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Host-Bacterial Associations in Marine Organisms
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Host-Bacterial Associations in Marine Organisms

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

Deadline for manuscript submissions: closed (1 May 2019) | Viewed by 19316

Special Issue Editors

Prof. Dr. Knut Rudi

E-Mail Website
Guest Editor
Department of Chemistry, Biotechnology and Food Science (IKBM), Norwegian University of Life Sciences, Chr. M. Falsensvei 1, Biotechnology Building, P.O. Box 5003, 1432 Ås, Norway
Interests: establishment of the infant gut microbiota; transition from infant to adult gut microbiota; the role of the commensal microbiota as a reservoir for antibiotic resistance; honey bees as a model for understanding spread of antibiotic resistance; dynamic interactions in the horse cecal microbiota; the salmon gut microbiota
Prof. Dr. Ingrid Bakke

E-Mail Website
Guest Editor
NTNU Norwegian University of Science and TechnologyInstitutt for bioteknologi og matvitenskap/Department of Biotechnology and Food ScienceSem Sælands vei 6-8N-7491 Trondheim, Norway
Interests: fish – microbe interactions; biological water treatment; microbial control and community dynamics in aquaculture systems
Prof. Dr. Olav Vadstein

E-Mail Website
Guest Editor
Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Sem Sælandsvei 8, N-7491 Trondheim, Norway
Interests: aquatic ecosystems; environmental biotechnology

Special Issue Information

Dear Colleagues,

Marine environments cover 90% of the earth’s biosphere, and represent half of the primary production. Most of our knowledge about host-bacterial associations, however, is derived from organism living in terrestrial environments. Due to fundamental differences in trophic interactions, environmental conditions, and dispersal barriers, knowledge about terrestrial host-bacterial associations cannot be directly transferred to marine systems. This particularly relates dispersal and tropic levels. In contrast to terrestrial environments, there are few dispersal barriers in marine environment, with the potential of global dispersal. The marine biomass is also heavily shifted towards consumers, rather than producers as in terrestrial environments. Furthermore, marine ecosystems have more tropic levels (longer food chains) than terrestrial systems. These issues, among others, influence how microorganisms associate differently with hosts in marine –, as compared to in terrestrial environments.

The focus of this special issue will therefore be to collect the current knowledge on mechanisms for host-bacterial associations in marine organisms. Papers related to all macroscopic marine organisms are welcome, including fish and invertebrates. Impact of host-bacterial associations in aquaculture are also covered.

Prof. Knut Rudi
Prof. Ingrid Bakke
Prof. Olav Vadstein
Guest Editors

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

  • Host-bacterial associations
  • Marine environment
  • Aquaculture
  • Ecology
  • Metagenomics
  • Tropic interactions

Published Papers (4 papers)

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Research

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21 pages, 1649 KiB  
Article
The Farmed Atlantic Salmon (Salmo salar) Skin–Mucus Proteome and Its Nutrient Potential for the Resident Bacterial Community
by Giusi Minniti, Simen Rød Sandve, János Tamás Padra, Live Heldal Hagen, Sara Lindén, Phillip B. Pope, Magnus Ø. Arntzen and Gustav Vaaje-Kolstad
Genes 2019, 10(7), 515; https://doi.org/10.3390/genes10070515 - 07 Jul 2019
Cited by 27 | Viewed by 4456
Abstract
Norway is the largest producer and exporter of farmed Atlantic salmon (Salmo salar) worldwide. Skin disorders correlated with bacterial infections represent an important challenge for fish farmers due to the economic losses caused. Little is known about this topic, thus studying [...] Read more.
Norway is the largest producer and exporter of farmed Atlantic salmon (Salmo salar) worldwide. Skin disorders correlated with bacterial infections represent an important challenge for fish farmers due to the economic losses caused. Little is known about this topic, thus studying the skin–mucus of Salmo salar and its bacterial community depict a step forward in understanding fish welfare in aquaculture. In this study, we used label free quantitative mass spectrometry to investigate the skin–mucus proteins associated with both Atlantic salmon and bacteria. In particular, the microbial temporal proteome dynamics during nine days of mucus incubation with sterilized seawater was investigated, in order to evaluate their capacity to utilize mucus components for growth in this environment. At the start of the incubation period, the largest proportion of proteins (~99%) belonged to the salmon and many of these proteins were assigned to protecting functions, confirming the defensive role of mucus. On the contrary, after nine days of incubation, most of the proteins detected were assigned to bacteria, mainly to the genera Vibrio and Pseudoalteromonas. Most of the predicted secreted proteins were affiliated with transport and metabolic processes. In particular, a large abundance and variety of bacterial proteases were observed, highlighting the capacity of bacteria to degrade the skin–mucus proteins of Atlantic salmon. Full article
(This article belongs to the Special Issue Host-Bacterial Associations in Marine Organisms)
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16 pages, 1648 KiB  
Article
Population Genetic Divergence and Environment Influence the Gut Microbiome in Oregon Threespine Stickleback
by Robert A. Steury, Mark C. Currey, William A. Cresko and Brendan J. M. Bohannan
Genes 2019, 10(7), 484; https://doi.org/10.3390/genes10070484 - 26 Jun 2019
Cited by 23 | Viewed by 3471
Abstract
Much of animal-associated microbiome research has been conducted in species for which little is known of their natural ecology and evolution. Microbiome studies that combine population genetic, environment, and geographic data for wild organisms can be very informative, especially in situations where host [...] Read more.
Much of animal-associated microbiome research has been conducted in species for which little is known of their natural ecology and evolution. Microbiome studies that combine population genetic, environment, and geographic data for wild organisms can be very informative, especially in situations where host genetic variation and the environment both influence microbiome variation. The few studies that have related population genetic and microbiome variation in wild populations have been constrained by observation-based kinship data or incomplete genomic information. Here we integrate population genomic and microbiome analyses in wild threespine stickleback fish distributed throughout western Oregon, USA. We found that gut microbiome diversity and composition partitioned more among than within wild host populations and was better explained by host population genetic divergence than by environment and geography. We also identified gut microbial taxa that were most differentially abundant across environments and across genetically divergent populations. Our findings highlight the benefits of studies that investigate host-associated microbiomes in wild organisms. Full article
(This article belongs to the Special Issue Host-Bacterial Associations in Marine Organisms)
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15 pages, 2075 KiB  
Article
Host-Associated Bacterial Succession during the Early Embryonic Stages and First Feeding in Farmed Gilthead Sea Bream (Sparus aurata)
by Eleni Nikouli, Alexandra Meziti, Efthimia Antonopoulou, Eleni Mente and Konstantinos Ar. Kormas
Genes 2019, 10(7), 483; https://doi.org/10.3390/genes10070483 - 26 Jun 2019
Cited by 26 | Viewed by 4098
Abstract
One of the most widely reared fish in the Mediterranean Sea is Sparus aurata. The succession of S. aurata whole-body microbiota in fertilized eggs, five, 15, 21 and 71 days post hatch (dph) larvae and the contribution of the rearing water and [...] Read more.
One of the most widely reared fish in the Mediterranean Sea is Sparus aurata. The succession of S. aurata whole-body microbiota in fertilized eggs, five, 15, 21 and 71 days post hatch (dph) larvae and the contribution of the rearing water and the provided feed (rotifers, Artemia sp. and commercial diet) to the host’s microbiota was investigated by 454 pyrosequencing of the 16S rRNA gene diversity. In total, 1917 bacterial operational taxonomic units (OTUs) were found in all samples. On average, between 93 ± 2.1 and 366 ± 9.2 bacterial OTUs per sample were found, with most of them belonging to Proteobacteria and Bacteroidetes. Ten OTUs were shared between all S. aurata stages and were also detected in the rearing water or diet. The highest OTU richness occurred at the egg stage and the lowest at the yolk sac stage (5 dph). The rearing water and diet microbial communities contributed in S. aurata microbiota without overlaps in their microbial composition and structure. The commercial diet showed higher contribution to the S. aurata microbiota than the rearing water. After stage D71 the observed microbiota showed similarities with that of adult S. aurata as indicated by the increased number of OTUs associated with γ-Proteobacteria and Firmicutes. Full article
(This article belongs to the Special Issue Host-Bacterial Associations in Marine Organisms)
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Review

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20 pages, 895 KiB  
Review
Overcoming Fish Defences: The Virulence Factors of Yersinia ruckeri
by Agnieszka Wrobel, Jack C. Leo and Dirk Linke
Genes 2019, 10(9), 700; https://doi.org/10.3390/genes10090700 - 11 Sep 2019
Cited by 36 | Viewed by 6848
Abstract
Yersinia ruckeri is the causative agent of enteric redmouth disease, a bacterial infection of marine and freshwater fish. The disease mainly affects salmonids, and outbreaks have significant economic impact on fish farms all over the world. Vaccination routines are in place against the [...] Read more.
Yersinia ruckeri is the causative agent of enteric redmouth disease, a bacterial infection of marine and freshwater fish. The disease mainly affects salmonids, and outbreaks have significant economic impact on fish farms all over the world. Vaccination routines are in place against the major serotypes of Y. ruckeri but are not effective in all cases. Despite the economic importance of enteric redmouth disease, a detailed molecular understanding of the disease is lacking. A considerable number of mostly omics-based studies have been performed in recent years to identify genes related to Y. ruckeri virulence. This review summarizes the knowledge on Y. ruckeri virulence factors. Understanding the molecular pathogenicity of Y. ruckeri will aid in developing more efficient vaccines and antimicrobial compounds directed against enteric redmouth disease. Full article
(This article belongs to the Special Issue Host-Bacterial Associations in Marine Organisms)
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