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Microorganisms
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Host–Bacteria Interactions in Aquaculture Systems
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Host–Bacteria Interactions in Aquaculture Systems

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 9515

Special Issue Editor

Dr. Pavlos Makridis

E-Mail Website
Guest Editor
Department of Biology, University of Patras, 26504 Rio, Greece
Interests: fish larvae; probiotics; miroalgae; oxygenation; recirculation aquaculture systems (RAS)
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In aquaculture systems (rearing systems for the culture of fish, crustacea, microalgae, or other aquatic organisms), there is an accumulation of organic load which promotes the proliferation of bacteria. These bacterial populations interact with host organisms in complex ways. Aquaculture is a fast-growing industry, and there is a need to describe these interactions of the microbiome in water, biofilms, and rearing systems in general with the microbiome of the cultured organisms, as this will help to alleviate and improve the conditions and increase the sustainability of the aquaculture industry worldwide.

Perturbations and imbalances of microbial communities often lead to the dominance of pathogens and disease problems. Several approaches have been suggested to avoid the use of chemotherapeutic agents in aquaculture. Manuscripts covering different aspects of the description of microbiomes in water, or organisms are welcome, including the effect of the use of probiotics, antimicrobial activity of microalgae, environmental factors influencing the microbiome, diet influencing microbiome, and outbreaks of pathogens under certain conditions.

Dr. Pavlos Makridis
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. Microorganisms 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 2700 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.

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Published Papers (6 papers)

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Research

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15 pages, 1318 KiB  
Article
Persistent Dysbiosis, Parasite Rise and Growth Impairment in Aquacultured European Seabass after Oxytetracycline Treatment
by Dimitris Rigas, Nikos Grivas, Aikaterini Nelli, Evangelia Gouva, Ioannis Skoufos, Konstantinos Kormas, Athina Tzora and Ilias Lagkouvardos
Microorganisms 2023, 11(9), 2302; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms11092302 - 13 Sep 2023
Viewed by 1719
Abstract
The use of antibiotics in open-water aquaculture is often unavoidable when faced with pathogens with high mortality rates. In addition, seasonal pathogen surges have become more common and more intense over the years. Apart from the apparent cost of antibiotic treatment, it has [...] Read more.
The use of antibiotics in open-water aquaculture is often unavoidable when faced with pathogens with high mortality rates. In addition, seasonal pathogen surges have become more common and more intense over the years. Apart from the apparent cost of antibiotic treatment, it has been observed that, in aquaculture practice, the surviving fish often display measurable growth impairment. To understand the role of gut microbiota on the observed growth impairment, in this study, we follow the incidence of Photobacterium damselae subsp. piscicida in a seabass commercial open-water aquaculture setting in Galaxidi (Greece). Fish around 10 months of age were fed with feed containing oxytetracycline (120 mg/kg/day) for twelve days, followed by a twelve-day withdrawal period, and another eighteen days of treatment. The fish were sampled 19 days before the start of the first treatment and one month after the end of the second treatment cycle. Sequencing of the 16S rRNA gene was used to measure changes in the gut microbiome. Overall, the gut microbiota community, even a month after treatment, was highly dysbiotic and characterized by very low alpha diversity. High abundances of alkalophilic bacteria in the post-antibiotic-treated fish indicated a rise in pH that was coupled with a significant increase in gut parasites. This study’s results indicate that oxytetracycline (OTC) treatment causes persistent dysbiosis even one month after withdrawal and provides a more suitable environment for an increase in parasites. These findings highlight the need for interventions to restore a healthy and protective gut microbiome. Full article
(This article belongs to the Special Issue Host–Bacteria Interactions in Aquaculture Systems)
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18 pages, 2772 KiB  
Article
Characterization of Host-Associated Microbiota and Isolation of Antagonistic Bacteria from Greater Amberjack (Seriola dumerili, Risso, 1810) Larvae
by Vasiliki Paralika, Fotini Kokou, Stelios Karapanagiotis and Pavlos Makridis
Microorganisms 2023, 11(8), 1889; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms11081889 - 26 Jul 2023
Viewed by 883
Abstract
Greater amberjack (Seriola dumerili) is a new species in marine aquaculture with high mortalities at the larval stages. The microbiota of amberjack larvae was analyzed using 16S rDNA sequencing in two groups, one added copepod nauplii (Acartia tonsa) in [...] Read more.
Greater amberjack (Seriola dumerili) is a new species in marine aquaculture with high mortalities at the larval stages. The microbiota of amberjack larvae was analyzed using 16S rDNA sequencing in two groups, one added copepod nauplii (Acartia tonsa) in the diet, and one without copepods (control). In addition, antagonistic bacteria were isolated from amberjack larvae and live food cultures. Proteobacteria was the most abundant phylum followed by Bacteroidota in amberjack larvae. The composition and diversity of the microbiota were influenced by age, but not by diet. Microbial community richness and diversity significantly increased over time. Rhodobacteraceae was the most dominant family followed by Vibrionaceae, which showed the highest relative abundance in larvae from the control group 31 days after hatching. Alcaligenes and Thalassobius genera exhibited a significantly higher relative abundance in the copepod group. Sixty-two antagonistic bacterial strains were isolated and screened for their ability to inhibit four fish pathogens (Aeromonas veronii, Vibrio harveyi, V. anguillarum, V. alginolyticus) using a double-layer test. Phaeobacter gallaeciensis, Phaeobacter sp., Ruegeria sp., and Rhodobacter sp. isolated from larvae and Artemia sp. inhibited the fish pathogens. These antagonistic bacteria could be used as host-derived probiotics to improve the growth and survival of the greater amberjack larvae. Full article
(This article belongs to the Special Issue Host–Bacteria Interactions in Aquaculture Systems)
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20 pages, 8700 KiB  
Article
Antibacterial Activity against Four Fish Pathogenic Bacteria of Twelve Microalgae Species Isolated from Lagoons in Western Greece
by Chrysa Androutsopoulou and Pavlos Makridis
Microorganisms 2023, 11(6), 1396; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms11061396 - 25 May 2023
Cited by 2 | Viewed by 1512
Abstract
Microalgae may produce a range of high-value bioactive substances, making them a promising resource for various applications. In this study, the antibacterial activity of twelve microalgae species isolated from lagoons in western Greece was examined against four fish pathogenic bacteria (Vibrio anguillarum [...] Read more.
Microalgae may produce a range of high-value bioactive substances, making them a promising resource for various applications. In this study, the antibacterial activity of twelve microalgae species isolated from lagoons in western Greece was examined against four fish pathogenic bacteria (Vibrio anguillarum, Aeromonas veronii, Vibrio alginolyticus, and Vibrio harveyi). Two experimental approaches were used to evaluate the inhibitory effect of microalgae on pathogenic bacteria. The first approach used bacteria-free microalgae cultures, whereas the second approach used filter-sterilized supernatant from centrifuged microalgae cultures. The results demonstrated that all microalgae had inhibitory effects against pathogenic bacteria in the first approach, particularly 4 days after inoculation, where Asteromonas gracilis and Tetraselmis sp. (red var., Pappas) exhibited the highest inhibitory activity, reducing bacterial growth by 1 to 3 log units. In the second approach, Tetraselmis sp. (red var., Pappas) showed significant inhibition against V. alginolyticus between 4 and 25 h after inoculation. Moreover, all tested cyanobacteria exhibited inhibitory activity against V. alginolyticus between 21 and 48 h after inoculation. Statistical analysis was performed using the independent samples t-test. These findings suggested that microalgae produce compounds with antibacterial activity, which could be useful in aquaculture. Full article
(This article belongs to the Special Issue Host–Bacteria Interactions in Aquaculture Systems)
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16 pages, 2165 KiB  
Article
Improvements to the Rapid Detection of the Marine Pathogenic Bacterium, Vibrio harveyi, Using Loop-Mediated Isothermal Amplification (LAMP) in Combination with SYBR Green
by Ahmad Mukhlis Abdul Rahman, Julian Ransangan and Vijay Kumar Subbiah
Microorganisms 2022, 10(12), 2346; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10122346 - 27 Nov 2022
Cited by 3 | Viewed by 1699
Abstract
The common methods that are presently used to identify Vibrio harveyi include microscopic examination and biochemical, immunological and PCR-based assays. These methods require technical expertise, and can be time-consuming. A rapid method is required for the high-throughput screening of large number of samples. [...] Read more.
The common methods that are presently used to identify Vibrio harveyi include microscopic examination and biochemical, immunological and PCR-based assays. These methods require technical expertise, and can be time-consuming. A rapid method is required for the high-throughput screening of large number of samples. As such, we have developed a rapid, simple yet sensitive and specific detection method based on the use of the loop-mediated isothermal amplification (LAMP) of DNA. A set of six primers, i.e., two outer, two inner and two loop primers, was designed based on the in silico analysis of a large pool of 39 strains of the toxR gene sequence of V. harveyi. The addition of the loop primers decreased the reaction time of the LAMP by more than half. Furthermore, with the application of SYBR Green, the result can be obtained as quickly as in 10 to 15 min without the need of gel electrophoresis. The specificity of the method primers was then determined by performing LAMP with Vibrio and non-Vibrio samples. LAMP has a greater sensitivity than PCR reaction. The sensitivity of PCR was at 0.6 pg concentration of V. harveyi recombinant plasmid DNA standard, while LAMP was able to detect lower amounts even at 0.6 fg. The development of the LAMP assay will provide a valuable tool for the high-throughput rapid detection of V. harveyi contamination both in laboratories and in the field. Full article
(This article belongs to the Special Issue Host–Bacteria Interactions in Aquaculture Systems)
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15 pages, 2125 KiB  
Article
The Gill Microbiota of Argopecten purpuratus Scallop Is Dominated by Symbiotic Campylobacterota and Upwelling Intensification Differentially Affects Their Abundance
by Roxana González, Carlos Henríquez-Castillo, Karin B. Lohrmann, María Soledad Romero, Laura Ramajo, Paulina Schmitt and Katherina Brokordt
Microorganisms 2022, 10(12), 2330; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10122330 - 25 Nov 2022
Cited by 3 | Viewed by 1701
Abstract
Despite the great importance of gills for bivalve mollusks (respiration, feeding, immunity), the microbiota associated with this tissue has barely been characterized in scallops. The scallop Argopecten purpuratus is an important economic resource that is cultivated in areas where coastal upwelling is intensifying [...] Read more.
Despite the great importance of gills for bivalve mollusks (respiration, feeding, immunity), the microbiota associated with this tissue has barely been characterized in scallops. The scallop Argopecten purpuratus is an important economic resource that is cultivated in areas where coastal upwelling is intensifying by climate change, potentially affecting host-microbiota interactions. Thus, we first characterized the bacterial community present in gills from cultivated scallops (by 16S rRNA gene amplicon sequencing) and assessed their stability and functional potential in animals under farm and laboratory conditions. Results showed that under both conditions the gill bacterial community is dominated by the phylum Campylobacterota (57%), which displays a chemoautotrophic potential that could contribute to scallop nutrition. Within this phylum, two phylotypes, namely symbionts A and B, were the most abundant; being, respectively, taxonomically affiliated to symbionts with nutritional functions in mussel gills, and to uncultured bacteria present in coral mucus. Additionally, in situ hybridization and scanning electron microscopy analyses allowed us to detect these symbionts in the gills of A. purpuratus. Given that shifts in upwelling phenology can cause disturbances to ecosystems, affecting bacteria that provide beneficial functions to the host, we further assessed the changes in the abundance of the two symbionts (via qPCR) in response to a simulated upwelling intensification. The exposure to combined decreasing values in the temperature, pH, and oxygen levels (upwelling conditions) favored the dominance of symbiont B over symbiont A; suggesting that symbiont abundances are modulated by these environmental changes. Overall, results showed that changes in the main Campylobacterota phylotypes in response to upwelling intensification could affect its symbiotic function in A. purpuratus under future climate change scenarios. These results provide the first insight into understanding how scallop gill-microbial systems adapt and respond to climate change stressors, which could be critical for managing health, nutrition, and scallop aquaculture productivity. Full article
(This article belongs to the Special Issue Host–Bacteria Interactions in Aquaculture Systems)
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Review

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27 pages, 508 KiB  
Review
Tools to Enumerate and Predict Distribution Patterns of Environmental Vibrio vulnificus and Vibrio parahaemolyticus
by Lisa A. Waidner and Trupti V. Potdukhe
Microorganisms 2023, 11(10), 2502; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms11102502 - 05 Oct 2023
Viewed by 1140
Abstract
Vibrio vulnificus (Vv) and Vibrio parahaemolyticus (Vp) are water- and foodborne bacteria that can cause several distinct human diseases, collectively called vibriosis. The success of oyster aquaculture is negatively impacted by high Vibrio abundances. Myriad environmental factors affect the [...] Read more.
Vibrio vulnificus (Vv) and Vibrio parahaemolyticus (Vp) are water- and foodborne bacteria that can cause several distinct human diseases, collectively called vibriosis. The success of oyster aquaculture is negatively impacted by high Vibrio abundances. Myriad environmental factors affect the distribution of pathogenic Vibrio, including temperature, salinity, eutrophication, extreme weather events, and plankton loads, including harmful algal blooms. In this paper, we synthesize the current understanding of ecological drivers of Vv and Vp and provide a summary of various tools used to enumerate Vv and Vp in a variety of environments and environmental samples. We also highlight the limitations and benefits of each of the measurement tools and propose example alternative tools for more specific enumeration of pathogenic Vv and Vp. Improvement of molecular methods can tighten better predictive models that are potentially important for mitigation in more controlled environments such as aquaculture. Full article
(This article belongs to the Special Issue Host–Bacteria Interactions in Aquaculture Systems)
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