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Zhao Y, Sun T, Li Y, Yang Z, Chen J, Wang J, Yu X, Tang X, Xiao H. The host sex contributes to the endophytic bacterial community in Sargassum thunbergii and their receptacles. Front Microbiol 2024; 15:1334918. [PMID: 38559345 PMCID: PMC10978810 DOI: 10.3389/fmicb.2024.1334918] [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: 11/08/2023] [Accepted: 02/14/2024] [Indexed: 04/04/2024] Open
Abstract
Endophytic bacteria have a complex coevolutionary relationship with their host macroalgae. Dioecious macroalgae are important producers in marine ecosystems, but there is still a lack of research on how sex influences their endophytic bacteria. In this study, the endophytic bacterial communities in male and female S. thunbergii and their reproductive tissues (receptacles) were compared using culture methods and high-throughput sequencing. The endophytic bacterial communities detected by the two methods were different. Among the 78 isolated strains, the dominant phylum, genus, and species were Bacillota, Alkalihalobacillus, and Alkalihalobacillus algicola, respectively, in the algal bodies, while in the receptacles, they were Bacillota, Vibrio, and Vibrio alginolyticus. However, 24 phyla and 349 genera of endophytic bacteria were identified by high-throughput sequencing, and the dominant phylum and genus were Pseudomonadota and Sva0996_ Marine_ Group, respectively, in both the algal body and the receptacles. The two methods showed similar compositions of endophytic bacterial communities between the samples of different sexes, but the relative abundances of dominant and specific taxa were different. The high-throughput sequencing results showed more clearly that the sex of the host alga had an effect on its endophyte community assembly and a greater effect on the endophytic bacterial community in the receptacles. Moreover, most specific bacteria and predicted functional genes that differed between the samples from the males and females were related to metabolism, suggesting that metabolic differences are the main causes of sex differences in the endophytic bacterial community. Our research is the first to show that host sex contributes to the composition of endophytic bacterial communities in dioecious marine macroalgae. The results enrich the database of endophytic bacteria of dioecious marine macroalgae and pave the way for better understanding the assembly mechanism of the endophytic bacterial community of algae.
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Affiliation(s)
- Yayun Zhao
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Tao Sun
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Qingdao Branch CCCC Water Transportation Consultants Co.,LTD, Qingdao, China
| | - Yang Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Shandong Marine Forecast and Hazard Mitigation Service, Qingdao, China
| | - Zhibo Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jun Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jing Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xinlong Yu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xuexi Tang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Hui Xiao
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
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Di Costanzo F, Di Dato V, Romano G. Diatom-Bacteria Interactions in the Marine Environment: Complexity, Heterogeneity, and Potential for Biotechnological Applications. Microorganisms 2023; 11:2967. [PMID: 38138111 PMCID: PMC10745847 DOI: 10.3390/microorganisms11122967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/28/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
Diatom-bacteria interactions evolved during more than 200 million years of coexistence in the same environment. In this time frame, they established complex and heterogeneous cohorts and consortia, creating networks of multiple cell-to-cell mutualistic or antagonistic interactions for nutrient exchanges, communication, and defence. The most diffused type of interaction between diatoms and bacteria is based on a win-win relationship in which bacteria benefit from the organic matter and nutrients released by diatoms, while these last rely on bacteria for the supply of nutrients they are not able to produce, such as vitamins and nitrogen. Despite the importance of diatom-bacteria interactions in the evolutionary history of diatoms, especially in structuring the marine food web and controlling algal blooms, the molecular mechanisms underlying them remain poorly studied. This review aims to present a comprehensive report on diatom-bacteria interactions, illustrating the different interplays described until now and the chemical cues involved in the communication and exchange between the two groups of organisms. We also discuss the potential biotechnological applications of molecules and processes involved in those fascinating marine microbial networks and provide information on novel approaches to unveiling the molecular mechanisms underlying diatom-bacteria interactions.
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Affiliation(s)
| | - Valeria Di Dato
- Stazione Zoologica Anton Dohrn Napoli, Ecosustainable Marine Biotechnology Department, Via Ammiraglio Ferdinando Acton 55, 80133 Napoli, Italy; (F.D.C.); (G.R.)
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3
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Syhapanha KS, Russo DA, Deng Y, Meyer N, Poulin RX, Pohnert G. Transcriptomics-guided identification of an algicidal protease of the marine bacterium Kordia algicida OT-1. Microbiologyopen 2023; 12:e1387. [PMID: 37877654 PMCID: PMC10565126 DOI: 10.1002/mbo3.1387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/26/2023] Open
Abstract
In recent years, interest in algicidal bacteria has risen due to their ecological importance and their potential as biotic regulators of harmful algal blooms. Algicidal bacteria shape the plankton communities of the oceans by inhibiting or lysing microalgae and by consuming the released nutrients. Kordia algicida strain OT-1 is a model marine algicidal bacterium that was isolated from a bloom of the diatom Skeletonema costatum. Previous work has suggested that algicidal activity is mediated by secreted proteases. Here, we utilize a transcriptomics-guided approach to identify the serine protease gene KAOT1_RS09515, hereby named alpA1 as a key element in the algicidal activity of K. algicida. The protease AlpA1 was expressed and purified from a heterologous host and used in in vitro bioassays to validate its activity. We also show that K. algicida is the only algicidal species within a group of four members of the Kordia genus. The identification of this algicidal protease opens the possibility of real-time monitoring of the ecological impact of algicidal bacteria in natural phytoplankton blooms.
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Affiliation(s)
- Kristy S. Syhapanha
- Institute for Inorganic and Analytical Chemistry, Bioorganic AnalyticsFriedrich Schiller University JenaJenaGermany
| | - David A. Russo
- Institute for Inorganic and Analytical Chemistry, Bioorganic AnalyticsFriedrich Schiller University JenaJenaGermany
| | - Yun Deng
- Institute for Inorganic and Analytical Chemistry, Bioorganic AnalyticsFriedrich Schiller University JenaJenaGermany
| | - Nils Meyer
- Institute for Inorganic and Analytical Chemistry, Bioorganic AnalyticsFriedrich Schiller University JenaJenaGermany
| | - Remington X. Poulin
- Institute for Inorganic and Analytical Chemistry, Bioorganic AnalyticsFriedrich Schiller University JenaJenaGermany
- Department of Chemistry and Biochemistry, Center for Marine ScienceUniversity of North Carolina WilmingtonWilmingtonNorth CarolinaUSA
| | - Georg Pohnert
- Institute for Inorganic and Analytical Chemistry, Bioorganic AnalyticsFriedrich Schiller University JenaJenaGermany
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Murúa P, Garvetto A, Egan S, Gachon CMM. The Reemergence of Phycopathology: When Algal Biology Meets Ecology and Biosecurity. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:231-255. [PMID: 37253694 DOI: 10.1146/annurev-phyto-020620-120425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Viruses, bacteria, and eukaryotic symbionts interact with algae in a variety of ways to cause disease complexes, often shaping marine and freshwater ecosystems. The advent of phyconomy (a.k.a. seaweed agronomy) represents a need for a greater understanding of algal disease interactions, where underestimated cryptic diversity and lack of phycopathological basis are prospective constraints for algal domestication. Here, we highlight the limited yet increasing knowledge of algal pathogen biodiversity and the ecological interaction with their algal hosts. Finally, we discuss how ecology and cultivation experience contribute to and reinforce aquaculture practice, with the potential to reshape biosecurity policies of seaweed cultivation worldwide.
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Affiliation(s)
- Pedro Murúa
- Instituto de Acuicultura, Universidad Austral de Chile-Sede Puerto Montt, Los Lagos, Chile;
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom
| | - Andrea Garvetto
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom
- Institute of Microbiology, Universität Innsbruck, Innsbruck, Tyrol, Austria
| | - Suhelen Egan
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Claire M M Gachon
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom
- Muséum National d'Histoire Naturelle, CNRS, Paris, France
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5
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Dynamic Diatom-Bacteria Consortia in Synthetic Plankton Communities. Appl Environ Microbiol 2022; 88:e0161922. [PMID: 36300970 PMCID: PMC9680611 DOI: 10.1128/aem.01619-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The marine food web is fueled by phototrophic phytoplankton. These algae are central primary producers responsible for the fixation of ca. 40% of the global CO
2
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Qixin L, Xuan F, Zhiya S, Wenxin S, Shuo W, Ji L. Enhanced wastewater treatment performance by understanding the interaction between algae and bacteria based on quorum sensing. BIORESOURCE TECHNOLOGY 2022; 354:127161. [PMID: 35429596 DOI: 10.1016/j.biortech.2022.127161] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/09/2022] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
In order to further obtain sustainable wastewater treatment technology, in-depth analysis based on algal-bacterial symbiosis, quorum sensing signal molecules and algal-bacterial relationship will lay the foundation for the synergistic algal-bacterial wastewater treatment process. The methods of enhancing algae and bacteria wastewater treatment technology were systematically explored, including promoting symbiosis, reducing algicidal behavior, eliminating the interference of quorum sensing inhibitor, and developing algae and bacteria granular sludge. These findings can provide guidance for sustainable economic and environmental development, and facilitate carbon emissions reduction by using algae and bacteria synergistic wastewater treatment technology in further attempts. The future work should be carried out in the following four aspects: (1) Screening of dominant microalgae and bacteria; (2) Coordination of stable (emerging) contaminants removal; (3) Utilization of algae to produce fertilizers and feed (additives), and (4) Constructing recombinant algae and bacteria for reducing carbon emissions and obtaining high value-added products.
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Affiliation(s)
- Liu Qixin
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Feng Xuan
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Sheng Zhiya
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton T6G 2W2, Canada
| | - Shi Wenxin
- College of Environment and Ecology, Chongqing University, Chongqing 400030, China
| | - Wang Shuo
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China; Jiangsu College of Water Treatment Technology and Material Collaborative Innovation Center, Suzhou 215009, China.
| | - Li Ji
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China; Jiangsu College of Water Treatment Technology and Material Collaborative Innovation Center, Suzhou 215009, China
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7
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Gibson K, Song H, Chen N. Metabarcoding analysis of microbiome dynamics during a Phaeocystis globosa bloom in the Beibu Gulf, China. HARMFUL ALGAE 2022; 114:102217. [PMID: 35550291 DOI: 10.1016/j.hal.2022.102217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 02/21/2022] [Accepted: 02/26/2022] [Indexed: 06/15/2023]
Abstract
Phaeocystis globosa is an ecologically important haptophyte that can form harmful algal blooms (HABs). In this study, we used 16S rDNA V3-V4 amplicon sequencing data to explore the ecological mechanisms underlying a P. globosa bloom in the Beibu Gulf, China. Using field samples collected from three time points of a bloom, we observed a distinct succession in the bacteria, archaea and phytoplankton community composition throughout the bloom. We also observed temporal variation in response to the bloom at the nucleotide level, which supports a previously underappreciated amount of intragroup variation in the niches taken up by microbes during HABs. We developed a preliminary model for the development and progression of the P. globosa bloom using the spatial-temporal dynamics of P. globosa and the bacteria, archaea, phytoplankton and environmental variables. We also identified microbes with putative interactions with P. globosa during the bloom by identifying microbes correlated with P. globosa in interaction networks, identifying particle-associated microbes and exploring the P. globosa colony microbiome using sequences from whole P. globosa colonies collected during the bloom. This study revealed novel insight into the development of P. globosa HABs and many testable hypotheses that will guide future research on the mechanisms of P. globosa HABs.
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Affiliation(s)
- Kate Gibson
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada
| | - Huiyin Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Nansheng Chen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada; CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
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8
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Vacant S, Benites LF, Salmeron C, Intertaglia L, Norest M, Cadoudal A, Sanchez F, Caceres C, Piganeau G. Long-Term Stability of Bacterial Associations in a Microcosm of Ostreococcus tauri (Chlorophyta, Mamiellophyceae). FRONTIERS IN PLANT SCIENCE 2022; 13:814386. [PMID: 35463414 PMCID: PMC9024300 DOI: 10.3389/fpls.2022.814386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
Phytoplankton-bacteria interactions rule over carbon fixation in the sunlit ocean, yet only a handful of phytoplanktonic-bacteria interactions have been experimentally characterized. In this study, we investigated the effect of three bacterial strains isolated from a long-term microcosm experiment with one Ostreococcus strain (Chlorophyta, Mamiellophyceae). We provided evidence that two Roseovarius strains (Alphaproteobacteria) had a beneficial effect on the long-term survival of the microalgae whereas one Winogradskyella strain (Flavobacteriia) led to the collapse of the microalga culture. Co-cultivation of the beneficial and the antagonistic strains also led to the loss of the microalga cells. Metagenomic analysis of the microcosm is consistent with vitamin B12 synthesis by the Roseovarius strains and unveiled two additional species affiliated to Balneola (Balneolia) and Muricauda (Flavobacteriia), which represent less than 4% of the reads, whereas Roseovarius and Winogradskyella recruit 57 and 39% of the reads, respectively. These results suggest that the low-frequency bacterial species may antagonize the algicidal effect of Winogradskyella in the microbiome of Ostreococcus tauri and thus stabilize the microalga persistence in the microcosm. Altogether, these results open novel perspectives into long-term stability of phytoplankton cultures.
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Affiliation(s)
- Sophie Vacant
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, Centre National de la Recherche Scientifique, Oceanological Observatory of Banyuls, Banyuls-sur-Mer, France
| | - L. Felipe Benites
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, Centre National de la Recherche Scientifique, Oceanological Observatory of Banyuls, Banyuls-sur-Mer, France
| | - Christophe Salmeron
- Sorbonne Université, Centre National de la Recherche Scientifique, Observatoire Océanologique de Banyuls, FR3724, Banyuls-sur-Mer, France
| | - Laurent Intertaglia
- Sorbonne Université, Centre National de la Recherche Scientifique, Observatoire Océanologique de Banyuls, FR3724, Banyuls-sur-Mer, France
| | - Manon Norest
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, Centre National de la Recherche Scientifique, Oceanological Observatory of Banyuls, Banyuls-sur-Mer, France
| | - Adrien Cadoudal
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, Centre National de la Recherche Scientifique, Oceanological Observatory of Banyuls, Banyuls-sur-Mer, France
| | - Frederic Sanchez
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, Centre National de la Recherche Scientifique, Oceanological Observatory of Banyuls, Banyuls-sur-Mer, France
| | - Carlos Caceres
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, Centre National de la Recherche Scientifique, Oceanological Observatory of Banyuls, Banyuls-sur-Mer, France
| | - Gwenael Piganeau
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, Centre National de la Recherche Scientifique, Oceanological Observatory of Banyuls, Banyuls-sur-Mer, France
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Park S, Lee JS, Kim W, Yoon JH. Kordia aestuariivivens sp. nov. and Olleya sediminilitoris sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2021; 71. [PMID: 34085922 DOI: 10.1099/ijsem.0.004815] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain-negative and non-flagellated bacteria, YSTF-M3T and YSTF-M6T, were isolated from a tidal flat from Yellow Sea, Republic of Korea, and subjected to a polyphasic taxonomic study. Neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strains YSTF-M3T and YSTF-M6T belong to the genera Kordia and Olleya of the family Flavobacteriaceae, respectively. The 16S rRNA gene sequence similarities between strain YSTF-M3T and the type strains of Kordia species and between strain YSTF-M6T and the type strains of Olleya species were 94.1-98.4 and 97.3-98.3 %, respectively. The ANI and dDDH values between genomic sequences of strain YSTF-M3T and the type strains of five Kordia species and between those of strain YSTF-M6T and the type strains of three Olleya species were in ranges of 77.0-83.2 and 20.7-27.1 % and 79.4-81.5 and 22.3-23.9 %, respectively. The DNA G+C contents of strain YSTF-M3T and YSTF-M6T from genomic sequences were 34.1 and 31.1 %, respectively. Both strains contained MK-6 as predominant menaquinone and phosphatidylethanolamine as only major phospholipid identified. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strains YSTF-M3T and YSTF-M6T are separated from recognized species of the genera Kordia and Olleya, respectively. On the basis of the data presented, strains YSTF-M3T (=KACC 21639T=NBRC 114499T) and YSTF-M6T (=KACC 21640T=NBRC 114500T) are considered to represent novel species of the genera Kordia and Olleya, respectively, for which the names Kordia aestuariivivens sp. nov. and Olleya sediminilitoris sp. nov. are proposed.
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Affiliation(s)
- Sooyeon Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Republic of Korea
| | - Jung-Sook Lee
- Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup, Republic of Korea
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, 84 Heukseok-ro, Dongjak-gu, Seoul, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Republic of Korea
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10
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Genome characteristics of Kordia antarctica IMCC3317 T and comparative genome analysis of the genus Kordia. Sci Rep 2020; 10:14715. [PMID: 32895436 PMCID: PMC7477175 DOI: 10.1038/s41598-020-71328-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 08/10/2020] [Indexed: 11/25/2022] Open
Abstract
The genus Kordia is one of many genera affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes, well known for its degradation of high molecular weight organic matters. The genus Kordia currently comprises eight species, type strains of which have been isolated from a diverse range of marine environments. As of this report, four genome sequences have been submitted for cultured strains of Kordia, but none are complete nor have they been analyzed comprehensively. In this study, we report the complete genome of Kordia antarctica IMCC3317T, isolated from coastal seawater off the Antarctic Peninsula. The complete genome of IMCC3317T consists of a single circular chromosome with 5.5 Mbp and a 33.2 mol% of G+C DNA content. The IMCC3317T genome showed features typical of chemoheterotrophic marine bacteria and similar to other Kordia genomes, such as complete gene sets for the Embden–Meyerhof–Parnas glycolysis pathway, tricarboxylic acid cycle and oxidative phosphorylation. The genome also encoded many carbohydrate-active enzymes, some of which were clustered into approximately seven polysaccharide utilization loci, thereby demonstrating the potential for polysaccharide utilization. Finally, a nosZ gene encoding nitrous oxide reductase, an enzyme that catalyzes the reduction of N2O to N2 gas, was also unique to the IMCC3317T genome.
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Schultz D, Zühlke D, Bernhardt J, Francis TB, Albrecht D, Hirschfeld C, Markert S, Riedel K. An optimized metaproteomics protocol for a holistic taxonomic and functional characterization of microbial communities from marine particles. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:367-376. [PMID: 32281239 DOI: 10.1111/1758-2229.12842] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 04/03/2020] [Indexed: 06/11/2023]
Abstract
This study aimed to establish a robust and reliable metaproteomics protocol for an in-depth characterization of marine particle-associated (PA) bacteria. To this end, we compared six well-established protein extraction protocols together with different MS-sample preparation techniques using particles sampled during a North Sea spring algae bloom in 2009. In the final optimized workflow, proteins are extracted using a combination of SDS-containing lysis buffer and cell disruption by bead-beating, separated by SDS-PAGE, in-gel digested and analysed by LC-MS/MS, before MASCOT search against a metagenome-based database and data processing/visualization with the in-house-developed bioinformatics tools Prophane and Paver. As an application example, free-living (FL) and particulate communities sampled in April 2009 were analysed, resulting in an as yet unprecedented number of 9354 and 5034 identified protein groups for FL and PA bacteria, respectively. Our data suggest that FL and PA communities appeared similar in their taxonomic distribution, with notable exceptions: eukaryotic proteins and proteins assigned to Flavobacteriia, Cyanobacteria, and some proteobacterial genera were found more abundant on particles, whilst overall proteins belonging to Proteobacteria were more dominant in the FL fraction. Furthermore, our data points to functional differences including proteins involved in polysaccharide degradation, sugar- and phosphorus uptake, adhesion, motility, and stress response.
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Affiliation(s)
- Doreen Schultz
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Daniela Zühlke
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Jörg Bernhardt
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | | | - Dirk Albrecht
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Claudia Hirschfeld
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Stephanie Markert
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
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12
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Royo-Llonch M, Sánchez P, González JM, Pedrós-Alió C, Acinas SG. Ecological and functional capabilities of an uncultured Kordia sp. Syst Appl Microbiol 2019; 43:126045. [PMID: 31831198 DOI: 10.1016/j.syapm.2019.126045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 10/28/2019] [Accepted: 11/12/2019] [Indexed: 01/07/2023]
Abstract
Cultivable bacteria represent only a fraction of the diversity in microbial communities. However, the official procedures for classification and characterization of a novel prokaryotic species still rely on isolates. Nevertheless, due to single cell genomics, it is possible to retrieve genomes from environmental samples by sequencing them individually, and to assign specific genes to a specific taxon, regardless of their ability to grow in culture. In this study, a complete description was performed for uncultured Kordia sp. TARA_039_SRF, a proposed novel species within the genus Kordia, using culture-independent techniques. The type material was a high-quality draft genome (94.97% complete, 4.65% gene redundancy) co-assembled using ten nearly identical single amplified genomes (SAGs) from surface seawater in the North Indian Ocean during the Tara Oceans Expedition. The assembly process was optimized to obtain the best possible assembly metrics and a less fragmented genome. The closest relative of the species was Kordia periserrulae, which shared 97.56% similarity of the 16S rRNA gene, 75% orthologs and 89.13% average nucleotide identity. The functional potential of the proposed novel species included proteorhodopsin, the ability to incorporate nitrate, cytochrome oxidases with high affinity for oxygen, and CAZymes that were unique features within the genus. Its abundance at different depths and size fractions was also evaluated together with its functional annotation, revealing that its putative ecological niche could be particles of phytoplanktonic origin. It could putatively attach to these particles and consume them while sinking to the deeper and oxygen depleted layers of the North Indian Ocean.
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Affiliation(s)
- M Royo-Llonch
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain
| | - P Sánchez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain
| | - J M González
- Department of Microbiology, University of La Laguna, La Laguna, Spain
| | - C Pedrós-Alió
- Systems Biology Program, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - S G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain.
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13
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Complete genome sequence of Dyadobacter sp. 32, isolated from a culture of the freshwater diatom Cymbella microcephala. Mar Genomics 2019; 52:100720. [PMID: 31704048 DOI: 10.1016/j.margen.2019.100720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 09/25/2019] [Accepted: 10/18/2019] [Indexed: 11/22/2022]
Abstract
Bacteria have been shown to be involved in different species-specific interactions with eukaryotic algae such as diatoms, impacting important ecosystem processes. Recently, a strain assigned to Dyadobacter, named 'species 32', has been shown to be involved in a number of ecologically relevant diatom processes, such as biofilm formation or growth enhancement, depending on the diatom species. This bacterium was originally isolated from a culture of freshwater benthic diatoms that originated from an epilithic biofilm, in which both bacteria and diatoms coexist. A single complete circular chromosome of Dyadobacter sp. 32 was assembled with a length of 7,101,228 bp, containing 6062 protein coding genes and 3 rRNA operons. A number of interesting genetic features were found, such as a putative zeaxanthin biosynthetic gene cluster. A large number of polysaccharide utilizing gene clusters were also detected, along with genes potentially acquired from other bacteria through horizontal gene transfer, and genes previously identified in other algae-bacteria interactions. These data serve to increase our understanding of specific interactions within freshwater biofilms, and identify a number of gene targets with which to study the molecular basis of diatom-bacteria interactions.
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14
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Kling JD, Lee MD, Fu F, Phan MD, Wang X, Qu P, Hutchins DA. Transient exposure to novel high temperatures reshapes coastal phytoplankton communities. ISME JOURNAL 2019; 14:413-424. [PMID: 31636366 DOI: 10.1038/s41396-019-0525-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 09/04/2019] [Accepted: 09/13/2019] [Indexed: 11/09/2022]
Abstract
Average sea surface temperatures are expected to rise 4° this century, and marine phytoplankton and bacterial community composition, biogeochemical rates, and trophic interactions are all expected to change in a future warmer ocean. Thermal experiments typically use constant temperatures; however, weather and hydrography cause marine temperatures to fluctuate on diel cycles and over multiple days. We incubated natural communities of phytoplankton collected from California coastal waters during spring, summer, and fall under present-day and future mean temperatures, using thermal treatments that were either constant or fluctuated on a 48 h cycle. As assayed by marker-gene sequencing, the emergent microbial communities were consistent within each season, except when culture temperatures exceeded the highest temperature recorded in a 10-year local thermal dataset. When temperature treatments exceeded the 10-year maximum the phytoplankton community shifted, becoming dominated by diatom amplicon sequence variants (ASVs) not seen at lower temperatures. When mean temperatures were above the 10-year maximum, constant and fluctuating regimes each selected for different ASVs. These findings suggest coastal microbial communities are largely adapted to the current range of temperatures they experience. They also suggest a general hypothesis whereby multiyear upper temperature limits may represent thresholds, beyond which large community restructurings may occur. Now inevitable future temperature increases that exceed these environmental thresholds, even temporarily, may fundamentally reshape marine microbial communities and therefore the biogeochemical cycles that they mediate.
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Affiliation(s)
- Joshua D Kling
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90007, USA
| | - Michael D Lee
- Exobiology Branch, NASA Ames Research Center, Moffett Blvd., Mountain View, CA, 94035, USA
| | - Feixue Fu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90007, USA
| | - Megan D Phan
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90007, USA
| | - Xinwei Wang
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90007, USA.,School of Life Sciences, Xiamen University, 361005, Xiamen, China
| | - Pingping Qu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90007, USA
| | - David A Hutchins
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90007, USA.
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15
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Pinder MIM, Johansson ON, Almstedt A, Kourtchenko O, Clarke AK, Godhe A, Töpel M. Genome Sequence of Kordia sp. Strain SMS9 Identified in a Non-Axenic Culture of the Diatom Skeletonema marinoi. J Genomics 2019; 7:46-49. [PMID: 31171940 PMCID: PMC6536808 DOI: 10.7150/jgen.35061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 04/18/2019] [Indexed: 01/10/2023] Open
Abstract
Initial efforts to sequence the genome of the marine diatom Skeletonema marinoi were hampered by the presence of genetic material from bacteria, and there was sufficient material from some of these bacteria to enable the assembly of full chromosomes. Here, we report the genome of strain SMS9, one such bacterial species identified in a non-axenic culture of S. marinoi strain ST54. Its 5,482,391 bp circular chromosome contains 4,641 CDSs, and has a G+C content of 35.6%. Based on 16S rRNA comparison, phylotaxonomic analysis, and the genome similarity metrics dDDH and OrthoANI, we place this strain in the genus Kordia, and to the best of our knowledge, this is the first Kordia species to be initially described from European waters. As attempts to culture this strain have failed, however, the specifics of its relationship with S. marinoi are still uncertain.
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Affiliation(s)
- Matthew I M Pinder
- Department of Marine Sciences, University of Gothenburg, Göteborg, Sweden
| | - Oskar N Johansson
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Alvar Almstedt
- Department of Marine Sciences, University of Gothenburg, Göteborg, Sweden.,Clinical Genomics Göteborg, SciLifeLab, Göteborg, Sweden
| | - Olga Kourtchenko
- Department of Marine Sciences, University of Gothenburg, Göteborg, Sweden
| | - Adrian K Clarke
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Anna Godhe
- Department of Marine Sciences, University of Gothenburg, Göteborg, Sweden
| | - Mats Töpel
- Department of Marine Sciences, University of Gothenburg, Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, Göteborg, Sweden
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16
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The Algicidal Bacterium Kordia algicida Shapes a Natural Plankton Community. Appl Environ Microbiol 2019; 85:AEM.02779-18. [PMID: 30737345 PMCID: PMC6585488 DOI: 10.1128/aem.02779-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 01/27/2019] [Indexed: 11/23/2022] Open
Abstract
Plankton communities change on a seasonal basis in temperate systems, with distinct succession patterns; this is mainly due to algal species that have their optimal timing relative to environmental conditions. We know that bacterial populations are also instrumental in the decay and termination of phytoplankton blooms. Here, we describe algicidal bacteria as modulators of this important species succession. Upon treatment of a natural plankton consortium with an algicidal bacterium, we observed a strong shift in the phytoplankton community structure, compared to controls, resulting in formation of a succeeding Phaeocystis bloom. Blooms of this alga have a substantial impact on global biogeochemical and ecological cycles, as they are responsible for a substantial proportion of primary production during spring in the North Sea. We propose that one of the key factors influencing such community shifts may be algicidal bacteria. Plankton communities consist of complex microbial consortia that change over time. These fluctuations can be only partially explained by limiting resources. Biotic factors such as herbivores and pathogens also contribute to the control of algal blooms. Here we address the effects of algicidal bacteria on a natural plankton community in an indoor enclosure experiment. The algicidal bacteria, introduced into plankton taken directly from the North Sea during a diatom bloom, caused the rapid decline of the bloom-forming Chaetoceros socialis within only 1 day. The haptophyte Phaeocystis, in contrast, is resistant to the lytic bacteria and could benefit from the removal of the competitor, as indicated by an onset of a bloom in the treated enclosures. This cascading effect caused by the bacterial pathogen accelerated the succession of Phaeocystis, which bloomed with a delay of only several weeks in the in situ waters at Helgoland Roads in the North Sea. The algicidal bacteria can thus modulate the community within the limits of the abiotic and biotic conditions of the local environment. Implications of our findings for plankton ecosystem functioning are discussed. IMPORTANCE Plankton communities change on a seasonal basis in temperate systems, with distinct succession patterns; this is mainly due to algal species that have their optimal timing relative to environmental conditions. We know that bacterial populations are also instrumental in the decay and termination of phytoplankton blooms. Here, we describe algicidal bacteria as modulators of this important species succession. Upon treatment of a natural plankton consortium with an algicidal bacterium, we observed a strong shift in the phytoplankton community structure, compared to controls, resulting in formation of a succeeding Phaeocystis bloom. Blooms of this alga have a substantial impact on global biogeochemical and ecological cycles, as they are responsible for a substantial proportion of primary production during spring in the North Sea. We propose that one of the key factors influencing such community shifts may be algicidal bacteria.
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17
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Algal Oxylipins Mediate the Resistance of Diatoms against Algicidal Bacteria. Mar Drugs 2018; 16:md16120486. [PMID: 30518148 PMCID: PMC6315584 DOI: 10.3390/md16120486] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/12/2018] [Accepted: 11/30/2018] [Indexed: 11/17/2022] Open
Abstract
Algicidal bacteria can lyse microalgal blooms and trigger shifts within plankton communities. Resistant algal species can escape lysis, and have the opportunity to dominate the phytoplankton after a bacterial infection. Despite their important function in ecosystem regulation, little is known about mechanisms of resistance. Here, we show that the diatom Chaetoceros didymus releases eicosanoid oxylipins into the medium, and that the lytic algicidal bacterium, Kordia algicida, induces the production of several wound-activated oxylipins in this resistant diatom. Neither releases nor an induction occurs in the susceptible diatom Skeletonema costatum that is lysed by the bacterium within a few days. Among the upregulated oxylipins, hydroxylated eicosapentaenoic acids (HEPEs) dominate. However, also, resolvins, known lipid mediators in mammals, increase upon exposure of the algae to the algicidal bacteria. The prevailing hydroxylated fatty acid, 15-HEPE, significantly inhibits growth of K. algicida at a concentration of approximately 1 µM. The oxylipin production may represent an independent line of defense of the resistant alga, acting in addition to the previously reported upregulation of proteases.
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18
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Huang X, Zhu J, Cai Z, Lao Y, Jin H, Yu K, Zhang B, Zhou J. Profiles of quorum sensing (QS)-related sequences in phycospheric microorganisms during a marine dinoflagellate bloom, as determined by a metagenomic approach. Microbiol Res 2018; 217:1-13. [PMID: 30384903 DOI: 10.1016/j.micres.2018.08.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Revised: 08/26/2018] [Accepted: 08/29/2018] [Indexed: 01/09/2023]
Abstract
The complicated relationships among environmental microorganisms are regulated by quorum sensing (QS). Understanding QS-based signals could shed light on the interactions between microbial communities in certain environments. Although QS characteristics have been widely discussed, few studies have been conducted on the role of QS in phycospheric microorganisms. Here, we used metagenomics to examine the profile of AI-1 (AinS, HdtS, LuxI) and AI-2 (LuxS) autoinducers from a deeply sequenced microbial database, obtained from a complete dinoflagellate bloom. A total of 3001 putative AI-1 homologs and 130 AI-2 homologs were identified. The predominant member among the AI groups was HdtS. The abundance of HdtS, AinS, and LuxS increased as the bloom developed, whereas the abundance of LuxI showed the opposite trend. Phylogenetic analysis suggested that HdtS and LuxI synthase originated mainly from alpha-, beta-, and gamma-Proteobacteria, whereas AinS synthase originated solely from Vibrionales. In comparison to AI-1, the sequences related to AI-2 (LuxS) demonstrated a much wider taxonomic coverage. Some significant correlations were found between dominant species and QS signals. In addition to the QS, we also performed parallel analysis of the quorum quenching (QQ) sequences. In comparison to QS, the relative abundance of QQ signals was lower; however, an obvious frequency correlation was observed. These results suggested that QS and QQ signals co-participate in regulating microbial communities during an algal bloom. These data helped to reveal the characteristic behavior of algal symbiotic bacteria, and facilitated a better understanding of microbial dynamics during an algal bloom event from a chemical ecological perspective.
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Affiliation(s)
- Xinqing Huang
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, The Graduate School at Shenzhen, Tsinghua University, Guangdong Province, Shenzhen, China
| | - Jianming Zhu
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, The Graduate School at Shenzhen, Tsinghua University, Guangdong Province, Shenzhen, China
| | - Zhonghua Cai
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, The Graduate School at Shenzhen, Tsinghua University, Guangdong Province, Shenzhen, China
| | - Yongmin Lao
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, The Graduate School at Shenzhen, Tsinghua University, Guangdong Province, Shenzhen, China
| | - Hui Jin
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, The Graduate School at Shenzhen, Tsinghua University, Guangdong Province, Shenzhen, China
| | - Ke Yu
- The Division of Environment and Energy, Graduate School at Shenzhen, Peking University, Guangdong Province, Shenzhen, China
| | - Boya Zhang
- The Division of Environment and Energy, Graduate School at Shenzhen, Peking University, Guangdong Province, Shenzhen, China
| | - Jin Zhou
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, The Graduate School at Shenzhen, Tsinghua University, Guangdong Province, Shenzhen, China.
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19
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Hespen CW, Bruegger JJ, Guo Y, Marletta MA. Native Alanine Substitution in the Glycine Hinge Modulates Conformational Flexibility of Heme Nitric Oxide/Oxygen (H-NOX) Sensing Proteins. ACS Chem Biol 2018; 13:1631-1639. [PMID: 29757599 DOI: 10.1021/acschembio.8b00248] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Heme nitric oxide/oxygen sensing (H-NOX) domains are direct NO sensors that regulate a variety of biological functions in both bacteria and eukaryotes. Previous work on H-NOX proteins has shown that upon NO binding, a conformational change occurs along two glycine residues on adjacent helices (termed the glycine hinge). Despite the apparent importance of the glycine hinge, it is not fully conserved in all H-NOX domains. Several H-NOX sensors from the family Flavobacteriaceae contain a native alanine substitution in one of the hinge residues. In this work, the effect of the increased steric bulk within the Ala-Gly hinge on H-NOX function was investigated. The hinge in Kordia algicida OT-1 ( Ka H-NOX) is composed of A71 and G145. Ligand-binding properties and signaling function for this H-NOX were characterized. The variant A71G was designed to convert the hinge region of Ka H-NOX to the typical Gly-Gly motif. In activity assays with its cognate histidine kinase (HnoK), the wild type displayed increased signal specificity compared to A71G. Increasing titrations of unliganded A71G gradually inhibits HnoK autophosphorylation, while increasing titrations of unliganded wild type H-NOX does not inhibit HnoK. Crystal structures of both wild type and A71G Ka H-NOX were solved to 1.9 and 1.6 Å, respectively. Regions of H-NOX domains previously identified as involved in protein-protein interactions with HnoK display significantly higher b-factors in A71G compared to wild-type H-NOX. Both biochemical and structural data indicate that the hinge region controls overall conformational flexibility of the H-NOX, affecting NO complex formation and regulation of its HnoK.
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Affiliation(s)
- Charles W. Hespen
- QB3 Institute, University of California—Berkeley, 356 Stanley Hall, Berkeley, California 94720-3220, United States
| | - Joel J. Bruegger
- QB3 Institute, University of California—Berkeley, 356 Stanley Hall, Berkeley, California 94720-3220, United States
| | - Yirui Guo
- QB3 Institute, University of California—Berkeley, 356 Stanley Hall, Berkeley, California 94720-3220, United States
| | - Michael A. Marletta
- QB3 Institute, University of California—Berkeley, 356 Stanley Hall, Berkeley, California 94720-3220, United States
- Department of Chemistry, Department of Molecular and Cell Biology, QB3 Institute, University of California—Berkeley, 374B Stanley Hall, Berkeley, California 94720-3220, United States
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20
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Meyer N, Bigalke A, Kaulfuß A, Pohnert G. Strategies and ecological roles of algicidal bacteria. FEMS Microbiol Rev 2018; 41:880-899. [PMID: 28961821 DOI: 10.1093/femsre/fux029] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 05/31/2017] [Indexed: 12/21/2022] Open
Abstract
In both freshwater and marine ecosystems, phytoplankton are the most dominant primary producers, contributing substantially to aquatic food webs. Algicidal bacteria that can associate to microalgae from the phytoplankton have the capability to control the proliferation and even to lyse them. These bacteria thus play an important role in shaping species composition in pelagic environments. In this review, we discuss and categorise strategies used by algicidal bacteria for the attack on microalgae. We highlight the complex regulation of algicidal activity and defence responses that govern alga-bacteria interactions. We also discuss how algicidal bacteria impact algal physiology and metabolism and survey the existing algicidal metabolites and enzymes. The review illustrates that the ecological role of algicidal bacteria is not yet fully understood and critically discusses the challenges in obtaining ecologically relevant data.
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Affiliation(s)
- Nils Meyer
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich-Schiller-Universität Jena, Lessingstrasse 8, D-07743 Jena, Germany
| | - Arite Bigalke
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich-Schiller-Universität Jena, Lessingstrasse 8, D-07743 Jena, Germany
| | - Anett Kaulfuß
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich-Schiller-Universität Jena, Lessingstrasse 8, D-07743 Jena, Germany
| | - Georg Pohnert
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich-Schiller-Universität Jena, Lessingstrasse 8, D-07743 Jena, Germany.,Max Planck Institute for Chemical Ecology, Hans Knöll Str. 8, D-07745 Jena, Germany
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21
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Kim DI, Lee JH, Kim MS, Seong CN. Kordia zosterae sp. nov., isolated from the seaweed, Zostera marina. Int J Syst Evol Microbiol 2017; 67:4790-4795. [DOI: 10.1099/ijsem.0.002379] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Dae In Kim
- Department of Biology, College of Life science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
- Environmentally Friendly Agriculture Center, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Ji Hee Lee
- Aquaculture Industry Research Division, South Sea Fisheries Research Institute, National Institute of Fisheries Science (NIFS), Yeosu 59780, Republic of Korea
| | - Mi Sun Kim
- Agricultural Sciences Institute, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Chi Nam Seong
- Department of Biology, College of Life science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
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22
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Lee JJ, Kim TY, Choi SH, Kim BS. Analysis of the bacterial microbiome in the small octopus, Octopus variabilis, from South Korea to detect the potential risk of foodborne illness and to improve product management. Food Res Int 2017; 102:51-60. [PMID: 29195979 DOI: 10.1016/j.foodres.2017.09.084] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 09/26/2017] [Accepted: 09/27/2017] [Indexed: 01/10/2023]
Abstract
The small octopus (Octopus variabilis) is a popular seafood in many countries including South Korea. Because it is often consumed uncooked, the microorganisms in it often cause food poisoning. Therefore, analyzing the microbiome of the small octopus can help to understand the risk of food poisoning and manage octopus products better. A total of 40 small octopuses were collected from four sites in November and August. The microbiota was analyzed using Illumina Miseq sequencing, and the amount of bacteria was quantified by real-time PCR. In addition, we analyzed the influence of Vibrio vulnificus infection on the microbiome of the small octopus through artificial infection experiments. Bacteroidetes was the predominant phylum in August, and Proteobacteria was predominant in November. The composition of the microbiota in octopus depended on sampling region and season. The potential risk of foodborne illness from small octopus consumption might be higher in August than in November due to the abundance of potential pathogens. In the infection experiment, the proportion of V. vulnificus increased only at 27°C. The composition and functional gene profiles of the microbiota varied in a similar manner between non-infected and infected samples over time at the same temperature. These results indicated that the indigenous microbiota in small octopus could inhibit colonization by V. vulnificus during storage. Although further studies are necessary to clarify these results, our results could help us better understand food poisoning through octopus ingestion and manage products.
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Affiliation(s)
- Jin-Jae Lee
- Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon, Gangwon-do 24252, Republic of Korea
| | - Tae-Yoon Kim
- Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon, Gangwon-do 24252, Republic of Korea
| | - Sang Ho Choi
- Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Seoul National University, Seoul 08826, Republic of Korea
| | - Bong-Soo Kim
- Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon, Gangwon-do 24252, Republic of Korea.
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23
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Stringent Expression Control of Pathogenic R-body Production in Legume Symbiont Azorhizobium caulinodans. mBio 2017; 8:mBio.00715-17. [PMID: 28743814 PMCID: PMC5527310 DOI: 10.1128/mbio.00715-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
R bodies are insoluble large polymers consisting of small proteins encoded by reb genes and are coiled into cylindrical structures in bacterial cells. They were first discovered in Caedibacter species, which are obligate endosymbionts of paramecia. Caedibacter confers a killer trait on the host paramecia. R-body-producing symbionts are released from their host paramecia and kill symbiont-free paramecia after ingestion. The roles of R bodies have not been explained in bacteria other than Caedibacter. Azorhizobium caulinodans ORS571, a microsymbiont of the legume Sesbania rostrata, carries a reb operon containing four reb genes that are regulated by the repressor PraR. Herein, deletion of the praR gene resulted in R-body formation and death of host plant cells. The rebR gene in the reb operon encodes an activator. Three PraR binding sites and a RebR binding site are present in the promoter region of the reb operon. Expression analyses using strains with mutations within the PraR binding site and/or the RebR binding site revealed that PraR and RebR directly control the expression of the reb operon and that PraR dominantly represses reb expression. Furthermore, we found that the reb operon is highly expressed at low temperatures and that 2-oxoglutarate induces the expression of the reb operon by inhibiting PraR binding to the reb promoter. We conclude that R bodies are toxic not only in paramecium symbiosis but also in relationships between other bacteria and eukaryotic cells and that R-body formation is controlled by environmental factors. Caedibacter species, which are obligate endosymbiotic bacteria of paramecia, produce R bodies, and R-body-producing endosymbionts that are released from their hosts are pathogenic to symbiont-free paramecia. Besides Caedibacter species, R bodies have also been observed in a few free-living bacteria, but the significance of R-body production in these bacteria is still unknown. Recent advances in genome sequencing technologies revealed that many Gram-negative bacteria possess reb genes encoding R-body components, and interestingly, many of them are animal and plant pathogens. Azorhizobium caulinodans, a microsymbiont of the tropical legume Sesbania rostrata, also possesses reb genes. In this study, we demonstrate that A. caulinodans has ability to kill the host plant cells by producing R bodies, suggesting that pathogenicity conferred by an R body might be universal in bacteria possessing reb genes. Furthermore, we provide the first insight into the molecular mechanism underlying the expression of R-body production in response to environmental factors, such as temperature and 2-oxoglutarate.
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24
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Royo-Llonch M, Ferrera I, Cornejo-Castillo FM, Sánchez P, Salazar G, Stepanauskas R, González JM, Sieracki ME, Speich S, Stemmann L, Pedrós-Alió C, Acinas SG. Exploring Microdiversity in Novel Kordia sp. (Bacteroidetes) with Proteorhodopsin from the Tropical Indian Ocean via Single Amplified Genomes. Front Microbiol 2017; 8:1317. [PMID: 28790980 PMCID: PMC5525439 DOI: 10.3389/fmicb.2017.01317] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 06/29/2017] [Indexed: 12/03/2022] Open
Abstract
Marine Bacteroidetes constitute a very abundant bacterioplankton group in the oceans that plays a key role in recycling particulate organic matter and includes several photoheterotrophic members containing proteorhodopsin. Relatively few marine Bacteroidetes species have been described and, moreover, they correspond to cultured isolates, which in most cases do not represent the actual abundant or ecologically relevant microorganisms in the natural environment. In this study, we explored the microdiversity of 98 Single Amplified Genomes (SAGs) retrieved from the surface waters of the underexplored North Indian Ocean, whose most closely related isolate is Kordia algicida OT-1. Using Multi Locus Sequencing Analysis (MLSA) we found no microdiversity in the tested conserved phylogenetic markers (16S rRNA and 23S rRNA genes), the fast-evolving Internal Transcribed Spacer and the functional markers proteorhodopsin and the beta-subunit of RNA polymerase. Furthermore, we carried out a Fragment Recruitment Analysis (FRA) with marine metagenomes to learn about the distribution and dynamics of this microorganism in different locations, depths and size fractions. This analysis indicated that this taxon belongs to the rare biosphere, showing its highest abundance after upwelling-induced phytoplankton blooms and sinking to the deep ocean with large organic matter particles. This uncultured Kordia lineage likely represents a novel Kordia species (Kordia sp. CFSAG39SUR) that contains the proteorhodopsin gene and has a widespread spatial and vertical distribution. The combination of SAGs and MLSA makes a valuable approach to infer putative ecological roles of uncultured abundant microorganisms.
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Affiliation(s)
- Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones CientíficasBarcelona, Spain
| | - Isabel Ferrera
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones CientíficasBarcelona, Spain
| | - Francisco M Cornejo-Castillo
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones CientíficasBarcelona, Spain
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones CientíficasBarcelona, Spain
| | - Guillem Salazar
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones CientíficasBarcelona, Spain
| | | | - José M González
- Department of Microbiology, University of La LagunaLa Laguna, Spain
| | | | - Sabrina Speich
- École Normale Supérieure, Département de Géosciences, Laboratoire de Météorologie Dynamique, UMR 8539 ENS-CNRS- École PolytechniqueParis, France
| | - Lars Stemmann
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire d'Océanographie de Villefranche (LOV) UMR7093, Observatoire OcéanologiqueVillefranche-sur-Mer, France
| | - Carlos Pedrós-Alió
- Systems Biology Program, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones CientíficasBarcelona, Spain.,Departament de Genética i de Microbiologia, Facultat de Biociències, Universitat Autònoma de BarcelonaBellaterra, Spain
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25
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A Diverse Community To Study Communities: Integration of Experiments and Mathematical Models To Study Microbial Consortia. J Bacteriol 2017; 199:JB.00865-16. [PMID: 28533216 PMCID: PMC5512218 DOI: 10.1128/jb.00865-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The last few years have seen the advancement of high-throughput experimental techniques that have produced an extraordinary amount of data. Bioinformatics and statistical analyses have become instrumental to interpreting the information coming from, e.g., sequencing data and often motivate further targeted experiments. The broad discipline of “computational biology” extends far beyond the well-established field of bioinformatics, but it is our impression that more theoretical methods such as the use of mathematical models are not yet as well integrated into the research studying microbial interactions. The empirical complexity of microbial communities presents challenges that are difficult to address with in vivo/in vitro approaches alone, and with microbiology developing from a qualitative to a quantitative science, we see stronger opportunities arising for interdisciplinary projects integrating theoretical approaches with experiments. Indeed, the addition of in silico experiments, i.e., computational simulations, has a discovery potential that is, unfortunately, still largely underutilized and unrecognized by the scientific community. This minireview provides an overview of mathematical models of natural ecosystems and emphasizes that one critical point in the development of a theoretical description of a microbial community is the choice of problem scale. Since this choice is mostly dictated by the biological question to be addressed, in order to employ theoretical models fully and successfully it is vital to implement an interdisciplinary view at the conceptual stages of the experimental design.
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Rolland JL, Stien D, Sanchez-Ferandin S, Lami R. Quorum Sensing and Quorum Quenching in the Phycosphere of Phytoplankton: a Case of Chemical Interactions in Ecology. J Chem Ecol 2016; 42:1201-1211. [PMID: 27822708 DOI: 10.1007/s10886-016-0791-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 09/20/2016] [Accepted: 10/05/2016] [Indexed: 12/28/2022]
Abstract
The interactions between bacteria and phytoplankton regulate many important biogeochemical reactions in the marine environment, including those in the global carbon, nitrogen, and sulfur cycles. At the microscopic level, it is now well established that important consortia of bacteria colonize the phycosphere, the immediate environment of phytoplankton cells. In this microscale environment, abundant bacterial cells are organized in a structured biofilm, and exchange information through the diffusion of small molecules called semiochemicals. Among these processes, quorum sensing plays a particular role as, when a sufficient abundance of cells is reached, it allows bacteria to coordinate their gene expression and physiology at the population level. In contrast, quorum quenching mechanisms are employed by many different types of microorganisms that limit the coordination of antagonistic bacteria. This review synthesizes quorum sensing and quorum quenching mechanisms evidenced to date in the phycosphere, emphasizing the implications that these signaling systems have for the regulation of bacterial communities and their activities. The diversity of chemical compounds involved in these processes is examined. We further review the bacterial functions regulated in the phycosphere by quorum sensing, which include biofilm formation, nutrient acquisition, and emission of algaecides. We also discuss quorum quenching compounds as antagonists of quorum sensing, their function in the phycosphere, and their potential biotechnological applications. Overall, the current state of the art demonstrates that quorum sensing and quorum quenching regulate a balance between a symbiotic and a parasitic way of life between bacteria and their phytoplankton host.
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Affiliation(s)
- Jean Luc Rolland
- Interactions-Hôtes-Pathogènes-Environnements (IHPE), Ifremer, CNRS, UPVD, Université de Montpellier, UMR 5244, 34090, Montpellier, France
| | - Didier Stien
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Sophie Sanchez-Ferandin
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire de Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Raphaël Lami
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, Banyuls-sur-Mer, France.
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Qi F, Huang Z, Lai Q, Li D, Shao Z. Kordia ulvae sp. nov., a bacterium isolated from the surface of green marine algae Ulva sp. Int J Syst Evol Microbiol 2016; 66:2623-2628. [DOI: 10.1099/ijsem.0.001098] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Feng Qi
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, PR China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation, Xiamen, PR China
- School of Marine Sciences, Ningbo University, Ningbo, PR China
- Third Institute of Oceanography, SOA, Xiamen 361005, PR China
| | - Zhaobin Huang
- Third Institute of Oceanography, SOA, Xiamen 361005, PR China
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation, Xiamen, PR China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, PR China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
- School of Marine Sciences, Ningbo University, Ningbo, PR China
| | - Qiliang Lai
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation, Xiamen, PR China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, PR China
- Third Institute of Oceanography, SOA, Xiamen 361005, PR China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Dengfeng Li
- School of Marine Sciences, Ningbo University, Ningbo, PR China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, PR China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
- Third Institute of Oceanography, SOA, Xiamen 361005, PR China
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation, Xiamen, PR China
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Du J, Liu Y, Lai Q, Dong C, Xie Y, Shao Z. Kordia zhangzhouensis sp. nov., isolated from surface freshwater. Int J Syst Evol Microbiol 2015; 65:3379-3383. [DOI: 10.1099/ijsem.0.000424] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, Gram-stain-negative, rod-shaped and non-motile bacterium, JS14SB-1T, was isolated from the surface freshwater of the Jiulong River, PR China. Strain JS14SB-1T grew at 15–38 °C (optimum, 28–35 °C), at pH 6.0–9.0 (optimum pH 7.0) and in the presence of 1.0–7.0 % (w/v) NaCl [optimum 3.0–5.0 % (w/v)]. Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that strain JS14SB-1T was affiliated to the genus Kordia, sharing low similarities (95.1–97.1 %) to all type strains of species of this genus. The digital DNA–DNA hybridization (DDH) value between strain JS14SB-1T and the closely related strain Kordia jejudonensis SSK3-3T was 20.70 ± 2.33 % and far below the 70 % DDH value taken as the gold standard for delineation of bacterial species. The major fatty acids were identified as iso-C15 : 0 and iso-C17 : 0 3-OH. The polar lipids were phosphatidylethanolamine, glycolipid, aminolipid, several unidentified phospholipids and lipids. The predominant menaquinone was MK-6. The G+C content of the genomic DNA was 33.8 mol%. Based on the phenotypic, phylogenetic and chemotaxonomic distinctiveness, strain JS14SB-1T is considered to represent a novel species of the genus Kordia, for which the name Kordia zhangzhouensis sp. nov. is proposed; the type strain is JS14SB-1T ( = MCCC 1A00726T = KCTC 42140T).
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Affiliation(s)
- Juan Du
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Yang Liu
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Qiliang Lai
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Chunming Dong
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Yanrong Xie
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
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29
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Lei X, Zhang H, Chen Y, Li Y, Chen Z, Lai Q, Zhang J, Zheng W, Xu H, Zheng T. Erythrobacter luteus sp. nov., isolated from mangrove sediment. Int J Syst Evol Microbiol 2015; 65:2472-2478. [PMID: 25911535 DOI: 10.1099/ijs.0.000283] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative, orange-pigmented, aerobic bacterial strain, designated KA37T, was isolated from a mangrove sediment sample collected from Yunxiao mangrove National Nature Reserve, Fujian Province, China. Growth was observed at 4-37 °C, 0-3% (w/v) NaCl and pH 5-10. Mg2+ ions were required for growth. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that the isolate was a member of the genus Erythrobacter, which belongs to the family Erythrobacteraceae. Strain KA37T was most closely related to Erythrobacter gangjinensis KCTC 22330T (96.9% sequence similarity), followed by Erythrobacter marinus KCTC 23554T (96.8%); similarity to other members of the genus was below 96.6%. The major fatty acids were C17 : 1ω6c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). Strain KA37T did not produce bacteriochlorophyll a. The predominant respiratory quinone was ubiquinone 10 (Q-10). The polar lipids of strain KA37T were sphingoglycolipid, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, five unknown lipids and one unidentified phospholipid. According to its morphology, physiology, fatty acid composition and 16S rRNA sequence, the novel strain most appropriately belongs to the genus Erythrobacter, but can be distinguished readily from species of the genus Erythrobacter with validly published names. The name Erythrobacter luteus sp. nov. is proposed, with strain KA37T ( = MCCC 1F01227T = KCTC 42179T) as the type strain.
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Affiliation(s)
- Xueqian Lei
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, PR China
| | - Huajun Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, PR China
| | - Yao Chen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, PR China
| | - Yi Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, PR China
| | - Zhangran Chen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, PR China
| | - Qiliang Lai
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, PR China.,Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, PR China
| | - Jingyan Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, PR China
| | - Wei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, PR China
| | - Hong Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, PR China
| | - Tianling Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, PR China
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30
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Adaptational properties and applications of cold-active lipases from psychrophilic bacteria. Extremophiles 2014; 19:235-47. [PMID: 25472009 DOI: 10.1007/s00792-014-0710-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 11/16/2014] [Indexed: 10/24/2022]
Abstract
Psychrophilic microorganisms are cold-adapted with distinct properties from other thermal classes thriving in cold conditions in large areas of the earth's cold environment. Maintenance of functional membranes, evolving cold-adapted enzymes and synthesizing a range of structural features are basic adaptive strategies of psychrophiles. Among the cold-evolved enzymes are the cold-active lipases, a group of microbial lipases with inherent stability-activity-flexibility property that have engaged the interest of researchers over the years. Current knowledge regarding these cold-evolved enzymes in psychrophilic bacteria proves a display of high catalytic efficiency with low thermal stability, which is a differentiating feature with that of their mesophilic and thermophilic counterparts. Improvement strategies of their adaptive structural features have significantly benefited the enzyme industry. Based on their homogeneity and purity, molecular characterizations of these enzymes have been successful and their properties make them unique biocatalysts for various industrial and biotechnological applications. Although, strong association of lipopolysaccharides from Antarctic microorganisms with lipid hydrolases pose a challenge in their purification, heterologous expression of the cold-adapted lipases with affinity tags simplifies purification with higher yield. The review discusses these cold-evolved lipases from bacteria and their peculiar properties, in addition to their potential biotechnological and industrial applications.
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31
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Buchan A, LeCleir GR, Gulvik CA, González JM. Master recyclers: features and functions of bacteria associated with phytoplankton blooms. Nat Rev Microbiol 2014; 12:686-98. [PMID: 25134618 DOI: 10.1038/nrmicro3326] [Citation(s) in RCA: 538] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Marine phytoplankton blooms are annual spring events that sustain active and diverse bloom-associated bacterial populations. Blooms vary considerably in terms of eukaryotic species composition and environmental conditions, but a limited number of heterotrophic bacterial lineages - primarily members of the Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria - dominate these communities. In this Review, we discuss the central role that these bacteria have in transforming phytoplankton-derived organic matter and thus in biogeochemical nutrient cycling. On the basis of selected field and laboratory-based studies of flavobacteria and roseobacters, distinct metabolic strategies are emerging for these archetypal phytoplankton-associated taxa, which provide insights into the underlying mechanisms that dictate their behaviours during blooms.
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Affiliation(s)
- Alison Buchan
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996-0845, USA
| | - Gary R LeCleir
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996-0845, USA
| | - Christopher A Gulvik
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - José M González
- Department of Microbiology, University of La Laguna, ES-38200 La Laguna, Spain
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Kordia
aquimaris sp. nov., a zeaxanthin-producing member of the family Flavobacteriaceae isolated from surface seawater, and emended description of the genus Kordia. Int J Syst Evol Microbiol 2013; 63:4790-4796. [DOI: 10.1099/ijs.0.056051-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative, strictly aerobic, rod-shaped, non-flagellated, non-spore-forming and gliding marine bacterium designated strain CC-AMZ-301T was isolated from coastal surface seawater near Taichung harbour, Taiwan. Strain CC-AMZ-301T predominantly synthesized zeaxanthin and thus formed yellow colonies on marine agar. The novel strain showed high pairwise 16S rRNA gene sequence similarity to
Kordia periserrulae
IMCC1412T (95.0 %),
K. algicida
KCTC 8814PT (94.4 %) and K. antarctica IMCC3317T (94.2 %), and formed a phylogenetic lineage tightly associated with species of the genus
Kordia
. The polar lipid profile of strain CC-AMZ-301T consisted of three unidentified lipids, three unidentified aminolipids and one unidentified phospholipid. The major fatty acids (>5 % of total) were iso-C17 : 0 3-OH, iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 9 (iso-C17 : 1ω9c and/or 10-methyl C16 : 0). The DNA G+C content was 36.4 mol%. Menaquinone 6 (MK-6) was the predominant respiratory quinone. The major polyamine was the triamine sym-homospermidine. Based on evidence from the present polyphasic study, strain CC-AMZ-301T is proposed to represent a novel species of the genus
Kordia
, for which the name
Kordia
aquimaris sp. nov. is proposed; the type strain is CC-AMZ-301T ( = JCM 18556T = BCRC 80464T). An emended description of the genus
Kordia
is also proposed.
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Park S, Jung YT, Yoon JH. Kordia jejudonensis sp. nov., isolated from the junction between the ocean and a freshwater spring, and emended description of the genus Kordia. Int J Syst Evol Microbiol 2013; 64:657-662. [PMID: 24170775 DOI: 10.1099/ijs.0.058776-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative, aerobic, non-spore-forming, non-flagellated, non-gliding and rod-shaped bacterial strain, SSK3-3(T), was isolated from the zone where the ocean and a freshwater spring meet at Jeju island, South Korea. Strain SSK3-3(T) grew optimally at 30 °C, at pH 7.0-8.0 and in the presence of 2.0% (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain SSK3-3(T) clustered with the type strains of species of the genus Kordia, with which it exhibited 96.5-97.2% 16S rRNA gene sequence similarity. Sequence similarities to the type strains of other recognized species were less than 92.2%. Strain SSK3-3(T) contained MK-6 as the predominant menaquinone and iso-C(15 : 0), iso-C(17 : 0) 3-OH, iso-C(15 : 0) 3-OH and summed feature 3 (C(16 : 1)ω7c and/or C(16 : 1)ω6c) as the major fatty acids. The major polar lipids of strain SSK3-3(T) were phosphatidylethanolamine, one unidentified lipid and one unidentified glycolipid. The DNA G+C content of strain SSK3-3(T) was 34.9 mol% and the mean DNA-DNA relatedness with Kordia periserrulae KACC 14311(T) was 12%. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain SSK3-3(T) is separate from other species of the genus Kordia. On the basis of the data presented, strain SSK3-3(T) is considered to represent a novel species of the genus Kordia, for which the name Kordia jejudonensis sp. nov. is proposed. The type strain is SSK3-3(T) ( = KCTC 32426(T) = CECT 8368(T)). An emended description of the genus Kordia is also provided.
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Affiliation(s)
- Sooyeon Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, South Korea
| | - Yong-Taek Jung
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, South Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, South Korea
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Baek K, Choi A, Kang I, Lee K, Cho JC. Kordia
antarctica sp. nov., isolated from Antarctic seawater. Int J Syst Evol Microbiol 2013; 63:3617-3622. [DOI: 10.1099/ijs.0.052738-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative, chemoheterotrophic, yellow-pigmented, non-motile, flexirubin-negative, facultatively anaerobic bacterium, designated strain IMCC3317T, was isolated from a coastal seawater sample from the Antarctic Penninsula. Optimal growth of strain IMCC3317T was observed at 20 °C, pH 8.0 and in the presence of 2–3 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain IMCC3317T belonged to the genus
Kordia
and was closely related to
Kordia algicida
OT-1T (96.7 % sequence similarity) and
Kordia periserrulae
IMCC1412T (96.1 % sequence similarity). The major fatty acids were 10-methyl C16 : 0 and/or iso-C16 : 1ω9c, iso-C17 : 0 3-OH, iso-C15 : 0 and anteiso-C15 : 0. The G+C content of the genomic DNA was 35.1 mol%. The strain contained menaquinone-6 (MK-6) as the respiratory quinone. The polar lipids detected in the strain were phosphatidylethanolamine and unknown aminophospholipids, aminolipids and polar lipids. On the basis of phylogenetic distinction and differential phenotypic characteristics, it is suggested that strain IMCC3317T ( = KCTC 32292T = NBRC 109401T) be assigned to the genus
Kordia
as the type strain of a novel species, for which the name
Kordia
antarctica sp. nov. is proposed.
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Affiliation(s)
- Kiwoon Baek
- Division of Biology and Ocean Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Ahyoung Choi
- Division of Biology and Ocean Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Ilnam Kang
- Division of Biology and Ocean Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Kiyoung Lee
- Division of Biology and Ocean Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Jang-Cheon Cho
- Division of Biology and Ocean Sciences, Inha University, Incheon 402-751, Republic of Korea
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Biradar YS, Jagatap S, Khandelwal KR, Singhania SS. Exploring of Antimicrobial Activity of Triphala Mashi-an Ayurvedic Formulation. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2013; 5:107-13. [PMID: 18317557 PMCID: PMC2249739 DOI: 10.1093/ecam/nem002] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2006] [Accepted: 09/26/2006] [Indexed: 11/22/2022]
Abstract
Triphala Mashi is an ayurvedic formulation that was prepared in our lab. Aqueous and alcoholic extracts of both Triphala and Triphala Mashi were used, to evaluate antimicrobial activity. Comparative phytochemical profile of Triphala and Triphala Mashi was done by preliminary phytochemical screening, total phenolic content and thin layer chromatography (TLC). Antimicrobial activity includes isolation of pathogens from clinical samples, its characterization, testing its multiple drug resistance against standard antibiotics and antimicrobial activity of aqueous and alcoholic extracts of both Triphala and Triphala Mashi against these organisms by using agar gel diffusion method. Triphala Mashi containing phenolic compounds, tannins exhibited comparable antimicrobial activity in relation to Triphala against all the microorganisms tested. It inhibits the dose-dependent growth of Gram-positive and Gram-negative bacteria. In conclusion, it appears that Triphala Mashi has non-specific antimicrobial activity.
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Affiliation(s)
- Yogesh S Biradar
- Department of Pharmacognosy, Poona College of Pharmacy, Bharati Vidyapeeth Deemed University, Erandwane, Pune 411 038, Department of Microbiology, University of Pune and Department of Management Sciences, University of Pune, Pune, Maharashtra, India
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Meziti A, Mente E, Kormas KA. Gut bacteria associated with different diets in reared Nephrops norvegicus. Syst Appl Microbiol 2012; 35:473-82. [PMID: 23040460 DOI: 10.1016/j.syapm.2012.07.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 07/26/2012] [Accepted: 07/27/2012] [Indexed: 11/17/2022]
Abstract
The impact of different diets on the gut microbiota of reared Nephrops norvegicus was investigated based on bacterial 16S rRNA gene diversity. Specimens were collected from Pagasitikos Gulf (Greece) and kept in experimental rearing tanks, under in situ conditions, for 6months. Treatments included three diets: frozen natural (mussel) food (M), dry formulated pellet (P) and starvation (S). Gut samples were collected at the initiation of the experiment, and after 3 and 6months. Tank water and diet samples were also analyzed for bacterial 16S rRNA gene diversity. Statistical analysis separated the two groups fed or starved (M and P vs. S samples). Most gut bacteria were not related to the water or diet bacteria, while bacterial diversity was higher in the starvation samples. M and P samples were dominated by Gammaproteobacteria, Epsilonproteobacteria and Tenericutes. Phylotypes clustering in Photobacterium leiognathi, Shewanella sp. and Entomoplasmatales had high frequencies in the M and P samples but low sequence frequencies in S samples. The study showed that feeding resulted in the selection of specific species, which also occurs in the natural population, and might be associated with the animal's nutrition.
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Affiliation(s)
- Alexandra Meziti
- Department of Ichthyology & Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46 Volos, Greece
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Lon protease of Azorhizobium caulinodans ORS571 is required for suppression of reb gene expression. Appl Environ Microbiol 2012; 78:6251-61. [PMID: 22752172 DOI: 10.1128/aem.01039-12] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial Lon proteases play important roles in a variety of biological processes in addition to housekeeping functions. In this study, we focused on the Lon protease of Azorhizobium caulinodans, which can fix nitrogen both during free-living growth and in stem nodules of the legume Sesbania rostrata. The nitrogen fixation activity of an A. caulinodans lon mutant in the free-living state was not significantly different from that of the wild-type strain. However, the stem nodules formed by the lon mutant showed little or no nitrogen fixation activity. By microscopic analyses, two kinds of host cells were observed in the stem nodules formed by the lon mutant. One type has shrunken host cells containing a high density of bacteria, and the other type has oval or elongated host cells containing a low density or no bacteria. This phenotype is similar to a praR mutant highly expressing the reb genes. Quantitative reverse transcription-PCR analyses revealed that reb genes were also highly expressed in the lon mutant. Furthermore, a lon reb double mutant formed stem nodules showing higher nitrogen fixation activity than the lon mutant, and shrunken host cells were not observed in these stem nodules. These results suggest that Lon protease is required to suppress the expression of the reb genes and that high expression of reb genes in part causes aberrance in the A. caulinodans-S. rostrata symbiosis. In addition to the suppression of reb genes, it was found that Lon protease was involved in the regulation of exopolysaccharide production and autoagglutination of bacterial cells.
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Powell SM, Chapman CC, Bermudes M, Tamplin ML. Use of a blocking primer allows selective amplification of bacterial DNA from microalgae cultures. J Microbiol Methods 2012; 90:211-3. [PMID: 22610103 DOI: 10.1016/j.mimet.2012.05.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 05/09/2012] [Accepted: 05/09/2012] [Indexed: 11/27/2022]
Abstract
The production of algae is a crucial component of many aquaculture systems and the role of bacteria in this process is an important although complex one. We report the development of a new blocking primer that allowed PCR amplification of bacterial DNA in the presence of algal chloroplast DNA.
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Affiliation(s)
- Shane M Powell
- Australian Seafood Cooperative Research Centre and the Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia.
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Teeling H, Fuchs BM, Becher D, Klockow C, Gardebrecht A, Bennke CM, Kassabgy M, Huang S, Mann AJ, Waldmann J, Weber M, Klindworth A, Otto A, Lange J, Bernhardt J, Reinsch C, Hecker M, Peplies J, Bockelmann FD, Callies U, Gerdts G, Wichels A, Wiltshire KH, Glockner FO, Schweder T, Amann R. Substrate-Controlled Succession of Marine Bacterioplankton Populations Induced by a Phytoplankton Bloom. Science 2012; 336:608-11. [DOI: 10.1126/science.1218344] [Citation(s) in RCA: 937] [Impact Index Per Article: 78.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Yu Y, Li HR, Zeng YX, Sun K, Chen B. Pricia antarctica gen. nov., sp. nov., a member of the family Flavobacteriaceae, isolated from Antarctic intertidal sediment. Int J Syst Evol Microbiol 2011; 62:2218-2223. [PMID: 22081722 DOI: 10.1099/ijs.0.037515-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A yellow-coloured, rod-shaped, Gram-reaction- and Gram-staining-negative, non-motile and aerobic bacterium, designated strain ZS1-8(T), was isolated from a sample of sandy intertidal sediment collected from the Antarctic coast. Flexirubin-type pigments were absent. In phylogenetic analyses based on 16S rRNA gene sequences, strain ZS1-8(T) formed a distinct phyletic line and the results indicated that the novel strain should be placed in a new genus within the family Flavobacteriaceae. In pairwise comparisons between strain ZS1-8(T) and recognized species, the levels of 16S rRNA gene sequence similarity were all <93.3 %. The strain required Ca(2+) and K(+) ions as well as NaCl for growth. Optimal growth was observed at pH 7.5-8.0, 17-19 °C and with 2-3 % (w/v) NaCl. The major fatty acids were iso-C(15 : 1) G, iso-C(15 : 0), summed feature 3 (iso-C(15 : 0) 2-OH and/or C(16 : 1)ω7c), an unknown acid with an equivalent chain-length of 13.565 and iso-C(17 : 0) 3-OH. The major respiratory quinone was MK-6. The predominant polar lipid was phosphatidylethanolamine. The genomic DNA G+C content was 43.9 mol%. Based on the phylogenetic, phenotypic and chemotaxonomic data, strain ZS1-8(T) represents a novel species in a new genus in the family Flavobacteriaceae for which the name Pricia antarctica gen. nov., sp. nov. is proposed. The type strain of the type species is ZS1-8(T) (= JCM 17291(T) = DSM 23421(T)).
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Affiliation(s)
- Yong Yu
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, PR China
| | - Hui-Rong Li
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, PR China
| | - Yin-Xin Zeng
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, PR China
| | - Kun Sun
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, PR China
| | - Bo Chen
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, PR China
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Shin YR, Lim KB, Chae JP, Kang DK. Characterization of Anti-Listerial Substance Produced by Lactobacillus salivarius LCH1227. Korean J Food Sci Anim Resour 2011. [DOI: 10.5851/kosfa.2011.31.4.609] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Paul C, Pohnert G. Interactions of the algicidal bacterium Kordia algicida with diatoms: regulated protease excretion for specific algal lysis. PLoS One 2011; 6:e21032. [PMID: 21695044 PMCID: PMC3117869 DOI: 10.1371/journal.pone.0021032] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Accepted: 05/16/2011] [Indexed: 11/18/2022] Open
Abstract
Interactions of planktonic bacteria with primary producers such as diatoms have great impact on plankton population dynamics. Several studies described the detrimental effect of certain bacteria on diatoms but the biochemical nature and the regulation mechanism involved in the production of the active compounds remained often elusive. Here, we investigated the interactions of the algicidal bacterium Kordia algicida with the marine diatoms Skeletonema costatum, Thalassiosira weissflogii, Phaeodactylum tricornutum, and Chaetoceros didymus. Algicidal activity was only observed towards the first three of the tested diatom species while C. didymus proved to be not susceptible. The cell free filtrate and the >30 kDa fraction of stationary K. algicida cultures is fully active, suggesting a secreted algicidal principle. The active supernatant from bacterial cultures exhibited high protease activity and inhibition experiments proved that these enzymes are involved in the observed algicidal action of the bacteria. Protease mediated interactions are not controlled by the presence of the alga but dependent on the cell density of the K. algicida culture. We show that protease release is triggered by cell free bacterial filtrates suggesting a quorum sensing dependent excretion mechanism of the algicidal protein. The K. algicida / algae interactions in the plankton are thus host specific and under the control of previously unidentified factors.
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Affiliation(s)
- Carsten Paul
- Institute for Inorganic and Analyticial Chemistry, Department for Bioorganic Analytics, Friedrich Schiller University Jena, Jena, Germany
| | - Georg Pohnert
- Institute for Inorganic and Analyticial Chemistry, Department for Bioorganic Analytics, Friedrich Schiller University Jena, Jena, Germany
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Thomas F, Hehemann JH, Rebuffet E, Czjzek M, Michel G. Environmental and gut bacteroidetes: the food connection. Front Microbiol 2011; 2:93. [PMID: 21747801 PMCID: PMC3129010 DOI: 10.3389/fmicb.2011.00093] [Citation(s) in RCA: 655] [Impact Index Per Article: 50.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 04/14/2011] [Indexed: 12/21/2022] Open
Abstract
Members of the diverse bacterial phylum Bacteroidetes have colonized virtually all types of habitats on Earth. They are among the major members of the microbiota of animals, especially in the gastrointestinal tract, can act as pathogens and are frequently found in soils, oceans and freshwater. In these contrasting ecological niches, Bacteroidetes are increasingly regarded as specialists for the degradation of high molecular weight organic matter, i.e., proteins and carbohydrates. This review presents the current knowledge on the role and mechanisms of polysaccharide degradation by Bacteroidetes in their respective habitats. The recent sequencing of Bacteroidetes genomes confirms the presence of numerous carbohydrate-active enzymes covering a large spectrum of substrates from plant, algal, and animal origin. Comparative genomics reveal specific Polysaccharide Utilization Loci shared between distantly related members of the phylum, either in environmental or gut-associated species. Moreover, Bacteroidetes genomes appear to be highly plastic and frequently reorganized through genetic rearrangements, gene duplications and lateral gene transfers (LGT), a feature that could have driven their adaptation to distinct ecological niches. Evidence is accumulating that the nature of the diet shapes the composition of the intestinal microbiota. We address the potential links between gut and environmental bacteria through food consumption. LGT can provide gut bacteria with original sets of utensils to degrade otherwise refractory substrates found in the diet. A more complete understanding of the genetic gateways between food-associated environmental species and intestinal microbial communities sheds new light on the origin and evolution of Bacteroidetes as animals’ symbionts. It also raises the question as to how the consumption of increasingly hygienic and processed food deprives our microbiota from useful environmental genes and possibly affects our health.
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Affiliation(s)
- François Thomas
- UMR 7139, Marine Plants and Biomolecules, Station Biologique de Roscoff, UPMC University Paris 6, Roscoff, France
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Abstract
Kordia algicida OT-1 is an algicidal bacterium against the bloom-forming microalgae. The genome sequence of K. algicida revealed a number of interesting features, including the degradation of macromolecules, the biosynthesis of carotenoid pigment and secondary metabolites, and the capacity for gliding motility, which might facilitate the understanding of algicidal mechanisms.
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Choi A, Oh HM, Yang SJ, Cho JC. Kordia periserrulae sp. nov., isolated from a marine polychaete Periserrula leucophryna, and emended description of the genus Kordia. Int J Syst Evol Microbiol 2010; 61:864-869. [PMID: 20495038 DOI: 10.1099/ijs.0.022764-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, chemoheterotrophic, yellow-pigmented, non-motile, flexirubin-negative, facultatively anaerobic bacterium, designated strain IMCC1412(T), was isolated from a marine polychaete Periserrula leucophryna inhabiting a tidal flat of the Yellow Sea, Korea. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain IMCC1412(T) was most closely related to Kordia algicida, with a sequence similarity of 96.7 %, but only distantly related to other species in the family Flavobacteriaceae (<92 % similarity). The G+C content of the DNA was 37.3 mol%. The strain contained MK-6 as the major respiratory quinone and phosphatidylethanolamine, unidentified aminolipids and unidentified polar lipids as the major polar lipids. On the basis of phylogenetic distinctiveness and differential phenotypic characteristics, strain IMCC1412(T) ( = KACC 14311(T) = KCTC 22801(T) = NBRC 106077(T)) should be assigned to the genus Kordia as the type strain of a novel species, for which the name Kordia periserrulae sp. nov. is proposed. An emended description of the genus Kordia is also presented.
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Affiliation(s)
- Ahyoung Choi
- Division of Biology and Ocean Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Hyun-Myung Oh
- Division of Biology and Ocean Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Seung-Jo Yang
- Division of Biology and Ocean Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Jang-Cheon Cho
- Division of Biology and Ocean Sciences, Inha University, Incheon 402-751, Republic of Korea
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Banning EC, Casciotti KL, Kujawinski EB. Novel strains isolated from a coastal aquifer suggest a predatory role for flavobacteria. FEMS Microbiol Ecol 2010; 73:254-70. [DOI: 10.1111/j.1574-6941.2010.00897.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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phrR-like gene praR of Azorhizobium caulinodans ORS571 is essential for symbiosis with Sesbania rostrata and is involved in expression of reb genes. Appl Environ Microbiol 2010; 76:3475-85. [PMID: 20382809 DOI: 10.1128/aem.00238-10] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
This study focuses on the function of the gene praR that encodes a putative transcription factor in Azorhizobium caulinodans ORS571, a microsymbiont of Sesbania rostrata. The praR gene is a homolog of the phrR gene of Sinorhizobium medicae WSM419, and the praR and phrR homologs are distributed throughout the class Alphaproteobacteria. The growth and nitrogen fixation activity of an A. caulinodans praR deletion mutant in the free-living state were not significantly different from those of the wild-type strain. However, the stem nodules formed by the praR mutant showed lower nitrogen fixation activity than the wild-type stem nodules. Microscopy revealed that infected host cells with an oval or elongated shape were observed at early stages in the nodules formed by the praR mutant, but these infected cells gradually fell into two types. One maintained an oval or elongated shape, but the vacuoles in these cells gradually enlarged and the bacteria gradually disappeared. The other cells were shrunken with bacteria remaining inside. Microarrays revealed that genes homologous to the reb genes of Caedibacter taeniospiralis were highly expressed in the praR mutant. Furthermore, the stem nodules formed by an A. caulinodans mutant with a deletion of praR and reb-homologous genes showed high nitrogen fixation activity, comparable to that of the wild-type stem nodules, and were filled with oval or elongated host cells. These results suggest that PraR controls the expression of the reb-homologous genes and that high expression of reb-homologous genes causes aberrance in A. caulinodans-S. rostrata symbiosis.
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Lee SH, Chae JP, Kim MJ, Kang DK. Isolation of Bacillus amyloliquefaciens ATC6 Producing Acidic Cellulase. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2010. [DOI: 10.5187/jast.2010.52.1.065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Becker PT, Gillan DC, Eeckhaut I. Characterization of the bacterial community associated with body wall lesions of Tripneustes gratilla (Echinoidea) using culture-independent methods. J Invertebr Pathol 2008; 100:127-30. [PMID: 19041326 DOI: 10.1016/j.jip.2008.11.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2008] [Revised: 10/22/2008] [Accepted: 11/05/2008] [Indexed: 11/24/2022]
Abstract
The bacterial community associated with skin lesions of the sea urchin Tripneustes gratilla was investigated using 16S ribosomal RNA gene cloning and fluorescent in situ hybridization (FISH). All clones were classified in the Alphaproteobacteria, Gammaproteobacteria and Cytophaga-Flexibacter-Bacteroides (CFB) bacteria. Most of the Alphaproteobacteria were related to the Roseobacter lineage and to bacteria implicated in marine diseases. The majority of the Gammaproteobacteria were identified as Vibrio while CFB represented only 9% of the total clones. FISH analyses showed that Alphaproteobacteria, CFB bacteria and Gammaproteobacteria accounted respectively for 43%, 38% and 19% of the DAPI counts. The importance of the methods used is emphasized.
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Affiliation(s)
- Pierre T Becker
- Laboratoire de biologie marine, Université de Mons-Hainaut, 6 Avenue du Champ de Mars, 7000 Mons, Belgium.
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Fulvibacter tottoriensis gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from marine sediment. Int J Syst Evol Microbiol 2008; 58:1670-4. [DOI: 10.1099/ijs.0.65554-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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