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Peña-Salinas ME, Speth DR, Utter DR, Spelz RM, Lim S, Zierenberg R, Caress DW, Núñez PG, Vázquez R, Orphan VJ. Thermotogota diversity and distribution patterns revealed in Auka and JaichMaa 'ja 'ag hydrothermal vent fields in the Pescadero Basin, Gulf of California. PeerJ 2024; 12:e17724. [PMID: 39175749 PMCID: PMC11340630 DOI: 10.7717/peerj.17724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 06/20/2024] [Indexed: 08/24/2024] Open
Abstract
Discovering new deep hydrothermal vent systems is one of the biggest challenges in ocean exploration. They are a unique window to elucidate the physical, geochemical, and biological processes that occur on the seafloor and are involved in the evolution of life on Earth. In this study, we present a molecular analysis of the microbial composition within the newly discovered hydrothermal vent field, JaichMaa 'ja 'ag, situated in the Southern Pescadero Basin within the Gulf of California. During the cruise expedition FK181031 in 2018, 33 sediment cores were collected from various sites within the Pescadero vent fields and processed for 16S rRNA amplicon sequence variants (ASVs) and geochemical analysis. Correlative analysis of the chemical composition of hydrothermal pore fluids and microbial abundances identified several sediment-associated phyla, including Thermotogota, that appear to be enriched in sediment horizons impacted by hydrothermal fluid flow. Comparative analysis of Thermotogota with the previously explored Auka hydrothermal vent field situated 2 km away displayed broad similarity between the two locations, although at finer scales (e.g., ASV level), there were notable differences that point to core-to-core and site-level factors revealing distinct patterns of distribution and abundance within these two sediment-hosted hydrothermal vent fields. These patterns are intricately linked to the specific physical and geochemical conditions defining each vent, illuminating the complexity of this unique deep ocean chemosynthetic ecosystem.
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Affiliation(s)
- Manet E. Peña-Salinas
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Ensenada, Baja California, Mexico
- Laboratorio de Astrobiología, Instituto de Astronomía, Universidad Nacional Autónoma de México, Ensenada, Baja California, Mexico
| | - Daan R. Speth
- Division of Microbial Ecology, Center for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States
| | - Daniel R. Utter
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States
| | - Ronald M. Spelz
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Ensenada, Baja California, Mexico
| | - Sujung Lim
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States
| | - Robert Zierenberg
- Department of Earth and Planetary Sciences, University of California, Davis, Davis, California, United States
| | - David W. Caress
- Science Division, Monterey Bay Aquarium Research Institute, Moss Landing, California, United States
| | - Patricia G. Núñez
- Laboratorio de Astrobiología, Instituto de Astronomía, Universidad Nacional Autónoma de México, Ensenada, Baja California, Mexico
| | - Roberto Vázquez
- Laboratorio de Astrobiología, Instituto de Astronomía, Universidad Nacional Autónoma de México, Ensenada, Baja California, Mexico
| | - Victoria J. Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States
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Farrell AA, Nesbø CL, Zhaxybayeva O. Early Divergence and Gene Exchange Highways in the Evolutionary History of Mesoaciditogales. Genome Biol Evol 2023; 15:evad156. [PMID: 37616556 PMCID: PMC10476701 DOI: 10.1093/gbe/evad156] [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: 06/23/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023] Open
Abstract
The placement of a nonhyperthermophilic order Mesoaciditogales as the earliest branching clade within the Thermotogota phylum challenges the prevailing hypothesis that the last common ancestor of Thermotogota was a hyperthermophile. Yet, given the long branch leading to the only two Mesoaciditogales described to date, the phylogenetic position of the order may be due to the long branch attraction artifact. By testing various models and applying data recoding in phylogenetic reconstructions, we observed that early branching of Mesoaciditogales within Thermotogota is strongly supported by the conserved marker genes assumed to be vertically inherited. However, based on the taxonomic content of 1,181 gene families and a phylogenetic analysis of 721 gene family trees, we also found that a substantial number of Mesoaciditogales genes are more closely related to species from the order Petrotogales. These genes contribute to coenzyme transport and metabolism, fatty acid biosynthesis, genes known to respond to heat and cold stressors, and include many genes of unknown functions. The Petrotogales comprise moderately thermophilic and mesophilic species with similar temperature tolerances to that of Mesoaciditogales. Our findings hint at extensive horizontal gene transfer (HGT) between, or parallel independent gene gains by, the two ecologically similar lineages and suggest that the exchanged genes may be important for adaptation to comparable temperature niches.
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Affiliation(s)
- Anne A Farrell
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
| | - Camilla L Nesbø
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
- Department of Computer Science, Dartmouth College, Hanover, New Hampshire, USA
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Pollo SMJ, Leon-Coria A, Liu H, Cruces-Gonzalez D, Finney CAM, Wasmuth JD. Transcriptional patterns of sexual dimorphism and in host developmental programs in the model parasitic nematode Heligmosomoides bakeri. Parasit Vectors 2023; 16:171. [PMID: 37246221 DOI: 10.1186/s13071-023-05785-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/24/2023] [Indexed: 05/30/2023] Open
Abstract
BACKGROUND Heligmosomoides bakeri (often mistaken for Heligmosomoides polygyrus) is a promising model for parasitic nematodes with the key advantage of being amenable to study and manipulation within a controlled laboratory environment. While draft genome sequences are available for this worm, which allow for comparative genomic analyses between nematodes, there is a notable lack of information on its gene expression. METHODS We generated biologically replicated RNA-seq datasets from samples taken throughout the parasitic life of H. bakeri. RNA from tissue-dwelling and lumen-dwelling worms, collected under a dissection microscope, was sequenced on an Illumina platform. RESULTS We find extensive transcriptional sexual dimorphism throughout the fourth larval and adult stages of this parasite and identify alternative splicing, glycosylation, and ubiquitination as particularly important processes for establishing and/or maintaining sex-specific gene expression in this species. We find sex-linked differences in transcription related to aging and oxidative and osmotic stress responses. We observe a starvation-like signature among transcripts whose expression is consistently upregulated in males, which may reflect a higher energy expenditure by male worms. We detect evidence of increased importance for anaerobic respiration among the adult worms, which coincides with the parasite's migration into the physiologically hypoxic environment of the intestinal lumen. Furthermore, we hypothesize that oxygen concentration may be an important driver of the worms encysting in the intestinal mucosa as larvae, which not only fully exposes the worms to their host's immune system but also shapes many of the interactions between the host and parasite. We find stage- and sex-specific variation in the expression of immunomodulatory genes and in anthelmintic targets. CONCLUSIONS We examine how different the male and female worms are at the molecular level and describe major developmental events that occur in the worm, which extend our understanding of the interactions between this parasite and its host. In addition to generating new hypotheses for follow-up experiments into the worm's behavior, physiology, and metabolism, our datasets enable future more in-depth comparisons between nematodes to better define the utility of H. bakeri as a model for parasitic nematodes in general.
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Affiliation(s)
- Stephen M J Pollo
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- Host-Parasite Interactions Research Training Network, University of Calgary, Calgary, AB, Canada
| | - Aralia Leon-Coria
- Host-Parasite Interactions Research Training Network, University of Calgary, Calgary, AB, Canada
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - Hongrui Liu
- Host-Parasite Interactions Research Training Network, University of Calgary, Calgary, AB, Canada
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - David Cruces-Gonzalez
- Host-Parasite Interactions Research Training Network, University of Calgary, Calgary, AB, Canada
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - Constance A M Finney
- Host-Parasite Interactions Research Training Network, University of Calgary, Calgary, AB, Canada
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - James D Wasmuth
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada.
- Host-Parasite Interactions Research Training Network, University of Calgary, Calgary, AB, Canada.
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Li X, Li D, Ma S, Yang Y. Integration of transcriptomic and proteomic analyses of cold shock response in Kosmotoga olearia, a typical thermophile with an incredible minimum growth temperature at 20 °C. Braz J Microbiol 2022; 53:71-88. [PMID: 34997565 PMCID: PMC8882551 DOI: 10.1007/s42770-021-00662-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 11/19/2021] [Indexed: 01/09/2023] Open
Abstract
Kosmotoga olearia TBF 19.5.1 is a typical thermophile with optimal growth at 65 °C and also exhibits visible growth at an incredible minimum temperature (20 °C). It is considered an ideal model for investigating the evolutionary transition from thermophiles to mesophiles within Thermotogae. However, knowledge relevant to molecular mechanisms of K. olearia responding to cold shock is still limited. In this study, transcriptomics and proteomics were integrated to investigate the global variations at the transcript and protein level during cold shock in K. olearia. As a result, total 734 differentially expressed genes and 262 differentially expressed proteins were identified. The cold-responsive genes and proteins were associated with signaling transduction, transcription, translation and repair, cell wall/membrane reconstruction, amino acid biosynthesis, and stress response. However, most genes and proteins, involved in carbon metabolism, fatty acid biosynthesis, and energy production, were repressed. This work provides the first integrative transcriptomics and proteomics analyses of the cold shock response in K. olearia, and it offered new insights into the mechanisms of cold adaptation and post-transcriptional regulation of the distinctive thermophile within Thermotogae.
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Affiliation(s)
- Xia Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 China ,Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041 China
| | - Dan Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 China ,School of Liquor-Making Engineering, Sichuan University Jinjiang College, Meishan, 620680 China
| | - Shichun Ma
- Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041 China
| | - Yi Yang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 China
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Nesbø CL, Charchuk R, Pollo SMJ, Budwill K, Kublanov IV, Haverkamp THA, Foght J. Genomic analysis of the mesophilic Thermotogae genusMesotogareveals phylogeographic structure and genomic determinants of its distinct metabolism. Environ Microbiol 2018; 21:456-470. [DOI: 10.1111/1462-2920.14477] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 10/15/2018] [Accepted: 11/06/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Camilla L. Nesbø
- Department of Biological Sciences; University of Alberta; Edmonton AB Canada
- BioZone, Department of Chemical Engineering and Applied Chemistry; Wallberg Building, University of Toronto; Toronto ON Canada
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences; University of Oslo; Blindern, Oslo Norway
| | - Rhianna Charchuk
- Department of Biological Sciences; University of Alberta; Edmonton AB Canada
| | - Stephen M. J. Pollo
- Department of Biological Sciences; University of Alberta; Edmonton AB Canada
| | | | - Ilya V. Kublanov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology; Russian Academy of Sciences; Moscow Russia
| | - Thomas H. A. Haverkamp
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences; University of Oslo; Blindern, Oslo Norway
- Norwegian Veterinary Institute; Oslo Norway
| | - Julia Foght
- Department of Biological Sciences; University of Alberta; Edmonton AB Canada
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