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Genomics of Marine and Aquatic Bacteria: A Focus on Novel...
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Genomics of Marine and Aquatic Bacteria: A Focus on Novel Taxa, Diversity and Biotechnological Potential, 3rd Edition

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

Deadline for manuscript submissions: 30 September 2026 | Viewed by 4755

Special Issue Editors

Dr. Alexander Machado Cardoso

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Guest Editor
Department of Biology, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
Interests: environmental biotechnology; environmental sciences; microbial diversity and metagenome
Special Issues, Collections and Topics in MDPI journals
Dr. Marina Isaeva

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Guest Editor
G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Russia
Interests: genomics; phylogeny; biochemistry; genome bioprospecting
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The current Special Issue is a continuation of the Special Issue “Genomics of Marine and Aquatic Bacteria: A Focus on Novel Taxa, Diversity and Biotechnological Potential” (https://www.mdpi.com/journal/microorganisms/special_issues/DQMJE03822).

Marine and aquatic bacteria represent an enormous portion of biodiversity and are a valuable bioprospecting source in the search for novel bioactive compounds, functional food ingredients, and polymers. Our knowledge regarding the bacterial world has been greatly advanced by exploring bacterial genome sequences, especially in bacterial systematics, genetic diversity, and microbial evolution. Advances in genomics promote the application of genetic information of bacteria in virtually unlimited areas. To describe new taxa, environmental microbiologists have to combine culture-dependent studies with genome sequence analyses. Research on bacteria recovered from underexplored, remote, and extreme environments, such as arctic seas, the deep sea, or underground waters and sediments, is a challenge for understanding microbial diversity, its conservation, and further biotechnological use. We firmly believe that new taxa will result in new genes, new knowledge, and new opportunities.

Dr. Alexander Machado Cardoso
Dr. Marina Isaeva
Guest Editors

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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.

Keywords

  • bacteria
  • diversity
  • bacterial communities
  • novel taxa
  • phylogeny
  • genome analysis
  • marine and aquatic environments

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Published Papers (5 papers)

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14 pages, 1172 KB  
Article
Genomic and Phenotypic Insights into Carbapenem-Resistant Pseudomonas aeruginosa in the Aquatic Environments of the Tibetan Plateau
by Dingxiang Lu, Lin Liu, Zhongwei Yang, Tianjiao Chen, Dong Yang, Danyang Shi, Shuqing Zhou, Junwen Li, Haibei Li and Min Jin
Microorganisms 2026, 14(5), 1094; https://doi.org/10.3390/microorganisms14051094 - 12 May 2026
Abstract
Carbapenem-resistant Pseudomonas aeruginosa is increasingly becoming a global health threat. However, although aquatic environments are key resistance reservoirs, data obtained from high-altitude ecosystems are scarce. Whole-genome sequencing of eight carbapenem-resistant P. aeruginosa isolates collected from aquatic environments in the Tibetan Plateau identified three [...] Read more.
Carbapenem-resistant Pseudomonas aeruginosa is increasingly becoming a global health threat. However, although aquatic environments are key resistance reservoirs, data obtained from high-altitude ecosystems are scarce. Whole-genome sequencing of eight carbapenem-resistant P. aeruginosa isolates collected from aquatic environments in the Tibetan Plateau identified three sequence types (STs), with ST1420 predominating (62.5%, 5/8). Phylogenetic analysis revealed a close clustering of isolates with those from distant clinical settings, suggesting potential cross-habitat transmission. All studied strains were multidrug-resistant, exhibiting 100% resistance to imipenem, ceftriaxone, and trimethoprim–sulfamethoxazole. This included the PA6 strain, which showed multiple-antibiotic resistance. Eight strains harbored the intrinsic carbapenemase gene blaOXA-50. The diverse virulence-gene profiles of strains PA2, PA4, and PA6 aligned with their high pathogenicity observed both in vitro and in vivo. However, virulence genotypes sometimes did not correlate with phenotypes, revealing the limitations of relying on static genetic information alone. This study highlights the aquatic environments of the Tibetan Plateau as reservoirs of carbapenem-resistant P. aeruginosa with substantial genetic diversity and divergent pathogenic potential, underscoring their public-health relevance. Full article
(This article belongs to the Special Issue Genomics of Marine and Aquatic Bacteria: A Focus on Novel Taxa, Diversity and Biotechnological Potential, 3rd Edition)
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16 pages, 2249 KB  
Article
Apolloniradiicaulis salifontis gen. nov., sp. nov., a New Prosthecate Aerobic Anoxygenic Phototroph Isolated from Lake Winnipegosis Region Salt Springs
by Katia Messner, Caleb Pereira, John A. Kyndt, Marike Palmer and Vladimir Yurkov
Microorganisms 2026, 14(3), 525; https://doi.org/10.3390/microorganisms14030525 - 25 Feb 2026
Viewed by 582
Abstract
A pink colored, rod-shaped, prosthecate, Gram-negative bacterial strain MS644T was discovered in saline spring water near Lake Winnipegosis, Manitoba, Canada. It produces bacteriochlorophyll a, which is incorporated into its reaction center and light harvesting I complex. Alongside no anaerobic or photoautotrophic [...] Read more.
A pink colored, rod-shaped, prosthecate, Gram-negative bacterial strain MS644T was discovered in saline spring water near Lake Winnipegosis, Manitoba, Canada. It produces bacteriochlorophyll a, which is incorporated into its reaction center and light harvesting I complex. Alongside no anaerobic or photoautotrophic growth, these features support its designation as an aerobic anoxygenic phototroph (AAP). Unlike most AAP, the photosynthetic apparatus is produced in significantly greater amounts compared to carotenoids. Sequence of the 16S rRNA gene identified relatedness to Glycocaulis albus (96.19%), Glycocaulis alkaliphilus (96.12%) and Glycocaulis abyssi (96.07%). The DNA G + C content was 66.01 mol %. Differences in salt tolerance and photosynthesis capability, alongside low average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization compared to other Maricauaceae, support the designation of the strain as a representative of a new genus. Therefore, we propose that strain MS644T (=NCIMB 15625T = DSM 121292T) be classified as the type species of a new genus Apolloniradiicaulis in Maricaulaceae with the name A. salifontis gen. nov., sp. nov. Full article
(This article belongs to the Special Issue Genomics of Marine and Aquatic Bacteria: A Focus on Novel Taxa, Diversity and Biotechnological Potential, 3rd Edition)
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25 pages, 2488 KB  
Article
Characterization of an Atypical GH19 Family Chitinase from Vibrio jasicida KMM 6832
by Yulia Noskova, Iuliia Pentekhina, Alexandra Seitkalieva, Olga Nedashkovskaya, Yulia Goroshkova and Larissa Balabanova
Microorganisms 2026, 14(2), 443; https://doi.org/10.3390/microorganisms14020443 - 12 Feb 2026
Viewed by 612
Abstract
The highly chitinolytic marine bacterium Vibrio jasicida KMM 6832, which exhibits potent antifungal activity, possesses an atypical Glycosyl Hydrolase family 19 (GH19) chitinase (ChitVjs). This is the first report of a GH19 gene in V. jasicida, an enzyme generally absent in this [...] Read more.
The highly chitinolytic marine bacterium Vibrio jasicida KMM 6832, which exhibits potent antifungal activity, possesses an atypical Glycosyl Hydrolase family 19 (GH19) chitinase (ChitVjs). This is the first report of a GH19 gene in V. jasicida, an enzyme generally absent in this species and rare within the Harveyi clade. Phylogenetically, ChitVjs-like enzymes from the genera Vibrio and Aeromonas form a distinct cluster, separate from typical plant and bacterial GH19 counterparts. Despite high sequence identity (80–94%) with characterized homologs from V. parahaemolyticus and V. cholerae, ChitVjs is distinguished by its obligate halophilicity (optimum 0.3–0.4 M NaCl), an acidic isoelectric point (pI 4.72), and a broader cation-activation profile (K+, Ni2+, Ca2+, Cu2+, Co2+). The recombinant ChitVjs was produced in E. coli as a soluble 63 kDa protein. It functions as a stable, salt-dependent endo-chitinase/chitosanase, exhibiting optimal activity at 40 °C and pH 7.0. The enzyme displays high affinity for colloidal chitin (KM 0.377 mg·mL−1), is activated by DTT and Tween 80, and shows moderate stability in organic solvents. Furthermore, unlike its primarily catabolic relatives, ChitVjs suppresses conidial germination in marine-derived Aspergillus strains. These findings suggest that ChitVjs significantly contributes to the competitive fitness of V. jasicida KMM 6832 in high-salinity marine environments through both nutrient acquisition and antagonism. Full article
(This article belongs to the Special Issue Genomics of Marine and Aquatic Bacteria: A Focus on Novel Taxa, Diversity and Biotechnological Potential, 3rd Edition)
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20 pages, 4363 KB  
Article
Genome-Based Reclassification of [Bizionia] algoritergicola Bowman and Nichols 2005 as Algorimicrobium algoritergicola gen. nov., comb. nov. and description of Algorimicrobium bowmanii sp. nov.
by Valeriya Kurilenko, Evgeniya Bystritskaya, Nadezhda Otstavnykh, Peter Velansky, Sergey Baldaev, Viacheslav Eremeev, Natalya Ageenko, Konstantin Kiselev, Olga Nedashkovskaya and Marina Isaeva
Microorganisms 2026, 14(1), 24; https://doi.org/10.3390/microorganisms14010024 - 21 Dec 2025
Cited by 1 | Viewed by 1046
Abstract
The genus Bizionia, a member of the Bacteroidota phylum, is considered a polyphyletic taxonomic group requiring a phylogenetic revision of its members. A novel strain 041-53-Ur-6T was isolated from the cavity fluid of the sea urchin Strongylocentrotus intermedius from the Sea [...] Read more.
The genus Bizionia, a member of the Bacteroidota phylum, is considered a polyphyletic taxonomic group requiring a phylogenetic revision of its members. A novel strain 041-53-Ur-6T was isolated from the cavity fluid of the sea urchin Strongylocentrotus intermedius from the Sea of Okhotsk. Analysis of the 16S rRNA gene sequence showed that 041-53-Ur-6T belongs to the family Flavobacteriaceae, and its closest neighbor is [Bizionia] algoritergicola with 97.5% sequence similarity. Phylogenomic analysis confirmed the phylogenetic heterogeneity of the genus Bizionia and the clear separation of the genera “Algorimicrobium” and Hanstruepera. The inter-genus AAI values between them were 74.0–76.4%, which is slightly lower than the inter-species AAI values observed for each genus. The strain 041-53-Ur-6T (= KMM 8389T) formed a separated branch within the [B.] algoritergicola clade, demonstrating the highest ANI/AAI values of 80.1/81.0% with the strain [B.] algoritergicola APA-1T. The dDDH values between strain KMM 8389T and representatives of the genus “Algorimicrobium” ranged from 22.6% to 26.7%. Major fatty acids were iso-C15:1 ω10c, iso-C15:0 and iso-C15:0 Δ2-OH. The polar lipids included a phosphatidylethanolamine, a phosphatidylglycerol, five unidentified lipids, two unidentified aminolipids, a phosphatidylcholine, and an unidentified aminophospholipid. The genome KMM 8389T is a circular chromosome of 3,031,910 bp in size with a DNA G + C content of 33.5%. It comprises 2702 protein-coding genes and four rrn operons. Functional genomic analysis indicated the potential of KMM 8389T for degrading starch, glycogen, and alginate due to the presence of genes encoding GH13, GH31, and GH65. Furthermore, KMM 8389T possessed PLs 6, 7, 12, and 17, specialized for alginate, confirming the potential adaptation of this strain to algal substrates and surfaces. On the basis of the results of genotypic, chemotaxonomic, and phenotypic analyses, it is clear that the strain KMM 8389T represents a novel species with [B.] algoritergicola, [B.] argentinensis, [B.] echini, [B.] hallyeonensis, [B.] myxarmorum, [B.] psychrotolerans, and [B.] sediminis as the nearest neighbors. These taxa are classified in a single novel genus, as Algorimicrobium algoritergicola gen. nov., comb. nov., A. argentinensis comb. nov., A. echini comb. nov., A. hallyeonensis comb. nov., A. myxarmorum comb. nov., A. psychrotolerans comb. nov., A. sediminis comb. nov., and Algorimicrobium bowmanii sp. nov. 041-53-Ur-6T (=KMM 8389T, =KCTC 72011T). Full article
(This article belongs to the Special Issue Genomics of Marine and Aquatic Bacteria: A Focus on Novel Taxa, Diversity and Biotechnological Potential, 3rd Edition)
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23 pages, 3860 KB  
Article
Alteromonas nitratireducens sp. nov., a Novel Nitrate-Reducing Bacterium Isolated from Marine Sediments, and the Evolution of Nitrate-Reducing Genes in the Genus Alteromonas
by Ying-Li Chang, Jia-Xi Li, Xing-Chen Wang, Yang Li, Yun-Fei Cao, Xiang-Wen Duan, Cong Sun, Can Chen and Lin Xu
Microorganisms 2025, 13(8), 1888; https://doi.org/10.3390/microorganisms13081888 - 13 Aug 2025
Cited by 4 | Viewed by 1906
Abstract
Nitrate reduction serves as a pivotal process in the global nitrogen cycle, playing a crucial role in natural ecosystems and industrial applications. Although the genus Alteromonas is not traditionally regarded as a nitrate reducer, several Alteromonas strains have recently been found to be [...] Read more.
Nitrate reduction serves as a pivotal process in the global nitrogen cycle, playing a crucial role in natural ecosystems and industrial applications. Although the genus Alteromonas is not traditionally regarded as a nitrate reducer, several Alteromonas strains have recently been found to be capable of doing so. However, the evolutionary trajectory of this capability remains undiscovered. In this study, 32 bacterial strains were isolated and cultivated from the tidal flat sediment in Hangzhou Bay and classified into the classes Cytophagia (n = 2), Alphaproteobacteria (n = 2), Gammaproteobacteria (n = 17), Flavobacteriia (n = 5), and Bacilli (n = 6). One nitrate-reducing strain, designated as CYL-A6T, was identified by polyphasic taxonomy and proposed as a novel Alteromonas species. Genomic analysis reveals that seven Alteromonas genomes encode the dissimilatory nitrate reduction genes narGHI. Evolutionary analysis showed that these three nitrate-reducing genes were present in the early common ancestor of the genus Alteromonas, while gene loss events occurred in the subsequent evolution. With the loss of nitrate-reducing genes in the ancestry nodes, a wide variety of genes related to energy production and conversion, as well as carbohydrate, nucleotide, coenzyme, and inorganic ion metabolism, were gained in those nodes, which enabled Alteromonas members to utilize diverse substrates for increased energy production. This study enhances the understanding of microbial diversity in marine tidal flat sediments, proposes a novel nitrate-reducing species of the genus Alteromonas, and highlights the ecological diversification and ecological niche breadth in the evolution of the microbial metabolic network. Full article
(This article belongs to the Special Issue Genomics of Marine and Aquatic Bacteria: A Focus on Novel Taxa, Diversity and Biotechnological Potential, 3rd Edition)
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