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Biofouling and Antifouling: Application of Omics Technologies
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Biofouling and Antifouling: Application of Omics Technologies

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 (30 October 2023) | Viewed by 7754

Special Issue Editors

Prof. Dr. Sergey Dobretsov

E-Mail
Guest Editor
Department of Marine Science and Fisheries, Sultan Qaboos University, Al Khoud 123, P.O. Box 34, Muscat, Oman
Interests: biofouling; antifouling; microbial biofilms; marine biotechnology; marine natural products; chemical ecology
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Daniel Rittschof

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Co-Guest Editor
Marine Science and Conservation, Marine Laboratory, Nicholas School, Duke University, 135 Duke Marine Lab Road, Beaufort, NC 28516, USA
Interests: environmental toxicology; marine fouling; environmentally benign antifoulants; plastic pollution
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Biofouling refers to the undesirable accumulation and deposition of living organisms on submerged hard surfaces. The initial stages of biofouling are represented by biofilms, which are composed of assemblages of different microorganisms incorporated into exopolymeric substances and attached to each other and to substrata. The bioactive compounds produced by the microbes in biofilms can induce or inhibit the larval recruitment of invertebrates. Biofouling causes significant problems to the maritime industries. Current antifouling technologies are based on using toxic biocides. Thus, novel environmentally benign antifouling solutions are urgently needed. In order to develop them, it is necessary to elucidate the molecular effects of antifouling compounds on marine organisms. “Omics” technologies, such as genomics, transcriptomics, proteomics, and metabolomics, can lead to innovative breakthroughs in antifouling technologies and can help us to understand the process of biofouling. This Special Issue targets research results focusing on the investigation of changes in biofouling communities including pro-fouling and anti-fouling using the novel “omics” approaches.

Prof. Dr. Sergey Dobretsov
Prof. Dr. Daniel Rittschof
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. 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

  • Biofouling
  • Inhibition of settlement
  • Microbial biofilm
  • Metagenomics
  • Metabolomics
  • Transcriptomics
  • Proteomics
  • Next generation sequencing

Published Papers (4 papers)

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Research

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14 pages, 4676 KiB  
Article
Two-Component System Response Regulator ompR Regulates Mussel Settlement through Exopolysaccharides
by Wei Ma, Xiaoyu Wang, Wen Zhang, Xiaomeng Hu, Jin-Long Yang and Xiao Liang
Int. J. Mol. Sci. 2023, 24(8), 7474; https://doi.org/10.3390/ijms24087474 - 18 Apr 2023
Cited by 5 | Viewed by 1323
Abstract
The outer membrane protein (OMP) is a kind of biofilm matrix component that widely exists in Gram-negative bacteria. However, the mechanism of OMP involved in the settlement of molluscs is still unclear. In this study, the mussel Mytilus coruscus was selected as a [...] Read more.
The outer membrane protein (OMP) is a kind of biofilm matrix component that widely exists in Gram-negative bacteria. However, the mechanism of OMP involved in the settlement of molluscs is still unclear. In this study, the mussel Mytilus coruscus was selected as a model to explore the function of ompR, a two-component system response regulator, on Pseudoalteromonas marina biofilm-forming capacity and the mussel settlement. The motility of the ΔompR strain was increased, the biofilm-forming capacity was decreased, and the inducing activity of the ΔompR biofilms in plantigrades decreased significantly (p < 0.05). The extracellular α-polysaccharide and β-polysaccharide of the ΔompR strain decreased by 57.27% and 62.63%, respectively. The inactivation of the ompR gene decreased the ompW gene expression and had no impact on envZ expression or c-di-GMP levels. Adding recombinant OmpW protein caused the recovery of biofilm-inducing activities, accompanied by the upregulation of exopolysaccharides. The findings deepen the understanding of the regulatory mechanism of bacterial two-component systems and the settlement of benthic animals. Full article
(This article belongs to the Special Issue Biofouling and Antifouling: Application of Omics Technologies)
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14 pages, 33881 KiB  
Article
TRPM7-Mediated Ca2+ Regulates Mussel Settlement through the CaMKKβ-AMPK-SGF1 Pathway
by Jian He, Peng Wang, Zhixuan Wang, Danqing Feng and Dun Zhang
Int. J. Mol. Sci. 2023, 24(6), 5399; https://doi.org/10.3390/ijms24065399 - 11 Mar 2023
Viewed by 1515
Abstract
Many marine invertebrates have planktonic larval and benthic juvenile/adult stages. When the planktonic larvae are fully developed, they must find a favorable site to settle and metamorphose into benthic juveniles. This transition from a planktonic to a benthic mode of life is a [...] Read more.
Many marine invertebrates have planktonic larval and benthic juvenile/adult stages. When the planktonic larvae are fully developed, they must find a favorable site to settle and metamorphose into benthic juveniles. This transition from a planktonic to a benthic mode of life is a complex behavioral process involving substrate searching and exploration. Although the mechanosensitive receptor in the tactile sensor has been implicated in sensing and responding to surfaces of the substrates, few have been unambiguously identified. Recently, we identified that the mechanosensitive transient receptor potential melastatin-subfamily member 7 (TRPM7) channel, highly expressed in the larval foot of the mussel Mytilospsis sallei, was involved in substrate exploration for settlement. Here, we show that the TRPM7-mediated Ca2+ signal was involved in triggering the larval settlement of M. sallei through the calmodulin-dependent protein kinase kinase β/AMP-activated protein kinase/silk gland factor 1 (CaMKKβ-AMPK-SGF1) pathway. It was found that M. sallei larvae preferred the stiff surfaces for settlement, on which TRPM7, CaMKKβ, AMPK, and SGF1 were highly expressed. These findings will help us to better understand the molecular mechanisms of larval settlement in marine invertebrates, and will provide insights into the potential targets for developing environmentally friendly antifouling coatings for fouling organisms. Full article
(This article belongs to the Special Issue Biofouling and Antifouling: Application of Omics Technologies)
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16 pages, 4573 KiB  
Article
Metabolomic Insights of Biosurfactant Activity from Bacillus niabensis against Planktonic Cells and Biofilm of Pseudomonas stutzeri Involved in Marine Biofouling
by Ilse Sánchez-Lozano, Luz Clarita Muñoz-Cruz, Claire Hellio, Christine J. Band-Schmidt, Yair Cruz-Narváez, Elvia Becerra-Martínez and Claudia J. Hernández-Guerrero
Int. J. Mol. Sci. 2023, 24(4), 4249; https://doi.org/10.3390/ijms24044249 - 20 Feb 2023
Cited by 1 | Viewed by 1910
Abstract
In marine environments, biofilm can cause negative impacts, including the biofouling process. In the search for new non-toxic formulations that inhibit biofilm, biosurfactants (BS) produced by the genus Bacillus have demonstrated considerable potential. To elucidate the changes that BS from B. niabensis promote [...] Read more.
In marine environments, biofilm can cause negative impacts, including the biofouling process. In the search for new non-toxic formulations that inhibit biofilm, biosurfactants (BS) produced by the genus Bacillus have demonstrated considerable potential. To elucidate the changes that BS from B. niabensis promote in growth inhibition and biofilm formation, this research performed a nuclear magnetic resonance (NMR) metabolomic profile analysis to compare the metabolic differences between planktonic cells and biofilms of Pseudomonas stutzeri, a pioneer fouling bacteria. The multivariate analysis showed a clear separation between groups with a higher concentration of metabolites in the biofilm than in planktonic cells of P. stutzeri. When planktonic and biofilm stages were treated with BS, some differences were found among them. In planktonic cells, the addition of BS had a minor effect on growth inhibition, but at a metabolic level, NADP+, trehalose, acetone, glucose, and betaine were up-regulated in response to osmotic stress. When the biofilm was treated with the BS, a clear inhibition was observed and metabolites such as glucose, acetic acid, histidine, lactic acid, phenylalanine, uracil, and NADP+ were also up-regulated, while trehalose and histamine were down-regulated in response to the antibacterial effect of the BS. Full article
(This article belongs to the Special Issue Biofouling and Antifouling: Application of Omics Technologies)
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Review

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20 pages, 1847 KiB  
Review
“Omics” Techniques Used in Marine Biofouling Studies
by Sergey Dobretsov and Daniel Rittschof
Int. J. Mol. Sci. 2023, 24(13), 10518; https://doi.org/10.3390/ijms241310518 - 23 Jun 2023
Cited by 3 | Viewed by 2004
Abstract
Biofouling is the growth of organisms on wet surfaces. Biofouling includes micro- (bacteria and unicellular algae) and macrofouling (mussels, barnacles, tube worms, bryozoans, etc.) and is a major problem for industries. However, the settlement and growth of some biofouling species, like oysters and [...] Read more.
Biofouling is the growth of organisms on wet surfaces. Biofouling includes micro- (bacteria and unicellular algae) and macrofouling (mussels, barnacles, tube worms, bryozoans, etc.) and is a major problem for industries. However, the settlement and growth of some biofouling species, like oysters and corals, can be desirable. Thus, it is important to understand the process of biofouling in detail. Modern “omic” techniques, such as metabolomics, metagenomics, transcriptomics, and proteomics, provide unique opportunities to study biofouling organisms and communities and investigate their metabolites and environmental interactions. In this review, we analyze the recent publications that employ metagenomic, metabolomic, and proteomic techniques for the investigation of biofouling and biofouling organisms. Specific emphasis is given to metagenomics, proteomics and publications using combinations of different “omics” techniques. Finally, this review presents the future outlook for the use of “omics” techniques in marine biofouling studies. Like all trans-disciplinary research, environmental “omics” is in its infancy and will advance rapidly as researchers develop the necessary expertise, theory, and technology. Full article
(This article belongs to the Special Issue Biofouling and Antifouling: Application of Omics Technologies)
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