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Derelle R, Verdonck R, Jacob S, Huet M, Akerman I, Philippe H, Legrand D. The macronuclear genomic landscape within Tetrahymena thermophila. Microb Genom 2024; 10:001175. [PMID: 38206129 PMCID: PMC10868616 DOI: 10.1099/mgen.0.001175] [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: 09/04/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
The extent of intraspecific genomic variation is key to understanding species evolutionary history, including recent adaptive shifts. Intraspecific genomic variation remains poorly explored in eukaryotic micro-organisms, especially in the nuclear dimorphic ciliates, despite their fundamental role as laboratory model systems and their ecological importance in many ecosystems. We sequenced the macronuclear genome of 22 laboratory strains of the oligohymenophoran Tetrahymena thermophila, a model species in both cellular biology and evolutionary ecology. We explored polymorphisms at the junctions of programmed eliminated sequences, and reveal their utility to barcode very closely related cells. As for other species of the genus Tetrahymena, we confirm micronuclear centromeres as gene diversification centres in T. thermophila, but also reveal a two-speed evolution in these regions. In the rest of the genome, we highlight recent diversification of genes coding for extracellular proteins and cell adhesion. We discuss all these findings in relation to this ciliate's ecology and cellular characteristics.
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Affiliation(s)
- Romain Derelle
- Station d’Ecologie Théorique et Expérimentale, UAR2029, CNRS, Moulis, France
- Present address: NIHR Health Protection Research Unit in Respiratory Infections, National Heart and Lung Institute, Imperial College London, London, UK
| | - Rik Verdonck
- Station d’Ecologie Théorique et Expérimentale, UAR2029, CNRS, Moulis, France
- Present address: Centre for Environmental Sciences, Environmental Biology, Hasselt University, Diepenbeek, Belgium
| | - Staffan Jacob
- Station d’Ecologie Théorique et Expérimentale, UAR2029, CNRS, Moulis, France
| | - Michèle Huet
- Station d’Ecologie Théorique et Expérimentale, UAR2029, CNRS, Moulis, France
| | - Ildem Akerman
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | - Hervé Philippe
- Station d’Ecologie Théorique et Expérimentale, UAR2029, CNRS, Moulis, France
| | - Delphine Legrand
- Station d’Ecologie Théorique et Expérimentale, UAR2029, CNRS, Moulis, France
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Bulannga RB, Schmidt S. Two Predators, One Prey - the Interaction Between Bacteriophage, Bacterivorous Ciliates, and Escherichia coli. MICROBIAL ECOLOGY 2023; 86:1620-1631. [PMID: 36723682 DOI: 10.1007/s00248-022-02163-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
Bacterivorous ciliates and lytic bacteriophages are two major predators in aquatic environments, competing for the same type of prey. This study investigated the possible interaction of these different microorganisms and their influence on the activity of each other. Therefore, two bacterivorous ciliates, Paramecium sp. RB1 and Tetrahymena sp. RB2, were used as representative ciliates; a T4-like Escherichia coli targeting lytic bacteriophage as a model virus; and E. coli ATCC 25922 as a susceptible bacterial host and prey. The growth of the two ciliates with E. coli ATCC 25922 as prey was affected by the presence of phage particles. The grazing activity of the two ciliates resulted in more than a 99% reduction of the phage titer and bacterial cell numbers. However, viable phage particles were recovered from individual washed cells of the two ciliates after membrane filtration. Therefore, ciliates such as Paramecium sp. RB1 and Tetrahymena sp. RB2 can remove bacteriophages present in natural and artificial waters by ingesting the viral particles and eliminating bacterial host cells required for viral replication. The ingestion of phage particles may marginally contribute to the nutrient supply of the ciliates. However, the interaction of phage particles with ciliate cells may contribute to the transmission of bacteriophages in aquatic environments.
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Affiliation(s)
- Rendani Bridghette Bulannga
- Discipline of Microbiology, School of Life Sciences, University of KwaZulu-Natal, Private Bag X01, Pietermaritzburg, 3209, South Africa
| | - Stefan Schmidt
- Discipline of Microbiology, School of Life Sciences, University of KwaZulu-Natal, Private Bag X01, Pietermaritzburg, 3209, South Africa.
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Protozoal food vacuoles enhance transformation in Vibrio cholerae through SOS-regulated DNA integration. THE ISME JOURNAL 2022; 16:1993-2001. [PMID: 35577916 PMCID: PMC9296650 DOI: 10.1038/s41396-022-01249-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 04/20/2022] [Accepted: 04/29/2022] [Indexed: 11/08/2022]
Abstract
Vibrio cholerae, the bacterial pathogen responsible for the diarrheal disease cholera, resides in the aquatic environment between outbreaks. For bacteria, genetic variation by lateral gene transfer (LGT) is important for survival and adaptation. In the aquatic environment, V. cholerae is predominantly found in biofilms associated with chitinous organisms or with chitin "rain". Chitin induces competency in V. cholerae, which can lead to LGT. In the environment, V. cholerae is also subjected to predation pressure by protist. Here we investigated whether protozoal predation affected LGT using the integron as a model. Integrons facilitate the integration of mobile DNA (gene cassettes) into the bacterial chromosome. We report that protozoal predation enhances transformation of a gene cassette by as much as 405-fold. We show that oxidative radicals produced in the protozoal phagosome induces the universal SOS response, which in turn upregulates the integron-integrase, the recombinase that facilitates cassette integration. Additionally, we show that during predation, V. cholerae requires the type VI secretion system to acquire the gene cassette from Escherichia coli. These results show that protozoal predation enhances LGT thus producing genetic variants that may have increased capacity to survive grazing. Additionally, the conditions in the food vacuole may make it a "hot spot" for LGT by accumulating diverse bacteria and inducing the SOS response helping drive genetic diversification and evolution.
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Abstract
Freshwater iron mats are dynamic geochemical environments with broad ecological diversity, primarily formed by the iron-oxidizing bacteria. The community features functional groups involved in biogeochemical cycles for iron, sulfur, carbon, and nitrogen. Despite this complexity, iron mat communities provide an excellent model system for exploring microbial ecological interactions and ecological theories in situ Syntrophies and competition between the functional groups in iron mats, how they connect cycles, and the maintenance of these communities by taxons outside bacteria (the eukaryota, archaea, and viruses) have been largely unstudied. Here, we review what is currently known about freshwater iron mat communities, the taxa that reside there, and the interactions between these organisms, and we propose ways in which future studies may uncover exciting new discoveries. For example, the archaea in these mats may play a greater role than previously thought as they are diverse and widespread in iron mats based on 16S rRNA genes and include methanogenic taxa. Studies with a holistic view of the iron mat community members focusing on their diverse interactions will expand our understanding of community functions, such as those involved in pollution removal. To begin addressing questions regarding the fundamental interactions and to identify the conditions in which they occur, more laboratory culturing techniques and coculture studies, more network and keystone species analyses, and the expansion of studies to more freshwater iron mat systems are necessary. Increasingly accessible bioinformatic, geochemical, and culturing tools now open avenues to address the questions that we pose herein.
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Affiliation(s)
- Chequita N Brooks
- Department of Biology, East Carolina University, Greenville, North Carolina, USA
| | - Erin K Field
- Department of Biology, East Carolina University, Greenville, North Carolina, USA
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George AS, Rehfuss MYM, Parker CT, Brandl MT. The transcriptome of Escherichia coli O157: H7 reveals a role for oxidative stress resistance in its survival from predation by Tetrahymena. FEMS Microbiol Ecol 2020; 96:5721237. [PMID: 32009174 DOI: 10.1093/femsec/fiaa014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/28/2020] [Indexed: 11/14/2022] Open
Abstract
Pathogenic E. coli remains undigested upon phagocytosis by Tetrahymena and is egested from the ciliate as viable cells in its fecal pellets. Factors that are involved in the survival of Shiga toxin-producing E. coli serovar O157: H7 (EcO157) from digestion by Tetrahymena were identified by microarray analysis of its transcriptome in the protozoan phagosome. Numerous genes belonging to anaerobic metabolism and various stress responses were upregulated significantly ≥ 2-fold in EcO157 cells in the food vacuoles compared with in planktonic cells that remained uningested by the protist. Among these were the oxidative stress response genes, ahpF and katG. Fluorescence microscopy and staining with CellROX® Orange confirmed the presence of reactive oxygen species in food vacuoles containing EcO157 cells. Frequency distribution analysis of the percentage of EcO157 viable cells in Tetrahymena fecal pellets revealed that the ΔahpCF and ΔahpCFΔkatG mutants were less fit than the wild type strain and ΔkatG mutant after passage through the protist. Given the broad use of oxidants as sanitizers in the food industry, our observation of the oxidative stress response in EcO157 during its interaction with Tetrahymena emphasizes the importance of furthering our knowledge of the physiology of this human pathogen in environments relevant to its ecology and to food safety.
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Affiliation(s)
- Andree Sherlon George
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, US Department of Agriculture, Albany, CA, USA
| | - Marc Yi Ming Rehfuss
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, US Department of Agriculture, Albany, CA, USA
| | - Craig Thomas Parker
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, US Department of Agriculture, Albany, CA, USA
| | - Maria Theresa Brandl
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, US Department of Agriculture, Albany, CA, USA
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Liang D, Wang X, Wang Y, Dong Z, Zhao X, Fan W. The dual effect of natural organic matter on the two-step internalization process of Au@Sio 2 in freshwater. WATER RESEARCH 2020; 184:116216. [PMID: 32721761 DOI: 10.1016/j.watres.2020.116216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 06/11/2023]
Abstract
Dissolved organic matter (DOM) in aquatic ecosystems reshapes the surface of nanoparticles (NPs) greatly. Understanding how these changes influence the bioavailability of NPs is critical for accurately predicting the ecological risks of NPs. A quantitative model based on the two-step internalization process enabled the differentiation between the adhesion ability of NPs to membranes and the internalization capacity. Using protozoa Tetrahymena thermophila as the test organism, fluorescein isothiocyanate-modified silica NPs (FITC-SiO2) and silica-coated gold NPs (Au@SiO2) were prepared to validate the model and study the influence of DOM on uptake. DOM reduced the ability of Au@SiO2 to adhere onto cell membranes and the inhibitory effect of bovine serum albumin (BSA) and β-lactoglobulin was higher due to their higher molecular weights and the weaker interaction. Moreover, DOM increased the internalization capacity. 80% Au@SiO2 was internalized in the presence of humic acid (HA), over 90% Au@SiO2 was internalized in the presence of the two proteins, whereas only 60% were internalized by the control group. Next, the specific recognition of the cell internalization in the presence of DOM was confirmed. We concluded that the traditional "accumulation" may misestimate the true biological effect caused by NPs coated with DOM. NPs coated with highly bioavailable DOM pose a greater risk to aquatic ecosystems because they are more likely to be internalized by living organisms.
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Affiliation(s)
- Dingyuan Liang
- School of Space and Environment, Beihang University, Beijing 100191, P.R. China
| | - Xiangrui Wang
- School of Space and Environment, Beihang University, Beijing 100191, P.R. China
| | - Ying Wang
- School of Space and Environment, Beihang University, Beijing 100191, P.R. China
| | - Zhaomin Dong
- School of Space and Environment, Beihang University, Beijing 100191, P.R. China
| | - Xiaoli Zhao
- Chinese Res Institute Environmental Science, State Key Lab Environmental Criteria & Risk Assessment, Beijing 100012
| | - Wenhong Fan
- School of Space and Environment, Beihang University, Beijing 100191, P.R. China; Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing 100191, P.R. China.
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Beinart R, Rotterová J, Čepička I, Gast R, Edgcomb V. The genome of an endosymbiotic methanogen is very similar to those of its free‐living relatives. Environ Microbiol 2018; 20:2538-2551. [DOI: 10.1111/1462-2920.14279] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- R.A. Beinart
- Department of Geology and Geophysics Woods Hole Oceanographic Institution Woods Hole MA USA
- Department of Biology Woods Hole Oceanographic Institution Woods Hole MA USA
| | - J. Rotterová
- Department of Zoology Charles University Prague Czech Republic
| | - I. Čepička
- Department of Zoology Charles University Prague Czech Republic
| | - R.J. Gast
- Department of Biology Woods Hole Oceanographic Institution Woods Hole MA USA
| | - V.P. Edgcomb
- Department of Geology and Geophysics Woods Hole Oceanographic Institution Woods Hole MA USA
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Sun S, Noorian P, McDougald D. Dual Role of Mechanisms Involved in Resistance to Predation by Protozoa and Virulence to Humans. Front Microbiol 2018; 9:1017. [PMID: 29867902 PMCID: PMC5967200 DOI: 10.3389/fmicb.2018.01017] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 04/30/2018] [Indexed: 12/12/2022] Open
Abstract
Most opportunistic pathogens transit in the environment between hosts and the environment plays a significant role in the evolution of protective traits. The coincidental evolution hypothesis suggests that virulence factors arose as a response to other selective pressures rather for virulence per se. This idea is strongly supported by the elucidation of bacterial-protozoal interactions. In response to protozoan predation, bacteria have evolved various defensive mechanisms which may also function as virulence factors. In this review, we summarize the dual role of factors involved in both grazing resistance and human pathogenesis, and compare the traits using model intracellular and extracellular pathogens. Intracellular pathogens rely on active invasion, blocking of the phagosome and lysosome fusion and resistance to phagocytic digestion to successfully invade host cells. In contrast, extracellular pathogens utilize toxin secretion and biofilm formation to avoid internalization by phagocytes. The complexity and diversity of bacterial virulence factors whose evolution is driven by protozoan predation, highlights the importance of protozoa in evolution of opportunistic pathogens.
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Affiliation(s)
- Shuyang Sun
- ithree Institute, University of Technology Sydney, Sydney, NSW, Australia
| | - Parisa Noorian
- ithree Institute, University of Technology Sydney, Sydney, NSW, Australia.,School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Diane McDougald
- ithree Institute, University of Technology Sydney, Sydney, NSW, Australia.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
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Aijaz I, Koudelka GB. Cheating, facilitation and cooperation regulate the effectiveness of phage-encoded exotoxins as antipredator molecules. Microbiologyopen 2018; 8:e00636. [PMID: 29675935 PMCID: PMC6391270 DOI: 10.1002/mbo3.636] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 03/09/2018] [Accepted: 03/09/2018] [Indexed: 01/28/2023] Open
Abstract
Temperate phage encoded Shiga toxin (Stx) kills the bacterivorous predator, Tetrahymena thermophila, providing Stx+Escherichia coli with a survival advantage over Stx− cells. Although bacterial death accompanies Stx release, since bacteria grow clonally the fitness benefits of predator killing accrue to the kin of the sacrificed organism, meaning Stx‐mediated protist killing is a form of self‐destructive cooperation. We show here that the fitness benefits of Stx production are not restricted to the kin of the phage‐encoding bacteria. Instead, nearby “free loading” bacteria, irrespective of their genotype, also reap the benefit of Stx‐mediated predator killing. This finding indicates that the phage‐borne Stx exotoxin behaves as a public good. Stx is encoded by a mobile phage. We find that Stx‐encoding phage can use susceptible bacteria in the population as surrogates to enhance toxin and phage production. Moreover, our findings also demonstrate that engulfment and concentration of Stx‐encoding and susceptible Stx− bacteria in the Tetrahymena phagosome enhances the transfer of Stx‐encoding temperate phage from the host to the susceptible bacteria. This transfer increases the population of cooperating bacteria within the community. Since these bacteria now encode Stx, the predation‐stimulated increase in phage transfer increases the population of toxin encoding bacteria in the environment.
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Affiliation(s)
- Iqbal Aijaz
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Gerald B Koudelka
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
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