1
|
Tekle YI, Tran H, Wang F, Singla M, Udu I. Omics of an Enigmatic Marine Amoeba Uncovers Unprecedented Gene Trafficking from Giant Viruses and Provides Insights into Its Complex Life Cycle. MICROBIOLOGY RESEARCH 2023; 14:656-672. [PMID: 37752971 PMCID: PMC10521059 DOI: 10.3390/microbiolres14020047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023] Open
Abstract
Amoebozoa include lineages of diverse ecology, behavior, and morphology. They are assumed to encompass members with the largest genome sizes of all living things, yet genomic studies in the group are limited. Trichosphaerium, a polymorphic, multinucleate, marine amoeba with a complicated life cycle, has puzzled experts for over a century. In an effort to explore the genomic diversity and investigate extraordinary behavior observed among the Amoebozoa, we used integrated omics approaches to study this enigmatic marine amoeba. Omics data, including single-cell transcriptomics and cytological data, demonstrate that Trichosphaerium sp. possesses the complete meiosis toolkit genes. These genes are expressed in life stages of the amoeba including medium and large cells. The life cycle of Trichosphaerium sp. involves asexual processes via binary fission and multiple fragmentation of giant cells, as well as sexual-like processes involving genes implicated in sexual reproduction and polyploidization. These findings are in stark contrast to a life cycle previously reported for this amoeba. Despite the extreme morphological plasticity observed in Trichosphaerium, our genomic data showed that populations maintain a species-level intragenomic variation. A draft genome of Trichosphaerium indicates elevated lateral gene transfer (LGT) from bacteria and giant viruses. Gene trafficking in Trichosphaerium is the highest within Amoebozoa and among the highest in microbial eukaryotes.
Collapse
Affiliation(s)
- Yonas I. Tekle
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
| | - Hanh Tran
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
| | - Fang Wang
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
| | - Mandakini Singla
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
| | - Isimeme Udu
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
| |
Collapse
|
2
|
Zurita-Artaloitia JM, Rivera J, Vinuesa P. Extensive Cryptic Diversity and Ecological Associations Uncovered among Mexican and Global Collections of Naegleria and Vermamoeba Species by 18S Ribosomal DNA, Internal Transcribed Spacer, and Cytochrome Oxidase Subunit I Sequence Analysis. Microbiol Spectr 2023; 11:e0379522. [PMID: 36943092 PMCID: PMC10100766 DOI: 10.1128/spectrum.03795-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 02/26/2023] [Indexed: 03/23/2023] Open
Abstract
Free-living amoebae (FLA) are phagocytic protists that play crucial roles in microbial communities as significant microbial grazers. However, our current knowledge of their diversity, ecology, and population genetic structures is marginal due to the shallow and biased sampling of ecosystems and the use of few, poorly resolving molecular markers. Thirty-two FLA were isolated from soil and water samples collected across representative ecosystems of the State of Morelos in Central Mexico, including the drinking water distribution system (DWDS) from the state capital. We classified our isolates as members of Acanthamoeba, Vermamoeba, Naegleria, and Tetramitus by 18S ribosomal DNA (rDNA) sequencing. Vermamoeba isolates were recovered exclusively from the DWDS samples. In contrast, Naegleria strains displayed a broad distribution in soil and water samples across the natural ecosystems. We used a combination of phylogenetic and population genetic analyses of internal transcribed spacer (ITS) and cytochrome oxidase subunit I (COI) sequences from our isolates and a comprehensive set of reference sequences to analyze the currently known diversity of Naegleria spp. Significant associations were uncovered between the most prevalent lineages of Naegleria and Vermamoeba and broad ecological and geographical variables at regional and global levels. The population structure and cryptic diversity within the Naegleria galeacystis-Naegleria americana and Vermamoeba vermiformis species complexes were thoroughly analyzed. Our results prove that the genus Vermamoeba, which was previously thought to consist of only one species, actually encompasses at least seven widely distributed species, as indicated by consistent evidence from Bayesian phylogenetics, two species-delimitation programs, and population genetics analyses. IMPORTANCE Our study sheds new light on the population genetic structure of V. vermiformis and diverse Naegleria species. Using improved molecular markers and advanced analytical approaches, we discovered that N. americana, previously considered a single species, actually contains multiple distinct lineages, as revealed by COI sequencing. These lineages are highly differentiated, with little gene flow between them. Our findings demonstrate that the genus Vermamoeba holds multiple cryptic species, requiring a significant taxonomic revision in light of multilocus sequence analyses. These results advance our understanding of the ecology, molecular systematics, and biogeography of these genera and species complexes at both regional and global scales. This study has significant implications for diagnosing amoebal infections and evaluating health risks associated with FLA in domestic and recreational waters.
Collapse
Affiliation(s)
| | - Javier Rivera
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| |
Collapse
|
3
|
A three-gene phylogeny supports taxonomic rearrangements in the family Didymiaceae (Myxomycetes). Mycol Prog 2023. [DOI: 10.1007/s11557-022-01858-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
4
|
Macher JN, Bloska DM, Holzmann M, Girard EB, Pawlowski J, Renema W. Mitochondrial cytochrome c oxidase subunit I (COI) metabarcoding of Foraminifera communities using taxon-specific primers. PeerJ 2022; 10:e13952. [PMID: 36093332 PMCID: PMC9454970 DOI: 10.7717/peerj.13952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 08/05/2022] [Indexed: 01/19/2023] Open
Abstract
Foraminifera are a species-rich phylum of rhizarian protists that are highly abundant in most marine environments. Molecular methods such as metabarcoding have revealed a high, yet undescribed diversity of Foraminifera. However, so far only one molecular marker, the 18S ribosomal RNA, was available for metabarcoding studies on Foraminifera. Primers that allow amplification of foraminiferal mitochondrial cytochrome oxidase I (COI) and identification of Foraminifera species were recently published. Here we test the performance of these primers for the amplification of whole foraminiferal communities, and compare their performance to that of the highly degenerate LerayXT primers, which amplify the same COI region in a wide range of eukaryotes. We applied metabarcoding to 48 samples taken along three transects spanning a North Sea beach in the Netherlands from dunes to the low tide level, and analysed both sediment samples and meiofauna samples, which contained taxa between 42 µm and 1 mm in body size obtained by decantation from sand samples. We used single-cell metabarcoding (Girard et al., 2022) to generate a COI reference library containing 32 species of Foraminifera, and used this to taxonomically annotate our community metabarcoding data. Our analyses show that the highly degenerate LerayXT primers do not amplify Foraminifera, while the Foraminifera primers are highly Foraminifera- specific, with about 90% of reads assigned to Foraminifera and amplifying taxa from all major groups, i.e., monothalamids, Globothalamea, and Tubothalamea. We identified 176 Foraminifera ASVs and found a change in Foraminifera community composition along the beach transects from high tide to low tide level, and a dominance of single-chambered monothalamid Foraminifera. Our results highlight that COI metabarcoding can be a powerful tool for assessing Foraminiferal communities.
Collapse
Affiliation(s)
- Jan-Niklas Macher
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands
| | | | - Maria Holzmann
- Department of Genetics & Evolution, University of Geneva, Geneva, Switzerland
| | - Elsa B. Girard
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands
- Department of Ecosystem & Landscape Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Jan Pawlowski
- Laboratory of Paleoceanography, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Willem Renema
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands
- Department of Ecosystem & Landscape Dynamics, University of Amsterdam, Amsterdam, Netherlands
| |
Collapse
|
5
|
Tekle YI, Wang F, Tran H, Hayes TD, Ryan JF. The draft genome of Cochliopodium minus reveals a complete meiosis toolkit and provides insight into the evolution of sexual mechanisms in Amoebozoa. Sci Rep 2022; 12:9841. [PMID: 35701521 PMCID: PMC9198077 DOI: 10.1038/s41598-022-14131-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/06/2022] [Indexed: 11/23/2022] Open
Abstract
To date, genomic analyses in amoebozoans have been mostly limited to model organisms or medically important lineages. Consequently, the vast diversity of Amoebozoa genomes remain unexplored. A draft genome of Cochliopodium minus, an amoeba characterized by extensive cellular and nuclear fusions, is presented. C. minus has been a subject of recent investigation for its unusual sexual behavior. Cochliopodium's sexual activity occurs during vegetative stage making it an ideal model for studying sexual development, which is sorely lacking in the group. Here we generate a C. minus draft genome assembly. From this genome, we detect a substantial number of lateral gene transfer (LGT) instances from bacteria (15%), archaea (0.9%) and viruses (0.7%) the majority of which are detected in our transcriptome data. We identify the complete meiosis toolkit genes in the C. minus genome, as well as the absence of several key genes involved in plasmogamy and karyogamy. Comparative genomics of amoebozoans reveals variation in sexual mechanism exist in the group. Similar to complex eukaryotes, C. minus (some amoebae) possesses Tyrosine kinases and duplicate copies of SPO11. We report a first example of alternative splicing in a key meiosis gene and draw important insights on molecular mechanism of sex in C. minus using genomic and transcriptomic data.
Collapse
Affiliation(s)
- Yonas I Tekle
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA, 30314, USA.
| | - Fang Wang
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA, 30314, USA
| | - Hanh Tran
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA, 30314, USA
| | - T Danielle Hayes
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
- Iowa State University, Ames, IA, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| |
Collapse
|
6
|
Is scale’s structure still a good character to delimitate species of Amoebozoa? case of the genus Korotnevella (Amoebozoa, Dactylopodida). ORG DIVERS EVOL 2021. [DOI: 10.1007/s13127-021-00521-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
7
|
Kudryavtsev A, Völcker E, Clauß S, Pawlowski J. Ovalopodium rosalinum sp. nov., Planopodium haveli gen. nov, sp. nov., Planopodium desertum comb. nov. and new insights into phylogeny of the deeply branching members of the order Himatismenida (Amoebozoa). Int J Syst Evol Microbiol 2021; 71. [PMID: 33709902 DOI: 10.1099/ijsem.0.004737] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The order Himatismenida (Amoebozoa, Discosea) comprises naked amoebae with an organic coat that is located on the dorsal surface of the cell. The phylogenetic relationships among deeply branching genera of the Himatismenida are unclear, as data on the species diversity of the himatismenid genera is largely restricted to the derived genus Cochliopodium. Here, we describe two new amoeba species that branch at the base of the order Himatismenida, evidenced by SSU rRNA gene and multigene analyses. Among them, a freshwater species Planopodium haveli gen. nov., sp. nov. has a dorsal cell coat consisting of flat, oval scales. This species forms a clade at the base of the Himatismenida, and the previously described Ovalopodium desertum, its closest relative, is transferred into the new genus as Planopodium desertum comb. nov. Although the two species are barely distinguishable by their sequence data, they are clearly distinct in morphology. Using this data, we can report the first evidence of a dorsal cell coat consisting of scales outside of the genus Cochliopodium. The other species has a marine origin and branches deeply, close to the root of the phylogenetic tree of Himatismenida. Based on the morphology of this amoeba, it should be described as Ovalopodium rosalinum sp. nov., a new species of the genus Ovalopodium. Analyses of the phylogenetic relationships and the ultrastructure of the deeply branching himatismenids, together with several of the newly obtained gene sequences of Parvamoeba and Cochliopodium, suggest that some elements of the dorsal cell coat of Ovalopodium may be ancestral for Himatismenida and have been partly retained in various more derived species of this clade, in particular, Cochliopodium gallicum. Although actin and Cox1 gene data do not resolve the higher-level relationships in Himatismenida, they correspond to the grouping of species within most genera.
Collapse
Affiliation(s)
- Alexander Kudryavtsev
- Department of Invertebrate Zoology, Faculty of Biology, Saint-Petersburg State University, Universitetskaya nab., 7/9 199034 Saint-Petersburg, Russia.,Laboratory of Cellular and Molecular Protistology, Zoological Institute RAS, Universitetskaya nab., 1 199034 Saint-Petersburg, Russia
| | | | | | - Jan Pawlowski
- Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland.,ID-Gene ecodiagnostics, Campus Biotech Innovation Park, 1202, Geneva, Switzerland.,Department of Genetics and Evolution, University of Geneva, Sciences III, 1211 Geneva, Switzerland
| |
Collapse
|
8
|
English CJ, Lima PC. Defining the aetiology of amoebic diseases of aquatic animals: trends, hurdles and best practices. DISEASES OF AQUATIC ORGANISMS 2020; 142:125-143. [PMID: 33269724 DOI: 10.3354/dao03537] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Disease caused by parasitic amoebae impacts a range of aquatic organisms including finfish, crustaceans, echinoderms and molluscs. Despite the significant economic impact caused in both aquaculture and fisheries, the aetiology of most aquatic amoebic diseases is uncertain, which then affects diagnosis, treatment and prevention. The main factors hampering research effort in this area are the confusion around amoeba taxonomy and the difficulty proving that a particular species causes specific lesions. These issues stem from morphological and genetic similarities between cryptic species and technical challenges such as establishing and maintaining pure amoeba cultures, scarcity of Amoebozoa sequence data, and the inability to trigger pathogenesis under experimental conditions. This review provides a critical analysis of how amoebae are commonly identified and defined as aetiological agents of disease in aquatic animals and highlights gaps in the available knowledge regarding determining pathogenic Amoebozoa.
Collapse
Affiliation(s)
- Chloe J English
- CSIRO Agriculture and Food, Livestock and Aquaculture, Queensland Bioscience Precinct, St. Lucia, QLD 4067, Australia
| | | |
Collapse
|
9
|
Udalov IA, Lotonin K, Volkova E. Description of a new species of marine amoeba Korotnevella mutabilis n. sp. (Amoebozoa, Dactylopodida). Eur J Protistol 2020; 75:125701. [DOI: 10.1016/j.ejop.2020.125701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 03/30/2020] [Accepted: 03/31/2020] [Indexed: 10/24/2022]
|
10
|
DNA Metabarcoding of Deep-Sea Sediment Communities Using COI: Community Assessment, Spatio-Temporal Patterns and Comparison with 18S rDNA. DIVERSITY-BASEL 2020. [DOI: 10.3390/d12040123] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Among the complex ecosystems and habitats that form the deep sea, submarine canyons and open slope systems are regarded as potential hotspots of biodiversity. We assessed the spatial and temporal patterns of biodiversity in sediment communities of a NW Mediterranean Canyon and its adjacent open slope (Blanes Canyon) with DNA metabarcoding. We sampled three layers of sediment and four different depths (900–1750 m) at two seasons, and used a fragment of the mitochondrial gene cytochrome c oxidase subunit I (COI) as a metabarcoding marker. The final dataset contained a total of 15,318 molecular operational taxonomic units (MOTUs). Metazoa, Stramenopiles and Archaeplastida were the dominant taxa and, within metazoans, Arthropoda, Nematoda and Cnidaria were the most diverse. There was a trend towards decreasing MOTU richness and diversity in the first few cm (1 to 5) of the sediment, with only 26.3% of the MOTUs shared across sediment layers. Our results show the presence of heterogeneous communities in the studied area, which was significantly different between zones, depths and seasons. We compared our results with the ones presented in a previous study, obtained using the v7 region of the 18S rRNA gene in the same samples. There were remarkable differences in the total number of MOTUs and in the most diverse taxa. COI recovered a higher number of MOTUs, but more remained unassigned taxonomically. However, the broad spatio-temporal patterns elucidated from both datasets coincided, with both markers retrieving the same ecological information. Our results showed that COI can be used to accurately characterize the studied communities and constitute a high-resolution method to detect ecological shifts. We also highlight that COI reference databases for deep-sea organisms have important gaps, and their completeness is essential in order to successfully apply metabarcoding techniques.
Collapse
|
11
|
Kudryavtsev A, Volkova E. Cunea russae n. sp. (Amoebozoa, Dactylopodida), another cryptic species of Cunea Kudryavtsev and Pawlowski, 2015, inhabits a continental brackish-water biotope. Eur J Protistol 2020; 73:125685. [PMID: 32114251 DOI: 10.1016/j.ejop.2020.125685] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 01/28/2020] [Accepted: 01/30/2020] [Indexed: 02/02/2023]
Abstract
The genus Cunea Kudryavtsev and Pawlowski, 2015 (Amoebozoa, Dactylopodida) was initially described from the oceanic benthos: C. profundata, from over 5 km depth in the Atlantic Ocean, and C. thuwala from the Red Sea benthos at ca. 60 m depth. Both species are identical to each other in morphology (including cell coat ultrastructure), but differ significantly in the gene sequence data, including barcoding loci of small subunit ribosomal RNA and cytochrome oxidase subunit 1 gene, as well as actin. This paper describes the third species of Cunea, C. russae n. sp. isolated from a brackish water habitat without a direct connection to the ocean, a small spring of brackish water (19‰) emerging from a 246 m deep hole in the earth. This species is morphologically identical to the previous two amoebae, but differs from them significantly in the gene sequence data and ecological preferences. In particular, this species has the broadest salinity tolerance range, being able to reproduce well already at 2.5‰. It is also capable of resisting cold temperatures, like C. profundata. The data obtained suggest that the genus Cunea may comprise a significant taxonomic diversity represented by morphologically identical, but quickly diverging species with significant ecological plasticity.
Collapse
Affiliation(s)
- Alexander Kudryavtsev
- Laboratory of Cellular and Molecular Protistology, Zoological Institute, Russian Academy of Sciences, 199034 St. Petersburg, Russia; Department of Invertebrate Zoology, Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia.
| | - Ekaterina Volkova
- Laboratory of Cellular and Molecular Protistology, Zoological Institute, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| |
Collapse
|
12
|
Melton JT, Singla M, Wood FC, Collins SJ, Tekle YI. Three New Freshwater Cochliopodium Species (Himatismenida, Amoebozoa) from the Southeastern United States. J Eukaryot Microbiol 2019; 67:154-166. [PMID: 31560817 DOI: 10.1111/jeu.12764] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/04/2019] [Accepted: 09/22/2019] [Indexed: 11/30/2022]
Abstract
Cochliopodium is a lens-shaped genus of Amoebozoa characterized by a flexible layer of microscopic dorsal scales. Recent taxonomic and molecular studies reported cryptic diversity in this group and suggested that the often-used scale morphology is not a reliable character for species delineation in the genus. Here, we described three freshwater Cochliopodium spp. from the southeastern United States based on morphological, immunocytochemistry (ICC), and molecular data. A maximum-likelihood phylogenetic analysis and pairwise comparison of COI sequences of Cochliopodium species showed that each of these monoclonal cultures were genetically distinct from each other and any described species with molecular data. Two of the new isolates, "crystal UK-YT2" (Cochliopodium crystalli n. sp.) and "crystal-like UK-YT3" (C. jaguari n. sp.), formed a clade with C. larifeili, which all share a prominent microtubule organizing center (MTOC) and have cubical-shaped crystals. The "Marrs Spring UK-YT4" isolate, C. marrii n. sp., was 100% identical to "Cochliopodium sp. SG-2014 KJ569724." These sequences formed a clade with C. actinophorum and C. arabianum. While the new isolates can be separated morphologically, most of the taxonomic features used in the group show plasticity; therefore, Cochliopodium species can only be reliably identified with the help of molecular data.
Collapse
Affiliation(s)
- James T Melton
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, Georgia, 30314
| | - Mandakini Singla
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, Georgia, 30314
| | - Fiona C Wood
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, Georgia, 30314
| | - Shawndasia J Collins
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, Georgia, 30314
| | - Yonas I Tekle
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, Georgia, 30314
| |
Collapse
|
13
|
Udalov IA, Lee WJ, Lotonin K, Smirnov A. Pseudoparamoeba garorimi n. sp., with Notes on Species Distinctions within the Genus. J Eukaryot Microbiol 2019; 67:132-139. [PMID: 31529735 DOI: 10.1111/jeu.12763] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 08/16/2019] [Accepted: 09/10/2019] [Indexed: 02/04/2023]
Abstract
A new marine species of naked lobose amoebae Pseudoparamoeba garorimi n. sp. (Amoebozoa, Dactylopodida) isolated from intertidal marine sediments of Garorim Bay, Korea was studied with light and transmission electron microscopy. This species has a typical set of morphological characters for a genus including the shape of the locomotive form, type of subpseudopodia and the tendency to form the single long waving pseudopodium in locomotion. Furthermore, it has the same cell surface structures as were described for the type species, Pseudoparamoeba pagei: blister-like glycostyles with hexagonal base and dome-shaped apex; besides, cell surface bears hair-like outgrowths. The new species described here lacks clear morphological distinctions from the two other Pseudoparamoeba species, but has considerable differences in the 18S rDNA and COX1 gene sequences. Phylogenetic analysis based on 18S rDNA placed P. garorimi n. sp. at the base of the Pseudoparamoeba clade with high PP/BS support. The level of COX1 sequence divergence was 22% between P. garorimi n. sp. and P. pagei and 25% between P. garorimi n. sp. and P. microlepis. Pseudoparamoeba species are hardly distinguishable by morphology alone, but display clear differences in 18S rDNA and COX1 gene sequences.
Collapse
Affiliation(s)
- Ilya A Udalov
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaya nab. 7/9, Saint Petersburg, 199034, Russia.,Laboratory of Cellular and Molecular Protistology, Zoological Institute RAS, Universitetskaya nab. 1, Saint Petersburg, 199034, Russia
| | - Won Je Lee
- Department of Environment and Energy Engineering, Kyungnam University, Changwon, Kyungnam, 51767, Korea
| | - Kirill Lotonin
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaya nab. 7/9, Saint Petersburg, 199034, Russia
| | - Alexey Smirnov
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaya nab. 7/9, Saint Petersburg, 199034, Russia
| |
Collapse
|
14
|
Tekle YI, Wood FC. A practical implementation of large transcriptomic data analysis to resolve cryptic species diversity problems in microbial eukaryotes. BMC Evol Biol 2018; 18:170. [PMID: 30445905 PMCID: PMC6240226 DOI: 10.1186/s12862-018-1283-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/30/2018] [Indexed: 01/09/2023] Open
Abstract
Background Transcriptome sequencing has become a method of choice for evolutionary studies in microbial eukaryotes due to low cost and minimal sample requirements. Transcriptome data has been extensively used in phylogenomic studies to infer ancient evolutionary histories. However, its utility in studying cryptic species diversity is not well explored. An empirical investigation was conducted to test the applicability of transcriptome data in resolving two major types of discordances at lower taxonomic levels. These include cases where species have the same morphology but different genetics (cryptic species) and species of different morphologies but have the same genetics. We built a species comparison bioinformatic pipeline that takes into account the nature of transcriptome data in amoeboid microbes exemplifying such discordances. Result Our analyses of known or suspected cryptic species yielded consistent results regardless of the methods of culturing, RNA collection or sequencing. Over 95% of the single copy genes analyzed in samples of the same species sequenced using different methods and cryptic species had intra- and interspecific divergences below 2%. Only a minority of groups (2.91–4.87%) had high distances exceeding 2% in these taxa, which was likely caused by low data quality. This pattern was also observed in suspected genetically similar species with different morphologies. Transcriptome data consistently delineated all taxa above species level, including cryptically diverse species. Using our approach we were able to resolve cryptic species problems, uncover misidentification and discover new species. We also identified several potential barcode markers with varying evolutionary rates that can be used in lineages with different evolutionary histories. Conclusion Our findings demonstrate that transcriptome data is appropriate for understanding cryptic species diversity in microbial eukaryotes. Electronic supplementary material The online version of this article (10.1186/s12862-018-1283-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yonas I Tekle
- Spelman College, 350 Spelman Lane Southwest, Atlanta, GA, 30314, USA.
| | - Fiona C Wood
- Spelman College, 350 Spelman Lane Southwest, Atlanta, GA, 30314, USA
| |
Collapse
|
15
|
English CJ, Tyml T, Botwright NA, Barnes AC, Wynne JW, Lima PC, Cook MT. A diversity of amoebae colonise the gills of farmed Atlantic salmon (Salmo salar) with amoebic gill disease (AGD). Eur J Protistol 2018; 67:27-45. [PMID: 30447480 DOI: 10.1016/j.ejop.2018.10.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/23/2018] [Accepted: 10/23/2018] [Indexed: 01/08/2023]
Abstract
Neoparamoeba perurans is the aetiological agent of amoebic gill disease (AGD) in salmonids, however multiple other amoeba species colonise the gills and their role in AGD is unknown. Taxonomic assessments of these accompanying amoebae on AGD-affected salmon have previously been based on gross morphology alone. The aim of the present study was to document the diversity of amoebae colonising the gills of AGD-affected farmed Atlantic salmon using a combination of morphological and sequence-based taxonomic methods. Amoebae were characterised morphologically via light microscopy and transmission electron microscopy, and by phylogenetic analyses based on the 18S rRNA gene and cytochrome oxidase subunit I (COI) gene. In addition to N. perurans, 11 other amoebozoans were isolated from the gills, and were classified within the genera Neoparamoeba, Paramoeba, Vexillifera, Pseudoparamoeba, Vannella and Nolandella. In some cases, such as Paramoeba eilhardi, this is the first time this species has been isolated from the gills of teleost fish. Furthermore, sequencing of both the 18S rRNA and COI gene revealed significant genetic variation within genera. We highlight that there is a far greater diversity of amoebae colonising AGD-affected gills than previously established.
Collapse
Affiliation(s)
- Chloe J English
- The University of Queensland, School of Biological Sciences, Brisbane, Queensland 4072, Australia; CSIRO Agriculture and Food, Integrated Sustainable Aquaculture Production, Bribie Island Research Centre, 144 North Street, Woorim, Queensland 4507, Australia.
| | - Tomáš Tyml
- Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Natasha A Botwright
- CSIRO Agriculture and Food, Integrated Sustainable Aquaculture Production, Queensland Biosciences Precinct, 306 Carmody Road, Brisbane, Queensland 4067, Australia
| | - Andrew C Barnes
- The University of Queensland, School of Biological Sciences, Brisbane, Queensland 4072, Australia
| | - James W Wynne
- CSIRO Agriculture and Food, Integrated Sustainable Aquaculture Production, Castray Esplanade, Battery Point, Tasmania 7004, Australia
| | - Paula C Lima
- CSIRO Agriculture and Food, Integrated Sustainable Aquaculture Production, Bribie Island Research Centre, 144 North Street, Woorim, Queensland 4507, Australia
| | - Mathew T Cook
- CSIRO Agriculture and Food, Integrated Sustainable Aquaculture Production, Queensland Biosciences Precinct, 306 Carmody Road, Brisbane, Queensland 4067, Australia
| |
Collapse
|
16
|
Kudryavtsev A, Pawlowski J, Smirnov A. More amoebae from the deep-sea: Two new marine species of Vexillifera (Amoebozoa, Dactylopodida) with notes on taxonomy of the genus. Eur J Protistol 2018; 66:9-25. [DOI: 10.1016/j.ejop.2018.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/04/2018] [Accepted: 07/04/2018] [Indexed: 10/28/2022]
|
17
|
Two new species of Ripella (Amoebozoa, Vannellida) and unusual intragenomic variability in the SSU rRNA gene of this genus. Eur J Protistol 2017; 61:92-106. [PMID: 28992523 DOI: 10.1016/j.ejop.2017.09.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Revised: 08/22/2017] [Accepted: 09/08/2017] [Indexed: 11/20/2022]
Abstract
Two new species, Ripella decalvata and R. tribonemae (Amoebozoa, Vannellida), are described and the diversity of known strains assigned to the genus analyzed. Ripella spp. are closely similar to each other in the light microscopic characters and sequences of small-subunit (SSU) ribosomal RNA gene, but differences in the cell coat structure and cytochrome oxidase (COI) gene sequences are more prominent. SSU rRNA in R. platypodia CCAP1589/2, R. decalvata and R. tribonemae demonstrates an unusual pattern of intragenomic variation. Sequencing of multiple molecular clones of this gene produced numerous sequence variants in a number of specific sites. These sites were usually terminal parts of several variable helices in all studied strains. Analysis of all known Ripella strains shows that SSU rRNA sites differing between strains of different origin are mainly restricted to these areas of the gene. There are only two sites, which differ between strains, but not within genomes. This intragenomic variability of the SSU rRNA gene, seemingly characteristic of all Ripella spp., was never reported to be so extensive in Amoebozoa. The data obtained show another example of complex organization of rRNA gene cluster in protists and emphasize caution needed when interpreting the metagenomic data based on this marker.
Collapse
|
18
|
Genetic structure of a morphological species within the amoeba genus Korotnevella (Amoebozoa: Discosea), revealed by the analysis of two genes. Eur J Protistol 2016; 56:102-111. [DOI: 10.1016/j.ejop.2016.08.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 07/30/2016] [Accepted: 08/01/2016] [Indexed: 11/20/2022]
|
19
|
Tekle YI, Williams JR. Cytoskeletal architecture and its evolutionary significance in amoeboid eukaryotes and their mode of locomotion. ROYAL SOCIETY OPEN SCIENCE 2016; 3:160283. [PMID: 27703691 PMCID: PMC5043310 DOI: 10.1098/rsos.160283] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/30/2016] [Indexed: 06/06/2023]
Abstract
The cytoskeleton is the hallmark of eukaryotic evolution. The molecular and architectural aspects of the cytoskeleton have been playing a prominent role in our understanding of the origin and evolution of eukaryotes. In this study, we seek to investigate the cytoskeleton architecture and its evolutionary significance in understudied amoeboid lineages belonging to Amoebozoa. These amoebae primarily use cytoplasmic extensions supported by the cytoskeleton to perform important cellular processes such as movement and feeding. Amoeboid structure has important taxonomic significance, but, owing to techniques used, its potential significance in understanding diversity of the group has been seriously compromised, leading to an under-appreciation of its value. Here, we used immunocytochemistry and confocal microscopy to study the architecture of microtubules (MTs) and F-actin in diverse groups of amoebae. Our results demonstrate that all Amoebozoa examined are characterized by a complex cytoskeletal array, unlike what has been previously thought to exist. Our results not only conclusively demonstrate that all amoebozoans possess complex cytoplasmic MTs, but also provide, for the first time, a potential synapomorphy for the molecularly defined Amoebozoa clade. Based on this evidence, the last common ancestor of amoebozoans is hypothesized to have had a complex interwoven MT architecture limited within the granular cell body. We also generate several cytoskeleton characters related to MT and F-actin, which are found to be robust for defining groups in deep and shallow nodes of Amoebozoa.
Collapse
|
20
|
Udalov IA. Pseudoparamoeba microlepis n. sp., Korotnevella fousta n. sp. (Amoebozoa, Dactylopodida), with notes on the evolution of scales among dactylopodid amoebae. Eur J Protistol 2016; 54:33-46. [DOI: 10.1016/j.ejop.2016.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 02/05/2016] [Accepted: 03/14/2016] [Indexed: 11/29/2022]
|
21
|
Oliverio AM, Lahr DJG, Grant J, Katz LA. Are microbes fundamentally different than macroorganisms? Convergence and a possible case for neutral phenotypic evolution in testate amoeba (Amoebozoa: Arcellinida). ROYAL SOCIETY OPEN SCIENCE 2015; 2:150414. [PMID: 27019725 PMCID: PMC4807447 DOI: 10.1098/rsos.150414] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 11/17/2015] [Indexed: 06/05/2023]
Abstract
This study reveals extensive phenotypic convergence based on the non-monophyly of genera and morphospecies of testate (shelled) amoebae. Using two independent markers, small subunit ribosomal DNA (ssu-rDNA) and mitochondrial cytochrome oxidase I (COI), we demonstrate discordance between morphology and molecules for 'core Nebela' species (Arcellinida; Amoebozoa). Prior work using just a single locus, ssu-rDNA, also supported the non-monophyly of the genera Hyalosphenia and Nebela as well as for several morphospecies within these genera. Here, we obtained COI gene sequences of 59 specimens from seven morphospecies and ssu-rDNA gene sequences of 50 specimens from six morphospecies of hyalosphenids. Our analyses corroborate the prior ssu-rDNA findings of morphological convergence in test (shell) morphologies, as COI and ssu-rDNA phylogenies are concordant. Further, the monophyly of morphospecies is rejected using approximately unbiased tests. Given that testate amoebae are used as bioindicators in both palaeoecological and contemporary studies of threatened ecosystems such as bogs and fens, understanding the discordance between morphology and genetics in the hyalosphenids is essential for interpretation of indicator species. Further, while convergence is normally considered the result of natural selection, it is possible that neutrality underlies phenotypic evolution in these microorganisms.
Collapse
Affiliation(s)
- Angela M. Oliverio
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA
| | - Daniel J. G. Lahr
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo 05508-090, Brazil
| | - Jessica Grant
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA
| | - Laura A. Katz
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA
- Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA 01003, USA
| |
Collapse
|
22
|
Fučíková K, Lahr DJG. Uncovering Cryptic Diversity in Two Amoebozoan Species Using Complete Mitochondrial Genome Sequences. J Eukaryot Microbiol 2015. [PMID: 26211788 DOI: 10.1111/jeu.12253] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The Amoebozoa are a major eukaryotic lineage that encompasses a wide range of amoeboid organisms. The group is understudied from a systematic perspective: molecular tools have only been applied in the last 15 yr. Hence, there is an undersampling of both genes and taxa in the group especially compared to plants, animals, and fungi. Here, we present the complete mitochondrial genomes of two ubiquitous and abundant morpho-species (Acanthamoeba castellanii and Vermamoeba vermiformis). Both have mitochondrial genomes of close relatives previously available, enabling insights into recent divergences at a genomic scale, while simultaneously offering comparisons with divergence estimates obtained from traditionally used single genes, SSU rDNA and cox1. The newly sequenced mt genomes are significantly divergent from their previously sequenced conspecifics (A. castellannii 16.4% divergence at nucleotide level and 10.4% amino acid; V. vermiformis 21.6% and 13.1%, respectively), while divergence at the small subunit ribosomal DNA is below 1% within both species. Morphological analyses determined that these lineages are indistinguishable from their previously sequenced counterparts. Phylogenetic reconstructions using 26 mt genes also indicate a level of divergence that is comparable to divergence among species, while reconstructions using the small subunit ribosomal DNA (SSU rDNA) do not. In addition, we demonstrate that between closely related taxa, there are high levels of synteny, which can be explored for primer design to obtain larger fragments than the traditional barcoding genes. We conclude that, although most systematic work has relied on SSU, this gene alone can severely underestimate diversity. Thus, we suggest that the mt genome emerges as an alternative for unraveling the lower level phylogenetic relationships of Amoebozoa.
Collapse
Affiliation(s)
- Karolina Fučíková
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Daniel J G Lahr
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, 05508-090, Brazil
| |
Collapse
|
23
|
Cunea n. g. (Amoebozoa, Dactylopodida) with two cryptic species isolated from different areas of the ocean. Eur J Protistol 2015; 51:197-209. [DOI: 10.1016/j.ejop.2015.04.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 03/30/2015] [Accepted: 04/01/2015] [Indexed: 11/17/2022]
|
24
|
Tekle YI, Gorfu LA, Anderson OR. Cochliopodium arabianum
n. sp. (Amorphea, Amoebozoa). J Eukaryot Microbiol 2015; 62:623-8. [DOI: 10.1111/jeu.12218] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 12/17/2014] [Accepted: 01/27/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Yonas I. Tekle
- Department of Biology; Spelman College; 350 Spelman Lane Southwest Atlanta Georgia 30314 USA
| | - Lydia A. Gorfu
- Department of Biology; Spelman College; 350 Spelman Lane Southwest Atlanta Georgia 30314 USA
| | - O. Roger Anderson
- Department of Biology; Lamont-Doherty Earth Observatory of Columbia University; Palisades NY 10964 USA
| |
Collapse
|
25
|
Tekle YI, Anderson OR, Lecky AF. Evidence of Parasexual Activity in “Asexual Amoebae” Cochliopodium spp. (Amoebozoa): Extensive Cellular and Nuclear Fusion. Protist 2014; 165:676-87. [DOI: 10.1016/j.protis.2014.07.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 07/15/2014] [Accepted: 07/17/2014] [Indexed: 11/30/2022]
|