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Journal Article
- Rhodobacteraceae are Prevalent and Ecologically Crucial Bacterial Members in Marine Biofloc Aquaculture.
- Meora Rajeev, Jang-Cheon Cho
- J. Microbiol. 2024;62(11):985-997. Published online November 15, 2024
- DOI: https://doi.org/10.1007/s12275-024-00187-0
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Abstract
- Bioflocs are microbial aggregates primarily composed of heterotrophic bacteria that play essential ecological roles in maintaining animal health, gut microbiota, and water quality in biofloc aquaculture systems. Despite the global adoption of biofloc aquaculture for shrimp and fish cultivation, our understanding of biofloc microbiota-particularly the dominant bacterial members and their ecological functions-remains limited. In this study, we employed integrated metataxonomic and metagenomic approaches to demonstrate that the family Rhodobacteraceae of Alphaproteobacteria consistently dominates the biofloc microbiota and plays essential ecological roles. We first analyzed a comprehensive metataxonomic dataset consisting of 200 16S rRNA gene amplicons collected across three Asian countries: South Korea, China, and Vietnam. Taxonomic investigation identified Rhodobacteraceae as the dominant and consistent bacterial members across the datasets. The predominance of this taxon was further validated through metagenomics approaches, including read taxonomy and read recruitment analyses. To explore the ecological roles of Rhodobacteraceae, we applied genome-centric metagenomics, reconstructing 45 metagenome-assembled genomes. Functional annotation of these genomes revealed that dominant Rhodobacteraceae genera, such as Marivita, Ruegeria, Dinoroseobacter, and Aliiroseovarius, are involved in vital ecological processes, including complex carbohydrate degradation, aerobic denitrification, assimilatory nitrate reduction, ammonium assimilation, and sulfur oxidation. Overall, our study reveals that the common practice of carbohydrate addition in biofloc aquaculture systems fosters the growth of specific heterotrophic bacterial communities, particularly Rhodobacteraceae. These bacteria contribute to maintaining water quality by removing toxic nitrogen and sulfur compounds and enhance animal health by colonizing gut microbiota and exerting probiotic effects.
Review
- [Minireview]Biodegradation of plastics: mining of plastic-degrading microorganisms and enzymes using metagenomics approaches
- Dae-Wi Kim , Jae-Hyung Ahn , Chang-Jun Cha
- J. Microbiol. 2022;60(10):969-976. Published online September 27, 2022
- DOI: https://doi.org/10.1007/s12275-022-2313-7
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- 17 Citations
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Abstract
- Plastic pollution exacerbated by the excessive use of synthetic plastics and its recalcitrance has been recognized among the most pressing global threats. Microbial degradation of plastics has gained attention as a possible eco-friendly countermeasure, as several studies have shown microbial metabolic capabilities as potential degraders of various synthetic plastics. However, still defined biochemical mechanisms of biodegradation for the most plastics remain elusive, because the widely used culture-dependent approach can access only a very limited amount of the metabolic potential in each microbiome. A culture-independent approach, including metagenomics, is becoming increasingly important in the mining of novel plastic-degrading enzymes, considering its more expanded coverage on the microbial metabolism in microbiomes. Here, we described the advantages and drawbacks associated with four different metagenomics approaches (microbial community analysis, functional metagenomics, targeted gene sequencing, and whole metagenome sequencing) for the mining of plastic-degrading microorganisms and enzymes from the plastisphere. Among these approaches, whole metagenome sequencing has been recognized among the most powerful tools that allow researchers access to the entire metabolic potential of a microbiome. Accordingly, we suggest strategies that will help to identify plastisphere-enriched sequences as de novo plastic-degrading enzymes using the whole metagenome sequencing approach. We anticipate that new strategies for metagenomics approaches will continue to be developed and facilitate to identify novel plastic-degrading microorganisms and enzymes from microbiomes.
Journal Article
- Sulfitobacter profundi sp. nov., isolated from deep seawater
- Jaeho Song , Hye-Jin Jang , Yochan Joung , Ilnam Kang , Jang-Cheon Cho
- J. Microbiol. 2019;57(8):661-667. Published online April 22, 2019
- DOI: https://doi.org/10.1007/s12275-019-9150-3
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- 9 Citations
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Abstract
- A Gram-stain-negative, rod-shaped, obligately aerobic, chemoheterotrophic bacterium which is motile by means of a single polar flagellum, designated SAORIC-263T, was isolated from deep seawater of the Pacific Ocean. Phylogenetic analyses based on 16S rRNA gene sequences and genomebased phylogeny revealed that strain SAORIC-263T belonged to the genus Sulfitobacter and shared 96.1–99.9% 16S rRNA gene sequence similarities with Sulfitobacter species. Wholegenome sequencing of strain SAORIC-263T revealed a genome size of 3.9Mbp and DNA G+C content of 61.3 mol%. The SAORIC-263T genome shared an average nucleotide identity and digital DNA-DNA hybridization of 79.1–88.5% and 18.9–35.0%, respectively, with other Sulfitobacter genomes. The SAORIC-263T genome contained the genes related to benzoate degradation, which are frequently found in deep-sea metagenome. The strain contained summed feature 8 (C18:1 ω7c), C18:1 ω7c 11-methyl, and C16:0 as the predominant cellular fatty acids as well as ubiquinone-10 (Q-10) as the major respiratory quinone. The major polar lipids of the strain were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, and aminolipid. On the basis of taxonomic data obtained in this study, it is suggested that strain SAORIC-263T represents a novel species of the genus Sulfitobacter, for which the name Sulfitobacter profundi sp. nov. is proposed. The type strain is SAORIC-263T (= KACC 21183T = NBRC 113428T).
Research Support, Non-U.S. Gov't
- Thalassobius aestuarii sp. nov., Isolated from Tidal Flat Sediment
- Hana Yi , Jongsik Chun
- J. Microbiol. 2006;44(2):171-176.
- DOI: https://doi.org/2368 [pii]
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Abstract
- A strictly aerobic, non-motile, ovoid-shaped Alphaproteobacteria, designated strain JC2049T,was isolated from a tidal flat sediment sample. The results of 16S rRNA gene sequence analysis indicated that this isolate belonged to the genus Thalassobius, with a sequence similarity of 96.9-97.3% to other valid Thalassobius spp. The cells required 1-7% NaCl for growth (optimum 2%) and accumulated poly-β-hydroxybutyrate. Nitrite was reduced to nitrogen, but nitrate was not reduced to nitrite. No genetic potential for aerobic anoxygenic photosynthesis was detected. The primary isoprenoid quinone (Ubiquinone-10), predominant cellular fatty acids (C18:1ω7c, 11 methyl C18:1ω7c and C16:0) and DNA G+C content (61 mol%) were all consistent with the assignment of this isolate to the genus Thalassobius. Several phenotypic characteristics clearly distinguished our isolate from other Thalassobius species. The degree of genomic relatedness between strain JC2049T and other Thalassobius species was in a range of 20-43%. The polyphasic data presented in this study indicates that our isolate should be classified as a novel species within the genus Thalassobius. The name Thalassobius aestuarii sp. nov. is therefore proposed for this isolate; the type strain is JC2049T (= IMSNU 14011T = KCTC 12049T = DSM 15283T).
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