101
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Mirdita M, Steinegger M, Breitwieser F, Söding J, Levy Karin E. Fast and sensitive taxonomic assignment to metagenomic contigs. Bioinformatics 2021; 37:3029-3031. [PMID: 33734313 PMCID: PMC8479651 DOI: 10.1093/bioinformatics/btab184] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/26/2021] [Accepted: 03/16/2021] [Indexed: 02/02/2023] Open
Abstract
SUMMARY MMseqs2 taxonomy is a new tool to assign taxonomic labels to metagenomic contigs. It extracts all possible protein fragments from each contig, quickly retains those that can contribute to taxonomic annotation, assigns them with robust labels and determines the contig's taxonomic identity by weighted voting. Its fragment extraction step is suitable for the analysis of all domains of life. MMseqs2 taxonomy is 2-18× faster than state-of-the-art tools and also contains new modules for creating and manipulating taxonomic reference databases as well as reporting and visualizing taxonomic assignments. AVAILABILITY AND IMPLEMENTATION MMseqs2 taxonomy is part of the MMseqs2 free open-source software package available for Linux, macOS and Windows at https://mmseqs.com. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- M Mirdita
- Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - M Steinegger
- School of Biological Sciences, Seoul National University, Seoul, South Korea,Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea,Artificial Intelligence Institute, Seoul National University, Seoul, South Korea
| | - F Breitwieser
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - J Söding
- Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany,Campus-Institut Data Science (CIDAS), Göttingen, Germany,To whom correspondence should be addressed. or
| | - E Levy Karin
- Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany,To whom correspondence should be addressed. or
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102
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Gao X, Bowler C, Kazamia E. Iron metabolism strategies in diatoms. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2165-2180. [PMID: 33693565 PMCID: PMC7966952 DOI: 10.1093/jxb/eraa575] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 03/03/2021] [Indexed: 05/28/2023]
Abstract
Diatoms are one of the most successful group of photosynthetic eukaryotes in the contemporary ocean. They are ubiquitously distributed and are the most abundant primary producers in polar waters. Equally remarkable is their ability to tolerate iron deprivation and respond to periodic iron fertilization. Despite their relatively large cell sizes, diatoms tolerate iron limitation and frequently dominate iron-stimulated phytoplankton blooms, both natural and artificial. Here, we review the main iron use strategies of diatoms, including their ability to assimilate and store a range of iron sources, and the adaptations of their photosynthetic machinery and architecture to iron deprivation. Our synthesis relies on published literature and is complemented by a search of 82 diatom transcriptomes, including information collected from seven representatives of the most abundant diatom genera in the world's oceans.
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Affiliation(s)
- Xia Gao
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Chris Bowler
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Elena Kazamia
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
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103
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Girgis HZ, James BT, Luczak BB. Identity: rapid alignment-free prediction of sequence alignment identity scores using self-supervised general linear models. NAR Genom Bioinform 2021; 3:lqab001. [PMID: 33554117 PMCID: PMC7850047 DOI: 10.1093/nargab/lqab001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 12/07/2020] [Accepted: 01/08/2021] [Indexed: 11/12/2022] Open
Abstract
Pairwise global alignment is a fundamental step in sequence analysis. Optimal alignment algorithms are quadratic-slow especially on long sequences. In many applications that involve large sequence datasets, all what is needed is calculating the identity scores (percentage of identical nucleotides in an optimal alignment-including gaps-of two sequences); there is no need for visualizing how every two sequences are aligned. For these applications, we propose Identity, which produces global identity scores for a large number of pairs of DNA sequences using alignment-free methods and self-supervised general linear models. For the first time, the new tool can predict pairwise identity scores in linear time and space. On two large-scale sequence databases, Identity provided the best compromise between sensitivity and precision while being faster than BLAST, Mash, MUMmer4 and USEARCH by 2-80 times. Identity was the best performing tool when searching for low-identity matches. While constructing phylogenetic trees from about 6000 transcripts, the tree due to the scores reported by Identity was the closest to the reference tree (in contrast to andi, FSWM and Mash). Identity is capable of producing pairwise identity scores of millions-of-nucleotides-long bacterial genomes; this task cannot be accomplished by any global-alignment-based tool. Availability: https://github.com/BioinformaticsToolsmith/Identity.
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Affiliation(s)
- Hani Z Girgis
- Bioinformatics Toolsmith Laboratory, Department of Electrical Engineering and Computer Science, Texas A&M University-Kingsville, 700 University Boulevard, Kingsville, TX 78363, USA
| | - Benjamin T James
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA
| | - Brian B Luczak
- Department of Mathematics, Vanderbilt University, 1326 Stevenson Center Lane, Nashville, TN 3721, USA
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104
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Turnšek J, Brunson JK, Viedma MDPM, Deerinck TJ, Horák A, Oborník M, Bielinski VA, Allen AE. Proximity proteomics in a marine diatom reveals a putative cell surface-to-chloroplast iron trafficking pathway. eLife 2021; 10:e52770. [PMID: 33591270 PMCID: PMC7972479 DOI: 10.7554/elife.52770] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 02/15/2021] [Indexed: 12/16/2022] Open
Abstract
Iron is a biochemically critical metal cofactor in enzymes involved in photosynthesis, cellular respiration, nitrate assimilation, nitrogen fixation, and reactive oxygen species defense. Marine microeukaryotes have evolved a phytotransferrin-based iron uptake system to cope with iron scarcity, a major factor limiting primary productivity in the global ocean. Diatom phytotransferrin is endocytosed; however, proteins downstream of this environmentally ubiquitous iron receptor are unknown. We applied engineered ascorbate peroxidase APEX2-based subcellular proteomics to catalog proximal proteins of phytotransferrin in the model marine diatom Phaeodactylum tricornutum. Proteins encoded by poorly characterized iron-sensitive genes were identified including three that are expressed from a chromosomal gene cluster. Two of them showed unambiguous colocalization with phytotransferrin adjacent to the chloroplast. Further phylogenetic, domain, and biochemical analyses suggest their involvement in intracellular iron processing. Proximity proteomics holds enormous potential to glean new insights into iron acquisition pathways and beyond in these evolutionarily, ecologically, and biotechnologically important microalgae.
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Affiliation(s)
- Jernej Turnšek
- Biological and Biomedical Sciences, The Graduate School of Arts and Sciences, Harvard UniversityCambridgeUnited States
- Department of Systems Biology, Harvard Medical SchoolBostonUnited States
- Wyss Institute for Biologically Inspired Engineering, Harvard UniversityBostonUnited States
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San DiegoLa JollaUnited States
- Center for Research in Biological Systems, University of California San DiegoLa JollaUnited States
- Microbial and Environmental Genomics, J. Craig Venter InstituteLa JollaUnited States
| | - John K Brunson
- Microbial and Environmental Genomics, J. Craig Venter InstituteLa JollaUnited States
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San DiegoLa JollaUnited States
| | | | - Thomas J Deerinck
- National Center for Microscopy and Imaging Research, University of California San DiegoLa JollaUnited States
| | - Aleš Horák
- Biology Centre CAS, Institute of ParasitologyČeské BudějoviceCzech Republic
- University of South Bohemia, Faculty of ScienceČeské BudějoviceCzech Republic
| | - Miroslav Oborník
- Biology Centre CAS, Institute of ParasitologyČeské BudějoviceCzech Republic
- University of South Bohemia, Faculty of ScienceČeské BudějoviceCzech Republic
| | - Vincent A Bielinski
- Synthetic Biology and Bioenergy, J. Craig Venter InstituteLa JollaUnited States
| | - Andrew Ellis Allen
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San DiegoLa JollaUnited States
- Microbial and Environmental Genomics, J. Craig Venter InstituteLa JollaUnited States
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105
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Kotabova E, Malych R, Pierella Karlusich JJ, Kazamia E, Eichner M, Mach J, Lesuisse E, Bowler C, Prášil O, Sutak R. Complex Response of the Chlorarachniophyte Bigelowiella natans to Iron Availability. mSystems 2021; 6:e00738-20. [PMID: 33563784 PMCID: PMC7883536 DOI: 10.1128/msystems.00738-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 01/10/2021] [Indexed: 11/20/2022] Open
Abstract
The productivity of the ocean is largely dependent on iron availability, and marine phytoplankton have evolved sophisticated mechanisms to cope with chronically low iron levels in vast regions of the open ocean. By analyzing the metabarcoding data generated from the Tara Oceans expedition, we determined how the global distribution of the model marine chlorarachniophyte Bigelowiella natans varies across regions with different iron concentrations. We performed a comprehensive proteomics analysis of the molecular mechanisms underpinning the adaptation of B. natans to iron scarcity and report on the temporal response of cells to iron enrichment. Our results highlight the role of phytotransferrin in iron homeostasis and indicate the involvement of CREG1 protein in the response to iron availability. Analysis of the Tara Oceans metagenomes and metatranscriptomes also points to a similar role for CREG1, which is found to be widely distributed among marine plankton but to show a strong bias in gene and transcript abundance toward iron-deficient regions. Our analyses allowed us to define a new subfamily of the CobW domain-containing COG0523 putative metal chaperones which are involved in iron metabolism and are restricted to only a few phytoplankton lineages in addition to B. natans At the physiological level, we elucidated the mechanisms allowing a fast recovery of PSII photochemistry after resupply of iron. Collectively, our study demonstrates that B. natans is well adapted to dynamically respond to a changing iron environment and suggests that CREG1 and COG0523 are important components of iron homeostasis in B. natans and other phytoplankton.IMPORTANCE Despite low iron availability in the ocean, marine phytoplankton require considerable amounts of iron for their growth and proliferation. While there is a constantly growing knowledge of iron uptake and its role in the cellular processes of the most abundant marine photosynthetic groups, there are still largely overlooked branches of the eukaryotic tree of life, such as the chlorarachniophytes. In the present work, we focused on the model chlorarachniophyte Bigelowiella natans, integrating physiological and proteomic analyses in culture conditions with the mining of omics data generated by the Tara Oceans expedition. We provide unique insight into the complex responses of B. natans to iron availability, including novel links to iron metabolism conserved in other phytoplankton lineages.
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Affiliation(s)
- Eva Kotabova
- Institute of Microbiology, Academy of Sciences, Centrum Algatech, Trebon, Czech Republic
| | - Ronald Malych
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Juan José Pierella Karlusich
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Elena Kazamia
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Meri Eichner
- Institute of Microbiology, Academy of Sciences, Centrum Algatech, Trebon, Czech Republic
| | - Jan Mach
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Emmanuel Lesuisse
- Jacques Monod Institute, UMR7592 CNRS, Paris Diderot University, Paris, France
| | - Chris Bowler
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Ondřej Prášil
- Institute of Microbiology, Academy of Sciences, Centrum Algatech, Trebon, Czech Republic
| | - Robert Sutak
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
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106
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Behnke J, Cohen AM, LaRoche J. N-linked glycosylation enzymes in the diatom Thalassiosira oceanica exhibit a diel cycle in transcript abundance and favor for NXT-type sites. Sci Rep 2021; 11:3227. [PMID: 33547363 PMCID: PMC7864949 DOI: 10.1038/s41598-021-82545-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 01/04/2021] [Indexed: 01/30/2023] Open
Abstract
N-linked glycosylation is a posttranslational modification affecting protein folding and function. The N-linked glycosylation pathway in algae is poorly characterized, and further knowledge is needed to understand the cell biology of algae and the evolution of N-linked glycosylation. This study investigated the N-linked glycosylation pathway in Thalassiosira oceanica, an open ocean diatom adapted to survive at growth-limiting iron concentrations. Here we identified and annotated the genes coding for the essential enzymes involved in the N-linked glycosylation pathway of T. oceanica. Transcript levels for genes coding for calreticulin, oligosaccharyltransferase (OST), N-acetylglucosaminyltransferase (GnT1), and UDP-glucose glucosyltransferase (UGGT) under high- and low-iron growth conditions revealed diel transcription patterns with a significant decrease of calreticulin and OST transcripts under iron-limitation. Solid-phase extraction of N-linked glycosylated peptides (SPEG) revealed 118 N-linked glycosylated peptides from cells grown in high- and low-iron growth conditions. The identified peptides had 81% NXT-type motifs, with X being any amino acids except proline. The presence of N-linked glycosylation sites in the iron starvation-induced protein 1a (ISIP1a) confirmed its predicted topology, contributing to the biochemical characterization of ISIP1 proteins. Analysis of extensive oceanic gene databases showed a global distribution of calreticulin, OST, and UGGT, reinforcing the importance of glycosylation in microalgae.
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Affiliation(s)
- Joerg Behnke
- grid.55602.340000 0004 1936 8200Department of Biology, Life Science Centre, Dalhousie University, 1355 Oxford Street, PO BOX 15000, Halifax, NS B3H 4R2 Canada
| | - Alejandro M. Cohen
- grid.55602.340000 0004 1936 8200Department of Biochemistry and Molecular Biology, Life Science Research Institute, Dalhousie University, 1344 Summer Street, PO Box 15000, Halifax, NS B3H 4R2 Canada
| | - Julie LaRoche
- grid.55602.340000 0004 1936 8200Department of Biology, Life Science Centre, Dalhousie University, 1355 Oxford Street, PO BOX 15000, Halifax, NS B3H 4R2 Canada
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107
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Dinoflagellates alter their carbon and nutrient metabolic strategies across environmental gradients in the central Pacific Ocean. Nat Microbiol 2021; 6:173-186. [PMID: 33398100 DOI: 10.1038/s41564-020-00814-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 10/13/2020] [Indexed: 01/28/2023]
Abstract
Marine microeukaryotes play a fundamental role in biogeochemical cycling through the transfer of energy to higher trophic levels and vertical carbon transport. Despite their global importance, microeukaryote physiology, nutrient metabolism and contributions to carbon cycling across offshore ecosystems are poorly characterized. Here, we observed the prevalence of dinoflagellates along a 4,600-km meridional transect extending across the central Pacific Ocean, where oligotrophic gyres meet equatorial upwelling waters rich in macronutrients yet low in dissolved iron. A combined multi-omics and geochemical analysis provided a window into dinoflagellate metabolism across the transect, indicating a continuous taxonomic dinoflagellate community that shifted its functional transcriptome and proteome as it extended from the euphotic to the mesopelagic zone. In euphotic waters, multi-omics data suggested that a combination of trophic modes were utilized, while mesopelagic metabolism was marked by cytoskeletal investments and nutrient recycling. Rearrangement in nutrient metabolism was evident in response to variable nitrogen and iron regimes across the gradient, with no associated change in community assemblage. Total dinoflagellate proteins scaled with particulate carbon export, with both elevated in equatorial waters, suggesting a link between dinoflagellate abundance and total carbon flux. Dinoflagellates employ numerous metabolic strategies that enable broad occupation of central Pacific ecosystems and play a dual role in carbon transformation through both photosynthetic fixation in the euphotic zone and remineralization in the mesopelagic zone.
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108
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McParland EL, Lee MD, Webb EA, Alexander H, Levine NM. DMSP synthesis genes distinguish two types of DMSP producer phenotypes. Environ Microbiol 2021; 23:1656-1669. [PMID: 33415763 DOI: 10.1111/1462-2920.15393] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/10/2020] [Accepted: 01/04/2021] [Indexed: 11/25/2022]
Abstract
Dimethylsulfoniopropionate (DMSP) is an important organic carbon and sulfur source in the surface ocean that fuels microbial activity and significantly impacts Earth's climate. After three decades of research, the cellular role(s) of DMSP and environmental drivers of production remain enigmatic. Recent work suggests that cellular DMSP concentrations, and changes in these concentrations in response to environmental stressors, define two major groups of DMSP producers: high DMSP producers that contain ≥ 50 mM intracellular DMSP and low DMSP producers that contain < 50 mM. Here we show that two recently described DMSP synthesis genes (DSYB and TpMT2) may differentiate these two DMSP phenotypes. A survey of prokaryotic and eukaryotic isolates found a significant correlation between the presence of DSYB and TpMT2 genes and previous measurements of high and low DMSP concentrations, respectively. Phylogenetic analysis demonstrated that DSYB and TpMT2 form two distinct clades. DSYB and TpMT2 were also found to be globally abundant in in situ surface communities, and their taxonomic annotations were similar to those observed for isolates. The strong correlation of the DSYB and TpMT2 synthesis genes with high and low producer phenotypes establishes a foundation for direct quantification of DMSP producers, enabling significantly improved predictions of DMSP in situ.
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Affiliation(s)
- Erin L McParland
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA.,Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Michael D Lee
- Exobiology Branch, NASA Ames Research Center, Mountain View, California, USA.,Blue Marble Space Institute of Science, Seattle, Washington, USA
| | - Eric A Webb
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Harriet Alexander
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Naomi M Levine
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
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109
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Zhu XY, Liu J, Xue CX, Tian J, Zhang XH. Shift and Metabolic Potentials of Microbial Eukaryotic Communities Across the Full Depths of the Mariana Trench. Front Microbiol 2021; 11:603692. [PMID: 33537012 PMCID: PMC7848797 DOI: 10.3389/fmicb.2020.603692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 12/15/2020] [Indexed: 12/04/2022] Open
Abstract
Microbial eukaryotes are widespread and play important roles in marine ecosystems. However, their ecological characteristics in the deep sea (>1,000 m), especially hadal trenches, were largely unknown. Here, we investigated the diversity and metabolic potentials of microbial eukaryotes along the whole water column of the Mariana Trench by metagenomics. Our results showed clear depth-related distribution of microbial eukaryotic community and associated metabolic potentials. Surface seawater was dominated by phototrophic/mixotrophic groups (e.g., Dinoflagellata) and genes involved in biosynthesis (photosynthesis and fatty acid biosynthesis), while deep (bathypelagic and/or hadal) seawaters were enriched with heterotrophic groups (e.g., Bicoecea) and genes related to digestion (lysosomal enzymes and V-type ATPase) and carbohydrate metabolism. Co-occurrence analysis revealed high intra-domain connectivity, indicating that microbial eukaryotic composition was more influenced by microbial eukaryotes themselves than bacteria. Increased abundance of genes associated with unsaturated fatty acid biosynthesis likely plays a role in resisting high hydrostatic pressure. Top1 and hupB genes, responsible for the formation and stabilization of DNA structure, were unique and abundant in the hadal zone and thus may be helpful to stabilize DNA structure in the deep sea. Overall, our results provide insights into the distribution and potential adaptability of microbial eukaryotes in the hadal zone.
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Affiliation(s)
- Xiao-Yu Zhu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jiwen Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Chun-Xu Xue
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jiwei Tian
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
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110
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Pierella Karlusich JJ, Bowler C, Biswas H. Carbon Dioxide Concentration Mechanisms in Natural Populations of Marine Diatoms: Insights From Tara Oceans. FRONTIERS IN PLANT SCIENCE 2021; 12:657821. [PMID: 33995455 PMCID: PMC8119650 DOI: 10.3389/fpls.2021.657821] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/23/2021] [Indexed: 05/08/2023]
Abstract
Marine diatoms, the most successful photoautotrophs in the ocean, efficiently sequester a significant part of atmospheric CO2 to the ocean interior through their participation in the biological carbon pump. However, it is poorly understood how marine diatoms fix such a considerable amount of CO2, which is vital information toward modeling their response to future CO2 levels. The Tara Oceans expeditions generated molecular data coupled with in situ biogeochemical measurements across the main ocean regions, and thus provides a framework to compare diatom genetic and transcriptional flexibility under natural CO2 variability. The current study investigates the interlink between the environmental variability of CO2 and other physicochemical parameters with the gene and transcript copy numbers of five key enzymes of diatom CO2 concentration mechanisms (CCMs): Rubisco activase and carbonic anhydrase (CA) as part of the physical pathway, together with phosphoenolpyruvate carboxylase, phosphoenolpyruvate carboxykinase, and malic enzyme as part of the potential C4 biochemical pathway. Toward this aim, we mined >200 metagenomes and >220 metatranscriptomes generated from samples of the surface layer of 66 globally distributed sampling sites and corresponding to the four main size fractions in which diatoms can be found: 0.8-5 μm, 5-20 μm, 20-180 μm, and 180-2,000 μm. Our analyses revealed that the transcripts for the enzymes of the putative C4 biochemical CCM did not in general display co-occurring profiles. The transcripts for CAs were the most abundant, with an order of magnitude higher values than the other enzymes, thus implying the importance of physical CCMs in diatom natural communities. Among the different classes of this enzyme, the most prevalent was the recently characterized iota class. Consequently, very little information is available from natural diatom assemblages about the distribution of this class. Biogeographic distributions for all the enzymes show different abundance hotspots according to the size fraction, pointing to the influence of cell size and aggregation in CCMs. Environmental correlations showed a complex pattern of responses to CO2 levels, total phytoplankton biomass, temperature, and nutrient concentrations. In conclusion, we propose that biophysical CCMs are prevalent in natural diatom communities.
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Affiliation(s)
- Juan José Pierella Karlusich
- Institut de Biologie de l’ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Chris Bowler
- Institut de Biologie de l’ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Haimanti Biswas
- CSIR National Institute of Oceanography, Biological Oceanography Division, Dona Paula, India
- *Correspondence: Haimanti Biswas,
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111
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Saito MA, Saunders JK, Chagnon M, Gaylord DA, Shepherd A, Held NA, Dupont C, Symmonds N, York A, Charron M, Kinkade DB. Development of an Ocean Protein Portal for Interactive Discovery and Education. J Proteome Res 2021; 20:326-336. [PMID: 32897077 PMCID: PMC8036901 DOI: 10.1021/acs.jproteome.0c00382] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Proteins are critical in catalyzing chemical reactions, forming key cellular structures, and in regulating cellular processes. Investigation of marine microbial proteins by metaproteomics methods enables the discovery of numerous aspects of microbial biogeochemical processes. However, these datasets present big data challenges as they often involve many samples collected across broad geospatial and temporal scales, resulting in thousands of protein identifications, abundances, and corresponding annotation information. The Ocean Protein Portal (OPP) was created to enable data sharing and discovery among multiple scientific domains and serve both research and education functions. The portal focuses on three use case questions: "Where is my protein of interest?", "Who makes it?", and "How much is there?" and provides profile and section visualizations, real-time taxonomic analysis, and links to metadata, sequence analysis, and other external resources to enable connections to be made between biogeochemical and proteomics datasets.
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Affiliation(s)
- Mak A Saito
- Woods Hole Oceanographic Institution, Woods Hole, Falmouth, Massachusetts 02543, United States
| | - Jaclyn K Saunders
- Woods Hole Oceanographic Institution, Woods Hole, Falmouth, Massachusetts 02543, United States
| | - Michael Chagnon
- RPS Group, South Kingston, Rhode Island 02879, United States
- Kaimika Technology, Cumberland, Rhode Island 02864, United States
| | - David A Gaylord
- Woods Hole Oceanographic Institution, Woods Hole, Falmouth, Massachusetts 02543, United States
| | - Adam Shepherd
- Woods Hole Oceanographic Institution, Woods Hole, Falmouth, Massachusetts 02543, United States
| | - Noelle A Held
- Woods Hole Oceanographic Institution, Woods Hole, Falmouth, Massachusetts 02543, United States
| | - Christopher Dupont
- Woods Hole Oceanographic Institute, Falmouth, Massachusetts 02543, United States
| | - Nicholas Symmonds
- Woods Hole Oceanographic Institution, Woods Hole, Falmouth, Massachusetts 02543, United States
| | - Amber York
- Woods Hole Oceanographic Institution, Woods Hole, Falmouth, Massachusetts 02543, United States
| | - Matthew Charron
- Kaimika Technology, Cumberland, Rhode Island 02864, United States
| | - Danie B Kinkade
- Woods Hole Oceanographic Institute, Falmouth, Massachusetts 02543, United States
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112
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Laso-Jadart R, Ambroise C, Peterlongo P, Madoui MA. metaVaR: Introducing metavariant species models for reference-free metagenomic-based population genomics. PLoS One 2020; 15:e0244637. [PMID: 33378381 PMCID: PMC7773188 DOI: 10.1371/journal.pone.0244637] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 12/14/2020] [Indexed: 11/18/2022] Open
Abstract
The availability of large metagenomic data offers great opportunities for the population genomic analysis of uncultured organisms, which represent a large part of the unexplored biosphere and play a key ecological role. However, the majority of these organisms lack a reference genome or transcriptome, which constitutes a technical obstacle for classical population genomic analyses. We introduce the metavariant species (MVS) model, in which a species is represented only by intra-species nucleotide polymorphism. We designed a method combining reference-free variant calling, multiple density-based clustering and maximum-weighted independent set algorithms to cluster intra-species variants into MVSs directly from multisample metagenomic raw reads without a reference genome or read assembly. The frequencies of the MVS variants are then used to compute population genomic statistics such as FST, in order to estimate genomic differentiation between populations and to identify loci under natural selection. The MVS construction was tested on simulated and real metagenomic data. MVSs showed the required quality for robust population genomics and allowed an accurate estimation of genomic differentiation (ΔFST < 0.0001 and <0.03 on simulated and real data respectively). Loci predicted under natural selection on real data were all detected by MVSs. MVSs represent a new paradigm that may simplify and enhance holistic approaches for population genomics and the evolution of microorganisms.
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Affiliation(s)
- Romuald Laso-Jadart
- Institut François Jacob, CEA, CNRS, Génomique Métabolique - UMR 8030, Univ Evry, Université Paris-Saclay, Evry, France
| | | | | | - Mohammed-Amin Madoui
- Institut François Jacob, CEA, CNRS, Génomique Métabolique - UMR 8030, Univ Evry, Université Paris-Saclay, Evry, France
- * E-mail:
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113
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Eukaryotic virus composition can predict the efficiency of carbon export in the global ocean. iScience 2020; 24:102002. [PMID: 33490910 PMCID: PMC7811142 DOI: 10.1016/j.isci.2020.102002] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 11/13/2020] [Accepted: 12/23/2020] [Indexed: 11/24/2022] Open
Abstract
The biological carbon pump, in which carbon fixed by photosynthesis is exported to the deep ocean through sinking, is a major process in Earth's carbon cycle. The proportion of primary production that is exported is termed the carbon export efficiency (CEE). Based on in-lab or regional scale observations, viruses were previously suggested to affect the CEE (i.e., viral “shunt” and “shuttle”). In this study, we tested associations between viral community composition and CEE measured at a global scale. A regression model based on relative abundance of viral marker genes explained 67% of the variation in CEE. Viruses with high importance in the model were predicted to infect ecologically important hosts. These results are consistent with the view that the viral shunt and shuttle functions at a large scale and further imply that viruses likely act in this process in a way dependent on their hosts and ecosystem dynamics. Eukaryotic virus community composition is shown to predict carbon export efficiency Tens of viruses are highly important in the prediction of the efficiency These viruses are inferred to infect ecologically important hosts
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114
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Compson ZG, McClenaghan B, Singer GAC, Fahner NA, Hajibabaei M. Metabarcoding From Microbes to Mammals: Comprehensive Bioassessment on a Global Scale. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.581835] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Global biodiversity loss is unprecedented, and threats to existing biodiversity are growing. Given pervasive global change, a major challenge facing resource managers is a lack of scalable tools to rapidly and consistently measure Earth's biodiversity. Environmental genomic tools provide some hope in the face of this crisis, and DNA metabarcoding, in particular, is a powerful approach for biodiversity assessment at large spatial scales. However, metabarcoding studies are variable in their taxonomic, temporal, or spatial scope, investigating individual species, specific taxonomic groups, or targeted communities at local or regional scales. With the advent of modern, ultra-high throughput sequencing platforms, conducting deep sequencing metabarcoding surveys with multiple DNA markers will enhance the breadth of biodiversity coverage, enabling comprehensive, rapid bioassessment of all the organisms in a sample. Here, we report on a systematic literature review of 1,563 articles published about DNA metabarcoding and summarize how this approach is rapidly revolutionizing global bioassessment efforts. Specifically, we quantify the stakeholders using DNA metabarcoding, the dominant applications of this technology, and the taxonomic groups assessed in these studies. We show that while DNA metabarcoding has reached global coverage, few studies deliver on its promise of near-comprehensive biodiversity assessment. We then outline how DNA metabarcoding can help us move toward real-time, global bioassessment, illustrating how different stakeholders could benefit from DNA metabarcoding. Next, we address barriers to widespread adoption of DNA metabarcoding, highlighting the need for standardized sampling protocols, experts and computational resources to handle the deluge of genomic data, and standardized, open-source bioinformatic pipelines. Finally, we explore how technological and scientific advances will realize the promise of total biodiversity assessment in a sample—from microbes to mammals—and unlock the rich information genomics exposes, opening new possibilities for merging whole-system DNA metabarcoding with (1) abundance and biomass quantification, (2) advanced modeling, such as species occupancy models, to improve species detection, (3) population genetics, (4) phylogenetics, and (5) food web and functional gene analysis. While many challenges need to be addressed to facilitate widespread adoption of environmental genomic approaches, concurrent scientific and technological advances will usher in methods to supplement existing bioassessment tools reliant on morphological and abiotic data. This expanded toolbox will help ensure that the best tool is used for the job and enable exciting integrative techniques that capitalize on multiple tools. Collectively, these new approaches will aid in addressing the global biodiversity crisis we now face.
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115
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Santos-Júnior CD, Sarmento H, de Miranda FP, Henrique-Silva F, Logares R. Uncovering the genomic potential of the Amazon River microbiome to degrade rainforest organic matter. MICROBIOME 2020; 8:151. [PMID: 33126925 PMCID: PMC7597016 DOI: 10.1186/s40168-020-00930-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/06/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND The Amazon River is one of the largest in the world and receives huge amounts of terrestrial organic matter (TeOM) from the surrounding rainforest. Despite this TeOM is typically recalcitrant (i.e. resistant to degradation), only a small fraction of it reaches the ocean, pointing to a substantial TeOM degradation by the river microbiome. Yet, microbial genes involved in TeOM degradation in the Amazon River were barely known. Here, we examined the Amazon River microbiome by analysing 106 metagenomes from 30 sampling points distributed along the river. RESULTS We constructed the Amazon River basin Microbial non-redundant Gene Catalogue (AMnrGC) that includes ~ 3.7 million non-redundant genes, affiliating mostly to bacteria. We found that the Amazon River microbiome contains a substantial gene-novelty compared to other relevant known environments (rivers and rainforest soil). Genes encoding for proteins potentially involved in lignin degradation pathways were correlated to tripartite tricarboxylates transporters and hemicellulose degradation machinery, pointing to a possible priming effect. Based on this, we propose a model on how the degradation of recalcitrant TeOM could be modulated by labile compounds in the Amazon River waters. Our results also suggest changes of the microbial community and its genomic potential along the river course. CONCLUSIONS Our work contributes to expand significantly our comprehension of the world's largest river microbiome and its potential metabolism related to TeOM degradation. Furthermore, the produced gene catalogue (AMnrGC) represents an important resource for future research in tropical rivers. Video abstract.
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Affiliation(s)
- Célio Dias Santos-Júnior
- Molecular Biology Laboratory, Department of Genetics and Evolution – DGE, Universidade Federal de São Carlos – UFSCar, Rod. Washington Luis KM 235 - Monjolinho, São Carlos, SP 13565-905 Brazil
- Institute of Science and Technology for Brain-Inspired Intelligence – ISTBI, Fudan University, Handan Rd 220, Wu Jiao Chang, Yangpu, Shanghai, 200433 China
| | - Hugo Sarmento
- Laboratory of Microbial Processes & Biodiversity, Department of Hydrobiology – DHB, Universidade Federal de São Carlos – UFSCar, Via Washington Luis KM 235 - Monjolinho, São Carlos, SP 13565-905 Brazil
| | - Fernando Pellon de Miranda
- Centro de Pesquisas e Desenvolvimento Leopoldo Américo Miguez de Mello, Petróleo Brasileiro S.A. (Petrobras), Av. Horácio Macedo 950, Rio de Janeiro, RJ 21941-915 Brazil
| | - Flávio Henrique-Silva
- Molecular Biology Laboratory, Department of Genetics and Evolution – DGE, Universidade Federal de São Carlos – UFSCar, Rod. Washington Luis KM 235 - Monjolinho, São Carlos, SP 13565-905 Brazil
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta 37-49, ES08003, Barcelona, Catalonia Spain
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116
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Phylogeny and Structure of Fatty Acid Photodecarboxylases and Glucose-Methanol-Choline Oxidoreductases. Catalysts 2020. [DOI: 10.3390/catal10091072] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Glucose-methanol-choline (GMC) oxidoreductases are a large and diverse family of flavin-binding enzymes found in all kingdoms of life. Recently, a new related family of proteins has been discovered in algae named fatty acid photodecarboxylases (FAPs). These enzymes use the energy of light to convert fatty acids to the corresponding Cn-1 alkanes or alkenes, and hold great potential for biotechnological application. In this work, we aimed at uncovering the natural diversity of FAPs and their relations with other GMC oxidoreductases. We reviewed the available GMC structures, assembled a large dataset of GMC sequences, and found that one active site amino acid, a histidine, is extremely well conserved among the GMC proteins but not among FAPs, where it is replaced with alanine. Using this criterion, we found several new potential FAP genes, both in genomic and metagenomic databases, and showed that related bacterial, archaeal and fungal genes are unlikely to be FAPs. We also identified several uncharacterized clusters of GMC-like proteins as well as subfamilies of proteins that lack the conserved histidine but are not FAPs. Finally, the analysis of the collected dataset of potential photodecarboxylase sequences revealed the key active site residues that are strictly conserved, whereas other residues in the vicinity of the flavin adenine dinucleotide (FAD) cofactor and in the fatty acid-binding pocket are more variable. The identified variants may have different FAP activity and selectivity and consequently may prove useful for new biotechnological applications, thereby fostering the transition from a fossil carbon-based economy to a bio-economy by enabling the sustainable production of hydrocarbon fuels.
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117
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Intriguing size distribution of the uncultured and globally widespread marine non-cyanobacterial diazotroph Gamma-A. ISME JOURNAL 2020; 15:124-128. [PMID: 32918066 DOI: 10.1038/s41396-020-00765-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 08/18/2020] [Accepted: 08/27/2020] [Indexed: 01/09/2023]
Abstract
Non-cyanobacterial diazotrophs (NCDs) have recently emerged as potentially important contributors to marine nitrogen fixation. One of the most widely distributed NCDs is Gamma-A, yet information about its autecology is still scarce and solely relies on the PCR-based detection of its nitrogenase (nifH) gene in seawater, since previous metagenomic surveys targeting free-living planktonic size fractions (<3 μm) have not detected it. Here, we explore the diversity, biogeography, size-distribution, and nitrogenase gene expression of Gamma-A across four larger planktonic size-fractions (0.8-5, 5-20, 20-180, and 180-2000 μm) using metagenomes and metatranscriptomes from the Tara Oceans. We detected a single variant of a complete Gamma-A nifH gene along with other nitrogenase-related genes (nifKDT) within a metatranscriptomic-based contig of the Marine Atlas of Tara Ocean Unigenes. Gamma-A was detected in tropical and subtropical oceanic regions across all the size-fractions. However, the highest gene and transcript abundances were found in the 0.8-5 and 5-20 μm size-fractions at the surface, whereas abundances at the deep chlorophyll maximum were lower and similar across all size-fractions. The ubiquitous presence of active Gamma-A in large planktonic size-fractions suggests a filamentous or particle-attached lifestyle and places its potential to fix nitrogen in larger planktonic compartments.
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118
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Saary P, Mitchell AL, Finn RD. Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC. Genome Biol 2020; 21:244. [PMID: 32912302 PMCID: PMC7488429 DOI: 10.1186/s13059-020-02155-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 08/24/2020] [Indexed: 12/23/2022] Open
Abstract
Microbial eukaryotes constitute a significant fraction of biodiversity and have recently gained more attention, but the recovery of high-quality metagenomic assembled eukaryotic genomes is limited by the current availability of tools. To help address this, we have developed EukCC, a tool for estimating the quality of eukaryotic genomes based on the automated dynamic selection of single copy marker gene sets. We demonstrate that our method outperforms current genome quality estimators, particularly for estimating contamination, and have applied EukCC to datasets derived from two different environments to enable the identification of novel eukaryote genomes, including one from the human skin.
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Affiliation(s)
- Paul Saary
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Alex L Mitchell
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
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119
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Sow SLS, Trull TW, Bodrossy L. Oceanographic Fronts Shape Phaeocystis Assemblages: A High-Resolution 18S rRNA Gene Survey From the Ice-Edge to the Equator of the South Pacific. Front Microbiol 2020; 11:1847. [PMID: 32849444 PMCID: PMC7424020 DOI: 10.3389/fmicb.2020.01847] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 07/15/2020] [Indexed: 01/01/2023] Open
Abstract
The cosmopolitan haptophyte Phaeocystis is recognized as a key contributor to marine biogeochemical cycling and important primary producer within polar marine environments. Yet, little is known about its solitary, non-colonial cell stages or its distribution during the colder, low-productivity seasons. We examined the biogeography of Phaeocystis along a high-resolution (0.5-degree latitudinal interval) transect from the Antarctic ice-edge to the equator of the South Pacific, in the austral autumn-winter. Using high-throughput 18S rRNA gene sequences with single nucleotide variable (zero-radius) operational taxonomic units (zOTUs) allowed us to explore the possibility of strain-level variation. From water samples within the upper water column, we show the presence of an abundant Phaeocystis assemblage that persisted during the colder months, contributing up to 9% of the microbial eukaryote community at high latitudes. The biogeography of Phaeocystis was strongly shaped by oceanographic boundaries, most prominently the polar and subantarctic fronts. Marked changes in dominant Phaeocystis antarctica zOTUs between different frontal zones support the concept that ecotypes may exist within the Phaeocystis assemblage. Our findings also show that the Phaeocystis assemblage did not abide by the classical latitudinal diversity gradient of increasing richness from the poles to the tropics; richness peaked at 30°S and declined to a minimum at 5°S. Another surprise was that P. globosa and P. cordata, previously thought to be restricted to the northern hemisphere, were detected at moderate abundances within the Southern Ocean. Our results emphasize the importance of oceanographic processes in shaping the biogeography of Phaeocystis and highlights the importance of genomics-based exploration of Phaeocystis, which have found the assemblage to be more complex than previously understood. The high winter relative abundance of the Phaeocystis assemblage suggests it could be involved in more complex ecological interactions during the less productive seasons, which should be considered in future studies to better understand the ecological role and strategies of this keystone species.
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Affiliation(s)
- Swan L S Sow
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia.,Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Hobart, TAS, Australia
| | - Thomas W Trull
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Hobart, TAS, Australia
| | - Levente Bodrossy
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Hobart, TAS, Australia
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120
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Faktorová D, Kaur B, Valach M, Graf L, Benz C, Burger G, Lukeš J. Targeted integration by homologous recombination enables in situ tagging and replacement of genes in the marine microeukaryote Diplonema papillatum. Environ Microbiol 2020; 22:3660-3670. [PMID: 32548939 DOI: 10.1111/1462-2920.15130] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/07/2020] [Accepted: 06/13/2020] [Indexed: 12/17/2022]
Abstract
Diplonemids are a group of highly diverse and abundant marine microeukaryotes that belong to the phylum Euglenozoa and form a sister clade to the well-studied, mostly parasitic kinetoplastids. Very little is known about the biology of diplonemids, as few species have been formally described and just one, Diplonema papillatum, has been studied to a decent extent at the molecular level. Following up on our previous results showing stable but random integration of delivered extraneous DNA, we demonstrate here homologous recombination in D. papillatum. Targeting various constructs to the intended position in the nuclear genome was successful when 5' and 3' homologous regions longer than 1 kbp were used, achieving N-terminal tagging with mCherry and gene replacement of α- and β-tubulins. For more convenient genetic manipulation, we designed a modular plasmid, pDP002, which bears a protein-A tag and used it to generate and express a C-terminally tagged mitoribosomal protein. Lastly, we developed an improved transformation protocol for broader applicability across laboratories. Our robust methodology allows the replacement, integration as well as endogenous tagging of D. papillatum genes, thus opening the door to functional studies in this species and establishing a basic toolkit for reverse genetics of diplonemids in general.
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Affiliation(s)
- Drahomíra Faktorová
- Czech Academy of Sciences, Institute of Parasitology, Biology Centre, Czech Republic.,Faculty of Sciences, University of South Bohemia, Cˇeské Budějovice (Budweis), Czech Republic
| | - Binnypreet Kaur
- Czech Academy of Sciences, Institute of Parasitology, Biology Centre, Czech Republic.,Faculty of Sciences, University of South Bohemia, Cˇeské Budějovice (Budweis), Czech Republic
| | - Matus Valach
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Canada
| | - Lena Graf
- Faculty of Sciences, University of South Bohemia, Cˇeské Budějovice (Budweis), Czech Republic.,Present address: Johannes Kepler University, Linz, Austria
| | - Corinna Benz
- Czech Academy of Sciences, Institute of Parasitology, Biology Centre, Czech Republic
| | - Gertraud Burger
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Canada
| | - Julius Lukeš
- Czech Academy of Sciences, Institute of Parasitology, Biology Centre, Czech Republic.,Faculty of Sciences, University of South Bohemia, Cˇeské Budějovice (Budweis), Czech Republic
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121
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Santoferrara L, Burki F, Filker S, Logares R, Dunthorn M, McManus GB. Perspectives from Ten Years of Protist Studies by High-Throughput Metabarcoding. J Eukaryot Microbiol 2020; 67:612-622. [PMID: 32498124 DOI: 10.1111/jeu.12813] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 05/29/2020] [Accepted: 05/29/2020] [Indexed: 01/07/2023]
Abstract
During the last decade, high-throughput metabarcoding became routine for analyzing protistan diversity and distributions in nature. Amid a multitude of exciting findings, scientists have also identified and addressed technical and biological limitations, although problems still exist for inference of meaningful taxonomic and ecological knowledge based on short DNA sequences. Given the extensive use of this approach, it is critical to settle our understanding on its strengths and weaknesses and to synthesize up-to-date methodological and conceptual trends. This article summarizes key scientific and technical findings, and identifies current and future directions in protist research that uses metabarcoding.
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Affiliation(s)
- Luciana Santoferrara
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA.,Department of Marine Sciences, University of Connecticut, Groton, CT, USA
| | - Fabien Burki
- Department of Organismal Biology, Program in Systematic Biology, and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sabine Filker
- Department of Molecular Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Micah Dunthorn
- Department of Eukaryotic Microbiology, University of Duisburg-Essen, Essen, Germany
| | - George B McManus
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
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122
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Chrismas N, Cunliffe M. Depth-dependent mycoplankton glycoside hydrolase gene activity in the open ocean-evidence from the Tara Oceans eukaryote metatranscriptomes. ISME JOURNAL 2020; 14:2361-2365. [PMID: 32494052 PMCID: PMC7608184 DOI: 10.1038/s41396-020-0687-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 11/09/2022]
Abstract
Mycoplankton are widespread components of marine ecosystems, yet the full extent of their functional role remains poorly known. Marine mycoplankton are likely functionally analogous to their terrestrial counterparts, including performing saprotrophy and degrading high-molecular weight organic substrates using carbohydrate-active enzymes (CAZymes). We investigated the prevalence of transcribed oceanic fungal CAZyme genes using the Marine Atlas of Tara Ocean Unigenes database. We revealed an abundance of unique transcribed fungal glycoside hydrolases in the open ocean, including a particularly high number that act upon cellulose in surface waters and the deep chlorophyll maximum (DCM). A variety of other glycoside hydrolases acting on a range of biogeochemically important polysaccharides including β-glucans and chitin were also found. This analysis demonstrates that mycoplankton are active saprotrophs in the open ocean and paves the way for future research into the depth-dependent roles of marine fungi in oceanic carbon cycling, including the biological carbon pump.
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Affiliation(s)
- Nathan Chrismas
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, UK. .,School of Geographical Sciences, University of Bristol, University Road, Bristol, UK.
| | - Michael Cunliffe
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, UK. .,School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK.
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123
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Armbrecht L, Herrando-Pérez S, Eisenhofer R, Hallegraeff GM, Bolch CJS, Cooper A. An optimized method for the extraction of ancient eukaryote DNA from marine sediments. Mol Ecol Resour 2020; 20:906-919. [PMID: 32277584 DOI: 10.1111/1755-0998.13162] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 03/17/2020] [Accepted: 03/26/2020] [Indexed: 12/19/2022]
Abstract
Marine sedimentary ancient DNA (sedaDNA) provides a powerful means to reconstruct marine palaeo-communities across the food web. However, currently there are few optimized sedaDNA extraction protocols available to maximize the yield of small DNA fragments typical of ancient DNA (aDNA) across a broad diversity of eukaryotes. We compared seven combinations of sedaDNA extraction treatments and sequencing library preparations using marine sediments collected at a water depth of 104 m off Maria Island, Tasmania, in 2018. These seven methods contrasted frozen versus refrigerated sediment, bead-beating induced cell lysis versus ethylenediaminetetraacetic acid (EDTA) incubation, DNA binding in silica spin columns versus in silica-solution, diluted versus undiluted DNA in shotgun library preparations to test potential inhibition issues during amplification steps, and size-selection of low molecular-weight (LMW) DNA to increase the extraction efficiency of sedaDNA. Maximum efficiency was obtained from frozen sediments subjected to a combination of EDTA incubation and bead-beating, DNA binding in silica-solution, and undiluted DNA in shotgun libraries, across 45 marine eukaryotic taxa. We present an optimized extraction protocol integrating these steps, with an optional post-library LMW size-selection step to retain DNA fragments of ≤500 base pairs. We also describe a stringent bioinformatic filtering approach for metagenomic data and provide a comprehensive list of contaminants as a reference for future sedaDNA studies. The new extraction and data-processing protocol should improve quantitative paleo-monitoring of eukaryotes from marine sediments, as well as other studies relying on the detection of highly fragmented and degraded eukaryote DNA in sediments.
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Affiliation(s)
- Linda Armbrecht
- School of Biological Sciences, Faculty of Sciences, Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA, Australia
| | - Salvador Herrando-Pérez
- School of Biological Sciences, Faculty of Sciences, Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA, Australia
| | - Raphael Eisenhofer
- School of Biological Sciences, Faculty of Sciences, Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA, Australia
| | - Gustaaf M Hallegraeff
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tas., Australia
| | - Christopher J S Bolch
- Institute for Marine and Antarctic Studies, University of Tasmania, Launceston, Tas., Australia
| | - Alan Cooper
- South Australian Museum, Adelaide, SA, Australia
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124
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Sunagawa S, Acinas SG, Bork P, Bowler C, Eveillard D, Gorsky G, Guidi L, Iudicone D, Karsenti E, Lombard F, Ogata H, Pesant S, Sullivan MB, Wincker P, de Vargas C. Tara Oceans: towards global ocean ecosystems biology. Nat Rev Microbiol 2020; 18:428-445. [PMID: 32398798 DOI: 10.1038/s41579-020-0364-5] [Citation(s) in RCA: 149] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2020] [Indexed: 12/14/2022]
Abstract
A planetary-scale understanding of the ocean ecosystem, particularly in light of climate change, is crucial. Here, we review the work of Tara Oceans, an international, multidisciplinary project to assess the complexity of ocean life across comprehensive taxonomic and spatial scales. Using a modified sailing boat, the team sampled plankton at 210 globally distributed sites at depths down to 1,000 m. We describe publicly available resources of molecular, morphological and environmental data, and discuss how an ecosystems biology approach has expanded our understanding of plankton diversity and ecology in the ocean as a planetary, interconnected ecosystem. These efforts illustrate how global-scale concepts and data can help to integrate biological complexity into models and serve as a baseline for assessing ecosystem changes and the future habitability of our planet in the Anthropocene epoch.
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Affiliation(s)
- Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland.
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences-CSIC, Barcelona, Spain
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.,Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Chris Bowler
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France
| | | | - Damien Eveillard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Université de Nantes, CNRS, UMR6004, LS2N, Nantes, France
| | - Gabriel Gorsky
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France
| | - Lionel Guidi
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France
| | | | - Eric Karsenti
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Directors' Research, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Fabien Lombard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Kyoto, Japan
| | - Stephane Pesant
- PANGAEA, University of Bremen, Bremen, Germany.,MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.,Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Patrick Wincker
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France.,Génomique Métabolique, Genoscope, Institut de Biologie Francois Jacob, Commissariat à l'Énergie Atomique, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Colomban de Vargas
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France. .,Sorbonne Université and CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Roscoff, France.
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125
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Ku C, Sheyn U, Sebé-Pedrós A, Ben-Dor S, Schatz D, Tanay A, Rosenwasser S, Vardi A. A single-cell view on alga-virus interactions reveals sequential transcriptional programs and infection states. SCIENCE ADVANCES 2020; 6:eaba4137. [PMID: 32490206 PMCID: PMC7239649 DOI: 10.1126/sciadv.aba4137] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/10/2020] [Indexed: 05/12/2023]
Abstract
The discovery of giant viruses infecting eukaryotes from diverse ecosystems has revolutionized our understanding of the evolution of viruses and their impact on protist biology, yet knowledge on their replication strategies and transcriptome regulation remains limited. Here, we profile single-cell transcriptomes of the globally distributed microalga Emiliania huxleyi and its specific giant virus during infection. We detected profound heterogeneity in viral transcript levels among individual cells. Clustering single cells based on viral expression profiles enabled reconstruction of the viral transcriptional trajectory. Reordering cells along this path unfolded highly resolved viral genetic programs composed of genes with distinct promoter elements that orchestrate sequential expression. Exploring host transcriptome dynamics across the viral infection states revealed rapid and selective shutdown of protein-encoding nuclear transcripts, while the plastid and mitochondrial transcriptomes persisted into later stages. Single-cell RNA-seq opens a new avenue to unravel the life cycle of giant viruses and their unique hijacking strategies.
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Affiliation(s)
- Chuan Ku
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Uri Sheyn
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Arnau Sebé-Pedrós
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Shifra Ben-Dor
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Daniella Schatz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Shilo Rosenwasser
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
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126
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Riccio G, De Luca D, Lauritano C. Monogalactosyldiacylglycerol and Sulfolipid Synthesis in Microalgae. Mar Drugs 2020; 18:md18050237. [PMID: 32370033 PMCID: PMC7281551 DOI: 10.3390/md18050237] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 04/23/2020] [Accepted: 04/27/2020] [Indexed: 12/24/2022] Open
Abstract
Microalgae, due to their huge taxonomic and metabolic diversity, have been shown to be a valuable and eco-friendly source of bioactive natural products. The increasing number of genomic and transcriptomic data will give a great boost for the study of metabolic pathways involved in the synthesis of bioactive compounds. In this study, we analyzed the presence of the enzymes involved in the synthesis of monogalactosyldiacylglycerols (MGDGs) and sulfoquinovosyldiacylglycerols (SQDG). Both compounds have important biological properties. MGDGs present both anti-inflammatory and anti-cancer activities while SQDGs present immunostimulatory activities and inhibit the enzyme glutaminyl cyclase, which is involved in Alzheimer’s disease. The Ocean Global Atlas (OGA) database and the Marine Microbial Eukaryotic Transcriptome Sequencing Project (MMETSP) were used to search MGDG synthase (MGD), UDP-sulfoquinovose synthase (SQD1), and sulfoquinovosyltransferase (SQD2) sequences along microalgal taxa. In silico 3D prediction analyses for the three enzymes were performed by Phyre2 server, while binding site predictions were performed by the COACH server. The analyzed enzymes are distributed across different taxa, which confirms the importance for microalgae of these two pathways for thylakoid physiology. MGD genes have been found across almost all analyzed taxa and can be separated in two different groups, similarly to terrestrial plant MGD. SQD1 and SQD2 genes are widely distributed along the analyzed taxa in a similar way to MGD genes with some exceptions. For Pinguiophyceae, Raphidophyceae, and Synurophyceae, only sequences coding for MGDG were found. On the contrary, sequences assigned to Ciliophora and Eustigmatophyceae were exclusively corresponding to SQD1 and SQD2. This study reports, for the first time, the presence/absence of these enzymes in available microalgal transcriptomes, which gives new insights on microalgal physiology and possible biotechnological applications for the production of bioactive lipids.
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Affiliation(s)
- Gennaro Riccio
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, CAP80121 Naples, Italy;
| | - Daniele De Luca
- Department of Humanities, Università degli Studi Suor Orsola Benincasa, CAP80135 Naples, Italy;
| | - Chiara Lauritano
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, CAP80121 Naples, Italy;
- Correspondence: ; Tel.: +39-081-5833-221
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127
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Ngugi DK, Ziegler M, Duarte CM, Voolstra CR. Genomic Blueprint of Glycine Betaine Metabolism in Coral Metaorganisms and Their Contribution to Reef Nitrogen Budgets. iScience 2020; 23:101120. [PMID: 32438323 PMCID: PMC7240134 DOI: 10.1016/j.isci.2020.101120] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 03/03/2020] [Accepted: 04/27/2020] [Indexed: 11/23/2022] Open
Abstract
The osmolyte glycine betaine (GB) ranks among the few widespread biomolecules in all three domains of life. In corals, tissue concentrations of GB are substantially higher than in the ambient seawater. However, the synthetic routes remain unresolved, questioning whether intracellular GB originates from de novo synthesis or heterotrophic input. Here we show that the genomic blueprint of coral metaorganisms encode the biosynthetic and degradation machinery for GB. Member organisms also adopted the prokaryotic high-affinity carrier-mediated uptake of exogenous GB, rendering coral reefs potential sinks of marine dissolved GB. The machinery metabolizing GB is highly expressed in the coral model Aiptasia and its microalgal symbionts, signifying GB's role in the cnidarian-dinoflagellate symbiosis. We estimate that corals store between 106–109 grams of GB globally, representing about 16% of their nitrogen biomass. Our findings provide a framework for further mechanistic studies addressing GB's role in coral biology and reef ecosystem nitrogen cycling. Coral tissues contain high concentrations of the osmolyte glycine betaine Corals and their microbial symbionts can produce and degrade glycine betaine High gene expression patterns signifies role in coral-microbial symbiosis Glycine betaine is estimated to encompass 16% of the coral's nitrogen biomass
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Affiliation(s)
- David K Ngugi
- Leibniz Institute DSMZ - German Culture Collection for Microorganisms and Cell Cultures, Braunschweig, Germany; Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| | - Maren Ziegler
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Department of Animal Ecology and Systematics, Justus-Liebig-University, Giessen, Germany
| | - Carlos M Duarte
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Christian R Voolstra
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Department of Biology, University of Konstanz, Konstanz 78457, Germany.
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128
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Caparco AA, Pelletier E, Petit JL, Jouenne A, Bommarius BR, Berardinis V, Zaparucha A, Champion JA, Bommarius AS, Vergne‐Vaxelaire C. Metagenomic Mining for Amine Dehydrogenase Discovery. Adv Synth Catal 2020. [DOI: 10.1002/adsc.202000094] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Adam A. Caparco
- School of Chemical & Biomolecular EngineeringGeorgia Institute of Technology Atlanta, GA USA
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 91057 Evry France
| | - Jean Louis Petit
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 91057 Evry France
| | - Aurélie Jouenne
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 91057 Evry France
| | - Bettina R. Bommarius
- School of Chemical & Biomolecular EngineeringGeorgia Institute of Technology Atlanta, GA USA
| | - Véronique Berardinis
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 91057 Evry France
| | - Anne Zaparucha
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 91057 Evry France
| | - Julie A. Champion
- School of Chemical & Biomolecular EngineeringGeorgia Institute of Technology Atlanta, GA USA
| | - Andreas S. Bommarius
- School of Chemical & Biomolecular EngineeringGeorgia Institute of Technology Atlanta, GA USA
| | - Carine Vergne‐Vaxelaire
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 91057 Evry France
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129
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Functional Genomics Differentiate Inherent and Environmentally Influenced Traits in Dinoflagellate and Diatom Communities. Microorganisms 2020; 8:microorganisms8040567. [PMID: 32326461 PMCID: PMC7232425 DOI: 10.3390/microorganisms8040567] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/07/2020] [Accepted: 04/09/2020] [Indexed: 12/13/2022] Open
Abstract
Dinoflagellates and diatoms are among the most prominent microeukaryotic plankton groups, and they have evolved different functional traits reflecting their roles within ecosystems. However, links between their metabolic processes and functional traits within different environmental contexts warrant further study. The functional biodiversity of dinoflagellates and diatoms was accessed with metatranscriptomics using Pfam protein domains as proxies for functional processes. Despite the overall geographic similarity of functional responses, abiotic (i.e., temperature and salinity; ~800 Pfam domains) and biotic (i.e., taxonomic group; ~1500 Pfam domains) factors influencing particular functional responses were identified. Salinity and temperature were identified as the main drivers of community composition. Higher temperatures were associated with an increase of Pfam domains involved in energy metabolism and a decrease of processes associated with translation and the sulfur cycle. Salinity changes were correlated with the biosynthesis of secondary metabolites (e.g., terpenoids and polyketides) and signal transduction processes, indicating an overall strong effect on the biota. The abundance of dinoflagellates was positively correlated with nitrogen metabolism, vesicular transport and signal transduction, highlighting their link to biotic interactions (more so than diatoms) and suggesting the central role of species interactions in the evolution of dinoflagellates. Diatoms were associated with metabolites (e.g., isoprenoids and carotenoids), as well as lysine degradation, which highlights their ecological role as important primary producers and indicates the physiological importance of these metabolic pathways for diatoms in their natural environment. These approaches and gathered information will support ecological questions concerning the marine ecosystem state and metabolic interactions in the marine environment.
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130
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Metegnier G, Paulino S, Ramond P, Siano R, Sourisseau M, Destombe C, Le Gac M. Species specific gene expression dynamics during harmful algal blooms. Sci Rep 2020; 10:6182. [PMID: 32277155 PMCID: PMC7148311 DOI: 10.1038/s41598-020-63326-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/20/2020] [Indexed: 01/10/2023] Open
Abstract
Harmful algal blooms are caused by specific members of microbial communities. Understanding the dynamics of these events requires comparing the strategies developed by the problematic species to cope with environmental fluctuations to the ones developed by the other members of the community. During three consecutive years, the meta-transcriptome of micro-eukaryote communities was sequenced during blooms of the toxic dinoflagellate Alexandrium minutum. The dataset was analyzed to investigate species specific gene expression dynamics. Major shifts in gene expression were explained by the succession of different species within the community. Although expression patterns were strongly correlated with fluctuation of the abiotic environment, and more specifically with nutrient concentration, transcripts specifically involved in nutrient uptake and metabolism did not display extensive changes in gene expression. Compared to the other members of the community, A. minutum displayed a very specific expression pattern, with lower expression of photosynthesis transcripts and central metabolism genes (TCA cycle, glucose metabolism, glycolysis…) and contrasting expression pattern of ion transporters across environmental conditions. These results suggest the importance of mixotrophy, cell motility and cell-to-cell interactions during A. minutum blooms.
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Affiliation(s)
- Gabriel Metegnier
- French Research Institute for Exploitation of the Sea, Ifremer DYNECO PELAGOS, 29280, Plouzané, France.,CNRS, Sorbonne Université, UC, UaCh, UMI 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, 29688, Roscoff, France
| | - Sauvann Paulino
- French Research Institute for Exploitation of the Sea, Ifremer DYNECO PELAGOS, 29280, Plouzané, France
| | - Pierre Ramond
- French Research Institute for Exploitation of the Sea, Ifremer DYNECO PELAGOS, 29280, Plouzané, France.,CNRS, Sorbonne Université, UMR 7144, Station Biologique de Roscoff, CS90074, 29688, Roscoff Cedex, France
| | - Raffaele Siano
- French Research Institute for Exploitation of the Sea, Ifremer DYNECO PELAGOS, 29280, Plouzané, France
| | - Marc Sourisseau
- French Research Institute for Exploitation of the Sea, Ifremer DYNECO PELAGOS, 29280, Plouzané, France
| | - Christophe Destombe
- CNRS, Sorbonne Université, UC, UaCh, UMI 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, 29688, Roscoff, France
| | - Mickael Le Gac
- French Research Institute for Exploitation of the Sea, Ifremer DYNECO PELAGOS, 29280, Plouzané, France.
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131
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Levy Karin E, Mirdita M, Söding J. MetaEuk-sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics. MICROBIOME 2020; 8:48. [PMID: 32245390 PMCID: PMC7126354 DOI: 10.1186/s40168-020-00808-x] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/14/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Metagenomics is revolutionizing the study of microorganisms and their involvement in biological, biomedical, and geochemical processes, allowing us to investigate by direct sequencing a tremendous diversity of organisms without the need for prior cultivation. Unicellular eukaryotes play essential roles in most microbial communities as chief predators, decomposers, phototrophs, bacterial hosts, symbionts, and parasites to plants and animals. Investigating their roles is therefore of great interest to ecology, biotechnology, human health, and evolution. However, the generally lower sequencing coverage, their more complex gene and genome architectures, and a lack of eukaryote-specific experimental and computational procedures have kept them on the sidelines of metagenomics. RESULTS MetaEuk is a toolkit for high-throughput, reference-based discovery, and annotation of protein-coding genes in eukaryotic metagenomic contigs. It performs fast searches with 6-frame-translated fragments covering all possible exons and optimally combines matches into multi-exon proteins. We used a benchmark of seven diverse, annotated genomes to show that MetaEuk is highly sensitive even under conditions of low sequence similarity to the reference database. To demonstrate MetaEuk's power to discover novel eukaryotic proteins in large-scale metagenomic data, we assembled contigs from 912 samples of the Tara Oceans project. MetaEuk predicted >12,000,000 protein-coding genes in 8 days on ten 16-core servers. Most of the discovered proteins are highly diverged from known proteins and originate from very sparsely sampled eukaryotic supergroups. CONCLUSION The open-source (GPLv3) MetaEuk software (https://github.com/soedinglab/metaeuk) enables large-scale eukaryotic metagenomics through reference-based, sensitive taxonomic and functional annotation. Video abstract.
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Affiliation(s)
- Eli Levy Karin
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.
| | - Milot Mirdita
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Johannes Söding
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.
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132
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Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics. Genome Res 2020; 30:647-659. [PMID: 32205368 PMCID: PMC7197479 DOI: 10.1101/gr.253070.119] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 03/18/2020] [Indexed: 11/25/2022]
Abstract
Large-scale metagenomic and metatranscriptomic data analyses are often restricted by their gene-centric approach, limiting the ability to understand organismal and community biology. De novo assembly of large and mosaic eukaryotic genomes from complex meta-omics data remains a challenging task, especially in comparison with more straightforward bacterial and archaeal systems. Here, we use a transcriptome reconstruction method based on clustering co-abundant genes across a series of metagenomic samples. We investigated the co-abundance patterns of ∼37 million eukaryotic unigenes across 365 metagenomic samples collected during the Tara Oceans expeditions to assess the diversity and functional profiles of marine plankton. We identified ∼12,000 co-abundant gene groups (CAGs), encompassing ∼7 million unigenes, including 924 metagenomics-based transcriptomes (MGTs, CAGs larger than 500 unigenes). We demonstrated the biological validity of the MGT collection by comparing individual MGTs with available references. We identified several key eukaryotic organisms involved in dimethylsulfoniopropionate (DMSP) biosynthesis and catabolism in different oceanic provinces, thus demonstrating the potential of the MGT collection to provide functional insights on eukaryotic plankton. We established the ability of the MGT approach to capture interspecies associations through the analysis of a nitrogen-fixing haptophyte-cyanobacterial symbiotic association. This MGT collection provides a valuable resource for analyses of eukaryotic plankton in the open ocean by giving access to the genomic content and functional potential of many ecologically relevant eukaryotic species.
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133
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Falciatore A, Jaubert M, Bouly JP, Bailleul B, Mock T. Diatom Molecular Research Comes of Age: Model Species for Studying Phytoplankton Biology and Diversity. THE PLANT CELL 2020; 32:547-572. [PMID: 31852772 PMCID: PMC7054031 DOI: 10.1105/tpc.19.00158] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 10/18/2019] [Accepted: 12/13/2019] [Indexed: 05/08/2023]
Abstract
Diatoms are the world's most diverse group of algae, comprising at least 100,000 species. Contributing ∼20% of annual global carbon fixation, they underpin major aquatic food webs and drive global biogeochemical cycles. Over the past two decades, Thalassiosira pseudonana and Phaeodactylum tricornutum have become the most important model systems for diatom molecular research, ranging from cell biology to ecophysiology, due to their rapid growth rates, small genomes, and the cumulative wealth of associated genetic resources. To explore the evolutionary divergence of diatoms, additional model species are emerging, such as Fragilariopsis cylindrus and Pseudo-nitzschia multistriata Here, we describe how functional genomics and reverse genetics have contributed to our understanding of this important class of microalgae in the context of evolution, cell biology, and metabolic adaptations. Our review will also highlight promising areas of investigation into the diversity of these photosynthetic organisms, including the discovery of new molecular pathways governing the life of secondary plastid-bearing organisms in aquatic environments.
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Affiliation(s)
- Angela Falciatore
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, UMR7238 Sorbonne Université, 75005 Paris, France
| | - Marianne Jaubert
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, UMR7238 Sorbonne Université, 75005 Paris, France
| | - Jean-Pierre Bouly
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, UMR7238 Sorbonne Université, 75005 Paris, France
| | - Benjamin Bailleul
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
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134
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Yu L, Zhang Y, Li M, Wang C, Lin X, Li L, Shi X, Guo C, Lin S. Comparative metatranscriptomic profiling and microRNA sequencing to reveal active metabolic pathways associated with a dinoflagellate bloom. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 699:134323. [PMID: 31522044 DOI: 10.1016/j.scitotenv.2019.134323] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/05/2019] [Accepted: 09/05/2019] [Indexed: 06/10/2023]
Abstract
Harmful algal blooms (HABs) have increased as a result of global climate and environmental changes, exerting increasing impacts on the aquatic ecosystem, coastal economy, and human health. Despite great research efforts, our understanding on the drivers of HABs is still limited in part because HAB species' physiology is difficult to probe in situ. Here, we used molecular ecological analyses to characterize a dinoflagellate bloom at Xiamen Harbor, China. Prorocentrum donghaiense was identified as the culprit, which nutrient bioassays showed were not nutrient-limited. Metatranscriptome profiling revealed that P. donghaiense highly expressed genes related to N- and P-nutrient uptake, phagotrophy, energy metabolism (photosynthesis, oxidative phophorylation, and rhodopsin) and carbohydrate metabolism (glycolysis/gluconeogenesis, TCA cycle and pentose phosphate) during the bloom. Many genes in P. donghaiense were up-regulated at night, including phagotrophy and environmental communication genes, and showed active expression in mitosis. Eight microbial defense genes were up-regulated in the bloom compared with previously analyzed laboratory cultures. Furthermore, 76 P. donghaiense microRNA were identified from the bloom, and their target genes exhibited marked differences in amino acid metabolism between the bloom and cultures and the potential of up-regulated antibiotic and cell communication capabilities. These findings, consistent with and complementary to recent reports, reveal major metabolic processes in P. donghaiense potentially important for bloom formation and provide a gene repertoire for developing bloom markers in future research.
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Affiliation(s)
- Liying Yu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Yaqun Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China
| | - Meizhen Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Cong Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Xin Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Xinguo Shi
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; College of Biological Science and Engineering, Fuzhou University, Fujian 350116, China
| | - Chentao Guo
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA.
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135
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Abstract
Photosynthesis evolved in the ocean more than 2 billion years ago and is now performed by a wide range of evolutionarily distinct organisms, including both prokaryotes and eukaryotes. Our appreciation of their abundance, distributions, and contributions to primary production in the ocean has been increasing since they were first discovered in the seventeenth century and has now been enhanced by data emerging from the Tara Oceans project, which performed a comprehensive worldwide sampling of plankton in the upper layers of the ocean between 2009 and 2013. Largely using recent data from Tara Oceans, here we review the geographic distributions of phytoplankton in the global ocean and their diversity, abundance, and standing stock biomass. We also discuss how omics-based information can be incorporated into studies of photosynthesis in the ocean and show the likely importance of mixotrophs and photosymbionts.
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Affiliation(s)
- Juan José Pierella Karlusich
- Institut de Biologie de l'École Normale Supérieure (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université de Recherche Paris Sciences et Lettres (Université PSL), 75005 Paris, France;
| | - Federico M Ibarbalz
- Institut de Biologie de l'École Normale Supérieure (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université de Recherche Paris Sciences et Lettres (Université PSL), 75005 Paris, France;
| | - Chris Bowler
- Institut de Biologie de l'École Normale Supérieure (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université de Recherche Paris Sciences et Lettres (Université PSL), 75005 Paris, France;
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136
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Ait-Mohamed O, Novák Vanclová AMG, Joli N, Liang Y, Zhao X, Genovesio A, Tirichine L, Bowler C, Dorrell RG. PhaeoNet: A Holistic RNAseq-Based Portrait of Transcriptional Coordination in the Model Diatom Phaeodactylum tricornutum. FRONTIERS IN PLANT SCIENCE 2020; 11:590949. [PMID: 33178253 PMCID: PMC7596299 DOI: 10.3389/fpls.2020.590949] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/15/2020] [Indexed: 05/04/2023]
Abstract
Transcriptional coordination is a fundamental component of prokaryotic and eukaryotic cell biology, underpinning the cell cycle, physiological transitions, and facilitating holistic responses to environmental stress, but its overall dynamics in eukaryotic algae remain poorly understood. Better understanding of transcriptional partitioning may provide key insights into the primary metabolism pathways of eukaryotic algae, which frequently depend on intricate metabolic associations between the chloroplasts and mitochondria that are not found in plants. Here, we exploit 187 publically available RNAseq datasets generated under varying nitrogen, iron and phosphate growth conditions to understand the co-regulatory principles underpinning transcription in the model diatom Phaeodactylum tricornutum. Using WGCNA (Weighted Gene Correlation Network Analysis), we identify 28 merged modules of co-expressed genes in the P. tricornutum genome, which show high connectivity and correlate well with previous microarray-based surveys of gene co-regulation in this species. We use combined functional, subcellular localization and evolutionary annotations to reveal the fundamental principles underpinning the transcriptional co-regulation of genes implicated in P. tricornutum chloroplast and mitochondrial metabolism, as well as the functions of diverse transcription factors underpinning this co-regulation. The resource is publically available as PhaeoNet, an advanced tool to understand diatom gene co-regulation.
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Affiliation(s)
- Ouardia Ait-Mohamed
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Anna M. G. Novák Vanclová
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Nathalie Joli
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Yue Liang
- Department of Oceanography, Dalhousie University, Halifax, NS, Canada
| | - Xue Zhao
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Université de Nantes, CNRS, UFIP, UMR 6286, Nantes, France
| | - Auguste Genovesio
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Leila Tirichine
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Université de Nantes, CNRS, UFIP, UMR 6286, Nantes, France
- *Correspondence: Leila Tirichine,
| | - Chris Bowler
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Chris Bowler,
| | - Richard G. Dorrell
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
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137
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Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nat Methods 2020; 17:481-494. [PMID: 32251396 PMCID: PMC7200600 DOI: 10.1038/s41592-020-0796-x] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 03/02/2020] [Indexed: 12/13/2022]
Abstract
Diverse microbial ecosystems underpin life in the sea. Among these microbes are many unicellular eukaryotes that span the diversity of the eukaryotic tree of life. However, genetic tractability has been limited to a few species, which do not represent eukaryotic diversity or environmentally relevant taxa. Here, we report on the development of genetic tools in a range of protists primarily from marine environments. We present evidence for foreign DNA delivery and expression in 13 species never before transformed and for advancement of tools for eight other species, as well as potential reasons for why transformation of yet another 17 species tested was not achieved. Our resource in genetic manipulation will provide insights into the ancestral eukaryotic lifeforms, general eukaryote cell biology, protein diversification and the evolution of cellular pathways.
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138
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Sordino P, D'Aniello S, Pelletier E, Wincker P, Nittoli V, Stemmann L, Mazzocchi MG, Lombard F, Iudicone D, Caputi L. Into the bloom: Molecular response of pelagic tunicates to fluctuating food availability. Mol Ecol 2019; 29:292-307. [PMID: 31793138 DOI: 10.1111/mec.15321] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 01/07/2023]
Abstract
The planktonic tunicates appendicularians and thaliaceans are highly efficient filter feeders on a wide range of prey size including bacteria and have shorter generation times than any other marine grazers. These traits allow some tunicate species to reach high population densities and ensure their success in a favourable environment. However, there are still few studies focusing on which genes and gene pathways are associated with responses of pelagic tunicates to environmental variability. Herein, we present the effect of food availability increase on tunicate community and gene expression at the Marquesas Islands (South-East Pacific Ocean). By using data from the Tara Oceans expedition, we show that changes in phytoplankton density and composition trigger the success of a dominant larvacean species (an undescribed appendicularian). Transcriptional signature to the autotroph bloom suggests key functions in specific physiological processes, i.e., energy metabolism, muscle contraction, membrane trafficking, and proteostasis. The relative abundance of reverse transcription-related Pfams was lower at bloom conditions, suggesting a link with adaptive genetic diversity in tunicates in natural ecosystems. Downstream of the bloom, pelagic tunicates were outcompeted by copepods. Our work represents the first metaomics study of the biological effects of phytoplankton bloom on a key zooplankton taxon.
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Affiliation(s)
| | | | - Eric Pelletier
- CEA - Institut Francois Jacob, Genoscope, Evry, France.,CNRS, UMR, Evry, France.,Université d'Evry Val d'Essonne, Université Paris-Saclay, Evry, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, Paris, France
| | - Patrick Wincker
- CEA - Institut Francois Jacob, Genoscope, Evry, France.,CNRS, UMR, Evry, France.,Université d'Evry Val d'Essonne, Université Paris-Saclay, Evry, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, Paris, France
| | | | - Lars Stemmann
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, Paris, France.,CNRS, UMR 7093, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, Sorbonne Université, Villefranche-sur-Mer, France
| | | | - Fabien Lombard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, Paris, France.,CNRS, UMR 7093, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, Sorbonne Université, Villefranche-sur-Mer, France
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139
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Salazar G, Paoli L, Alberti A, Huerta-Cepas J, Ruscheweyh HJ, Cuenca M, Field CM, Coelho LP, Cruaud C, Engelen S, Gregory AC, Labadie K, Marec C, Pelletier E, Royo-Llonch M, Roux S, Sánchez P, Uehara H, Zayed AA, Zeller G, Carmichael M, Dimier C, Ferland J, Kandels S, Picheral M, Pisarev S, Poulain J, Acinas SG, Babin M, Bork P, Bowler C, de Vargas C, Guidi L, Hingamp P, Iudicone D, Karp-Boss L, Karsenti E, Ogata H, Pesant S, Speich S, Sullivan MB, Wincker P, Sunagawa S. Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome. Cell 2019; 179:1068-1083.e21. [PMID: 31730850 PMCID: PMC6912165 DOI: 10.1016/j.cell.2019.10.014] [Citation(s) in RCA: 181] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 07/26/2019] [Accepted: 10/11/2019] [Indexed: 12/02/2022]
Abstract
Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms. VIDEO ABSTRACT.
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Affiliation(s)
- Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Lucas Paoli
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid 28223, Spain; Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Miguelangel Cuenca
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Christopher M Field
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China; Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China; Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Corinne Cruaud
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Stefan Engelen
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Ann C Gregory
- Department of Microbiology, the Ohio State University, Columbus, OH 43210, USA
| | - Karine Labadie
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Claudie Marec
- Département de biologie, Université Laval, QC G1V 0A6, Canada; Laboratoire d'Oceanographie Physique et Spatiale, UMR 6523, CNRS-IFREMER-IRD-UBO, Plouzané, France
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France
| | - Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Barcelona 08003, Spain
| | - Simon Roux
- Department of Microbiology, the Ohio State University, Columbus, OH 43210, USA
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Barcelona 08003, Spain
| | - Hideya Uehara
- Institute for Chemical Research, Kyoto Univerisity, Gokasho, Uji 611-0011, Japan; Hewlett-Packard Japan, 2-2-1, Ojima, Koto-ku, Tokyo 136-8711, Japan
| | - Ahmed A Zayed
- Department of Microbiology, the Ohio State University, Columbus, OH 43210, USA
| | - Georg Zeller
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Margaux Carmichael
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université & CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Céline Dimier
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefanche, LOV, Villefranche-sur-mer 06230, France; Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris 75005, France
| | - Joannie Ferland
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Takuvik Joint International Laboratory, CNRS-Université Laval, QC G1V 0A6, Canada
| | - Stefanie Kandels
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Marc Picheral
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefanche, LOV, Villefranche-sur-mer 06230, France
| | - Sergey Pisarev
- Shirshov Institute of Oceanology, Russian Academy of Sciences, Moscow 117997, Russia
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Barcelona 08003, Spain
| | - Marcel Babin
- Takuvik Joint International Laboratory, CNRS-Université Laval, QC G1V 0A6, Canada
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany; Max Delbrück Centre for Molecular Medicine, Berlin 13125, Germany; Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Chris Bowler
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris 75005, France
| | - Colomban de Vargas
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université & CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Lionel Guidi
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université & CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France; Department of Oceanography, University of Hawaii, Honolulu, HI 96822, USA
| | - Pascal Hingamp
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | | | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, ME 04469, USA
| | - Eric Karsenti
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris 75005, France; Directors' Research European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto Univerisity, Gokasho, Uji 611-0011, Japan
| | - Stephane Pesant
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany; PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany
| | | | - Matthew B Sullivan
- Department of Microbiology, the Ohio State University, Columbus, OH 43210, USA; Department of Civil, Environmental and Geodetic Engineering, the Ohio State University, Columbus, OH 43214, USA; Center for RNA Biology, the Ohio State University, Columbus, OH 43214, USA
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland.
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140
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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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141
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Han KY, Maciszewski K, Graf L, Yang JH, Andersen RA, Karnkowska A, Yoon HS. Dictyochophyceae Plastid Genomes Reveal Unusual Variability in Their Organization. JOURNAL OF PHYCOLOGY 2019; 55:1166-1180. [PMID: 31325913 DOI: 10.1111/jpy.12904] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/01/2019] [Indexed: 05/22/2023]
Abstract
Dictyochophyceae (silicoflagellates) are unicellular freshwater and marine algae (Heterokontophyta, stramenopiles). Despite their abundance in global oceans and potential ecological significance, discovered in recent years, neither nuclear nor organellar genomes of representatives of this group were sequenced until now. Here, we present the first complete plastid genome sequences of Dictyochophyceae, obtained from four species: Dictyocha speculum, Rhizochromulina marina, Florenciella parvula and Pseudopedinella elastica. Despite their comparable size and genetic content, these four plastid genomes exhibit variability in their organization: plastid genomes of F. parvula and P. elastica possess conventional quadripartite structure with a pair of inverted repeats, R. marina instead possesses two direct repeats with the same orientation and D. speculum possesses no repeats at all. We also observed a number of unusual traits in the plastid genome of D. speculum, including expansion of the intergenic regions, presence of an intron in the otherwise non-intron-bearing psaA gene, and an additional copy of the large subunit of RuBisCO gene (rbcL), the last of which has never been observed in any plastid genome. We conclude that despite noticeable gene content similarities between the plastid genomes of Dictyochophyceae and their relatives (pelagophytes, diatoms), the number of distinctive features observed in this lineage strongly suggests that additional taxa require further investigation.
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Affiliation(s)
- Kwi Young Han
- Department of Biological Science, Sungkyunkwan University, Suwon, 16419, Korea
| | - Kacper Maciszewski
- Department of Molecular Phylogenetics and Evolution, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Louis Graf
- Department of Biological Science, Sungkyunkwan University, Suwon, 16419, Korea
| | - Ji Hyun Yang
- Department of Biological Science, Sungkyunkwan University, Suwon, 16419, Korea
| | - Robert A Andersen
- Friday Harbor Laboratories, University of Washington, Friday Harbor, Washington, 98250, USA
| | - Anna Karnkowska
- Department of Molecular Phylogenetics and Evolution, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Hwan Su Yoon
- Department of Biological Science, Sungkyunkwan University, Suwon, 16419, Korea
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142
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Planes S, Allemand D, Agostini S, Banaigs B, Boissin E, Boss E, Bourdin G, Bowler C, Douville E, Flores JM, Forcioli D, Furla P, Galand PE, Ghiglione JF, Gilson E, Lombard F, Moulin C, Pesant S, Poulain J, Reynaud S, Romac S, Sullivan MB, Sunagawa S, Thomas OP, Troublé R, de Vargas C, Vega Thurber R, Voolstra CR, Wincker P, Zoccola D. The Tara Pacific expedition-A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean. PLoS Biol 2019; 17:e3000483. [PMID: 31545807 PMCID: PMC6776362 DOI: 10.1371/journal.pbio.3000483] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 10/03/2019] [Indexed: 02/01/2023] Open
Abstract
Coral reefs are the most diverse habitats in the marine realm. Their productivity, structural complexity, and biodiversity critically depend on ecosystem services provided by corals that are threatened because of climate change effects-in particular, ocean warming and acidification. The coral holobiont is composed of the coral animal host, endosymbiotic dinoflagellates, associated viruses, bacteria, and other microeukaryotes. In particular, the mandatory photosymbiosis with microalgae of the family Symbiodiniaceae and its consequences on the evolution, physiology, and stress resilience of the coral holobiont have yet to be fully elucidated. The functioning of the holobiont as a whole is largely unknown, although bacteria and viruses are presumed to play roles in metabolic interactions, immunity, and stress tolerance. In the context of climate change and anthropogenic threats on coral reef ecosystems, the Tara Pacific project aims to provide a baseline of the "-omics" complexity of the coral holobiont and its ecosystem across the Pacific Ocean and for various oceanographically distinct defined areas. Inspired by the previous Tara Oceans expeditions, the Tara Pacific expedition (2016-2018) has applied a pan-ecosystemic approach on coral reefs throughout the Pacific Ocean, drawing an east-west transect from Panama to Papua New Guinea and a south-north transect from Australia to Japan, sampling corals throughout 32 island systems with local replicates. Tara Pacific has developed and applied state-of-the-art technologies in very-high-throughput genetic sequencing and molecular analysis to reveal the entire microbial and chemical diversity as well as functional traits associated with coral holobionts, together with various measures on environmental forcing. This ambitious project aims at revealing a massive amount of novel biodiversity, shedding light on the complex links between genomes, transcriptomes, metabolomes, organisms, and ecosystem functions in coral reefs and providing a reference of the biological state of modern coral reefs in the Anthropocene.
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Affiliation(s)
- Serge Planes
- Laboratoire d’Excellence “CORAIL,” PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE, Paris, France
- * E-mail:
| | - Denis Allemand
- Centre Scientifique de Monaco, Monte Carlo, Principality of Monaco
| | | | - Bernard Banaigs
- Laboratoire d’Excellence “CORAIL,” PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France
| | - Emilie Boissin
- Laboratoire d’Excellence “CORAIL,” PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, Maine, United States of America
| | - Guillaume Bourdin
- School of Marine Sciences, University of Maine, Orono, Maine, United States of America
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France
| | - Chris Bowler
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE, Paris, France
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l’Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, Gif-sur-Yvette, France
| | - J. Michel Flores
- Weizmann Institute of Science, Dept. Earth and Planetary Science, Rehovot, Israel
| | - Didier Forcioli
- Université Côte d'Azur-CNRS-INSERM, IRCAN, Medical School, Nice, France and Department of Medical Genetics, CHU of Nice, Nice, France
| | - Paola Furla
- Université Côte d'Azur-CNRS-INSERM, IRCAN, Medical School, Nice, France and Department of Medical Genetics, CHU of Nice, Nice, France
| | - Pierre E. Galand
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE, Paris, France
- Sorbonne Université, CNRS, Laboratoire d’Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls sur mer, France
| | - Jean-François Ghiglione
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE, Paris, France
- Sorbonne Université Laboratoire d’Océanographie Microbienne LOMIC, UMR 7621, Observatoire Océanologique de Banyuls, Banyuls sur mer, France
| | - Eric Gilson
- Université Côte d'Azur-CNRS-INSERM, IRCAN, Medical School, Nice, France and Department of Medical Genetics, CHU of Nice, Nice, France
| | - Fabien Lombard
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-Mer, France
| | | | - Stephane Pesant
- PANGEA, Data Publisher for Earth and Environment Science, Bremen, Germany
- MARUM—Center for Marine Environmental Sciences, Universität Bremen, Bremen, Germany
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | | | - Sarah Romac
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Matthew B. Sullivan
- Departments of Microbiology and Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, Ohio, United States of America
| | - Shinichi Sunagawa
- Department of Biology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | - Olivier P. Thomas
- Marine Biodiscovery Laboratory, School of Chemistry and Ryan Institute, National University of Ireland, Galway (NUI Galway), Galway, Ireland
| | - Romain Troublé
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE, Paris, France
- La Fondation Tara Expéditions, “Base Tara” 11, Paris, France
| | - Colomban de Vargas
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Rebecca Vega Thurber
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
| | | | - Patrick Wincker
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE, Paris, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Didier Zoccola
- Centre Scientifique de Monaco, Monte Carlo, Principality of Monaco
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143
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Villar E, Vannier T, Vernette C, Lescot M, Cuenca M, Alexandre A, Bachelerie P, Rosnet T, Pelletier E, Sunagawa S, Hingamp P. The Ocean Gene Atlas: exploring the biogeography of plankton genes online. Nucleic Acids Res 2019; 46:W289-W295. [PMID: 29788376 PMCID: PMC6030836 DOI: 10.1093/nar/gky376] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/02/2018] [Indexed: 12/27/2022] Open
Abstract
The Ocean Gene Atlas is a web service to explore the biogeography of genes from marine planktonic organisms. It allows users to query protein or nucleotide sequences against global ocean reference gene catalogs. With just one click, the abundance and location of target sequences are visualized on world maps as well as their taxonomic distribution. Interactive results panels allow for adjusting cutoffs for alignment quality and displaying the abundances of genes in the context of environmental features (temperature, nutrients, etc.) measured at the time of sampling. The ease of use enables non-bioinformaticians to explore quantitative and contextualized information on genes of interest in the global ocean ecosystem. Currently the Ocean Gene Atlas is deployed with (i) the Ocean Microbial Reference Gene Catalog (OM-RGC) comprising 40 million non-redundant mostly prokaryotic gene sequences associated with both Tara Oceans and Global Ocean Sampling (GOS) gene abundances and (ii) the Marine Atlas of Tara Ocean Unigenes (MATOU) composed of >116 million eukaryote unigenes. Additional datasets will be added upon availability of further marine environmental datasets that provide the required complement of sequence assemblies, raw reads and contextual environmental parameters. Ocean Gene Atlas is a freely-available web service at: http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/.
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Affiliation(s)
- Emilie Villar
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin UMR7144, Station Biologique de Roscoff, Roscoff, France.,Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Thomas Vannier
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Caroline Vernette
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Magali Lescot
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Miguelangel Cuenca
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Aurélien Alexandre
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Paul Bachelerie
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Thomas Rosnet
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut de Biologie François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Pascal Hingamp
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
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144
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Nakayama T, Nomura M, Takano Y, Tanifuji G, Shiba K, Inaba K, Inagaki Y, Kawata M. Single-cell genomics unveiled a cryptic cyanobacterial lineage with a worldwide distribution hidden by a dinoflagellate host. Proc Natl Acad Sci U S A 2019; 116:15973-15978. [PMID: 31235587 PMCID: PMC6689939 DOI: 10.1073/pnas.1902538116] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cyanobacteria are one of the most important contributors to oceanic primary production and survive in a wide range of marine habitats. Much effort has been made to understand their ecological features, diversity, and evolution, based mainly on data from free-living cyanobacterial species. In addition, symbiosis has emerged as an important lifestyle of oceanic microbes and increasing knowledge of cyanobacteria in symbiotic relationships with unicellular eukaryotes suggests their significance in understanding the global oceanic ecosystem. However, detailed characteristics of these cyanobacteria remain poorly described. To gain better insight into marine cyanobacteria in symbiosis, we sequenced the genome of cyanobacteria collected from a cell of a pelagic dinoflagellate that is known to host cyanobacterial symbionts within a specialized chamber. Phylogenetic analyses using the genome sequence revealed that the cyanobacterium represents an underdescribed lineage within an extensively studied, ecologically important group of marine cyanobacteria. Metagenomic analyses demonstrated that this cyanobacterial lineage is globally distributed and strictly coexists with its host dinoflagellates, suggesting that the intimate symbiotic association allowed the cyanobacteria to escape from previous metagenomic studies. Furthermore, a comparative analysis of the protein repertoire with related species indicated that the lineage has independently undergone reductive genome evolution to a similar extent as Prochlorococcus, which has the most reduced genomes among free-living cyanobacteria. Discovery of this cyanobacterial lineage, hidden by its symbiotic lifestyle, provides crucial insights into the diversity, ecology, and evolution of marine cyanobacteria and suggests the existence of other undiscovered cryptic cyanobacterial lineages.
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Affiliation(s)
- Takuro Nakayama
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8578, Japan;
| | - Mami Nomura
- Shimoda Marine Research Center, University of Tsukuba, Shimoda 415-0025, Japan
| | - Yoshihito Takano
- Faculty of Science and Technology, Kochi University, Nankoku 783-8502, Japan
| | - Goro Tanifuji
- Department of Zoology, National Museum of Nature and Science, Tsukuba 305-0005, Japan
| | - Kogiku Shiba
- Shimoda Marine Research Center, University of Tsukuba, Shimoda 415-0025, Japan
| | - Kazuo Inaba
- Shimoda Marine Research Center, University of Tsukuba, Shimoda 415-0025, Japan
| | - Yuji Inagaki
- Center for Computational Sciences, University of Tsukuba, Tsukuba 305-8577, Japan
| | - Masakado Kawata
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8578, Japan
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145
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Li Y, Endo H, Gotoh Y, Watai H, Ogawa N, Blanc-Mathieu R, Yoshida T, Ogata H. The Earth Is Small for "Leviathans": Long Distance Dispersal of Giant Viruses across Aquatic Environments. Microbes Environ 2019; 34:334-339. [PMID: 31378760 PMCID: PMC6759346 DOI: 10.1264/jsme2.me19037] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Giant viruses of ‘Megaviridae’ have the ability to widely disperse around the globe. We herein examined ‘Megaviridae’ communities in four distinct aquatic environments (coastal and offshore seawater, brackish water, and hot spring freshwater), which are distantly located from each other (between 74 and 1,765 km), using a meta-barcoding method. We identified between 593 and 3,627 OTUs in each sample. Some OTUs were detected in all five samples tested as well as in many of the Tara Oceans metagenomes, suggesting the existence of viruses of this family in a wide range of habitats and the ability to circulate on the planet.
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Affiliation(s)
- Yanze Li
- Institute for Chemical Research, Kyoto University
| | - Hisashi Endo
- Institute for Chemical Research, Kyoto University
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University
| | | | - Nana Ogawa
- Graduate School of Agriculture, Kyoto University
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146
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Tan S, Liu J, Fang Y, Hedlund BP, Lian ZH, Huang LY, Li JT, Huang LN, Li WJ, Jiang HC, Dong HL, Shu WS. Insights into ecological role of a new deltaproteobacterial order Candidatus Acidulodesulfobacterales by metagenomics and metatranscriptomics. THE ISME JOURNAL 2019; 13:2044-2057. [PMID: 30962514 PMCID: PMC6776010 DOI: 10.1038/s41396-019-0415-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 02/15/2019] [Accepted: 03/24/2019] [Indexed: 12/21/2022]
Abstract
Several abundant but yet uncultivated bacterial groups exist in extreme iron- and sulfur-rich environments, and the physiology, biodiversity, and ecological roles of these bacteria remain a mystery. Here we retrieved four metagenome-assembled genomes (MAGs) from an artificial acid mine drainage (AMD) system, and propose they belong to a new deltaproteobacterial order, Candidatus Acidulodesulfobacterales. The distribution pattern of Ca. Acidulodesulfobacterales in AMDs across Southeast China correlated strongly with ferrous iron. Reconstructed metabolic pathways and gene expression profiles showed that they were likely facultatively anaerobic autotrophs capable of nitrogen fixation. In addition to dissimilatory sulfate reduction, encoded by dsrAB, dsrD, dsrL, and dsrEFH genes, these microorganisms might also oxidize sulfide, depending on oxygen concentration and/or oxidation reduction potential. Several genes with homology to those involved in iron metabolism were also identified, suggesting their potential role in iron cycling. In addition, the expression of abundant resistance genes revealed the mechanisms of adaptation and response to the extreme environmental stresses endured by these organisms in the AMD environment. These findings shed light on the distribution, diversity, and potential ecological role of the new order Ca. Acidulodesulfobacterales in nature.
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Affiliation(s)
- Sha Tan
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Jun Liu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
- Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, 45056, USA
| | - Yun Fang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Zheng-Han Lian
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
- Guangdong Magigene Biotechnology Co. Ltd., 510000, Guangzhou, China
| | - Li-Ying Huang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Jin-Tian Li
- School of Life Sciences, South China Normal University, 510631, Guangzhou, China
| | - Li-Nan Huang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Hong-Chen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Hai-Liang Dong
- Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, 45056, USA.
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 100083, Beijing, China.
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, 510631, Guangzhou, China.
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147
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Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection. ISME JOURNAL 2019; 13:2817-2833. [PMID: 31320727 PMCID: PMC6794264 DOI: 10.1038/s41396-019-0472-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 06/11/2019] [Accepted: 06/15/2019] [Indexed: 01/06/2023]
Abstract
Phytoplankton and associated microbial communities provide organic carbon to oceanic food webs and drive ecosystem dynamics. However, capturing those dynamics is challenging. Here, an in situ, semi-Lagrangian, robotic sampler profiled pelagic microbes at 4 h intervals over ~2.6 days in North Pacific high-nutrient, low-chlorophyll waters. We report on the community structure and transcriptional dynamics of microbes in an operationally large size class (>5 μm) predominantly populated by dinoflagellates, ciliates, haptophytes, pelagophytes, diatoms, cyanobacteria (chiefly Synechococcus), prasinophytes (chiefly Ostreococcus), fungi, archaea, and proteobacteria. Apart from fungi and archaea, all groups exhibited 24-h periodicity in some transcripts, but larger portions of the transcriptome oscillated in phototrophs. Periodic photosynthesis-related transcripts exhibited a temporal cascade across the morning hours, conserved across diverse phototrophic lineages. Pronounced silica:nitrate drawdown, a high flavodoxin to ferredoxin transcript ratio, and elevated expression of other Fe-stress markers indicated Fe-limitation. Fe-stress markers peaked during a photoperiodically adaptive time window that could modulate phytoplankton response to seasonal Fe-limitation. Remarkably, we observed viruses that infect the majority of abundant taxa, often with total transcriptional activity synchronized with putative hosts. Taken together, these data reveal a microbial plankton community that is shaped by recycled production and tightly controlled by Fe-limitation and viral activity.
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148
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Busseni G, Vieira FRJ, Amato A, Pelletier E, Pierella Karlusich JJ, Ferrante MI, Wincker P, Rogato A, Bowler C, Sanges R, Maiorano L, Chiurazzi M, d'Alcalà MR, Caputi L, Iudicone D. Meta-omics reveals genetic flexibility of diatom nitrogen transporters in response to environmental changes. Mol Biol Evol 2019; 36:2522-2535. [PMID: 31259367 PMCID: PMC6805229 DOI: 10.1093/molbev/msz157] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/05/2019] [Accepted: 06/22/2019] [Indexed: 01/27/2023] Open
Abstract
Diatoms (Bacillariophyta), one of the most abundant and diverse groups of marine phytoplankton, respond rapidly to the supply of new nutrients, often out-competing other phytoplankton. Herein, we integrated analyses of the evolution, distribution and expression modulation of two gene families involved in diatom nitrogen uptake (DiAMT1 and DiNRT2), in order to infer the main drivers of divergence in a key functional trait of phytoplankton. Our results suggest that major steps in the evolution of the two gene families reflected key events triggering diatom radiation and diversification. Their expression is modulated in the contemporary ocean by seawater temperature, nitrate and iron concentrations. Moreover, the differences in diversity and expression of these gene families throughout the water column hint at a possible link with bacterial activity. This study represents a proof-of-concept of how a holistic approach may shed light on the functional biology of organisms in their natural environment.
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Affiliation(s)
- Greta Busseni
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy
| | - Fabio Rocha Jimenez Vieira
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
| | - Alberto Amato
- Laboratoire de Physiologie Cellulaire et Végétale, Univ. Grenoble Alpes, CEA, INRA, CNRS. BIG, 17 rue des Martyrs Grenoble cedex 9, France
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France.,FR2022/Tara Oceans-GOSEE, 3 rue Michel-Ange, Paris, France
| | - Juan J Pierella Karlusich
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
| | | | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France.,FR2022/Tara Oceans-GOSEE, 3 rue Michel-Ange, Paris, France
| | - Alessandra Rogato
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy.,Institute of Biosciences and BioResources, CNR, Via P. Castellino 111, Naples, Italy
| | - Chris Bowler
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
| | - Remo Sanges
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy.,Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, Trieste, Italy
| | - Luigi Maiorano
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy.,Dipartimento di Biologia e Biotecnologie "Charles Darwin", Università di Roma "La Sapienza", Viale dell'Università 32, Roma, Italy
| | - Maurizio Chiurazzi
- Institute of Biosciences and BioResources, CNR, Via P. Castellino 111, Naples, Italy
| | | | - Luigi Caputi
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy
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149
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Debeljak P, Toulza E, Beier S, Blain S, Obernosterer I. Microbial iron metabolism as revealed by gene expression profiles in contrasted Southern Ocean regimes. Environ Microbiol 2019; 21:2360-2374. [PMID: 30958628 PMCID: PMC6618146 DOI: 10.1111/1462-2920.14621] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 03/18/2019] [Accepted: 04/01/2019] [Indexed: 11/28/2022]
Abstract
Iron (Fe) is a limiting nutrient in large regions of the ocean, but the strategies of prokaryotes to cope with this micronutrient are poorly known. Using a gene-specific approach from metatranscriptomics data, we investigated seven Fe-related metabolic pathways in microbial communities from high nutrient low chlorophyll and naturally Fe-fertilized waters in the Southern Ocean. We observed major differences in the contribution of prokaryotic groups at different taxonomic levels to transcripts encoding Fe-uptake mechanisms, intracellular Fe storage and replacement and Fe-related pathways in the tricarboxylic acid (TCA) cycle. The composition of the prokaryotic communities contributing to the transcripts of a given Fe-related pathway was overall independent of the in situ Fe supply, indicating that microbial taxa utilize distinct Fe-related metabolic processes. Only a few prokaryotic groups contributed to the transcripts of more than one Fe-uptake mechanism, suggesting limited metabolic versatility. Taxa-specific expression of individual genes varied among prokaryotic groups and was substantially higher for all inspected genes in Fe-limited as compared to naturally fertilized waters, indicating the link between transcriptional state and Fe regime. Different metabolic strategies regarding low Fe concentrations in the Southern Ocean are discussed for two abundant prokaryotic groups, Pelagibacteraceae and Flavobacteriaceae.
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Affiliation(s)
- Pavla Debeljak
- Sorbonne UniversitéCNRS, Laboratoire d'Océanographie Microbienne, LOMICF‐66650 Banyuls/merFrance
- Department of Limnology and Bio‐OceanographyUniversity of Vienna, A‐1090ViennaAustria
| | - Eve Toulza
- Université Perpignan Via DomitiaIHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, F‐66860PerpignanFrance
| | - Sara Beier
- Leibniz Institute for Baltic Sea ResearchWarnemündeGermany
| | - Stephane Blain
- Sorbonne UniversitéCNRS, Laboratoire d'Océanographie Microbienne, LOMICF‐66650 Banyuls/merFrance
| | - Ingrid Obernosterer
- Sorbonne UniversitéCNRS, Laboratoire d'Océanographie Microbienne, LOMICF‐66650 Banyuls/merFrance
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150
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Steinegger M, Mirdita M, Söding J. Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold. Nat Methods 2019; 16:603-606. [PMID: 31235882 DOI: 10.1038/s41592-019-0437-4] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 03/15/2019] [Accepted: 05/05/2019] [Indexed: 12/25/2022]
Abstract
The open-source de novo protein-level assembler, Plass ( https://plass.mmseqs.com ), assembles six-frame-translated sequencing reads into protein sequences. It recovers 2-10 times more protein sequences from complex metagenomes and can assemble huge datasets. We assembled two redundancy-filtered reference protein catalogs, 2 billion sequences from 640 soil samples (soil reference protein catalog) and 292 million sequences from 775 marine eukaryotic metatranscriptomes (marine eukaryotic reference catalog), the largest free collections of protein sequences.
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Affiliation(s)
- Martin Steinegger
- Quantitative and Computational Biology Group, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany. .,Department of Chemistry, Seoul National University, Seoul, Korea. .,Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA.
| | - Milot Mirdita
- Quantitative and Computational Biology Group, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Johannes Söding
- Quantitative and Computational Biology Group, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany.
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