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Becker R, Ulrich K, Behrendt U, Schneck V, Ulrich A. Genomic Characterization of Aureimonas altamirensis C2P003-A Specific Member of the Microbiome of Fraxinus excelsior Trees Tolerant to Ash Dieback. PLANTS (BASEL, SWITZERLAND) 2022; 11:3487. [PMID: 36559599 PMCID: PMC9781493 DOI: 10.3390/plants11243487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Some European ash trees show tolerance towards dieback caused by the invasive pathogen Hymenoscyphus fraxineus. The microbiome of these trees harbours a range of specific bacterial groups. One of these groups belonging to the species Aureimonas altamirensis was studied in detail by genome analysis and a plant inoculation trial. The strain group was shown to be phylogenetically distinct from clinical isolates by 16S rRNA analysis and phylogenomics. Genome analysis of a representative strain C2P003 resulted in a large number of unique gene sequences in comparison to other well-studied strains of the species. A functional analysis of the genome revealed features associated with the synthesis of exopolysaccharides, protein secretion and biofilm production as well as genes for stress adaptation, suggesting the ability of C2P003 to effectively colonize ash leaves. The inoculation of ash seedlings with C2P003 showed a significant positive effect on the plant health of the seedlings that were exposed to H. fraxineus infection. This effect was maintained over a period of three years and was accompanied by a significant shift in the bacterial microbiome composition one year after inoculation. Overall, the results indicate that C2P003 may suppress H. fraxineus in or on ash leaves via colonization resistance or indirectly by affecting the microbiome.
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Affiliation(s)
- Regina Becker
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), 15374 Müncheberg, Germany
| | - Kristina Ulrich
- Institute of Forest Genetics, Johann Heinrich von Thünen Institute, 15377 Waldsieversdorf, Germany
| | - Undine Behrendt
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), 15374 Müncheberg, Germany
| | - Volker Schneck
- Institute of Forest Genetics, Johann Heinrich von Thünen Institute, 15377 Waldsieversdorf, Germany
| | - Andreas Ulrich
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), 15374 Müncheberg, Germany
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Silva R, Padovani K, Góes F, Alves R. geneRFinder: gene finding in distinct metagenomic data complexities. BMC Bioinformatics 2021; 22:87. [PMID: 33632132 PMCID: PMC7905635 DOI: 10.1186/s12859-021-03997-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 02/04/2021] [Indexed: 12/01/2022] Open
Abstract
Background Microbes perform a fundamental economic, social, and environmental role in our society. Metagenomics makes it possible to investigate microbes in their natural environments (the complex communities) and their interactions. The way they act is usually estimated by looking at the functions they play in those environments and their responsibility is measured by their genes. The advances of next-generation sequencing technology have facilitated metagenomics research however it also creates a heavy computational burden. Large and complex biological datasets are available as never before. There are many gene predictors available that can aid the gene annotation process though they lack handling appropriately metagenomic data complexities. There is no standard metagenomic benchmark data for gene prediction. Thus, gene predictors may inflate their results by obfuscating low false discovery rates. Results We introduce geneRFinder, an ML-based gene predictor able to outperform state-of-the-art gene prediction tools across this benchmark by using only one pre-trained Random Forest model. Average prediction rates of geneRFinder differed in percentage terms by 54% and 64%, respectively, against Prodigal and FragGeneScan while handling high complexity metagenomes. The specificity rate of geneRFinder had the largest distance against FragGeneScan, 79 percentage points, and 66 more than Prodigal. According to McNemar’s test, all percentual differences between predictors performances are statistically significant for all datasets with a 99% confidence interval. Conclusions We provide geneRFinder, an approach for gene prediction in distinct metagenomic complexities, available at gitlab.com/r.lorenna/generfinder and https://osf.io/w2yd6/, and also we provide a novel, comprehensive benchmark data for gene prediction—which is based on The Critical Assessment of Metagenome Interpretation (CAMI) challenge, and contains labeled data from gene regions—available at https://sourceforge.net/p/generfinder-benchmark.
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Affiliation(s)
- Raíssa Silva
- Vale Institute of Technology, Boaventura da Silva, 955, Belém, BR, 66055-090, Brazil.,PPGCC, Federal University of Pará, Augusto Corrêa, 01, Belém, BR, 66075-110, Brazil
| | - Kleber Padovani
- PPGCC, Federal University of Pará, Augusto Corrêa, 01, Belém, BR, 66075-110, Brazil
| | - Fabiana Góes
- ICMC, University of São Paulo, Trab. São Carlense, 400, São Carlos, BR, 13566-590, Brazil
| | - Ronnie Alves
- Vale Institute of Technology, Boaventura da Silva, 955, Belém, BR, 66055-090, Brazil. .,PPGCC, Federal University of Pará, Augusto Corrêa, 01, Belém, BR, 66075-110, Brazil.
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Kokane SB, Bhose S, Kokane A, Gubyad M, Ghosh DK. Molecular detection, identification, and sequence analysis of ' Candidatus Liberibacter asiaticus' associated with Huanglongbing disease of citrus in North India. 3 Biotech 2020; 10:341. [PMID: 32714736 DOI: 10.1007/s13205-020-02334-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 07/11/2020] [Indexed: 01/20/2023] Open
Abstract
Huanglongbing (HLB, Citrus greening), caused by a phloem-limited fastidious gram-negative bacterium, "Candidatus Liberibacter spp.", is one of the devastating diseases of citrus worldwide. The pathogen belongs to the alpha-proteobacteria group and is classified on the basis of its geographical origin and 16S rRNA sequence diversity. Although the disease has been reported from all citrus growing states of India, the status and the molecular variability among the isolates from the Northern part of the country is unknown. A total of five different HLB isolates originating from Northern India showing variable symptoms were studied. The genomic regions of four different genes, i.e., 16S rRNA, intergenic 16S/23S rRNA spacer region, rplA-rplJ, and CLIBASIA_01645 were amplified by PCR, sequenced, and variations in these sequences were assessed. Analysis of 16S rRNA clearly indicated that all five isolates fit in to 'Candidatus Liberibacter asiaticus' (CLas) group. However, 16S/23S rRNA intergenic spacer region-based analysis failed to segregate these isolates beyond species level. Sequence analysis of rplA-rplJ gene and CLIBASIA_01645 loci also confirmed the existence of diversity among the 'CLas' in the surveyed areas. Further, 16S rRNA and rplA-rplJ-based SNP analysis revealed that some isolates segregated into three new lineages, two on the basis of 16Sr (16Sr-XV and 16Sr-XVI), and one based on β-rp (rp-IV), respectively. A tandem repeat number (TRN) at CLIBASIA_01645 region were TRN = 5, 6 and 13; with TRN = 6 being common in three 'CLas' isolates. Overall, the study demonstrated that all examined five HLB isolates belonged to 'CLas' group. However, these isolates showed distinct sequence variability in three out of four genomic regions. The results provide a robust framework for understanding differences in pathogenicity among different HLB isolates as it is plausibly related to their genomic variation, and evolutionary history.
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Comin HB, Domingues R, Gaspar EB, Santos JRGDL, Cardoso FF. Genetic differences among Moraxella bovis and Moraxella bovoculi isolates from infectious bovine keratoconjunctivitis (IBK) outbreaks in southern Brazil. Genet Mol Biol 2020; 43:e20180380. [PMID: 32478794 PMCID: PMC7271659 DOI: 10.1590/1678-4685-gmb-2018-0380] [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: 01/16/2019] [Accepted: 06/28/2019] [Indexed: 12/05/2022] Open
Abstract
The objective of this study was to evaluate the genetic diversity of
Moraxella bovis and Moraxella bovoculi
bacteria isolated from infectious bovine keratoconjunctivitis (IBK) outbreaks in
the state of Rio Grande do Sul, Brazil. The genetic diversity among
Moraxella spp. was evaluated by RAPD-PCR, JWP1-JWOPA07-PCR,
ERIC-PCR and by sequencing the 16S-23S intergenic regions. Based on the
dendrogram, two genetically differentiated clades were observed; 14 isolates
were classified as M. bovis and 17 as M.
bovoculi. Genetic distances between the M. bovis
samples ranged from 0.0379 to 0.4285, while for M. bovoculi the
dissimilarities ranged from zero to 0.7297. Alternatively, based on sequencing
analyses of the 16S-23S intergenic region, M. bovis and
M. bovoculi isolates were grouped into the same two
different clades, but it was not possible to differentiate between isolates
within clades. PCR techniques were demonstrated to be a satisfactory tool to
unravel the genetic variability among Moraxella spp., while
sequencing of the 16S-23S intergenic region was only able to differentiate two
species of the Moraxella genus. Despite sampling geographically
close regions, we demonstrate considerable genetic diversity in M.
bovis and M. bovoculi strains and genetically
distinct M. bovis strains co-infecting the same animal.
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Affiliation(s)
- Helena Brocardo Comin
- Universidade Federal de Pelotas, Programa de Pós-Graduação em Zootecnia, Pelotas, RS, Brazil
| | | | | | | | - Fernando Flores Cardoso
- Embrapa Pecuária Sul, Bagé, RS, Brazil.,Universidade Federal de Pelotas, Departamento de Zootecnia, Pelotas, RS, Brazil
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Joglekar P, Mesa CP, Richards VA, Polson SW, Wommack KE, Fuhrmann JJ. Polyphasic analysis reveals correlation between phenotypic and genotypic analysis in soybean bradyrhizobia (Bradyrhizobium spp.). Syst Appl Microbiol 2020; 43:126073. [PMID: 32139173 PMCID: PMC7894101 DOI: 10.1016/j.syapm.2020.126073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 02/07/2020] [Accepted: 02/09/2020] [Indexed: 10/25/2022]
Abstract
Soybean bradyrhizobia (Bradyrhizobium spp.) are bacteria that fix atmospheric nitrogen within the root nodules of soybean, a crop critical for meeting global nutritional protein demand. Members of this group differ in symbiotic effectiveness, and historically both phenotypic and genotypic approaches have been used to assess bradyrhizobial diversity. However, agreement between various approaches of assessment is poorly known. A collection (n=382) of soybean bradyrhizobia (Bradyrhizobium japonicum, B. diazoefficiens, and B. elkanii) were characterized by Internal Transcribed Spacer - Restriction Fragment Length Polymorphism (ITS-RFLP), cellular fatty acid composition (fatty acid methyl esters, FAME), and serological reactions to assess agreement between phenotypic and genotypic methods. Overall, 76% of the accessions demonstrated identical clustering with each of these techniques. FAME was able to identify all 382 accessions, whereas 14% were non-reactive serologically. One ITS-RFLP group, containing 36 Delaware isolates, produced multiple ITS amplicons indicating they possess multiple ribosomal RNA (rrn) operons. Cloning and sequencing revealed that these strains contained as many as three heterogenous rrn operons, a trait previously unknown in bradyrhizobia. A representative subset of 96 isolates was further characterized using 16S rRNA and Internal Transcribed Spacer (ITS) amplicon sequencing. ITS sequences showed better inter- and intra-species discrimination (65-99% identity) than 16S sequences (96-99% identity). This study shows that phenotypic and genotypic approaches are strongly correlated at the species level but should be approached with caution. We also suggest using combined 16S and ITS genotyping data to obtain better inter- and intra-species resolution in bradyrhizobia classification.
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Affiliation(s)
- P Joglekar
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - C P Mesa
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware, USA
| | - V A Richards
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - S W Polson
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA; Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
| | - K E Wommack
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA; Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware, USA; Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
| | - J J Fuhrmann
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA; Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware, USA.
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Fossou RK, Ziegler D, Zézé A, Barja F, Perret X. Two Major Clades of Bradyrhizobia Dominate Symbiotic Interactions with Pigeonpea in Fields of Côte d'Ivoire. Front Microbiol 2016; 7:1793. [PMID: 27891120 PMCID: PMC5104742 DOI: 10.3389/fmicb.2016.01793] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 10/25/2016] [Indexed: 12/03/2022] Open
Abstract
In smallholder farms of Côte d'Ivoire, particularly in the northeast of the country, Cajanus cajan (pigeonpea) has become an important crop because of its multiple beneficial facets. Pigeonpea seeds provide food to make ends meet, are sold on local markets, and aerial parts serve as forage for animals. Since it fixes atmospheric nitrogen in symbiosis with soil bacteria collectively known as rhizobia, C. cajan also improves soil fertility and reduces fallow time. Yet, seed yields remain low mostly because farmers cannot afford chemical fertilizers. To identify local rhizobial strains susceptible to be used as bio-inoculants to foster pigeonpea growth, root nodules were collected in six fields of three geographically distant regions of Côte d'Ivoire. Nodule bacteria were isolated and characterized using various molecular techniques including matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry (MS) and DNA sequencing. These molecular analyses showed that 63 out of 85 nodule isolates belonged to two major clades of bradyrhizobia, one of which is known as the Bradyrhizobium elkanii super clade. Phylogenies of housekeeping (16S-ITS-23S, rpoB) and symbiotic (nifH) genes were not always congruent suggesting that lateral transfer of nitrogen fixation genes also contributed to define the genome of these bradyrhizobial isolates. Interestingly, no field-, plant-, or cultivar-specific effect was found to shape the profiles of symbiotic strains. In addition, nodule isolates CI-1B, CI-36E, and CI-41A that belong to distinct species, showed similar symbiotic efficiencies suggesting that any of these strains might serve as a proficient inoculant for C. cajan.
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Affiliation(s)
- Romain K Fossou
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva Geneva, Switzerland
| | - Dominik Ziegler
- Microbiology Unit, Department of Botany and Plant Biology, University of GenevaGeneva, Switzerland; Mabritec AGRiehen, Switzerland
| | - Adolphe Zézé
- Laboratoire de Biotechnologies Végétale et Microbienne, Unité Mixte de Recherche et d'Innovation en Sciences Agronomiques et Génie Rural, Institut National Polytechnique Félix Houphouët-Boigny (INPHB) Yamoussoukro, Côte d'Ivoire
| | - François Barja
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva Geneva, Switzerland
| | - Xavier Perret
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva Geneva, Switzerland
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