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Cho A, Lax G, Keeling PJ. Phylogenomic analyses of ochrophytes (stramenopiles) with an emphasis on neglected lineages. Mol Phylogenet Evol 2024; 198:108120. [PMID: 38852907 DOI: 10.1016/j.ympev.2024.108120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 05/13/2024] [Accepted: 06/04/2024] [Indexed: 06/11/2024]
Abstract
Ochrophyta is a photosynthetic lineage that crowns the phylogenetic tree of stramenopiles, one of the major eukaryotic supergroups. Due to their ecological impact as a major primary producer, ochrophytes are relatively well-studied compared to the rest of the stramenopiles, yet their evolutionary relationships remain poorly understood. This is in part due to a number of missing lineages in large-scale multigene analyses, and an apparently rapid radiation leading to many short internodes between ochrophyte subgroups in the tree. These short internodes are also found across deep-branching lineages of stramenopiles with limited phylogenetic signal, leaving many relationships controversial overall. We have addressed this issue with other deep-branching stramenopiles recently, and now examine whether contentious relationships within the ochrophytes may be resolved with the help of filling in missing lineages in an updated phylogenomic dataset of ochrophytes, along with exploring various gene filtering criteria to identify the most phylogenetically informative genes. We generated ten new transcriptomes from various culture collections and a single-cell isolation from an environmental sample, added these to an existing phylogenomic dataset, and examined the effects of selecting genes with high phylogenetic signal or low phylogenetic noise. For some previously contentious relationships, we find a variety of analyses and gene filtering criteria consistently unite previously unstable groupings with strong statistical support. For example, we recovered a robust grouping of Eustigmatophyceae with Raphidophyceae-Phaeophyceae-Xanthophyceae while Olisthodiscophyceae formed a sister-lineage to Pinguiophyceae. Selecting genes with high phylogenetic signal or data quality recovered more stable topologies. Overall, we find that adding under-represented groups across different lineages is still crucial in resolving phylogenetic relationships, and discrete gene properties affect lineages of stramenopiles differently. This is something which may be explored to further our understanding of the molecular evolution of stramenopiles.
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Affiliation(s)
- Anna Cho
- Department of Botany, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada.
| | - Gordon Lax
- Department of Botany, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada
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2
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Tedersoo L, Hosseyni Moghaddam MS, Mikryukov V, Hakimzadeh A, Bahram M, Nilsson RH, Yatsiuk I, Geisen S, Schwelm A, Piwosz K, Prous M, Sildever S, Chmolowska D, Rueckert S, Skaloud P, Laas P, Tines M, Jung JH, Choi JH, Alkahtani S, Anslan S. EUKARYOME: the rRNA gene reference database for identification of all eukaryotes. Database (Oxford) 2024; 2024:baae043. [PMID: 38865431 PMCID: PMC11168333 DOI: 10.1093/database/baae043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 03/14/2024] [Accepted: 05/23/2024] [Indexed: 06/14/2024]
Abstract
Molecular identification of micro- and macroorganisms based on nuclear markers has revolutionized our understanding of their taxonomy, phylogeny and ecology. Today, research on the diversity of eukaryotes in global ecosystems heavily relies on nuclear ribosomal RNA (rRNA) markers. Here, we present the research community-curated reference database EUKARYOME for nuclear ribosomal 18S rRNA, internal transcribed spacer (ITS) and 28S rRNA markers for all eukaryotes, including metazoans (animals), protists, fungi and plants. It is particularly useful for the identification of arbuscular mycorrhizal fungi as it bridges the four commonly used molecular markers-ITS1, ITS2, 18S V4-V5 and 28S D1-D2 subregions. The key benefits of this database over other annotated reference sequence databases are that it is not restricted to certain taxonomic groups and it includes all rRNA markers. EUKARYOME also offers a number of reference long-read sequences that are derived from (meta)genomic and (meta)barcoding-a unique feature that can be used for taxonomic identification and chimera control of third-generation, long-read, high-throughput sequencing data. Taxonomic assignments of rRNA genes in the database are verified based on phylogenetic approaches. The reference datasets are available in multiple formats from the project homepage, http://www.eukaryome.org.
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Affiliation(s)
- Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Liivi 2, Tartu 50400, Estonia
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, Tartu 50400, Estonia
- Department of Zoology, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
| | | | - Vladimir Mikryukov
- Mycology and Microbiology Center, University of Tartu, Liivi 2, Tartu 50400, Estonia
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, Tartu 50400, Estonia
| | - Ali Hakimzadeh
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, Tartu 50400, Estonia
| | - Mohammad Bahram
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, Tartu 50400, Estonia
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, Uppsala 75651, Sweden
| | - R Henrik Nilsson
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Box 461, Göteborg 40530, Sweden
| | - Iryna Yatsiuk
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, Tartu 50400, Estonia
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
| | - Arne Schwelm
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
- Department of Environment, Soils and Land-Use, Teagasc, Oak Park House, Wexford R93 XE12, Ireland
| | - Kasia Piwosz
- National Marine Fisheries Research Institute, Kołłątaja 1, Gdynia 81332, Poland
| | - Marko Prous
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, Tartu 50400, Estonia
- Ecology and Genetics Research Unit, University of Oulu, Box 8000, Oulu 90014, Finland
| | - Sirje Sildever
- Department of Marine Systems, Tallinn University of Technology, Mäealuse 14a, Tallinn 12618, Estonia
| | - Dominika Chmolowska
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, Kraków 31016, Poland
| | - Sonja Rueckert
- Eukaryotic Microbiology, Faculty of Biology, University of Duisburg-Essen, Universitätsstraße 1, Essen, Nordrhein-Westfalen 45141, Germany
| | - Pavel Skaloud
- Department of Botany, Faculty of Science, Charles University, Benatska 2, Praha 12800, Czech Republic
| | - Peeter Laas
- Department of Marine Systems, Tallinn University of Technology, Mäealuse 14a, Tallinn 12618, Estonia
- Institute of Technology, University of Tartu, Nooruse 1, Tartu 50400, Estonia
| | - Marco Tines
- Department for Biological Sciences, Institute for Ecology, Evolution, and Diversity, Goethe University Frankfurt am Main, Max-von-Laue-Str. 13, Frankfurt am Main 60438, Germany
- Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Straße 14-16, Frankfurt am Main 60325, Germany
| | - Jae-Ho Jung
- Department of Biology, Gangneung-Wonju National University, Jukheon-gil 7, Gangneung 25457, South Korea
| | - Ji Hye Choi
- Department of Biology, Gangneung-Wonju National University, Jukheon-gil 7, Gangneung 25457, South Korea
| | - Saad Alkahtani
- Department of Zoology, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, Tartu 50400, Estonia
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Jirsová D, Wideman JG. Integrated overview of stramenopile ecology, taxonomy, and heterotrophic origin. THE ISME JOURNAL 2024; 18:wrae150. [PMID: 39077993 PMCID: PMC11412368 DOI: 10.1093/ismejo/wrae150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 06/12/2024] [Accepted: 07/29/2024] [Indexed: 07/31/2024]
Abstract
Stramenopiles represent a significant proportion of aquatic and terrestrial biota. Most biologists can name a few, but these are limited to the phototrophic (e.g. diatoms and kelp) or parasitic species (e.g. oomycetes, Blastocystis), with free-living heterotrophs largely overlooked. Though our attention is slowly turning towards heterotrophs, we have only a limited understanding of their biology due to a lack of cultured models. Recent metagenomic and single-cell investigations have revealed the species richness and ecological importance of stramenopiles-especially heterotrophs. However, our lack of knowledge of the cell biology and behaviour of these organisms leads to our inability to match species to their particular ecological functions. Because photosynthetic stramenopiles are studied independently of their heterotrophic relatives, they are often treated separately in the literature. Here, we present stramenopiles as a unified group with shared synapomorphies and evolutionary history. We introduce the main lineages, describe their important biological and ecological traits, and provide a concise update on the origin of the ochrophyte plastid. We highlight the crucial role of heterotrophs and mixotrophs in our understanding of stramenopiles with the goal of inspiring future investigations in taxonomy and life history. To understand each of the many diversifications within stramenopiles-towards autotrophy, osmotrophy, or parasitism-we must understand the ancestral heterotrophic flagellate from which they each evolved. We hope the following will serve as a primer for new stramenopile researchers or as an integrative refresher to those already in the field.
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Affiliation(s)
- Dagmar Jirsová
- Center for Mechanisms of Evolution, Biodesign Institute, School of Life Sciences, Arizona State University, 1001 S McAllister Avenue, Tempe, Arizona, 85287-7701, United States
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 31, České Budějovice 37005, Czech Republic
| | - Jeremy G Wideman
- Center for Mechanisms of Evolution, Biodesign Institute, School of Life Sciences, Arizona State University, 1001 S McAllister Avenue, Tempe, Arizona, 85287-7701, United States
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Ramond P, Siano R, Sourisseau M, Logares R. Assembly processes and functional diversity of marine protists and their rare biosphere. ENVIRONMENTAL MICROBIOME 2023; 18:59. [PMID: 37443126 PMCID: PMC10347826 DOI: 10.1186/s40793-023-00513-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023]
Abstract
BACKGROUND The mechanisms shaping the rare microbial biosphere and its role in ecosystems remain unclear. We developed an approach to study ecological patterns in the rare biosphere and use it on a vast collection of marine microbiomes, sampled in coastal ecosystems at a regional scale. We study the assembly processes, and the ecological strategies constituting the rare protistan biosphere. Using the phylogeny and morpho-trophic traits of these protists, we also explore their functional potential. RESULTS Taxonomic community composition remained stable along rank abundance curves. Conditionally rare taxa, driven by selection processes, and transiently rare taxa, with stochastic distributions, were evidenced along the rank abundance curves of all size-fractions. Specific taxa within the divisions Sagenista, Picozoa, Telonemia, and Choanoflagellida were rare across time and space. The distribution of traits along rank abundance curves outlined a high functional redundancy between rare and abundant protists. Nevertheless, trophic traits illustrated an interplay between the trophic groups of different size-fractions. CONCLUSIONS Our results suggest that rare and abundant protists are evolutionary closely related, most notably due to the high microdiversity found in the rare biosphere. We evidenced a succession of assembly processes and strategies of rarity along rank abundance curves that we hypothesize to be common to most microbiomes at the regional scale. Despite high functional redundancy in the rare protistan biosphere, permanently rare protists were evidenced, and they could play critical functions as bacterivores and decomposers from within the rare biosphere. Finally, changes in the composition of the rare protistan biosphere could be influenced by the trophic regime of aquatic ecosystems. Our work contributes to understanding the role of rare protists in microbiomes.
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Affiliation(s)
- Pierre Ramond
- Institute of Marine Sciences (ICM), Department of Marine Biology and Oceanography, CSIC, Barcelona, Catalunya, 08003, Spain.
| | - Raffaele Siano
- DYNECO/Pelagos, Ifremer-Centre de Brest, Technopôle Brest Iroise, Plouzané, 29280, France
| | - Marc Sourisseau
- DYNECO/Pelagos, Ifremer-Centre de Brest, Technopôle Brest Iroise, Plouzané, 29280, France
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), Department of Marine Biology and Oceanography, CSIC, Barcelona, Catalunya, 08003, Spain
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Obiol A, López-Escardó D, Salomaki ED, Wiśniewska MM, Forn I, Sà E, Vaqué D, Kolísko M, Massana R. Gene expression dynamics of natural assemblages of heterotrophic flagellates during bacterivory. MICROBIOME 2023; 11:134. [PMID: 37322519 PMCID: PMC10268365 DOI: 10.1186/s40168-023-01571-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 05/12/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Marine heterotrophic flagellates (HF) are dominant bacterivores in the ocean, where they represent the trophic link between bacteria and higher trophic levels and participate in the recycling of inorganic nutrients for regenerated primary production. Studying their activity and function in the ecosystem is challenging since most of the HFs in the ocean are still uncultured. In the present work, we investigated gene expression of natural HF communities during bacterivory in four unamended seawater incubations. RESULTS The most abundant species growing in our incubations belonged to the taxonomic groups MAST-4, MAST-7, Chrysophyceae, and Telonemia. Gene expression dynamics were similar between incubations and could be divided into three states based on microbial counts, each state displaying distinct expression patterns. The analysis of samples where HF growth was highest revealed some highly expressed genes that could be related to bacterivory. Using available genomic and transcriptomic references, we identified 25 species growing in our incubations and used those to compare the expression levels of these specific genes. Video Abstract CONCLUSIONS: Our results indicate that several peptidases, together with some glycoside hydrolases and glycosyltransferases, are more expressed in phagotrophic than in phototrophic species, and thus could be used to infer the process of bacterivory in natural assemblages.
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Affiliation(s)
- Aleix Obiol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, Barcelona, Catalonia, 08003, Spain.
| | - David López-Escardó
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, Barcelona, Catalonia, 08003, Spain
| | - Eric D Salomaki
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Monika M Wiśniewska
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Irene Forn
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, Barcelona, Catalonia, 08003, Spain
| | - Elisabet Sà
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, Barcelona, Catalonia, 08003, Spain
| | - Dolors Vaqué
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, Barcelona, Catalonia, 08003, Spain
| | - Martin Kolísko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, Barcelona, Catalonia, 08003, Spain.
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Higuera A, Salas-Leiva DE, Curtis B, Patiño LH, Zhao D, Jerlström-Hultqvist J, Dlutek M, Muñoz M, Roger AJ, Ramírez JD. Draft genomes of Blastocystis subtypes from human samples of Colombia. Parasit Vectors 2023; 16:52. [PMID: 36732768 PMCID: PMC9896827 DOI: 10.1186/s13071-022-05619-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 12/14/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Blastocystis is one of the most common eukaryotic microorganisms colonizing the intestines of both humans and animals, but the conditions under which it may be a pathogen are unclear. METHODS To study the genomic characteristics of circulating subtypes (ST) in Colombia, we established nine xenic cultures from Blastocystis isolated from human fecal samples, we identified 10 different subtypes, since one sample had a mixed infection. Thus, the genomes of the subtypes ST1 (n = 3), ST2 (n = 1), ST3 (n = 2), ST6 (n = 1), ST7 (n = 1), and ST8 (n = 2) were sequenced using Illumina and Oxford Nanopore Technologies (ONT). RESULTS Analyses of these draft nuclear genomes indicated remarkable diversity in terms of genome size and guanine-cytosine (GC) content among the compared STs. Illumina sequencing-only draft genomes contained 824 to 2077 scaffolds, with total genome size ranging from 12 to 13.2 Mb and N50 values ranging from 10,585 to 29,404 base pairs (bp). The genome of one ST1 isolate was sequenced using ONT. This assembly was more contiguous, with a size of 20 million base pairs (Mb) spread over 116 scaffolds, and an N50 of 248,997 bp. CONCLUSION This work represents one of the few large-scale comparative genomic analyses of Blastocystis isolates, providing an additional glimpse into its genomic diversity.
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Affiliation(s)
- Adriana Higuera
- grid.412191.e0000 0001 2205 5940Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Dayana E. Salas-Leiva
- grid.5335.00000000121885934Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge, CB2 1QW United Kingdom
| | - Bruce Curtis
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Luz H. Patiño
- grid.412191.e0000 0001 2205 5940Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Dandan Zhao
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Jon Jerlström-Hultqvist
- grid.8993.b0000 0004 1936 9457Department of Cell and Molecular Biology, BMC, Uppsala Universitet, Box 596, 751 24 Uppsala, Sweden
| | - Marlena Dlutek
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Marina Muñoz
- grid.412191.e0000 0001 2205 5940Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Andrew J. Roger
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Juan David Ramírez
- grid.412191.e0000 0001 2205 5940Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia ,grid.59734.3c0000 0001 0670 2351Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY USA
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Saati-Santamaría Z, Baroncelli R, Rivas R, García-Fraile P. Comparative Genomics of the Genus Pseudomonas Reveals Host- and Environment-Specific Evolution. Microbiol Spectr 2022; 10:e0237022. [PMID: 36354324 PMCID: PMC9769992 DOI: 10.1128/spectrum.02370-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/24/2022] [Indexed: 11/12/2022] Open
Abstract
Each Earth ecosystem has unique microbial communities. Pseudomonas bacteria have evolved to occupy a plethora of different ecological niches, including living hosts, such as animals and plants. Many genes necessary for the Pseudomonas-niche interaction and their encoded functions remain unknown. Here, we describe a comparative genomic study of 3,274 genomes with 19,056,667 protein-coding sequences from Pseudomonas strains isolated from diverse environments. We detected functional divergence of Pseudomonas that depends on the niche. Each group of strains from a certain environment harbored a distinctive set of metabolic pathways or functions. The horizontal transfer of genes, which mainly proceeded between closely related taxa, was dependent on the isolation source. Finally, we detected thousands of undescribed proteins and functions associated with each Pseudomonas lifestyle. This research represents an effort to reveal the mechanisms underlying the ecology, pathogenicity, and evolution of Pseudomonas, and it will enable clinical, ecological, and biotechnological advances. IMPORTANCE Microbes play important roles in the health of living beings and in the environment. The knowledge of these functions may be useful for the development of new clinical and biotechnological applications and the restoration and preservation of natural ecosystems. However, most mechanisms implicated in the interaction of microbes with the environment remain poorly understood; thus, this field of research is very important. Here, we try to understand the mechanisms that facilitate the differential adaptation of Pseudomonas-a large and ubiquitous bacterial genus-to the environment. We analyzed more than 3,000 Pseudomonas genomes and searched for genetic patterns that can be related with their coevolution with different hosts (animals, plants, or fungi) and environments. Our results revealed that thousands of genes and genetic features are associated with each niche. Our data may be useful to develop new technical and theoretical advances in the fields of ecology, health, and industry.
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Affiliation(s)
- Zaki Saati-Santamaría
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), Villamayor, Salamanca, Spain
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Prague, Czech Republic
| | - Riccardo Baroncelli
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Raúl Rivas
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), Villamayor, Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, USAL-CSIC (IRNASA), Salamanca, Spain
| | - Paula García-Fraile
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), Villamayor, Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, USAL-CSIC (IRNASA), Salamanca, Spain
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Li Z, Wang X, Zhang Y, Yu Z, Zhang T, Dai X, Pan X, Jing R, Yan Y, Liu Y, Gao S, Li F, Huang Y, Tian J, Yao J, Xing X, Shi T, Ning J, Yao B, Huang H, Jiang Y. Genomic insights into the phylogeny and biomass-degrading enzymes of rumen ciliates. THE ISME JOURNAL 2022; 16:2775-2787. [PMID: 35986094 PMCID: PMC9666518 DOI: 10.1038/s41396-022-01306-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 08/04/2022] [Accepted: 08/09/2022] [Indexed: 12/15/2022]
Abstract
Understanding the biodiversity and genetics of gut microbiomes has important implications for host physiology and industrial enzymes, whereas most studies have been focused on bacteria and archaea, and to a lesser extent on fungi and viruses. One group, still underexplored and elusive, is ciliated protozoa, despite its importance in shaping microbiota populations. Integrating single-cell sequencing and an assembly-and-identification pipeline, we acquired 52 high-quality ciliate genomes of 22 rumen morphospecies from 11 abundant morphogenera. With these genomes, we resolved the taxonomic and phylogenetic framework that revised the 22 morphospecies into 19 species spanning 13 genera and reassigned the genus Dasytricha from Isotrichidae to a new family Dasytrichidae. Comparative genomic analyses revealed that extensive horizontal gene transfers and gene family expansion provided rumen ciliate species with a broad array of carbohydrate-active enzymes (CAZymes) to degrade all major kinds of plant and microbial carbohydrates. In particular, the genomes of Diplodiniinae and Ophryoscolecinae species encode as many CAZymes as gut fungi, and ~80% of their degradative CAZymes act on plant cell-wall. The activities of horizontally transferred cellulase and xylanase of ciliates were experimentally verified and were 2-9 folds higher than those of the inferred corresponding bacterial donors. Additionally, the new ciliate dataset greatly facilitated rumen metagenomic analyses by allowing ~12% of the metagenomic sequencing reads to be classified as ciliate sequences.
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Affiliation(s)
- Zongjun Li
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiangnan Wang
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yu Zhang
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Zhongtang Yu
- Department of Animal Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Tingting Zhang
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xuelei Dai
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiangyu Pan
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Ruoxi Jing
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
- College of Animal Engineering, Yangling Vocational & Technical College, Yangling, 712100, China
| | - Yueyang Yan
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yangfan Liu
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Shan Gao
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Fei Li
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Youqin Huang
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Jian Tian
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Junhu Yao
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - XvPeng Xing
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China
| | - Tao Shi
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Jifeng Ning
- College of Information Engineering, Northwest A&F University, Yangling, 712100, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Yu Jiang
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
- Center for Functional Genomics, Institute of Future Agriculture, Northwest A&F University, Yangling, 712100, China.
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9
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Koppelle S, López-Escardó D, Brussaard CPD, Huisman J, Philippart CJM, Massana R, Wilken S. Mixotrophy in the bloom-forming genus Phaeocystis and other haptophytes. HARMFUL ALGAE 2022; 117:102292. [PMID: 35944956 DOI: 10.1016/j.hal.2022.102292] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 05/13/2023]
Abstract
Phaeocystis is a globally widespread marine phytoplankton genus, best known for its colony-forming species that can form large blooms and odorous foam during bloom decline. In the North Sea, Phaeocystis globosa typically becomes abundant towards the end of the spring bloom, when nutrients are depleted and the share of mixotrophic protists increases. Although mixotrophy is widespread across the eukaryotic tree of life and is also found amongst haptophytes, a mixotrophic nutrition has not yet been demonstrated in Phaeocystis. Here, we sampled two consecutive Phaeocystis globosa spring blooms in the coastal North Sea. In both years, bacterial cells were observed inside 0.6 - 2% of P. globosa cells using double CARD-FISH hybridizations in combination with laser scanning confocal microscopy. Incubation experiments manipulating light and nutrient availability showed a trend towards higher occurrence of intracellular bacteria under P-deplete conditions. Based on counts of bacteria inside P. globosa cells in combination with theoretical values of prey digestion times, maximum ingestion rates of up to 0.08 bacteria cell-1 h-1 were estimated. In addition, a gene-based predictive model was applied to the transcriptome assemblies of seven Phaeocystis strains and 24 other haptophytes to assess their trophic mode. This model predicted a phago-mixotrophic feeding strategy in several (but not all) strains of P. globosa, P. antarctica and other haptophytes that were previously assumed to be autotrophic. The observation of bacterial cells inside P. globosa and the gene-based model predictions strongly suggest that the phago-mixotrophic feeding strategy is widespread among members of the Phaeocystis genus and other haptophytes, and might contribute to their remarkable success to form nuisance blooms under nutrient-limiting conditions.
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Affiliation(s)
- Sebastiaan Koppelle
- Department of Freshwater and Marine Ecology (FAME), Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, P.O. Box 94920, 1090 XH, Amsterdam, The Netherlands.
| | - David López-Escardó
- Ecology of Marine Microbes, Institut de Ciènces del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
| | - Corina P D Brussaard
- Department of Freshwater and Marine Ecology (FAME), Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, P.O. Box 94920, 1090 XH, Amsterdam, The Netherlands; Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands
| | - Jef Huisman
- Department of Freshwater and Marine Ecology (FAME), Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, P.O. Box 94920, 1090 XH, Amsterdam, The Netherlands
| | - Catharina J M Philippart
- Department of Coastal Systems, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands; Department of Physical Geography, Utrecht University, P.O. Box 80115, 3508 TC, Utrecht, The Netherlands
| | - Ramon Massana
- Ecology of Marine Microbes, Institut de Ciènces del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
| | - Susanne Wilken
- Department of Freshwater and Marine Ecology (FAME), Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, P.O. Box 94920, 1090 XH, Amsterdam, The Netherlands.
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10
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Abstract
Environmental community sequencing is suitable for producing metagenome assembled genomes (MAGs) of prokaryotes, but there is the perception that it cannot work for eukaryotes. In this issue of Cell Genomics, Delmont et al1 process a massive sequencing dataset from marine plankton to produce 683 eukaryotic MAGs; the study also includes useful functional information.
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Affiliation(s)
- Ramon Massana
- Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
| | - David López-Escardó
- Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
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11
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Gann ER, Truchon AR, Papoulis SE, Dyhrman ST, Gobler CJ, Wilhelm SW. Aureococcus anophagefferens (Pelagophyceae) genomes improve evaluation of nutrient acquisition strategies involved in brown tide dynamics. JOURNAL OF PHYCOLOGY 2022; 58:146-160. [PMID: 34773248 DOI: 10.1111/jpy.13221] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 06/13/2023]
Abstract
The pelagophyte Aureococcus anophagefferens causes harmful brown tide blooms in marine embayments on three continents. Aureococcus anophagefferens was the first harmful algal bloom species to have its genome sequenced, an advance that evidenced genes important for adaptation to environmental conditions that prevail during brown tides. To expand the genomic tools available for this species, genomes for four strains were assembled, including three newly sequenced strains and one assembled from publicly available data. These genomes ranged from 57.11 to 73.62 Mb, encoding 13,191-17,404 potential proteins. All strains shared ~90% of their encoded proteins as determined by homology searches and shared most functional orthologs as determined by KEGG, although each strain also possessed coding sequences with unique functions. Like the original reference genome, the genomes assembled in this study possessed genes hypothesized to be important in bloom proliferation, including genes involved in organic compound metabolism and growth at low light. Cross-strain informatics and culture experiments suggest that the utilization of purines is a potentially important source of organic nitrogen for brown tides. Analyses of metatranscriptomes from a brown tide event demonstrated that use of a single genome yielded a lower read mapping percentage (~30% of library reads) as compared to a database generated from all available genomes (~43%), suggesting novel information about bloom ecology can be gained from expanding genomic space. This work demonstrates the continued need to sequence ecologically relevant algae to understand the genomic potential and their ecology in the environment.
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Affiliation(s)
- Eric R Gann
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, 37996, USA
| | - Alexander R Truchon
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, 37996, USA
| | - Spiridon E Papoulis
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, 37996, USA
| | - Sonya T Dyhrman
- Biology and Paleo Environment Division, Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York, 10964, USA
- Department of Earth and Environmental Sciences, Columbia University, Palisades, New York, 10964, USA
| | - Christopher J Gobler
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, 11790, USA
| | - Steven W Wilhelm
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, 37996, USA
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12
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Abstract
Cation and anion channelrhodopsins (CCRs and ACRs, respectively) primarily from two algal species, Chlamydomonas reinhardtii and Guillardia theta, have become widely used as optogenetic tools to control cell membrane potential with light. We mined algal and other protist polynucleotide sequencing projects and metagenomic samples to identify 75 channelrhodopsin homologs from four channelrhodopsin families, including one revealed in dinoflagellates in this study. We carried out electrophysiological analysis of 33 natural channelrhodopsin variants from different phylogenetic lineages and 10 metagenomic homologs in search of sequence determinants of ion selectivity, photocurrent desensitization, and spectral tuning in channelrhodopsins. Our results show that association of a reduced number of glutamates near the conductance path with anion selectivity depends on a wider protein context, because prasinophyte homologs with a glutamate pattern identical to that in cryptophyte ACRs are cation selective. Desensitization is also broadly context dependent, as in one branch of stramenopile ACRs and their metagenomic homologs, its extent roughly correlates with phylogenetic relationship of their sequences. Regarding spectral tuning, we identified two prasinophyte CCRs with red-shifted spectra to 585 nm. They exhibit a third residue pattern in their retinal-binding pockets distinctly different from those of the only two types of red-shifted channelrhodopsins known (i.e., the CCR Chrimson and RubyACRs). In cryptophyte ACRs we identified three specific residue positions in the retinal-binding pocket that define the wavelength of their spectral maxima. Lastly, we found that dinoflagellate rhodopsins with a TCP motif in the third transmembrane helix and a metagenomic homolog exhibit channel activity.
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13
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Latorre F, Deutschmann IM, Labarre A, Obiol A, Krabberød AK, Pelletier E, Sieracki ME, Cruaud C, Jaillon O, Massana R, Logares R. Niche adaptation promoted the evolutionary diversification of tiny ocean predators. Proc Natl Acad Sci U S A 2021; 118:e2020955118. [PMID: 34155140 PMCID: PMC8237690 DOI: 10.1073/pnas.2020955118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Unicellular eukaryotic predators play a crucial role in the functioning of the ocean ecosystem by recycling nutrients and energy that are channeled to upper trophic levels. Traditionally, these evolutionarily diverse organisms have been combined into a single functional group (heterotrophic flagellates), overlooking their organismal differences. Here, we investigated four evolutionarily related species belonging to one cosmopolitan group of uncultured marine picoeukaryotic predators: marine stramenopiles (MAST)-4 (species A, B, C, and E). Co-occurrence and distribution analyses in the global surface ocean indicated contrasting patterns in MAST-4A and C, suggesting adaptation to different temperatures. We then investigated whether these spatial distribution patterns were mirrored by MAST-4 genomic content using single-cell genomics. Analyses of 69 single cells recovered 66 to 83% of the MAST-4A/B/C/E genomes, which displayed substantial interspecies divergence. MAST-4 genomes were similar in terms of broad gene functional categories, but they differed in enzymes of ecological relevance, such as glycoside hydrolases (GHs), which are part of the food degradation machinery in MAST-4. Interestingly, MAST-4 species featuring a similar GH composition (A and C) coexcluded each other in the surface global ocean, while species with a different set of GHs (B and C) appeared to be able to coexist, suggesting further niche diversification associated with prey digestion. We propose that differential niche adaptation to temperature and prey type has promoted adaptive evolutionary diversification in MAST-4. We show that minute ocean predators from the same phylogenetic group may have different biogeography and genomic content, which needs to be accounted for to better comprehend marine food webs.
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Affiliation(s)
- Francisco Latorre
- Institute of Marine Sciences (ICM), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona E-08003, Spain;
| | - Ina M Deutschmann
- Institute of Marine Sciences (ICM), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona E-08003, Spain
| | - Aurélie Labarre
- Institute of Marine Sciences (ICM), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona E-08003, Spain
| | - Aleix Obiol
- Institute of Marine Sciences (ICM), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona E-08003, Spain
| | - Anders K Krabberød
- Department of Biosciences, Section for Genetics and Evolutionary Biology, University of Oslo, Oslo N-0316, Norway
| | - Eric Pelletier
- Metabolic Genomics, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology & Evolution, FR2022/Tara Oceans Global Ocean System Ecology & Evolution, 75016 Paris, France
| | - Michael E Sieracki
- Ocean Science Division, National Science Foundation, Alexandria, VA 22314
| | - Corinne Cruaud
- Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique, Université Paris-Saclay, 91000 Evry, France
| | - Olivier Jaillon
- Metabolic Genomics, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology & Evolution, FR2022/Tara Oceans Global Ocean System Ecology & Evolution, 75016 Paris, France
| | - Ramon Massana
- Institute of Marine Sciences (ICM), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona E-08003, Spain
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona E-08003, Spain;
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