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Nair S, Zhang Z, Li H, Zhao H, Shen H, Kao SJ, Jiao N, Zhang Y. Inherent tendency of Synechococcus and heterotrophic bacteria for mutualism on long-term coexistence despite environmental interference. SCIENCE ADVANCES 2022; 8:eabf4792. [PMID: 36179022 PMCID: PMC9524826 DOI: 10.1126/sciadv.abf4792] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 08/17/2022] [Indexed: 06/12/2023]
Abstract
Mutualism between Synechococcus and heterotrophic bacteria has been found to support their prolonged survival in nutrient-depleted conditions. However, environmental interference on the fate of their mutualism is not understood. Here, we show that exogenous nutrients disrupt their established mutualism. Once the exogenous nutrients were exhausted, Synechococcus and heterotrophic bacteria gradually reestablished their metabolic mutualism during 450 days of culture, which revived unhealthy Synechococcus cells. Using metagenomics, metatranscriptomics, and the 15N tracer method, we reveal that the associated bacterial nitrogen fixation triggered the reestablishment of the mutualism and revival of Synechococcus health. During this process, bacterial community structure and functions underwent tremendous adjustments to achieve the driving effect, and a cogeneration of nitrogen, phosphorus, iron, and vitamin by the heterotrophic bacteria sustained Synechococcus's prolonged healthy growth. Our findings suggest that Synechococcus and heterotrophic bacteria may have an inherent tendency toward mutualism despite environmental interference. This may exhibit their coevolutionary adaptations in nutrient-deficient environments.
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Affiliation(s)
- Shailesh Nair
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zenghu Zhang
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongmei Li
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hanshuang Zhao
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Shen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361101, China
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou 570228, China
| | - Shuh-Ji Kao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361101, China
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou 570228, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361101, China
| | - Yongyu Zhang
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Gibson K, Song H, Chen N. Metabarcoding analysis of microbiome dynamics during a Phaeocystis globosa bloom in the Beibu Gulf, China. HARMFUL ALGAE 2022; 114:102217. [PMID: 35550291 DOI: 10.1016/j.hal.2022.102217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 02/21/2022] [Accepted: 02/26/2022] [Indexed: 06/15/2023]
Abstract
Phaeocystis globosa is an ecologically important haptophyte that can form harmful algal blooms (HABs). In this study, we used 16S rDNA V3-V4 amplicon sequencing data to explore the ecological mechanisms underlying a P. globosa bloom in the Beibu Gulf, China. Using field samples collected from three time points of a bloom, we observed a distinct succession in the bacteria, archaea and phytoplankton community composition throughout the bloom. We also observed temporal variation in response to the bloom at the nucleotide level, which supports a previously underappreciated amount of intragroup variation in the niches taken up by microbes during HABs. We developed a preliminary model for the development and progression of the P. globosa bloom using the spatial-temporal dynamics of P. globosa and the bacteria, archaea, phytoplankton and environmental variables. We also identified microbes with putative interactions with P. globosa during the bloom by identifying microbes correlated with P. globosa in interaction networks, identifying particle-associated microbes and exploring the P. globosa colony microbiome using sequences from whole P. globosa colonies collected during the bloom. This study revealed novel insight into the development of P. globosa HABs and many testable hypotheses that will guide future research on the mechanisms of P. globosa HABs.
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Affiliation(s)
- Kate Gibson
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada
| | - Huiyin Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Nansheng Chen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada; CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
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3
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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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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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5
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Phelps CM, McMahon K, Bissett A, Bernasconi R, Steinberg PD, Thomas T, Marzinelli EM, Huggett MJ. The surface bacterial community of an Australian kelp shows cross-continental variation and relative stability within regions. FEMS Microbiol Ecol 2021; 97:fiab089. [PMID: 34156064 DOI: 10.1093/femsec/fiab089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 06/18/2021] [Indexed: 11/12/2022] Open
Abstract
Epiphytic microbial communities often have a close relationship with their eukaryotic host, assisting with defence, health, disease prevention and nutrient transfer. Shifts in the structure of microbial communities could therefore have negative effects on the individual host and indirectly impact the surrounding ecosystem, particularly for major habitat-forming hosts, such as kelps in temperate rocky shores. Thus, an understanding of the structure and dynamics of host-associated microbial communities is essential for monitoring and assessing ecosystem changes. Here, samples were taken from the ecologically important kelp, Ecklonia radiata, over a 17-month period, from six different sites in two distinct geographic regions (East and West coasts of Australia), separated by ∼3,300 kms, to understand variation in the kelp bacterial community and its potential environmental drivers. Differences were observed between kelp bacterial communities between the largely disconnected geographical regions. In contrast, within each region and over time the bacterial communities were considerably more stable, despite substantial seasonal changes in environmental conditions.
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Affiliation(s)
- Charlie M Phelps
- Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, 270 Joondalup Drive, Joondalup, WA, 6027, Australia
| | - Kathryn McMahon
- Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, 270 Joondalup Drive, Joondalup, WA, 6027, Australia
| | - Andrew Bissett
- CSIRO Oceans and Atmosphere, Castray Esp, Battery Point, Tas, 7004, Australia
| | - Rachele Bernasconi
- Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, 270 Joondalup Drive, Joondalup, WA, 6027, Australia
| | - Peter D Steinberg
- Sydney Institute of Marine Science, 19 Chowder Bay Rd, Mosman, NSW, 2088, Australia
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, High St, Kensington, NSW, 2052, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Dr, Singapore 637551
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, High St, Kensington, NSW, 2052, Australia
| | - Ezequiel M Marzinelli
- Sydney Institute of Marine Science, 19 Chowder Bay Rd, Mosman, NSW, 2088, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Dr, Singapore 637551
- The University of Sydney, School of Life and Environmental Sciences, Coastal and Marine Ecosystems, City Rd, Camperdown, NSW, 2006, Australia
| | - Megan J Huggett
- Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, 270 Joondalup Drive, Joondalup, WA, 6027, Australia
- School of Environmental and Life Sciences, University of Newcastle, 10 Chittaway Rd, Ourimbah, NSW, 2258, Australia
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6
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Kuhlisch C, Althammer J, Sazhin AF, Jakobsen HH, Nejstgaard JC, Pohnert G. Metabolomics-derived marker metabolites to characterize Phaeocystis pouchetii physiology in natural plankton communities. Sci Rep 2020; 10:20444. [PMID: 33235278 PMCID: PMC7686483 DOI: 10.1038/s41598-020-77169-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 10/28/2020] [Indexed: 01/07/2023] Open
Abstract
Phaeocystis pouchetii (Hariot) Lagerheim, 1893 regularly dominates phytoplankton blooms in higher latitudes spanning from the English Channel to the Arctic. Through zooplankton grazing and microbial activity, it is considered to be a key resource for the entire marine food web, but the actual relevance of biomass transfer to higher trophic levels is still under discussion. Cell physiology and algal nutritional state are suggested to be major factors controlling the observed variability in zooplankton grazing. However, no data have so far yielded insights into the metabolic state of Phaeocystis populations that would allow testing this hypothesis. Therefore, endometabolic markers of different growth phases were determined in laboratory batch cultures using comparative metabolomics and quantified in different phytoplankton blooms in the field. Metabolites, produced during exponential, early and late stationary growth of P. pouchetii, were profiled using gas chromatography-mass spectrometry. Then, metabolites were characterized that correlate with the growth phases using multivariate statistical analysis. Free amino acids characterized the exponential growth, whereas the early stationary phase was correlated with sugar alcohols, mono- and disaccharides. In the late stationary phase, free fatty acids, sterols and terpenes increased. These marker metabolites were then traced in Phaeocystis blooms during a cruise in the Barents Sea and North Norwegian fjords. About 50 endometabolites of P. pouchetii were detected in natural phytoplankton communities. Mannitol, scyllo-inositol, 24-methylcholesta-5,22-dien-3β-ol, and several free fatty acids were characteristic for Phaeocystis-dominated blooms but showed variability between them. Distinct metabolic profiles were detected in the nutrient-depleted community in the inner Porsangerfjord (< 0.5 µM NO3-, < 0.1 µM PO 4 3- ), with high relative amounts of free mono- and disaccharides indicative for a limited culture. This study thereby shows how the variable physiology of phytoplankton can alter the metabolic landscape of entire plankton communities.
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Affiliation(s)
- Constanze Kuhlisch
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstraße 8, 07743, Jena, Germany.,Department of Plant and Environmental Sciences, Weizmann Institute of Science, 234 Herzl Street, 7610001, Rehovot, Israel
| | - Julia Althammer
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstraße 8, 07743, Jena, Germany.,JenaBios GmbH, Löbstedter Straße 80, 07749, Jena, Germany
| | - Andrey F Sazhin
- Shirshov Institute of Oceanology, Russian Academy of Sciences, Nakhimovsky Prospect 36, Moscow, Russia
| | - Hans H Jakobsen
- Department of Bioscience, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Jens C Nejstgaard
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Dep. 3, Alte Fischerhütte 2, 16775, Stechlin, Germany
| | - Georg Pohnert
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstraße 8, 07743, Jena, Germany.
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7
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Derilus D, Rahman MZ, Pinero F, Massey SE. Synergism between the Black Queen effect and the proteomic constraint on genome size reduction in the photosynthetic picoeukaryotes. Sci Rep 2020; 10:8918. [PMID: 32488045 PMCID: PMC7265537 DOI: 10.1038/s41598-020-65476-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 05/05/2020] [Indexed: 01/01/2023] Open
Abstract
The photosynthetic picoeukaryotes (PPEs) comprise a rare example of free-living eukaryotes that have undergone genome reduction. Here, we examine a duality in the process; the proposed driver of genome reduction (the Black Queen hypothesis, BQH), and the resultant impact of genome information loss (the Proteomic Constraint hypothesis, PCH). The BQH predicts that some metabolites may be shared in the open ocean, thus driving loss of redundant metabolic pathways in individual genomes. In contrast, the PCH predicts that as the information content of a genome is reduced, the total mutation load is also reduced, leading to loss of DNA repair genes due to the resulting reduction in selective constraint. Consistent with the BQH, we observe that biosynthetic pathways involved with soluble metabolites such as amino acids and carotenoids are preferentially lost from the PPEs, in contrast to biosynthetic pathways involved with insoluble metabolites, such as lipids, which are retained. Consistent with the PCH, a correlation between proteome size and the number of DNA repair genes, and numerous other informational categories, is observed. While elevated mutation rates resulting from the loss of DNA repair genes have been linked to reduced effective population sizes in intracellular bacteria, this remains to be established. This study shows that in microbial species with large population sizes, an underlying factor in modulating their DNA repair capacity appears to be information content.
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Affiliation(s)
- D Derilus
- Environmental Sciences Department, University of Puerto Rico - Rio Piedras, San Juan, Puerto Rico
| | - M Z Rahman
- Biology Department, University of Puerto Rico - Rio Piedras, San Juan, Puerto Rico
| | - F Pinero
- Mathematics Department, University of Puerto Rico - Ponce, Ponce, Puerto Rico
| | - S E Massey
- Biology Department, University of Puerto Rico - Rio Piedras, San Juan, Puerto Rico.
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8
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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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9
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Marcellin-Gros R, Piganeau G, Stien D. Metabolomic Insights into Marine Phytoplankton Diversity. Mar Drugs 2020; 18:E78. [PMID: 31991720 PMCID: PMC7074452 DOI: 10.3390/md18020078] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 01/10/2020] [Accepted: 01/22/2020] [Indexed: 02/08/2023] Open
Abstract
The democratization of sequencing technologies fostered a leap in our knowledge of the diversity of marine phytoplanktonic microalgae, revealing many previously unknown species and lineages. The evolutionary history of the diversification of microalgae can be inferred from the analysis of their genome sequences. However, the link between the DNA sequence and the associated phenotype is notoriously difficult to assess, all the more so for marine phytoplanktonic microalgae for which the lab culture and, thus, biological experimentation is very tedious. Here, we explore the potential of a high-throughput untargeted metabolomic approach to explore the phenotypic-genotypic gap in 12 marine microalgae encompassing 1.2 billion years of evolution. We identified species- and lineage-specific metabolites. We also provide evidence of a very good correlation between the molecular divergence, inferred from the DNA sequences, and the metabolomic divergence, inferred from the complete metabolomic profiles. These results provide novel insights into the potential of chemotaxonomy in marine phytoplankton and support the hypothesis of a metabolomic clock, suggesting that DNA and metabolomic profiles co-evolve.
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Affiliation(s)
- Rémy Marcellin-Gros
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologie Microbiennes, LBBM, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France;
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Gwenaël Piganeau
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Didier Stien
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologie Microbiennes, LBBM, Observatoire Océanologique, 66650 Banyuls-sur-Mer, France;
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10
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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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11
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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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12
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Contributions of the microbial community to algal biomass and biofuel productivity in a wastewater treatment lagoon system. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101461] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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13
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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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14
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Richter LV, Mansfeldt CB, Kuan MM, Cesare AE, Menefee ST, Richardson RE, Ahner BA. Altered Microbiome Leads to Significant Phenotypic and Transcriptomic Differences in a Lipid Accumulating Chlorophyte. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:6854-6863. [PMID: 29750518 DOI: 10.1021/acs.est.7b06581] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Given the challenges facing the economically favorable production of products from microalgae, understanding factors that might impact productivity rates including growth rates and accumulation of desired products, for example, triacylglycerols (TAG) for biodiesel feedstock, remains critical. Although operational parameters such as media composition and reactor design can clearly effect growth rates, the role of microbe-microbe interactions is just beginning to be elucidated. In this study an oleaginous marine algae Chlorella spp. C596 culture is shown to be better described as a microbial community. Perturbations to this microbial community showed a significant impact on phenotypes including sustained differences in growth rate and TAG accumulation of 2.4 and 2.5 fold, respectively. Characterization of the associated community using Illumina 16S rRNA amplicon and random shotgun transcriptomic analyses showed that the fast growth rate correlated with two specific bacterial species ( Ruegeria and Rhodobacter spp). The transcriptomic response of the Chlorella species revealed that the slower growing algal consortium C596-S1 upregulated genes associated with photosynthesis and resource scavenging and decreased the expression of genes associated with transcription and translation relative to the initial C596-R1. Our studies advance the appreciation of the effects microbiomes can have on algal growth in bioreactors and suggest that symbiotic interactions are involved in a range of critical processes including nitrogen, carbon cycling, and oxidative stress.
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Affiliation(s)
- Lubna V Richter
- Department of Biological and Environmental Engineering , Cornell University , Ithaca , New York 14853 , United States
| | - Cresten B Mansfeldt
- School of Civil and Environmental Engineering , Cornell University , Ithaca , New York 14853 , United States
| | - Michael M Kuan
- Department of Biological and Environmental Engineering , Cornell University , Ithaca , New York 14853 , United States
| | - Alexandra E Cesare
- Department of Biological and Environmental Engineering , Cornell University , Ithaca , New York 14853 , United States
| | - Stephen T Menefee
- Department of Biological and Environmental Engineering , Cornell University , Ithaca , New York 14853 , United States
| | - Ruth E Richardson
- School of Civil and Environmental Engineering , Cornell University , Ithaca , New York 14853 , United States
| | - Beth A Ahner
- Department of Biological and Environmental Engineering , Cornell University , Ithaca , New York 14853 , United States
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15
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Behringer G, Ochsenkühn MA, Fei C, Fanning J, Koester JA, Amin SA. Bacterial Communities of Diatoms Display Strong Conservation Across Strains and Time. Front Microbiol 2018; 9:659. [PMID: 29681892 PMCID: PMC5897529 DOI: 10.3389/fmicb.2018.00659] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 03/21/2018] [Indexed: 11/13/2022] Open
Abstract
Interactions between phytoplankton and bacteria play important roles in shaping the microenvironment surrounding these organisms and in turn influence global biogeochemical cycles. This microenvironment, known as the phycosphere, is presumed to shape the bacterial diversity around phytoplankton and thus stimulate a diverse array of interactions between both groups. Although many studies have attempted to characterize bacterial communities that associate and interact with phytoplankton, bias in bacterial cultivation and consistency and persistence of bacterial communities across phytoplankton isolates likely impede the understanding of these microbial associations. Here, we isolate four strains of the diatom Asterionellopsis glacialis and three strains of the diatom Nitzschia longissima and show through metabarcoding of the bacterial 16S rDNA gene that though each species possesses a unique bacterial community, the bacterial composition across strains from the same species are highly conserved at the genus level. Cultivation of all seven strains in the laboratory for longer than 1 year resulted in only small changes to the bacterial composition, suggesting that despite strong pressures from laboratory culturing conditions associations between these diatoms and their bacterial communities are robust. Specific operational taxonomic units (OTUs) belonging to the Roseobacter-clade appear to be conserved across all strains and time, suggesting their importance to diatoms. In addition, we isolate a range of cultivable bacteria from one of these cultures, A. glacialis strain A3, including several strains of Shimia marina and Nautella sp. that appear closely related to OTUs conserved across all strains and times. Coculturing of A3 with some of its cultivable bacteria as well as other diatom-associated bacteria shows a wide range of responses that include enhancing diatom growth. Cumulatively, these findings suggest that phytoplankton possess unique microbiomes that are consistent across strains and temporal scales.
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Affiliation(s)
- Gregory Behringer
- Marine Microbial Ecology Lab, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Michael A. Ochsenkühn
- Marine Microbial Ecology Lab, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Cong Fei
- Marine Microbial Ecology Lab, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- College of Resources and Environmental Science, Nanjing Agriculture University, Nanjing, China
| | - Jhamal Fanning
- Marine Microbial Ecology Lab, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Julie A. Koester
- Department of Biology and Marine Biology, University of North Carolina at Wilmington, Wilmington, NC, United States
| | - Shady A. Amin
- Marine Microbial Ecology Lab, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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16
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Serive B, Nicolau E, Bérard JB, Kaas R, Pasquet V, Picot L, Cadoret JP. Community analysis of pigment patterns from 37 microalgae strains reveals new carotenoids and porphyrins characteristic of distinct strains and taxonomic groups. PLoS One 2017; 12:e0171872. [PMID: 28231253 PMCID: PMC5322898 DOI: 10.1371/journal.pone.0171872] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 01/26/2017] [Indexed: 11/26/2022] Open
Abstract
Phytoplankton, with an estimated 30 000 to 1 000 000 species clustered in 12 phyla, presents a high taxonomic and ecophysiological diversity, reflected by the complex distribution of pigments among the different algal classes. High performance liquid chromatography is the gold standard method for qualitative and quantitative analysis of phytoplankton pigments in seawater and culture samples, but only a few pigments can be used as robust chemotaxonomic markers. A major challenge is thus to identify new ones, characteristic of a strain, species, class or taxon that cannot be currently identified on the basis of its pigment signature. Using an optimized extraction process coupled to a HPLC de-replication strategy, we examined the pigment composition of 37 microalgae strains, representative of the broad taxonomic diversity of marine and freshwater species (excluding cyanobacteria). For each species, the major pigments already described were unambiguously identified. We also observed the presence of several minor unidentified pigments in each chromatogram. The global analysis of pigment compositions revealed a total of 124 pigments, including 98 pigments or derivatives unidentified using the standards. Absorption spectra indicated that 35 corresponded to chlorophyll/porphyrin derivatives, 57 to carotenoids and six to derivatives having both spectral signatures. Sixty-one of these unidentified or new carotenoids and porphyrin derivatives were characteristic of particular strains or species, indicating their possible use as highly specific chemotaxonomic markers capable of identifying one strain out of the 37 selected. We developed a graphical analysis using Gephi software to give a clear representation of pigment communities among the various phytoplankton strains, and to reveal strain-characteristic and shared pigments. This made it possible to reconstruct the taxonomic evolution of microalgae classes, on the basis of the conservation, loss, and/or appearance of pigments.
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Affiliation(s)
- Benoît Serive
- Laboratoire de Physiologie et Biotechnologie des Algues, IFREMER, BP, Nantes, France
- * E-mail: (BS); (EN)
| | - Elodie Nicolau
- Laboratoire de Physiologie et Biotechnologie des Algues, IFREMER, BP, Nantes, France
- * E-mail: (BS); (EN)
| | - Jean-Baptiste Bérard
- Laboratoire de Physiologie et Biotechnologie des Algues, IFREMER, BP, Nantes, France
| | - Raymond Kaas
- Laboratoire de Physiologie et Biotechnologie des Algues, IFREMER, BP, Nantes, France
| | - Virginie Pasquet
- UMRi CNRS 7266 LIENSs, Université de la Rochelle, La Rochelle, France
| | - Laurent Picot
- UMRi CNRS 7266 LIENSs, Université de la Rochelle, La Rochelle, France
| | - Jean-Paul Cadoret
- Laboratoire de Physiologie et Biotechnologie des Algues, IFREMER, BP, Nantes, France
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17
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Nazir R, Mazurier S, Yang P, Lemanceau P, van Elsas JD. The Ecological Role of Type Three Secretion Systems in the Interaction of Bacteria with Fungi in Soil and Related Habitats Is Diverse and Context-Dependent. Front Microbiol 2017; 8:38. [PMID: 28197129 PMCID: PMC5282467 DOI: 10.3389/fmicb.2017.00038] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/06/2017] [Indexed: 12/14/2022] Open
Abstract
Bacteria and fungi constitute important organisms in many ecosystems, in particular terrestrial ones. Both organismal groups contribute significantly to biogeochemical cycling processes. Ecological theory postulates that bacteria capable of receiving benefits from host fungi are likely to evolve efficient association strategies. The purpose of this review is to examine the mechanisms that underpin the bacterial interactions with fungi in soil and other systems, with special focus on the type III secretion system (T3SS). Starting with a brief description of the versatility of the T3SS as an interaction system with diverse eukaryotic hosts, we subsequently examine the recent advances made in our understanding of its contribution to interactions with soil fungi. The analysis used data sets ranging from circumstantial evidence to gene-knockout-based experimental data. The initial finding that the abundance of T3SSs in microbiomes is often enhanced in fungal-affected habitats like the mycosphere and the mycorrhizosphere is now substantiated with in-depth knowledge of the specific systems involved. Different fungal–interactive bacteria, in positive or negative associations with partner fungi, harbor and express T3SSs, with different ecological outcomes. In some particular cases, bacterial T3SSs have been shown to modulate the physiology of its fungal partner, affecting its ecological characteristics and consequently shaping its own habitat. Overall, the analyses of the collective data set revealed that diverse T3SSs have assumed diverse roles in the interactions of bacteria with host fungi, as driven by ecological and evolutionary niche requirements.
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Affiliation(s)
- Rashid Nazir
- Department of Environmental Sciences, COMSATS Institute of Information TechnologyAbbottabad, Pakistan; Department of Soil Environmental Science, Research Centre for Eco-environmental Sciences - Chinese Academy of SciencesBeijing, China
| | - Sylvie Mazurier
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté Dijon, France
| | - Pu Yang
- Department of Microbial Ecology, GELIFES, University of Groningen Groningen, Netherlands
| | - Philippe Lemanceau
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté Dijon, France
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, GELIFES, University of Groningen Groningen, Netherlands
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18
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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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19
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Lupette J, Lami R, Krasovec M, Grimsley N, Moreau H, Piganeau G, Sanchez-Ferandin S. Marinobacter Dominates the Bacterial Community of the Ostreococcus tauri Phycosphere in Culture. Front Microbiol 2016; 7:1414. [PMID: 27656176 PMCID: PMC5013054 DOI: 10.3389/fmicb.2016.01414] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 08/26/2016] [Indexed: 11/13/2022] Open
Abstract
Microalgal–bacterial interactions are commonly found in marine environments and are well known in diatom cultures maintained in laboratory. These interactions also exert strong effects on bacterial and algal diversity in the oceans. Small green eukaryote algae of the class Mamiellophyceae (Chlorophyta) are ubiquitous and some species, such as Ostreococcus spp., are particularly important in Mediterranean coastal lagoons, and are observed as dominant species during phytoplankton blooms in open sea. Despite this, little is known about the diversity of bacteria that might facilitate or hinder O. tauri growth. We show, using rDNA 16S sequences, that the bacterial community found in O. tauri RCC4221 laboratory cultures is dominated by γ-proteobacteria from the Marinobacter genus, regardless of the growth phase of O. tauri RCC4221, the photoperiod used, or the nutrient conditions (limited in nitrogen or phosphorous) tested. Several strains of Marinobacter algicola were detected, all closely related to strains found in association with taxonomically distinct organisms, particularly with dinoflagellates and coccolithophorids. These sequences were more distantly related to M. adhaerens, M. aquaeoli and bacteria usually associated to euglenoids. This is the first time, to our knowledge, that distinct Marinobacter strains have been found to be associated with a green alga in culture.
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Affiliation(s)
- Josselin Lupette
- Sorbonne Universités, Université Pierre et Marie Curie Paris 06, UMR 7232 Biologie Intégrative des Organismes Marins, Observatoire OcéanologiqueBanyuls-sur-Mer, France; Centre National de la Recherche Scientifique, UMR 7232 Biologie Intégrative des Organismes Marins, Observatoire OcéanologiqueBanyuls-sur-Mer, France; CEA/CNRS/INRA/Université Grenoble Alpes, UMR 5168 Laboratoire Physiologie Cellulaire VégétaleGrenoble, France
| | - Raphaël Lami
- Sorbonne Universités, Université Pierre et Marie Curie Paris 06, USR 3579 Laboratoire de Biodiversité et Biotechnologies Microbiennes, Observatoire OcéanologiqueBanyuls-sur-Mer, France; Centre National de la Recherche Scientifique, USR 3579 Laboratoire de Biodiversité et Biotechnologies Microbiennes, Observatoire OcéanologiqueBanyuls-sur-Mer, France
| | - Marc Krasovec
- Sorbonne Universités, Université Pierre et Marie Curie Paris 06, UMR 7232 Biologie Intégrative des Organismes Marins, Observatoire OcéanologiqueBanyuls-sur-Mer, France; Centre National de la Recherche Scientifique, UMR 7232 Biologie Intégrative des Organismes Marins, Observatoire OcéanologiqueBanyuls-sur-Mer, France
| | - Nigel Grimsley
- Sorbonne Universités, Université Pierre et Marie Curie Paris 06, UMR 7232 Biologie Intégrative des Organismes Marins, Observatoire OcéanologiqueBanyuls-sur-Mer, France; Centre National de la Recherche Scientifique, UMR 7232 Biologie Intégrative des Organismes Marins, Observatoire OcéanologiqueBanyuls-sur-Mer, France
| | - Hervé Moreau
- Sorbonne Universités, Université Pierre et Marie Curie Paris 06, UMR 7232 Biologie Intégrative des Organismes Marins, Observatoire OcéanologiqueBanyuls-sur-Mer, France; Centre National de la Recherche Scientifique, UMR 7232 Biologie Intégrative des Organismes Marins, Observatoire OcéanologiqueBanyuls-sur-Mer, France
| | - Gwenaël Piganeau
- Sorbonne Universités, Université Pierre et Marie Curie Paris 06, UMR 7232 Biologie Intégrative des Organismes Marins, Observatoire OcéanologiqueBanyuls-sur-Mer, France; Centre National de la Recherche Scientifique, UMR 7232 Biologie Intégrative des Organismes Marins, Observatoire OcéanologiqueBanyuls-sur-Mer, France
| | - Sophie Sanchez-Ferandin
- Sorbonne Universités, Université Pierre et Marie Curie Paris 06, UMR 7232 Biologie Intégrative des Organismes Marins, Observatoire OcéanologiqueBanyuls-sur-Mer, France; Centre National de la Recherche Scientifique, UMR 7232 Biologie Intégrative des Organismes Marins, Observatoire OcéanologiqueBanyuls-sur-Mer, France
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20
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Egan S, Gardiner M. Microbial Dysbiosis: Rethinking Disease in Marine Ecosystems. Front Microbiol 2016; 7:991. [PMID: 27446031 PMCID: PMC4914501 DOI: 10.3389/fmicb.2016.00991] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 06/09/2016] [Indexed: 11/16/2022] Open
Abstract
With growing environmental pressures placed on our marine habitats there is concern that the prevalence and severity of diseases affecting marine organisms will increase. Yet relative to terrestrial systems, we know little about the underlying causes of many of these diseases. Moreover, factors such as saprophytic colonizers and a lack of baseline data on healthy individuals make it difficult to accurately assess the role of specific microbial pathogens in disease states. Emerging evidence in the field of medicine suggests that a growing number of human diseases result from a microbiome imbalance (or dysbiosis), questioning the traditional view of a singular pathogenic agent. Here we discuss the possibility that many diseases seen in marine systems are, similarly, the result of microbial dysbiosis and the rise of opportunistic or polymicrobial infections. Thus, understanding and managing disease in the future will require us to also rethink definitions of disease and pathogenesis for marine systems. We suggest that a targeted, multidisciplinary approach that addresses the questions of microbial symbiosis in both healthy and diseased states, and at that the level of the holobiont, will be key to progress in this area.
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Affiliation(s)
- Suhelen Egan
- Centre for Marine Bio-Innovation, School of Biological, Earth and Environmental Sciences, The University of New South Wales, SydneyNSW, Australia
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21
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Farnelid HM, Turk-Kubo KA, Zehr JP. Identification of Associations between Bacterioplankton and Photosynthetic Picoeukaryotes in Coastal Waters. Front Microbiol 2016; 7:339. [PMID: 27148165 PMCID: PMC4834442 DOI: 10.3389/fmicb.2016.00339] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 03/03/2016] [Indexed: 01/10/2023] Open
Abstract
Photosynthetic picoeukaryotes are significant contributors to marine primary productivity. Associations between marine bacterioplankton and picoeukaryotes frequently occur and can have large biogeochemical impacts. We used flow cytometry to sort cells from seawater to identify non-eukaryotic phylotypes that are associated with photosynthetic picoeukaryotes. Samples were collected at the Santa Cruz wharf on Monterey Bay, CA, USA during summer and fall, 2014. The phylogeny of associated microbes was assessed through 16S rRNA gene amplicon clone and Illumina MiSeq libraries. The most frequently detected bacterioplankton phyla within the photosynthetic picoeukaryote sorts were Proteobacteria (Alphaproteobacteria and Gammaproteobacteria) and Bacteroidetes. Intriguingly, the presence of free-living bacterial genera in the photosynthetic picoeukaryote sorts could suggest that some of the photosynthetic picoeukaryotes were mixotrophs. However, the occurrence of bacterial sequences, which were not prevalent in the corresponding bulk seawater samples, indicates that there was also a selection for specific OTUs in association with photosynthetic picoeukaryotes suggesting specific functional associations. The results show that diverse bacterial phylotypes are found in association with photosynthetic picoeukaryotes. Taxonomic identification of these associations is a prerequisite for further characterizing and to elucidate their metabolic pathways and ecological functions.
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Affiliation(s)
- Hanna M Farnelid
- Ocean Sciences Department, University of California at Santa CruzSanta Cruz, CA, USA; Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus UniversityKalmar, Sweden
| | - Kendra A Turk-Kubo
- Ocean Sciences Department, University of California at Santa Cruz Santa Cruz, CA, USA
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California at Santa Cruz Santa Cruz, CA, USA
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Cooper MB, Smith AG. Exploring mutualistic interactions between microalgae and bacteria in the omics age. CURRENT OPINION IN PLANT BIOLOGY 2015; 26:147-53. [PMID: 26318329 DOI: 10.1016/j.pbi.2015.07.003] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 07/05/2015] [Accepted: 07/13/2015] [Indexed: 05/27/2023]
Abstract
Microalgae undertake a wide range of mutualistic interactions with bacteria. Here we consider how transcriptomic, metagenomic and metabolomic approaches have been combined with microbiological and biochemical analyses to expand our understanding of algal-bacterial interactions. Identification of the major bacterial species associated with algae indicates that specific bacterial groups, particularly the alpha-Proteobacteria, are found more frequently, suggesting that these may have the means to initiate and maintain symbiotic relationships. Nutrient exchange is frequently the basis of algal-bacterial mutualism, and as the compounds involved are characterised, evidence is accumulating that these are complex and specific molecules, offering opportunities for signalling processes and regulation rather than merely passive diffusion. At the same time, it is clear that the interactions are not static, but can be initiated and broken in response to environmental and developmental cues.
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Affiliation(s)
- Matthew B Cooper
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Alison G Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK.
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Blanc-Mathieu R, Verhelst B, Derelle E, Rombauts S, Bouget FY, Carré I, Château A, Eyre-Walker A, Grimsley N, Moreau H, Piégu B, Rivals E, Schackwitz W, Van de Peer Y, Piganeau G. An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies. BMC Genomics 2014; 15:1103. [PMID: 25494611 PMCID: PMC4378021 DOI: 10.1186/1471-2164-15-1103] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 11/19/2014] [Indexed: 12/17/2022] Open
Abstract
Background Cost effective next generation sequencing technologies now enable the production of genomic datasets for many novel planktonic eukaryotes, representing an understudied reservoir of genetic diversity. O. tauri is the smallest free-living photosynthetic eukaryote known to date, a coccoid green alga that was first isolated in 1995 in a lagoon by the Mediterranean sea. Its simple features, ease of culture and the sequencing of its 13 Mb haploid nuclear genome have promoted this microalga as a new model organism for cell biology. Here, we investigated the quality of genome assemblies of Illumina GAIIx 75 bp paired-end reads from Ostreococcus tauri, thereby also improving the existing assembly and showing the genome to be stably maintained in culture. Results The 3 assemblers used, ABySS, CLCBio and Velvet, produced 95% complete genomes in 1402 to 2080 scaffolds with a very low rate of misassembly. Reciprocally, these assemblies improved the original genome assembly by filling in 930 gaps. Combined with additional analysis of raw reads and PCR sequencing effort, 1194 gaps have been solved in total adding up to 460 kb of sequence. Mapping of RNAseq Illumina data on this updated genome led to a twofold reduction in the proportion of multi-exon protein coding genes, representing 19% of the total 7699 protein coding genes. The comparison of the DNA extracted in 2001 and 2009 revealed the fixation of 8 single nucleotide substitutions and 2 deletions during the approximately 6000 generations in the lab. The deletions either knocked out or truncated two predicted transmembrane proteins, including a glutamate-receptor like gene. Conclusion High coverage (>80 fold) paired-end Illumina sequencing enables a high quality 95% complete genome assembly of a compact ~13 Mb haploid eukaryote. This genome sequence has remained stable for 6000 generations of lab culture. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1103) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Gwenaël Piganeau
- CNRS, UMR 7232, Observatoire Océanologique, Avenue du Fontaulé, BP44, 66650 Banyuls-sur-Mer, France.
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