Draft genome sequences of four potential new species of the genus Bradyrhizobium isolated from root nodules of native legumes in Costa Rican forests

  1. Rachelle Fernández-Vargas
  2. Sara Jiménez-Alpízar
  3. Valeria Leandro-Arce
  4. Bradd Mendoza
  5. Keilor Rojas-Jimenez

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Abstract

Here we report the draft genome sequences of four Bradyrhizobium spp. isolates obtained from root nodules of the native legumes Pentaclethra macroloba, Chamaecrista nictitans, Erythrina fusca, and Zygia engelsingii in tropical forests of Costa Rica. Genomes ranged from 8.6 to 9.8 Mb with GC contents between 62.8% and 63.8%. Phylogenomic analysis, along with Average Nucleotide Identity (ANI) and digital DNA-DNA hybridization (dDDH) comparisons, confirmed these isolates represent potential new species. ANI values ranged from 88.3% to 90.3%, and dDDH values from 28.8% to 41.8%, compared to their closest Bradyrhizobium sp. references. Functional annotation revealed some genes related to nitrogen fixation (nifA, nifB, nifH) and nodulation capacity (nodB, nodC, nodJ). These results provide insights into the diversity and symbiotic capabilities of Bradyrhizobium in tropical ecosystems.

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  1. Access Microbiology

    I am pleased to tell you that your article has now been accepted for publication in Access Microbiology. The work presented is clear and the arguments well formed and this study will be a valuable contribution to the existing literature. You have addressed the reviewers’ comments sufficiently after revision. The raw data are accessible and will be helpful for the community.

  2. Version published to 10.1099/acmi.0.000990.v2 on Access Microbiology
  3. Access Microbiology

    This study would be a valuable contribution to the existing literature. This is a study that would be of interest to the field and community. The reviewers have highlighted major concerns with the work presented. Please ensure that you address their comments. Please include more rigour criteria and resources in your methods section, as highlighted by the SciScore reports. Including RRIDs and negative statements to explain why things were not performed should increase the rigour and reproducibility of your work. You can find tips on how to improve your article here: https://sciscore.com/reports/Core-Report.php

  4. Access Microbiology

    Comments to Author

    The ms by Fernández-Vargas et al describes the genomic sequences of 4 new Bradyrhizobium strains from the tropical forest in Costa Rica, which are compared to other Bradyrhizobium species suggesting they probably represent new species. I have just one small comment Line 122 Referencias should be References.

    Please rate the manuscript for methodological rigour

    Very good

    Please rate the quality of the presentation and structure of the manuscript

    Very good

    To what extent are the conclusions supported by the data?

    Strongly support

    Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?

    No

    Is there a potential financial or other conflict of interest between yourself and the author(s)?

    No

    If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?

    Yes

  5. Access Microbiology

    Comments to Author

    Draft genome sequences of four potential new species of the genus Bradyrhizobium isolated from root nodules of native legumes in Costa Rican forests The manuscript shows four draft genome sequences of Bradyrhizobium strains isolated from poorly studied leguminous species of tropical Costa Rican forests. Based on phylogenomic, ANI, and dDDH comparisons, the strains are distant from other Bradyrhizobium species available, indicating putative new species. However, further studies are needed to elucidate this hypothesis. Line 26: The term "references" is confusing regarding other validly published species. Replace "closest Bradyrhizobium sp. references" with "closest Bradyrhizobium species". Lines 30-37: Please cite each strain's specific accession number of SRA, genomic sequences, and 16S rRNA sequences. Lines 43-44: The strains were isolated from nodules of leguminous plants in Costa Rica, right? It would be interesting to specify it in this sentence. Lines 48-50: It would be interesting to include information about the soils where the plants were growing in the nurseries, e.g. if it was previously inoculated, if it is from an agronomic or preservation area, city, or state. Line 53: Superscript -1 and -2 from "(10-1 and 10-2)". Line 62-68: Specify the versions used for fastp, Seqtk, Quast, and CheckM2 programs. Line 70-73: This step of GenFlow pipeline is confusing. Is it used to choose the NCBI closest genomic sequences to your sequences? Please rewrite to improve the sentence's clarity. As you indicated that strains under study are putative new species, it would be interesting to use only type strains of described species of Bradyrhizobium. Line 74-75: Explain the geometric and functional index threshold. Lines 70-78: Include the version of programs used in this analysis. Table 1: Concerning N50, length, and number of CDS rows, separate the numbers with a dot instead of a space. Table 1: Fix the scientific names as follows: Bradyrhizobium betae (italic) PL7HG1 (not italic) T (T=type strain, superscript). Figure 1: Before Figure 1, it would be interesting to construct a phylogenetic tree using 16S rRNA sequences with type strains of all Bradyrhizobium species, since you have this data. Figure 1: When the sequence is from a type strain, indicate with a T superscript after the culture collection accession number. Figure 1: When the sequence is from a not validly published species, use a double quotation mark to identify them, e.g. "Bradyrhizobium forestalis" INPA54B Figure 1: Change the bootstrap values to percentages in the figure legend and tree nodes. Lines 88-94: Include the number of gene sequences used to construct the phylogenetic tree. Lines 91-93: How did you select the closest type strains used to construct the phylogenetic tree? Currently, there is at least one genomic sequence of a type strain for 63 of the 89 described Bradyrhizobium species (available on LPSN). I suggest constructing a phylogenetic tree using all these sequences, improving the robustness of the analysis. Lines 97-99: Construct a table showing the ANI and dDDH including the comparisons between strains under study and the closest species in the phylogenetic tree, instead of keeping the "ANI value for the most related species (%)" and "dDHH (d4 in %)" rows in table 1. Lines 97-99: Include a rationale the strains under study are considered putative new species based on ANI and dDDH comparisons. Line 100: Replace "varying" with "various".

    Please rate the manuscript for methodological rigour

    Satisfactory

    Please rate the quality of the presentation and structure of the manuscript

    Good

    To what extent are the conclusions supported by the data?

    Partially support

    Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?

    No

    Is there a potential financial or other conflict of interest between yourself and the author(s)?

    No

    If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?

    Yes

  6. Version published to 10.1099/acmi.0.000990.v1 on Access Microbiology