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Thøgersen MS, Zervas A, Stougaard P, Ellegaard-Jensen L. Investigating eukaryotic and prokaryotic diversity and functional potential in the cold and alkaline ikaite columns in Greenland. Front Microbiol 2024; 15:1358787. [PMID: 38655082 PMCID: PMC11035741 DOI: 10.3389/fmicb.2024.1358787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/08/2024] [Indexed: 04/26/2024] Open
Abstract
The ikaite columns in the Ikka Fjord, SW Greenland, represent a permanently cold and alkaline environment known to contain a rich bacterial diversity. 16S and 18S rRNA gene amplicon and metagenomic sequencing was used to investigate the microbial diversity in the columns and for the first time, the eukaryotic and archaeal diversity in ikaite columns were analyzed. The results showed a rich prokaryotic diversity that varied across columns as well as within each column. Seven different archaeal phyla were documented in multiple locations inside the columns. The columns also contained a rich eukaryotic diversity with 27 phyla representing microalgae, protists, fungi, and small animals. Based on metagenomic sequencing, 25 high-quality MAGs were assembled and analyzed for the presence of genes involved in cycling of nitrogen, sulfur, and phosphorous as well as genes encoding carbohydrate-active enzymes (CAZymes), showing a potentially very bioactive microbial community.
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Taxonomic and Bioactivity Characterizations of Mameliella alba Strain LZ-28 Isolated from Highly Toxic Marine Dinoflagellate Alexandrium catenella LZT09. Mar Drugs 2022; 20:md20050321. [PMID: 35621971 PMCID: PMC9147911 DOI: 10.3390/md20050321] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/28/2022] [Accepted: 05/10/2022] [Indexed: 01/15/2023] Open
Abstract
Microalgae host varied microbial consortium harboring cross-kingdom interactions with fundamental ecological significance in aquatic ecosystems. Revealing the complex biofunctions of the cultivable bacteria of phycosphere microbiota is one vital basis for deeply understanding the mechanisms governing these dynamic associations. In this study, a new light-yellow pigmented bacterial strain LZ-28 was isolated from the highly-toxic and harmful algal bloom-forming dinoflagellate Alexandrium catenella LZT09. Collective phenotypic and genotypic profiles were obtained to confidently identify this strain as a new Mameliellaalba member. Comparative genomic analysis showed that strain LZ-28 shared highly similar functional features with other four marine algae-derived M. alba strains in spite of their distinctive isolation sources. Based on the bioactivity assaying, the mutual growth-promoting effects between bacterial strain LZ-28 and algal strain LZT09 were observed. After the culture conditions were optimized, strain LZ-28 demonstrated an extraordinary production ability for its bioflocculanting exopolysaccharides (EPS). Moreover, the portions of two monosaccharides glucose and fucose of the EPS were found to positively contribute to the bioflocculanting capacity. Therefore, the present study sheds light on the similar genomic features among the selected M. alba strains, and it also reveals the potential pharmaceutical, environmental and biotechnological implications of active EPS produced by this new Mameliella alba strain LZ-28 recovered from toxic bloom-forming marine dinoflagellate.
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Antarctica as a reservoir of planetary analogue environments. Extremophiles 2021; 25:437-458. [PMID: 34586500 DOI: 10.1007/s00792-021-01245-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/08/2021] [Indexed: 10/20/2022]
Abstract
One of the main objectives of astrobiological research is the investigation of the habitability of other planetary bodies. Since space exploration missions are expensive and require long-term organization, the preliminary study of terrestrial environments is an essential step to prepare and support exploration missions. The Earth hosts a multitude of extreme environments whose characteristics resemble celestial bodies in our Solar System. In these environments, the physico-chemical properties partly match extraterrestrial environments and could clarify limits and adaptation mechanisms of life, the mineralogical or geochemical context, and support and interpret data sent back from planetary bodies. One of the best terrestrial analogues is Antarctica, whose conditions lie on the edge of habitability. It is characterized by a cold and dry climate (Onofri et al., Nova Hedwigia 68:175-182, 1999), low water availability, strong katabatic winds, salt concentration, desiccation, and high radiation. Thanks to the harsh conditions like those in other celestial bodies, Antarctica offers good terrestrial analogues for celestial body (Mars or icy moons; Léveillé, CR Palevol 8:637-648, https://doi.org/10.1016/j.crpv.2009.03.005 , 2009). The continent could be distinguished into several habitats, each with characteristics similar to those existing on other bodies. Here, we reported a description of each simulated parameter within the habitats, in relation to each of the simulated extraterrestrial environments.
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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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Production of Polyunsaturated Fatty Acids and Lipids from Autotrophic, Mixotrophic and Heterotrophic cultivation of Galdieria sp. strain USBA-GBX-832. Sci Rep 2019; 9:10791. [PMID: 31346188 PMCID: PMC6658668 DOI: 10.1038/s41598-019-46645-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 06/28/2019] [Indexed: 01/31/2023] Open
Abstract
A search for extremophile organisms producing bioactive compounds led us to isolate a microalga identified as Galdieria sp. USBA-GBX-832 from acidic thermal springs. We have cultured Galdieria sp. USBA-GBX-832 under autotrophic, mixotrophic and heterotrophic conditions and determined variations of its production of biomass, lipids and PUFAs. Greatest biomass and PUFA production occurred under mixotrophic and heterotrophic conditions, but the highest concentration of lipids occurred under autotrophic conditions. Effects of variations of carbon sources and temperature on biomass and lipid production were evaluated and factorial experiments were used to analyze the effects of substrate concentration, temperature, pH, and organic and inorganic nitrogen on biomass production, lipids and PUFAs. Production of biomass and lipids was significantly dependent on temperature and substrate concentration. Greatest accumulation of PUFAs occurred at the lowest temperature tested. PUFA profiles showed trace concentrations of arachidonic acid (C20:4) and eicosapentaenoic acid (C20:5). This is the first time synthesis of these acids has been reported in Galdieria. These findings demonstrate that under heterotrophic conditions this microalga’s lipid profile is significantly different from those observed in other species of this genus which indicates that the culture conditions evaluated are key determinants of these organisms’ responses to stress conditions and accumulation of these metabolites.
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KleinJan H, Jeanthon C, Boyen C, Dittami SM. Exploring the Cultivable Ectocarpus Microbiome. Front Microbiol 2017; 8:2456. [PMID: 29312170 PMCID: PMC5732352 DOI: 10.3389/fmicb.2017.02456] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/27/2017] [Indexed: 01/08/2023] Open
Abstract
Coastal areas form the major habitat of brown macroalgae, photosynthetic multicellular eukaryotes that have great ecological value and industrial potential. Macroalgal growth, development, and physiology are influenced by the microbial community they accommodate. Studying the algal microbiome should thus increase our fundamental understanding of algal biology and may help to improve culturing efforts. Currently, a freshwater strain of the brown macroalga Ectocarpus subulatus is being developed as a model organism for brown macroalgal physiology and algal microbiome studies. It can grow in high and low salinities depending on which microbes it hosts. However, the molecular mechanisms involved in this process are still unclear. Cultivation of Ectocarpus-associated bacteria is the first step toward the development of a model system for in vitro functional studies of brown macroalgal–bacterial interactions during abiotic stress. The main aim of the present study is thus to provide an extensive collection of cultivable E. subulatus-associated bacteria. To meet the variety of metabolic demands of Ectocarpus-associated bacteria, several isolation techniques were applied, i.e., direct plating and dilution-to-extinction cultivation techniques, each with chemically defined and undefined bacterial growth media. Algal tissue and algal growth media were directly used as inoculum, or they were pretreated with antibiotics, by filtration, or by digestion of algal cell walls. In total, 388 isolates were identified falling into 33 genera (46 distinct strains), of which Halomonas (Gammaproteobacteria), Bosea (Alphaproteobacteria), and Limnobacter (Betaproteobacteria) were the most abundant. Comparisons with 16S rRNA gene metabarcoding data showed that culturability in this study was remarkably high (∼50%), although several cultivable strains were not detected or only present in extremely low abundance in the libraries. These undetected bacteria could be considered as part of the rare biosphere and they may form the basis for the temporal changes in the Ectocarpus microbiome.
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Affiliation(s)
- Hetty KleinJan
- Sorbonne Universités, CNRS-UPMC, Station Biologique de Roscoff, UMR8227, Integrative Biology of Marine Models, Roscoff, France
| | - Christian Jeanthon
- CNRS, Station Biologique de Roscoff, UMR7144, Adaptation et Diversité en Milieu Marin, Roscoff, France.,Sorbonne Universités, UPMC Univ Paris 06, Station Biologique de Roscoff, UMR7144, Adaptation et Diversité en Milieu Marin, Roscoff, France
| | - Catherine Boyen
- Sorbonne Universités, CNRS-UPMC, Station Biologique de Roscoff, UMR8227, Integrative Biology of Marine Models, Roscoff, France
| | - Simon M Dittami
- Sorbonne Universités, CNRS-UPMC, Station Biologique de Roscoff, UMR8227, Integrative Biology of Marine Models, Roscoff, France
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7
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Kang I, Kim S, Islam MR, Cho JC. The first complete genome sequences of the acI lineage, the most abundant freshwater Actinobacteria, obtained by whole-genome-amplification of dilution-to-extinction cultures. Sci Rep 2017; 7:42252. [PMID: 28186143 PMCID: PMC5301498 DOI: 10.1038/srep42252] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 01/06/2017] [Indexed: 02/07/2023] Open
Abstract
The acI lineage of the phylum Actinobacteria is the most abundant bacterial group in most freshwater lakes. However, due to difficulties in laboratory cultivation, only two mixed cultures and some incomplete single-amplified or metagenome-derived genomes have been reported for the lineage. Here, we report the initial cultivation and complete genome sequences of four novel strains of the acI lineage from the tribes acI-A1, -A4, -A7, and -C1. The acI strains, initially isolated by dilution-to-extinction culturing, eventually failed to be maintained as axenic cultures. However, the first complete genomes of the acI lineage were successfully obtained from these initial cultures through whole genome amplification applied to more than hundreds of cultured acI cells. The genome sequences exhibited features of genome streamlining and showed that the strains are aerobic chemoheterotrophs sharing central metabolic pathways, with some differences among tribes that may underlie niche diversification within the acI lineage. Actinorhodopsin was found in all strains, but retinal biosynthesis was complete in only A1 and A4 tribes.
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Affiliation(s)
- Ilnam Kang
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Suhyun Kim
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Md Rashedul Islam
- 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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8
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The value of cultures to modern microbiology. Antonie van Leeuwenhoek 2017; 110:1247-1256. [DOI: 10.1007/s10482-017-0840-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 01/31/2017] [Indexed: 02/02/2023]
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9
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Al-Amoudi S, Essack M, Simões MF, Bougouffa S, Soloviev I, Archer JAC, Lafi FF, Bajic VB. Bioprospecting Red Sea Coastal Ecosystems for Culturable Microorganisms and Their Antimicrobial Potential. Mar Drugs 2016; 14:md14090165. [PMID: 27626430 PMCID: PMC5039536 DOI: 10.3390/md14090165] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Revised: 08/10/2016] [Accepted: 08/10/2016] [Indexed: 01/19/2023] Open
Abstract
Microorganisms that inhabit unchartered unique soil such as in the highly saline and hot Red Sea lagoons on the Saudi Arabian coastline, represent untapped sources of potentially new bioactive compounds. In this study, a culture-dependent approach was applied to three types of sediments: mangrove mud (MN), microbial mat (MM), and barren soil (BS), collected from Rabigh harbor lagoon (RHL) and Al-Kharrar lagoon (AKL). The isolated bacteria were evaluated for their potential to produce bioactive compounds. The phylogenetic characterization of 251 bacterial isolates based on the 16S rRNA gene sequencing, supported their assignment to five different phyla: Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Planctomycetes. Fifteen putative novel species were identified based on a 16S rRNA gene sequence similarity to other strain sequences in the NCBI database, being ≤98%. We demonstrate that 49 of the 251 isolates exhibit the potential to produce antimicrobial compounds. Additionally, at least one type of biosynthetic gene sequence, responsible for the synthesis of secondary metabolites, was recovered from 25 of the 49 isolates. Moreover, 10 of the isolates had a growth inhibition effect towards Staphylococcus aureus, Salmonella typhimurium and Pseudomonas syringae. We report the previously unknown antimicrobial activity of B. borstelensis, P. dendritiformis and M. salipaludis against all three indicator pathogens. Our study demonstrates the evidence of diverse cultured microbes associated with the Red Sea harbor/lagoon environments and their potential to produce antimicrobial compounds.
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Affiliation(s)
- Soha Al-Amoudi
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Saudi Arabia.
| | - Magbubah Essack
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Saudi Arabia.
| | - Marta F Simões
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Saudi Arabia.
- Biology Department, Edge Hill University, St. Helens Road, Lancashire, Ormskirk L39 4QP, UK.
| | - Salim Bougouffa
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Saudi Arabia.
| | - Irina Soloviev
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Saudi Arabia.
| | - John A C Archer
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Saudi Arabia.
| | - Feras F Lafi
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Saudi Arabia.
| | - Vladimir B Bajic
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Saudi Arabia.
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Bálint M, Bahram M, Eren AM, Faust K, Fuhrman JA, Lindahl B, O'Hara RB, Öpik M, Sogin ML, Unterseher M, Tedersoo L. Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes. FEMS Microbiol Rev 2016; 40:686-700. [DOI: 10.1093/femsre/fuw017] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2016] [Indexed: 11/13/2022] Open
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12
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Cold-Active, Heterotrophic Bacteria from the Highly Oligotrophic Waters of Lake Vanda, Antarctica. Microorganisms 2015; 3:391-406. [PMID: 27682095 PMCID: PMC5023249 DOI: 10.3390/microorganisms3030391] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 07/05/2015] [Accepted: 07/09/2015] [Indexed: 11/16/2022] Open
Abstract
The permanently ice-covered lakes of the McMurdo Dry Valleys, Antarctica are distinctive ecosystems that consist strictly of microbial communities. In this study, water samples were collected from Lake Vanda, a stratified Dry Valley lake whose upper waters (from just below the ice cover to nearly 60 m) are highly oligotrophic, and used to establish enrichment cultures. Six strains of psychrotolerant, heterotrophic bacteria were isolated from lake water samples from a depth of 50 or 55 m. Phylogenetic analyses showed the Lake Vanda strains to be species of Nocardiaceae, Caulobacteraceae, Sphingomonadaceae, and Bradyrhizobiaceae. All Lake Vanda strains grew at temperatures near or below 0 °C, but optimal growth occurred from 18 to 24 °C. Some strains showed significant halotolerance, but no strains required NaCl for growth. The isolates described herein include cold-active species not previously reported from Dry Valley lakes, and their physiological and phylogenetic characterization broadens our understanding of these limnologically unique lakes.
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Sosa OA, Gifford SM, Repeta DJ, DeLong EF. High molecular weight dissolved organic matter enrichment selects for methylotrophs in dilution to extinction cultures. ISME JOURNAL 2015; 9:2725-39. [PMID: 25978545 PMCID: PMC4817625 DOI: 10.1038/ismej.2015.68] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 03/04/2015] [Accepted: 03/18/2015] [Indexed: 02/06/2023]
Abstract
The role of bacterioplankton in the cycling of marine dissolved organic matter (DOM) is central to the carbon and energy balance in the ocean, yet there are few model organisms available to investigate the genes, metabolic pathways, and biochemical mechanisms involved in the degradation of this globally important carbon pool. To obtain microbial isolates capable of degrading semi-labile DOM for growth, we conducted dilution to extinction cultivation experiments using seawater enriched with high molecular weight (HMW) DOM. In total, 93 isolates were obtained. Amendments using HMW DOM to increase the dissolved organic carbon concentration 4x (280 μM) or 10x (700 μM) the ocean surface water concentrations yielded positive growth in 4–6% of replicate dilutions, whereas <1% scored positive for growth in non-DOM-amended controls. The majority (71%) of isolates displayed a distinct increase in cell yields when grown in increasing concentrations of HMW DOM. Whole-genome sequencing was used to screen the culture collection for purity and to determine the phylogenetic identity of the isolates. Eleven percent of the isolates belonged to the gammaproteobacteria including Alteromonadales (the SAR92 clade) and Vibrio. Surprisingly, 85% of isolates belonged to the methylotrophic OM43 clade of betaproteobacteria, bacteria thought to metabolically specialize in degrading C1 compounds. Growth of these isolates on methanol confirmed their methylotrophic phenotype. Our results indicate that dilution to extinction cultivation enriched with natural sources of organic substrates has a potential to reveal the previously unsuspected relationships between naturally occurring organic nutrients and the microorganisms that consume them.
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Affiliation(s)
- Oscar A Sosa
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI, USA.,Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Scott M Gifford
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Daniel J Repeta
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Edward F DeLong
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI, USA.,Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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López G, Chow J, Bongen P, Lauinger B, Pietruszka J, Streit WR, Baena S. A novel thermoalkalostable esterase from Acidicaldus sp. strain USBA-GBX-499 with enantioselectivity isolated from an acidic hot springs of Colombian Andes. Appl Microbiol Biotechnol 2014; 98:8603-16. [PMID: 24818691 DOI: 10.1007/s00253-014-5775-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 04/09/2014] [Accepted: 04/12/2014] [Indexed: 12/28/2022]
Abstract
Several thermo- and mesoacidophilic bacterial strains that revealed high lipolytic activity were isolated from water samples derived from acidic hot springs in Los Nevados National Natural Park (Colombia). A novel lipolytic enzyme named 499EST was obtained from the thermoacidophilic alpha-Proteobacterium Acidicaldus USBA-GBX-499. The gene estA encoded a 313-amino-acid protein named 499EST. The deduced amino acid sequence showed the highest identity (58 %) with a putative α/β hydrolase from Acidiphilium sp. (ZP_08632277.1). Sequence alignments and phylogenetic analysis indicated that 499EST is a new member of the bacterial esterase/lipase family IV. The esterase reveals its optimum catalytic activity at 55 °C and pH 9.0. Kinetic studies showed that 499EST preferentially hydrolyzed middle-length acyl chains (C6-C8), especially p-nitrophenyl (p-NP) caproate (C6). Its thermostability and activity were strongly enhanced by adding 6 mM FeCl3. High stability in the presence of water-miscible solvents such as dimethyl sulfoxide and glycerol was observed. This enzyme also exhibits stability under harsh environmental conditions and enantioselectivity towards naproxen and ibuprofen esters, yielding the medically relevant (S)-enantiomers. In conclusion, according to our knowledge, 499EST is the first thermoalkalostable esterase derived from a Gram-negative thermoacidophilic bacterium.
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Affiliation(s)
- Gina López
- Unidad de Saneamiento y Biotecnología Ambiental, Departamento de Biología, Pontificia Universidad Javeriana, POB 56710, Bogotá, DC, Colombia
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Chong CW, Goh YS, Convey P, Pearce D, Tan IKP. Spatial pattern in Antarctica: what can we learn from Antarctic bacterial isolates? Extremophiles 2013; 17:733-45. [PMID: 23812890 DOI: 10.1007/s00792-013-0555-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 06/13/2013] [Indexed: 11/30/2022]
Abstract
A range of small- to moderate-scale studies of patterns in bacterial biodiversity have been conducted in Antarctica over the last two decades, most suggesting strong correlations between the described bacterial communities and elements of local environmental heterogeneity. However, very few of these studies have advanced interpretations in terms of spatially associated patterns, despite increasing evidence of patterns in bacterial biogeography globally. This is likely to be a consequence of restricted sampling coverage, with most studies to date focusing only on a few localities within a specific Antarctic region. Clearly, there is now a need for synthesis over a much larger spatial to consolidate the available data. In this study, we collated Antarctic bacterial culture identities based on the 16S rRNA gene information available in the literature and the GenBank database (n > 2,000 sequences). In contrast to some recent evidence for a distinct Antarctic microbiome, our phylogenetic comparisons show that a majority (~75 %) of Antarctic bacterial isolates were highly similar (≥99 % sequence similarity) to those retrieved from tropical and temperate regions, suggesting widespread distribution of eurythermal mesophiles in Antarctic environments. However, across different Antarctic regions, the dominant bacterial genera exhibit some spatially distinct diversity patterns analogous to those recently proposed for Antarctic terrestrial macroorganisms. Taken together, our results highlight the threat of cross-regional homogenisation in Antarctic biodiversity, and the imperative to include microbiota within the framework of biosecurity measures for Antarctica.
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Affiliation(s)
- Chun Wie Chong
- Department of Life Sciences, International Medical University, Kuala Lumpur, Malaysia.
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Michaud L, Caruso C, Mangano S, Interdonato F, Bruni V, Lo Giudice A. Predominance ofFlavobacterium,Pseudomonas, andPolaromonaswithin the prokaryotic community of freshwater shallow lakes in the northern Victoria Land, East Antarctica. FEMS Microbiol Ecol 2012; 82:391-404. [DOI: 10.1111/j.1574-6941.2012.01394.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 04/06/2012] [Accepted: 04/13/2012] [Indexed: 11/24/2022] Open
Affiliation(s)
- Luigi Michaud
- Department of Animal Biology and Marine Ecology (DBAEM); University of Messina; Messina; Italy
| | - Consolazione Caruso
- Department of Animal Biology and Marine Ecology (DBAEM); University of Messina; Messina; Italy
| | - Santina Mangano
- Department of Animal Biology and Marine Ecology (DBAEM); University of Messina; Messina; Italy
| | - Filippo Interdonato
- Department of Animal Biology and Marine Ecology (DBAEM); University of Messina; Messina; Italy
| | - Vivia Bruni
- Department of Animal Biology and Marine Ecology (DBAEM); University of Messina; Messina; Italy
| | - Angelina Lo Giudice
- Department of Animal Biology and Marine Ecology (DBAEM); University of Messina; Messina; Italy
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Margesin R, Miteva V. Diversity and ecology of psychrophilic microorganisms. Res Microbiol 2010; 162:346-61. [PMID: 21187146 DOI: 10.1016/j.resmic.2010.12.004] [Citation(s) in RCA: 231] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Accepted: 11/08/2010] [Indexed: 10/18/2022]
Abstract
Cold environments represent the majority of the biosphere on Earth and have been successfully colonized by psychrophilic microorganisms that are able to thrive at low temperatures and to survive and even maintain metabolic activity at subzero temperatures. These microorganisms play key ecological roles in their habitats and include a wide diversity of representatives of all three domains (Bacteria, Archaea, Eukarya). In this review, we summarize recent knowledge on the abundance, on the taxonomic and functional biodiversity, on low temperature adaptation and on the biogeography of microbial communities in a range of aquatic and terrestrial cold environments.
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Affiliation(s)
- Rosa Margesin
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria.
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A guide to successful bioprospecting: informed by actinobacterial systematics. Antonie van Leeuwenhoek 2010; 98:119-42. [PMID: 20582471 DOI: 10.1007/s10482-010-9460-2] [Citation(s) in RCA: 256] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Accepted: 05/14/2010] [Indexed: 11/26/2022]
Abstract
New structurally diverse natural products are discovered when novel screening procedures are introduced or when high quality biological materials from new sources are examined in existing screens, hence it is important to foster these two aspects of novelty in drug discovery programmes. Amongst prokaryotes, actinomycetes, notably streptomycetes, remain a rich source of new natural products though it has become increasingly difficult to find such metabolites from common actinomycetes as screening 'old friends' leads to the costly rediscovery of known compounds. The bioprospecting strategy which is the subject of this review is based upon the premise that new secondary metabolites can be found by screening relatively small numbers of dereplicated, novel actinomycetes isolated from marine sediments. The success of the strategy is exemplified by the discovery of a range of novel bioactive compounds, notably atrop-abyssomicin C and proximicins A, B and C from Verrucosispora strains isolated from sediment samples taken from the Sea of Japan and the Raune Fjord, respectively, and the dermacozines derived from Dermacoccus strains isolated from the Challenger Deep of the Mariana Trench in the Pacific Ocean. The importance of current advances in prokaryotic systematics in work of this nature is stressed and a plea made that resources be sought to train, support and employ the next generation of actinobacterial systematists.
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Abstract
Molecular ecology methods are now well established for the culture-independent characterization of complex bacterial communities associated with various environmental and animal habitats and are revealing the extent of their diversity. By comparison, it has become clear that only a small minority of microorganisms are readily cultivated in vitro, with the majority of all bacteria remaining 'unculturable' using standard methods. Yet, it is only through the isolation of bacterial species in pure culture that they may be fully characterized, both for their physiological and pathological properties. Hence, the endeavour to devise novel cultivation methods for microorganisms that appear to be inherently resistant to artificial culture is a most important one. This minireview discusses the possible reasons for 'unculturability' and evaluates advances in the cultivation of previously unculturable bacteria from complex bacterial communities. Methods include the use of dilute nutrient media particularly suited for the growth of bacteria adapted to oligotrophic conditions, and the provision of simulated natural environmental conditions for bacterial culture. This has led to the recovery of 'unculturables' from soil and aquatic environments, likely to be due to the inclusion of essential nutrients and/or signalling molecules from the native environment.
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Affiliation(s)
- Sonia R Vartoukian
- King's College London Dental Institute, Infection Research Group, London, UK
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Song J, Oh HM, Cho JC. Improved culturability of SAR11 strains in dilution-to-extinction culturing from the East Sea, West Pacific Ocean. FEMS Microbiol Lett 2009; 295:141-7. [PMID: 19459973 DOI: 10.1111/j.1574-6968.2009.01623.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Although the SAR11 clade of the Alphaproteobacteria represents the most abundant and ubiquitous bacterioplankton in the ocean, very few laboratories have successfully cultured SAR11 cells. All of the SAR11 strains isolated thus far have been retrieved from the Oregon coast and the Sargasso Sea. In this study, a modified dilution-to-extinction culturing with prolonged incubation at low temperature was applied in an effort to cultivate major bacterioplankton lineages in the East Sea, Western Pacific Ocean. Five to 10 cells were inoculated into each well of 48-well plates, followed by the incubation of the plates at 10 degrees C for 4, 8, 20, and 24 weeks. Among a total of 35 isolated strains, 18 strains assigned to the SAR11 clade were isolated after 8, 20, and 24 weeks of incubation, whereas no SAR11 cells were detected in the samples after 4 weeks of incubation. The SAR11 isolates, noticeably, comprised 64-82% of the total isolates from the plates incubated for 20 and 24 weeks. Extinction cultures belonging to the Roseobacter, OM43, and SAR92 clades were also cultivated. The results of this study suggest that long-term incubation at low temperatures might prove an alternative for the efficient cultivation of new variants of the members of the SAR11 clade.
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Affiliation(s)
- Jaeho Song
- Division of Biology and Ocean Sciences, Inha University, Incheon, Korea
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