Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
7.8
5.6
Journals
IJMS
Special Issues
Bacteria Present in Nitrogen-Fixing Nodules
ijms-logo
Submit to IJMS Review for IJMS Propose a Special Issue

Journal Menu

► Journal Menu

Journal Browser

► Journal Browser
share announcement

Bacteria Present in Nitrogen-Fixing Nodules

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (15 May 2023) | Viewed by 6186

Special Issue Editor

Prof. Dr. Katharina Pawlowski

E-Mail Website
Guest Editor
Department of Ecology, Environment and Plant Sciences, Stockholm University, 10691 Stockholm, Sweden
Interests: actinorhizal nodules; legume nodules; Frankia evolution; arbuscular mycorrhiza; plant endophytes

Special Issue Information

Dear Colleagues,

Two groups of nitrogen-fixing soil bacteria can enter root nodule symbioses with members of Fabales, Fagales, Cucurbitales, and Rosales: a diverse group of alpha- and beta-proteobacteria, collectively called rhizobia can enter symbioses with legumes and Parasponia (Cannabaceae, Rosales), while actinobacteria of the genus Frankia can enter symbioses with actinorhizal plants. Root nodule symbioses render the host plants independent of soil nitrogen and, thus, in the case of agricultural plants, of nitrogen fertilizer.

Rhizobia and Frankia strains are not the only bacteria hosted in these nodules. Apart from the dominant nitrogen-fixing microsymbionts, bacteria from several different taxa have been isolated repeatedly from surface-sterilized, nitrogen-fixing root nodules induced by rhizobia or Frankia strains. Some of those bacteria have even been detected inside infected cells. It is known that some soil bacteria improve nodulation, e.g., by interfering with plant ethylene production. In this context, we ask the following questions surrounding their ecological role: Are there other ways for nodule bacteria to improve symbiosis? Conversely, can we identify bacteria which simply exploit the nodule as an ecological niche?

This Special Issue will combine reviews and research articles addressing novel questions in the context of nitrogen-fixing root nodule symbioses. Suitable topics include but are not limited to the following themes and questions:

  • Analysis of nodule metagenomes, or 16S profiles, of surface-sterilized legume or actinorhizal nodules: which bacterial groups are commonly present? Which factors determine the composition of the non-rhizobial or non-Frankia communities?
  • Which soil bacteria improve nodulation, and which soil bacteria end up inside nodule tissues? Do these groups overlap?
  • How do non-rhizobia in legume nodules—or non-Frankia bacteria in actinorhizal nodules—affect the nodule metabolome or the nodule transcriptome?
  • Is there evidence for interactions between nitrogen-fixing microsymbionts and other nodule bacteria?

Moreover, the methodological aspect should not be neglected: which DNA isolation methods are best suited to explore the diversity of bacteria in nodules?

Kind Regards,
Prof. Dr. Katharina Pawlowski
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • legume
  • actinorhiza
  • root nodule
  • rhizobia
  • Frankia
  • metagenome
  • co-inoculation
  • endophytic
  • PGPB

Published Papers (3 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

30 pages, 2885 KiB  
Article
Pleiotropic Effects of PhaR Regulator in Bradyrhizobium diazoefficiens Microaerobic Metabolism
by Juan I. Quelas, Juan J. Cabrera, Rocío Díaz-Peña, Lucía Sánchez-Schneider, Andrea Jiménez-Leiva, Germán Tortosa, María J. Delgado, M. Julia Pettinari, Aníbal R. Lodeiro, Coral del Val and Socorro Mesa
Int. J. Mol. Sci. 2024, 25(4), 2157; https://doi.org/10.3390/ijms25042157 - 10 Feb 2024
Viewed by 928
Abstract
Bradyrhizobium diazoefficiens can live inside soybean root nodules and in free-living conditions. In both states, when oxygen levels decrease, cells adjust their protein pools by gene transcription modulation. PhaR is a transcription factor involved in polyhydroxyalkanoate (PHA) metabolism but also plays a role [...] Read more.
Bradyrhizobium diazoefficiens can live inside soybean root nodules and in free-living conditions. In both states, when oxygen levels decrease, cells adjust their protein pools by gene transcription modulation. PhaR is a transcription factor involved in polyhydroxyalkanoate (PHA) metabolism but also plays a role in the microaerobic network of this bacterium. To deeply uncover the function of PhaR, we applied a multipronged approach, including the expression profile of a phaR mutant at the transcriptional and protein levels under microaerobic conditions, and the identification of direct targets and of proteins associated with PHA granules. Our results confirmed a pleiotropic function of PhaR, affecting several phenotypes, in addition to PHA cycle control. These include growth deficiency, regulation of carbon and nitrogen allocation, and bacterial motility. Interestingly, PhaR may also modulate the microoxic-responsive regulatory network by activating the expression of fixK2 and repressing nifA, both encoding two transcription factors relevant for microaerobic regulation. At the molecular level, two PhaR-binding motifs were predicted and direct control mediated by PhaR determined by protein-interaction assays revealed seven new direct targets for PhaR. Finally, among the proteins associated with PHA granules, we found PhaR, phasins, and other proteins, confirming a dual function of PhaR in microoxia. Full article
(This article belongs to the Special Issue Bacteria Present in Nitrogen-Fixing Nodules)
►▼ Show Figures

Figure 1

16 pages, 3182 KiB  
Article
Frankia alni Carbonic Anhydrase Regulates Cytoplasmic pH of Nitrogen-Fixing Vesicles
by Petar Pujic, Lorena Carro, Pascale Fournier, Jean Armengaud, Guylaine Miotello, Nathalie Dumont, Caroline Bourgeois, Xavier Saupin, Patrick Jame, Gabriela Vuletin Selak, Nicole Alloisio and Philippe Normand
Int. J. Mol. Sci. 2023, 24(11), 9162; https://doi.org/10.3390/ijms24119162 - 23 May 2023
Viewed by 1384
Abstract
A phyloprofile of Frankia genomes was carried out to identify those genes present in symbiotic strains of clusters 1, 1c, 2 and 3 and absent in non-infective strains of cluster 4. At a threshold of 50% AA identity, 108 genes were retrieved. Among [...] Read more.
A phyloprofile of Frankia genomes was carried out to identify those genes present in symbiotic strains of clusters 1, 1c, 2 and 3 and absent in non-infective strains of cluster 4. At a threshold of 50% AA identity, 108 genes were retrieved. Among these were known symbiosis-associated genes such as nif (nitrogenase), and genes which are not know as symbiosis-associated genes such as can (carbonic anhydrase, CAN). The role of CAN, which supplies carbonate ions necessary for carboxylases and acidifies the cytoplasm, was thus analyzed by staining cells with pH-responsive dyes; assaying for CO2 levels in N-fixing propionate-fed cells (that require a propionate-CoA carboxylase to yield succinate-CoA), fumarate-fed cells and N-replete propionate-fed cells; conducting proteomics on N-fixing fumarate and propionate-fed cells and direct measurement of organic acids in nodules and in roots. The interiors of both in vitro and nodular vesicles were found to be at a lower pH than that of hyphae. CO2 levels in N2-fixing propionate-fed cultures were lower than in N-replete ones. Proteomics of propionate-fed cells showed carbamoyl-phosphate synthase (CPS) as the most overabundant enzyme relative to fumarate-fed cells. CPS combines carbonate and ammonium in the first step of the citrulline pathway, something which would help manage acidity and NH4+. Nodules were found to have sizeable amounts of pyruvate and acetate in addition to TCA intermediates. This points to CAN reducing the vesicles’ pH to prevent the escape of NH3 and to control ammonium assimilation by GS and GOGAT, two enzymes that work in different ways in vesicles and hyphae. Genes with related functions (carboxylases, biotin operon and citrulline-aspartate ligase) appear to have undergone decay in non-symbiotic lineages. Full article
(This article belongs to the Special Issue Bacteria Present in Nitrogen-Fixing Nodules)
►▼ Show Figures

Figure 1

21 pages, 3512 KiB  
Article
Microbiome of Nodules and Roots of Soybean and Common Bean: Searching for Differences Associated with Contrasting Performances in Symbiotic Nitrogen Fixation
by Flávia Raquel Bender, Leonardo Cardoso Alves, João Fernando Marques da Silva, Renan Augusto Ribeiro, Giuliano Pauli, Marco Antonio Nogueira and Mariangela Hungria
Int. J. Mol. Sci. 2022, 23(19), 12035; https://doi.org/10.3390/ijms231912035 - 10 Oct 2022
Cited by 11 | Viewed by 3201
Abstract
Biological nitrogen fixation (BNF) is a key process for the N input in agriculture, with outstanding economic and environmental benefits from the replacement of chemical fertilizers. However, not all symbioses are equally effective in fixing N2, and a major example relies [...] Read more.
Biological nitrogen fixation (BNF) is a key process for the N input in agriculture, with outstanding economic and environmental benefits from the replacement of chemical fertilizers. However, not all symbioses are equally effective in fixing N2, and a major example relies on the high contribution associated with the soybean (Glycine max), contrasting with the low rates reported with the common bean (Phaseolus vulgaris) crop worldwide. Understanding these differences represents a major challenge that can help to design strategies to increase the contribution of BNF, and next-generation sequencing (NGS) analyses of the nodule and root microbiomes may bring new insights to explain differential symbiotic performances. In this study, three treatments evaluated in non-sterile soil conditions were investigated in both legumes: (i) non-inoculated control; (ii) inoculated with host-compatible rhizobia; and (iii) co-inoculated with host-compatible rhizobia and Azospirillum brasilense. In the more efficient and specific symbiosis with soybean, Bradyrhizobium presented a high abundance in nodules, with further increases with inoculation. Contrarily, the abundance of the main Rhizobium symbiont was lower in common bean nodules and did not increase with inoculation, which may explain the often-reported lack of response of this legume to inoculation with elite strains. Co-inoculation with Azospirillum decreased the abundance of the host-compatible rhizobia in nodules, probably because of competitiveness among the species at the rhizosphere, but increased in root microbiomes. The results showed that several other bacteria compose the nodule microbiomes of both legumes, including nitrogen-fixing, growth-promoters, and biocontrol agents, whose contribution to plant growth deserves further investigation. Several genera of bacteria were detected in root microbiomes, and this microbial community might contribute to plant growth through a variety of microbial processes. However, massive inoculation with elite strains should be better investigated, as it may affect the root microbiome, verified by both relative abundance and diversity indices, that might impact the contribution of microbial processes to plant growth. Full article
(This article belongs to the Special Issue Bacteria Present in Nitrogen-Fixing Nodules)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-3
Back to TopTop