Blue Microbiology—Aquatic Microbial Resources for Sustainable Life on Earth

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

Deadline for manuscript submissions: closed (31 March 2022) | Viewed by 17369

Special Issue Editors


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Guest Editor
Laboratoire de Chimie des Substances Naturelles et des Sciences des Aliments, ESIROI Département Agroalimentaire, Université de La Réunion, 2 Rue Joseph Wetzell, F‐97490 Sainte‐Clotilde, La Réunion, France
Interests: sustainable textile; microbial biotechnology; microbial production of pigments and colorants; fermentation; bioprocess engineering and fermentation technology
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Biological Oceanography Division (BOD), National Institute of oceanography (CSIR-NIO), Dona Paula-403004, Goa, India
Interests: bioluminescence; fluorescence; pigments; evolution of life; marine molecular ecology

Special Issue Information

Dear Colleagues,

Biotechnology is the exploitation or manipulation of living organisms, systems, and processes for the benefit of society, the environment, and industry. We all know the color code developed by Kafarski (2012) to differentiate the main areas of biotechnology: white (industrial), green (agricultural), blue (marine and fresh water), red (pharmaceutical), brown (desert biotechnology), and purple (patents and inventions), among others. More recently, insect biotechnology, an emerging field of applied entomology that covers the use of insects in drug discovery, food, and feed has been coded yellow.

Blue biotechnology seeks to explore and use marine and fresh-water biodiversity as, for example, a source of new products, bioprospecting the environment and using molecular biology and microbial ecology in fresh-water and marine organisms to obtain beneficial advances for humanity (Barcelos et al., 2018).

In this Special Issue, we have decided to restrict the scope to blue microbiology, limiting the papers to those involving archaea, bacteria, cyanobacteria, yeasts, and filamentous fungi.

Contributions may belong to:

  • Bioprospecting for novel strains;
  • Microbial diversity, interactions, and ecological functions (polar, hydrothermal vents, deep-sea, coastal, etc.);
  • Novel bioactive compound characterization, scale-up, safety assessment, production;
  • Food industry applications;
  • Cosmetic industry;
  • Biopolymers;
  • Human and animal health and wellness;
  • Plant production and health;
  • Biofuels and bioenergy;
  • Sustainable production of biosourced chemical products (e.g., 1,3-propanediol, acrylic acid, succinic acid, glycerol);
  • Microbial fatty acids (e.g., Omega-3, Omega-6, polyunsaturated fatty acids PUFAs);
  • Vitamins;
  • Flavors, pigments, and colorants;
  • Surfactants;
  • Bio-adhesives;
  • Biodegradable plastics;
  • Novel methods in the production of “blue” microbial compounds.

References

Kafarski, P. Rainbow code of biotechnology. Chemik 2012, 66, 814–816.

Barcelos, M.C.S.; Lupki, F.B.; Campolina, G.A.; Nelson, D.L.; Molina, G. The colors of biotechnology: General overview and developments of white, green and blue areas. FEMS Microbiology Letters 2018, 365, fny239.

Prof. Dr. Laurent Dufossé
Dr. Ramesh Chatragadda
Guest Editors

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Published Papers (6 papers)

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Editorial

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2 pages, 201 KiB  
Editorial
Blue Microbiology—Aquatic Microbial Resources for Sustainable Life on Earth
by Chatragadda Ramesh and Laurent Dufossé
Microorganisms 2023, 11(3), 808; https://doi.org/10.3390/microorganisms11030808 - 22 Mar 2023
Viewed by 1285
Abstract
The exploration of the microbial world in research continues to be fascinating and unending in several aspects of taxonomy, genomics, evolution, and industrial applications [...] Full article

Research

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13 pages, 2367 KiB  
Article
Isolation and Properties of the Bacterial Strain Janthinobacterium sp. SLB01
by Lubov Chernogor, Kseniya Bakhvalova, Alina Belikova and Sergei Belikov
Microorganisms 2022, 10(5), 1071; https://doi.org/10.3390/microorganisms10051071 - 23 May 2022
Cited by 5 | Viewed by 2631
Abstract
Bacteria of the genus Janthinobacterium are widespread in soils and freshwater ecosystems and belong to the phylum Proteobacteria. The Janthinobacterium sp. SLB01 strain was isolated from diseased freshwater Lubomirskia baicalensis (Pallas, 1776) sponge, and the draft genome was published previously. However, the properties [...] Read more.
Bacteria of the genus Janthinobacterium are widespread in soils and freshwater ecosystems and belong to the phylum Proteobacteria. The Janthinobacterium sp. SLB01 strain was isolated from diseased freshwater Lubomirskia baicalensis (Pallas, 1776) sponge, and the draft genome was published previously. However, the properties of the SLB01 strain are not known. The aim of the study is to describe some properties of the Janthinobacterium sp. SLB01 strain, isolated from L. baicalensis sponge. The identification of the SLB01 strain was established as Gram-negative, motile, rod-shaped, and psychrotolerant, with growth at 3 and 22 °C. We found that the SLB01 strain has proteolytic, lipolytic, and saccharolytic activity and can use citrates and reduce nitrates. The bacteria Janthinobacterium sp. SLB01 strain can grow, form biofilms, and produce the violet pigment violacein. We identified the pigments violacein and deoxyviolacein by chromatography and mass spectrometry. These metabolites may be of interest to biotechnology in the future. The studied characteristics of the Janthinobacterium sp. SLB01 strain are an important addition to previous studies of the genome of this strain. This study will help us to understand the relationship between the microbial communities of Lake Baikal and sponges. Full article
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10 pages, 923 KiB  
Article
Identification and Characterization of Marine Microorganisms by Tandem Mass Spectrometry Proteotyping
by Clément Lozano, Mélodie Kielbasa, Jean-Charles Gaillard, Guylaine Miotello, Olivier Pible and Jean Armengaud
Microorganisms 2022, 10(4), 719; https://doi.org/10.3390/microorganisms10040719 - 26 Mar 2022
Cited by 16 | Viewed by 3021
Abstract
The vast majority of marine microorganisms and their functions are yet to be explored. The considerable diversity they encompass is an endless source of knowledge and wealth that can be valued on an industrial scale, emphasizing the need to develop rapid and efficient [...] Read more.
The vast majority of marine microorganisms and their functions are yet to be explored. The considerable diversity they encompass is an endless source of knowledge and wealth that can be valued on an industrial scale, emphasizing the need to develop rapid and efficient identification and characterization techniques. In this study, we identified 26 microbial isolates from coastal water of the NW Mediterranean Sea, using phylopeptidomics, a cutting-edge tandem mass spectrometry proteotyping technique. Taxonomical identification at the species level was successfully conducted for all isolates. The presence of strains belonging to the newly described Balneolaeota phylum, yet uncharacterized at the proteomics scale, was noted. The very first proteomics-based investigation of a representative of the Balneolaeota phylum, Balneola vulgaris, is proposed, demonstrating the use of our proteotyping workflow for the rapid identification and in-depth molecular characterization, in a single MS/MS analytical run. Tandem mass spectrometry proteotyping is a valuable asset for culturomic programs as the methodology is able to quickly classify the most atypical isolates. Full article
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17 pages, 4048 KiB  
Article
Complete Genome Analysis of Undecylprodigiosin Pigment Biosynthesizing Marine Streptomyces Species Displaying Potential Bioactive Applications
by Chatragadda Ramesh, Maile Anwesh, Nambali Valsalan Vinithkumar, Ramalingam Kirubagaran and Laurent Dufossé
Microorganisms 2021, 9(11), 2249; https://doi.org/10.3390/microorganisms9112249 - 28 Oct 2021
Cited by 5 | Viewed by 3010
Abstract
Marine Streptomyces species are underexplored for their pigment molecules and genes. In this study, we report the genome of the undecylprodigiosin biosynthesizing gene cluster carrying Streptomyces sp. strain BSE6.1, displaying antioxidant, antimicrobial, and staining properties. This Gram-positive obligate aerobic bacterium was isolated from [...] Read more.
Marine Streptomyces species are underexplored for their pigment molecules and genes. In this study, we report the genome of the undecylprodigiosin biosynthesizing gene cluster carrying Streptomyces sp. strain BSE6.1, displaying antioxidant, antimicrobial, and staining properties. This Gram-positive obligate aerobic bacterium was isolated from the coastal sediment of the Andaman and Nicobar Islands, India. Pink to reddish pigmented colonies with whitish powdery spores on both agar and broth media are the important morphological characteristics of this bacterium. Growth tolerance to NaCl concentrations was 2 to 7%. The assembled genome of Streptomyces sp. BSE6.1 contains one linear chromosome 8.02 Mb in length with 7157 protein-coding genes, 82 tRNAs, 3 rRNAs and at least 11 gene clusters related to the synthesis of various secondary metabolites, including undecylprodigiosin. This strain carries type I, type II, and type III polyketide synthases (PKS) genes. Type I PKS gene cluster is involved in the biosynthesis of red pigment undecylprodigiosin of BSE6.1, similar to the one found in the S. coelicolor A3(2). This red pigment was reported to have various applications in the food and pharmaceutical industries. The genome of Streptomyces sp. BSE6.1 was submitted to NCBI with a BioProject ID of PRJNA514840 (Sequence Read Archive ID: SRR10849367 and Genome accession ID: CP085300). Full article
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Review

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17 pages, 2050 KiB  
Review
Marine Bioprospecting, Biocatalysis and Process Development
by Carlos J. C. Rodrigues and Carla C. C. R. de Carvalho
Microorganisms 2022, 10(10), 1965; https://doi.org/10.3390/microorganisms10101965 - 5 Oct 2022
Cited by 2 | Viewed by 2976
Abstract
Oceans possess tremendous diversity in microbial life. The enzymatic machinery that marine bacteria present is the result of extensive evolution to assist cell survival under the harsh and continuously changing conditions found in the marine environment. Several bacterial cells and enzymes are already [...] Read more.
Oceans possess tremendous diversity in microbial life. The enzymatic machinery that marine bacteria present is the result of extensive evolution to assist cell survival under the harsh and continuously changing conditions found in the marine environment. Several bacterial cells and enzymes are already used at an industrial scale, but novel biocatalysts are still needed for sustainable industrial applications, with benefits for both public health and the environment. Metagenomic techniques have enabled the discovery of novel biocatalysts, biosynthetic pathways, and microbial identification without their cultivation. However, a key stage for application of novel biocatalysts is the need for rapid evaluation of the feasibility of the bioprocess. Cultivation of not-yet-cultured bacteria is challenging and requires new methodologies to enable growth of the bacteria present in collected environmental samples, but, once a bacterium is isolated, its enzyme activities are easily measured. High-throughput screening techniques have also been used successfully, and innovative in vitro screening platforms to rapidly identify relevant enzymatic activities continue to improve. Small-scale approaches and process integration could improve the study and development of new bioprocesses to produce commercially interesting products. In this work, the latest studies related to (i) the growth of marine bacteria under laboratorial conditions, (ii) screening techniques for bioprospecting, and (iii) bioprocess development using microreactors and miniaturized systems are reviewed and discussed. Full article
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Other

16 pages, 1842 KiB  
Perspective
Pathways for Understanding Blue Carbon Microbiomes with Amplicon Sequencing
by Valentina Hurtado-McCormick, Stacey M. Trevathan-Tackett, Jennifer L. Bowen, Rod M. Connolly, Carlos M. Duarte and Peter I. Macreadie
Microorganisms 2022, 10(11), 2121; https://doi.org/10.3390/microorganisms10112121 - 26 Oct 2022
Cited by 3 | Viewed by 2703
Abstract
The capacity of Blue Carbon Ecosystems to act as carbon sinks is strongly influenced by the metabolism of soil-associated microbes, which ultimately determine how much carbon is accumulated or returned to the atmosphere. The rapid evolution of sequencing technologies has facilitated the generation [...] Read more.
The capacity of Blue Carbon Ecosystems to act as carbon sinks is strongly influenced by the metabolism of soil-associated microbes, which ultimately determine how much carbon is accumulated or returned to the atmosphere. The rapid evolution of sequencing technologies has facilitated the generation of tremendous amounts of data on what taxa comprise belowground microbial assemblages, largely available as isolated datasets, offering an opportunity for synthesis research that informs progress on understanding Blue Carbon microbiomes. We identified questions that can be addressed with a synthesis approach, including the high variability across datasets, space, and time due to differing sampling techniques, ecosystem or vegetation specificity, and the relationship between microbiome community and edaphic properties, particularly soil carbon. To address these questions, we collated 34 16S rRNA amplicon sequencing datasets, including bulk soil or rhizosphere from seagrass, mangroves, and saltmarshes within publicly available repositories. We identified technical and theoretical challenges that precluded a synthesis of multiple studies with currently available data, and opportunities for addressing the knowledge gaps within Blue Carbon microbial ecology going forward. Here, we provide a standardisation toolbox that supports enacting tasks for the acquisition, management, and integration of Blue Carbon-associated sequencing data and metadata to potentially elucidate novel mechanisms behind Blue Carbon dynamics. Full article
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