1
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Pestana CJ, Santos AA, Capelo-Neto J, Melo VMM, Reis KC, Oliveira S, Rogers R, Pacheco ABF, Hui J, Skillen NC, Barros MUG, Edwards C, Azevedo SMFO, Robertson PKJ, Irvine JTS, Lawton LA. Suppressing cyanobacterial dominance by UV-LED TiO 2-photocatalysis in a drinking water reservoir: A mesocosm study. WATER RESEARCH 2022; 226:119299. [PMID: 36323220 DOI: 10.1016/j.watres.2022.119299] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 10/21/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
Cyanobacteria and their toxic secondary metabolites present challenges for water treatment globally. In this study we have assessed TiO2 immobilized onto recycled foamed glass beads by a facile calcination method, combined in treatment units with 365 nm UV-LEDs. The treatment system was deployed in mesocosms within a eutrophic Brazilian drinking water reservoir. The treatment units were deployed for 7 days and suppressed cyanobacterial abundance by 85% while at the same time enhancing other water quality parameters; turbidity and transparency improved by 40 and 81% respectively. Genomic analysis of the microbiota in the treated mesocosms revealed that the composition of the cyanobacterial community was affected and the abundance of Bacteroidetes and Proteobacteria increased during cyanobacterial suppression. The effect of the treatment on zooplankton and other eukaryotes was also monitored. The abundance of zooplankton decreased while Chrysophyte and Alveolata loadings increased. The results of this proof-of-concept study demonstrate the potential for full-scale, in-reservoir application of advanced oxidation processes as complementary water treatment processes.
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Affiliation(s)
- Carlos J Pestana
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen, UK.
| | - Allan A Santos
- Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - José Capelo-Neto
- Department of Hydraulic and Environmental Engineering, Federal University of Ceará, Fortaleza, Brazil
| | - Vânia M M Melo
- Department of Biology, Federal University of Ceará, Fortaleza, Brazil
| | - Kelly C Reis
- Department of Hydraulic and Environmental Engineering, Federal University of Ceará, Fortaleza, Brazil
| | - Samylla Oliveira
- Department of Hydraulic and Environmental Engineering, Federal University of Ceará, Fortaleza, Brazil
| | - Ricardo Rogers
- Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ana B F Pacheco
- Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jianing Hui
- School of Chemistry, University of St. Andrews, St. Andrews, UK
| | - Nathan C Skillen
- School of Chemistry and Chemical Engineering, Queen's University Belfast, Belfast, UK
| | - Mário U G Barros
- Ceára Water Resources Management Company (COGERH), Fortaleza, Brazil
| | - Christine Edwards
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen, UK
| | - Sandra M F O Azevedo
- Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Peter K J Robertson
- School of Chemistry and Chemical Engineering, Queen's University Belfast, Belfast, UK
| | - John T S Irvine
- School of Chemistry, University of St. Andrews, St. Andrews, UK
| | - Linda A Lawton
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen, UK
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2
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High molecular diversity in the functional group of small bacterivorous non-scaled chrysomonad flagellates. Eur J Protistol 2022; 86:125915. [DOI: 10.1016/j.ejop.2022.125915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/19/2022] [Accepted: 08/21/2022] [Indexed: 11/21/2022]
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3
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Hammond M, Dorrell RG, Speijer D, Lukeš J. Eukaryotic cellular intricacies shape mitochondrial proteomic complexity. Bioessays 2022; 44:e2100258. [PMID: 35318703 DOI: 10.1002/bies.202100258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 12/17/2022]
Abstract
Mitochondria have been fundamental to the eco-physiological success of eukaryotes since the last eukaryotic common ancestor (LECA). They contribute essential functions to eukaryotic cells, above and beyond classical respiration. Mitochondria interact with, and complement, metabolic pathways occurring in other organelles, notably diversifying the chloroplast metabolism of photosynthetic organisms. Here, we integrate existing literature to investigate how mitochondrial metabolism varies across the landscape of eukaryotic evolution. We illustrate the mitochondrial remodelling and proteomic changes undergone in conjunction with major evolutionary transitions. We explore how the mitochondrial complexity of the LECA has been remodelled in specific groups to support subsequent evolutionary transitions, such as the acquisition of chloroplasts in photosynthetic species and the emergence of multicellularity. We highlight the versatile and crucial roles played by mitochondria during eukaryotic evolution, extending from its huge contribution to the development of the LECA itself to the dynamic evolution of individual eukaryote groups, reflecting both their current ecologies and evolutionary histories.
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Affiliation(s)
- Michael Hammond
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Richard G Dorrell
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Dave Speijer
- Medical Biochemistry, UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
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4
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Cho A, Tikhonenkov DV, Hehenberger E, Karnkowska A, Mylnikov AP, Keeling PJ. Monophyly of Diverse Bigyromonadea and their Impact on Phylogenomic Relationships Within Stramenopiles. Mol Phylogenet Evol 2022; 171:107468. [DOI: 10.1016/j.ympev.2022.107468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 02/11/2022] [Accepted: 02/22/2022] [Indexed: 10/18/2022]
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5
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Gastineau R, Yilmaz E, Solak CN, Lemieux C, Turmel M, Witkowski A. Complete chloroplast genome of the mixotrophic chrysophyte Poterioochromonas malhamensis (Ochromonadales, Synurophyceae) from Van Lake in Eastern Anatolia. Mitochondrial DNA B Resour 2021; 6:2719-2721. [PMID: 34471690 PMCID: PMC8405094 DOI: 10.1080/23802359.2021.1923416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Romain Gastineau
- Institute of Marine and Environmental Sciences, University of Szczecin, Szczecin, Poland
| | - Elif Yilmaz
- Institute of Marine and Environmental Sciences, University of Szczecin, Szczecin, Poland
- Department of Biology, Arts and Science Faculty, Dumlupinar University, Kütahya, Turkey
| | - Cüneyt Nadir Solak
- Department of Biology, Arts and Science Faculty, Dumlupinar University, Kütahya, Turkey
| | - Claude Lemieux
- Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
| | - Monique Turmel
- Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
| | - Andrzej Witkowski
- Institute of Marine and Environmental Sciences, University of Szczecin, Szczecin, Poland
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6
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Abstract
The origin of plastids (chloroplasts) by endosymbiosis stands as one of the most important events in the history of eukaryotic life. The genetic, biochemical, and cell biological integration of a cyanobacterial endosymbiont into a heterotrophic host eukaryote approximately a billion years ago paved the way for the evolution of diverse algal groups in a wide range of aquatic and, eventually, terrestrial environments. Plastids have on multiple occasions also moved horizontally from eukaryote to eukaryote by secondary and tertiary endosymbiotic events. The overall picture of extant photosynthetic diversity can best be described as “patchy”: Plastid-bearing lineages are spread far and wide across the eukaryotic tree of life, nested within heterotrophic groups. The algae do not constitute a monophyletic entity, and understanding how, and how often, plastids have moved from branch to branch on the eukaryotic tree remains one of the most fundamental unsolved problems in the field of cell evolution. In this review, we provide an overview of recent advances in our understanding of the origin and spread of plastids from the perspective of comparative genomics. Recent years have seen significant improvements in genomic sampling from photosynthetic and nonphotosynthetic lineages, both of which have added important pieces to the puzzle of plastid evolution. Comparative genomics has also allowed us to better understand how endosymbionts become organelles.
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Affiliation(s)
- Shannon J Sibbald
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - John M Archibald
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
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7
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Lalla C, Calvaruso R, Dick S, Reyes-Prieto A. Winogradsky columns as a strategy to study typically rare microbial eukaryotes. Eur J Protistol 2021; 80:125807. [PMID: 34091379 DOI: 10.1016/j.ejop.2021.125807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 05/05/2021] [Accepted: 05/11/2021] [Indexed: 11/28/2022]
Abstract
Winogradsky columns have been widely used to study soil microbial communities, but the vast majority of those investigations have focused on the ecology and diversity of bacteria. In contrast, microbial eukaryotes (ME) have been regularly overlooked in studies based on experimental soil columns. Despite the recognized ecological relevance of ME in soil communities, investigations focused on ME diversity and the abundance of certain groups of interest are still scarce. In the present study, we used DNA metabarcoding (high-throughput sequencing of the V4 region of the 18S rRNA locus) to survey the ME diversity and abundance in an experimental Winogradsky soil column. Consistent with previous surveys in natural soils, our survey identified members of Cercozoa (Rhizaria; 31.2%), Apicomplexa and Ciliophora (Alveolata; 12.5%) as the predominant ME groups, but at particular depths we also detected the abundant presence of ME lineages that are typically rare in natural environments, such as members of the Vampyrellida (Rhizaria) and Breviatea (Amorphea). Our survey demonstrates that experimental soil columns are an efficient enrichment-culture approach that can enhance investigations about the diversity and ecology of ME in soils.
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Affiliation(s)
- Clarissa Lalla
- Department of Biology, University of New Brunswick, Fredericton. 10 Bailey Drive, Fredericton, New Brunswick E3B 5A3, Canada
| | - Rossella Calvaruso
- Department of Biology, University of New Brunswick, Fredericton. 10 Bailey Drive, Fredericton, New Brunswick E3B 5A3, Canada
| | - Sophia Dick
- Department of Biology, University of New Brunswick, Fredericton. 10 Bailey Drive, Fredericton, New Brunswick E3B 5A3, Canada
| | - Adrian Reyes-Prieto
- Department of Biology, University of New Brunswick, Fredericton. 10 Bailey Drive, Fredericton, New Brunswick E3B 5A3, Canada.
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8
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9
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Majda S, Beisser D, Boenigk J. Nutrient-driven genome evolution revealed by comparative genomics of chrysomonad flagellates. Commun Biol 2021; 4:328. [PMID: 33712682 PMCID: PMC7954800 DOI: 10.1038/s42003-021-01781-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 01/28/2021] [Indexed: 01/31/2023] Open
Abstract
Phototrophic eukaryotes have evolved mainly by the primary or secondary uptake of photosynthetic organisms. A return to heterotrophy occurred multiple times in various protistan groups such as Chrysophyceae, despite the expected advantage of autotrophy. It is assumed that the evolutionary shift to mixotrophy and further to heterotrophy is triggered by a differential importance of nutrient and carbon limitation. We sequenced the genomes of 16 chrysophyte strains and compared them in terms of size, function, and sequence characteristics in relation to photo-, mixo- and heterotrophic nutrition. All strains were sequenced with Illumina and partly with PacBio. Heterotrophic taxa have reduced genomes and a higher GC content of up to 59% as compared to phototrophic taxa. Heterotrophs have a large pan genome, but a small core genome, indicating a differential specialization of the distinct lineages. The pan genome of mixotrophs and heterotrophs taken together but not the pan genome of the mixotrophs alone covers the complete functionality of the phototrophic strains indicating a random reduction of genes. The observed ploidy ranges from di- to tetraploidy and was found to be independent of taxonomy or trophic mode. Our results substantiate an evolution driven by nutrient and carbon limitation.
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Affiliation(s)
- Stephan Majda
- Department of Biodiversity, University of Duisburg-Essen, Essen, Germany.
| | - Daniela Beisser
- Department of Biodiversity, University of Duisburg-Essen, Essen, Germany
| | - Jens Boenigk
- Department of Biodiversity, University of Duisburg-Essen, Essen, Germany
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10
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Jeong M, Kim JI, Nam SW, Shin W. Molecular Phylogeny and Taxonomy of the Genus Spumella (Chrysophyceae) Based on Morphological and Molecular Evidence. FRONTIERS IN PLANT SCIENCE 2021; 12:758067. [PMID: 34764972 PMCID: PMC8577464 DOI: 10.3389/fpls.2021.758067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/04/2021] [Indexed: 05/08/2023]
Abstract
The genus Spumella, established by Cienkowsky in 1870, is characterized by omnivory, two (rarely three) flagella, a short stick-like structure beneath the flagella, a threadlike stalk, cell division via constriction and cyst formation. Since the first phylogenetic study of Spumella-like flagellates, their paraphyly has consistently been shown, with separation into several genera. More recently, Spumella was carefully investigated using molecular and morphological data to propose seven new species. Classification of this genus and knowledge of its species diversity remain limited because Spumella-like flagellates are extremely difficult to identify based on limited morphological characters. To understand the phylogeny and taxonomy of Spumella, we analyzed molecular and morphological data from 47 strains, including 18 strains isolated from Korean ponds or swamps. Nuclear SSU, ITS and LSU rDNA data were used for maximum likelihood and Bayesian analyses. The molecular data divided the strains into 15 clades, including seven new lineages, each with unique molecular signatures for nuclear SSU rRNA from the E23-2 to E23-5 domains, the spacer between the E23-8 and E23-9 domains of the V4 region and domain 29 of the V5 region. Our results revealed increased species diversity in Spumella. In contrast to the molecular phylogeny results, the taxa showed very similar cell morphologies, suggesting morphological convergence into simple nanoflagellates to enable heterotrophy. Three new species produced stomatocysts in culture. Aspects of stomatocyst morphology, including collar structure, surface ornamentation, and cyst shape, were very useful in differentiating the three species. The general ultrastructure of Spumella bureschii strain Baekdongje012018B8 and S. benthica strain Hwarim032418A5 showed the typical chrysophyte form for the leucoplast, a vestigial chloroplast surrounded by four envelope membranes, supporting the hypothesis that Spumella evolved from a phototroph to a heterotroph via the loss of its photosynthetic ability. Seven new species are proposed: S. benthica, S. communis, S. longicolla, S. oblata, S. rotundata, S. similis, and S. sinechrysos.
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Affiliation(s)
- Minseok Jeong
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - Jong Im Kim
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - Seung Won Nam
- Nakdonggang National Institute of Biological Resources, Sangju-si, South Korea
| | - Woongghi Shin
- Department of Biology, Chungnam National University, Daejeon, South Korea
- *Correspondence: Woongghi Shin,
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11
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Abstract
Most secondary nonphotosynthetic eukaryotes have retained residual plastids whose physiological role is often still unknown. One such example is Euglena longa, a close nonphotosynthetic relative of Euglena gracilis harboring a plastid organelle of enigmatic function. By mining transcriptome data from E. longa, we finally provide an overview of metabolic processes localized to its elusive plastid. The organelle plays no role in the biosynthesis of isoprenoid precursors and fatty acids and has a very limited repertoire of pathways concerning nitrogen-containing metabolites. In contrast, the synthesis of phospholipids and glycolipids has been preserved, curiously with the last step of sulfoquinovosyldiacylglycerol synthesis being catalyzed by the SqdX form of an enzyme so far known only from bacteria. Notably, we show that the E. longa plastid synthesizes tocopherols and a phylloquinone derivative, the first such report for nonphotosynthetic plastids studied so far. The most striking attribute of the organelle could be the presence of a linearized Calvin-Benson (CB) pathway, including RuBisCO yet lacking the gluconeogenetic part of the standard cycle, together with ferredoxin-NADP+ reductase (FNR) and the ferredoxin/thioredoxin system. We hypothesize that the ferredoxin/thioredoxin system activates the linear CB pathway in response to the redox status of the E. longa cell and speculate on the role of the pathway in keeping the redox balance of the cell. Altogether, the E. longa plastid defines a new class of relic plastids that is drastically different from the best-studied organelle of this category, the apicoplast.IMPORTANCE Colorless plastids incapable of photosynthesis evolved in many plant and algal groups, but what functions they perform is still unknown in many cases. Here, we study the elusive plastid of Euglena longa, a nonphotosynthetic cousin of the familiar green flagellate Euglena gracilis We document an unprecedented combination of metabolic functions that the E. longa plastid exhibits in comparison with previously characterized nonphotosynthetic plastids. For example, and truly surprisingly, it has retained the synthesis of tocopherols (vitamin E) and a phylloquinone (vitamin K) derivative. In addition, we offer a possible solution of the long-standing conundrum of the presence of the CO2-fixing enzyme RuBisCO in E. longa Our work provides a detailed account on a unique variant of relic plastids, the first among nonphotosynthetic plastids that evolved by secondary endosymbiosis from a green algal ancestor, and suggests that it has persisted for reasons not previously considered in relation to nonphotosynthetic plastids.
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12
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Kim JI, Jeong M, Archibald JM, Shin W. Comparative Plastid Genomics of Non-Photosynthetic Chrysophytes: Genome Reduction and Compaction. FRONTIERS IN PLANT SCIENCE 2020; 11:572703. [PMID: 33013997 PMCID: PMC7511666 DOI: 10.3389/fpls.2020.572703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/24/2020] [Indexed: 05/11/2023]
Abstract
Spumella-like heterotrophic chrysophytes are important eukaryotic microorganisms that feed on bacteria in aquatic and soil environments. They are characterized by their lack of pigmentation, naked cell surface, and extremely small size. Although Spumella-like chrysophytes have lost their photosynthetic ability, they still possess a leucoplast and retain a plastid genome. We have sequenced the plastid genomes of three non-photosynthetic chrysophytes, Spumella sp. Baeckdong012018B8, Pedospumella sp. Jangsampo120217C5 and Poteriospumella lacustris Yongseonkyo072317C3, and compared them to the previously sequenced plastid genome of "Spumella" sp. NIES-1846 and photosynthetic chrysophytes. We found the plastid genomes of Spumella-like flagellates to be generally conserved with respect to genome structure and housekeeping gene content. We nevertheless also observed lineage-specific gene rearrangements and duplication of partial gene fragments at the boundary of the inverted repeat and single copy regions. Most gene losses correspond to genes for proteins involved in photosynthesis and carbon fixation, except in the case of petF. The newly sequenced plastid genomes range from ~55.7 kbp to ~62.9 kbp in size and share a core set of 45 protein-coding genes, 3 rRNAs, and 32 to 34 tRNAs. Our results provide insight into the evolutionary history of organelle genomes via genome reduction and gene loss related to loss of photosynthesis in chrysophyte evolution.
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Affiliation(s)
- Jong Im Kim
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - Minseok Jeong
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - John M. Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Woongghi Shin
- Department of Biology, Chungnam National University, Daejeon, South Korea
- *Correspondence: Woongghi Shin,
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13
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Muñoz-Gómez SA, Durnin K, Eme L, Paight C, Lane CE, Saffo MB, Slamovits CH. Nephromyces Represents a Diverse and Novel Lineage of the Apicomplexa That Has Retained Apicoplasts. Genome Biol Evol 2019; 11:2727-2740. [PMID: 31328784 PMCID: PMC6777426 DOI: 10.1093/gbe/evz155] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2019] [Indexed: 12/13/2022] Open
Abstract
A most interesting exception within the parasitic Apicomplexa is Nephromyces, an extracellular, probably mutualistic, endosymbiont found living inside molgulid ascidian tunicates (i.e., sea squirts). Even though Nephromyces is now known to be an apicomplexan, many other questions about its nature remain unanswered. To gain further insights into the biology and evolutionary history of this unusual apicomplexan, we aimed to 1) find the precise phylogenetic position of Nephromyces within the Apicomplexa, 2) search for the apicoplast genome of Nephromyces, and 3) infer the major metabolic pathways in the apicoplast of Nephromyces. To do this, we sequenced a metagenome and a metatranscriptome from the molgulid renal sac, the specialized habitat where Nephromyces thrives. Our phylogenetic analyses of conserved nucleus-encoded genes robustly suggest that Nephromyces is a novel lineage sister to the Hematozoa, which comprises both the Haemosporidia (e.g., Plasmodium) and the Piroplasmida (e.g., Babesia and Theileria). Furthermore, a survey of the renal sac metagenome revealed 13 small contigs that closely resemble the genomes of the nonphotosynthetic reduced plastids, or apicoplasts, of other apicomplexans. We show that these apicoplast genomes correspond to a diverse set of most closely related but genetically divergent Nephromyces lineages that co-inhabit a single tunicate host. In addition, the apicoplast of Nephromyces appears to have retained all biosynthetic pathways inferred to have been ancestral to parasitic apicomplexans. Our results shed light on the evolutionary history of the only probably mutualistic apicomplexan known, Nephromyces, and provide context for a better understanding of its life style and intricate symbiosis.
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Affiliation(s)
- Sergio A Muñoz-Gómez
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Keira Durnin
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Laura Eme
- Unité d'Ecologie, Sistématique et Evolution, CNRS, Université Paris-Sud, France
| | | | | | - Mary B Saffo
- Smithsonian National Museum of Natural History, Washington, District of Columbia
| | - Claudio H Slamovits
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
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14
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Majda S, Boenigk J, Beisser D. Intraspecific Variation in Protists: Clues for Microevolution from Poteriospumella lacustris (Chrysophyceae). Genome Biol Evol 2019; 11:2492-2504. [PMID: 31384914 PMCID: PMC6738136 DOI: 10.1093/gbe/evz171] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2019] [Indexed: 12/19/2022] Open
Abstract
Species delimitation in protists is still a challenge, attributable to the fact that protists are small, difficult to observe and many taxa are poor in morphological characters, whereas most current phylogenetic approaches only use few marker genes to measure genetic diversity. To address this problem, we assess genome-level divergence and microevolution in strains of the protist Poteriospumella lacustris, one of the first free-living, nonmodel organisms to study genome-wide intraspecific variation. Poteriospumella lacustris is a freshwater protist belonging to the Chrysophyceae with an assumed worldwide distribution. We examined three strains from different geographic regions (New Zealand, China, and Austria) by sequencing their genomes with the Illumina and PacBio platforms. The assembled genomes were small with 49-55 Mb but gene-rich with 16,000-19,000 genes, of which ∼8,000 genes could be assigned to functional categories. At least 68% of these genes were shared by all three species. Genetic variation occurred predominantly in genes presumably involved in ecological niche adaptation. Most surprisingly, we detected differences in genome ploidy between the strains (diploidy, triploidy, and tetraploidy). In analyzing intraspecific variation, several mechanisms of diversification were identified including SNPs, change of ploidy and genome size reduction.
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Affiliation(s)
| | - Jens Boenigk
- Department of Biodiversity, Duisburg-Essen, Germany
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15
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Bråte J, Fuss J, Jakobsen KS, Klaveness D. Draft genome assembly and transcriptome sequencing of the golden algae Hydrurus foetidus (Chrysophyceae). F1000Res 2019; 8:401. [DOI: 10.12688/f1000research.16734.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/27/2019] [Indexed: 11/20/2022] Open
Abstract
Hydrurus foetidus is a freshwater chrysophyte alga. It thrives in cold rivers in polar and high alpine regions. It has several morphological traits reminiscent of single-celled eukaryotes, but can also form macroscopic thalli. Despite its ability to produce polyunsaturated fatty acids, its life under cold conditions and its variable morphology, very little is known about its genome and transcriptome. Here, we present an extensive set of next-generation sequencing data, including genomic short reads from Illumina sequencing and long reads from Nanopore sequencing, as well as full length cDNAs from PacBio IsoSeq sequencing and a small RNA dataset (smaller than 200 bp) sequenced with Illumina. The genome sequences were combined to produce an assembly consisting of 5069 contigs, with a total assembly size of 171 Mb and a 77% BUSCO completeness. The new data generated here may contribute to a better understanding of the evolution and ecological roles of chrysophyte algae, as well as to resolve the branching patterns at a larger phylogenetic scale.
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16
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Beisser D, Bock C, Hahn MW, Vos M, Sures B, Rahmann S, Boenigk J. Interaction-Specific Changes in the Transcriptome of Polynucleobacter asymbioticus Caused by Varying Protistan Communities. Front Microbiol 2019; 10:1498. [PMID: 31354646 PMCID: PMC6629928 DOI: 10.3389/fmicb.2019.01498] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 06/14/2019] [Indexed: 11/29/2022] Open
Abstract
We studied the impact of protist grazing and exudation on the growth and transcriptomic response of the prokaryotic prey species Polynucleobacter asymbioticus. Different single- and multi-species communities of chrysophytes were used to determine a species-specific response to the predators and the effect of chrysophyte diversity. We sequenced the mRNA of Pn. asymbioticus in communities with three single chrysophyte species (Chlorochromonas danica, Poterioochromonas malhamensis and Poteriospumella lacustris) and all combinations. The molecular responses of Pn. asymbioticus significantly changed in the presence of predators with different trophic modes and combinations of species. In the single-species samples we observed significant differences related to the relative importance of grazing and exudation in the protist-bacteria interaction, i.e., to the presence of either the heterotrophic Ps. lacustris or the mixotrophic C. danica. When grazing dominates the interaction, as in the presence of Ps. lacustris, genes acting in stress response are up-regulated. Further genes associated with transcription and translation are down-regulated indicating a reduced growth of Pn. asymbioticus. In contrast, when the potential use of algal exudates dominates the interaction, genes affiliated with iron transport are up-regulated. Rapid phototrophic growth of chrysophytes, with a high demand on soluble iron, could thus lead to iron-limitation and cause changes in the iron metabolism of Pn. asymbioticus. Additionally, we observe a benefit for Pn. asymbioticus from a more diverse protistan community, which could be due to shifts in the relative importance of phototrophy in the mixotrophic chrysophytes when competing for food with other species. Our study highlights the importance of biotic interactions and the specificity of such interactions, in particular the differential effect of grazing and algal exudation in the interaction of bacteria with mixotrophic protists.
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Affiliation(s)
| | - Christina Bock
- Biodiversity, University of Duisburg-Essen, Essen, Germany
| | - Martin W. Hahn
- Research Institute for Limnology, University of Innsbruck, Mondsee, Austria
| | - Matthijs Vos
- Theoretical and Applied Biodiversity, Ruhr-University Bochum, Bochum, Germany
| | - Bernd Sures
- Aquatic Ecology, University of Duisburg-Essen, Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | - Sven Rahmann
- Genome Informatics, University of Duisburg-Essen, Essen, Germany
| | - Jens Boenigk
- Biodiversity, University of Duisburg-Essen, Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
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Bråte J, Fuss J, Mehrota S, Jakobsen KS, Klaveness D. Draft genome assembly and transcriptome sequencing of the golden algae Hydrurus foetidus (Chrysophyceae). F1000Res 2019; 8:401. [PMID: 31632652 PMCID: PMC6784874 DOI: 10.12688/f1000research.16734.3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/03/2019] [Indexed: 01/01/2023] Open
Abstract
Hydrurusfoetidus is a freshwater chrysophyte alga. It thrives in cold rivers in polar and high alpine regions. It has several morphological traits reminiscent of single-celled eukaryotes, but can also form macroscopic thalli. Despite its ability to produce polyunsaturated fatty acids, its life under cold conditions and its variable morphology, very little is known about its genome and transcriptome. Here, we present an extensive set of next-generation sequencing data, including genomic short reads from Illumina sequencing and long reads from Nanopore sequencing, as well as full length cDNAs from PacBio IsoSeq sequencing and a small RNA dataset (smaller than 200 bp) sequenced with Illumina. The genome sequences were combined to produce an assembly consisting of 5069 contigs, with a total assembly size of 171 Mb and a 77% BUSCO completeness. The new data generated here may contribute to a better understanding of the evolution and ecological roles of chrysophyte algae, as well as to resolve the branching patterns at a larger phylogenetic scale.
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Affiliation(s)
- Jon Bråte
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Oslo, 0316, Norway
| | - Janina Fuss
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, 24118, Germany
| | - Shruti Mehrota
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Oslo, 0316, Norway.,Section for Aquatic Biology and Toxicology (AQUA), Department of Biosciences, University of Oslo, Oslo, 0316, Norway
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, 0316, Norway
| | - Dag Klaveness
- Section for Aquatic Biology and Toxicology (AQUA), Department of Biosciences, University of Oslo, Oslo, 0316, Norway
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Principles of plastid reductive evolution illuminated by nonphotosynthetic chrysophytes. Proc Natl Acad Sci U S A 2019; 116:6914-6923. [PMID: 30872488 DOI: 10.1073/pnas.1819976116] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The division of life into producers and consumers is blurred by evolution. For example, eukaryotic phototrophs can lose the capacity to photosynthesize, although they may retain vestigial plastids that perform other essential cellular functions. Chrysophyte algae have undergone a particularly large number of photosynthesis losses. Here, we present a plastid genome sequence from a nonphotosynthetic chrysophyte, "Spumella" sp. NIES-1846, and show that it has retained a nearly identical set of plastid-encoded functions as apicomplexan parasites. Our transcriptomic analysis of 12 different photosynthetic and nonphotosynthetic chrysophyte lineages reveals remarkable convergence in the functions of these nonphotosynthetic plastids, along with informative lineage-specific retentions and losses. At one extreme, Cornospumella fuschlensis retains many photosynthesis-associated proteins, although it appears to have lost the reductive pentose phosphate pathway and most plastid amino acid metabolism pathways. At the other extreme, Paraphysomonas lacks plastid-targeted proteins associated with gene expression and all metabolic pathways that require plastid-encoded partners, indicating a complete loss of plastid DNA in this genus. Intriguingly, some of the nucleus-encoded proteins that once functioned in the expression of the Paraphysomonas plastid genome have been retained. These proteins were likely to have been dual targeted to the plastid and mitochondria of the chrysophyte ancestor, and are uniquely targeted to the mitochondria in Paraphysomonas Our comparative analyses provide insights into the process of functional reduction in nonphotosynthetic plastids.
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Kraus D, Chi J, Boenigk J, Beisser D, Graupner N, Dunthorn M. Putatively asexual chrysophytes have meiotic genes: evidence from transcriptomic data. PeerJ 2019; 6:e5894. [PMID: 30671284 PMCID: PMC6339481 DOI: 10.7717/peerj.5894] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 10/08/2018] [Indexed: 01/06/2023] Open
Abstract
Chrysophytes are a large group of heterotrophic, phototrophic, or even mixotrophic protists that are abundant in aquatic as well as terrestrial environments. Although much is known about chrysophyte biology and ecology, it is unknown if they are sexual or not. Here we use available transcriptomes of 18 isolates of 15 putatively asexual species to inventory the presence of genes used in meiosis. Since we were able to detect a set of nine meiosis-specific and 29 meiosis-related genes shared by the chrysophytes, we conclude that they are secretively sexual and therefore should be investigated further using genome sequencing to uncover any missed genes from the transcriptomes.
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Affiliation(s)
- Diana Kraus
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Jingyun Chi
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Jens Boenigk
- Department of Biodiversity, University of Duisburg-Essen, Essen, Germany
| | - Daniela Beisser
- Department of Biodiversity, University of Duisburg-Essen, Essen, Germany.,Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | - Nadine Graupner
- Department of Biodiversity, University of Duisburg-Essen, Essen, Germany
| | - Micah Dunthorn
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany.,Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany.,Department of Eukaryotic Microbiology, University of Duisburg-Essen, Essen, Germany
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