean genotypes previously described in the Grand Maghreb countries
(Morocco and Tunisia) and in Europe (France) but without clear separations from
other cluster 2 genotypes.
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Affiliation(s)
- Abdellatif Gueddou
- USCR Bactériologie Moléculaire &
Génomique, Institut National des Sciences Appliquées et de Technologie, Université
de Carthage, Tunisia
| | - Imed Sbissi
- LR Ecologie Pastorale, Institut des
Régions Arides, Médenine, Tunisia
| | - Moussa Louati
- USCR Bactériologie Moléculaire &
Génomique, Institut National des Sciences Appliquées et de Technologie, Université
de Carthage, Tunisia
| | - Faten Ghodhbane-Gtari
- USCR Bactériologie Moléculaire &
Génomique, Institut National des Sciences Appliquées et de Technologie, Université
de Carthage, Tunisia,Institut Supérieur de Biotechnologie de
Sidi Thabet, Université la Manouba, Tunisia
| | - Hafsa Cherif-Silini
- LR Microbiologie Appliquée, FNLS,
Université Ferhat Abbas Alegria, Sétif, Alegria
| | - Maher Gtari
- USCR Bactériologie Moléculaire &
Génomique, Institut National des Sciences Appliquées et de Technologie, Université
de Carthage, Tunisia,Maher Gtari, Universite de Carthage,
Institut National des Sciences Appliquées et de Technologie Centre Urbain Nord
BP 676-1080 Tunis Cedex, Tunis, 1054, Tunisia.
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Li Z, Wen W, Qin M, He Y, Xu D, Li L. Biosynthetic Mechanisms of Secondary Metabolites Promoted by the Interaction Between Endophytes and Plant Hosts. Front Microbiol 2022; 13:928967. [PMID: 35898919 PMCID: PMC9309545 DOI: 10.3389/fmicb.2022.928967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/21/2022] [Indexed: 12/28/2022] Open
Abstract
Endophytes is a kind of microorganism resource with great potential medicinal value. The interactions between endophytes and host not only promote the growth and development of each other but also drive the biosynthesis of many new medicinal active substances. In this review, we summarized recent reports related to the interactions between endophytes and hosts, mainly regarding the research progress of endophytes affecting the growth and development of host plants, physiological stress and the synthesis of new compounds. Then, we also discussed the positive effects of multiomics analysis on the interactions between endophytes and their hosts, as well as the application and development prospects of metabolites synthesized by symbiotic interactions. This review may provide a reference for the further development and utilization of endophytes and the study of their interactions with their hosts.
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Affiliation(s)
- Zhaogao Li
- Department of Cell Biology, Zunyi Medical University, Zunyi, China
| | - Weie Wen
- Department of Cell Biology, Zunyi Medical University, Zunyi, China
| | - Ming Qin
- Department of Immunology, Zunyi Medical University, Zunyi, China
| | - Yuqi He
- Engineering Research Center of Key Technology Development for Gui Zhou Provincial Dendrobium Nobile Industry, Zunyi Medical University, Zunyi, China
- *Correspondence: Yuqi He,
| | - Delin Xu
- Department of Cell Biology, Zunyi Medical University, Zunyi, China
- Delin Xu,
| | - Lin Li
- Department of Cell Biology, Zunyi Medical University, Zunyi, China
- Lin Li,
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7
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Nouioui I, Pötter G, Jando M, Goodfellow M. Nocardia noduli sp. nov., a novel actinobacterium with biotechnological potential. Arch Microbiol 2022; 204:260. [PMID: 35419662 PMCID: PMC9007811 DOI: 10.1007/s00203-022-02878-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 11/25/2022]
Abstract
A genome-based polyphasic study was undertaken to establish the taxonomic status of an actinobacterium strain isolated from an actinorhizal root nodule. Strain ncl1T was found to have chemotaxonomic, cultural and morphological properties characteristic of members of the genus Nocardia. The strain was closely related to Nocardia aurea in the phylogenetic trees based on 16S rRNA gene and genome sequences. The draft genome of the strain is 8.9 Mbp in size, has a genomic DNA G + C content of 67.0% and was predicted to contain at least 19 biosynthetic gene clusters encoding for specialized metabolites. Strain ncl1T was distinguished from its closest neighbour, N. aurea DSM 103986T, by a broad range of phenotypic properties and by low average nucleotide identity and digital DNA-DNA hybridization scores. Consequently, the strain represents a novel Nocardia species for which the name Nocardia noduli sp. nov. is proposed. The type strain is ncl1T (CECT 30123T = DSM 110878T). The present study provides further evidence that actinorhizal nodules are a source of novel species of Nocardia.
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Affiliation(s)
- Imen Nouioui
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124, Braunschweig, Germany.
| | - Gabriele Pötter
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124, Braunschweig, Germany
| | - Marlen Jando
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124, Braunschweig, Germany
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
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