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Bonacolta AM, Krause-Massaguer J, Smit NJ, Sikkel PC, Del Campo J. A new and widespread group of fish apicomplexan parasites. Curr Biol 2024; 34:2748-2755.e3. [PMID: 38821048 DOI: 10.1016/j.cub.2024.04.084] [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: 01/10/2024] [Revised: 03/12/2024] [Accepted: 04/30/2024] [Indexed: 06/02/2024]
Abstract
Apicomplexans are obligate intracellular parasites that have evolved from a free-living, phototrophic ancestor. They have been reported from marine environmental samples in high numbers,1 with several clades of apicomplexan-related lineages (ARLs) having been described from environmental sequencing data (16S rRNA gene metabarcoding).2 The most notable of these are the corallicolids (previously ARL-V), which possess chlorophyll-biosynthesis genes in their relic chloroplast (apicoplast) and are geographically widespread and abundant symbionts of anthozoans.3 Corallicolids are related to the Eimeriorina, a suborder of apicomplexan coccidians that include other notable members such as Toxoplasma gondii.4Ophioblennius macclurei, the redlip blenny, along with other tropical reef fishes, is known to be infected by Haemogregarina-like and Haemohormidium-like parasites5 supposedly belonging to the Adeleorina; however, phylogenetics shows that these parasites are instead related to the Eimeriorina.6,7 Hybrid genomic sequencing of apicomplexan-infected O. macclurei blood recovered the entire rRNA operon of this apicomplexan parasite along with the complete mitochondrion and apicoplast genomes. Phylogenetic analyses using this new genomic information consistently place these fish-infecting apicomplexans, hereby informally named ichthyocolids, sister to the corallicolids within Coccidia. The apicoplast genome did not contain chlorophyll biosynthesis genes, providing evidence for another independent loss of this pathway within Apicomplexa. Based on the 16S rRNA gene found in the apicoplast, this group corresponds to the previously described ARL-VI. Screening of fish microbiome studies using the plastid 16S rRNA gene shows these parasites to be geographically and taxonomically widespread in fish species across the globe with implications for commercial fisheries and oceanic food webs.
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Affiliation(s)
- Anthony M Bonacolta
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, FL 33149, USA; Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Pg. Marítim de la Barceloneta, 37-49, 08003 Barcelona, Catalonia, Spain
| | - Joana Krause-Massaguer
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Pg. Marítim de la Barceloneta, 37-49, 08003 Barcelona, Catalonia, Spain
| | - Nico J Smit
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, FL 33149, USA; Water Research Group, Unit for Environmental Sciences and Management, North-West University, Private Bag X6001, Potchefstroom 2520, South Africa
| | - Paul C Sikkel
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, FL 33149, USA; Water Research Group, Unit for Environmental Sciences and Management, North-West University, Private Bag X6001, Potchefstroom 2520, South Africa
| | - Javier Del Campo
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, FL 33149, USA; Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Pg. Marítim de la Barceloneta, 37-49, 08003 Barcelona, Catalonia, Spain.
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2
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Na I, Campos C, Lax G, Kwong WK, Keeling PJ. Phylogenomics reveals Adeleorina are an ancient and distinct subgroup of Apicomplexa. Mol Phylogenet Evol 2024; 195:108060. [PMID: 38485105 DOI: 10.1016/j.ympev.2024.108060] [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: 10/25/2023] [Revised: 02/21/2024] [Accepted: 03/11/2024] [Indexed: 03/17/2024]
Abstract
Apicomplexans are a diverse phylum of unicellular eukaryotes that share obligate relationships with terrestrial and aquatic animal hosts. Many well-studied apicomplexans are responsible for several deadly zoonotic and human diseases, most notably malaria caused by Plasmodium. Interest in the evolutionary origin of apicomplexans has also spurred recent work on other more deeply-branching lineages, especially gregarines and sister groups like squirmids and chrompodellids. But a full picture of apicomplexan evolution is still lacking several lineages, and one major, diverse lineage that is notably absent is the adeleorinids. Adeleorina apicomplexans comprises hundreds of described species that infect invertebrate and vertebrate hosts across the globe. Although historically considered coccidians, phylogenetic trees based on limited data have shown conflicting branch positions for this subgroup, leaving this question unresolved. Phylogenomic trees and large-scale analyses comparing cellular functions and metabolism between major subgroups of apicomplexans have not incorporated Adeleorina because only a handful of molecular markers and a couple organellar genomes are available, ultimately excluding this group from contributing to our understanding of apicomplexan evolution and biology. To address this gap, we have generated complete genomes from mitochondria and plastids, as well as multiple deep-coverage single-cell transcriptomes of nuclear genes from two Adeleorina species, Klossia helicina and Legerella nova, and inferred a 206-protein phylogenomic tree of Apicomplexa. We observed distinct structures reported in species descriptions as remnant host structures surrounding adeleorinid oocysts. Klossia helicina and L. nova branched, as expected, with monoxenous adeleorinids within the Adeleorina and their mitochondrial and plastid genomes exhibited similarity to published organellar adeleorinid genomes. We show with a phylogeneomic tree and subsequent phylogenomic analyses that Adeleorina are not closely related to any of the currently sampled apicomplexan subgroups, and instead fall as a sister to a large clade encompassing Coccidia, Protococcidia, Hematozoa, and Nephromycida, collectively. This resolves Adeleorina as a key independently-branching group, separate from coccidians, on the tree of Apicomplexa, which now has all known major lineages sampled.
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Affiliation(s)
- Ina Na
- Department of Botany, University of British Columbia, Vancouver, BC, Canada.
| | - Claudia Campos
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal
| | - Gordon Lax
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Waldan K Kwong
- Department of Botany, University of British Columbia, Vancouver, BC, Canada; Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC, Canada.
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3
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Hooper PM, Bass D, Feil EJ, Vincent WF, Lovejoy C, Owen CJ, Tsola SL, Jungblut AD. Arctic cyanobacterial mat community diversity decreases with latitude across the Canadian Arctic. FEMS Microbiol Ecol 2024; 100:fiae067. [PMID: 38653723 DOI: 10.1093/femsec/fiae067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 04/15/2024] [Accepted: 04/22/2024] [Indexed: 04/25/2024] Open
Abstract
Cyanobacterial mats are commonly reported as hotspots of microbial diversity across polar environments. These thick, multilayered microbial communities provide a refuge from extreme environmental conditions, with many species able to grow and coexist despite the low allochthonous nutrient inputs. The visibly dominant phototrophic biomass is dependent on internal nutrient recycling by heterotrophic organisms within the mats; however, the specific contribution of heterotrophic protists remains little explored. In this study, mat community diversity was examined along a latitudinal gradient (55-83°N), spanning subarctic taiga, tundra, polar desert, and the High Arctic ice shelves. The prokaryotic and eukaryotic communities were targeted, respectively, by V4 16S ribosomal RNA (rRNA) and V9 18S rRNA gene amplicon high-throughput sequencing. Prokaryotic and eukaryotic richness decreased, in tandem with decreasing temperatures and shorter seasons of light availability, from the subarctic to the High Arctic. Taxonomy-based annotation of the protist community revealed diverse phototrophic, mixotrophic, and heterotrophic genera in all mat communities, with fewer parasitic taxa in High Arctic communities. Co-occurrence network analysis identified greater heterogeneity in eukaryotic than prokaryotic community structure among cyanobacterial mats across the Canadian Arctic. Our findings highlight the sensitivity of microbial eukaryotes to environmental gradients across northern high latitudes.
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Affiliation(s)
- Patrick M Hooper
- Science Department, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom
| | - David Bass
- Science Department, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Barrack Road, Weymouth, DT4 8UB, United Kingdom
- Centre for Sustainable Aquaculture Futures, University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom
| | - Edward J Feil
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom
| | - Warwick F Vincent
- Département de Biologie, Takuvik International Research Laboratory and Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre d'études nordiques (CEN), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Connie Lovejoy
- Département de Biologie, Takuvik International Research Laboratory and Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre d'études nordiques (CEN), Université Laval, Québec, QC, G1V 0A6, Canada
- Québec Océan, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Christopher J Owen
- UCL Genetics Institute, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Stephania L Tsola
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, United Kingdom
| | - Anne D Jungblut
- Science Department, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom
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4
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Useros F, García-Cunchillos I, Henry N, Berney C, Lara E. How good are global DNA-based environmental surveys for detecting all protist diversity? Arcellinida as an example of biased representation. Environ Microbiol 2024; 26:e16606. [PMID: 38509748 DOI: 10.1111/1462-2920.16606] [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: 10/19/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024]
Abstract
Metabarcoding approaches targeting microeukaryotes have deeply changed our vision of protist environmental diversity. The public repository EukBank consists of 18S v4 metabarcodes from 12,672 samples worldwide. To estimate how far this database provides a reasonable overview of all eukaryotic diversity, we used Arcellinida (lobose testate amoebae) as a case study. We hypothesised that (1) this approach would allow the discovery of unexpected diversity, but also that (2) some groups would be underrepresented because of primer/sequencing biases. Most of the Arcellinida sequences appeared in freshwater and soil, but their abundance and diversity appeared underrepresented. Moreover, 84% of ASVs belonged to the suborder Phryganellina, a supposedly species-poor clade, whereas the best-documented suborder (Glutinoconcha, 600 described species) was only marginally represented. We explored some possible causes of these biases. Mismatches in the primer-binding site seem to play a minor role. Excessive length of the target region could explain some of these biases, but not all. There must be some other unknown factors involved. Altogether, while metabarcoding based on ribosomal genes remains a good first approach to document microbial eukaryotic clades, alternative approaches based on other genes or sequencing techniques must be considered for an unbiased picture of the diversity of some groups.
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Affiliation(s)
| | - Iván García-Cunchillos
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Nicolas Henry
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, Paris, France
- CNRS, FR2424, ABiMS, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Cédric Berney
- CNRS, FR2424, ABiMS, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
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5
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Schwarz D, Lourido S. The multifaceted roles of Myb domain-containing proteins in apicomplexan parasites. Curr Opin Microbiol 2023; 76:102395. [PMID: 37866202 PMCID: PMC10872578 DOI: 10.1016/j.mib.2023.102395] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/17/2023] [Accepted: 09/19/2023] [Indexed: 10/24/2023]
Abstract
Apicomplexan parasites are a large and diverse clade of protists responsible for significant diseases of humans and animals. Central to the ability of these parasites to colonize their host and evade immune responses is an expanded repertoire of gene-expression programs that requires the coordinated action of complex transcriptional networks. DNA-binding proteins and chromatin regulators are essential orchestrators of apicomplexan gene expression that often act in concert. Although apicomplexan genomes encode various families of putative DNA-binding proteins, most remain functionally and mechanistically unexplored. This review highlights the versatile role of myeloblastosis (Myb) domain-containing proteins in apicomplexan parasites as transcription factors and chromatin regulators. We explore the diversity of Myb domain structure and use phylogenetic analysis to identify common features across the phylum. This provides a framework to discuss functional heterogeneity and regulation of Myb domain-containing proteins particularly emphasizing their role in parasite differentiation.
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Affiliation(s)
- Dominic Schwarz
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Sebastian Lourido
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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6
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Van Steenkiste NWL, Wakeman KC, Söderström B, Leander BS. Patterns of host-parasite associations between marine meiofaunal flatworms (Platyhelminthes) and rhytidocystids (Apicomplexa). Sci Rep 2023; 13:21050. [PMID: 38030717 PMCID: PMC10687266 DOI: 10.1038/s41598-023-48233-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/23/2023] [Indexed: 12/01/2023] Open
Abstract
Microturbellarians are abundant and ubiquitous members of marine meiofaunal communities around the world. Because of their small body size, these microscopic animals are rarely considered as hosts for parasitic organisms. Indeed, many protists, both free-living and parasitic ones, equal or surpass meiofaunal animals in size. Despite several anecdotal records of "gregarines", "sporozoans", and "apicomplexans" parasitizing microturbellarians in the literature-some of them dating back to the nineteenth century-these single-celled parasites have never been identified and characterized. More recently, the sequencing of eukaryotic microbiomes in microscopic invertebrates have revealed a hidden diversity of protist parasites infecting microturbellarians and other meiofaunal animals. Here we show that apicomplexans isolated from twelve taxonomically diverse rhabdocoel taxa and one species of proseriate collected in four geographically distinct areas around the Pacific Ocean (Okinawa, Hokkaido, and British Columbia) and the Caribbean Sea (Curaçao) all belong to the apicomplexan genus Rhytidocystis. Based on comprehensive molecular phylogenies of Rhabdocoela and Proseriata inferred from both 18S and 28S rDNA sequences, as well as a molecular phylogeny of Marosporida inferred from 18S rDNA sequences, we determine the phylogenetic positions of the microturbellarian hosts and their parasites. Multiple lines of evidence, including morphological and molecular data, show that at least nine new species of Rhytidocystis infect the microturbellarian hosts collected in this study, more than doubling the number of previously recognized species of Rhytidocystis, all of which infect polychaete hosts. A cophylogenetic analysis examining patterns of phylosymbiosis between hosts and parasites suggests a complex picture of overall incongruence between host and parasite phylogenies, and varying degrees of geographic signals and taxon specificity.
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Affiliation(s)
- Niels W L Van Steenkiste
- Departments of Botany and Zoology, University of British Columbia, Vancouver, BC, Canada.
- Hakai Institute, Heriot Bay, Quadra Island, BC, Canada.
| | - Kevin C Wakeman
- Institute for the Advancement of High Education, Hokkaido University, Sapporo, Japan.
| | - Bill Söderström
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, Australia
| | - Brian S Leander
- Departments of Botany and Zoology, University of British Columbia, Vancouver, BC, Canada
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7
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Xu Z, Chen J, Li Y, Shekarriz E, Wu W, Chen B, Liu H. High Microeukaryotic Diversity in the Cold-Seep Sediment. MICROBIAL ECOLOGY 2023; 86:2003-2020. [PMID: 36973438 DOI: 10.1007/s00248-023-02212-y] [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: 10/29/2022] [Accepted: 03/22/2023] [Indexed: 06/18/2023]
Abstract
Microeukaryotic diversity, community structure, and their regulating mechanisms remain largely unclear in chemosynthetic ecosystems. Here, using high-throughput sequencing data of 18S rRNA genes, we explored microeukaryotic communities from the Haima cold seep in the northern South China Sea. We compared three distinct habitats: active, less active, and non-seep regions, with vertical layers (0-25 cm) from sediment cores. The results showed that seep regions harbored more abundant and diverse parasitic microeukaryotes (e.g., Apicomplexa and Syndiniales) as indicator species, compared to nearby non-seep region. Microeukaryotic community heterogeneity was larger between habitats than within habitat, and greatly increased when considering molecular phylogeny, suggesting the local diversification in cold-seep sediments. Microeukaryotic α-diversity at cold seeps was positively increased by metazoan richness and dispersal rate of microeukaryotes, while its β-diversity was promoted by heterogeneous selection mainly from metazoan communities (as potential hosts). Their combined effects led to the significant higher γ-diversity (i.e., total diversity in a region) at cold seeps than non-seep regions, suggesting cold-seep sediment as a hotspot for microeukaryotic diversity. Our study highlights the importance of microeukaryotic parasitism in cold-seep sediment and has implications for the roles of cold seep in maintaining and promoting marine biodiversity.
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Affiliation(s)
- Zhimeng Xu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Jiawei Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Yingdong Li
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Erfan Shekarriz
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Wenxue Wu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Bingzhang Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Mathematics and Statistics, University of Strathclyde, Glasgow, UK
| | - Hongbin Liu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China.
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China.
- CAS-HKUST Sanya Joint Laboratory of Marine Science Research, Sanya, China.
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8
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Geisen S, Lara E, Mitchell E. Contemporary issues, current best practice and ways forward in soil protist ecology. Mol Ecol Resour 2023; 23:1477-1487. [PMID: 37259890 DOI: 10.1111/1755-0998.13819] [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: 10/31/2022] [Revised: 02/23/2023] [Accepted: 05/17/2023] [Indexed: 06/02/2023]
Abstract
Soil protists are increasingly studied due to a release from previous methodological constraints and the acknowledgement of their immense diversity and functional importance in ecosystems. However, these studies often lack sufficient depth in knowledge, which is visible in the form of falsely used terms and false- or over-interpreted data with conclusions that cannot be drawn from the data obtained. As we welcome that also non-experts include protists in their still mostly bacterial and/or fungal-focused studies, our aim here is to help avoid some common errors. We provide suggestions for current terms to use when working on soil protists, like protist instead of protozoa, predator instead of grazer, microorganisms rather than microflora and other terms to be used to describe the prey spectrum of protists. We then highlight some dos and don'ts in soil protist ecology including challenges related to interpreting 18S rRNA gene amplicon sequencing data. We caution against the use of standard bioinformatic settings optimized for bacteria and the uncritical reliance on incomplete and partly erroneous reference databases. We also show why causal inferences cannot be drawn from sequence-based correlation analyses or any sampling/monitoring, study in the field without thorough experimental confirmation and sound understanding of the biology of taxa. Together, we envision this work to help non-experts to more easily include protists in their soil ecology analyses and obtain more reliable interpretations from their protist data and other biodiversity data that, in the end, will contribute to a better understanding of soil ecology.
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Affiliation(s)
- Stefan Geisen
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
| | | | - Edward Mitchell
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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9
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Zimmermann HH, Stoof-Leichsenring KR, Dinkel V, Harms L, Schulte L, Hütt MT, Nürnberg D, Tiedemann R, Herzschuh U. Marine ecosystem shifts with deglacial sea-ice loss inferred from ancient DNA shotgun sequencing. Nat Commun 2023; 14:1650. [PMID: 36964154 PMCID: PMC10039020 DOI: 10.1038/s41467-023-36845-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 02/20/2023] [Indexed: 03/26/2023] Open
Abstract
Sea ice is a key factor for the functioning and services provided by polar marine ecosystems. However, ecosystem responses to sea-ice loss are largely unknown because time-series data are lacking. Here, we use shotgun metagenomics of marine sedimentary ancient DNA off Kamchatka (Western Bering Sea) covering the last ~20,000 years. We traced shifts from a sea ice-adapted late-glacial ecosystem, characterized by diatoms, copepods, and codfish to an ice-free Holocene characterized by cyanobacteria, salmon, and herring. By providing information about marine ecosystem dynamics across a broad taxonomic spectrum, our data show that ancient DNA will be an important new tool in identifying long-term ecosystem responses to climate transitions for improvements of ocean and cryosphere risk assessments. We conclude that continuing sea-ice decline on the northern Bering Sea shelf might impact on carbon export and disrupt benthic food supply and could allow for a northward expansion of salmon and Pacific herring.
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Affiliation(s)
- Heike H Zimmermann
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, D-14473, Potsdam, Germany
- Department of Glaciology and Climate, Geological Survey of Denmark and Greenland (GEUS), DK-1350, Copenhagen, Denmark
| | - Kathleen R Stoof-Leichsenring
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, D-14473, Potsdam, Germany
| | - Viktor Dinkel
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, D-14473, Potsdam, Germany
- Constructor University Bremen, Computational Systems Biology, Bremen, D-28759, Germany
| | - Lars Harms
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Data Science Support, D-27568, Bremerhaven, Germany
| | - Luise Schulte
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, D-14473, Potsdam, Germany
| | - Marc-Thorsten Hütt
- Constructor University Bremen, Computational Systems Biology, Bremen, D-28759, Germany
| | - Dirk Nürnberg
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Ocean circulation and climate dynamics, D-24148, Kiel, Germany
| | - Ralf Tiedemann
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Marine Geology, D-27568, Bremerhaven, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, D-28334, Bremen, Germany
| | - Ulrike Herzschuh
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, D-14473, Potsdam, Germany.
- University of Potsdam, Institute of Biochemistry and Biology, D-14476, Potsdam, Germany.
- University of Potsdam, Institute of Environmental Sciences and Geography, D-14476, Potsdam, Germany.
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10
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Grierson J, Flies EJ, Bissett A, Ammitzboll H, Jones P. Which soil microbiome? Bacteria, fungi, and protozoa communities show different relationships with urban green space type and use-intensity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 863:160468. [PMID: 36464041 DOI: 10.1016/j.scitotenv.2022.160468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/20/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
Exposure to diverse microbial communities early in life can help support healthy human immune function. Soil microbiomes in public and private urban green spaces are potentially important sources of contact with diverse microbiomes for much of the global population. However, we lack understanding of how soil microbial communities vary across and within urban green spaces, and whether these patterns vary across microbial kingdoms; closing this knowledge gap may help us optimise green spaces' capacities to provide this ecosystem service. Here we explore the diversity and community compositions of soil microbiomes across urban green space types in Tasmania, Australia. Specifically, we analysed soil bacterial, fungal, and protozoan diversity and composition across private backyards and public parks. Within parks, we conducted separate sampling for areas of high and low intensity use. We found that: (i) bacteria, fungi, and protozoa showed different patterns of variation, (ii) bacterial alpha-diversity was lowest in low-intensity use areas of parks, (iii) there was relatively little variation in the community composition across backyards, and high and low intensity-use park areas and (iv) neither human-associated bacteria, nor potential microbial community function of bacteria and fungi differed significantly across green space types. To our knowledge, this is the first urban soil microbiome analysis which analyses these three soil microbial kingdoms simultaneously across public and private green space types and within public spaces according to intensity of use. These findings demonstrate how green space type and use intensity may impact on soil microbial diversity and composition, and thus may influence our opportunity to gain healthy exposure to diverse environmental microbiomes.
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Affiliation(s)
- Jessica Grierson
- Menzies Institute for Medical Research, University of Tasmania, Hobart 7001, Australia; School of Natural Sciences, University of Tasmania, Hobart 7001, Australia; Healthy Landscapes Research Group, University of Tasmania, Hobart 7001, Australia.
| | - Emily J Flies
- School of Natural Sciences, University of Tasmania, Hobart 7001, Australia; Healthy Landscapes Research Group, University of Tasmania, Hobart 7001, Australia
| | - Andrew Bissett
- Oceans and Atmosphere, CSIRO, Hobart, TAS 7000, Australia
| | - Hans Ammitzboll
- School of Natural Sciences, University of Tasmania, Hobart 7001, Australia
| | - Penelope Jones
- Menzies Institute for Medical Research, University of Tasmania, Hobart 7001, Australia; School of Natural Sciences, University of Tasmania, Hobart 7001, Australia; Healthy Landscapes Research Group, University of Tasmania, Hobart 7001, Australia
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11
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Holt CC, Boscaro V, Van Steenkiste NWL, Herranz M, Mathur V, Irwin NAT, Buckholtz G, Leander BS, Keeling PJ. Microscopic marine invertebrates are reservoirs for cryptic and diverse protists and fungi. MICROBIOME 2022; 10:161. [PMID: 36180959 PMCID: PMC9523941 DOI: 10.1186/s40168-022-01363-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Microbial symbioses in marine invertebrates are commonplace. However, characterizations of invertebrate microbiomes are vastly outnumbered by those of vertebrates. Protists and fungi run the gamut of symbiosis, yet eukaryotic microbiome sequencing is rarely undertaken, with much of the focus on bacteria. To explore the importance of microscopic marine invertebrates as potential symbiont reservoirs, we used a phylogenetic-focused approach to analyze the host-associated eukaryotic microbiomes of 220 animal specimens spanning nine different animal phyla. RESULTS Our data expanded the traditional host range of several microbial taxa and identified numerous undescribed lineages. A lack of comparable reference sequences resulted in several cryptic clades within the Apicomplexa and Ciliophora and emphasized the potential for microbial invertebrates to harbor novel protistan and fungal diversity. CONCLUSIONS Microscopic marine invertebrates, spanning a wide range of animal phyla, host various protist and fungal sequences and may therefore serve as a useful resource in the detection and characterization of undescribed symbioses. Video Abstract.
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Affiliation(s)
- Corey C Holt
- Department of Botany, University of British Columbia, Vancouver, Canada.
- Hakai Institute, Heriot Bay, Canada.
| | - Vittorio Boscaro
- Department of Botany, University of British Columbia, Vancouver, Canada
- Hakai Institute, Heriot Bay, Canada
| | - Niels W L Van Steenkiste
- Department of Botany, University of British Columbia, Vancouver, Canada
- Hakai Institute, Heriot Bay, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
| | - Maria Herranz
- Department of Botany, University of British Columbia, Vancouver, Canada
- Hakai Institute, Heriot Bay, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Varsha Mathur
- Department of Botany, University of British Columbia, Vancouver, Canada
| | | | - Gracy Buckholtz
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Brian S Leander
- Department of Botany, University of British Columbia, Vancouver, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, Canada.
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12
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Cahoon AB, VanGundy RD. Alveolates (dinoflagellates, ciliates and apicomplexans) and Rhizarians are the most common microbial eukaryotes in temperate Appalachian karst caves. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:538-548. [PMID: 35388620 PMCID: PMC9542216 DOI: 10.1111/1758-2229.13060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 03/02/2022] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
The purpose of this study was to survey the eukaryotic microbiome of two karst caves in the Valley and Ridge physiographic region of the Appalachian Mountains. Caves are known to harbour eukaryotic microbes but their very low densities and small cell size make them difficult to collect and identify. Microeukaryotes were surveyed using two methodologies, filtering water and submerging glass microscope slides mounted in periphytometers in cave pools. The periphyton sampling yielded 13.5 times more unique amplicon sequence variants (ASVs) than filtered water. The most abundant protist supergroup was Alveolata with large proportions of the ASVs belonging to dinoflagellate, ciliate and apicomplexan clades. The next most abundant were Rhizarians followed by Stramenopiles (diatoms and chrysophytes) and Ameobozoans. Very few of the ASVs, 1.5%, matched curated protist sequences with greater than 99% identity and only 2.5% could be identified from surface plankton samples collected in the same region. The overall composition of the eukaryotic microbiome appears to be a combination of bacterial grazers and parasitic species that could possibly survive underground as well as cells, cysts and spores probably transported from the surface.
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Affiliation(s)
- A. Bruce Cahoon
- Department of Natural SciencesThe University of Virginia's College at WiseWiseVA24293USA
| | - Robert D. VanGundy
- Department of Natural SciencesThe University of Virginia's College at WiseWiseVA24293USA
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13
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Sridhar S, Fukagawa T. Kinetochore Architecture Employs Diverse Linker Strategies Across Evolution. Front Cell Dev Biol 2022; 10:862637. [PMID: 35800888 PMCID: PMC9252888 DOI: 10.3389/fcell.2022.862637] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 05/23/2022] [Indexed: 01/09/2023] Open
Abstract
The assembly of a functional kinetochore on centromeric chromatin is necessary to connect chromosomes to the mitotic spindle, ensuring accurate chromosome segregation. This connecting function of the kinetochore presents multiple internal and external structural challenges. A microtubule interacting outer kinetochore and centromeric chromatin interacting inner kinetochore effectively confront forces from the external spindle and centromere, respectively. While internally, special inner kinetochore proteins, defined as "linkers," simultaneously interact with centromeric chromatin and the outer kinetochore to enable association with the mitotic spindle. With the ability to simultaneously interact with outer kinetochore components and centromeric chromatin, linker proteins such as centromere protein (CENP)-C or CENP-T in vertebrates and, additionally CENP-QOkp1-UAme1 in yeasts, also perform the function of force propagation within the kinetochore. Recent efforts have revealed an array of linker pathways strategies to effectively recruit the largely conserved outer kinetochore. In this review, we examine these linkages used to propagate force and recruit the outer kinetochore across evolution. Further, we look at their known regulatory pathways and implications on kinetochore structural diversity and plasticity.
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Affiliation(s)
- Shreyas Sridhar
- Laboratory of Chromosome Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Tatsuo Fukagawa
- Laboratory of Chromosome Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
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14
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Abstract
The goals of the Earth Biogenome Project-to sequence the genomes of all eukaryotic life on earth-are as daunting as they are ambitious. The Darwin Tree of Life Project was founded to demonstrate the credibility of these goals and to deliver at-scale genome sequences of unprecedented quality for a biogeographic region: the archipelago of islands that constitute Britain and Ireland. The Darwin Tree of Life Project is a collaboration between biodiversity organizations (museums, botanical gardens, and biodiversity institutes) and genomics institutes. Together, we have built a workflow that collects specimens from the field, robustly identifies them, performs sequencing, generates high-quality, curated assemblies, and releases these openly for the global community to use to build future science and conservation efforts.
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15
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Rojas-Pirela M, Medina L, Rojas MV, Liempi AI, Castillo C, Pérez-Pérez E, Guerrero-Muñoz J, Araneda S, Kemmerling U. Congenital Transmission of Apicomplexan Parasites: A Review. Front Microbiol 2021; 12:751648. [PMID: 34659187 PMCID: PMC8519608 DOI: 10.3389/fmicb.2021.751648] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 09/01/2021] [Indexed: 12/17/2022] Open
Abstract
Apicomplexans are a group of pathogenic protists that cause various diseases in humans and animals that cause economic losses worldwide. These unicellular eukaryotes are characterized by having a complex life cycle and the ability to evade the immune system of their host organism. Infections caused by some of these parasites affect millions of pregnant women worldwide, leading to various adverse maternal and fetal/placental effects. Unfortunately, the exact pathogenesis of congenital apicomplexan diseases is far from being understood, including the mechanisms of how they cross the placental barrier. In this review, we highlight important aspects of the diseases caused by species of Plasmodium, Babesia, Toxoplasma, and Neospora, their infection during pregnancy, emphasizing the possible role played by the placenta in the host-pathogen interaction.
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Affiliation(s)
- Maura Rojas-Pirela
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile.,Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile.,Facultad de Farmacia y Bioanálisis, Universidad de Los Andes, Mérida, Venezuela
| | - Lisvaneth Medina
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Maria Verónica Rojas
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Ana Isabel Liempi
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Christian Castillo
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile.,Núcleo de Investigación Aplicada en Ciencias Veterinarias y Agronómicas, Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Santiago, Chile
| | | | - Jesús Guerrero-Muñoz
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Sebastian Araneda
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile.,Facultad de Salud y Odontología, Universidad Diego Portales, Santiago, Chile
| | - Ulrike Kemmerling
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
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16
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Mazel F, Malard L, Niculita-Hirzel H, Yashiro E, Mod HK, Mitchell EAD, Singer D, Buri A, Pinto E, Guex N, Lara E, Guisan A. Soil protist function varies with elevation in the Swiss Alps. Environ Microbiol 2021; 24:1689-1702. [PMID: 34347350 PMCID: PMC9290697 DOI: 10.1111/1462-2920.15686] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 07/06/2021] [Accepted: 07/25/2021] [Indexed: 11/29/2022]
Abstract
Protists are abundant and play key trophic functions in soil. Documenting how their trophic contributions vary across large environmental gradients is essential to understand and predict how biogeochemical cycles will be impacted by global changes. Here, using amplicon sequencing of environmental DNA in open habitat soil from 161 locations spanning 2600 m of elevation in the Swiss Alps (from 400 to 3000 m), we found that, over the whole study area, soils are dominated by consumers, followed by parasites and phototrophs. In contrast, the proportion of these groups in local communities shows large variations in relation to elevation. While there is, on average, three times more consumers than parasites at low elevation (400–1000 m), this ratio increases to 12 at high elevation (2000–3000 m). This suggests that the decrease in protist host biomass and diversity toward mountains tops impact protist functional composition. Furthermore, the taxonomic composition of protists that infect animals was related to elevation while that of protists that infect plants or of protist consumers was related to soil pH. This study provides a first step to document and understand how soil protist functions vary along the elevational gradient.
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Affiliation(s)
- Florent Mazel
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland
| | - Lucie Malard
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland
| | - Hélène Niculita-Hirzel
- Department of Occupational Health and Environment, Center for Primary Care and Public Health (Unisanté), University of Lausanne, Epalinges, CH-1066, Switzerland
| | - Erika Yashiro
- Center for Microbial Communities, Section of Biotechnology, Aalborg University, Aalborg, Denmark
| | - Heidi K Mod
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
| | - Edward A D Mitchell
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel, CH-2000, Switzerland.,Jardin Botanique de Neuchâtel, Chemin du Perthuis-du-Sault 58, Neuchâtel, CH-2000, Switzerland
| | - David Singer
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel, CH-2000, Switzerland.,UMR CNRS 6112 LPG-BIAF, Université d'Angers, Angers Cedex 1, France
| | - Aline Buri
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, 1015, Switzerland
| | - Eric Pinto
- Terrabiom Association, Dörflistrasse 32, Oberrieden, Zürich, 8942, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
| | - Enrique Lara
- Real Jardín Botánico, CSIC, Plaza de Murillo 2, Madrid, 28014, Spain
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland.,Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, 1015, Switzerland
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17
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Sediment archives reveal irreversible shifts in plankton communities after World War II and agricultural pollution. Curr Biol 2021; 31:2682-2689.e7. [PMID: 33887182 DOI: 10.1016/j.cub.2021.03.079] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 02/12/2021] [Accepted: 03/23/2021] [Indexed: 01/04/2023]
Abstract
To evaluate the stability and resilience1 of coastal ecosystem communities to perturbations that occurred during the Anthropocene,2 pre-industrial biodiversity baselines inferred from paleoarchives are needed.3,4 The study of ancient DNA (aDNA) from sediments (sedaDNA)5 has provided valuable information about past dynamics of microbial species6-8 and communities9-18 in relation to ecosystem variations. Shifts in planktonic protist communities might significantly affect marine ecosystems through cascading effects,19-21 and therefore the analysis of this compartment is essential for the assessment of ecosystem variations. Here, sediment cores collected from different sites of the Bay of Brest (northeast Atlantic, France) allowed ca. 1,400 years of retrospective analyses of the effects of human pollution on marine protists. Comparison of sedaDNA extractions and metabarcoding analyses with different barcode regions (V4 and V7 18S rDNA) revealed that protist assemblages in ancient sediments are mainly composed of species known to produce resting stages. Heavy-metal pollution traces in sediments were ascribed to the World War II period and coincided with community shifts within dinoflagellates and stramenopiles. After the war and especially from the 1980s to 1990s, protist genera shifts followed chronic contaminations of agricultural origin. Community composition reconstruction over time showed that there was no recovery to a Middle Ages baseline composition. This demonstrates the irreversibility of the observed shifts after the cumulative effect of war and agricultural pollutions. Developing a paleoecological approach, this study highlights how human contaminations irreversibly affect marine microbial compartments, which contributes to the debate on coastal ecosystem preservation and restoration.
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18
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Schoenle A, Hohlfeld M, Hermanns K, Mahé F, de Vargas C, Nitsche F, Arndt H. High and specific diversity of protists in the deep-sea basins dominated by diplonemids, kinetoplastids, ciliates and foraminiferans. Commun Biol 2021; 4:501. [PMID: 33893386 PMCID: PMC8065057 DOI: 10.1038/s42003-021-02012-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 03/08/2021] [Indexed: 02/02/2023] Open
Abstract
Heterotrophic protists (unicellular eukaryotes) form a major link from bacteria and algae to higher trophic levels in the sunlit ocean. Their role on the deep seafloor, however, is only fragmentarily understood, despite their potential key function for global carbon cycling. Using the approach of combined DNA metabarcoding and cultivation-based surveys of 11 deep-sea regions, we show that protist communities, mostly overlooked in current deep-sea foodweb models, are highly specific, locally diverse and have little overlap to pelagic communities. Besides traditionally considered foraminiferans, tiny protists including diplonemids, kinetoplastids and ciliates were genetically highly diverse considerably exceeding the diversity of metazoans. Deep-sea protists, including many parasitic species, represent thus one of the most diverse biodiversity compartments of the Earth system, forming an essential link to metazoans.
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Affiliation(s)
- Alexandra Schoenle
- University of Cologne, Institute of Zoology, General Ecology, Cologne, Germany.
| | - Manon Hohlfeld
- University of Cologne, Institute of Zoology, General Ecology, Cologne, Germany
| | - Karoline Hermanns
- University of Cologne, Institute of Zoology, General Ecology, Cologne, Germany
| | - Frédéric Mahé
- CIRAD, UMR BGPI, Montpellier, France
- BGPI, Univ Montpellier, CIRAD, IRD, Montpellier SupAgro, Montpellier, France
| | - Colomban de Vargas
- CNRS, Sorbonne Université, Station Biologique de Roscoff, UMR7144, ECOMAP-Ecology of Marine Plankton, Roscoff, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara GOSEE, Paris, France
| | - Frank Nitsche
- University of Cologne, Institute of Zoology, General Ecology, Cologne, Germany
| | - Hartmut Arndt
- University of Cologne, Institute of Zoology, General Ecology, Cologne, Germany.
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19
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Salomaki ED, Terpis KX, Rueckert S, Kotyk M, Varadínová ZK, Čepička I, Lane CE, Kolisko M. Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans. BMC Biol 2021; 19:77. [PMID: 33863338 PMCID: PMC8051059 DOI: 10.1186/s12915-021-01007-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 03/19/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Apicomplexa is a diverse phylum comprising unicellular endobiotic animal parasites and contains some of the most well-studied microbial eukaryotes including the devastating human pathogens Plasmodium falciparum and Cryptosporidium hominis. In contrast, data on the invertebrate-infecting gregarines remains sparse and their evolutionary relationship to other apicomplexans remains obscure. Most apicomplexans retain a highly modified plastid, while their mitochondria remain metabolically conserved. Cryptosporidium spp. inhabit an anaerobic host-gut environment and represent the known exception, having completely lost their plastid while retaining an extremely reduced mitochondrion that has lost its genome. Recent advances in single-cell sequencing have enabled the first broad genome-scale explorations of gregarines, providing evidence of differential plastid retention throughout the group. However, little is known about the retention and metabolic capacity of gregarine mitochondria. RESULTS Here, we sequenced transcriptomes from five species of gregarines isolated from cockroaches. We combined these data with those from other apicomplexans, performed detailed phylogenomic analyses, and characterized their mitochondrial metabolism. Our results support the placement of Cryptosporidium as the earliest diverging lineage of apicomplexans, which impacts our interpretation of evolutionary events within the phylum. By mapping in silico predictions of core mitochondrial pathways onto our phylogeny, we identified convergently reduced mitochondria. These data show that the electron transport chain has been independently lost three times across the phylum, twice within gregarines. CONCLUSIONS Apicomplexan lineages show variable functional restructuring of mitochondrial metabolism that appears to have been driven by adaptations to parasitism and anaerobiosis. Our findings indicate that apicomplexans are rife with convergent adaptations, with shared features including morphology, energy metabolism, and intracellularity.
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Affiliation(s)
- Eric D Salomaki
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Kristina X Terpis
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
| | - Sonja Rueckert
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, Scotland, UK
| | - Michael Kotyk
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | | | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Christopher E Lane
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA.
| | - Martin Kolisko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.
- Department of Molecular Biology and Genetics, University of South Bohemia, České Budějovice, Czech Republic.
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20
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Rappemonads are haptophyte phytoplankton. Curr Biol 2021; 31:2395-2403.e4. [PMID: 33773100 DOI: 10.1016/j.cub.2021.03.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/12/2021] [Accepted: 03/03/2021] [Indexed: 11/20/2022]
Abstract
Rapidly accumulating genetic data from environmental sequencing approaches have revealed an extraordinary level of unsuspected diversity within marine phytoplankton,1-11 which is responsible for around 50% of global net primary production.12,13 However, the phenotypic identity of many of the organisms distinguished by environmental DNA sequences remains unclear. The rappemonads represent a plastid-bearing protistan lineage that to date has only been identified by environmental plastid 16S rRNA sequences.14-17 The phenotypic identity of this group, which does not confidently cluster in any known algal clades in 16S rRNA phylogenetic reconstructions,15 has remained unknown since the first report of environmental sequences over two decades ago. We show that rappemonads are closely related to a haptophyte microalga, Pavlomulina ranunculiformis gen. nov. et sp. nov., and belong to a new haptophyte class, the Rappephyceae. Organellar phylogenomic analyses provide strong evidence for the inclusion of this lineage within the Haptophyta as a sister group to the Prymnesiophyceae. Members of this new class have a cosmopolitan distribution in coastal and oceanic regions. The relative read abundance of Rappephyceae in a large environmental barcoding dataset was comparable to, or greater than, those of major haptophyte species, such as the bloom-forming Gephyrocapsa huxleyi and Prymnesium parvum, and this result indicates that they likely have a significant impact as primary producers. Detailed characterization of Pavlomulina allowed for reconstruction of the ancient evolutionary history of the Haptophyta, a group that is one of the most important components of extant marine phytoplankton communities.
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21
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Kwong WK, Irwin NAT, Mathur V, Na I, Okamoto N, Vermeij MJA, Keeling PJ. Taxonomy of the Apicomplexan Symbionts of Coral, including Corallicolida ord. nov., Reassignment of the Genus Gemmocystis, and Description of New Species Corallicola aquarius gen. nov. sp. nov. and Anthozoaphila gnarlus gen. nov. sp. nov. J Eukaryot Microbiol 2021; 68:e12852. [PMID: 33768669 DOI: 10.1111/jeu.12852] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/27/2021] [Accepted: 03/12/2021] [Indexed: 11/30/2022]
Abstract
Corals (Metazoa; Cnidaria; Anthozoa) have recently been shown to play host to a widespread and diverse group of intracellular symbionts of the phylum Apicomplexa. These symbionts, colloquially called "corallicolids", are mostly known through molecular analyses, and no formal taxonomy has been proposed. Another apicomplexan, Gemmocystis cylindrus (described from the coral Dendrogyra cylindrus), may be related to corallicolids, but lacks molecular data. Here, we isolate and describe motile trophozoite (feeding) corallicolids cells using microscopic (light, SEM, and TEM) and molecular phylogenetic analysis to provide the basis for a formal description. Phylogenetic analyses using nuclear and plastid rRNA operons, and three mitochondrial protein sequences derived from single cell transcriptomes, all confirm that these organisms fall into a discrete deep-branching clade within the Apicomplexa not closely related to any known species or major subgroup. As a result, we assign this clade to a new order, Corallicolida ord. nov., and family, Corallicolidae fam. nov. We describe a type species, Corallicola aquarius gen. nov. sp. nov. from its Rhodactis sp. host, and also describe a second species, Anthozoaphila gnarlus gen. nov. sp. nov., from the coral host Madracis mirabilis. Finally, we propose reassigning the incertae sedis taxon G. cylindrus from the order Agamococcidiorida to the Corallicolida, based on similarities in morphology and host localization to that of the corallicolids.
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Affiliation(s)
- Waldan K Kwong
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Nicholas A T Irwin
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Varsha Mathur
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Ina Na
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Noriko Okamoto
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Mark J A Vermeij
- Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 700, Amsterdam, 1098 XH, The Netherlands
- CARMABI Foundation, PO Box 2090, Piscaderabaai z/n, Willemstad, Curaçao
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
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22
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Florent I, Chapuis MP, Labat A, Boisard J, Leménager N, Michel B, Desportes-Livage I. Integrative taxonomy confirms that Gregarina garnhami and G. acridiorum (Apicomplexa, Gregarinidae), parasites of Schistocerca gregaria and Locusta migratoria (Insecta, Orthoptera), are distinct species. ACTA ACUST UNITED AC 2021; 28:12. [PMID: 33620310 PMCID: PMC7901526 DOI: 10.1051/parasite/2021009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 02/02/2021] [Indexed: 11/27/2022]
Abstract
Orthoptera are infected by about 60 species of gregarines assigned to the genus Gregarina Dufour, 1828. Among these species, Gregarina garnhami Canning, 1956 from Schistocerca gregaria (Forsskål, 1775) was considered by Lipa et al. in 1996 to be synonymous with Gregarina acridiorum (Léger 1893), a parasite of several orthopteran species including Locusta migratoria (Linné, 1758). Here, a morphological study and molecular analyses of the SSU rDNA marker demonstrate that specimens of S. gregaria and specimens of L. migratoria are infected by two distinct Gregarina species, G. garnhami and G. acridiorum, respectively. Validation of the species confirms that molecular analyses provide useful taxonomical information. Phenotypic plasticity was clearly observed in the case of G. garnhami: the morphology of its trophozoites, gamonts and syzygies varied according to the geographical location of S. gregaria and the subspecies infected.
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Affiliation(s)
- Isabelle Florent
- Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR 7245 CNRS), Département Adaptations du vivant (AVIV), Muséum National d'Histoire Naturelle, CNRS, CP 52, 57 rue Cuvier, 75231 Paris Cedex 05, France
| | - Marie Pierre Chapuis
- CBGP, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34060 Montpellier, France - CIRAD, UMR CBGP, 34398 Montpellier, France
| | - Amandine Labat
- Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR 7245 CNRS), Département Adaptations du vivant (AVIV), Muséum National d'Histoire Naturelle, CNRS, CP 52, 57 rue Cuvier, 75231 Paris Cedex 05, France
| | - Julie Boisard
- Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR 7245 CNRS), Département Adaptations du vivant (AVIV), Muséum National d'Histoire Naturelle, CNRS, CP 52, 57 rue Cuvier, 75231 Paris Cedex 05, France - Structure et instabilité des génomes (STRING UMR 7196 CNRS/INSERM U1154), Département Adaptations du vivant (AVIV), Muséum National d'Histoire Naturelle, CNRS, INSERM, CP 26, 57 rue Cuvier, 75231 Paris Cedex 05, France
| | - Nicolas Leménager
- CBGP, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34060 Montpellier, France - CIRAD, UMR CBGP, 34398 Montpellier, France
| | - Bruno Michel
- CBGP, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34060 Montpellier, France - CIRAD, UMR CBGP, 34398 Montpellier, France
| | - Isabelle Desportes-Livage
- Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR 7245 CNRS), Département Adaptations du vivant (AVIV), Muséum National d'Histoire Naturelle, CNRS, CP 52, 57 rue Cuvier, 75231 Paris Cedex 05, France
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23
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Sapkota R, Santos S, Farias P, Krogh PH, Winding A. Insights into the earthworm gut multi-kingdom microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 727:138301. [PMID: 32330704 DOI: 10.1016/j.scitotenv.2020.138301] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/27/2020] [Accepted: 03/27/2020] [Indexed: 06/11/2023]
Abstract
Earthworms are widely known to impact soil health, having a key role in nutrient cycling and are often referred to as soil engineers. They are vital for soil microbial assemblages particularly through their feeding and burrowing activity in soil. Earthworms feed on soil organic matter and litter, and the resulting casts alter the soil microbial community. However, the gut microbiome of earthworms remains less known. In this study, we used amplicon sequencing of the 16S rRNA gene for bacteria and 18S rRNA gene for eukaryotes to assess the gut community assemblages of earthworm species within three genera Aporrectodea, Allolobophora and Lumbricus that represent different life forms sharing the same habitat. The objective was to compare the gut microbiome profiles of eukaryotic and prokaryotic organisms to assess significance of earthworm life forms, and to explore the cross kingdom networks in an attempt to identify keystone species. We found a high eukaryotic diversity with a dominance of the SAR supergroup along with fungi and metazoan in the earthworm gut. The bacterial community were dominated by members of Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes, and Verrucomicrobia. The eukaryotic and prokaryotic communities showed similar differences in alpha diversity, being lowest in Lumbricus herculeus. The beta diversity showed earthworm species as a key factor in shaping gut microbiomes with L. herculeus harboring distinct microbiomes compared to species of Aporrectodea caliginosa, A. longa, A. tuberculata and Allolobophora chlorotica. Cross kingdom networks showed high interactions between several protist and bacterial OTUs. In conclusion, this study suggested that the community assemblages of gut microbiomes were shaped by earthworm species and life form, and such assemblage consists of cross kingdom interactions among eukaryotes and prokaryotes.
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Affiliation(s)
- Rumakanta Sapkota
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Susana Santos
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Pedro Farias
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Paul Henning Krogh
- Department of Bioscience, Aarhus University, Vejlsøvej 25, 8600 Silkeborg, Denmark
| | - Anne Winding
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark.
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24
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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: 39] [Impact Index Per Article: 9.8] [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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25
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Bass D, Del Campo J. Microeukaryotes in animal and plant microbiomes: Ecologies of disease? Eur J Protistol 2020; 76:125719. [PMID: 32736314 DOI: 10.1016/j.ejop.2020.125719] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/28/2020] [Accepted: 05/25/2020] [Indexed: 02/06/2023]
Abstract
Studies of animal and plant microbiomes are burgeoning, but the majority of these focus on bacteria and rarely include microeukaryotes other than fungi. However, there is growing evidence that microeukaryotes living on and in larger organisms (e.g. plants, animals, macroalgae) are diverse and in many cases abundant. We present here a new combination of 'anti-metazoan' primers: 574*f-UNonMet_DB that amplify a wide diversity of microeukaryotes including some groups that are difficult to amplify using other primer combinations. While many groups of microeukaryotic parasites are recognised, myriad other microeukaryotes are associated with hosts as previously unknown parasites (often genetically divergent so difficult to amplify using standard PCR primers), opportunistic parasites, commensals, and other ecto- and endo-symbionts, across the 'symbiotic continuum'. These fulfil a wide range of roles from pathogenesis to mutually beneficial symbioses, but mostly their roles are unknown and likely fall somewhere along this spectrum, with the potential to switch the nature of their interactions with the host under different conditions. The composition and dynamics of host-associated microbial communities are also increasingly recognised as important moderators of host health. This 'pathobiome' approach to understanding disease is beginning to supercede a one-pathogen-one-disease paradigm, which cannot sufficiently explain many disease scenarios.
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Affiliation(s)
- David Bass
- Centre for Environment, Aquaculture and Fisheries Science (Cefas), Barrack Road, Weymouth, Dorset DT4 8UB, UK; Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; Sustainable Aquaculture Futures, University of Exeter, Exeter EX4 4QD, UK; Biosciences, University of Exeter, Stocker Road, Exeter EX4 4HB, UK.
| | - Javier Del Campo
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA
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26
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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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27
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Boisard J, Florent I. Why the -omic future of Apicomplexa should include gregarines. Biol Cell 2020; 112:173-185. [PMID: 32176937 DOI: 10.1111/boc.202000006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/03/2020] [Accepted: 03/10/2020] [Indexed: 12/15/2022]
Abstract
Gregarines, a polyphyletic group of apicomplexan parasites infecting mostly non-vertebrates hosts, remains poorly known at taxonomic, phylogenetic and genomic levels. However, it represents an essential group for understanding evolutionary history and adaptive capacities of apicomplexan parasites to the remarkable diversity of their hosts. Because they have a mostly extracellular lifestyle, gregarines have developed other cellular developmental forms and host-parasite interactions, compared with their much better studied apicomplexan cousins, intracellular parasites of vertebrates (Hemosporidia, Coccidia, Cryptosporidia). This review highlights the promises offered by the molecular exploration of gregarines, that have been until now left on the side of the road of the comparative -omic exploration of apicomplexan parasites. Elucidating molecular bases for both their ultrastructural, functional and behavioural similarities and differences, compared with those of the typical apicomplexan models, is expected to provide entirely novel clues on the adaptive capacities developed by Apicomplexa over evolution. A challenge remains to identify which gregarines should be explored in priority, as recent metadata from open and host-associated environments have confirmed how underestimated is our current view on true gregarine biodiversity. It is now time to turn to gregarines to widen the currently highly skewed view we have of adaptive mechanisms developed by Apicomplexa.
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Affiliation(s)
- Julie Boisard
- Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR 7245), Département Adaptations du Vivant (AVIV), Muséum National d'Histoire Naturelle, CNRS, Paris, Cedex 05, France.,Structure et instabilité des génomes (STRING UMR 7196 CNRS / INSERM U1154), Département Adaptations du Vivant (AVIV), Muséum National d'Histoire Naturelle, Paris, Cedex 05, France
| | - Isabelle Florent
- Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR 7245), Département Adaptations du Vivant (AVIV), Muséum National d'Histoire Naturelle, CNRS, Paris, Cedex 05, France
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