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Lee JH, Oh HM. Effects of Light and Dark Conditions on the Transcriptome of Aging Cultures of Candidatus Puniceispirillum marinum IMCC1322. J Microbiol 2024; 62:297-314. [PMID: 38662311 DOI: 10.1007/s12275-024-00125-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/19/2024] [Accepted: 02/19/2024] [Indexed: 04/26/2024]
Abstract
To elucidate the function of proteorhodopsin in Candidatus Puniceispirillum marinum strain IMCC1322, a cultivated representative of SAR116, we produced RNA-seq data under laboratory conditions. We examined the transcriptomes of six different cultures, including sets of expression changes under constant dark (DD), constant light (LL), and diel-cycled (LD; 14 h light: 10 h dark) conditions at the exponential and stationary/death phases. Prepared mRNA extracted from the six samples was analyzed on the Solexa Genome Analyzer with 36 cycles. Differentially expressed genes on the IMCC1322 genome were distinguished as four clusters by K-mean clustering and each CDS (n = 2546) was annotated based on the KEGG BRITE hierarchy. Cluster 0 (n = 1573) covered most constitutive genes including proteorhodopsin, retinoids, and glycolysis/TCA cycle. Cluster 1 genes (n = 754) were upregulated in stationary/death phase under constant dark conditions and included genes associated with bacterial defense, membrane transporters, nitrogen metabolism, and senescence signaling. Cluster 2 genes (n = 197) demonstrated upregulation in exponential phase cultures and included genes involved in genes for oxidative phosphorylation, translation factors, and transcription machinery. Cluster 3 (n = 22) contained light-stimulated upregulated genes expressed under stationary/phases. Stringent response genes belonged to cluster 2, but affected genes spanned various cellular processes such as amino acids, nucleotides, translation, transcription, glycolysis, fatty acids, and cell wall components. The coordinated expression of antagonistic stringent genes, including mazG, ppx/gppA, and spoT/relA may provide insight into the controlled cultural response observed between constant light and constant dark conditions in IMCC1322 cultures, regardless of cell numbers and biomass.
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Affiliation(s)
- Ji Hyen Lee
- Department of Pediatrics, Ewha Womans University School of Medicine, Seoul, 07804, Republic of Korea
| | - Hyun-Myung Oh
- Institute of Liberal Arts Education, Pukyong National University, Busan, 48547, Republic of Korea.
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2
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Hardies SC, Cho BC, Jang GI, Wang Z, Hwang CY. Identification of Structural and Morphogenesis Genes of Sulfitobacter Phage ΦGT1 and Placement within the Evolutionary History of the Podoviruses. Viruses 2023; 15:1475. [PMID: 37515163 PMCID: PMC10386132 DOI: 10.3390/v15071475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/23/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
ΦGT1 is a lytic podovirus of an alphaproteobacterial Sulfitobacter species, with few closely matching sequences among characterized phages, thus defying a useful description by simple sequence clustering methods. The history of the ΦGT1 core structure module was reconstructed using timetrees, including numerous related prospective prophages, to flesh out the evolutionary lineages spanning from the origin of the ejectosomal podovirus >3.2 Gya to the present genes of ΦGT1 and its closest relatives. A peculiarity of the ΦGT1 structural proteome is that it contains two paralogous tubular tail A (tubeA) proteins. The origin of the dual tubeA arrangement was traced to a recombination between two more ancient podoviral lineages occurring ~0.7 Gya in the alphaproteobacterial order Rhizobiales. Descendants of the ancestral dual A recombinant were tracked forward forming both temperate and lytic phage clusters and exhibiting both vertical transmission with patchy persistence and horizontal transfer with respect to host taxonomy. The two ancestral lineages were traced backward, making junctions with a major metagenomic podoviral family, the LUZ24-like gammaproteobacterial phages, and Myxococcal phage Mx8, and finally joining near the origin of podoviruses with P22. With these most conservative among phage genes, deviations from uncomplicated vertical and nonrecombinant descent are numerous but countable. The use of timetrees allowed conceptualization of the phage's evolution in the context of a sequence of ancestors spanning the time of life on Earth.
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Affiliation(s)
- Stephen C Hardies
- Department of Biochemistry and Structural Biology, UT Health, San Antonio, TX 78229, USA
| | - Byung Cheol Cho
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
- Saemangeum Environmental Research Center, Kunsan National University, Gunsan 54150, Republic of Korea
| | - Gwang Il Jang
- Aquatic Disease Control Division, National Fishery Products Quality Management Service, Busan 46083, Republic of Korea
| | - Zhiqing Wang
- National Cryo-EM Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Chung Yeon Hwang
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
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3
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Auladell A, Barberán A, Logares R, Garcés E, Gasol JM, Ferrera I. Seasonal niche differentiation among closely related marine bacteria. THE ISME JOURNAL 2022; 16:178-189. [PMID: 34285363 PMCID: PMC8692485 DOI: 10.1038/s41396-021-01053-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 02/07/2023]
Abstract
Bacteria display dynamic abundance fluctuations over time in marine environments, where they play key biogeochemical roles. Here, we characterized the seasonal dynamics of marine bacteria in a coastal oligotrophic time series station, tested how similar the temporal niche of closely related taxa is, and what are the environmental parameters modulating their seasonal abundance patterns. We further explored how conserved the niche is at higher taxonomic levels. The community presented recurrent patterns of seasonality for 297 out of 6825 amplicon sequence variants (ASVs), which constituted almost half of the total relative abundance (47%). For certain genera, niche similarity decreased as nucleotide divergence in the 16S rRNA gene increased, a pattern compatible with the selection of similar taxa through environmental filtering. Additionally, we observed evidence of seasonal differentiation within various genera as seen by the distinct seasonal patterns of closely related taxa. At broader taxonomic levels, coherent seasonal trends did not exist at the class level, while the order and family ranks depended on the patterns that existed at the genus level. This study identifies the coexistence of closely related taxa for some bacterial groups and seasonal differentiation for others in a coastal marine environment subjected to a strong seasonality.
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Affiliation(s)
- Adrià Auladell
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, Spain.
| | - Albert Barberán
- Department of Environmental Science, University of Arizona, Tucson, AZ, USA
| | - Ramiro Logares
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, Spain
| | - Esther Garcés
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, Spain
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, Spain.
- Center for Marine Ecosystems Research, School of Science, Edith Cowan University, Joondalup, WA, Australia.
| | - Isabel Ferrera
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, Spain.
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, IEO-CSIC, Fuengirola, Málaga, Spain.
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4
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Kobiyama A, Rashid J, Reza MS, Ikeda Y, Yamada Y, Kudo T, Mizusawa N, Yanagisawa S, Ikeda D, Sato S, Ogata T, Ikeo K, Kaga S, Watanabe S, Naiki K, Kaga Y, Segawa S, Tada Y, Musashi T, Mineta K, Gojobori T, Watabe S. Seasonal and annual changes in the microbial communities of Ofunato Bay, Japan, based on metagenomics. Sci Rep 2021; 11:17277. [PMID: 34446773 PMCID: PMC8390468 DOI: 10.1038/s41598-021-96641-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 08/12/2021] [Indexed: 02/07/2023] Open
Abstract
Five years of datasets from 2015 to 2019 of whole genome shotgun sequencing for cells trapped on 0.2-µm filters of seawater collected monthly from Ofunato Bay, an enclosed bay in Japan, were analysed, which included the 2015 data that we had reported previously. Nucleotide sequences were determined for extracted DNA from three locations for both the upper (1 m) and deeper (8 or 10 m) depths. The biotic communities analysed at the domain level comprised bacteria, eukaryotes, archaea and viruses. The relative abundance of bacteria was over 60% in most months for the five years. The relative abundance of the SAR86 cluster was highest in the bacterial group, followed by Candidatus Pelagibacter and Planktomarina. The relative abundance of Ca. Pelagibacter showed no relationship with environmental factors, and those of SAR86 and Planktomarina showed positive correlations with salinity and dissolved oxygen, respectively. The bacterial community diversity showed seasonal changes, with high diversity around September and low diversity around January for all five years. Nonmetric multidimensional scaling analysis also revealed that the bacterial communities in the bay were grouped in a season-dependent manner and linked with environmental variables such as seawater temperature, salinity and dissolved oxygen.
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Affiliation(s)
- Atsushi Kobiyama
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Jonaira Rashid
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
- Bangladesh Fisheries Research Institute, Freshwater Station, Mymensingh, 2201, Bangladesh
| | - Md Shaheed Reza
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
- Department of Fisheries Technology, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Yuri Ikeda
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Yuichiro Yamada
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Toshiaki Kudo
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Nanami Mizusawa
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Saki Yanagisawa
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Daisuke Ikeda
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Shigeru Sato
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Takehiko Ogata
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Kazuho Ikeo
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
- National Institute of Genetics, Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Shinnosuke Kaga
- Iwate Fisheries Technology Center, Kamaishi, Iwate, 026-0001, Japan
| | - Shiho Watanabe
- Iwate Fisheries Technology Center, Kamaishi, Iwate, 026-0001, Japan
| | - Kimiaki Naiki
- Iwate Inland Fisheries Technology Center, Hachimantai, Iwate, 028-7302, Japan
| | - Yoshimasa Kaga
- Iwate Inland Fisheries Technology Center, Hachimantai, Iwate, 028-7302, Japan
| | - Satoshi Segawa
- Iwate Fisheries Technology Center, Kamaishi, Iwate, 026-0001, Japan
| | - Yumiko Tada
- Iwate Fisheries Technology Center, Kamaishi, Iwate, 026-0001, Japan
| | - Tatsuya Musashi
- Iwate Fisheries Technology Center, Kamaishi, Iwate, 026-0001, Japan
| | - Katsuhiko Mineta
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Takashi Gojobori
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia.
| | - Shugo Watabe
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan.
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Kim S, Islam MR, Kang I, Cho JC. Cultivation of Dominant Freshwater Bacterioplankton Lineages Using a High-Throughput Dilution-to-Extinction Culturing Approach Over a 1-Year Period. Front Microbiol 2021; 12:700637. [PMID: 34385989 PMCID: PMC8353197 DOI: 10.3389/fmicb.2021.700637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/09/2021] [Indexed: 11/13/2022] Open
Abstract
Although many culture-independent molecular analyses have elucidated a great diversity of freshwater bacterioplankton, the ecophysiological characteristics of several abundant freshwater bacterial groups are largely unknown due to the scarcity of cultured representatives. Therefore, a high-throughput dilution-to-extinction culturing (HTC) approach was implemented herein to enable the culture of these bacterioplankton lineages using water samples collected at various seasons and depths from Lake Soyang, an oligotrophic reservoir located in South Korea. Some predominant freshwater bacteria have been isolated from Lake Soyang via HTC (e.g., the acI lineage); however, large-scale HTC studies encompassing different seasons and water depths have not been documented yet. In this HTC approach, bacterial growth was detected in 14% of 5,376 inoculated wells. Further, phylogenetic analyses of 16S rRNA genes from a total of 605 putatively axenic bacterial cultures indicated that the HTC isolates were largely composed of Actinobacteria, Bacteroidetes, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Verrucomicrobia. Importantly, the isolates were distributed across diverse taxa including phylogenetic lineages that are widely known cosmopolitan and representative freshwater bacterial groups such as the acI, acIV, LD28, FukuN57, MNG9, and TRA3-20 lineages. However, some abundant bacterial groups including the LD12 lineage, Chloroflexi, and Acidobacteria could not be domesticated. Among the 71 taxonomic groups in the HTC isolates, representative strains of 47 groups could either form colonies on agar plates or be revived from frozen glycerol stocks. Additionally, season and water depth significantly affected bacterial community structure, as demonstrated by 16S rRNA gene amplicon sequencing analyses. Therefore, our study successfully implemented a dilution-to-extinction cultivation strategy to cultivate previously uncultured or underrepresented freshwater bacterial groups, thus expanding the basis for future multi-omic studies.
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Affiliation(s)
- Suhyun Kim
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, South Korea
| | - Md Rashedul Islam
- Bacteriophage Biology Laboratory, Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
| | - Ilnam Kang
- Department of Biological Sciences, Center for Molecular and Cell Biology, Inha University, Incheon, South Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, South Korea
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Thrash JC. Towards culturing the microbe of your choice. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:36-41. [PMID: 33073476 DOI: 10.1111/1758-2229.12898] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 10/15/2020] [Indexed: 06/11/2023]
Affiliation(s)
- J Cameron Thrash
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
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7
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Steiner PA, Geijo J, Fadeev E, Obiol A, Sintes E, Rattei T, Herndl GJ. Functional Seasonality of Free-Living and Particle-Associated Prokaryotic Communities in the Coastal Adriatic Sea. Front Microbiol 2020; 11:584222. [PMID: 33304331 PMCID: PMC7701263 DOI: 10.3389/fmicb.2020.584222] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/23/2020] [Indexed: 01/04/2023] Open
Abstract
Marine snow is an important habitat for microbes, characterized by chemical and physical properties contrasting those of the ambient water. The higher nutrient concentrations in marine snow lead to compositional differences between the ambient water and the marine snow-associated prokaryotic community. Whether these compositional differences vary due to seasonal environmental changes, however, remains unclear. Thus, we investigated the seasonal patterns of the free-living and marine snow-associated microbial community composition and their functional potential in the northern Adriatic Sea. Our data revealed seasonal patterns in both, the free-living and marine snow-associated prokaryotes. The two assemblages were more similar to each other in spring and fall than in winter and summer. The taxonomic distinctness resulted in a contrasting functional potential. Motility and adaptations to low temperature in winter and partly anaerobic metabolism in summer characterized the marine snow-associated prokaryotes. Free-living prokaryotes were enriched in genes indicative for functions related to phosphorus limitation in winter and in genes tentatively supplementing heterotrophic growth with proteorhodopsins and CO-oxidation in summer. Taken together, the results suggest a strong influence of environmental parameters on both free-living and marine snow-associated prokaryotic communities in spring and fall leading to higher similarity between the communities, while the marine snow habitat in winter and summer leads to a specific prokaryotic community in marine snow in these two seasons.
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Affiliation(s)
- Paul A. Steiner
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Javier Geijo
- Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, University of Vienna, Vienna, Austria
| | - Eduard Fadeev
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Aleix Obiol
- Institut de Ciències del Mar, Institut de Ci ncies del Mar – Consejo Superior de Investigaciones Cient ficas (ICM-CSIC), Barcelona, Spain
| | - Eva Sintes
- Instituto Español de Oceanografia, Centre Oceanogràfic de les Balears, Palma, Spain
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, University of Vienna, Vienna, Austria
| | - Gerhard J. Herndl
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Microbiology and Biogeochemistry, Utrecht University, Utrecht, Netherlands
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8
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Kim S, Park MS, Song J, Kang I, Cho JC. High-throughput cultivation based on dilution-to-extinction with catalase supplementation and a case study of cultivating acI bacteria from Lake Soyang. J Microbiol 2020; 58:893-905. [PMID: 33125668 DOI: 10.1007/s12275-020-0452-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 09/22/2020] [Indexed: 12/12/2022]
Abstract
Multi-omics approaches, including metagenomics and single-cell amplified genomics, have revolutionized our understanding of the hidden diversity and function of microbes in nature. Even in the omics age, cultivation is an essential discipline in microbial ecology since microbial cultures are necessary to assess the validity of an in silico prediction about the microbial metabolism and to isolate viruses infecting bacteria and archaea. However, the ecophysiological characteristics of predominant freshwater bacterial lineages remain largely unknown due to the scarcity of cultured representatives. In an ongoing effort to cultivate the uncultured majority of freshwater bacteria, the most abundant freshwater Actinobacteria acI clade has recently been cultivated from Lake Soyang through catalase-supplemented high-throughput cultivation based on dilution-to-extinction. This method involves physical isolation of target microbes from mixed populations, culture media simulating natural habitats, and removal of toxic compounds. In this protocol, we describe detailed procedures for isolating freshwater oligotrophic microbes, as well as the essence of the dilution-to-extinction culturing. As a case study employing the catalase-supplemented dilution-to-extinction protocol, we also report a cultivation trial using a water sample collected from Lake Soyang. Of the 480 cultivation wells inoculated with a single lake-water sample, 75 new acI strains belonging to 8 acI tribes (acI-A1, A2, A4, A5, A6, A7, B1, B4, C1, and C2) were cultivated, and each representative strain per subclade could be revived from glycerol stocks. These cultivation results demonstrate that the protocol described in this study is efficient in isolating freshwater bacterioplankton harboring streamlined genomes.
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Affiliation(s)
- Suhyun Kim
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea
| | - Miri S Park
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea
| | - Jaeho Song
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea
| | - Ilnam Kang
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea.
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9
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Expanding the Diversity of Bacterioplankton Isolates and Modeling Isolation Efficacy with Large-Scale Dilution-to-Extinction Cultivation. Appl Environ Microbiol 2020; 86:AEM.00943-20. [PMID: 32561583 PMCID: PMC7440811 DOI: 10.1128/aem.00943-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/13/2020] [Indexed: 12/13/2022] Open
Abstract
Even before the coining of the term “great plate count anomaly” in the 1980s, scientists had noted the discrepancy between the number of microorganisms observed under the microscope and the number of colonies that grew on traditional agar media. New cultivation approaches have reduced this disparity, resulting in the isolation of some of the “most wanted” bacterial lineages. Nevertheless, the vast majority of microorganisms remain uncultured, hampering progress toward answering fundamental biological questions about many important microorganisms. Furthermore, few studies have evaluated the underlying factors influencing cultivation success, limiting our ability to improve cultivation efficacy. Our work details the use of dilution-to-extinction (DTE) cultivation to expand the phylogenetic and geographic diversity of available axenic cultures. We also provide a new model of the DTE approach that uses cultivation results and natural abundance information to predict taxon-specific viability and iteratively constrain DTE experimental design to improve cultivation success. Cultivated bacterioplankton representatives from diverse lineages and locations are essential for microbiology, but the large majority of taxa either remain uncultivated or lack isolates from diverse geographic locales. We paired large-scale dilution-to-extinction (DTE) cultivation with microbial community analysis and modeling to expand the phylogenetic and geographic diversity of cultivated bacterioplankton and to evaluate DTE cultivation success. Here, we report results from 17 DTE experiments totaling 7,820 individual incubations over 3 years, yielding 328 repeatably transferable isolates. Comparison of isolates to microbial community data for source waters indicated that we successfully isolated 5% of the observed bacterioplankton community throughout the study; 43% and 26% of our isolates matched operational taxonomic units and amplicon single-nucleotide variants, respectively, within the top 50 most abundant taxa. Isolates included those from previously uncultivated clades such as SAR11 LD12 and Actinobacteria acIV, as well as geographically novel members from other ecologically important groups like SAR11 subclade IIIa, SAR116, and others, providing isolates in eight putatively new genera and seven putatively new species. Using a newly developed DTE cultivation model, we evaluated taxon viability by comparing relative abundance with cultivation success. The model (i) revealed the minimum attempts required for successful isolation of taxa amenable to growth on our media and (ii) identified possible subpopulation viability variation in abundant taxa such as SAR11 that likely impacts cultivation success. By incorporating viability in experimental design, we can now statistically constrain the effort necessary for successful cultivation of specific taxa on a defined medium. IMPORTANCE Even before the coining of the term “great plate count anomaly” in the 1980s, scientists had noted the discrepancy between the number of microorganisms observed under the microscope and the number of colonies that grew on traditional agar media. New cultivation approaches have reduced this disparity, resulting in the isolation of some of the “most wanted” bacterial lineages. Nevertheless, the vast majority of microorganisms remain uncultured, hampering progress toward answering fundamental biological questions about many important microorganisms. Furthermore, few studies have evaluated the underlying factors influencing cultivation success, limiting our ability to improve cultivation efficacy. Our work details the use of dilution-to-extinction (DTE) cultivation to expand the phylogenetic and geographic diversity of available axenic cultures. We also provide a new model of the DTE approach that uses cultivation results and natural abundance information to predict taxon-specific viability and iteratively constrain DTE experimental design to improve cultivation success.
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10
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Li SH, Song J, Kang I, Hwang J, Cho JC. Aequoribacter fuscus gen. nov., sp. nov., a new member of the family Halieaceae, isolated from coastal seawater. J Microbiol 2020; 58:463-471. [PMID: 32462487 DOI: 10.1007/s12275-020-0206-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/04/2020] [Accepted: 05/04/2020] [Indexed: 11/29/2022]
Abstract
A Gram-stain-negative, rod-shaped, obligately aerobic, nonflagellated, and chemoheterotrophic bacterium, designated IMCC3088T, was isolated from coastal seawater of the Yellow Sea. The 16S rRNA gene sequence analysis indicated that this strain belonged to the family Halieaceae which shared the highest sequence similarities with Luminiphilus syltensis NOR5-1BT (94.5%) and Halioglobus pacificus S1-72T (94.5%), followed by 92.3-94.3% sequence similarities with other species within the aforementioned family. Phylogenetic analyses demonstrated that strain IMCC3088T was robustly clustered with Luminiphilus syltensis NOR5-1BT within the family Halieaceae. However, average amino acid identity (AAI), percentages of conserved proteins (POCP), average nucleotide identity (ANI), and alignment fraction (AF) between strain IMCC3088T and Luminiphilus syltensis NOR5-1BT were 54.5%, 47.7%, 68.0%, and 16.5%, respectively, suggesting that they belonged to different genera. Whole-genome sequencing of strain IMCC3088T revealed a 3.1 Mbp genome size with a DNA G + C content of 51.7 mol%. The genome encoded diverse metabolic pathways including sulfur oxidation, phenol degradation, and proteorhodopsin phototrophy. Mono-unsaturated fatty acids were found to be the predominant cellular fatty acid components in the strain. Phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol were the primarily identified polar lipids, and ubiquinone-8 was identified as a major respiratory quinone. The taxonomic data collected herein suggested that strain IMCC3088T represented a novel genus and species of the family Halieaceae, for which the name Aequoribacter fuscus gen. nov., sp. nov. is proposed with the type strain (= KACC 15529T = NBRC 108213T).
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Affiliation(s)
- Shan-Hui Li
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea
| | - Jaeho Song
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea
| | - Ilnam Kang
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea
| | - Juchan Hwang
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea.
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11
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Konstantinidis KT, Rosselló‐Móra R, Amann R. Advantages outweigh concerns about using genome sequence as type material for prokaryotic taxonomy. Environ Microbiol 2020; 22:819-822. [DOI: 10.1111/1462-2920.14934] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 01/27/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Konstantinos T. Konstantinidis
- School of Civil and Environmental Engineering and School of Biological Sciences, Georgia Institute of Technology Atlanta GA USA
| | - Ramon Rosselló‐Móra
- Marine Microbiology Group, Institut Mediterrani d'Estudis Avançats (IMEDEA; CSIC‐UIB) E‐07190 Esporles Spain
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology D‐28359 Bremen Germany
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