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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: 2nd Edition

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

Deadline for manuscript submissions: 15 March 2025 | Viewed by 7160

Special Issue Editor

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

Special Issue Information

Dear Colleagues,

The current issue is a continuation of the Special Issue “Genomics of Marine and Aquatic Bacteria: A Focus on Novel Taxa, Diversity and Biotechnological Potential”.

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
Guest Editor

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Keywords

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

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Published Papers (7 papers)

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Research

19 pages, 3078 KiB  
Article
Sulfate-Reducing Bacteria Isolated from an Oil Field in Kazakhstan and a Description of Pseudodesulfovibrio karagichevae sp. nov.
by Salimat K. Bidzhieva, Tatyana P. Tourova, Denis S. Grouzdev, Salima R. Samigullina, Diyana S. Sokolova, Andrey B. Poltaraus, Alexander N. Avtukh, Vera M. Tereshina, Andrey V. Mardanov, Nurlan S. Zhaparov and Tamara N. Nazina
Microorganisms 2024, 12(12), 2552; https://doi.org/10.3390/microorganisms12122552 - 11 Dec 2024
Viewed by 444
Abstract
Sulfidogenic bacteria cause numerous issues in the oil industry since they produce sulfide, corroding steel equipment, reducing oil quality, and worsening the environmental conditions in oil fields. The purpose of this work was to isolate and taxonomically identify the sulfidogenic bacteria responsible for [...] Read more.
Sulfidogenic bacteria cause numerous issues in the oil industry since they produce sulfide, corroding steel equipment, reducing oil quality, and worsening the environmental conditions in oil fields. The purpose of this work was to isolate and taxonomically identify the sulfidogenic bacteria responsible for the corrosion of steel equipment at the Karazhanbas oil field (Kazakhstan). In this study, we characterized five sulfidogenic strains of the genera Pseudodesulfovibrio, Oleidesulfovibrio, and Acetobacterium isolated from the formation water of the Karazhanbas oil field (Kazakhstan). Sulfate-reducing strain 9FUST revealed 98.9% similarity of the 16S rRNA gene sequence with the closely related strain ‘Pseudodesulfovibrio methanolicus’ 5S69T and was studied in detail to enhance the taxonomic resolution. Strain 9FUST grew optimally at 23–28 °C, pH 6.5, and 0–2% (w/v) NaCl. The strain used lactate, pyruvate, methanol, ethanol, fructose, ribose, and H2/CO2 (in the presence of acetate) as carbon and energy sources for sulfate reduction. Iso-C17:1 ω11, C15:0, iso-C15:0, and C16:0 were the predominant fatty acids. The genome is 4.20 Mbp with a G + C content of 64.0%. The average nucleotide identity and digital DNA–DNA hybridization values with Pseudodesulfovibrio spp. genomes were 72.5–91.6% (<95%) and 18.5–45.0% (<70%), respectively, and supported our conclusion that 9FUST (=VKM B-3654T = KCTC 25498T) belonged to a novel Pseudodesulfovibrio species, for which the name Pseudodesulfovibrio karagichevae sp. nov. is proposed. Pangenome analysis of sixteen Pseudodesulfovibrio species and functional annotation analysis of identified genes revealed complete modules of enzymes of the main metabolic pathways, characteristic of bacteria of this genus, and unique genes highlighting the adaptations of strain 9FUST in carbohydrate metabolism, nutrient uptake, and environmental stress response. Isolation of these strains expands our understanding of the diversity of sulfidogens in oil reservoirs and can be used to test the effectiveness of biocides used in an oil field. Full article
(This article belongs to the Special Issue Genomics of Marine and Aquatic Bacteria: A Focus on Novel Taxa, Diversity and Biotechnological Potential: 2nd Edition)
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10 pages, 3532 KiB  
Article
Genomic Insights into Stutzerimonas kunmingensis TFRC-KFRI-1 Isolated from Manila Clam (Ruditapes philippinarum): Functional and Phylogenetic Analysis
by Myunglip Lee, Sunghun Yi, Jiho Choi, Yukyoung Pak, Chaehyeon Lim and Yucheol Kim
Microorganisms 2024, 12(12), 2402; https://doi.org/10.3390/microorganisms12122402 - 23 Nov 2024
Viewed by 466
Abstract
Stutzerimonas kunmingensis TFRC-KFRI-1, isolated from the gut of Manila Clam in the sediment of the West Sea of Korea, was investigated for its potential as a probiotic bacterium. This strain, belonging to the family Pseudomonadaceae, was previously classified as Pseudomonas kunmingensis but [...] Read more.
Stutzerimonas kunmingensis TFRC-KFRI-1, isolated from the gut of Manila Clam in the sediment of the West Sea of Korea, was investigated for its potential as a probiotic bacterium. This strain, belonging to the family Pseudomonadaceae, was previously classified as Pseudomonas kunmingensis but later reclassified to the genus Stutzerimonas, known for species with bioremediation and probiotic properties. To evaluate its genomic features and potential applications, we performed draft-genome sequencing and analysis. The genome of S. kunmingensis TFRC-KFRI-1 was assembled into a 4,756,396 bp sequence with a 62.8% GC content. Genomic analysis suggested potential genes for carbohydrate degradation and lactic acid production. The strain exhibited high average nucleotide identity (ANI) and 16S rRNA similarity with S. kunmingensis HL22-2T, further supporting its potential as a probiotic. This genome sequence provides valuable insights into the functional capabilities of S. kunmingensis TFRC-KFRI-1 and its potential applications in various industries, including aquaculture and food biotechnology. The genome sequence is available under GenBank accession number JBGJJB000000000.1, with related project information under BioProject PRJNA1147901 and Bio-Sample SAMN43173893. Full article
(This article belongs to the Special Issue Genomics of Marine and Aquatic Bacteria: A Focus on Novel Taxa, Diversity and Biotechnological Potential: 2nd Edition)
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12 pages, 1382 KiB  
Article
Salinarimonas chemoclinalis, an Aerobic Anoxygenic Phototroph Isolated from a Saline, Sulfate-Rich Meromictic Lake
by Katia Messner, John A. Kyndt and Vladimir Yurkov
Microorganisms 2024, 12(11), 2359; https://doi.org/10.3390/microorganisms12112359 - 19 Nov 2024
Viewed by 504
Abstract
A pink-pigmented, ovoid-rod-shaped, Gram-negative bacterial strain ML10T was previously isolated in a study of a meromictic lake in British Columbia, Canada. It produces bacteriochlorophyll a, which is incorporated into the reaction center and light harvesting I complexes. This alongside no anaerobic [...] Read more.
A pink-pigmented, ovoid-rod-shaped, Gram-negative bacterial strain ML10T was previously isolated in a study of a meromictic lake in British Columbia, Canada. It produces bacteriochlorophyll a, which is incorporated into the reaction center and light harvesting I complexes. This alongside no anaerobic or photoautotrophic growth supports the designation of the strain as an aerobic anoxygenic phototroph. The cells produce wavy polar flagellum and accumulate clear, refractive granules, presumed to be polyhydroxyalkanoate. Sequence of the 16S rRNA gene identified close relatedness to Salinarimonas rosea (97.85%), Salinarimonas ramus (97.92%) and Saliniramus fredricksonii (94.61%). The DNA G + C content was 72.06 mol %. Differences in cellular fatty acids and some physiological tests compared to Salinarimonadaceae members, as well as average nucleotide identity and digital DNA-DNA hybridization, define the strain as a new species in Salinarimonas. Therefore, we propose that ML10T (=NCIMB 15586T = DSM 118510T) be classified as the type strain of a new species in the genus with the name Salinarimonas chemoclinalis 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: 2nd Edition)
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10 pages, 3817 KiB  
Article
Brevundimonas aurifodinae, sp. nov., an Aerobic Anoxygenic Phototroph Resistant to Metalloid Oxyanions Isolated from Gold Mine Tailings
by Chris Maltman, Katia Messner, John A. Kyndt and Vladimir Yurkov
Microorganisms 2024, 12(11), 2167; https://doi.org/10.3390/microorganisms12112167 - 27 Oct 2024
Cited by 1 | Viewed by 828
Abstract
A polyphasic taxonomic study was carried out on the rod-shaped, orange-pigmented strain C11T, isolated from gold mine tailings. Sequencing of the 16S rRNA gene showed a relatedness to Brevundimonas, with a 98.4% and 98.2% similarity to Brevundimonas bacteroides and Brevundimonas [...] Read more.
A polyphasic taxonomic study was carried out on the rod-shaped, orange-pigmented strain C11T, isolated from gold mine tailings. Sequencing of the 16S rRNA gene showed a relatedness to Brevundimonas, with a 98.4% and 98.2% similarity to Brevundimonas bacteroides and Brevundimonas variabilis, respectively. The average nucleotide identity and a digital DNA–DNA hybridization with the closest phylogenetic neighbor of strain C11T indicate distinction at the species level, further confirmed by the differences in physiology. C18:1 ω7c is the dominant cellular fatty acid. Its DNA G + C content is 68.3 mol %. Its predominant ubiquinone is Q-10; 1,2-Di-O-acyl-3-O-α-D-glucopyranuronosyl glycerol, phosphatidylglycerol, 1,2-di-O-acyl-3-O-α-D-glucopyranosyl glycerol, and 1,2-di-O-acyl-3-O-[D-glucopyranosyl-(1→4)-α-D-glucopyranuronosyl] glycerol are its major polar lipid constituents. This bacterium produces bacteriochlorophyll a and tolerates high concentrations of (μg/mL) the following: tellurium (>1500), selenium (1000 to >5000), and vanadium (>5000) oxyanions. The data support the inclusion of the strain C11T into the genus Brevundimonas as a new species with the proposed name Brevundimonas aurifodinae sp. nov. (C11T = NRRL B-61758T; =DSM 118059T). Full article
(This article belongs to the Special Issue Genomics of Marine and Aquatic Bacteria: A Focus on Novel Taxa, Diversity and Biotechnological Potential: 2nd Edition)
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15 pages, 2991 KiB  
Article
The Phylogeny and Metabolic Potentials of an Aromatics-Degrading Marivivens Bacterium Isolated from Intertidal Seawater in East China Sea
by Chengwen Sun, Zekai Wang, Xi Yu, Hongcai Zhang, Junwei Cao, Jiasong Fang, Jiahua Wang and Li Zhang
Microorganisms 2024, 12(7), 1308; https://doi.org/10.3390/microorganisms12071308 - 27 Jun 2024
Viewed by 1235
Abstract
Lignocellulosic materials, made up of cellulose, hemicellulose, and lignin, constitute some of the most prevalent types of biopolymers in marine ecosystems. The degree to which marine microorganisms participate in the breakdown of lignin and their impact on the cycling of carbon in the [...] Read more.
Lignocellulosic materials, made up of cellulose, hemicellulose, and lignin, constitute some of the most prevalent types of biopolymers in marine ecosystems. The degree to which marine microorganisms participate in the breakdown of lignin and their impact on the cycling of carbon in the oceans is not well understood. Strain LCG002, a novel Marivivens species isolated from Lu Chao Harbor’s intertidal seawater, is distinguished by its ability to metabolize lignin and various aromatic compounds, including benzoate, 3-hydroxybenzoate, 4-hydroxybenzoate and phenylacetate. It also demonstrates a broad range of carbon source utilization, including carbohydrates, amino acids and carboxylates. Furthermore, it can oxidize inorganic gases, such as hydrogen and carbon monoxide, providing alternative energy sources in diverse marine environments. Its diversity of nitrogen metabolism is supported by nitrate/nitrite, urea, ammonium, putrescine transporters, as well as assimilatory nitrate reductase. For sulfur assimilation, it employs various pathways to utilize organic and inorganic substrates, including the SOX system and DSMP utilization. Overall, LCG002’s metabolic versatility and genetic profile contribute to its ecological significance in marine environments, particularly in the degradation of lignocellulosic material and aromatic monomers. Full article
(This article belongs to the Special Issue Genomics of Marine and Aquatic Bacteria: A Focus on Novel Taxa, Diversity and Biotechnological Potential: 2nd Edition)
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15 pages, 4331 KiB  
Article
Functional Genes and Transcripts Indicate the Existent and Active Microbial Mercury-Methylating Community in Mangrove Intertidal Sediments of an Urbanized Bay
by Guofang Feng and Sanqiang Gong
Microorganisms 2024, 12(6), 1245; https://doi.org/10.3390/microorganisms12061245 - 20 Jun 2024
Viewed by 918
Abstract
Mercury (Hg) methylation in mangrove sediments can result in the accumulation of neurotoxic methylmercury (MeHg). Identification of Hg methyltransferase gene hgcA provides the means to directly characterize the microbial Hg-methylating consortia in environments. Hitherto, the microbial Hg-methylating community in mangrove sediments was scarcely [...] Read more.
Mercury (Hg) methylation in mangrove sediments can result in the accumulation of neurotoxic methylmercury (MeHg). Identification of Hg methyltransferase gene hgcA provides the means to directly characterize the microbial Hg-methylating consortia in environments. Hitherto, the microbial Hg-methylating community in mangrove sediments was scarcely investigated. An effort to assess the diversity and abundance of hgcA genes and transcripts and link them to Hg and MeHg contents was made in the mangrove intertidal sediments along the urbanized Shenzhen Bay, China. The hgcA genes and transcripts associated with Thermodesulfobacteria [mainly Geobacteraceae, Syntrophorhabdaceae, Desulfobacterales, and Desulfarculales (these four lineages were previously classified into the Deltaproteobacteria taxon)], as well as Euryarchaeota (mainly Methanomicrobia and Theionarchaea) dominated the hgcA-harboring communities, while Chloroflexota, Nitrospirota, Planctomycetota, and Lentisphaerota-like hgcA sequences accounted for a small proportion. The hgcA genes appeared in greater abundance and diversity than their transcript counterparts in each sampling site. Correlation analysis demonstrated that the MeHg content rather than Hg content significantly correlated with the structure of the existent/active hgcA-harboring community and the abundance of hgcA genes/transcripts. These findings provide better insights into the microbial Hg methylation drivers in mangrove sediments, which could be helpful for understanding the MeHg biotransformation therein. Full article
(This article belongs to the Special Issue Genomics of Marine and Aquatic Bacteria: A Focus on Novel Taxa, Diversity and Biotechnological Potential: 2nd Edition)
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22 pages, 5201 KiB  
Article
A Novel View on the Taxonomy of Sulfate-Reducing Bacterium ‘Desulfotomaculum salinum’ and a Description of a New Species Desulfofundulus salinus sp. nov.
by Tamara N. Nazina, Tatyana P. Tourova, Denis S. Grouzdev, Salimat K. Bidzhieva and Andrey B. Poltaraus
Microorganisms 2024, 12(6), 1115; https://doi.org/10.3390/microorganisms12061115 - 30 May 2024
Cited by 2 | Viewed by 1012
Abstract
Two thermophilic spore-forming sulfate-reducing strains, 435T and 781, were isolated from oil and gas reservoirs in Western Siberia (Russia) about 50 years ago. Both strains were found to be neutrophilic, chemoorganotrophic, anaerobic bacteria, growing at 45–70 °C (optimum, 55–60 °C) and with [...] Read more.
Two thermophilic spore-forming sulfate-reducing strains, 435T and 781, were isolated from oil and gas reservoirs in Western Siberia (Russia) about 50 years ago. Both strains were found to be neutrophilic, chemoorganotrophic, anaerobic bacteria, growing at 45–70 °C (optimum, 55–60 °C) and with 0–4.5% (w/v) NaCl (optimum, 0.5–1% NaCl). The major fatty acids were iso-C15:0, iso-C17:0, C16:0, and C18:0. In sulfate-reducing conditions, the strains utilized H2/CO2, formate, lactate, pyruvate, malate, fumarate, succinate, methanol, ethanol, propanol, butanol, butyrate, valerate, and palmitate. In 2005, based on phenotypic characteristics and a 16S rRNA gene sequence analysis, the strains were described as ‘Desulfotomaculum salinum’ sp. nov. However, this species was not validly published because the type strain was not deposited in two culture collections. In this study, a genomic analysis of strain 435T was carried out to determine its taxonomic affiliation. The genome size of strain 435T was 2.886 Mb with a 55.1% genomic G + C content. The average nucleotide identity and digital DNA–DNA hybridization values were highest between strain 435T and members of the genus Desulfofundulus, 78.7–93.3% and 25.0–52.2%, respectively; these values were below the species delineation cut-offs (<95–96% and <70%). The cumulative phenotypic and phylogenetic data indicate that two strains represent a novel species within the genus Desulfofundulus, for which the name Desulfofundulus salinus sp. nov. is proposed. The type strain is 435T (=VKM B-1492T = DSM 23196T). A genome analysis of strain 435T revealed the genes for dissimilatory sulfate reduction, autotrophic carbon fixation via the Wood–Ljungdahl pathway, hydrogen utilization, methanol and organic acids metabolism, and sporulation, which were confirmed by cultivation studies. Full article
(This article belongs to the Special Issue Genomics of Marine and Aquatic Bacteria: A Focus on Novel Taxa, Diversity and Biotechnological Potential: 2nd Edition)
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