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Abate R, Oon YL, Oon YS, Bi Y, Mi W, Song G, Gao Y. Diverse interactions between bacteria and microalgae: A review for enhancing harmful algal bloom mitigation and biomass processing efficiency. Heliyon 2024; 10:e36503. [PMID: 39286093 PMCID: PMC11402748 DOI: 10.1016/j.heliyon.2024.e36503] [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: 02/16/2024] [Revised: 08/15/2024] [Accepted: 08/16/2024] [Indexed: 09/19/2024] Open
Abstract
The interactions between bacteria and microalgae play pivotal roles in resource allocation, biomass accumulation, nutrient recycling, and species succession in aquatic systems, offering ample opportunities to solve several social problems. The escalating threat of harmful algal blooms (HABs) in the aquatic environment and the lack of cheap and eco-friendly algal-biomass processing methods have been among the main problems, demanding efficient and sustainable solutions. In light of this, the application of algicidal bacteria to control HABs and enhance algal biomass processing has been promoted in the past few decades as potentially suitable mechanisms to solve those problems. Hence, this comprehensive review aims to explore the diverse interaction modes between bacteria and microalgae, ranging from synergistic to antagonistic, and presents up-to-date information and in-depth analysis of their potential biotechnological applications, particularly in controlling HABs and enhancing microalgal biomass processing. For instance, several studies revealed that algicidal bacteria can effectively inhibit the growth of Microcystis aeruginosa, a notorious freshwater HAB species, with an antialgal efficiency of 24.87 %-98.8 %. The review begins with an overview of the mechanisms behind algae-bacteria interactions, including the environmental factors influencing these dynamics and their broader implications for aquatic ecosystems. It then provides a detailed analysis of the role of algicidal bacteria in controlling harmful algal blooms, as well as their role in bioflocculation and the pretreatment of microalgal biomass. Additionally, the review identifies and discusses the constraints and challenges in the biotechnological application of these interactions. By exploring the strategic use of algicidal bacteria, this review not only underscores their importance in maintaining aquatic environmental health but also in enhancing biomass processing efficiency. It offers valuable insights into future research avenues and the potential scalability of these applications, both in situ and at an industrial level.
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Affiliation(s)
- Rediat Abate
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- College of Natural and Computatinal Science, Arba Minch University, Ethiopia
| | - Yoong-Ling Oon
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China
| | - Yoong-Sin Oon
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China
| | - Yonghong Bi
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Wujuan Mi
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Gaofei Song
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yahui Gao
- School of Life Sciences, Xiamen University, Xiamen, 361102, China
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2
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A joint bacterial effort to produce vitamin B 12. Nature 2024:10.1038/d41586-024-02474-7. [PMID: 39085632 DOI: 10.1038/d41586-024-02474-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2024]
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3
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Yang X, Liu Z, Zhang Y, Shi X, Wu Z. Dinoflagellate-Bacteria Interactions: Physiology, Ecology, and Evolution. BIOLOGY 2024; 13:579. [PMID: 39194517 DOI: 10.3390/biology13080579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/09/2024] [Accepted: 07/12/2024] [Indexed: 08/29/2024]
Abstract
Dinoflagellates and heterotrophic bacteria are two major micro-organism groups within marine ecosystems. Their coexistence has led to a co-evolutionary relationship characterized by intricate interactions that not only alter their individual behaviors but also exert a significant influence on the broader biogeochemical cycles. Our review commenced with an analysis of bacterial populations, both free-living and adherent to dinoflagellate surfaces. Members of Alphaproteobacteria, Gammaproteobacteria, and the Cytophaga-Flavobacterium-Bacteroides group are repeatedly found to be associated with dinoflagellates, with representation by relatively few genera, such as Methylophaga, Marinobacter, and Alteromonas. These bacterial taxa engage with dinoflagellates in a limited capacity, involving nutrient exchange, the secretion of pathogenic substances, or participation in chemical production. Furthermore, the genomic evolution of dinoflagellates has been profoundly impacted by the horizontal gene transfer from bacteria. The integration of bacterial genes into dinoflagellates has been instrumental in defining their biological characteristics and nutritional strategies. This review aims to elucidate the nuanced interactions between dinoflagellates and their associated bacteria, offering a detailed perspective on their complex relationship.
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Affiliation(s)
- Xiaohong Yang
- Guangzhou Marine Geological Survey, Guangzhou 511458, China
| | - Zijian Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
- Microbial Processes and Interactions (MiPI), TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
| | - Yanwen Zhang
- Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
| | - Xinguo Shi
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
| | - Zhen Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
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4
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Judd M, Wira J, Place AR, Bachvaroff T. Long-Read Sequencing Unlocks New Insights into the Amphidinium carterae Microbiome. Mar Drugs 2024; 22:342. [PMID: 39195458 DOI: 10.3390/md22080342] [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: 06/21/2024] [Revised: 07/16/2024] [Accepted: 07/22/2024] [Indexed: 08/29/2024] Open
Abstract
Dinoflagellates are one of the largest groups of marine microalgae and exhibit diverse trophic strategies. Some dinoflagellates can produce secondary metabolites that are known to be toxic, which can lead to ecologically harmful blooms. Amphidinium carterae is one species of dinoflagellate that produces toxic compounds and is used as a model for dinoflagellate studies. The impact of the microbiome on A. carterae growth and metabolite synthesis is not yet fully understood, nor is the impact of bacterial data on sequencing and assembly. An antibiotic cocktail was previously shown to eliminate 16S amplification from the dinoflagellate culture. Even with drastically reduced bacterial numbers during antibiotic treatment, bacterial sequences were still present. In this experiment, we used novel Nanopore long-read sequencing techniques on A. carterae cultures to assemble 15 full bacterial genomes ranging from 2.9 to 6.0 Mb and found that the use of antibiotics decreased the percentage of reads mapping back to bacteria. We also identified shifts in the microbiome composition and identified a potentially deleterious bacterial species arising in the absence of the antibiotic treatment. Multiple antibiotic resistance genes were identified, as well as evidence that the bacterial population does not contribute to toxic secondary metabolite synthesis.
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Affiliation(s)
- Miranda Judd
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
| | - Jens Wira
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
| | - Allen R Place
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
| | - Tsvetan Bachvaroff
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
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5
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Martínez-Pérez C, Zweifel ST, Pioli R, Stocker R. Space, the final frontier: The spatial component of phytoplankton-bacterial interactions. Mol Microbiol 2024. [PMID: 38970428 DOI: 10.1111/mmi.15293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 06/17/2024] [Accepted: 06/24/2024] [Indexed: 07/08/2024]
Abstract
Microscale interactions between marine phytoplankton and bacteria shape the microenvironment of individual cells, impacting their physiology and ultimately influencing global-scale biogeochemical processes like carbon and nutrient cycling. In dilute environments such as the ocean water column, metabolic exchange between microorganisms likely requires close proximity between partners. However, the biological strategies to achieve this physical proximity remain an understudied aspect of phytoplankton-bacterial associations. Understanding the mechanisms by which these microorganisms establish and sustain spatial relationships and the extent to which spatial proximity is necessary for interactions to occur, is critical to learning how spatial associations influence the ecology of phytoplankton and bacterial communities. Here, we provide an overview of current knowledge on the role of space in shaping interactions among ocean microorganisms, encompassing behavioural and metabolic evidence. We propose that characterising phytoplankton-bacterial interactions from a spatial perspective can contribute to a mechanistic understanding of the establishment and maintenance of these associations and, consequently, an enhanced ability to predict the impact of microscale processes on ecosystem-wide phenomena.
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Affiliation(s)
- Clara Martínez-Pérez
- Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Sophie T Zweifel
- Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Roberto Pioli
- Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Roman Stocker
- Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
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Abate R, Oon YS, Oon YL, Bi Y. Microalgae-bacteria nexus for environmental remediation and renewable energy resources: Advances, mechanisms and biotechnological applications. Heliyon 2024; 10:e31170. [PMID: 38813150 PMCID: PMC11133723 DOI: 10.1016/j.heliyon.2024.e31170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 04/25/2024] [Accepted: 05/11/2024] [Indexed: 05/31/2024] Open
Abstract
Microalgae and bacteria, known for their resilience, rapid growth, and proximate ecological partnerships, play fundamental roles in environmental and biotechnological advancements. This comprehensive review explores the synergistic interactions between microalgae and bacteria as an innovative approach to address some of the most pressing environmental issues and the demands of clean and renewable freshwater and energy sources. Studies indicated that microalgae-bacteria consortia can considerably enhance the output of biotechnological applications; for instance, various reports showed during wastewater treatment the COD removal efficiency increased by 40%-90.5 % due to microalgae-bacteria consortia, suggesting its great potential amenability in biotechnology. This review critically synthesizes research works on the microalgae and bacteria nexus applied in the advancements of renewable energy generation, with a special focus on biohydrogen, reclamation of wastewater and desalination processes. The mechanisms of underlying interactions, the environmental factors influencing consortia performance, and the challenges and benefits of employing these bio-complexes over traditional methods are also discussed in detail. This paper also evaluates the biotechnological applications of these microorganism consortia for the augmentation of biomass production and the synthesis of valuable biochemicals. Furthermore, the review sheds light on the integration of microalgae-bacteria systems in microbial fuel cells for concurrent energy production, waste treatment, and resource recovery. This review postulates microalgae-bacteria consortia as a sustainable and efficient solution for clean water and energy, providing insights into future research directions and the potential for industrial-scale applications.
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Affiliation(s)
- Rediat Abate
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yoong-Sin Oon
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China
| | - Yoong-Ling Oon
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China
| | - Yonghong Bi
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
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Wienhausen G, Moraru C, Bruns S, Tran DQ, Sultana S, Wilkes H, Dlugosch L, Azam F, Simon M. Ligand cross-feeding resolves bacterial vitamin B 12 auxotrophies. Nature 2024; 629:886-892. [PMID: 38720071 DOI: 10.1038/s41586-024-07396-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 04/08/2024] [Indexed: 05/24/2024]
Abstract
Cobalamin (vitamin B12, herein referred to as B12) is an essential cofactor for most marine prokaryotes and eukaryotes1,2. Synthesized by a limited number of prokaryotes, its scarcity affects microbial interactions and community dynamics2-4. Here we show that two bacterial B12 auxotrophs can salvage different B12 building blocks and cooperate to synthesize B12. A Colwellia sp. synthesizes and releases the activated lower ligand α-ribazole, which is used by another B12 auxotroph, a Roseovarius sp., to produce the corrin ring and synthesize B12. Release of B12 by Roseovarius sp. happens only in co-culture with Colwellia sp. and only coincidently with the induction of a prophage encoded in Roseovarius sp. Subsequent growth of Colwellia sp. in these conditions may be due to the provision of B12 by lysed cells of Roseovarius sp. Further evidence is required to support a causative role for prophage induction in the release of B12. These complex microbial interactions of ligand cross-feeding and joint B12 biosynthesis seem to be widespread in marine pelagic ecosystems. In the western and northern tropical Atlantic Ocean, bacteria predicted to be capable of salvaging cobinamide and synthesizing only the activated lower ligand outnumber B12 producers. These findings add new players to our understanding of B12 supply to auxotrophic microorganisms in the ocean and possibly in other ecosystems.
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Affiliation(s)
- Gerrit Wienhausen
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany.
- Scripps Institution of Oceanography, Marine Biology Research Division, University of California San Diego, La Jolla, CA, USA.
| | - Cristina Moraru
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Stefan Bruns
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Den Quoc Tran
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Sabiha Sultana
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Heinz Wilkes
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Leon Dlugosch
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Farooq Azam
- Scripps Institution of Oceanography, Marine Biology Research Division, University of California San Diego, La Jolla, CA, USA
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany.
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Oldenburg, Germany.
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8
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Arslan Topal EI, Öbek E, Topal M. Is Cladophora fracta an efficient tool of accumulating critical raw materials from wastewater and there a potential health risk of use of algae as organic fertilizer? INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2024; 34:1977-1994. [PMID: 37097044 DOI: 10.1080/09603123.2023.2203905] [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: 10/24/2022] [Accepted: 04/12/2023] [Indexed: 05/03/2023]
Abstract
In this study investigation of accumulations of critical raw materials (cobalt (Co), antimony (Sb), vanadium (V), lanthanum (La) and tungsten (W)) from wastewater by using C. fracta were aimed. Besides, assessment of the potential health risks in terms of the use of organic fertilizer obtained from the macroalga to be harvested from the treatment were also aimed. Highest Co, Sb, V, La and W accumulations by algae in reactor were 125±6.2%, 201.25±10%, 318.18±15%, 357.97±18%, and 500±25%, respectively. When compared with control, Co, Sb, V, La and W in algae increased 2.25, 3.01, 4.18, 4.58, and 6 times, respectively. The algae was very high bioaccumulative for Co and La. Highest MPI was calculated as 3.94. Non-carcinogenic risk of CRMs according to different exposure types (ingestion, inhalation, and dermal) were calculated for man, woman and child. There is not any non-carcinogenic risk from the investigated exposure ways of algae as organic fertilizer.
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Affiliation(s)
- E Işıl Arslan Topal
- Department of Environmental Engineering, Faculty of Engineering, Firat University, Elazığ, Turkey
| | - Erdal Öbek
- Department of Bioengineering, Faculty of Engineering, Firat University, Elazığ, Turkey
| | - Murat Topal
- Department of Chemistry Processing Technologies, Tunceli Vocation School, Munzur University, Tunceli, Turkey
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Tran DQ, Milke F, Niggemann J, Simon M. The diatom Thalassiosira rotula induces distinct growth responses and colonization patterns of Roseobacteraceae, Flavobacteria and Gammaproteobacteria. Environ Microbiol 2023; 25:3536-3555. [PMID: 37705313 DOI: 10.1111/1462-2920.16506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/03/2023] [Indexed: 09/15/2023]
Abstract
Diatoms as important phytoplankton components interact with and are colonized by heterotrophic bacteria. This colonization has been studied extensively in the past but a distinction between the bacterial colonization directly on diatom cells or on the aggregated organic material, exopolymeric substances (EPS), was little addressed. Here we show that the diatom Thalassiosira rotula and EPS were differently colonized by strains of Roseobacteraceae and Flavobacteriaceae in two and tree partner treatments and an enriched natural bacterial community as inoculum. In two partner treatments, the algae and EPS were generally less colonized than in the three partner treatments. Two strains benefitted greatly from the presence of another partner as the proportions of their subpopulations colonizing the diatom cell and the EPS were much enhanced relative to their two partner treatments. Highest proportions of bacteria colonizing the diatom and EPS occurred in the treatment inoculated with the enriched natural bacterial community. Dissolved organic carbon, amino acids and carbohydrates produced by T. rotula were differently used by the bacteria in the two and three partner treatments and most efficiently by the enriched natural bacterial community. Our approach is a valid model system to study physico-chemical bacteria-diatom interactions with increasing complexity.
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Affiliation(s)
- Den Quoc Tran
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Felix Milke
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Jutta Niggemann
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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10
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Den TQ, Neu TR, Sultana S, Giebel HA, Simon M, Billerbeck S. Distinct glycoconjugate cell surface structures make the pelagic diatom Thalassiosira rotula an attractive habitat for bacteria. JOURNAL OF PHYCOLOGY 2023; 59:309-322. [PMID: 36471567 DOI: 10.1111/jpy.13308] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/14/2022] [Indexed: 05/28/2023]
Abstract
Interactions between marine diatoms and bacteria have been studied for decades. However, the visualization of physical interactions between these diatoms and their colonizers is still limited. To enhance our understanding of these specific interactions, a new Thalassiosira rotula isolate from the North Sea (strain 8673) was characterized by scanning electron microscopy and confocal laser scanning microscopy (CLSM) after staining with fluorescently labeled lectins targeting specific glycoconjugates. To investigate defined interactions of this strain with bacteria the new strain was made axenic and co-cultivated with a natural bacterial community and in two- or three-partner consortia with different bacteria of the Roseobacter group, Gammaproteobacteria and Bacteroidetes. The CLSM analysis of the consortia identified six out of 78 different lectins as very suitable to characterize glycoconjugates of T. rotula. The resulting images show that fucose-containing threads were the dominant glycoconjugates secreted by the T. rotula cells but chitin and to a lesser extent other glycoconjugates were also identified. Bacteria attached predominantly to the fucose glycoconjugates. The colonizing bacteria showed various attachment patterns such as adhering to the diatom threads in aggregates only or attaching to both the surfaces and the threads of the diatom. Interestingly the colonization patterns of single bacteria differed strikingly from those of bacterial co-cultures, indicating that interactions between two bacterial species impacted the colonization of the diatom. Our observations help to better understand physical interactions and specific colonization patterns of distinct bacterial mono- and co-cultures with an abundant diatom of costal seas.
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Affiliation(s)
- Tran Quoc Den
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Thomas R Neu
- Helmholtz Centre for Environmental Research - UFZ, Magdeburg, Germany
| | - Sabiha Sultana
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Helge-A Giebel
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Sara Billerbeck
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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Sultana S, Bruns S, Wilkes H, Simon M, Wienhausen G. Vitamin B 12 is not shared by all marine prototrophic bacteria with their environment. THE ISME JOURNAL 2023; 17:836-845. [PMID: 36914732 DOI: 10.1038/s41396-023-01391-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 02/20/2023] [Accepted: 02/23/2023] [Indexed: 03/14/2023]
Abstract
Vitamin B12 (cobalamin, herein B12) is an essential cofactor involved in amino acid synthesis and carbon resupply to the TCA cycle for most prokaryotes, eukaryotic microorganisms, and animals. Despite being required by most, B12 is produced by only a minor fraction of prokaryotes and therefore leads to complex interaction between prototrophs and auxotrophs. However, it is unknown how B12 is provided by prototrophs to auxotrophs. In this study, 33 B12 prototrophic alphaproteobacterial strains were grown in co-culture with Thalassiosira pseudonana, a B12 auxotrophic diatom, to determine the bacterial ability to support the growth of the diatom by sharing B12. Among these strains, 18 were identified to share B12 with the diatom, while nine were identified to retain B12 and not support growth of the diatom. The other bacteria either shared B12 with the diatom only with the addition of substrate or inhibited the growth of the diatom. Extracellular B12 measurements of B12-provider and B12-retainer strains confirmed that the cofactor could only be detected in the environment of the tested B12-provider strains. Intracellular B12 was measured by LC-MS and showed that the concentrations of the different B12-provider as well as B12-retainer strains differed substantially. Although B12 is essential for the vast majority of microorganisms, mechanisms that export this essential cofactor are still unknown. Our results suggest that a large proportion of bacteria that can synthesise B12 de novo cannot share the cofactor with their environment.
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Affiliation(s)
- Sabiha Sultana
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl von Ossietzky Str. 9-11, D-26129, Oldenburg, Germany
| | - Stefan Bruns
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl von Ossietzky Str. 9-11, D-26129, Oldenburg, Germany
| | - Heinz Wilkes
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl von Ossietzky Str. 9-11, D-26129, Oldenburg, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl von Ossietzky Str. 9-11, D-26129, Oldenburg, Germany.,Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heerstraße 231, D-26129, Oldenburg, Germany
| | - Gerrit Wienhausen
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl von Ossietzky Str. 9-11, D-26129, Oldenburg, Germany. .,Institute for Medical Microbiology and Virology, Carl von Ossietzky University Oldenburg, D-26129, Oldenburg, Germany.
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12
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Soto MA, Desai D, Bannon C, LaRoche J, Bertrand EM. Cobalamin producers and prokaryotic consumers in the Northwest Atlantic. Environ Microbiol 2023. [PMID: 36861357 DOI: 10.1111/1462-2920.16363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 02/26/2023] [Indexed: 03/03/2023]
Abstract
Cobalamin availability can influence primary productivity and ecological interactions in marine microbial communities. The characterization of cobalamin sources and sinks is a first step in investigating cobalamin dynamics and its impact on productivity. Here, we identify potential cobalamin sources and sinks on the Scotian Shelf and Slope in the Northwest Atlantic Ocean. Functional and taxonomic annotation of bulk metagenomic reads, combined with analysis of genome bins, were used to identify potential cobalamin sources and sinks. Cobalamin synthesis potential was mainly attributed to Rhodobacteraceae, Thaumarchaeota, and cyanobacteria (Synechococcus and Prochlorococcus). Cobalamin remodelling potential was mainly attributed to Alteromonadales, Pseudomonadales, Rhizobiales, Oceanospirilalles, Rhodobacteraceae, and Verrucomicrobia, while potential cobalamin consumers include Flavobacteriaceae, Actinobacteria, Porticoccaceae, Methylophiliaceae, and Thermoplasmatota. These complementary approaches identified taxa with the potential to be involved in cobalamin cycling on the Scotian Shelf and revealed genomic information required for further characterization. The Cob operon of Rhodobacterales bacterium HTCC2255, a strain with known importance in cobalamin cycling, was similar to a major cobalamin producer bin, suggesting that a related strain may represent a critical cobalamin source in this region. These results enable future inquiries that will enhance our understanding of how cobalamin shapes microbial interdependencies and productivity in this region.
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Affiliation(s)
- Maria A Soto
- Department of Biology and Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Dhwani Desai
- Department of Biology and Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Catherine Bannon
- Department of Biology and Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Julie LaRoche
- Department of Biology and Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Erin M Bertrand
- Department of Biology and Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
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Macey MC, Ramkissoon NK, Cogliati S, Toubes-Rodrigo M, Stephens BP, Kucukkilic-Stephens E, Schwenzer SP, Pearson VK, Preston LJ, Olsson-Francis K. Habitability and Biosignature Formation in Simulated Martian Aqueous Environments. ASTROBIOLOGY 2023; 23:144-154. [PMID: 36577028 DOI: 10.1089/ast.2021.0197] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Water present on early Mars is often assumed to have been habitable. In this study, experiments were performed to investigate the habitability of well-defined putative martian fluids and to identify the accompanying potential formation of biosignatures. Simulated martian environments were developed by combining martian fluid and regolith simulants based on the chemistry of the Rocknest sand shadow at Gale Crater. The simulated chemical environment was inoculated with terrestrial anoxic sediment from the Pyefleet mudflats (United Kingdom). These enrichments were cultured for 28 days and subsequently subcultured seven times to ensure that the microbial community was solely grown on the defined, simulated chemistry. The impact of the simulated chemistries on the microbial community was assessed by cell counts and sequencing of 16S rRNA gene profiles. Associated changes to the fluid and precipitate chemistries were established by using ICP-OES, IC, FTIR, and NIR. The fluids were confirmed as habitable, with the enriched microbial community showing a reduction in abundance and diversity over multiple subcultures relating to the selection of specific metabolic groups. The final community comprised sulfate-reducing, acetogenic, and other anaerobic and fermentative bacteria. Geochemical characterization and modeling of the simulant and fluid chemistries identified clear differences between the biotic and abiotic experiments. These differences included the elimination of sulfur owing to the presence of sulfate-reducing bacteria and more general changes in pH associated with actively respiring cells that impacted the mineral assemblages formed. This study confirmed that a system simulating the fluid chemistry of Gale Crater could support a microbial community and that variation in chemistries under biotic and abiotic conditions can be used to inform future life-detection missions.
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Affiliation(s)
- Michael C Macey
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Nisha K Ramkissoon
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Simone Cogliati
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Mario Toubes-Rodrigo
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Ben P Stephens
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Ezgi Kucukkilic-Stephens
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Susanne P Schwenzer
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Victoria K Pearson
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Louisa J Preston
- Mullard Space Science Laboratory, Department of Space and Climate Physics, University College London, London, United Kingdom
| | - Karen Olsson-Francis
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, United Kingdom
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14
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Synergy between microalgae and microbiome in polluted waters. Trends Microbiol 2023; 31:9-21. [PMID: 35985939 DOI: 10.1016/j.tim.2022.06.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 11/22/2022]
Abstract
Microalga-microbiome interactions are central to both health and disease of aquatic environments. Despite impressive advances in deciphering how microorganisms participate in and impact aquatic ecosystems, the evolution and ecological involvement of microalgae and the microbiome in polluted waters are typically studied independently. Here, the phycosphere (i.e., the consortia of microalgae and the related microbiome) is regarded as an independent and integrated life form, and we summarize the survival strategies exhibited by this symbiont when exposed to anthropogenic pollution. We highlight the cellular strategies and discuss the modulation at the transcriptional and population levels, which reciprocally alters community structure or genome composition for medium-term acclimation or long-term adaptation. We propose a 'PollutantBiome' concept to help the understanding of microalga-microbiome interactions and development of beneficial microbial synthetic communities for pollutant remediation.
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15
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Abstract
The skin microbiome is a key player in human health, with diverse functions ranging from defense against pathogens to education of the immune system. While recent studies have begun to shed light on the valuable role that skin microorganisms have in maintaining the skin barrier, a detailed understanding of the complex interactions that shape healthy skin microbial communities is limited. Cobamides, the vitamin B12 class of cofactor, are essential for organisms across the tree of life. Because this vitamin is only produced by a limited fraction of prokaryotes, cobamide sharing is predicted to mediate community dynamics within microbial communities. Here, we provide the first large-scale metagenomic assessment of cobamide biosynthesis and utilization in the skin microbiome. We show that while numerous and diverse taxa across the major bacterial phyla on the skin encode cobamide-dependent enzymes, relatively few species encode de novo cobamide biosynthesis. We show that cobamide producers and users are integrated into the network structure of microbial communities across the different microenvironments of the skin and that changes in microbiome community structure and diversity are associated with the abundance of cobamide producers in the Corynebacterium genus, for both healthy and diseased skin states. Finally, we find that de novo cobamide biosynthesis is enriched only in Corynebacterium species associated with hosts, including those prevalent on human skin. We confirm that the cofactor is produced in excess through quantification of cobamide production by human skin-associated species isolated in the laboratory. Taken together, our results reveal the potential for cobamide sharing within skin microbial communities, which we hypothesize mediates microbiome community dynamics and host interactions. IMPORTANCE The skin microbiome is essential for maintaining skin health and function. However, the microbial interactions that dictate microbiome structure, stability, and function are not well understood. Here, we investigate the biosynthesis and use of cobamides, a cofactor needed by many organisms but only produced by select prokaryotes, within the human skin microbiome. We found that while a large proportion of skin taxa encode cobamide-dependent enzymes, only a select few encode de novo cobamide biosynthesis. Further, the abundance of cobamide-producing Corynebacterium species is associated with skin microbiome diversity and structure, and within this genus, de novo biosynthesis is enriched in host-associated species compared to environment-associated species. These findings identify cobamides as a potential mediator of skin microbiome dynamics and skin health.
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16
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Sanchez-Garcia S, Wang H, Wagner-Döbler I. The microbiome of the dinoflagellate Prorocentrum cordatum in laboratory culture and its changes at higher temperatures. Front Microbiol 2022; 13:952238. [PMID: 36246277 PMCID: PMC9555710 DOI: 10.3389/fmicb.2022.952238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
In the ocean, phytoplankton are dependent on communities of bacteria living in the phycosphere, a hot spot of metabolic and genetic exchange. Many types of interactions between phytoplankton and phycosphere bacteria have been shown, but it is unclear if the microbial communities associated with microalgae strains in culture collections are beneficial or harmful to the host strain. Here, we studied the microbial communities associated with four strains of the dinoflagellate Prorocentrum cordatum that had been isolated from distant geographical locations and maintained in culture collection for hundreds of generations. Community composition was determined by 16S rRNA gene amplicon sequencing. The dinoflagellate host strain was the strongest parameter separating communities, while growth phase, lifestyle (particle-attached versus free-living) and temperature had only a modulating effect. Although the strains had been isolated from distant locations in the Atlantic and Pacific Ocean, 14 ASVs were shared among all strains, the most abundant ones being Gilvibacter, Marivita, uncultivated Rhodobacteraceae, Marinobacter, Hyphomonadaceae, Cupriavidus, Variovorax, and Paucibacter. Adaptation to higher temperatures resulted in specific changes in each phycosphere microbiome, including increased abundance of rare community members. We then compared the growth of the four xenic cultures to that of the axenic P. cordatum CCMP1329. At 20°C, growth of the xenic cultures was similar or slower than that of CCMP1329. At 26°C, all four xenic cultures experienced a death phase, while the axenic culture stably remained in the stationary phase. At 30°C, only two of the xenic cultures were able to grow. A shift of dinoflagellate metabolism from autotrophy to mixotrophy and competition between dinoflagellate and bacteria for limiting nutrients, including essential vitamins, may contribute to these differences in growth patterns.
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Affiliation(s)
| | | | - Irene Wagner-Döbler
- Institute of Microbiology, Technical University of Braunschweig, Braunschweig, Germany
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17
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Lin S, Hu Z, Song X, Gobler CJ, Tang YZ. Vitamin B 12-auxotrophy in dinoflagellates caused by incomplete or absent cobalamin-independent methionine synthase genes ( metE). FUNDAMENTAL RESEARCH 2022; 2:727-737. [PMID: 38933134 PMCID: PMC11197592 DOI: 10.1016/j.fmre.2021.12.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 12/17/2021] [Accepted: 12/28/2021] [Indexed: 10/19/2022] Open
Abstract
Dinoflagellates are responsible for most marine harmful algal blooms (HABs) and play vital roles in many ocean processes. More than 90% of dinoflagellates are vitamin B12 auxotrophs and that B12 availability can control dinoflagellate HABs, yet the genetic basis of B12 auxotrophy in dinoflagellates in the framework of the ecology of dinoflagellates and particularly HABs, which was the objective of this work. Here, we investigated the presence, phylogeny, and transcription of two methionine synthase genes (B12-dependent metH and B12-independent metE) via searching and assembling transcripts and genes from transcriptomic and genomic databases, cloning 38 cDNA isoforms of the two genes from 14 strains of dinoflagellates, measuring the expression at different scenarios of B12, and comprehensive phylogenetic analyses of more than 100 organisms. We found that 1) metH was present in all 58 dinoflagellates accessible and metE was present in 40 of 58 species, 2) all metE genes lacked N-terminal domains, 3) metE of dinoflagellates were phylogenetically distinct from other known metE genes, and 4) expression of metH in dinoflagellates was responsive to exogenous B12 levels while expression of metE was not responding as that of genuine metE genes. We conclude that most, hypothetically all, dinoflagellates have either non-functional metE genes lacking N-terminal domain for most species, or do not possess metE for other species, which provides the genetic basis for the widespread nature of B12 auxotrophy in dinoflagellates. The work elucidated a fundamental aspect of the nutritional ecology of dinoflagellates.
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Affiliation(s)
- Siheng Lin
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Current address: Department of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou 363000, China
| | - Zhangxi Hu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for 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
| | - Xiaoying Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Ying Zhong Tang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for 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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18
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Bunbury F, Deery E, Sayer AP, Bhardwaj V, Harrison EL, Warren MJ, Smith AG. Exploring the onset of B 12 -based mutualisms using a recently evolved Chlamydomonas auxotroph and B 12 -producing bacteria. Environ Microbiol 2022; 24:3134-3147. [PMID: 35593514 PMCID: PMC9545926 DOI: 10.1111/1462-2920.16035] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/28/2022] [Accepted: 04/29/2022] [Indexed: 12/01/2022]
Abstract
Cobalamin (vitamin B12 ) is a cofactor for essential metabolic reactions in multiple eukaryotic taxa, including major primary producers such as algae, and yet only prokaryotes can produce it. Many bacteria can colonize the algal phycosphere, forming stable communities that gain preferential access to photosynthate and in return provide compounds such as B12 . Extended coexistence can then drive gene loss, leading to greater algal-bacterial interdependence. In this study, we investigate how a recently evolved B12 -dependent strain of Chlamydomonas reinhardtii, metE7, forms a mutualism with certain bacteria, including the rhizobium Mesorhizobium loti and even a strain of the gut bacterium E. coli engineered to produce cobalamin. Although metE7 was supported by B12 producers, its growth in co-culture was slower than the B12 -independent wild-type, suggesting that high bacterial B12 provision may be necessary to favour B12 auxotrophs and their evolution. Moreover, we found that an E. coli strain that releases more B12 makes a better mutualistic partner, and although this trait may be more costly in isolation, greater B12 release provided an advantage in co-cultures. We hypothesize that, given the right conditions, bacteria that release more B12 may be selected for, particularly if they form close interactions with B12 -dependent algae.
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Affiliation(s)
- Freddy Bunbury
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Evelyne Deery
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NH, UK
| | - Andrew P Sayer
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Vaibhav Bhardwaj
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Ellen L Harrison
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NH, UK.,Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Alison G Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
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19
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Srinivas S, Berger M, Brinkhoff T, Niggemann J. Impact of Quorum Sensing and Tropodithietic Acid Production on the Exometabolome of Phaeobacter inhibens. Front Microbiol 2022; 13:917969. [PMID: 35801100 PMCID: PMC9253639 DOI: 10.3389/fmicb.2022.917969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/03/2022] [Indexed: 11/29/2022] Open
Abstract
Microbial interactions shape ecosystem diversity and chemistry through production and exchange of organic compounds, but the impact of regulatory mechanisms on production and release of these exometabolites is largely unknown. We studied the extent and nature of impact of two signaling molecules, tropodithietic acid (TDA) and the quorum sensing molecule acyl homoserine lactone (AHL) on the exometabolome of the model bacterium Phaeobacter inhibens DSM 17395, a member of the ubiquitous marine Roseobacter group. Exometabolomes of the wild type, a TDA and a QS (AHL-regulator) negative mutant were analyzed via Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Based on a total of 996 reproducibly detected molecular masses, exometabolomes of the TDA and QS negative mutant were ∼70% dissimilar to each other, and ∼90 and ∼60% dissimilar, respectively, to that of the wild type. Moreover, at any sampled growth phase, 40–60% of masses detected in any individual exometabolome were unique to that strain, while only 10–12% constituted a shared “core exometabolome.” Putative annotation revealed exometabolites of ecological relevance such as vitamins, amino acids, auxins, siderophore components and signaling compounds with different occurrence patterns in the exometabolomes of the three strains. Thus, this study demonstrates that signaling molecules, such as AHL and TDA, extensively impact the composition of bacterial exometabolomes with potential consequences for species interactions in microbial communities.
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Affiliation(s)
- Sujatha Srinivas
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Martine Berger
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Jutta Niggemann
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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20
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Availability of vitamin B 12 and its lower ligand intermediate α-ribazole impact prokaryotic and protist communities in oceanic systems. THE ISME JOURNAL 2022; 16:2002-2014. [PMID: 35585186 PMCID: PMC9296465 DOI: 10.1038/s41396-022-01250-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 04/28/2022] [Accepted: 05/06/2022] [Indexed: 01/22/2023]
Abstract
Genome analyses predict that the cofactor cobalamin (vitamin B12, called B12 herein) is produced by only one-third of all prokaryotes but almost all encode at least one B12-dependent enzyme, in most cases methionine synthase. This implies that the majority of prokaryotes relies on exogenous B12 supply and interacts with producers. B12 consists of a corrin ring centred around a cobalt ion and the lower ligand 5’6-dimethylbenzimidazole (DMB). It has never been tested whether availability of this pivotal cofactor, DMB or its intermediate α-ribazole affect growth and composition of prokaryotic microbial communities. Here we show that in the subtropical, equatorial and polar frontal Pacific Ocean supply of B12 and α-ribazole enhances heterotrophic prokaryotic production and alters the composition of prokaryotic and heterotrophic protist communities. In the polar frontal Pacific, the SAR11 clade and Oceanospirillales increased their relative abundances upon B12 supply. In the subtropical Pacific, Oceanospirillales increased their relative abundance upon B12 supply as well but also downregulated the transcription of the btuB gene, encoding the outer membrane permease for B12. Surprisingly, Prochlorococcus, known to produce pseudo-B12 and not B12, exhibited significant upregulation of genes encoding key proteins of photosystem I + II, carbon fixation and nitrate reduction upon B12 supply in the subtropical Pacific. These findings show that availability of B12 and α-ribazole affect growth and composition of prokaryotic and protist communities in oceanic systems thus revealing far-reaching consequences of methionine biosynthesis and other B12-dependent enzymatic reactions on a community level.
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21
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Hosseini H, Al-Jabri HM, Moheimani NR, Siddiqui SA, Saadaoui I. Marine microbial bioprospecting: Exploitation of marine biodiversity towards biotechnological applications-a review. J Basic Microbiol 2022; 62:1030-1043. [PMID: 35467037 DOI: 10.1002/jobm.202100504] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 03/14/2022] [Accepted: 04/07/2022] [Indexed: 11/09/2022]
Abstract
The increase in the human population causes an increase in the demand for nutritional supplies and energy resources. Thus, the novel, natural, and renewable resources became of great interest. Here comes the optimistic role of bioprospecting as a promising tool to isolate novel and interesting molecules and microorganisms from the marine environment as alternatives to the existing resources. Bioprospecting of marine metabolites and microorganisms with high biotechnological potentials has gained wide interest due to the variability and richness of the marine environment. Indeed, the existence of extreme conditions that increases the adaptability of marine organisms, especially planktons, allow the presence of interesting biological species that are able to produce novel compounds with multiple health benefits and high economical value. This review aims to provide a comprehensive overview of marine microbial bioprospecting as a growing field of interest. It emphasizes functional bioprospecting that facilitates the discovery of interesting metabolites. Marine bioprospecting was also discussed from a legal aspect for the first time, focusing on the shortcomings of international law. We also summarized the challenges facing bioprospecting in the marine environment including economic feasibility issues.
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Affiliation(s)
- Hoda Hosseini
- Algal Technologies Program, Centre for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Hareb M Al-Jabri
- Algal Technologies Program, Centre for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar.,Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Navid R Moheimani
- Algae R&D Centre, Harry Buttler Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Simil A Siddiqui
- Algal Technologies Program, Centre for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Imen Saadaoui
- Algal Technologies Program, Centre for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar.,Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
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22
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Wang Y, Coyne KJ. Metabolomic Insights of the Effects of Bacterial Algicide IRI-160AA on Dinoflagellate Karlodinium veneficum. Metabolites 2022; 12:metabo12040317. [PMID: 35448504 PMCID: PMC9030264 DOI: 10.3390/metabo12040317] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 03/29/2022] [Indexed: 11/16/2022] Open
Abstract
Shewanella sp. IRI-160 is an algicidal bacterium that secretes an algicide, IRI-160AA. This algicide specifically targets dinoflagellates, while having no adverse effects on other algal species tested. Dinoflagellates exposed to IRI-160AA exhibited increased production of reactive oxygen species (ROS), DNA damage, and cell cycle arrest, implying a programmed pathway leading to cell death (PCD). Here, a metabolomic analysis was conducted on dinoflagellate Karlodinium veneficum and a control cryptophyte species Rhodomonas exposed to IRI-160AA to investigate the cellular mechanisms behind the physiological effects and the specificity of this algicide. Results of this research supported previous observations about physiological responses to the algicide. A suite of metabolites was identified that increased in the cell pellets of K. veneficum but not in Rhodomonas, including oxidative stress biomarkers, antioxidants, and compounds involved in DNA damage and PCD. Overall, the results of this study illustrated the metabolomic mechanisms underlying the algicidal effects of IRI-160AA on dinoflagellates. This research also provided insights and future directions for studies on the cellular response of dinoflagellates exposed to antagonistic bacteria in the environment.
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23
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Hamouda RA, Abd El Latif A, Elkaw EM, Alotaibi AS, Alenzi AM, Hamza HA. Assessment of Antioxidant and Anticancer Activities of Microgreen Alga Chlorella vulgaris and Its Blend with Different Vitamins. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27051602. [PMID: 35268702 PMCID: PMC8911722 DOI: 10.3390/molecules27051602] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/19/2022] [Accepted: 02/23/2022] [Indexed: 01/09/2023]
Abstract
There is a very vital antioxidant extracted from microgreen alga. Chlorella vulgaris has major advantages and requires high yield worldwide. Some microalgae require vitamins for their growth promotion. This study was held to determine the impact of different vitamins including Thiamine (B1), Riboflavin (B2), Pyridoxine (B6), and Ascorbic acid (c) at concentrations of 0.02, 0.04, 0.06, and 0.08 mg/L of each. Each vitamin was added to the BG11 growth medium to determine the effect on growth, total carbohydrate, total protein, pigments content, antioxidant activities of Chlorella vulgaris. Moreover, antitumor effects of methanol extract of C. vulgaris without and with the supplement of thiamine against Human prostate cancer (PC-3), Hepatocellular carcinoma (HEPG-2), Colorectal carcinoma (HCT-116) and Epitheliod Carcinoma (Hela) was estimated in vitro. C. vulgaris supplemented with various vitamins showed a significant increase in biomass, pigment content, total protein, and total carbohydrates in comparison to the control. Thiamine was the best vitamin influencing as an antioxidant. C. vulgaris supplemented with thiamine had high antitumor effects in vitro. So, it’s necessary to add vitamins to BG11 media for enhancement of the growth and metabolites.
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Affiliation(s)
- Ragaa A. Hamouda
- Department of Biology, College of Sciences and Arts, Khulis, University of Jeddah, Jeddah 21959, Saudi Arabia
- Department of Microbial Biotechnology, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat 32897, Egypt; (E.M.E.); (H.A.H.)
- Correspondence: or
| | - Amera Abd El Latif
- Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh 33516, Egypt;
| | - Ebtihal M. Elkaw
- Department of Microbial Biotechnology, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat 32897, Egypt; (E.M.E.); (H.A.H.)
| | - Amenah S. Alotaibi
- Biology Department, College of Sciences, Tabuk University, Tabuk 71491, Saudi Arabia; (A.S.A.); (A.M.A.)
| | - Asma Massad Alenzi
- Biology Department, College of Sciences, Tabuk University, Tabuk 71491, Saudi Arabia; (A.S.A.); (A.M.A.)
| | - Hanafy A. Hamza
- Department of Microbial Biotechnology, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat 32897, Egypt; (E.M.E.); (H.A.H.)
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24
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Zhang Y, Zheng L, Wang S, Zhao Y, Xu X, Han B, Hu T. Quorum Sensing Bacteria in the Phycosphere of HAB Microalgae and Their Ecological Functions Related to Cross-Kingdom Interactions. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 19:ijerph19010163. [PMID: 35010421 PMCID: PMC8750903 DOI: 10.3390/ijerph19010163] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/06/2021] [Accepted: 12/11/2021] [Indexed: 12/28/2022]
Abstract
It has been proven that the relationship between microalgae and bacteria affects the dynamic process of harmful algal blooms (HABs). Microalgae-associated microorganisms widely exist in the phycosphere and play an essential role in algae-bacteria cross-kingdom interactions. Among these processes, quorum sensing (QS), as a communication system of bacteria, is thought to participate in algae-bacteria interactions. However, the species of QS bacteria in the phycosphere and their ecological function are still unknown. In this study, microalgae-associated microorganisms with a QS system were screened by the biosensor method and identified based on 16S rRNA gene analysis. The types and number of acyl-L-homoserine lactone (AHL) signalling molecules produced by QS bacteria were analysed by thin layer chromatography (TLC) bioautography and gas chromatography-mass spectrometer (GC-MS). The film formation, β-dimethylmercaptopropionic (DMSP) degradation and algae growth effects of QS bacteria were investigated. The results showed that 113 QS bacteria were isolated from 842 microalgae-associated bacteria. Detection of AHL molecules in 10 different species of QS bacteria showed that most of them were N-(3-Oxodecanoyl)-L-homoserine lactone (OC10-HSL), N-Octanoyl-L-homoserine lactone (C8-HSL) and N-(3-Oxooctanoyl)-L-homoserine lactone (OC8-HSL). All 10 QS bacteria had film-forming ability, and they could degrade DMSP (except strain E26). The crude metabolic extracts of the 10 QS bacteria can inhibit or promote microalgae growth to different degrees. Our study is helpful to understand the role of microalgae-associated microorganisms with the QS system in algae-bacteria interactions and community succession of HAB microalgae.
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Affiliation(s)
- Yanchao Zhang
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; (Y.Z.); (Y.Z.)
| | - Li Zheng
- Key Laboratory of Marine Ecological Environment Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China; (S.W.); (X.X.); (T.H.)
- Qingdao National Laboratory of Marine Science and Technology Pilot, Functional Laboratory of Marine Ecology and Environmental Science, Qingdao 266071, China;
- Correspondence:
| | - Shuai Wang
- Key Laboratory of Marine Ecological Environment Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China; (S.W.); (X.X.); (T.H.)
| | - Yangguo Zhao
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; (Y.Z.); (Y.Z.)
| | - Xiyuan Xu
- Key Laboratory of Marine Ecological Environment Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China; (S.W.); (X.X.); (T.H.)
| | - Bin Han
- Qingdao National Laboratory of Marine Science and Technology Pilot, Functional Laboratory of Marine Ecology and Environmental Science, Qingdao 266071, China;
| | - Tianyi Hu
- Key Laboratory of Marine Ecological Environment Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China; (S.W.); (X.X.); (T.H.)
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Microbial Plankton Community Structure and Function Responses to Vitamin B 12 and B 1 Amendments in an Upwelling System. Appl Environ Microbiol 2021; 87:e0152521. [PMID: 34495690 PMCID: PMC8552899 DOI: 10.1128/aem.01525-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
B vitamins are essential cofactors for practically all living organisms on Earth and are produced by a selection of microorganisms. An imbalance between high demand and limited production, in concert with abiotic processes, may explain the low availability of these vitamins in marine systems. Natural microbial communities from surface shelf water in the productive area off northwestern Spain were enclosed in mesocosms in winter, spring, and summer 2016. In order to explore the impact of B-vitamin availability on microbial community composition (16S and 18S rRNA gene sequence analysis) and bacterial function (metatranscriptomics analysis) in different seasons, enrichment experiments were conducted with seawater from the mesocosms. Our findings revealed that significant increases in phytoplankton or prokaryote biomass associated with vitamin B12 and/or B1 amendments were not accompanied by significant changes in community composition, suggesting that most of the microbial taxa benefited from the external B-vitamin supply. Metatranscriptome analysis suggested that many bacteria were potential consumers of vitamins B12 and B1, although the relative abundance of reads related to synthesis was ca. 3.6-fold higher than that related to uptake. Alteromonadales and Oceanospirillales accounted for important portions of vitamin B1 and B12 synthesis gene transcription, despite accounting for only minor portions of the bacterial community. Flavobacteriales appeared to be involved mostly in vitamin B12 and B1 uptake, and Pelagibacterales expressed genes involved in vitamin B1 uptake. Interestingly, the relative expression of vitamin B12 and B1 synthesis genes among bacteria strongly increased upon inorganic nutrient amendment. Collectively, these findings suggest that upwelling events intermittently occurring during spring and summer in productive ecosystems may ensure an adequate production of these cofactors to sustain high levels of phytoplankton growth and biomass. IMPORTANCE B vitamins are essential growth factors for practically all living organisms on Earth that are produced by a selection of microorganisms. An imbalance between high demand and limited production may explain the low concentration of these compounds in marine systems. In order to explore the impact of B-vitamin availability on bacteria and algae in the coastal waters off northwestern Spain, six experiments were conducted with natural surface water enclosed in winter, spring, and summer. Our findings revealed that increases in phytoplankton or bacterial growth associated with B12 and/or B1 amendments were not accompanied by significant changes in community composition, suggesting that most microorganisms benefited from the B-vitamin supply. Our analyses confirmed the role of many bacteria as consumers of vitamins B12 and B1, although the relative abundance of genes related to synthesis was ca. 3.6-fold higher than that related to uptake. Interestingly, prokaryote expression of B12 and B1 synthesis genes strongly increased when inorganic nutrients were added. Collectively, these findings suggest that upwelling of cold and nutrient-rich waters occurring during spring and summer in this coastal area may ensure an adequate production of B vitamins to sustain high levels of algae growth and biomass.
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Long-Term Survival of Synechococcus and Heterotrophic Bacteria without External Nutrient Supply after Changes in Their Relationship from Antagonism to Mutualism. mBio 2021; 12:e0161421. [PMID: 34465027 PMCID: PMC8406228 DOI: 10.1128/mbio.01614-21] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marine phytoplankton and heterotrophic bacteria share a very close but usually changeable relationship. However, the ultimate fate of their unstable relationship on a long-term scale is unclear. Here, the relationship between Synechococcus and heterotrophic bacterial communities underwent a dramatic shift from antagonism to commensalism and eventually to mutualism during long-term cocultivation. The relationship change is attributed to the different (even opposite) effects of diverse bacterial members on Synechococcus and the ratio of beneficial to harmful bacteria. Different bacterial members also interact with each other (e.g., quorum-sensing communication, hostility, or mutual promotion) and drive a dynamic succession in the entire community structure that corresponds exactly to the shift in its relationship with Synechococcus. In the final mutualism stage, a self-sufficient nitrogen cycle, including nitrogen fixation, denitrification, and organic nitrogen degradation, contributed to the healthy survival of Synechococcus for 2 years without an exogenous nutrient supply. This natural selective trait of Synechococcus and heterotrophic bacteria toward mutualism under long-term coexistence provides a novel clue for understanding the ubiquity and competitive advantage of Synechococcus in global oceans.
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Thompson HF, Gutierrez T. Detection of hydrocarbon-degrading bacteria on deepwater corals of the northeast Atlantic using CARD-FISH. J Microbiol Methods 2021; 187:106277. [PMID: 34237402 DOI: 10.1016/j.mimet.2021.106277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/30/2021] [Accepted: 06/30/2021] [Indexed: 11/28/2022]
Abstract
Recently, studies have begun to identify oil-degrading bacteria and host-taxon specific bacterial assemblages associated with the coral holobiont, including deep-sea cold-water corals, which are thought to provide metabolic functions and additional carbon sources to their coral hosts. Here, we describe the identification of Marinobacter on the soft tissue of Lophelia pertusa coral polyps by Catalyzed Reporter Deposition Fluorescence in situ Hybridization (CARD-FISH). L. pertusa samples from three reef sites in the northeast Atlantic (Logachev, Mingulay and Pisces) were collected at depth by vacuum seal to eliminate contamination issues. After decalcification, histological processing and sagittal sectioning of the soft coral polyp tissues, the 16S rRNA-targeted oligonucleotide HRP-labelled probe Mrb-0625-a, and Cyanine 3 (Cy3)-labelled tyramides, were used to identify members of the hydrocarbon-degrading genus Marinobacter. Mrb-0625-a-hybridized bacterial cell signals were detected in different anatomical sites of all polyps collected from each of the three reef sites, suggesting a close, possibly intimate, association between them, but the purpose of which remains unknown. We posit that Marinobacter, and possibly other hydrocarbon-degrading bacteria associated with Lophelia, may confer the coral with the ability to cope with toxic levels of hydrocarbons in regions of natural oil seepage and where there is an active oil and gas industry presence.
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Affiliation(s)
- Haydn Frank Thompson
- Institute of Mechanical, Process and Energy Engineering, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
| | - Tony Gutierrez
- Institute of Mechanical, Process and Energy Engineering, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom.
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Lin Q, Shang L, Wang X, Hu Z, Du H, Wang H. Different dimethylsulphoniopropionate-producing ability of dinoflagellates could affect the structure of their associated bacterial community. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Kundra P, Rachmühl C, Lacroix C, Geirnaert A. Role of Dietary Micronutrients on Gut Microbial Dysbiosis and Modulation in Inflammatory Bowel Disease. Mol Nutr Food Res 2021. [DOI: 10.1002/mnfr.201901271] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Palni Kundra
- Laboratory of Food Biotechnology Institute of Food Nutrition and Health Schmelzbergstrasse 7 Zürich 8092 Switzerland
| | - Carole Rachmühl
- Laboratory of Food Biotechnology Institute of Food Nutrition and Health Schmelzbergstrasse 7 Zürich 8092 Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology Institute of Food Nutrition and Health Schmelzbergstrasse 7 Zürich 8092 Switzerland
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology Institute of Food Nutrition and Health Schmelzbergstrasse 7 Zürich 8092 Switzerland
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Loss of Motility as a Non-Lethal Mechanism for Intercolony Inhibition ("Sibling Rivalry") in Marinobacter. Microorganisms 2021; 9:microorganisms9010103. [PMID: 33466273 PMCID: PMC7824750 DOI: 10.3390/microorganisms9010103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/23/2020] [Accepted: 12/30/2020] [Indexed: 11/17/2022] Open
Abstract
Bacteria from the genus Marinobacter are ubiquitous throughout the worlds' oceans as "opportunitrophs" capable of surviving a wide range of conditions, including colonization of surfaces of marine snow and algae. To prevent too many bacteria from occupying this ecological niche simultaneously, some sort of population dependent control must be operative. Here, we show that while Marinobacter do not produce or utilize an acylhomoserine lactone (AHL)-based quorum sensing system, "sibling" colonies of many species of Marinobacter exhibit a form of non-lethal chemical communication that prevents colonies from overrunning each other's niche space. Evidence suggests that this inhibition is the result of a loss in motility for cells at the colony interfaces. Although not the signal itself, we have identified a protein, glycerophosphoryl diester phosphodiesterase, that is enriched in the inhibition zone between the spreading colonies that may be part of the overall response.
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Hu X, Wei X, Ling J, Chen J. Cobalt: An Essential Micronutrient for Plant Growth? FRONTIERS IN PLANT SCIENCE 2021; 12:768523. [PMID: 34868165 PMCID: PMC8635114 DOI: 10.3389/fpls.2021.768523] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 09/29/2021] [Indexed: 05/19/2023]
Abstract
Cobalt is a transition metal located in the fourth row of the periodic table and is a neighbor of iron and nickel. It has been considered an essential element for prokaryotes, human beings, and other mammals, but its essentiality for plants remains obscure. In this article, we proposed that cobalt (Co) is a potentially essential micronutrient of plants. Co is essential for the growth of many lower plants, such as marine algal species including diatoms, chrysophytes, and dinoflagellates, as well as for higher plants in the family Fabaceae or Leguminosae. The essentiality to leguminous plants is attributed to its role in nitrogen (N) fixation by symbiotic microbes, primarily rhizobia. Co is an integral component of cobalamin or vitamin B12, which is required by several enzymes involved in N2 fixation. In addition to symbiosis, a group of N2 fixing bacteria known as diazotrophs is able to situate in plant tissue as endophytes or closely associated with roots of plants including economically important crops, such as barley, corn, rice, sugarcane, and wheat. Their action in N2 fixation provides crops with the macronutrient of N. Co is a component of several enzymes and proteins, participating in plant metabolism. Plants may exhibit Co deficiency if there is a severe limitation in Co supply. Conversely, Co is toxic to plants at higher concentrations. High levels of Co result in pale-colored leaves, discolored veins, and the loss of leaves and can also cause iron deficiency in plants. It is anticipated that with the advance of omics, Co as a constitute of enzymes and proteins and its specific role in plant metabolism will be exclusively revealed. The confirmation of Co as an essential micronutrient will enrich our understanding of plant mineral nutrition and improve our practice in crop production.
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Affiliation(s)
- Xiu Hu
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Xiangying Wei
- Institute of Oceanography, Minjiang University, Fuzhou, China
- Xiangying Wei
| | - Jie Ling
- He Xiangning College of Art and Design, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Jianjun Chen
- Department of Environmental Horticulture and Mid-Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Apopka, FL, United States
- *Correspondence: Jianjun Chen
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Subong BJJ, Lluisma AO, Azanza RV, Salvador-Reyes LA. Differentiating Two Closely Related Alexandrium Species Using Comparative Quantitative Proteomics. Toxins (Basel) 2020; 13:toxins13010007. [PMID: 33374829 PMCID: PMC7823455 DOI: 10.3390/toxins13010007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 01/21/2023] Open
Abstract
Alexandrium minutum and Alexandrium tamutum are two closely related harmful algal bloom (HAB)-causing species with different toxicity. Using isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomics and two-dimensional differential gel electrophoresis (2D-DIGE), a comprehensive characterization of the proteomes of A. minutum and A. tamutum was performed to identify the cellular and molecular underpinnings for the dissimilarity between these two species. A total of 1436 proteins and 420 protein spots were identified using iTRAQ-based proteomics and 2D-DIGE, respectively. Both methods revealed little difference (10-12%) between the proteomes of A. minutum and A. tamutum, highlighting that these organisms follow similar cellular and biological processes at the exponential stage. Toxin biosynthetic enzymes were present in both organisms. However, the gonyautoxin-producing A. minutum showed higher levels of osmotic growth proteins, Zn-dependent alcohol dehydrogenase and type-I polyketide synthase compared to the non-toxic A. tamutum. Further, A. tamutum had increased S-adenosylmethionine transferase that may potentially have a negative feedback mechanism to toxin biosynthesis. The complementary proteomics approach provided insights into the biochemistry of these two closely related HAB-causing organisms. The identified proteins are potential biomarkers for organismal toxicity and could be explored for environmental monitoring.
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Affiliation(s)
- Bryan John J Subong
- Marine Science Institute, University of the Philippines- Diliman, Velasquez Street, Quezon City 1101, Philippines
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo City, Tokyo 113-8654, Japan
| | - Arturo O Lluisma
- Marine Science Institute, University of the Philippines- Diliman, Velasquez Street, Quezon City 1101, Philippines
| | - Rhodora V Azanza
- Marine Science Institute, University of the Philippines- Diliman, Velasquez Street, Quezon City 1101, Philippines
| | - Lilibeth A Salvador-Reyes
- Marine Science Institute, University of the Philippines- Diliman, Velasquez Street, Quezon City 1101, Philippines
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Liu B, Eltanahy EE, Liu H, Chua ET, Thomas-Hall SR, Wass TJ, Pan K, Schenk PM. Growth-promoting bacteria double eicosapentaenoic acid yield in microalgae. BIORESOURCE TECHNOLOGY 2020; 316:123916. [PMID: 32768998 DOI: 10.1016/j.biortech.2020.123916] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 05/26/2023]
Abstract
High-yielding microalgae present an important commodity to sustainably satisfy burgeoning food, feed and biofuel demands. Because algae-associated bacteria can significantly enhance or reduce yields, we isolated, identified and selected highly-effective "probiotic" bacterial strains associated with Nannochloropsis oceanica, a high-yielding microalga rich in eicosapentaenoic acid (EPA). Xenic algae growth was significantly enhanced by co-cultivation with ten isolated bacteria that improved culture density and biomass by 2.2- and 1.56-fold, respectively (1.39 × 108 cells mL-1; 0.82 g L-1). EPA contents increased up to 2.25-fold (to 39.68% of total fatty acids). Added probiotic bacteria possessed multiple growth-stimulating characteristics, including atmospheric nitrogen fixation, growth hormone production and phosphorous solubilization. Core N. oceanica-dominant bacterial microbiomes at different cultivation scales included Sphingobacteria, Flavobacteria (Bacteroidetes), and α, γ-Proteobacteria, and added probiotic bacteria could be maintained. We conclude that the supplementation with probiotic algae-associated bacteria can significantly enhance biomass and EPA production of N. oceanica.
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Affiliation(s)
- Bingli Liu
- Laboratory of Applied Microalgae Biology, Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Algae Biotechnology Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Eladl E Eltanahy
- Algae Biotechnology Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia; Phycology Laboratory, Botany Department, Faculty of Science, Mansoura University, Mansoura 35516, Egypt
| | - Hongwei Liu
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales 2751, Australia
| | - Elvis T Chua
- Algae Biotechnology Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Skye R Thomas-Hall
- Algae Biotechnology Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Taylor J Wass
- Algae Biotechnology Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Kehou Pan
- Laboratory of Applied Microalgae Biology, Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Peer M Schenk
- Algae Biotechnology Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia.
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Zhou J, Zhang BY, Yu K, Du XP, Zhu JM, Zeng YH, Cai ZH. Functional profiles of phycospheric microorganisms during a marine dinoflagellate bloom. WATER RESEARCH 2020; 173:115554. [PMID: 32028248 DOI: 10.1016/j.watres.2020.115554] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/14/2019] [Accepted: 01/25/2020] [Indexed: 06/10/2023]
Abstract
Harmful algal blooms (HABs) are an ecological concern but relatively few studies have investigated the functional potential of bacterioplankton over a complete algal bloom cycle, which is critical for determining their contribution to the fate of algal blooms. To address this point, we carried out a time-series metagenomic analysis of the functional features of microbial communities at three different Gymnodinium catenatum bloom stages (pre-, peak-, and post-bloom). Different microbial composition were observed during the blooming stages. The environmental parameters and correlation networks co-contribute to microbial variability, and the former explained 38.4% of total variations of the bacterioplankton community composition. Functionally, a range of pathways involved in carbon, nitrogen, phosphorus and sulfur cycling were significantly different during the various HAB stages. Genes associated with carbohydrate-active enzymes, denitrification, and iron oxidation were enriched at the pre-bloom stage; genes involved in reductive citrate cycle for carbon fixation, carbon degradation, nitrification and phosphate transport were enhanced at the peak stage; and relative gene abundance related to sulfur oxidation, vitamin synthesis, and iron transport and storage was increased at the post-bloom stage. The ecological linkage analysis has shown that microbial functional potential especially the C/P/Fe metabolism were significantly linked to the fate of the algal blooms. Taken together, our results demonstrated that microorganisms displayed successional patterns not only at the community level, but also in the metabolic potential on HAB's progression. This work contributes to a growing understanding of microbial structural elasticity and functional plasticity and shed light on the potential mechanisms of microbial-mediated HAB trajectory.
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Affiliation(s)
- Jin Zhou
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, The Shenzhen International Graduate School, Tsinghua University, Shenzhen, China; The Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Bo-Ya Zhang
- The School of Environment and Energy, Graduate School at Shenzhen, Peking University, Guangdong Province, Shenzhen, China
| | - Ke Yu
- The School of Environment and Energy, Graduate School at Shenzhen, Peking University, Guangdong Province, Shenzhen, China
| | - Xiao-Peng Du
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, The Shenzhen International Graduate School, Tsinghua University, Shenzhen, China; The Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Jian-Ming Zhu
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, The Shenzhen International Graduate School, Tsinghua University, Shenzhen, China; The Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Yan-Hua Zeng
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, The Shenzhen International Graduate School, Tsinghua University, Shenzhen, China; The Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Zhong-Hua Cai
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, The Shenzhen International Graduate School, Tsinghua University, Shenzhen, China; The Shenzhen International Graduate School, Tsinghua University, Shenzhen, China.
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Wu PF, Li DX, Kong LF, Li YY, Zhang H, Xie ZX, Lin L, Wang DZ. The diversity and biogeography of microeukaryotes in the euphotic zone of the northwestern Pacific Ocean. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 698:134289. [PMID: 31514034 DOI: 10.1016/j.scitotenv.2019.134289] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/12/2019] [Accepted: 09/03/2019] [Indexed: 06/10/2023]
Abstract
Microeukaryotes are the key ecosystem drivers mediating marine productivity, the food web and biogeochemical cycles. The northwestern Pacific Ocean (NWPO), as one of the world's largest oligotrophic regions, remains largely unexplored regarding diversity and biogeography of microeukaryotes. Here, we investigated the community composition and geographical distribution of microeukaryotes collected from the euphotic zone of three different regions in the NWPO using high-throughput sequencing of the 18S rRNA gene and quantified the contributions of environmental factors on the distributions of microeukaryotes. The relative abundance of different group taxa, except for Ciliophora, presented distinct patterns in each region, and Metazoa and Dinoflagellata dominated the community, contributing approximately half of reads abundance. Spatial and environmental factors explained 66.01% of community variation in the NWPO. Temperature was the most important environmental factor significantly correlated with community structure. Bacterial biomass was also significantly correlated with microeukaryotic distribution, especially for Dinoflagellata and Diatomea. Network analysis showed strong correlations between microeukaryotic groups and free-living bacteria and different bacterial taxa were correlated with specific microeukaryotic groups, indicating that their interactions enabled microeukaryotic groups to adapt to diverse environments. This study provides a first glance at the diversity and geographical distribution of microeukaryotes in the NWPO and sheds light on the biotic and abiotic factors in shaping the microeukaryotic community in the ocean.
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Affiliation(s)
- Peng-Fei Wu
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Dong-Xu Li
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Ling-Fen Kong
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Yuan-Yuan Li
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Hao Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Zhang-Xian Xie
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Lin Lin
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China; Key Laboratory of Marine Ecology & Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
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36
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Rambo IM, Dombrowski N, Constant L, Erdner D, Baker BJ. Metabolic relationships of uncultured bacteria associated with the microalgae Gambierdiscus. Environ Microbiol 2019; 22:1764-1783. [PMID: 31775181 DOI: 10.1111/1462-2920.14878] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 11/13/2019] [Accepted: 11/25/2019] [Indexed: 12/14/2022]
Abstract
Microbial communities inhabit algae cell surfaces and produce a variety of compounds that can impact the fitness of the host. These interactions have been studied via culturing, single-gene diversity and metagenomic read survey methods that are limited by culturing biases and fragmented genetic characterizations. Higher-resolution frameworks are needed to resolve the physiological interactions within these algal-bacterial communities. Here, we infer the encoded metabolic capabilities of four uncultured bacterial genomes (reconstructed using metagenomic assembly and binning) associated with the marine dinoflagellates Gambierdiscus carolinianus and G. caribaeus. Phylogenetic analyses revealed that two of the genomes belong to the commonly algae-associated families Rhodobacteraceae and Flavobacteriaceae. The other two genomes belong to the Phycisphaeraceae and include the first algae-associated representative within the uncultured SM1A02 group. Analyses of all four genomes suggest these bacteria are facultative aerobes, with some capable of metabolizing phytoplanktonic organosulfur compounds including dimethylsulfoniopropionate and sulfated polysaccharides. These communities may biosynthesize compounds beneficial to both the algal host and other bacteria, including iron chelators, B vitamins, methionine, lycopene, squalene and polyketides. These findings have implications for marine carbon and nutrient cycling and provide a greater depth of understanding regarding the genetic potential for complex physiological interactions between microalgae and their associated bacteria.
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Affiliation(s)
- Ian M Rambo
- Department of Marine Science, University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX, 78373, USA
| | - Nina Dombrowski
- Department of Marine Science, University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX, 78373, USA.,NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, Den Burg, The Netherlands
| | - Lauren Constant
- Department of Marine Science, University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX, 78373, USA
| | - Deana Erdner
- Department of Marine Science, University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX, 78373, USA
| | - Brett J Baker
- Department of Marine Science, University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX, 78373, USA
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Genomic blueprints of sponge-prokaryote symbiosis are shared by low abundant and cultivatable Alphaproteobacteria. Sci Rep 2019; 9:1999. [PMID: 30760820 PMCID: PMC6374434 DOI: 10.1038/s41598-019-38737-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 01/09/2019] [Indexed: 02/07/2023] Open
Abstract
Marine sponges are early-branching, filter-feeding metazoans that usually host complex microbiomes comprised of several, currently uncultivatable symbiotic lineages. Here, we use a low-carbon based strategy to cultivate low-abundance bacteria from Spongia officinalis. This approach favoured the growth of Alphaproteobacteria strains in the genera Anderseniella, Erythrobacter, Labrenzia, Loktanella, Ruegeria, Sphingorhabdus, Tateyamaria and Pseudovibrio, besides two likely new genera in the Rhodobacteraceae family. Mapping of complete genomes against the metagenomes of S. officinalis, seawater, and sediments confirmed the rare status of all the above-mentioned lineages in the marine realm. Remarkably, this community of low-abundance Alphaproteobacteria possesses several genomic attributes common to dominant, presently uncultivatable sponge symbionts, potentially contributing to host fitness through detoxification mechanisms (e.g. heavy metal and metabolic waste removal, degradation of aromatic compounds), provision of essential vitamins (e.g. B6 and B12 biosynthesis), nutritional exchange (especially regarding the processing of organic sulphur and nitrogen) and chemical defence (e.g. polyketide and terpenoid biosynthesis). None of the studied taxa displayed signs of genome reduction, indicative of obligate mutualism. Instead, versatile nutrient metabolisms along with motility, chemotaxis, and tight-adherence capacities - also known to confer environmental hardiness – were inferred, underlying dual host-associated and free-living life strategies adopted by these diverse sponge-associated Alphaproteobacteria.
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Cobaviruses - a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems. ISME JOURNAL 2019; 13:1404-1421. [PMID: 30718806 PMCID: PMC6775973 DOI: 10.1038/s41396-019-0362-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 01/15/2019] [Accepted: 01/22/2019] [Indexed: 11/13/2022]
Abstract
Bacteriophages are widely considered to influence bacterial communities, however most phages are still unknown or not studied well enough to understand their ecological roles. We have isolated two phages infecting Lentibacter sp. SH36, affiliated with the marine Roseobacter group, and retrieved similar phage genomes from publicly available metagenomics databases. Phylogenetic analysis placed the new phages within the Cobavirus group, in the here newly proposed genus Siovirus and subfamily Riovirinae of the Podoviridae. Gene composition and presence of direct terminal repeats in cultivated cobaviruses point toward a genome replication and packaging strategy similar to the T7 phage. Investigation of the genomes suggests that viral lysis of the cell proceeds via the canonical holin-endolysin pathway. Cobaviral hosts include members of the genera Lentibacter, Sulfitobacter and Celeribacter of the Roseobacter group within the family Rhodobacteraceae (Alphaproteobacteria). Screening more than 5,000 marine metagenomes, we found cobaviruses worldwide from temperate to tropical waters, in the euphotic zone, mainly in bays and estuaries, but also in the open ocean. The presence of cobaviruses in protist metagenomes as well as the phylogenetic neighborhood of cobaviruses in glutaredoxin and ribonucleotide reductase trees suggest that cobaviruses could infect bacteria associated with phototrophic or grazing protists. With this study, we expand the understanding of the phylogeny, classification, genomic organization, biogeography and ecology of this phage group infecting marine Rhodobacteraceae.
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Zheng Q, Lu J, Wang Y, Jiao N. Genomic reconstructions and potential metabolic strategies of generalist and specialist heterotrophic bacteria associated with an estuarySynechococcusculture. FEMS Microbiol Ecol 2019; 95:5303724. [DOI: 10.1093/femsec/fiz017] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 01/26/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Qiang Zheng
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, People's Republic of China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, People's Republic of China
| | - Jiayao Lu
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, People's Republic of China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, People's Republic of China
| | - Yu Wang
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, People's Republic of China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, People's Republic of China
| | - Nianzhi Jiao
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, People's Republic of China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, People's Republic of China
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Crenn K, Duffieux D, Jeanthon C. Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations. Front Microbiol 2018; 9:2879. [PMID: 30564203 PMCID: PMC6288172 DOI: 10.3389/fmicb.2018.02879] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 11/09/2018] [Indexed: 12/26/2022] Open
Abstract
Interactions between phytoplankton and bacteria play a central role in mediating biogeochemical cycling and food web structure in the ocean. The cosmopolitan diatoms Thalassiosira and Chaetoceros often dominate phytoplankton communities in marine systems. Past studies of diatom-bacterial associations have employed community-level methods and culture-based or natural diatom populations. Although bacterial assemblages attached to individual diatoms represents tight associations little is known on their makeup or interactions. Here, we examined the epibiotic bacteria of 436 Thalassiosira and 329 Chaetoceros single cells isolated from natural samples and collection cultures, regarded here as short- and long-term associations, respectively. Epibiotic microbiota of single diatom hosts was analyzed by cultivation and by cloning-sequencing of 16S rRNA genes obtained from whole-genome amplification products. The prevalence of epibiotic bacteria was higher in cultures and dependent of the host species. Culture approaches demonstrated that both diatoms carry distinct bacterial communities in short- and long-term associations. Bacterial epibonts, commonly associated with phytoplankton, were repeatedly isolated from cells of diatom collection cultures but were not recovered from environmental cells. Our results suggest that in controlled laboratory culture conditions bacterial–diatom and bacterial–bacterial interactions select for a simplified, but specific, epibiotic microbiota shaped and adapted for long-term associations.
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Affiliation(s)
- Klervi Crenn
- CNRS, Sorbonne Université, Station Biologique de Roscoff, Adaptation et Diversité en Milieu Marin, Roscoff, France
| | - Delphine Duffieux
- CNRS, Sorbonne Université, Station Biologique de Roscoff, Adaptation et Diversité en Milieu Marin, Roscoff, France
| | - Christian Jeanthon
- CNRS, Sorbonne Université, Station Biologique de Roscoff, Adaptation et Diversité en Milieu Marin, Roscoff, France
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Kojadinovic-Sirinelli M, Villain A, Puppo C, Fon Sing S, Prioretti L, Hubert P, Grégori G, Zhang Y, Sassi JF, Claverie JM, Blanc G, Gontero B. Exploring the microbiome of the "star" freshwater diatom Asterionella formosa in a laboratory context. Environ Microbiol 2018; 20:3601-3615. [PMID: 30063098 DOI: 10.1111/1462-2920.14337] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 05/29/2018] [Accepted: 06/21/2018] [Indexed: 11/30/2022]
Abstract
Most of our knowledge on the mechanisms underlying diatom-bacterial interactions has been acquired through studies involving isolation of culturable partners. Here, we established a laboratory model of intermediate complexity between complex natural communities and laboratory pure culture models. We investigated the whole community formed by the freshwater diatom Asterionella formosa and its associated bacteria in a laboratory context, including both culturable and unculturable bacteria. Combining cellular and molecular approaches, we showed that in laboratory cultures, A. formosa microbiome was dynamic and comprised of numerous bacterial species (mainly Proteobacteria and Bacteroidetes). Using metagenomics, we explored several metabolic potentials present within the bacterial community. Our analyses suggested that bacteria were heterotrophic although a third of them (Alpha- and Beta-proteobacteria) could also be phototrophic. About 60% of the bacteria, phylogenetically diverse, could metabolize glycolate. The capacity to synthesize molecules such as B vitamins appeared unevenly distributed among bacteria. Altogether, our results brought insights into the bacterial diversity found in diatom-bacterial communities and hinted at metabolic interdependencies within the community that could result in diatom-bacterial and bacterial-bacterial interactions. The present work allowed us to explore the functional architecture of the bacterial community associated with A. formosa in culture and is complementary to field studies.
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Affiliation(s)
| | - Adrien Villain
- Aix Marseille Univ, CNRS, IGS, UMR 7256, Marseille, France
| | - Carine Puppo
- Aix Marseille Univ, CNRS, BIP, UMR 7281, Marseille, France
| | - Sophie Fon Sing
- CEA Cadarache, Groupe Biomasse 3G, Saint-Paul-lez-Durance, F-13108, France
| | | | - Pierre Hubert
- Aix Marseille Univ, CNRS, LISM, UMR 7255, Marseille, France
| | - Gérald Grégori
- Aix Marseille Univ, University of Toulon, CNRS, IRD, MIO, UM 110, Marseille, France
| | - Yizhi Zhang
- Aix Marseille Univ, CNRS, BIP, UMR 7281, Marseille, France
| | | | - Jean-Michel Claverie
- Aix Marseille Univ, CNRS, IGS, UMR 7256, Marseille, France.,Assistance Publique des Hôpitaux de Marseille (APHM), Marseille, France
| | - Guillaume Blanc
- Aix Marseille Univ, University of Toulon, CNRS, IRD, MIO, UM 110, Marseille, France
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Yao S, Lyu S, An Y, Lu J, Gjermansen C, Schramm A. Microalgae-bacteria symbiosis in microalgal growth and biofuel production: a review. J Appl Microbiol 2018; 126:359-368. [PMID: 30168644 DOI: 10.1111/jam.14095] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 06/24/2018] [Accepted: 08/22/2018] [Indexed: 01/19/2023]
Abstract
Photosynthetic microalgae can capture solar energy and convert it to bioenergy and biochemical products. In nature or industrial processes, microalgae live together with bacterial communities and may maintain symbiotic relationships. In general interactions, microalgae exude dissolved organic carbon that becomes available to bacteria. In return, the bacteria remineralize sulphur, nitrogen and phosphorous to support the further growth of microalgae. In specific interactions, heterotrophic bacteria supply B vitamins as organic cofactors or produce siderophores to bind iron, which could be utilized by microalgae, while the algae supply fixed carbon to the bacteria in return. In this review, we focus on mutualistic relationship between microalgae and bacteria, summarizing recent studies on the mechanisms involved in microalgae-bacteria symbiosis. Symbiotic bacteria on promoting microalgal growth are described and the relevance of microalgae-bacteria interactions for biofuel production processes is discussed. Symbiotic microalgae-bacteria consortia could be utilized to improve microalgal biomass production and to enrich the biomass with valuable chemical and energy compounds. The suitable control of such biological interactions between microalgae and bacteria will help to improve the microalgae-based biomass and biofuel production in the future.
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Affiliation(s)
- S Yao
- Microbiology Group, College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, China.,Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus C, Denmark
| | - S Lyu
- Microbiology Group, College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, China
| | - Y An
- Microbiology Group, College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, China
| | - J Lu
- Microbial Engineering Group, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Roskilde, Denmark
| | - C Gjermansen
- Microbial Engineering Group, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Roskilde, Denmark
| | - A Schramm
- Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus C, Denmark
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Guidi F, Pezzolesi L, Vanucci S. Microbial dynamics during harmful dinoflagellate Ostreopsis cf. ovata growth: Bacterial succession and viral abundance pattern. Microbiologyopen 2018; 7:e00584. [PMID: 29484854 PMCID: PMC6079179 DOI: 10.1002/mbo3.584] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Revised: 12/13/2017] [Accepted: 12/19/2017] [Indexed: 12/13/2022] Open
Abstract
Algal-bacterial interactions play a major role in shaping diversity of algal associated bacterial communities. Temporal variation in bacterial phylogenetic composition reflects changes of these complex interactions which occur during the algal growth cycle as well as throughout the lifetime of algal blooms. Viruses are also known to cause shifts in bacterial community diversity which could affect algal bloom phases. This study investigated on changes of bacterial and viral abundances, bacterial physiological status, and on bacterial successional pattern associated with the harmful benthic dinoflagellate Ostreopsis cf. ovata in batch cultures over the algal growth cycle. Bacterial community phylogenetic structure was assessed by 16S rRNA gene ION torrent sequencing. A comparison between bacterial community retrieved in cultures and that one co-occurring in situ during the development of the O. cf. ovata bloom from where the algal strain was isolated was also reported. Bacterial community growth was characterized by a biphasic pattern with the highest contributions (~60%) of highly active bacteria found at the two bacterial exponential growth steps. An alphaproteobacterial consortium composed by the Rhodobacteraceae Dinoroseobacter (22.2%-35.4%) and Roseovarius (5.7%-18.3%), together with Oceanicaulis (14.2-40.3%), was strongly associated with O. cf. ovata over the algal growth. The Rhodobacteraceae members encompassed phylotypes with an assessed mutualistic-pathogenic bimodal behavior. Fabibacter (0.7%-25.2%), Labrenzia (5.6%-24.3%), and Dietzia (0.04%-1.7%) were relevant at the stationary phase. Overall, the successional pattern and the metabolic and functional traits of the bacterial community retrieved in culture mirror those ones underpinning O. cf. ovata bloom dynamics in field. Viral abundances increased synoptically with bacterial abundances during the first bacterial exponential growth step while being stationary during the second step. Microbial trends also suggest that viruses induced some shifts in bacterial community composition.
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Affiliation(s)
- Flavio Guidi
- Department of Biological, Geological and Environmental Sciences (BiGeA)University of BolognaRavennaItaly
| | - Laura Pezzolesi
- Department of Biological, Geological and Environmental Sciences (BiGeA)University of BolognaRavennaItaly
| | - Silvana Vanucci
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences (ChiBioFarAm)University of MessinaMessinaItaly
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González-Olalla JM, Medina-Sánchez JM, Lozano IL, Villar-Argaiz M, Carrillo P. Climate-driven shifts in algal-bacterial interaction of high-mountain lakes in two years spanning a decade. Sci Rep 2018; 8:10278. [PMID: 29980756 PMCID: PMC6035198 DOI: 10.1038/s41598-018-28543-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/22/2018] [Indexed: 01/02/2023] Open
Abstract
Algal-bacterial interactions include mutualism, commensalism, and predation. However, how multiple environmental conditions that regulate the strength and prevalence of a given interaction remains unclear. Here, we test the hypothesis that the prevailing algal-bacterial interaction shifted in two years (2005 versus 2015), due to increased temperature (T) and Saharan dust depositions in high-mountain lakes of Sierra Nevada (S Spain). Our results support the starting hypothesis that the nature of the prevailing algal-bacterial interaction shifted from a bacterivory control exerted by algae to commensalism, coinciding with a higher air and water T as well as the lower ratio sestonic nitrogen (N): phosphorous (P), related to greater aerosol inputs. Projected global change conditions in Mediterranean region could decline the functional diversity and alter the role of mixotrophy as a carbon (C) by-pass in the microbial food web, reducing the biomass-transfer efficiency up the web by increasing the number of trophic links.
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Affiliation(s)
| | | | - Ismael L Lozano
- Departamento de Ecología, Facultad de Ciencias, Universidad de Granada, 18071, Granada, Spain
| | - Manuel Villar-Argaiz
- Departamento de Ecología, Facultad de Ciencias, Universidad de Granada, 18071, Granada, Spain
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Simons AL, Churches N, Nuzhdin S. High turnover of faecal microbiome from algal feedstock experimental manipulations in the Pacific oyster (Crassostrea gigas). Microb Biotechnol 2018; 11:848-858. [PMID: 29749083 PMCID: PMC6116748 DOI: 10.1111/1751-7915.13277] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 04/08/2018] [Accepted: 04/11/2018] [Indexed: 11/29/2022] Open
Abstract
The composition of digestive microbiomes is known to be a significant factor in the health of a variety of hosts, including animal livestock. Therefore, it is important to ascertain how readily the microbiome can be significantly altered. To this end, the role of changing diet on the digestive microbiome of the Pacific oyster (Crassostrea gigas) was assessed via weekly faecal sampling. Over the course of 12 weeks, isolated individual oysters were fed either a control diet of Tetraselmis algae (Tet) or a treatment diet which shifted in composition every 4 weeks. Weekly faecal samples from all oysters were taken to characterize their digestive bacterial microbiota. Concurrent weekly sampling of the algal feed cultures was performed to assess the effect of algal microbiomes, independent of the algal type, on the microbiomes observed in the oyster samples. Changing the algal feed was found to be significantly associated with changes in the faecal microbiome over a timescale of weeks between control and treatment groups. No significant differences between individual microbiomes were found within control and treatment groups. This suggests the digestive microbiome of the Pacific oyster can be quickly and reproducibly manipulated.
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Affiliation(s)
- Ariel Levi Simons
- Marine and Environmental Biology, University of Southern California, Los Angeles, CA, USA
| | - Nathan Churches
- Molecular and Computation Biology, University of Southern California Dana and David Dornsife College of Letters Arts and Sciences, Los Angeles, CA, USA
| | - Sergey Nuzhdin
- Molecular and Computation Biology, University of Southern California Dana and David Dornsife College of Letters Arts and Sciences, Los Angeles, CA, USA
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Zheng Q, Wang Y, Xie R, Lang AS, Liu Y, Lu J, Zhang X, Sun J, Suttle CA, Jiao N. Dynamics of Heterotrophic Bacterial Assemblages within Synechococcus Cultures. Appl Environ Microbiol 2018; 84:e01517-17. [PMID: 29150500 PMCID: PMC5772231 DOI: 10.1128/aem.01517-17] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 11/02/2017] [Indexed: 02/01/2023] Open
Abstract
Interactions between photoautotrophic and heterotrophic microorganisms are central to the marine microbial ecosystem. Lab cultures of one of the dominant marine photoautotrophs, Synechococcus, have historically been difficult to render axenic, presumably because these bacteria depend upon other organisms to grow under these conditions. These tight associations between Synechococcus and heterotrophic bacteria represent a good relevant system to study interspecies interactions. Ten individual Synechococcus strains, isolated from eutrophic and oligotrophic waters, were chosen for investigation. Four to six dominant associated heterotrophic bacteria were detected in the liquid cultures of each Synechococcus isolate, comprising members of the Cytophaga-Flavobacteria-Bacteroides (CFB) group (mainly from Flavobacteriales and Cytophagales), Alphaproteobacteria (mainly from the Roseobacter clade), Gammaproteobacteria (mainly from the Alteromonadales and Pseudomonadales), and Actinobacteria The presence of the CFB group, Gammaproteobacteria, and Actinobacteria showed clear geographic patterns related to the isolation environments of the Synechococcus bacteria. An investigation of the population dynamics within a growing culture (XM-24) of one of the isolates, including an evaluation of the proportions of cells that were free-living versus aggregated/attached, revealed interesting patterns for different bacterial groups. In Synechococcus sp. strain XM-24 culture, flavobacteria, which was the most abundant group throughout the culture period, tended to be aggregated or attached to the Synechococcus cells, whereas the actinobacteria demonstrated a free-living lifestyle, and roseobacters displayed different patterns depending on the culture growth phase. Factors contributing to these succession patterns for the heterotrophs likely include interactions among the culture community members, their relative abilities to utilize different compounds produced by Synechococcus cells and changes in the compounds released as culture growth proceeds, and their responses to other changes in the environmental conditions throughout the culture period.IMPORTANCE Marine microbes exist within an interactive ecological network, and studying their interactions is an important part of understanding their roles in global biogeochemical cycling and the determinants of microbial diversity. In this study, the dynamic relationships between Synechococcus spp. and their associated heterotrophic bacteria were investigated. Synechococcus-associated heterotrophic bacteria had similar geographic distribution patterns as their "host" and displayed different lifestyles (free-living versus attached/aggregated) according to the Synechococcus culture growth phases. Combined organic carbon composition and bacterial lifestyle data indicated a potential for succession in carbon utilization patterns by the dominant associated heterotrophic bacteria. Comprehending the interactions between photoautotrophs and heterotrophs and the patterns of organic carbon excretion and utilization is critical to understanding their roles in oceanic biogeochemical cycling.
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Affiliation(s)
- Qiang Zheng
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, People's Republic of China
| | - Yu Wang
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, People's Republic of China
| | - Rui Xie
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, People's Republic of China
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Yanting Liu
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, People's Republic of China
| | - Jiayao Lu
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, People's Republic of China
| | - Xiaodong Zhang
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, People's Republic of China
| | - Jun Sun
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, People's Republic of China
| | - Curtis A Suttle
- Departments of Earth, Ocean and Atmospheric Sciences, Microbiology and Immunology, and Botany and Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, British Columbia, Canada
- Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario, Canada
| | - Nianzhi Jiao
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, People's Republic of China
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Assunção J, Guedes AC, Malcata FX. Biotechnological and Pharmacological Applications of Biotoxins and Other Bioactive Molecules from Dinoflagellates. Mar Drugs 2017; 15:E393. [PMID: 29261163 PMCID: PMC5742853 DOI: 10.3390/md15120393] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/12/2017] [Accepted: 12/15/2017] [Indexed: 12/26/2022] Open
Abstract
The long-lasting interest in bioactive molecules (namely toxins) produced by (microalga) dinoflagellates has risen in recent years. Exhibiting wide diversity and complexity, said compounds are well-recognized for their biological features, with great potential for use as pharmaceutical therapies and biological research probes. Unfortunately, provision of those compounds is still far from sufficient, especially in view of an increasing demand for preclinical testing. Despite the difficulties to establish dinoflagellate cultures and obtain reasonable productivities of such compounds, intensive research has permitted a number of advances in the field. This paper accordingly reviews the characteristics of some of the most important biotoxins (and other bioactive substances) produced by dinoflagellates. It also presents and discusses (to some length) the main advances pertaining to dinoflagellate production, from bench to large scale-with an emphasis on material published since the latest review available on the subject. Such advances encompass improvements in nutrient formulation and light supply as major operational conditions; they have permitted adaptation of classical designs, and aided the development of novel configurations for dinoflagellate growth-even though shearing-related issues remain a major challenge.
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Affiliation(s)
- Joana Assunção
- LEPABE-Laboratory of Process Engineering, Environment, Biotechnology and Energy, Rua Dr. Roberto Frias, s/n, P-4200-465 Porto, Portugal.
| | - A Catarina Guedes
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, P-4450-208 Matosinhos, Portugal.
| | - F Xavier Malcata
- LEPABE-Laboratory of Process Engineering, Environment, Biotechnology and Energy, Rua Dr. Roberto Frias, s/n, P-4200-465 Porto, Portugal.
- Department of Chemical Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, P-4200-465 Porto, Portugal.
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Liu CL, Place AR, Jagus R. Use of Antibiotics for Maintenance of Axenic Cultures of Amphidinium carterae for the Analysis of Translation. Mar Drugs 2017; 15:E242. [PMID: 28763019 PMCID: PMC5577597 DOI: 10.3390/md15080242] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 07/17/2017] [Accepted: 07/27/2017] [Indexed: 11/16/2022] Open
Abstract
Most dinoflagellates in culture are bacterized, complicating the quantification of protein synthesis, as well as the analysis of its regulation. In bacterized cultures of Amphidinium carterae Hulbert, up to 80% of protein synthetic activity appears to be predominantly bacterial based on responses to inhibitors of protein synthesis. To circumvent this, axenic cultures of A. carterae were obtained and shown to respond to inhibitors of protein synthesis in a manner characteristic of eukaryotes. However, these responses changed with time in culture correlating with the reappearance of bacteria. Here we show that culture with kanamycin (50 μg/mL), carbenicillin (100 μg/mL), and streptomycin sulfate (50 μg/mL) (KCS), but not 100 units/mL of penicillin and streptomycin (PS), prevents the reappearance of bacteria and allows A. carterae protein synthesis to be quantified without the contribution of an associated bacterial community. We demonstrate that A. carterae can grow in the absence of a bacterial community. Furthermore, maintenance in KCS does not inhibit the growth of A. carterae cultures but slightly extends the growth phase and allows accumulation to somewhat higher saturation densities. We also show that cultures of A. carterae maintained in KCS respond to the eukaryotic protein synthesis inhibitors cycloheximide, emetine, and harringtonine. Establishment of these culture conditions will facilitate our ability to use polysome fractionation and ribosome profiling to study mRNA recruitment. Furthermore, this study shows that a simple and fast appraisal of the presence of a bacterial community in A. carterae cultures can be made by comparing responses to cycloheximide and chloramphenicol rather than depending on lengthier culture-based assessments.
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Affiliation(s)
- Chieh-Lun Liu
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, 701 E. Pratt Street, Baltimore, MD 21202, USA.
| | - Allen R Place
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, 701 E. Pratt Street, Baltimore, MD 21202, USA.
| | - Rosemary Jagus
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, 701 E. Pratt Street, Baltimore, MD 21202, USA.
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Caron DA, Alexander H, Allen AE, Archibald JM, Armbrust EV, Bachy C, Bell CJ, Bharti A, Dyhrman ST, Guida SM, Heidelberg KB, Kaye JZ, Metzner J, Smith SR, Worden AZ. Probing the evolution, ecology and physiology of marine protists using transcriptomics. Nat Rev Microbiol 2016; 15:6-20. [DOI: 10.1038/nrmicro.2016.160] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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