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Microbe-Host Interaction
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Microbe-Host Interaction

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: closed (20 September 2022) | Viewed by 8019

Special Issue Editor

Prof. Dr. Zengtao Zhong

E-Mail Website
Guest Editor
Department of Microbiology, School of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
Interests: rhizobium; bacteria–plant interactions; horizontal gene transfer; quorum sensing; biofilm

Special Issue Information

Dear Colleagues,

More than a century ago, Robert Koch illuminated that some infectious diseases are caused by microbes. At the same time, Ilya Mechnikov found that 'lactic-acid bacteria' might have beneficial effects on human health. Hermann Hellriegel discovered a symbiotic structure—root nodules on legume plants. Since then, a tremendous amount of pathogenic or beneficial microbes have been isolated from their hosts (microbes, plants and animals), and their physiological and molecular genetic functions were well-studied in vitro. However, there is less work on how they interact with their hosts. In the last ten years, high-throughput sequencing results have changed our views of microbe–host interaction. Gut microbes play an important role in human health. Legume plants employ sRNAs that regulate nodule formation; on the contrary, rhizobia use sRNAs that affect the nodulation signal pathway of hosts. The aim of the work on microbe–host interaction is simple: hosts’ health or disease.

This Special Issue aims to provide an overview of the current understanding of the molecular biology, genetics, cell biology and genomics of “Microbe–Host interaction”. To progress in the knowledge of such intricate issues, contributions by experts in the field in the form of research papers and critical reviews are called for.

Prof. Dr. Zengtao Zhong
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. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). 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

  • molecular and cell biology of microbes
  • host response to microbes
  • gene expression
  • signal transduction

Published Papers (4 papers)

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Research

12 pages, 1923 KiB  
Article
PAS Domain-Containing Chemoreceptors Influence the Signal Sensing and Intestinal Colonization of Vibrio cholerae
by Rundong Shu, Chaoqun Yuan, Bojun Liu, Yang Song, Leqi Hou, Panpan Ren, Hui Wang and Chunhong Cui
Genes 2022, 13(12), 2224; https://doi.org/10.3390/genes13122224 - 27 Nov 2022
Cited by 1 | Viewed by 1277
Abstract
Bacterial chemotaxis is the phenomenon in which bacteria migrate toward a more favorable niche in response to chemical cues in the environment. The methyl-accepting chemotaxis proteins (MCPs) are the principal sensory receptors of the bacterial chemotaxis system. Aerotaxis is a special form of [...] Read more.
Bacterial chemotaxis is the phenomenon in which bacteria migrate toward a more favorable niche in response to chemical cues in the environment. The methyl-accepting chemotaxis proteins (MCPs) are the principal sensory receptors of the bacterial chemotaxis system. Aerotaxis is a special form of chemotaxis in which oxygen serves as the signaling molecule; the process is dependent on the aerotaxis receptors (Aer) containing the Per-Arnt-Sim (PAS) domain. Over 40 MCPs are annotated on the genome of Vibrio cholerae; however, little is known about their functions. We investigated six MCPs containing the PAS domain in V. cholerae El Tor C6706, namely aer2, aer3, aer4, aer5, aer6, and aer7. Deletion analyses of each aer homolog gene indicated that these Aer receptors are involved in aerotaxis, chemotaxis, biofilm formation, and intestinal colonization. Swarming motility assay indicated that the aer2 gene was responsible for sensing the oxygen gradient independent of the other five homologs. When bile salts and mucin were used as chemoattractants, each Aer receptor influenced the chemotaxis differently. Biofilm formation was enhanced by overexpression of the aer6 and aer7 genes. Moreover, deletion of the aer2 gene resulted in better bacterial colonization of the mutant in adult mice; however, virulence gene expression was unaffected. These data suggest distinct roles for different Aer homologs in V. cholerae physiology. Full article
(This article belongs to the Special Issue Microbe-Host Interaction)
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15 pages, 2262 KiB  
Article
Effects of Bradyrhizobium Co-Inoculated with Bacillus and Paenibacillus on the Structure and Functional Genes of Soybean Rhizobacteria Community
by Pengfei Xing, Yubin Zhao, Dawei Guan, Li Li, Baisuo Zhao, Mingchao Ma, Xin Jiang, Changfu Tian, Fengming Cao and Jun Li
Genes 2022, 13(11), 1922; https://doi.org/10.3390/genes13111922 - 22 Oct 2022
Cited by 13 | Viewed by 2513
Abstract
Plant growth-promoting rhizobacteria (PGPR) are widely used to improve soil nutrients and promote plant growth and health. However, the growth-promoting effect of a single PGPR on plants is limited. Here, we evaluated the effect of applying rhizobium Bradyrhizobium japonicum 5038 (R5038) and two [...] Read more.
Plant growth-promoting rhizobacteria (PGPR) are widely used to improve soil nutrients and promote plant growth and health. However, the growth-promoting effect of a single PGPR on plants is limited. Here, we evaluated the effect of applying rhizobium Bradyrhizobium japonicum 5038 (R5038) and two PGPR strains, Bacillus aryabhattai MB35-5 (BA) and Paenibacillus mucilaginosus 3016 (PM), alone or in different combinations on the soil properties and rhizosphere bacterial community composition of soybean (Glycine max). Additionally, metagenomic sequencing was performed to elucidate the profile of functional genes. Inoculation with compound microbial inoculant containing R5038 and BA (RB) significantly improved nodule nitrogenase activity and increased soil nitrogen content, and urease activity increased the abundance of the nitrogen cycle genes and Betaproteobacteria and Chitinophagia in the rhizosphere. In the treatment of inoculant-containing R5038 and PM (RP), significant changes were found for the abundance of Deltaproteobacteria and Gemmatimonadetes and the phosphorus cycle genes, and soil available phosphorus and phosphatase activity were increased. The RBP inoculants composed of three strains (R5038, BA and PM) significantly affected soybean biomass and the N and P contents of the rhizosphere. Compared with RB and RP, RBP consistently increased soybean nitrogen content, and dry weight. Overall, these results showed that several PGPR with different functions could be combined into composite bacterial inoculants, which coordinately modulate the rhizosphere microbial community structure and improve soybean growth. Full article
(This article belongs to the Special Issue Microbe-Host Interaction)
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16 pages, 4112 KiB  
Article
A Novel Module Promotes Horizontal Gene Transfer in Azorhizobium caulinodans ORS571
by Mingxu Li, Qianqian Chen, Chuanhui Wu, Yiyang Li, Sanle Wang, Xuelian Chen, Bowen Qiu, Yuxin Li, Dongmei Mao, Hong Lin, Daogeng Yu, Yajun Cao, Zhi Huang, Chunhong Cui and Zengtao Zhong
Genes 2022, 13(10), 1895; https://doi.org/10.3390/genes13101895 - 19 Oct 2022
Cited by 2 | Viewed by 1881
Abstract
Azorhizobium caulinodans ORS571 contains an 87.6 kb integrative and conjugative element (ICEAc) that conjugatively transfers symbiosis genes to other rhizobia. Many hypothetical redundant gene fragments (rgfs) are abundant in ICEAc, but their potential function in horizontal gene transfer [...] Read more.
Azorhizobium caulinodans ORS571 contains an 87.6 kb integrative and conjugative element (ICEAc) that conjugatively transfers symbiosis genes to other rhizobia. Many hypothetical redundant gene fragments (rgfs) are abundant in ICEAc, but their potential function in horizontal gene transfer (HGT) is unknown. Molecular biological methods were employed to delete hypothetical rgfs, expecting to acquire a minimal ICEAc and consider non-functional rgfs as editable regions for inserting genes related to new symbiotic functions. We determined the significance of rgf4 in HGT and identified the physiological function of genes designated rihF1a (AZC_3879), rihF1b (AZC_RS26200), and rihR (AZC_3881). In-frame deletion and complementation assays revealed that rihF1a and rihF1b work as a unit (rihF1) that positively affects HGT frequency. The EMSA assay and lacZ-based reporter system showed that the XRE-family protein RihR is not a regulator of rihF1 but promotes the expression of the integrase (intC) that has been reported to be upregulated by the LysR-family protein, AhaR, through sensing host’s flavonoid. Overall, a conservative module containing rihF1 and rihR was characterized, eliminating the size of ICEAc by 18.5%. We propose the feasibility of constructing a minimal ICEAc element to facilitate the exchange of new genetic components essential for symbiosis or other metabolic functions between soil bacteria. Full article
(This article belongs to the Special Issue Microbe-Host Interaction)
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17 pages, 3995 KiB  
Article
Transcription Regulation of Cell Cycle Regulatory Genes Mediated by NtrX to Affect Sinorhizobium meliloti Cell Division
by Shenghui Xing, Wenjia Zheng, Fang An, Leqi Huang, Xinwei Yang, Shuang Zeng, Ningning Li, Khadidja Ouenzar, Liangliang Yu and Li Luo
Genes 2022, 13(6), 1066; https://doi.org/10.3390/genes13061066 - 15 Jun 2022
Cited by 1 | Viewed by 1759
Abstract
The cell division of the alfalfa symbiont, Sinorhizobium meliloti, is dictated by a cell cycle regulatory pathway containing the key transcription factors CtrA, GcrA, and DnaA. In this study, we found that NtrX, one of the regulators of nitrogen metabolism, can directly [...] Read more.
The cell division of the alfalfa symbiont, Sinorhizobium meliloti, is dictated by a cell cycle regulatory pathway containing the key transcription factors CtrA, GcrA, and DnaA. In this study, we found that NtrX, one of the regulators of nitrogen metabolism, can directly regulate the expression of ctrA, gcrA, and dnaA from the cell cycle pathway. Three sets of S. meliloti ntrX mutants showed similar cell division defects, such as slow growth, abnormal morphology of some cells, and delayed DNA synthesis. Transcription of ctrA and gcrA was upregulated, whereas the transcription of dnaA and ftsZ1 was downregulated in the insertion mutant and the strain of Sm1021 expressing ntrXD53E. Correspondingly, the inducible transcription of ntrX activates the expression of dnaA and ftsZ1, but represses ctrA and gcrA in the depletion strain. The expression levels of CtrA and GcrA were confirmed by Western blotting. The transcription regulation of these genes requires phosphorylation of the conserved 53rd aspartate in the NtrX protein that binds directly to the promoter regions of ctrA, gcrA, dnaA, and ftsZ1 by recognizing the characteristic sequence CAAN2-5TTG. Our findings suggest that NtrX affects S. meliloti cell division by regulating the transcription of the key cell cycle regulatory genes. Full article
(This article belongs to the Special Issue Microbe-Host Interaction)
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