1
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Cho A, Lax G, Livingston SJ, Masukagami Y, Naumova M, Millar O, Husnik F, Keeling PJ. Genomic analyses of Symbiomonas scintillans show no evidence for endosymbiotic bacteria but does reveal the presence of giant viruses. PLoS Genet 2024; 20:e1011218. [PMID: 38557755 PMCID: PMC11008856 DOI: 10.1371/journal.pgen.1011218] [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: 12/04/2023] [Revised: 04/11/2024] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
Symbiomonas scintillans Guillou et Chrétiennot-Dinet, 1999 is a tiny (1.4 μm) heterotrophic microbial eukaryote. The genus was named based on the presence of endosymbiotic bacteria in its endoplasmic reticulum, however, like most such endosymbionts neither the identity nor functional association with its host were known. We generated both amplification-free shotgun metagenomics and whole genome amplification sequencing data from S. scintillans strains RCC257 and RCC24, but were unable to detect any sequences from known lineages of endosymbiotic bacteria. The absence of endobacteria was further verified with FISH analyses. Instead, numerous contigs in assemblies from both RCC24 and RCC257 were closely related to prasinoviruses infecting the green algae Ostreococcus lucimarinus, Bathycoccus prasinos, and Micromonas pusilla (OlV, BpV, and MpV, respectively). Using the BpV genome as a reference, we assembled a near-complete 190 kbp draft genome encoding all hallmark prasinovirus genes, as well as two additional incomplete assemblies of closely related but distinct viruses from RCC257, and three similar draft viral genomes from RCC24, which we collectively call SsVs. A multi-gene tree showed the three SsV genome types branched within highly supported clades with each of BpV2, OlVs, and MpVs, respectively. Interestingly, transmission electron microscopy also revealed a 190 nm virus-like particle similar the morphology and size of the endosymbiont originally reported in S. scintillans. Overall, we conclude that S. scintillans currently does not harbour an endosymbiotic bacterium, but is associated with giant viruses.
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Affiliation(s)
- Anna Cho
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gordon Lax
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Samuel J. Livingston
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yumiko Masukagami
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Mariia Naumova
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Olivia Millar
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Filip Husnik
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Patrick J. Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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2
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Baylous HR, Gladfelter MF, Gardner MI, Foley M, Wilson AE, Steffen MM. Indole-3-acetic acid promotes growth in bloom-forming Microcystis via an antioxidant response. HARMFUL ALGAE 2024; 133:102575. [PMID: 38485434 DOI: 10.1016/j.hal.2024.102575] [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: 10/20/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 03/19/2024]
Abstract
Interactions between bacteria and phytoplankton in the phycosphere facilitate and constrain biogeochemical cycling in aquatic ecosystems. Indole-3-acetic acid (IAA) is a bacterially produced chemical signal that promotes growth of phytoplankton and plants. Here, we explored the impact of IAA on bloom-forming cyanobacteria and their associated bacteria. Exposure to IAA and its precursor, tryptophan, resulted in a strong growth response in a bloom of the freshwater cyanobacterium, Microcystis. Metatranscriptome analysis revealed the induction of an antioxidant response in Microcystis upon exposure to IAA, potentially allowing populations to increase photosynthetic rate and overcome internally generated reactive oxygen. Our data reveal that co-occurring bacteria within the phycosphere microbiome exhibit a division of labor for supportive functions, such as nutrient mineralization and transport, vitamin synthesis, and reactive oxygen neutralization. These complex dynamics within the Microcystis phycosphere microbiome are an example of interactions within a microenvironment that can have ecosystem-scale consequences.
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Affiliation(s)
- Hunter R Baylous
- Department of Biology, James Madison University, Harrisonburg, VA 22801, USA
| | - Matthew F Gladfelter
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Malia I Gardner
- Department of Biology, James Madison University, Harrisonburg, VA 22801, USA
| | - Madalynn Foley
- Department of Biology, James Madison University, Harrisonburg, VA 22801, USA
| | - Alan E Wilson
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Morgan M Steffen
- Department of Biology, James Madison University, Harrisonburg, VA 22801, USA.
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3
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Miller IR, Bui H, Wood JB, Fields MW, Gerlach R. Understanding phycosomal dynamics to improve industrial microalgae cultivation. Trends Biotechnol 2024:S0167-7799(23)00342-6. [PMID: 38184438 DOI: 10.1016/j.tibtech.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 01/08/2024]
Abstract
Algal-bacterial interactions are ubiquitous in both natural and industrial systems, and the characterization of these interactions has been reinvigorated by potential applications in biosystem productivity. Different growth conditions can be used for operational functions, such as the use of low-quality water or high pH/alkalinity, and the altered operating conditions likely constrain microbial community structure and function in unique ways. However, research is necessary to better understand whether consortia can be designed to improve the productivity, processing, and sustainability of industrial-scale cultivations through different controls that can constrain microbial interactions for maximal light-driven outputs. The review highlights current knowledge and gaps for relevant operating conditions, as well as suggestions for near-term and longer-term improvements for large-scale cultivation and polyculture engineering.
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Affiliation(s)
- Isaac R Miller
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA; Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA
| | - Huyen Bui
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA
| | - Jessica B Wood
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA; Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA
| | - Matthew W Fields
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA; Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA; Department of Civil Engineering, Montana State University, Bozeman, MT, USA; Energy Research Institute, Montana State University, Bozeman, MT, USA.
| | - Robin Gerlach
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA; Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA; Energy Research Institute, Montana State University, Bozeman, MT, USA; Department of Biological and Chemical Engineering, Bozeman, MT, USA
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4
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Mayali X, Samo TJ, Kimbrel JA, Morris MM, Rolison K, Swink C, Ramon C, Kim YM, Munoz-Munoz N, Nicora C, Purvine S, Lipton M, Stuart RK, Weber PK. Single-cell isotope tracing reveals functional guilds of bacteria associated with the diatom Phaeodactylum tricornutum. Nat Commun 2023; 14:5642. [PMID: 37704622 PMCID: PMC10499878 DOI: 10.1038/s41467-023-41179-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/24/2023] [Indexed: 09/15/2023] Open
Abstract
Bacterial remineralization of algal organic matter fuels algal growth but is rarely quantified. Consequently, we cannot currently predict whether some bacterial taxa may provide more remineralized nutrients to algae than others. Here, we quantified bacterial incorporation of algal-derived complex dissolved organic carbon and nitrogen and algal incorporation of remineralized carbon and nitrogen in fifteen bacterial co-cultures growing with the diatom Phaeodactylum tricornutum at the single-cell level using isotope tracing and nanoSIMS. We found unexpected strain-to-strain and cell-to-cell variability in net carbon and nitrogen incorporation, including non-ubiquitous complex organic nitrogen utilization and remineralization. We used these data to identify three distinct functional guilds of metabolic interactions, which we termed macromolecule remineralizers, macromolecule users, and small-molecule users, the latter exhibiting efficient growth under low carbon availability. The functional guilds were not linked to phylogeny and could not be elucidated strictly from metabolic capacity as predicted by comparative genomics, highlighting the need for direct activity-based measurements in ecological studies of microbial metabolic interactions.
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Affiliation(s)
- Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
| | - Ty J Samo
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jeff A Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Megan M Morris
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Kristina Rolison
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Courtney Swink
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Christina Ramon
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Young-Mo Kim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Nathalie Munoz-Munoz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Carrie Nicora
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Sam Purvine
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Mary Lipton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Rhona K Stuart
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
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5
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Xiao X, Li W, Li S, Zuo X, Liu J, Guo L, Lu X, Zhang L. The Growth Inhibition of Polyethylene Nanoplastics on the Bait-Microalgae Isochrysis galbana Based on the Transcriptome Analysis. Microorganisms 2023; 11:1108. [PMID: 37317083 DOI: 10.3390/microorganisms11051108] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 04/20/2023] [Accepted: 04/20/2023] [Indexed: 06/16/2023] Open
Abstract
The adverse effects of microplastics on microalgae species have been extensively studied, but their impact on the bait microalgae entering the food chain has not been well understood. This study investigated the cytological and physiological response of Isochrysis galbana to polyethylene microplastics (PE-MPs, 10 μm) and nanoplastics (PE-NPs, 50 nm). The results showed that PE-MPs had no significant impact on I. galbana, while PsE-NPs obviously inhibited cell growth, reduced chlorophyll content, and caused a decline in carotenoids and soluble protein. These changes in the quality of I. galbana could negatively affect its use as aquaculture feed. To understand the molecular response mechanism of I. galbana to PE-NPs, transcriptome sequencing was performed. The result revealed that the TCA cycle, purine metabolism, and some key amino acid syntheses were down-regulated by PE-NPs, while the Calvin cycle and fatty acid metabolism were up-regulated to tolerate PE-NP pressure. Microbial analysis showed that the bacterial community structure associated with I. galbana was significantly altered at the species level by PE-NPs. In conclusion, this study provides new insights into the physiological stress response caused by microplastic pollution based on transcriptome and bacterial community analysis. The findings highlight the need to mitigate the release of microplastics into the environment to prevent their harmful effects on aquatic ecosystems and will be helpful in understanding the impact of polyethylene nanoplastics on the bait microalgae.
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Affiliation(s)
- Xinfeng Xiao
- College of Safety & Environmental Engineering, Shandong University of Science & Technology, Qingdao 266510, China
| | - Wenfang Li
- College of Safety & Environmental Engineering, Shandong University of Science & Technology, Qingdao 266510, China
| | - Shuangwei Li
- College of Safety & Environmental Engineering, Shandong University of Science & Technology, Qingdao 266510, China
| | - Xingsheng Zuo
- College of Safety & Environmental Engineering, Shandong University of Science & Technology, Qingdao 266510, China
| | - Jie Liu
- College of Safety & Environmental Engineering, Shandong University of Science & Technology, Qingdao 266510, China
| | - Linke Guo
- College of Safety & Environmental Engineering, Shandong University of Science & Technology, Qingdao 266510, China
| | - Xiao Lu
- College of Safety & Environmental Engineering, Shandong University of Science & Technology, Qingdao 266510, China
| | - Linlin Zhang
- College of Safety & Environmental Engineering, Shandong University of Science & Technology, Qingdao 266510, China
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6
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Steinrücken P, Jackson S, Müller O, Puntervoll P, Kleinegris DMM. A closer look into the microbiome of microalgal cultures. Front Microbiol 2023; 14:1108018. [PMID: 36778846 PMCID: PMC9908576 DOI: 10.3389/fmicb.2023.1108018] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 01/10/2023] [Indexed: 01/27/2023] Open
Abstract
Although bacteria are commonly co-occurring in microalgal cultivation and production systems, little is known about their community structure and how it might be affected by specific microalgal groups or growth conditions. A better understanding about the underlying factors that determine the growth of specific bacterial populations is not only important for optimizing microalgal production processes, but also in the context of product quality when the algal biomass is to be used for future food or feed. We analyzed the bacterial community composition associated with nine microalgal strains in stock culture, maintained in two different growth media, to explore how specific taxonomic microalgal groups, microalgal origin, or the growth medium affect the bacterial community composition. Furthermore, we monitored the bacterial community composition for three Phaeodactylum strains during batch cultivation in bubble columns to examine if the bacterial composition alters during cultivation. Our results reveal that different microalgal genera, kept at the same cultivation conditions over many years, displayed separate and unique bacterial communities, and that different strains of the same genus had very similar bacterial community compositions, despite originating from different habitats. However, when maintained in a different growth medium, the bacterial composition changed for some. During batch cultivation, the bacterial community structure remained relatively stable for each Phaeodactylum strain. This indicates that microalgae seem to impact the development of the associated bacterial communities and that different microalgal genera could create distinct conditions that select for dominance of specific bacteria. However, other factors such as the composition of growth medium also affect the formation of the bacterial community structure.
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Affiliation(s)
- Pia Steinrücken
- Department of Biological Sciences, University of Bergen, Bergen, Norway,NORCE Climate & Environment - NORCE Norwegian Research Centre AS, Bergen, Norway,*Correspondence: Pia Steinrücken, ✉
| | - Steve Jackson
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Oliver Müller
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Pål Puntervoll
- NORCE Climate & Environment - NORCE Norwegian Research Centre AS, Bergen, Norway
| | - Dorinde M. M. Kleinegris
- Department of Biological Sciences, University of Bergen, Bergen, Norway,NORCE Climate & Environment - NORCE Norwegian Research Centre AS, Bergen, Norway
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7
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Deng Y, Wang K, Hu Z, Hu Q, Tang YZ. Identification and implications of a core bacterial microbiome in 19 clonal cultures laboratory-reared for months to years of the cosmopolitan dinoflagellate Karlodinium veneficum. Front Microbiol 2022; 13:967610. [PMID: 36033882 PMCID: PMC9416233 DOI: 10.3389/fmicb.2022.967610] [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: 06/14/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Identification of a core microbiome (a group of taxa commonly present and consistently abundant in most samples of host populations) is important to capture the key microbes closely associated with a host population, as this process may potentially contribute to further revealing their spatial distribution, temporal stability, ecological influence, and even impacts on their host’s functions and fitness. The naked dinoflagellate Karlodinium veneficum is a cosmopolitan and toxic species, which is also notorious in forming harmful algal blooms (HABs) and causing massive fish-kills. Here we reported the core microbiome tightly associated with 19 strains of K. veneficum that were originally isolated from 6 geographic locations along the coast of China and from an estuary of Chesapeake Bay, United States, and have been maintained in the laboratory for several months to over 14 years. Using high-throughput metabarcoding of the partial 16S rRNA gene amplicons, a total of 1,417 prokaryotic features were detected in the entire bacterial microbiome, which were assigned to 17 phyla, 35 classes, 90 orders, 273 families, and 716 genera. Although the bacterial communities associated with K. veneficum cultures displayed heterogeneity in feature (sequences clustered at 100% sequence similarity) composition among strains, a core set of 6 genera were found persistent in their phycospheres, which could contribute up to 74.54% of the whole bacterial microbiome. Three γ-proteobacteria members of the “core,” namely, Alteromonas, Marinobacter, and Methylophaga, were the predominant core genera and made up 83.25% of the core bacterial microbiome. The other 3 core genera, Alcanivorax, Thalassospira, and Ponticoccus, are reported to preferably utilize hydrocarbons as sole or major source of carbon and energy, and two of which (Alcanivorax and Ponticoccus) are recognized as obligate hydrocarbonoclastic bacteria (OHCB). Since OHCB generally present in extremely low abundance in marine water and elevate their abundance mostly in petroleum-impacted water, our detection in K. veneficum cultures suggests that the occurrence of obligate and generalist hydrocarbon-degrading bacteria living with dinoflagellates may be more frequent in nature. Our work identified a core microbiome with stable association with the harmful alga K. veneficum and opened a window for further characterization of the physiological mechanisms and ecological implications for the dinoflagellate-bacteria association.
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Affiliation(s)
- Yunyan Deng
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Kui Wang
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Zhangxi Hu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Qiang Hu
- Faculty of Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Ying Zhong Tang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- *Correspondence: Ying Zhong Tang,
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8
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Vacant S, Benites LF, Salmeron C, Intertaglia L, Norest M, Cadoudal A, Sanchez F, Caceres C, Piganeau G. Long-Term Stability of Bacterial Associations in a Microcosm of Ostreococcus tauri (Chlorophyta, Mamiellophyceae). FRONTIERS IN PLANT SCIENCE 2022; 13:814386. [PMID: 35463414 PMCID: PMC9024300 DOI: 10.3389/fpls.2022.814386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
Phytoplankton-bacteria interactions rule over carbon fixation in the sunlit ocean, yet only a handful of phytoplanktonic-bacteria interactions have been experimentally characterized. In this study, we investigated the effect of three bacterial strains isolated from a long-term microcosm experiment with one Ostreococcus strain (Chlorophyta, Mamiellophyceae). We provided evidence that two Roseovarius strains (Alphaproteobacteria) had a beneficial effect on the long-term survival of the microalgae whereas one Winogradskyella strain (Flavobacteriia) led to the collapse of the microalga culture. Co-cultivation of the beneficial and the antagonistic strains also led to the loss of the microalga cells. Metagenomic analysis of the microcosm is consistent with vitamin B12 synthesis by the Roseovarius strains and unveiled two additional species affiliated to Balneola (Balneolia) and Muricauda (Flavobacteriia), which represent less than 4% of the reads, whereas Roseovarius and Winogradskyella recruit 57 and 39% of the reads, respectively. These results suggest that the low-frequency bacterial species may antagonize the algicidal effect of Winogradskyella in the microbiome of Ostreococcus tauri and thus stabilize the microalga persistence in the microcosm. Altogether, these results open novel perspectives into long-term stability of phytoplankton cultures.
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Affiliation(s)
- Sophie Vacant
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, Centre National de la Recherche Scientifique, Oceanological Observatory of Banyuls, Banyuls-sur-Mer, France
| | - L. Felipe Benites
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, Centre National de la Recherche Scientifique, Oceanological Observatory of Banyuls, Banyuls-sur-Mer, France
| | - Christophe Salmeron
- Sorbonne Université, Centre National de la Recherche Scientifique, Observatoire Océanologique de Banyuls, FR3724, Banyuls-sur-Mer, France
| | - Laurent Intertaglia
- Sorbonne Université, Centre National de la Recherche Scientifique, Observatoire Océanologique de Banyuls, FR3724, Banyuls-sur-Mer, France
| | - Manon Norest
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, Centre National de la Recherche Scientifique, Oceanological Observatory of Banyuls, Banyuls-sur-Mer, France
| | - Adrien Cadoudal
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, Centre National de la Recherche Scientifique, Oceanological Observatory of Banyuls, Banyuls-sur-Mer, France
| | - Frederic Sanchez
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, Centre National de la Recherche Scientifique, Oceanological Observatory of Banyuls, Banyuls-sur-Mer, France
| | - Carlos Caceres
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, Centre National de la Recherche Scientifique, Oceanological Observatory of Banyuls, Banyuls-sur-Mer, France
| | - Gwenael Piganeau
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, Centre National de la Recherche Scientifique, Oceanological Observatory of Banyuls, Banyuls-sur-Mer, France
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9
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Zoccarato L, Sher D, Miki T, Segrè D, Grossart HP. A comparative whole-genome approach identifies bacterial traits for marine microbial interactions. Commun Biol 2022; 5:276. [PMID: 35347228 PMCID: PMC8960797 DOI: 10.1038/s42003-022-03184-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/30/2021] [Indexed: 12/11/2022] Open
Abstract
Microbial interactions shape the structure and function of microbial communities with profound consequences for biogeochemical cycles and ecosystem health. Yet, most interaction mechanisms are studied only in model systems and their prevalence is unknown. To systematically explore the functional and interaction potential of sequenced marine bacteria, we developed a trait-based approach, and applied it to 473 complete genomes (248 genera), representing a substantial fraction of marine microbial communities. We identified genome functional clusters (GFCs) which group bacterial taxa with common ecology and life history. Most GFCs revealed unique combinations of interaction traits, including the production of siderophores (10% of genomes), phytohormones (3-8%) and different B vitamins (57-70%). Specific GFCs, comprising Alpha- and Gammaproteobacteria, displayed more interaction traits than expected by chance, and are thus predicted to preferentially interact synergistically and/or antagonistically with bacteria and phytoplankton. Linked trait clusters (LTCs) identify traits that may have evolved to act together (e.g., secretion systems, nitrogen metabolism regulation and B vitamin transporters), providing testable hypotheses for complex mechanisms of microbial interactions. Our approach translates multidimensional genomic information into an atlas of marine bacteria and their putative functions, relevant for understanding the fundamental rules that govern community assembly and dynamics.
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Affiliation(s)
- Luca Zoccarato
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 16775, Stechlin, Germany.
| | - Daniel Sher
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, 3498838, Haifa, Israel.
| | - Takeshi Miki
- Faculty of Advanced Science and Technology, Ryukoku University, 520-2194, Otsu, Japan
| | - Daniel Segrè
- Departments of Biology, Biomedical Engineering, Physics, Boston University, 02215, Boston, MA, USA
- Bioinformatics Program & Biological Design Center, Boston University, 02215, Boston, MA, USA
| | - Hans-Peter Grossart
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 16775, Stechlin, Germany.
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195, Berlin, Germany.
- Institute of Biochemistry and Biology, Potsdam University, 14476, Potsdam, Germany.
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10
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Xu S, Wang X, Liu J, Zhou F, Guo K, Chen S, Wang ZH, Wang Y. Bacteria Associated With Phaeocystis globosa and Their Influence on Colony Formation. Front Microbiol 2022; 13:826602. [PMID: 35250943 PMCID: PMC8891983 DOI: 10.3389/fmicb.2022.826602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/04/2022] [Indexed: 11/13/2022] Open
Abstract
Phaeocystis globosa (P. globosa) is one of the dominant algae during harmful algal blooms (HABs) in coastal regions of Southern China. P. globosa exhibits complex heteromorphic life cycles that could switch between solitary cells and colonies. The ecological success of P. globosa has been attributed to its colony formation, although underlying mechanisms remain unknown. Here, we investigated different bacterial communities associated with P. globosa colonies and their influence on colony formation of two P. globosa strains isolated from coastal waters of Guangxi (GX) and Shantou (ST). Eight operational taxonomic units (OTUs) were observed in ST co-cultures and were identified as biomarkers based on Linear discriminant analysis Effect Size (LEfSe) analysis, while seven biomarkers were identified in P. globosa GX co-cultures. Bacterial communities associated with the P. globosa GX were more diverse than those of the ST strain. The most dominant phylum in the two co-cultures was Proteobacteria, within which Marinobacter was the most abundant genus in both GX and ST co-cultures. Bacteroidota were only observed in the GX co-cultures and Planctomycetota were only observed in the ST co-cultures. Co-culture experiments revealed that P. globosa colony formation was not influenced by low and medium cell densities of Marinobacter sp. GS7, but was inhibited by high cell densities of Marinobacter sp. GS7. Overall, these results indicated that the associated bacteria are selected by different P. globosa strains, which may affect the colony formation and development of P. globosa.
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Affiliation(s)
- Shuaishuai Xu
- College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Xiaodong Wang
- College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Jie Liu
- College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Fengli Zhou
- College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Kangli Guo
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Songze Chen
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Zhao-hui Wang
- College of Life Science and Technology, Jinan University, Guangzhou, China
- *Correspondence: Zhao-hui Wang,
| | - Yan Wang
- College of Life Science and Technology, Jinan University, Guangzhou, China
- Yan Wang,
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11
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Lian J, Steinert G, de Vree J, Meijer S, Heryanto C, Bosma R, Wijffels RH, Barbosa MJ, Smidt H, Sipkema D. Bacterial diversity in different outdoor pilot plant photobioreactor types during production of the microalga Nannochloropsis sp. CCAP211/78. Appl Microbiol Biotechnol 2022; 106:2235-2248. [PMID: 35166894 PMCID: PMC8930801 DOI: 10.1007/s00253-022-11815-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 12/22/2021] [Accepted: 01/29/2022] [Indexed: 11/25/2022]
Abstract
As large-scale outdoor production cannot be done in complete containment, cultures are (more) open for bacteria, which may affect the productivity and stability of the algae production process. We investigated the bacterial diversity in two indoor reactors and four pilot-scale outdoor reactors for the production of Nannochloropsis sp. CCAP211/78 spanning four months of operation from July to October. Illumina sequencing of 16S rRNA gene amplicons demonstrated that a wide variety of bacteria were present in all reactor types, with predominance of Bacteroidetes and Alphaproteobacteria. Bacterial communities were significantly different between all reactor types (except between the horizontal tubular reactor and the vertical tubular reactor) and also between runs in each reactor. Bacteria common to the majority of samples included one member of the Saprospiraceae family and one of the NS11-12_marine group (both Bacteroidetes). Hierarchical clustering analysis revealed two phases during the cultivation period separated by a major shift in bacterial community composition in the horizontal tubular reactor, the vertical tubular reactor and the raceway pond with a strong decrease of the Saprospiraceae and NS11-12_marine group that initially dominated the bacterial communities. Furthermore, we observed a less consistent pattern of bacterial taxa appearing in different reactors and runs, most of which belonging to the classes Deltaproteobacteria and Flavobacteriia. In addition, canonical correspondence analysis showed that the bacterial community composition was significantly correlated with the nitrate concentration. This study contributes to our understanding of bacterial diversity and composition in different types of outdoor reactors exposed to a range of dynamic biotic and abiotic factors. Key points • Reactor types had significantly different bacterial communities except HT and VT • The inoculum source and physiochemical factors together affect bacterial community • The bacterial family Saprospiraceae is positively correlated to microalgal growth.
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Affiliation(s)
- Jie Lian
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Georg Steinert
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Jeroen de Vree
- Bioprocess Engineering, AlgaePARC, Wageningen University & Research, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - Sven Meijer
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Christa Heryanto
- Bioprocess Engineering, AlgaePARC, Wageningen University & Research, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - Rouke Bosma
- Bioprocess Engineering, AlgaePARC, Wageningen University & Research, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - René H Wijffels
- Bioprocess Engineering, AlgaePARC, Wageningen University & Research, PO Box 16, 6700 AA, Wageningen, The Netherlands
- Faculty of Biosciences and Aquaculture, Nord University, N8049, Bodø, Norway
| | - Maria J Barbosa
- Bioprocess Engineering, AlgaePARC, Wageningen University & Research, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
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12
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Xia X, Zheng Q, Leung SK, Wang Y, Lee PY, Jing H, Jiao N, Liu H. Distinct metabolic strategies of the dominant heterotrophic bacterial groups associated with marine Synechococcus. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 798:149208. [PMID: 34375229 DOI: 10.1016/j.scitotenv.2021.149208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/08/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
The marine Synechococcus is a major primary producer in the global oceans. It is phylogenetically highly diverse, and its major phylogenetic lineages display clear spatial segregation among different marine environments. Here, we showed that the composition of the associated bacterial communities was related to the geographic origin of the different Synechococcus strains, and it was stable during long-term lab incubation. Of all the Synechococcus cultures investigated, the Rhodobacteraceae had a relatively high abundance and was the core bacterial family of the associated bacterial communities. In contrast, the Flavobacteriaceae were only abundant in the cultures collected from the South China Sea (which is warm and oligotrophic), whereas those of the Alteromonadaceae were abundant in the cultures from the coastal waters off Hong Kong and Xiamen. We also found that the Rhodobacteraceae had more ABC transporters and utilized a wider spectrum of carbon sources than did the Flavobacteriaceae and Alteromonadaceae. Moreover, the Alteromonadaceae had more transporters for importing phosphate and amino acids, but fewer transporters for importing oligosaccharides, polyol, and lipid, than the Flavobacteriaceae. Furthermore, metagenomic analysis demonstrated that bacteria involved in nitrate-ammonification prevailed in all the cultures. These results imply that networks formed by phytoplankton and heterotrophic bacteria might vary across habitats, and that different dominant bacterial groups play different roles in the phycosphere. This study provides new insight into the unique interactive and interdependent bond between phytoplankton and their associated microbiome, which may enhance our understanding of carbon and nutrient cycling in marine environments.
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Affiliation(s)
- Xiaomin Xia
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), PR China; CAS-HKUST Sanya Joint Laboratory of Marine Science Research, Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya, PR China.
| | - Qiang Zheng
- State Key Laboratory for Marine Environmental Sciences, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, PR China
| | - Sze Ki Leung
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Yu Wang
- State Key Laboratory for Marine Environmental Sciences, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, PR China
| | - Pui Yin Lee
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China
| | - Nianzhi Jiao
- State Key Laboratory for Marine Environmental Sciences, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, PR China
| | - Hongbin Liu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China; Hong Kong Branch of Southern Marine Science & Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China.
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13
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Maréchal E. Grand Challenges in Microalgae Domestication. FRONTIERS IN PLANT SCIENCE 2021; 12:764573. [PMID: 34630500 PMCID: PMC8495258 DOI: 10.3389/fpls.2021.764573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
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Pinto J, Lami R, Krasovec M, Grimaud R, Urios L, Lupette J, Escande ML, Sanchez F, Intertaglia L, Grimsley N, Piganeau G, Sanchez-Brosseau S. Features of the Opportunistic Behaviour of the Marine Bacterium Marinobacter algicola in the Microalga Ostreococcus tauri Phycosphere. Microorganisms 2021; 9:microorganisms9081777. [PMID: 34442856 PMCID: PMC8399681 DOI: 10.3390/microorganisms9081777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/07/2021] [Accepted: 08/10/2021] [Indexed: 11/16/2022] Open
Abstract
Although interactions between microalgae and bacteria are observed in both natural environment and the laboratory, the modalities of coexistence of bacteria inside microalgae phycospheres in laboratory cultures are mostly unknown. Here, we focused on well-controlled cultures of the model green picoalga Ostreococcus tauri and the most abundant member of its phycosphere, Marinobacter algicola. The prevalence of M. algicola in O. tauri cultures raises questions about how this bacterium maintains itself under laboratory conditions in the microalga culture. The results showed that M. algicola did not promote O. tauri growth in the absence of vitamin B12 while M. algicola depended on O. tauri to grow in synthetic medium, most likely to obtain organic carbon sources provided by the microalgae. M. algicola grew on a range of lipids, including triacylglycerols that are known to be produced by O. tauri in culture during abiotic stress. Genomic screening revealed the absence of genes of two particular modes of quorum-sensing in Marinobacter genomes which refutes the idea that these bacterial communication systems operate in this genus. To date, the ‘opportunistic’ behaviour of M. algicola in the laboratory is limited to several phytoplanktonic species including Chlorophyta such as O. tauri. This would indicate a preferential occurrence of M. algicola in association with these specific microalgae under optimum laboratory conditions.
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Affiliation(s)
- Jordan Pinto
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650 Banyuls-sur-Mer, France; (J.P.); (M.K.); (J.L.); (F.S.); (N.G.); (G.P.)
| | - Raphaël Lami
- Sorbonne Université, CNRS, USR 3579 Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, 66650 Banyuls-sur-Mer, France;
| | - Marc Krasovec
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650 Banyuls-sur-Mer, France; (J.P.); (M.K.); (J.L.); (F.S.); (N.G.); (G.P.)
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | - Régis Grimaud
- Université de Pau et des Pays de l’Adour, E2S UPPA, CNRS, IPREM, 64000 Pau, France; (R.G.); (L.U.)
| | - Laurent Urios
- Université de Pau et des Pays de l’Adour, E2S UPPA, CNRS, IPREM, 64000 Pau, France; (R.G.); (L.U.)
| | - Josselin Lupette
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650 Banyuls-sur-Mer, France; (J.P.); (M.K.); (J.L.); (F.S.); (N.G.); (G.P.)
- Université de Bordeaux, CNRS, UMR 5200 Laboratoire de Biogenèse Membranaire, 33140 Villenave d’Ornon, France
| | - Marie-Line Escande
- Sorbonne Université, CNRS, FR 3724, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France; (M.-L.E.); (L.I.)
| | - Frédéric Sanchez
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650 Banyuls-sur-Mer, France; (J.P.); (M.K.); (J.L.); (F.S.); (N.G.); (G.P.)
| | - Laurent Intertaglia
- Sorbonne Université, CNRS, FR 3724, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France; (M.-L.E.); (L.I.)
| | - Nigel Grimsley
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650 Banyuls-sur-Mer, France; (J.P.); (M.K.); (J.L.); (F.S.); (N.G.); (G.P.)
| | - Gwenaël Piganeau
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650 Banyuls-sur-Mer, France; (J.P.); (M.K.); (J.L.); (F.S.); (N.G.); (G.P.)
| | - Sophie Sanchez-Brosseau
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650 Banyuls-sur-Mer, France; (J.P.); (M.K.); (J.L.); (F.S.); (N.G.); (G.P.)
- Correspondence:
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15
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Lian J, Schimmel P, Sanchez‐Garcia S, Wijffels RH, Smidt H, Sipkema D. Different co-occurring bacteria enhance or decrease the growth of the microalga Nannochloropsis sp. CCAP211/78. Microb Biotechnol 2021; 14:1159-1170. [PMID: 33683803 PMCID: PMC8085966 DOI: 10.1111/1751-7915.13784] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 02/12/2021] [Accepted: 02/15/2021] [Indexed: 11/29/2022] Open
Abstract
Marine photosynthetic microalgae are ubiquitously associated with bacteria in nature. However, the influence of these bacteria on algal cultures in bioreactors is still largely unknown. In this study, eighteen different bacterial strains were isolated from cultures of Nannochloropsis sp. CCAP211/78 in two outdoor pilot-scale tubular photobioreactors. The majority of isolates was affiliated with the classes Alphaproteobacteria and Flavobacteriia. To assess the impact of the eighteen strains on the growth of Nannochloropsis sp. CCAP211/78, 24-well plates coupled with custom-made LED boxes were used to simultaneously compare replicate axenic microalgal cultures with addition of individual bacterial isolates. Co-culturing of Nannochloropsis sp. CCAP211/78 with these strains demonstrated distinct responses, which shows that the technique we developed is an efficient method for screening the influence of harmful/beneficial bacteria. Two of the tested strains, namely a strain of Maritalea porphyrae (DMSP31) and a Labrenzia aggregata strain (YP26), significantly enhanced microalgal growth with a 14% and 12% increase of the chlorophyll concentration, respectively, whereas flavobacterial strain YP206 greatly inhibited the growth of the microalga with 28% reduction of the chlorophyll concentration. Our study suggests that algal production systems represent a 'natural' source to isolate and study microorganisms that can either benefit or harm algal cultures.
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Affiliation(s)
- Jie Lian
- Laboratory of MicrobiologyWageningen University & ResearchStippeneng 4Wageningen6708 WEThe Netherlands
| | - Patrick Schimmel
- Laboratory of MicrobiologyWageningen University & ResearchStippeneng 4Wageningen6708 WEThe Netherlands
| | - Selene Sanchez‐Garcia
- Laboratory of MicrobiologyWageningen University & ResearchStippeneng 4Wageningen6708 WEThe Netherlands
| | - Rene H. Wijffels
- Bioprocess Engineering Group, AlgaePARCWageningen University & ResearchPO Box 16Wageningen6700 AAThe Netherlands
- Faculty of Biosciences and AquacultureNord UniversityBodøN‐8049Norway
| | - Hauke Smidt
- Laboratory of MicrobiologyWageningen University & ResearchStippeneng 4Wageningen6708 WEThe Netherlands
| | - Detmer Sipkema
- Laboratory of MicrobiologyWageningen University & ResearchStippeneng 4Wageningen6708 WEThe Netherlands
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16
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Mönnich J, Tebben J, Bergemann J, Case R, Wohlrab S, Harder T. Niche-based assembly of bacterial consortia on the diatom Thalassiosira rotula is stable and reproducible. THE ISME JOURNAL 2020; 14:1614-1625. [PMID: 32203123 PMCID: PMC7242391 DOI: 10.1038/s41396-020-0631-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 03/03/2020] [Accepted: 03/10/2020] [Indexed: 12/22/2022]
Abstract
With each cell division, phytoplankton create new space for primary colonization by marine bacteria. Although this surface microenvironment is available to all planktonic bacterial colonizers, we show the assembly of bacterial consortia on a cosmopolitan marine diatom to be highly specific and reproducible. While phytoplankton-bacteria interactions play fundamental roles in marine ecosystems, namely primary production and the carbon cycle, the ecological paradigm behind epiphytic microbiome assembly remains poorly understood. In a replicated and repeated primary colonization experiment, we exposed the axenic diatom Thalassiosira rotula to several complex and compositionally different bacterial inocula derived from phytoplankton species of varying degrees of relatedness to the axenic Thalassiosira host or natural seawater. This revealed a convergent assembly of diverse and compositionally different bacterial inocula, containing up to 2071 operational taxonomic units (OTUs), towards a stable and reproducible core community. Four of these OTUs already accounted for a cumulative abundance of 60%. This core community was dominated by Rhodobacteraceae (30.5%), Alteromonadaceae (27.7%), and Oceanospirillales (18.5%) which was qualitatively and quantitatively most similar to its conspecific original. These findings reject a lottery assembly model of bacterial colonization and suggest selective microhabitat filtering. This is likely due to diatom host traits such as surface properties and different levels of specialization resulting in reciprocal stable-state associations.
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Affiliation(s)
- Julian Mönnich
- Marine Chemistry, Department of Chemistry and Biology, University of Bremen, 28359, Bremen, Germany
| | - Jan Tebben
- Section Ecological Chemistry, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570, Bremerhaven, Germany
| | - Jennifer Bergemann
- Marine Chemistry, Department of Chemistry and Biology, University of Bremen, 28359, Bremen, Germany
| | - Rebecca Case
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, 637551, Singapore
| | - Sylke Wohlrab
- Section Ecological Chemistry, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity, 23129, Oldenburg, Germany
| | - Tilmann Harder
- Marine Chemistry, Department of Chemistry and Biology, University of Bremen, 28359, Bremen, Germany.
- Section Ecological Chemistry, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570, Bremerhaven, Germany.
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17
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The Puzzling Conservation and Diversification of Lipid Droplets from Bacteria to Eukaryotes. Results Probl Cell Differ 2020; 69:281-334. [PMID: 33263877 DOI: 10.1007/978-3-030-51849-3_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Membrane compartments are amongst the most fascinating markers of cell evolution from prokaryotes to eukaryotes, some being conserved and the others having emerged via a series of primary and secondary endosymbiosis events. Membrane compartments comprise the system limiting cells (one or two membranes in bacteria, a unique plasma membrane in eukaryotes) and a variety of internal vesicular, subspherical, tubular, or reticulated organelles. In eukaryotes, the internal membranes comprise on the one hand the general endomembrane system, a dynamic network including organelles like the endoplasmic reticulum, the Golgi apparatus, the nuclear envelope, etc. and also the plasma membrane, which are linked via direct lateral connectivity (e.g. between the endoplasmic reticulum and the nuclear outer envelope membrane) or indirectly via vesicular trafficking. On the other hand, semi-autonomous organelles, i.e. mitochondria and chloroplasts, are disconnected from the endomembrane system and request vertical transmission following cell division. Membranes are organized as lipid bilayers in which proteins are embedded. The budding of some of these membranes, leading to the formation of the so-called lipid droplets (LDs) loaded with hydrophobic molecules, most notably triacylglycerol, is conserved in all clades. The evolution of eukaryotes is marked by the acquisition of mitochondria and simple plastids from Gram-positive bacteria by primary endosymbiosis events and the emergence of extremely complex plastids, collectively called secondary plastids, bounded by three to four membranes, following multiple and independent secondary endosymbiosis events. There is currently no consensus view of the evolution of LDs in the Tree of Life. Some features are conserved; others show a striking level of diversification. Here, we summarize the current knowledge on the architecture, dynamics, and multitude of functions of the lipid droplets in prokaryotes and in eukaryotes deriving from primary and secondary endosymbiosis events.
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18
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Benites LF, Poulton N, Labadie K, Sieracki ME, Grimsley N, Piganeau G. Single cell ecogenomics reveals mating types of individual cells and ssDNA viral infections in the smallest photosynthetic eukaryotes. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190089. [PMID: 31587637 DOI: 10.1098/rstb.2019.0089] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Planktonic photosynthetic organisms of the class Mamiellophyceae include the smallest eukaryotes (less than 2 µm), are globally distributed and form the basis of coastal marine ecosystems. Eight complete fully annotated 13-22 Mb genomes from three genera, Ostreococcus, Bathycoccus and Micromonas, are available from previously isolated clonal cultured strains and provide an ideal resource to explore the scope and challenges of analysing single cell amplified genomes (SAGs) isolated from a natural environment. We assembled data from 12 SAGs sampled during the Tara Oceans expedition to gain biological insights about their in situ ecology, which might be lost by isolation and strain culture. Although the assembled nuclear genomes were incomplete, they were large enough to infer the mating types of four Ostreococcus SAGs. The systematic occurrence of sequences from the mitochondria and chloroplast, representing less than 3% of the total cell's DNA, intimates that SAGs provide suitable substrates for detection of non-target sequences, such as those of virions. Analysis of the non-Mamiellophyceae assemblies, following filtering out cross-contaminations during the sequencing process, revealed two novel 1.6 and 1.8 kb circular DNA viruses, and the presence of specific Bacterial and Oomycete sequences suggests that these organisms might co-occur with the Mamiellales. This article is part of a discussion meeting issue 'Single cell ecology'.
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Affiliation(s)
- L Felipe Benites
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, CNRS, Oceanological Observatory of Banyuls, 66650 Banyuls-sur-Mer, France
| | - Nicole Poulton
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544, USA
| | - Karine Labadie
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique, université Paris Saclay, 9105 Evry, France
| | | | - Nigel Grimsley
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, CNRS, Oceanological Observatory of Banyuls, 66650 Banyuls-sur-Mer, France
| | - Gwenael Piganeau
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, CNRS, Oceanological Observatory of Banyuls, 66650 Banyuls-sur-Mer, France
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19
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Host selection and stochastic effects influence bacterial community assembly on the microalgal phycosphere. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101489] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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20
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Li S, Chen M, Chen Y, Tong J, Wang L, Xu Y, Hu Z, Chen H. Epibiotic bacterial community composition in red-tide dinoflagellate Akashiwo sanguinea culture under various growth conditions. FEMS Microbiol Ecol 2019; 95:5481520. [DOI: 10.1093/femsec/fiz057] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 04/25/2019] [Indexed: 12/14/2022] Open
Affiliation(s)
- Shuangfei Li
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Minchun Chen
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Yufei Chen
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Jing Tong
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Liyan Wang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Ying Xu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Zhangli Hu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Huirong Chen
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
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21
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Hampel JJ, McCarthy MJ, Neudeck M, Bullerjahn GS, McKay RML, Newell SE. Ammonium recycling supports toxic Planktothrix blooms in Sandusky Bay, Lake Erie: Evidence from stable isotope and metatranscriptome data. HARMFUL ALGAE 2019; 81:42-52. [PMID: 30638497 DOI: 10.1016/j.hal.2018.11.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 08/10/2018] [Accepted: 11/16/2018] [Indexed: 05/03/2023]
Abstract
Sandusky Bay, Lake Erie, receives high nutrient loadings (nitrogen and phosphorus) from the Sandusky River, which drains an agricultural watershed. Eutrophication and cyanobacterial harmful algal blooms (cyanoHABs) persist throughout summer. Planktothrix agardhii is the dominant bloom-forming species and the main producer of microcystins in Sandusky Bay. Non-N2 fixing cyanobacteria, such as Planktothrix and Microcystis, thrive on chemically reduced forms of nitrogen, such as ammonium (NH4+) and urea. Ammonium regeneration and potential uptake rates and total microbial community demand for NH4+ were quantified in Sandusky Bay. Potential NH4+ uptake rates in the light increased from June to August at all stations. Dark uptake rates also increased seasonally and, by the end of August, were on par with light uptake rates. Regeneration rates followed a similar pattern and were significantly higher in August than June. Ammonium uptake kinetics during a Planktothrix-dominated bloom in Sandusky Bay and a Microcystis-dominated bloom in Maumee Bay were also compared. The highest half saturation constant (Km) in Sandusky Bay was measured in June and decreased throughout the season. In contrast, Km values in Maumee Bay were lowest at the beginning of summer and increased in October. A significant increase in Vmax in Sandusky Bay was observed between July and the end of August, reflective of intense competition for depleted NH4+. Metatranscriptome results from Sandusky Bay show a shift from cyanophycin synthetase (luxury NH4+ uptake; cphA1) expression in early summer to cyanophycinase (intracellular N mobilization; cphB/cphA2) expression in August, supporting the interpretation that the microbial community is nitrogen-starved in late summer. Combined, our results show that, in late summer, when nitrogen concentrations are low, cyanoHABs in Sandusky Bay rely on regenerated NH4+ to support growth and toxin production. Increased dark NH4+ uptake late in summer suggests an important heterotrophic contribution to NH4+ depletion in the phycosphere. Kinetic experiments in the two bays suggest a competitive advantage for Planktothrix over Microcystis in Sandusky Bay due to its higher affinity for NH4+ at low concentrations.
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Affiliation(s)
- Justyna J Hampel
- Department of Earth & Environmental Sciences, Wright State University, Dayton, OH, United States.
| | - Mark J McCarthy
- Department of Earth & Environmental Sciences, Wright State University, Dayton, OH, United States
| | - Michelle Neudeck
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, United States
| | - George S Bullerjahn
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, United States
| | - Robert Michael L McKay
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, United States
| | - Silvia E Newell
- Department of Earth & Environmental Sciences, Wright State University, Dayton, OH, United States
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22
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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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23
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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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24
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Hirth M, Liverani S, Mahlow S, Bouget FY, Pohnert G, Sasso S. Metabolic profiling identifies trehalose as an abundant and diurnally fluctuating metabolite in the microalga Ostreococcus tauri. Metabolomics 2017; 13:68. [PMID: 28473745 PMCID: PMC5392535 DOI: 10.1007/s11306-017-1203-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 03/31/2017] [Indexed: 12/18/2022]
Abstract
INTRODUCTION The picoeukaryotic alga Ostreococcus tauri (Chlorophyta) belongs to the widespread group of marine prasinophytes. Despite its ecological importance, little is known about the metabolism of this alga. OBJECTIVES In this work, changes in the metabolome were quantified when O. tauri was grown under alternating cycles of 12 h light and 12 h darkness. METHODS Algal metabolism was analyzed by gas chromatography-mass spectrometry. Using fluorescence-activated cell sorting, the bacteria associated with O. tauri were depleted to below 0.1% of total cells at the time of metabolic profiling. RESULTS Of 111 metabolites quantified over light-dark cycles, 20 (18%) showed clear diurnal variations. The strongest fluctuations were found for trehalose. With an intracellular concentration of 1.6 mM in the dark, this disaccharide was six times more abundant at night than during the day. This fluctuation pattern of trehalose may be a consequence of starch degradation or of the synchronized cell cycle. On the other hand, maltose (and also sucrose) was below the detection limit (~10 μM). Accumulation of glycine in the light is in agreement with the presence of a classical glycolate pathway of photorespiration. We also provide evidence for the presence of fatty acid methyl and ethyl esters in O. tauri. CONCLUSIONS This study shows how the metabolism of O. tauri adapts to day and night and gives new insights into the configuration of the carbon metabolism. In addition, several less common metabolites were identified.
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Affiliation(s)
- Matthias Hirth
- 0000 0001 1939 2794grid.9613.dInstitute of General Botany and Plant Physiology, Friedrich Schiller University, Jena, Germany
| | - Silvia Liverani
- 0000 0001 0724 6933grid.7728.aDepartment of Mathematics, Brunel University London, Uxbridge, UK
| | - Sebastian Mahlow
- 0000 0001 1939 2794grid.9613.dInstitute of General Botany and Plant Physiology, Friedrich Schiller University, Jena, Germany
| | - François-Yves Bouget
- 0000 0001 2369 4306grid.463752.1Sorbonne Universités, UPMC Univ Paris 06 & Centre National pour la Recherche Scientifique CNRS, UMR 7621, Laboratoire d’Océanographie Microbienne, Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Georg Pohnert
- 0000 0001 1939 2794grid.9613.dInstitute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- 0000 0004 0491 7131grid.418160.aMax Planck Institute for Chemical Ecology, Jena, Germany
| | - Severin Sasso
- 0000 0001 1939 2794grid.9613.dInstitute of General Botany and Plant Physiology, Friedrich Schiller University, Jena, Germany
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