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Ahmed Shazib SU, Cote-L’Heureux A, Ahsan R, Muñoz-Gómez SA, Lee J, Katz LA, Shin MK. Phylogeny and species delimitation of ciliates in the genus Spirostomum (Class, Heterotrichea) using single-cell transcriptomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596006. [PMID: 38854132 PMCID: PMC11160781 DOI: 10.1101/2024.05.29.596006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Ciliates are single-celled microbial eukaryotes that diverged from other eukaryotic lineages over a billion years ago. The extensive evolutionary timespan of ciliate has led to enormous genetic and phenotypic changes, contributing significantly to their high level of diversity. Recent analyses based on molecular data have revealed numerous cases of cryptic species complexes in different ciliate lineages, demonstrating the need for a robust approach to delimit species boundaries and elucidate phylogenetic relationships. Heterotrich ciliate species of the genus Spirostomum are abundant in freshwater and brackish environments and are commonly used as biological indicators for assessing water quality. However, some Spirostomum species are difficult to identify due to a lack of distinguishable morphological characteristics, and the existence of cryptic species in this genus remains largely unexplored. Previous phylogenetic studies have focused on only a few loci, namely the ribosomal RNA genes, alpha-tubulin, and mitochondrial CO1. In this study, we obtained single-cell transcriptome of 25 Spirostomum species populations (representing six morphospecies) sampled from South Korea and the USA, and used concatenation- and coalescent-based methods for species tree inference and delimitation. Phylogenomic analysis of 37 Spirostomum populations and 265 protein-coding genes provided a robustious insight into the evolutionary relationships among Spirostomum species and confirmed that species with moniliform and compact macronucleus each form a distinct monophyletic lineage. Furthermore, the multispecies coalescent (MSC) model suggests that there are at least nine cryptic species in the Spirostomum genus, three in S. minus, two in S. ambiguum, S. subtilis, and S. teres each. Overall, our fine sampling of closely related Spirostomum populations and wide scRNA-seq allowed us to demonstrate the hidden crypticity of species within the genus Spirostomum, and to resolve and provide much stronger support than hitherto to the phylogeny of this important ciliate genus.
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Affiliation(s)
- Shahed Uddin Ahmed Shazib
- Department of Biological Sciences, University of Ulsan, Ulsan 44610, South Korea
- Department of Biological Sciences, Smith College, Northampton, Massachusetts 01063, USA
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
| | - Auden Cote-L’Heureux
- Department of Biological Sciences, Smith College, Northampton, Massachusetts 01063, USA
| | - Ragib Ahsan
- Department of Biological Sciences, University of Ulsan, Ulsan 44610, South Korea
- Department of Biological Sciences, Smith College, Northampton, Massachusetts 01063, USA
- University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, Massachusetts, USA
| | - Sergio A. Muñoz-Gómez
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
| | - JunMo Lee
- Department of Oceanography, Kyungpook National University, Daegu 41566, South Korea
- Kyungpook Institute of Oceanography, Kyungpook National University, Daegu 41566, South Korea
| | - Laura A. Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts 01063, USA
- University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, Massachusetts, USA
| | - Mann Kyoon Shin
- Department of Biological Sciences, University of Ulsan, Ulsan 44610, South Korea
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Rondello Bonatti T, Vidal Siqueira-Castro IC, Averaldo Guiguet Leal D, Durigan M, Pedroso Dias RJ, Bueno Franco RM. Molecular characterization of waterborne protozoa in surface water and sediment in Brazil: a taxonomic survey of ciliated protozoa and their correlation with Giardia duodenalis and Cryptosporidium spp. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:470. [PMID: 36922479 DOI: 10.1007/s10661-023-11065-4] [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: 12/05/2022] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
The detection of Giardia duodenalis and Cryptosporidium spp. was performed, along with the identification of the ciliated protozoa biodiversity, to evaluate the correlation between these protozoa in freshwater quality monitoring. Water and sediment samples from two sites in the Atibaia River (Campinas, São Paulo, Brazil) were collected monthly for 2 years (n = 96). Pathogenic protozoa in water and sediment were detected by using immunomagnetic separation, followed by visualization by immunofluorescence assay (IFA). All positive aliquots in IFA were subjected to DNA extraction and subsequently nested PCR. Qualitative (in vivo observation and silver impregnation) and quantitative (in vivo enumeration) analyses were performed for the ciliated protozoa. Giardia cysts were detected in 62.5% of the surface water samples and Cryptosporidium spp. in 25.0%. In the sediment, cysts were detected in 35.4% samples and oocysts in 16.6%. A total of 57 samples positive for Giardia cysts were subjected to sequencing, 40 of which were harboring G. duodenalis (24 were characterized as sub-assemblage AII). For ciliated protozoa, 73 taxa belonging to 53 genera were identified over the period of the study. These results revealed a high degree of contamination by waterborne protozoa in the main water source which supplies drinking water for more than one million people in Campinas (São Paulo), highlighting the need for continuous monitoring of this catchment site. In addition, the present study provides important data regarding the sources of the water body degradation, i.e., fecal contamination of human origin, in addition to the survey of the ciliated protozoa.
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Affiliation(s)
- Taís Rondello Bonatti
- Laboratório de Protozoologia, Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, PO Box: 6109, CEP: 13083-970, São Paulo, Brazil.
| | - Isabel Cristina Vidal Siqueira-Castro
- Laboratório de Protozoologia, Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, PO Box: 6109, CEP: 13083-970, São Paulo, Brazil
| | | | - Maurício Durigan
- Laboratório de Protozoologia, Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, PO Box: 6109, CEP: 13083-970, São Paulo, Brazil
| | | | - Regina Maura Bueno Franco
- Laboratório de Protozoologia, Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, PO Box: 6109, CEP: 13083-970, São Paulo, Brazil
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Shazib SUA, Vďačný P, Slovák M, Gentekaki E, Shin MK. Deciphering phylogenetic relationships and delimiting species boundaries using a Bayesian coalescent approach in protists: A case study of the ciliate genus Spirostomum (Ciliophora, Heterotrichea). Sci Rep 2019; 9:16360. [PMID: 31704993 PMCID: PMC6841689 DOI: 10.1038/s41598-019-52722-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 10/22/2019] [Indexed: 11/09/2022] Open
Abstract
The ciliate genus Spirostomum comprises eight morphospecies, inhabiting diverse aquatic environments worldwide, where they can be used as water quality indicators. Although Spirostomum species are relatively easily identified using morphological methods, the previous nuclear rDNA-based phylogenies indicated several conflicts in morphospecies delineation. Moreover, the single locus phylogenies and previous analytical approaches could not unambiguously resolve phylogenetic relationships among Spirostomum morphospecies. Here, we attempt to investigate species boundaries and evolutionary history of Spirostomum taxa, using 166 new sequences from multiple populations employing one mitochondrial locus (CO1 gene) and two nuclear loci (rRNA operon and alpha-tubulin gene). In accordance with previous studies, relationships among the eight Spirostomum morphospecies were poorly supported statistically in individual gene trees. To overcome this problem, we utilised for the first time in ciliates the Bayesian coalescent approach, which accounts for ancestral polymorphisms, incomplete lineage sorting, and recombination. This strategy enabled us to robustly resolve deep relationships between Spirostomum species and to support the hypothesis that taxa with compact macronucleus and taxa with moniliform macronucleus each form a distinct lineage. Bayesian coalescent-based delimitation analyses strongly statistically supported the traditional morphospecies concept but also indicated that there are two S. minus-like cryptic species and S. teres is non-monophyletic. Spirostomum teres was very likely defined by a set of ancestral features of lineages that also gave rise to S. yagiui and S. dharwarensis. However, molecular data from type populations of the morphospecies S. minus and S. teres are required to unambiguously resolve the taxonomic problems.
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Affiliation(s)
| | - Peter Vďačný
- Department of Zoology, Comenius University in Bratislava, 842 15, Bratislava, Slovakia
| | - Marek Slovák
- Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, 845 23, Bratislava, Slovakia.,Department of Botany, Charles University, 128 01, Prague, Czech Republic
| | - Eleni Gentekaki
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Mann Kyoon Shin
- Department of Biological Science, University of Ulsan, Ulsan, 44610, South Korea.
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Hines HN, Onsbring H, Ettema TJ, Esteban GF. Molecular Investigation of the Ciliate Spirostomum semivirescens, with First Transcriptome and New Geographical Records. Protist 2018; 169:875-886. [DOI: 10.1016/j.protis.2018.08.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/06/2018] [Accepted: 08/09/2018] [Indexed: 11/26/2022]
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Molecular phylogeny and species delimitation within the ciliate genus Spirostomum (Ciliophora, Postciliodesmatophora, Heterotrichea), using the internal transcribed spacer region. Mol Phylogenet Evol 2016; 102:128-44. [DOI: 10.1016/j.ympev.2016.05.041] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 05/23/2016] [Accepted: 05/31/2016] [Indexed: 11/23/2022]
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Focusing on Genera to Improve Species Identification: Revised Systematics of the Ciliate Spirostomum. Protist 2014; 165:527-41. [DOI: 10.1016/j.protis.2014.05.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 05/18/2014] [Accepted: 05/21/2014] [Indexed: 11/20/2022]
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Bowes MJ, Smith JT, Neal C, Leach DV, Scarlett PM, Wickham HD, Harman SA, Armstrong LK, Davy-Bowker J, Haft M, Davies CE. Changes in water quality of the River Frome (UK) from 1965 to 2009: is phosphorus mitigation finally working? THE SCIENCE OF THE TOTAL ENVIRONMENT 2011; 409:3418-30. [PMID: 21624642 DOI: 10.1016/j.scitotenv.2011.04.049] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 04/21/2011] [Accepted: 04/26/2011] [Indexed: 05/21/2023]
Abstract
The water quality of the River Frome, Dorset, southern England, was monitored at weekly intervals from 1965 until 2009. Determinands included phosphorus, nitrogen, silicon, potassium, calcium, sodium, magnesium, pH, alkalinity and temperature. Nitrate-N concentrations increased from an annual average of 2.4 mg l⁻¹ in the mid to late 1960s to 6.0 mg l⁻¹ in 2008-2009, but the rate of increase was beginning to slow. Annual soluble reactive phosphorus (SRP) concentrations increased from 101 μg l⁻¹ in the mid 1960s to a maximum of 190 μg l⁻¹ in 1989. In 2002, there was a step reduction in SRP concentration (average=88 μg l⁻¹ in 2002-2005), with further improvement in 2007-2009 (average=49 μg l⁻¹), due to the introduction of phosphorus stripping at sewage treatment works. Phosphorus and nitrate concentrations showed clear annual cycles, related to the timing of inputs from the catchment, and within-stream bioaccumulation and release. Annual depressions in silicon concentration each spring (due to diatom proliferation) reached a maximum between 1980 and 1991, (the period of maximum SRP concentration) indicating that algal biomass had increased within the river. The timing of these silicon depressions was closely related to temperature. Excess carbon dioxide partial pressures (EpCO₂) of 60 times atmospheric CO₂ were also observed through the winter periods from 1980 to 1992, when phosphorus concentration was greatest, indicating very high respiration rates due to microbial decomposition of this enhanced biomass. Declining phosphorus concentrations since 2002 reduced productivity and algal biomass in the summer, and EpCO₂ through the winter, indicating that sewage treatment improvements had improved riverine ecology. Algal blooms were limited by phosphorus, rather than silicon concentration. The value of long-term water quality data sets is discussed. The data from this monitoring programme are made freely available to the wider science community through the CEH data portal (http://gateway.ceh.ac.uk/).
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Affiliation(s)
- M J Bowes
- Centre for Ecology and Hydrology, Maclean Building, Crowmarsh Gifford, Wallingford, Oxfordshire OX108BB, UK.
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