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Zhang X, Bi L, Gentekaki E, Zhao J, Shen P, Zhang Q. Culture-Independent Single-Cell PacBio Sequencing Reveals Epibiotic Variovorax and Nucleus Associated Mycoplasma in the Microbiome of the Marine Benthic Protist Geleia sp. YT (Ciliophora, Karyorelictea). Microorganisms 2023; 11:1500. [PMID: 37375002 DOI: 10.3390/microorganisms11061500] [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: 04/24/2023] [Revised: 05/19/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
Microbes in marine sediments constitute up to five-sixths of the planet's total biomass, but their diversity is little explored, especially for those forming associations with unicellular protists. Heterotrophic ciliates are among the most dominant and diversified marine benthic protists and comprise hotspot niches of bacterial colonization. To date, studies using culture-independent single-cell approaches to explore microbiomes of marine benthic ciliates in nature are almost absent, even for the most ubiquitous species. Here, we characterize the major bacterial groups associated with a representative marine benthic ciliate, Geleia sp. YT, collected directly from the coastal zone of Yantai, China. PacBio sequencing of the nearly full-length 16Sr RNA genes was performed on single cells of Geleia. Fluorescence in situ hybridization (FISH) analysis with genus-specific probes was further applied to locate the dominant bacterial groups. We identified a Variovorax-like bacterium as the major epibiotic symbiont residing in the kineties of the ciliate host. We provide evidence of a nucleus-associated bacterium related to the human pathogen Mycoplasma, which appeared prevalently in the local populations of Geleia sp. YT for 4 months. The most abundant bacterial taxa associated with Geleia sp. YT likely represent its core microbiome, hinting at the important roles of the ciliate-bacteria consortium in the marine benthos. Overall, this work has contributed to the knowledge of the diversity of life in the enigmatic marine benthic ciliate and its symbioses.
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Affiliation(s)
- Xiaoxin Zhang
- School of Ocean, Yantai University, Yantai 264003, China
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Luping Bi
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Eleni Gentekaki
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
- Gut Microbiome Research Group, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Jianmin Zhao
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Pingping Shen
- School of Ocean, Yantai University, Yantai 264003, China
| | - Qianqian Zhang
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
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Sandmeier FC, Leonard KL, Weitzman CL, Tracy CR. Potential Facilitation Between a Commensal and a Pathogenic Microbe in a Wildlife Disease. ECOHEALTH 2022; 19:427-438. [PMID: 35752710 DOI: 10.1007/s10393-022-01603-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
We assessed the potential for microbial interactions influencing a well-documented host-pathogen system. Mycoplasma agassizii is the known etiological agent of upper respiratory tract disease in Mojave desert tortoises (Gopherus agassizii), but disease in wild animals is extremely heterogeneous. For example, a much larger proportion of animals harbor M. agassizii than those that develop disease. With the availability of a new quantitative PCR assay for a microbe that had previously been implicated in disease, Pasteurella testudinis, we tested 389 previously collected samples of nasal microbes from tortoise populations across the Mojave desert. We showed that P. testudinis is a common commensal microbe. However, we did find that its presence was associated with higher levels of M. agassizii among the tortoises positive for this pathogen. The best predictor of P. testudinis prevalence in tortoise populations was average size of tortoises, suggesting that older populations have higher levels of P. testudinis. The prevalence of co-infection in populations was associated with the prevalence of URTD, providing additional evidence for an indirect interaction between the two microbes and inflammatory disease. We showed that URTD, like many chronic, polymicrobial diseases involving mucosal surfaces, shows patterns of a polymicrobial etiology.
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Affiliation(s)
- Franziska C Sandmeier
- Biology Department, LS 210, Colorado State University - Pueblo, 2100 Bonforte Blvd, Pueblo, CO, 81001, USA.
| | - Kendra L Leonard
- Biology Department, LS 210, Colorado State University - Pueblo, 2100 Bonforte Blvd, Pueblo, CO, 81001, USA
| | - Chava L Weitzman
- Biology Department, Virginia Polytechnic Institute and State University, Blacksburg, USA
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Luzuriaga-Neira A, Sandmeier FC, Weitzman CL, Tracy CR, Bauschlicher SN, Tillett RL, Alvarez-Ponce D. Mycoplasma agassizii, an opportunistic pathogen of tortoises, shows very little genetic variation across the Mojave and Sonoran Deserts. PLoS One 2021; 16:e0245895. [PMID: 33534823 PMCID: PMC7857612 DOI: 10.1371/journal.pone.0245895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 01/10/2021] [Indexed: 12/01/2022] Open
Abstract
Mycoplasma agassizii is a common cause of upper respiratory tract disease in Mojave desert tortoises (Gopherus agassizii). So far, only two strains of this bacterium have been sequenced, and very little is known about its patterns of genetic diversity. Understanding genetic variability of this pathogen is essential to implement conservation programs for their threatened, long-lived hosts. We used next generation sequencing to explore the genomic diversity of 86 cultured samples of M. agassizii collected from mostly healthy Mojave and Sonoran desert tortoises in 2011 and 2012. All samples with enough sequencing coverage exhibited a higher similarity to M. agassizii strain PS6T (collected in Las Vegas Valley, Nevada) than to strain 723 (collected in Sanibel Island, Florida). All eight genomes with a sequencing coverage over 2x were subjected to multiple analyses to detect single-nucleotide polymorphisms (SNPs). Strikingly, even though we detected 1373 SNPs between strains PS6T and 723, we did not detect any SNP between PS6T and our eight samples. Our whole genome analyses reveal that M. agassizii strain PS6T may be present across a wide geographic extent in healthy Mojave and Sonoran desert tortoises.
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Affiliation(s)
- Agusto Luzuriaga-Neira
- Department of Biology, University of Nevada Reno, Reno, Nevada, United States of America
| | - Franziska C. Sandmeier
- Biology Department, Colorado State University, Pueblo, Colorado, United States of America
- * E-mail: (FCS); (DAP)
| | - Chava L. Weitzman
- Department of Biological Sciences, Virginia Polytechnic Institute, Blacksburg, Virginia, United States of America
| | - C. Richard Tracy
- Department of Biology, University of Nevada Reno, Reno, Nevada, United States of America
| | - Shalyn N. Bauschlicher
- Biology Department, Colorado State University, Pueblo, Colorado, United States of America
| | - Richard L. Tillett
- Nevada Center for Bioinformatics, University of Nevada, Reno, Nevada, United States of America
| | - David Alvarez-Ponce
- Department of Biology, University of Nevada Reno, Reno, Nevada, United States of America
- * E-mail: (FCS); (DAP)
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