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Molecular Bacteria-Invertebrate Interactions
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Molecular Bacteria-Invertebrate Interactions

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

Deadline for manuscript submissions: closed (25 December 2022) | Viewed by 12480

Special Issue Editor

Dr. Sergei A. Subbotin

E-Mail Website
Guest Editor
California Department of Food and Agriculture, Plant Pest Diagnostic Center, 3294 Meadowview Road, Sacramento, CA 95832, USA
Interests: nematology; molecular systematics; phylogenetics; molecular diagnostics; phylogeography; phylogenomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In recent years, due to many research projects, it has become increasingly clear that bacteria form associations with many invertebrates. Bacteria may be facultative or obligate symbionts and perform an important role in maintaining invertebrate health. These associations have been largely overlooked because of difficulties in their detection and problems in bacteria cultivation. However, the widespread application of genetic and genomic approaches has revealed a spectacular bacterial world with high ubiquity and diversity. A growing area of research in bacterium–invertebrate interactions is to elucidate the role of bacteria in facilitation of invertebrate evolution, speciation, mechanisms of manipulation of host physiology and development, regulation of inter-domain metabolism, and genome formation and also influence on pathogenicity, parasitism, and transmission in parasitic invertebrates. This Special Issue will focus on recent advances in all aspects of molecular biological studies of bacterium–invertebrate interactions, covering genomics, proteomics, coevolution, biodiversity, and other research directions.

Dr. Sergei A. Subbotin
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

  • bacterial parasitism
  • host evolution
  • host physiology
  • inter-domain metabolism
  • genome formation

Published Papers (6 papers)

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Research

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14 pages, 3527 KiB  
Article
Distribution of Bacterial Endosymbionts of the Cardinium Clade in Plant-Parasitic Nematodes
by Sergey V. Tarlachkov, Boris D. Efeykin, Pablo Castillo, Lyudmila I. Evtushenko and Sergei A. Subbotin
Int. J. Mol. Sci. 2023, 24(3), 2905; https://doi.org/10.3390/ijms24032905 - 2 Feb 2023
Cited by 1 | Viewed by 1977
Abstract
Bacteria of the genus “Candidatus Cardinium” and related organisms composing the Cardinium clade are intracellular endosymbionts frequently occurring in several arthropod groups, freshwater mussels and plant-parasitic nematodes. Phylogenetic analyses based on two gene sequences (16S rRNA and gyrB) showed that the [...] Read more.
Bacteria of the genus “Candidatus Cardinium” and related organisms composing the Cardinium clade are intracellular endosymbionts frequently occurring in several arthropod groups, freshwater mussels and plant-parasitic nematodes. Phylogenetic analyses based on two gene sequences (16S rRNA and gyrB) showed that the Cardinium clade comprised at least five groups: A, B, C, D and E. In this study, a screening of 142 samples of plant-parasitic nematodes belonging to 93 species from 12 families and two orders using PCR with specific primers and sequencing, revealed bacteria of Cardinium clade in 14 nematode samples belonging to 12 species of cyst nematodes of the family Heteroderidae. Furthermore, in this study, the genome of the Cardinium cHhum from the hop cyst nematode, Heterodera humuli, was also amplified, sequenced and analyzed. The comparisons of the average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values for the strain Cardinium cHhum with regard to related organisms with available genomes, combined with the data on 16S rRNA and gyrB gene sequence identities, showed that this strain represents a new candidate species within the genus “Candidatus Paenicardinium”. The phylogenetic position of endosymbionts of the Cardinium clade detected in nematode hosts was also compared to known representatives of this clade from other metazoans. Phylogenetic reconstructions based on analysis of 16S rRNA, gyrB, sufB, gloEL, fusA, infB genes and genomes and estimates of genetic distances both indicate that the endosymbiont of the root-lesion nematode Pratylenchus penetrans represented a separate lineage and is designated herein as a new group F. The phylogenetic analysis also confirmed that endosymbionts of ostracods represent the novel group G. Evolutionary relationships of bacterial endosymbionts of the Cardinium clade within invertebrates are presented and discussed. Full article
(This article belongs to the Special Issue Molecular Bacteria-Invertebrate Interactions)
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17 pages, 2798 KiB  
Article
Exploring the Potential of Metatranscriptomics to Describe Microbial Communities and Their Effects in Molluscs
by Magalí Rey-Campos, Raquel Ríos-Castro, Cristian Gallardo-Escárate, Beatriz Novoa and Antonio Figueras
Int. J. Mol. Sci. 2022, 23(24), 16029; https://doi.org/10.3390/ijms232416029 - 16 Dec 2022
Cited by 3 | Viewed by 1651
Abstract
Metatranscriptomics has emerged as a very useful technology for the study of microbiomes from RNA-seq reads. This method provides additional information compared to the sequencing of ribosomal genes because the gene expression can also be analysed. In this work, we used the metatranscriptomic [...] Read more.
Metatranscriptomics has emerged as a very useful technology for the study of microbiomes from RNA-seq reads. This method provides additional information compared to the sequencing of ribosomal genes because the gene expression can also be analysed. In this work, we used the metatranscriptomic approach to study the whole microbiome of mussels, including bacteria, viruses, fungi, and protozoans, by mapping the RNA-seq reads to custom assembly databases (including the genomes of microorganisms publicly available). This strategy allowed us not only to describe the diversity of microorganisms but also to relate the host transcriptome and microbiome, finding the genes more affected by the pathogen load. Although some bacteria abundant in the metatranscriptomic analysis were undetectable by 16S rRNA sequencing, a common core of the taxa was detected by both methodologies (62% of the metatranscriptomic detections were also identified by 16S rRNA sequencing, the Oceanospirillales, Flavobacteriales and Vibrionales orders being the most relevant). However, the differences in the microbiome composition were observed among different tissues of Mytilus galloprovincialis, with the fungal kingdom being especially diverse, or among molluscan species. These results confirm the potential of a meta-analysis of transcriptome data to obtain new information on the molluscs’ microbiome. Full article
(This article belongs to the Special Issue Molecular Bacteria-Invertebrate Interactions)
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23 pages, 2741 KiB  
Article
An Intestinal Symbiotic Bacterial Strain of Oscheius chongmingensis Modulates Host Viability at Both Global and Post-Transcriptional Levels
by Chengxiu Zhan, Long Chen, Dandan Guo, Jing Sun, Yunbin Duan, Panjie Zhang, Pengpeng Li, Lijun Ma, Man Xu, Ying Wang, Haoran Bao, Guofu Gao, Liwang Liu and Keyun Zhang
Int. J. Mol. Sci. 2022, 23(23), 14692; https://doi.org/10.3390/ijms232314692 - 24 Nov 2022
Viewed by 1122
Abstract
A rhabditid entomopathogenic nematode (EPN), Oscheius chongmingensis, has a stable symbiotic relationship with the bacterial strain Serratia nematodiphila S1 harbored in its intestines and drastically reduced viability when associated with a non-native strain (186) of the same bacterial species. This nematode is [...] Read more.
A rhabditid entomopathogenic nematode (EPN), Oscheius chongmingensis, has a stable symbiotic relationship with the bacterial strain Serratia nematodiphila S1 harbored in its intestines and drastically reduced viability when associated with a non-native strain (186) of the same bacterial species. This nematode is thus a good model for understanding the molecular mechanisms and interactions involved between a nematode host and a member of its intestinal microbiome. Transcriptome analysis and RNA-seq data indicated that expression levels of the majority (8797, 87.59%) of mRNAs in the non-native combination of O. chongmingensis and S. nematodiphila 186 were downregulated compared with the native combination, including strain S1. Accordingly, 88.84% of the total uniq-sRNAs mapped in the O. chongmingensis transcriptome were specific between the two combinations. Six DEGs, including two transcription factors (oc-daf-16 and oc-goa-1) and four kinases (oc-pdk-1, oc-akt-1, oc-rtk, and oc-fak), as well as an up-regulated micro-RNA, oc-miR-71, were found to demonstrate the regulatory mechanisms underlying diminished host viability induced by a non-native bacterial strain. Oc-rtk and oc-fak play key roles in the viability regulation of O. chongmingensis by positively mediating the expression of oc-daf-16 to indirectly impact its longevity and stress tolerances and by negatively regulating the expression of oc-goa-1 to affect the olfactory chemotaxis and fecundity. In response to the stress of invasion by the non-native strain, the expression of oc-miR-71 in the non-native combination was upregulated to downregulate the expression of its targeting oc-pdk-1, which might improve the localization and activation of the transcription factor DAF-16 in the nucleus to induce longevity extension and stress resistance enhancement to some extent. Our findings provide novel insight into comprehension of how nematodes deal with the stress of encountering novel potential bacterial symbionts at the physiological and molecular genetic levels and contribute to improved understanding of host–symbiont relationships generally. Full article
(This article belongs to the Special Issue Molecular Bacteria-Invertebrate Interactions)
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18 pages, 3534 KiB  
Article
Long-Term Heat Selection of the Coral Endosymbiont Cladocopium C1acro (Symbiodiniaceae) Stabilizes Associated Bacterial Communities
by Patrick Buerger, Ruby T. Vanstone, Justin Maire and Madeleine J. H. van Oppen
Int. J. Mol. Sci. 2022, 23(9), 4913; https://doi.org/10.3390/ijms23094913 - 28 Apr 2022
Cited by 10 | Viewed by 2227
Abstract
Heat-tolerant strains of the coral endosymbiont, Cladocopium C1acro (Symbiodiniaceae), have previously been developed via experimental evolution. Here, we examine physiological responses and bacterial community composition (using 16S rRNA gene metabarcoding) in cultures of 10 heat-evolved (SS) and 9 wild-type (WT) strains, which [...] Read more.
Heat-tolerant strains of the coral endosymbiont, Cladocopium C1acro (Symbiodiniaceae), have previously been developed via experimental evolution. Here, we examine physiological responses and bacterial community composition (using 16S rRNA gene metabarcoding) in cultures of 10 heat-evolved (SS) and 9 wild-type (WT) strains, which had been exposed for 6 years to 31 °C and 27 °C, respectively. We also examine whether the associated bacterial communities were affected by a three-week reciprocal transplantation to both temperatures. The SS strains had bacterial communities with lower diversities that showed more stability and lower variability when exposed to elevated temperatures compared with the WT strains. Amplicon sequence variants (ASVs) of the bacterial genera Labrenzia, Algiphilus, Hyphobacterium and Roseitalea were significantly more associated with the SS strains compared with the WT strains. WT strains showed higher abundance of ASVs assigned to the genera Fabibacter and Tropicimonas. We hypothesize that these compositional differences in associated bacterial communities between SS and WT strains also contribute to the thermal tolerance of the microalgae. Future research should explore functional potential between bacterial communities using metagenomics to unravel specific genomic adaptations. Full article
(This article belongs to the Special Issue Molecular Bacteria-Invertebrate Interactions)
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17 pages, 2273 KiB  
Article
Narrow Genetic Diversity of Wolbachia Symbionts in Acrididae Grasshopper Hosts (Insecta, Orthoptera)
by Yury Ilinsky, Mary Demenkova, Roman Bykov and Alexander Bugrov
Int. J. Mol. Sci. 2022, 23(2), 853; https://doi.org/10.3390/ijms23020853 - 13 Jan 2022
Cited by 3 | Viewed by 1818
Abstract
Bacteria of the Wolbachia genus are maternally inherited symbionts of Nematoda and numerous Arthropoda hosts. There are approximately 20 lineages of Wolbachia, which are called supergroups, and they are designated alphabetically. Wolbachia strains of the supergroups A and B are predominant in [...] Read more.
Bacteria of the Wolbachia genus are maternally inherited symbionts of Nematoda and numerous Arthropoda hosts. There are approximately 20 lineages of Wolbachia, which are called supergroups, and they are designated alphabetically. Wolbachia strains of the supergroups A and B are predominant in arthropods, especially in insects, and supergroup F seems to rank third. Host taxa have been studied very unevenly for Wolbachia symbionts, and here, we turn to one of largely unexplored insect families: Acrididae. On the basis of five genes subject to multilocus sequence typing, we investigated the incidence and genetic diversity of Wolbachia in 41 species belonging three subfamilies (Gomphocerinae, Oedipodinae, and Podisminae) collected in Turkey, Kazakhstan, Tajikistan, Russia, and Japan, making 501 specimens in total. Our results revealed a high incidence and very narrow genetic diversity of Wolbachia. Although only the strains belonging to supergroups A and B are commonly present in present, the Acrididae hosts here proved to be infected with supergroups B and F without A-supergroup variants. The only trace of an A-supergroup lineage was noted in one case of an inter-supergroup recombinant haplotype, where the ftsZ gene came from supergroup A, and the others from supergroup B. Variation in the Wolbachia haplotypes in Acrididae hosts within supergroups B and F was extremely low. A comprehensive genetic analysis of Wolbachia diversity confirmed specific features of the Wolbachia allelic set in Acrididae hosts. This result can help to elucidate the crucial issue of Wolbachia biology: the route(s) and mechanism(s) of Wolbachia horizontal transmission. Full article
(This article belongs to the Special Issue Molecular Bacteria-Invertebrate Interactions)
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Review

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14 pages, 2500 KiB  
Review
Nocturnal Acidification: A Coordinating Cue in the Euprymna scolopes–Vibrio fischeri Symbiosis
by Brian L. Pipes and Michele K. Nishiguchi
Int. J. Mol. Sci. 2022, 23(7), 3743; https://doi.org/10.3390/ijms23073743 - 29 Mar 2022
Cited by 2 | Viewed by 2787
Abstract
The Vibrio fischeri–Euprymna scolopes symbiosis has become a powerful model for the study of specificity, initiation, and maintenance between beneficial bacteria and their eukaryotic partner. In this invertebrate model system, the bacterial symbionts are acquired every generation from the surrounding seawater [...] Read more.
The Vibrio fischeri–Euprymna scolopes symbiosis has become a powerful model for the study of specificity, initiation, and maintenance between beneficial bacteria and their eukaryotic partner. In this invertebrate model system, the bacterial symbionts are acquired every generation from the surrounding seawater by newly hatched squid. These symbionts colonize a specialized internal structure called the light organ, which they inhabit for the remainder of the host’s lifetime. The V. fischeri population grows and ebbs following a diel cycle, with high cell densities at night producing bioluminescence that helps the host avoid predation during its nocturnal activities. Rhythmic timing of the growth of the symbionts and their production of bioluminescence only at night is critical for maintaining the symbiosis. V. fischeri symbionts detect their population densities through a behavior termed quorum-sensing, where they secrete and detect concentrations of autoinducer molecules at high cell density when nocturnal production of bioluminescence begins. In this review, we discuss events that lead up to the nocturnal acidification of the light organ and the cues used for pre-adaptive behaviors that both host and symbiont have evolved. This host–bacterium cross talk is used to coordinate networks of regulatory signals (such as quorum-sensing and bioluminescence) that eventually provide a unique yet stable environment for V. fischeri to thrive and be maintained throughout its life history as a successful partner in this dynamic symbiosis. Full article
(This article belongs to the Special Issue Molecular Bacteria-Invertebrate Interactions)
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