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Price CTD, Hanford HE, Al-Quadan T, Santic M, Shin CJ, Da'as MSJ, Abu Kwaik Y. Amoebae as training grounds for microbial pathogens. mBio 2024; 15:e0082724. [PMID: 38975782 PMCID: PMC11323580 DOI: 10.1128/mbio.00827-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024] Open
Abstract
Grazing of amoebae on microorganisms represents one of the oldest predator-prey dynamic relationships in nature. It represents a genetic "melting pot" for an ancient and continuous multi-directional inter- and intra-kingdom horizontal gene transfer between amoebae and its preys, intracellular microbial residents, endosymbionts, and giant viruses, which has shaped the evolution, selection, and adaptation of microbes that evade degradation by predatory amoeba. Unicellular phagocytic amoebae are thought to be the ancient ancestors of macrophages with highly conserved eukaryotic processes. Selection and evolution of microbes within amoeba through their evolution to target highly conserved eukaryotic processes have facilitated the expansion of their host range to mammals, causing various infectious diseases. Legionella and environmental Chlamydia harbor an immense number of eukaryotic-like proteins that are involved in ubiquitin-related processes or are tandem repeats-containing proteins involved in protein-protein and protein-chromatin interactions. Some of these eukaryotic-like proteins exhibit novel domain architecture and novel enzymatic functions absent in mammalian cells, such as ubiquitin ligases, likely acquired from amoebae. Mammalian cells and amoebae may respond similarly to microbial factors that target highly conserved eukaryotic processes, but mammalian cells may undergo an accidental response to amoeba-adapted microbial factors. We discuss specific examples of microbes that have evolved to evade amoeba predation, including the bacterial pathogens- Legionella, Chlamydia, Coxiella, Rickettssia, Francisella, Mycobacteria, Salmonella, Bartonella, Rhodococcus, Pseudomonas, Vibrio, Helicobacter, Campylobacter, and Aliarcobacter. We also discuss the fungi Cryptococcus, and Asperigillus, as well as amoebae mimiviruses/giant viruses. We propose that amoeba-microbe interactions will continue to be a major "training ground" for the evolution, selection, adaptation, and emergence of microbial pathogens equipped with unique pathogenic tools to infect mammalian hosts. However, our progress will continue to be highly dependent on additional genomic, biochemical, and cellular data of unicellular eukaryotes.
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Affiliation(s)
- Christopher T. D. Price
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Hannah E. Hanford
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Tasneem Al-Quadan
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | | | - Cheon J. Shin
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Manal S. J. Da'as
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Yousef Abu Kwaik
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
- Center for Predictive Medicine, College of Medicine, University of Louisville, Louisville, Kentucky, USA
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Sajid S, Zhang G, Zhang Z, Lu Y, Chen L, Cai L. Spartinivicinus poritis sp. nov., a red pigment-producing bacterium isolated from a scleractinian coral Porites lutea. Int J Syst Evol Microbiol 2024; 74. [PMID: 38963416 DOI: 10.1099/ijsem.0.006444] [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] [Indexed: 07/05/2024] Open
Abstract
A Gram-stain-negative, red pigment-producing, aerobic, and rod-shaped bacterial strain (A2-2T) was isolated from a bleached scleractinian coral (Porites lutea). Strain A2-2T grew with 1.0-7.0 % (w/v) NaCl (optimum, 3.0 %), at pH 6.0-11.0 (optimum, pH 8.0), and at 18-41 °C (optimum, 35 °C). Results of phylogenetic analysis based on 16S rRNA gene sequences suggested that strain A2-2T fell within the genus Spartinivicinus and was closely related to Spartinivicinus ruber S2-4-1HT (98.1 % sequence similarity) and Spartinivicinus marinus SM1973T (98.0 % sequence similarity). The predominant cellular fatty acids of strain A2-2T were C16 : 0 (31.0 %), summed feature 3 (29.0 %), summed feature 8 (11.7 %), C12 : 0 3-OH (6.4 %), and C10 : 0 3-OH (5.5 %), while the major respiratory quinone was Q-9. The polar lipids mainly comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and an unidentified phospholipid. The genome size of strain A2-2T was 6.8 Mb, with a G+C content of 40.2 mol%. The DNA-DNA hybridization value was 24.2 % between A2-2T and S. ruber S2-4-1HT and 36.9 % between A2-2T and S. marinus SM1973T, while the average nucleotide identity values were 80.1 and 88.8 %, respectively. Based on these findings, strain A2-2T could be recognized to represent a novel species of the genus Spartinivicinus, for which the name Spartinivicinus poritis sp. nov. is proposed. The type strain is A2-2T (=MCCC 1K08228T=KCTC 8323T).
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Affiliation(s)
- Sumbal Sajid
- Shenzhen Institute of Guangdong Ocean University, Binhai 2nd Road, Shenzhen, 518120, PR China
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China
| | - Guoqiang Zhang
- Shenzhen Institute of Guangdong Ocean University, Binhai 2nd Road, Shenzhen, 518120, PR China
| | - Zongyao Zhang
- Shenzhen Institute of Guangdong Ocean University, Binhai 2nd Road, Shenzhen, 518120, PR China
| | - Yishan Lu
- Shenzhen Institute of Guangdong Ocean University, Binhai 2nd Road, Shenzhen, 518120, PR China
| | - Lianguo Chen
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China
| | - Lin Cai
- Shenzhen Institute of Guangdong Ocean University, Binhai 2nd Road, Shenzhen, 518120, PR China
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Marzouk AM, Mashaly MI, Reda ES, El-Naggar MM. The record of Vannella species (Vannellidae, Discosea, Amoebozoa) from freshwater sources in Dakahlyia Governorate, Egypt. Arch Microbiol 2024; 206:113. [PMID: 38376635 PMCID: PMC10879259 DOI: 10.1007/s00203-024-03837-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 02/21/2024]
Abstract
The River Nile is the main source of fresh water in Egypt, where its water is used for irrigation, drinking, fisheries, industrial uses, and recreation. For sustainable utilization of the River Nile and its branches in the Nile Delta region, it is necessary to monitor regular investigation for the biodiversity of protozoan fauna in the Damietta branch and other freshwater canals in Dakahlyia Governorate. Water samples were collected monthly from different water sources, for 1 year, and examined for protozoans, using phase-contrast microscopy and recorded video films, The genus Vannella Bovee 1965 is recorded for the first time in four freshwater localities: Demietta branch of the River Nile, Mansouria Canal, Bouhia Canal, and Bahr El-Saghir Canal. A detailed morphological description with a brief report of their locomotion has been given for four morphologically different Vannella species. The locomotive form of Vannella sp.1 has a long pointed posterior tail and 2 lateral posterior processes. Such a tail was absent in other Vannella species. Vannella sp.2 is unique among other recorded species, where its locomotive form possesses a long posterior rounded tail region and a frontal hyaloplasm provided with a wavy surface that forms several lobes and finger-like processes during locomotion. In addition, the hyaloplasm produces several transverse waves that vary in thickness and density. The floating form of Vannella sp.2 is of a radial type and has comparatively long hyaline pointed and spiral pseudopodia. The process of transformation of locomotive form to floating form in Vannella sp.2 has been followed up using several recorded video films. The locomotive form of Vannella sp.3 is bear-shaped, while that of Vannella sp.4 has variable shapes from semicircular to rectangular and sometimes fan-shaped. During movement in vivo, locomotive cells of all Vannella species, except Vannella sp.1, move in nearly a straight line, but there were variations in their rate of locomotion. Vannella sp.4 recorded the highest rate (6.8 µm/s), followed by Vannella sp.2 (4.5 µm/s), Vannella sp.3 (2.4 µm/s), and finally Vannella sp.1 (1.0 µm/s). Molecular studies and transmission electron microscope examinations are still needed to confirm the precise identity of each Vannella species.
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Affiliation(s)
- Asmaa M Marzouk
- Zoology Department, Faculty of Science, Mansoura University, Mansoura, Egypt
| | - Mohamed I Mashaly
- Zoology Department, Faculty of Science, Mansoura University, Mansoura, Egypt.
| | - Enayat S Reda
- Zoology Department, Faculty of Science, Mansoura University, Mansoura, Egypt
| | - Mohamed M El-Naggar
- Zoology Department, Faculty of Science, Mansoura University, Mansoura, Egypt
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The Porifera microeukaryome: Addressing the neglected associations between sponges and protists. Microbiol Res 2022; 265:127210. [PMID: 36183422 DOI: 10.1016/j.micres.2022.127210] [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: 05/02/2022] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 11/22/2022]
Abstract
While bacterial and archaeal communities of sponges are intensively studied, given their importance to the animal's physiology as well as sources of several new bioactive molecules, the potential and roles of associated protists remain poorly known. Historically, culture-dependent approaches dominated the investigations of sponge-protist interactions. With the advances in omics techniques, these associations could be visualized at other equally important scales. Of the few existing studies, there is a strong tendency to focus on interactions with photosynthesizing taxa such as dinoflagellates and diatoms, with fewer works dissecting the interactions with other less common groups. In addition, there are bottlenecks and inherent biases in using primer pairs and bioinformatics approaches in the most commonly used metabarcoding studies. Thus, this review addresses the issues underlying this association, using the term "microeukaryome" to refer exclusively to protists associated with an animal host. We aim to highlight the diversity and community composition of protists associated with sponges and place them on the same level as other microorganisms already well studied in this context. Among other shortcomings, it could be observed that the biotechnological potential of the microeukaryome is still largely unexplored, possibly being a valuable source of new pharmacological compounds, enzymes and metabolic processes.
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Sousa-Ramos D, Reyes-Batlle M, Bellini NK, Rodríguez-Expósito RL, Martín-Real C, Piñero JE, Lorenzo-Morales J. Pathogenic free-living amoebae from water sources in Cape Verde. Parasitol Res 2022; 121:2399-2404. [PMID: 35660958 PMCID: PMC9279231 DOI: 10.1007/s00436-022-07563-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/28/2022] [Indexed: 12/01/2022]
Abstract
Free-living amoebae (FLA) are protozoa which have been reported in different countries worldwide from diverse sources (water, soil, dust, air), contributing to the environmental microbiological contamination. Most of the FLA species present a life cycle with two different phases: an active vegetative and physiologically form named trophozoite, and an extremely resistant phase called cyst. Acanthamoeba spp., Naegleria fowleri, Balamuthia mandrillaris, Sapinia pedata, Vahlkampfia spp., Paravahlkampfia spp. and Vermamoeba vermiformis have been reported not only as causal agents of several opportunistic diseases including fatal encephalitis or epithelial disorders, but also as capable to favour the intracellular survival of common pathogenic bacteria, which could avoid the typical water disinfection systems, non-effective against FLAs cysts. Even though Santiago Island possesses high levels of humidity compared to the rest of the archipelago of Cape Verde, the water resources are scarce. Therefore, it is important to carry out proper microbiological quality controls, which currently do not contemplate the FLA presence in most of the countries. In the present work, we have reported the presence of Acanthamoeba spp. (69.2%); Vannella spp. (15.4%); Vermamoeba vermiformis (7.7%) and the recently discovered Stenamoeba dejonckheerei (7.7%) in different water sources of Santiago Island.
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Affiliation(s)
- Djeniffer Sousa-Ramos
- Instituto Universitario de Enfermedades Tropicales Y Salud Pública de Canarias (IUETSPC), Universidad de La Laguna (ULL), Avda. Astrofísico Fco. Sánchez S/N, 38203, La Laguna, Tenerife, Spain
- Departamento de Obstetricia Y Ginecología, Pediatría, Medicina Preventiva Y Salud Pública, Toxicología, Medicina Legal Y Forense Y Parasitología, Universidad de La Laguna (ULL), San Cristóbal de La Laguna, Tenerife, Spain
| | - María Reyes-Batlle
- Instituto Universitario de Enfermedades Tropicales Y Salud Pública de Canarias (IUETSPC), Universidad de La Laguna (ULL), Avda. Astrofísico Fco. Sánchez S/N, 38203, La Laguna, Tenerife, Spain
- Departamento de Obstetricia Y Ginecología, Pediatría, Medicina Preventiva Y Salud Pública, Toxicología, Medicina Legal Y Forense Y Parasitología, Universidad de La Laguna (ULL), San Cristóbal de La Laguna, Tenerife, Spain
- Red de Investigación Cooperativa en Enfermedades Tropicales (RICET), Madrid, Spain
| | - Natalia Karla Bellini
- Instituto de Física de São Carlos, Universidade de São Paulo, Caixa Postal 369, São Carlos, SP, 13560-590, Brazil
| | - Rubén L Rodríguez-Expósito
- Instituto Universitario de Enfermedades Tropicales Y Salud Pública de Canarias (IUETSPC), Universidad de La Laguna (ULL), Avda. Astrofísico Fco. Sánchez S/N, 38203, La Laguna, Tenerife, Spain
- Departamento de Obstetricia Y Ginecología, Pediatría, Medicina Preventiva Y Salud Pública, Toxicología, Medicina Legal Y Forense Y Parasitología, Universidad de La Laguna (ULL), San Cristóbal de La Laguna, Tenerife, Spain
- Red de Investigación Cooperativa en Enfermedades Tropicales (RICET), Madrid, Spain
| | - Christian Martín-Real
- Instituto Universitario de Enfermedades Tropicales Y Salud Pública de Canarias (IUETSPC), Universidad de La Laguna (ULL), Avda. Astrofísico Fco. Sánchez S/N, 38203, La Laguna, Tenerife, Spain
| | - José E Piñero
- Instituto Universitario de Enfermedades Tropicales Y Salud Pública de Canarias (IUETSPC), Universidad de La Laguna (ULL), Avda. Astrofísico Fco. Sánchez S/N, 38203, La Laguna, Tenerife, Spain.
- Departamento de Obstetricia Y Ginecología, Pediatría, Medicina Preventiva Y Salud Pública, Toxicología, Medicina Legal Y Forense Y Parasitología, Universidad de La Laguna (ULL), San Cristóbal de La Laguna, Tenerife, Spain.
- Red de Investigación Cooperativa en Enfermedades Tropicales (RICET), Madrid, Spain.
- Consorcio Centro de Investigación Biomédica En Red M.P. (CIBER) de Enfermedades Infecciosas (CIBERINFEC), Inst. de Salud Carlos III, 28006, Madrid, Spain.
| | - Jacob Lorenzo-Morales
- Instituto Universitario de Enfermedades Tropicales Y Salud Pública de Canarias (IUETSPC), Universidad de La Laguna (ULL), Avda. Astrofísico Fco. Sánchez S/N, 38203, La Laguna, Tenerife, Spain.
- Departamento de Obstetricia Y Ginecología, Pediatría, Medicina Preventiva Y Salud Pública, Toxicología, Medicina Legal Y Forense Y Parasitología, Universidad de La Laguna (ULL), San Cristóbal de La Laguna, Tenerife, Spain.
- Red de Investigación Cooperativa en Enfermedades Tropicales (RICET), Madrid, Spain.
- Consorcio Centro de Investigación Biomédica En Red M.P. (CIBER) de Enfermedades Infecciosas (CIBERINFEC), Inst. de Salud Carlos III, 28006, Madrid, Spain.
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Sousa-Ramos D, Reyes-Batlle M, Bellini NK, Rodríguez-Expósito RL, Piñero JE, Lorenzo-Morales J. Free-Living Amoebae in Soil Samples from Santiago Island, Cape Verde. Microorganisms 2021; 9:microorganisms9071460. [PMID: 34361894 PMCID: PMC8306126 DOI: 10.3390/microorganisms9071460] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 11/16/2022] Open
Abstract
Free-Living Amoebae (FLA) are widely distributed protozoa, which contain some groups considered as pathogenic microorganisms. These members are able to produce several opportunistic diseases including epithelial disorders, such as keratitis and fatal encephalitis. Even though they have been reported in numerous sources, such as soils, dust and water, there is no legislation related to the presence of these protozoa in soil-related environments worldwide. Therefore, there are no established prevention or disinfection protocols to advise the population regarding FLA infections or eliminate these microorganisms from human-related environments to date. Acanthamoeba spp. are the most common FLA isolated in soil samples, which is also the most common genera found in clinical cases. Thus, the aim of the present study was to evaluate the presence of potentially pathogenic FLA in human-related soil samples of Santiago Island, Cabo Verde. A total of 26 soil samples were seeded in non-nutrient agar plates (2%), incubated at 26 °C, and monitored daily to evaluate the presence of FLA. DNA was extracted from those plates on which there was suspected FLA growth, and PCR amplification of the 18S rRNA gene was carried out. A total of 17 from the 26 analysed samples were positive for FLA, where Acanthamoeba is the most abundant isolated genus (14/17; 82.4%), with the T4 genotype being the most common (13/14; 92.9%), followed by the T5 genotype, A. lenticulata (1/14; 7.1%). Moreover, Vermamoeba vermiformis, Stenamoeba dejonckheerei and Vannella pentlandi were isolated in three other samples. To the best of our knowledge, this is the first report of FLA presence in Cape Verde and the first report of V. vermiformis in beach sand worldwide.
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Affiliation(s)
- Djeniffer Sousa-Ramos
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC), Universidad de La Laguna (ULL), Avda. Astrofísico Fco. Sánchez s/n, 38203 San Cristóbal de La Laguna, Tenerife, Spain; (D.S.-R.); (N.K.B.); (R.L.R.-E.)
| | - María Reyes-Batlle
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC), Universidad de La Laguna (ULL), Avda. Astrofísico Fco. Sánchez s/n, 38203 San Cristóbal de La Laguna, Tenerife, Spain; (D.S.-R.); (N.K.B.); (R.L.R.-E.)
- Red de Investigación Cooperativa en Enfermedades Tropicales (RICET), Universidad de Salamanca, 37008 Salamanca, Spain
- Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna (ULL), 38200 San Cristóbal de La Laguna, Tenerife, Spain
- Correspondence: (M.R.-B.); (J.E.P.); (J.L.-M.)
| | - Natália K. Bellini
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC), Universidad de La Laguna (ULL), Avda. Astrofísico Fco. Sánchez s/n, 38203 San Cristóbal de La Laguna, Tenerife, Spain; (D.S.-R.); (N.K.B.); (R.L.R.-E.)
- Instituto de Física de São Carlos, Universidade de São Paulo, Caixa Postal 369, São Carlos 13560-590, SP, Brazil
| | - Rubén L. Rodríguez-Expósito
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC), Universidad de La Laguna (ULL), Avda. Astrofísico Fco. Sánchez s/n, 38203 San Cristóbal de La Laguna, Tenerife, Spain; (D.S.-R.); (N.K.B.); (R.L.R.-E.)
- Red de Investigación Cooperativa en Enfermedades Tropicales (RICET), Universidad de Salamanca, 37008 Salamanca, Spain
- Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna (ULL), 38200 San Cristóbal de La Laguna, Tenerife, Spain
| | - José E. Piñero
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC), Universidad de La Laguna (ULL), Avda. Astrofísico Fco. Sánchez s/n, 38203 San Cristóbal de La Laguna, Tenerife, Spain; (D.S.-R.); (N.K.B.); (R.L.R.-E.)
- Red de Investigación Cooperativa en Enfermedades Tropicales (RICET), Universidad de Salamanca, 37008 Salamanca, Spain
- Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna (ULL), 38200 San Cristóbal de La Laguna, Tenerife, Spain
- Correspondence: (M.R.-B.); (J.E.P.); (J.L.-M.)
| | - Jacob Lorenzo-Morales
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC), Universidad de La Laguna (ULL), Avda. Astrofísico Fco. Sánchez s/n, 38203 San Cristóbal de La Laguna, Tenerife, Spain; (D.S.-R.); (N.K.B.); (R.L.R.-E.)
- Red de Investigación Cooperativa en Enfermedades Tropicales (RICET), Universidad de Salamanca, 37008 Salamanca, Spain
- Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna (ULL), 38200 San Cristóbal de La Laguna, Tenerife, Spain
- Correspondence: (M.R.-B.); (J.E.P.); (J.L.-M.)
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Saini N, Gupta RS. A robust phylogenetic framework for members of the order Legionellales and its main genera (Legionella, Aquicella, Coxiella and Rickettsiella) based on phylogenomic analyses and identification of molecular markers demarcating different clades. Antonie van Leeuwenhoek 2021; 114:957-982. [PMID: 33881638 DOI: 10.1007/s10482-021-01569-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/01/2021] [Indexed: 12/29/2022]
Abstract
The order Legionellales contains several clinically important microorganisms. Although members of this order are well-studied for their pathogenesis, there is a paucity of reliable characteristics distinguishing members of this order and its constituent genera. Genome sequences are now available for 73 Legionellales species encompassing ≈90% of known members from different genera. With the aim of understanding evolutionary relationships and identifying reliable molecular characteristics that are specific for this order and its constituent genera, detailed phylogenetic and comparative analyses were conducted on the protein sequences from these genomes. A phylogenomic tree was constructed based on 393 single copy proteins that are commonly shared by the members of this order to delineate the evolutionary relationships among its members. In parallel, comparative analyses were performed on protein sequences from Legionellales genomes to identify novel molecular markers consisting of conserved signature indels (CSIs) that are specific for different clades and genera. In the phylogenomic tree and in an amino acid identity matrix based on core proteins, members of the genera Aquicella, Coxiella, Legionella and Rickettsiella formed distinct clades confirming their monophyly. In these studies, Diplorickettsia massiliensis exhibited a close relationship to members of the genus Rickettsiella. The results of our comparative genomic analyses have identified 59 highly specific molecular markers consisting of CSIs in diverse proteins that are uniquely shared by different members of this order. Four of these CSIs are specific for all Legionellales species, except the two deeper-branching "Candidatus Berkiella" species, providing means for identifying members of this order in molecular terms. Twenty four, 7 and 6 CSIs are uniquely shared by members of the genera Legionella, Coxiella and Aquicella, respectively, identifying these groups in molecular terms. The descriptions of these three genera are emended to include information for their novel molecular characteristics. We also describe 12 CSIs that are uniquely shared by D. massiliensis and different members of the genus Rickettsiella. Based on these results, we are proposing an integration of the genus Diplorickettsia with Rickettsiella. Three other CSIs suggest that members of the genera Coxiella and Rickettsiella shared a common ancestor exclusive of other Legionellales. The described molecular markers, due to their exclusivity for the indicated taxa/genera, provide important means for the identification of these clinically important microorganisms and for discovering novel properties unique to them.
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Affiliation(s)
- Navneet Saini
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada.
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Farnelid H, Turk‐Kubo K, Zehr JP. Cell sorting reveals few novel prokaryote and photosynthetic picoeukaryote associations in the oligotrophic ocean. Environ Microbiol 2021; 23:1469-1480. [PMID: 33295132 PMCID: PMC8048811 DOI: 10.1111/1462-2920.15351] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 12/04/2020] [Indexed: 11/28/2022]
Abstract
Close associations between single-celled marine organisms can have a central role in biogeochemical processes and are of great interest for understanding the evolution of organisms. The global significance of such associations raises the question of whether unidentified associations are yet to be discovered. In this study, fluorescence-activated cell sorted photosynthetic picoeukayote (PPE) populations and single cells were analysed by sequencing of 16S rRNA genes in the oligotrophic North Pacific Subtropical Gyre. Samples were collected during two cruises, spanning depths near the deep chlorophyll maximum, where the abundance of PPEs was highest. The association between the widespread and significant nitrogen (N2 )-fixing cyanobacterium, UCYN-A and its prymnesiophyte host was prevalent in both population and single-cell sorts. Several bacterial sequences, affiliating with previously described symbiotic taxa were detected but their detection was rare and not well replicated, precluding identification of novel tightly linked species-specific associations. Similarly, no enrichment of dominant seawater taxa such as Prochlorococcus, SAR11 or Synechococcus was observed suggesting that these were not systematically ingested by the PPE in this study. The results indicate that apart from the UCYN-A symbiosis, similar tight species-specific associations with PPEs are unusual in the oligotrophic ocean.
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Affiliation(s)
- Hanna Farnelid
- Ocean Sciences DepartmentUniversity of CaliforniaSanta CruzCAUSA
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS)Linnaeus UniversityKalmarSweden
| | - Kendra Turk‐Kubo
- Ocean Sciences DepartmentUniversity of CaliforniaSanta CruzCAUSA
| | - Jonathan P. Zehr
- Ocean Sciences DepartmentUniversity of CaliforniaSanta CruzCAUSA
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Abstract
Amoebae are protists that have complicated relationships with bacteria, covering the whole spectrum of symbiosis. Amoeba-bacterium interactions contribute to the study of predation, symbiosis, pathogenesis, and human health. Given the complexity of their relationships, it is necessary to understand the ecology and evolution of their interactions. In this paper, we provide an updated review of the current understanding of amoeba-bacterium interactions. We start by discussing the diversity of amoebae and their bacterial partners. We also define three types of ecological interactions between amoebae and bacteria and discuss their different outcomes. Finally, we focus on the implications of amoeba-bacterium interactions on human health, horizontal gene transfer, drinking water safety, and the evolution of symbiosis. In conclusion, amoeba-bacterium interactions are excellent model systems to investigate a wide range of scientific questions. Future studies should utilize advanced techniques to address research gaps, such as detecting hidden diversity, lack of amoeba genomes, and the impacts of amoeba predation on the microbiome.
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Oren A, Garrity GM, Parker CT, Chuvochina M, Trujillo ME. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2020; 70:3956-4042. [DOI: 10.1099/ijsem.0.003789] [Citation(s) in RCA: 782] [Impact Index Per Article: 195.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evolutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current proposals to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes.
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Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M. Garrity
- NamesforLife, LLC, PO Box 769, Okemos MI 48805-0769, USA
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
| | | | - Maria Chuvochina
- Australian Centre for Ecogenomics, University of Queensland, St. Lucia QLD 4072, Brisbane, Australia
| | - Martha E. Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, Universidad de Salamanca, 37007, Salamanca, Spain
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Cartography of Free-Living Amoebae in Soil in Guadeloupe (French West Indies) Using DNA Metabarcoding. Pathogens 2020; 9:pathogens9060440. [PMID: 32512696 PMCID: PMC7350318 DOI: 10.3390/pathogens9060440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/02/2020] [Accepted: 05/03/2020] [Indexed: 12/20/2022] Open
Abstract
Free-living amoebae (FLA) are ubiquitous protists. Pathogenic FLA such as N. fowleri can be found in hot springs in Guadeloupe, soil being the origin of this contamination. Herein, we analyzed the diversity and distribution of FLA in soil using a targeted metataxonomic analysis. Soil samples (n = 107) were collected from 40 sites. DNA was extracted directly from soil samples or from FLA cultivated at different temperatures (30, 37 and 44 °C). Metabarcoding studies were then conducted through FLA 18SrDNA amplicons sequencing; amplicon sequence variants (ASV) were extracted from each sample and taxonomy assigned against SILVA database using QIIME2 and SHAMAN pipelines. Vermamoeba were detected in DNA extracted directly from the soil, but to detect other FLA an amoebal enrichment step was necessary. V. vermiformis was by far the most represented species of FLA, being detected throughout the islands. Although Naegleria were mainly found in Basse-Terre region, N. fowleri was also detected in Grand Terre and Les Saintes Islands. Acanthamoeba were mainly found in areas where temperature is approx. 30 °C. Vannella and Vahlkampfia were randomly found in Guadeloupe islands. FLA detected in Guadeloupe include both pathogenic genera and genera that can putatively harbor microbial pathogens, therefore posing a potential threat to human health.
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12
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Abstract
Soil ecosystems harbor diverse microorganisms and yet remain only partially characterized as neither single-cell sequencing nor whole-community sequencing offers a complete picture of these complex communities. Thus, the genetic and metabolic potential of this "uncultivated majority" remains underexplored. To address these challenges, we applied a pooled-cell-sorting-based mini-metagenomics approach and compared the results to bulk metagenomics. Informatic binning of these data produced 200 mini-metagenome assembled genomes (sorted-MAGs) and 29 bulk metagenome assembled genomes (MAGs). The sorted and bulk MAGs increased the known phylogenetic diversity of soil taxa by 7.2% with respect to the Joint Genome Institute IMG/M database and showed clade-specific sequence recruitment patterns across diverse terrestrial soil metagenomes. Additionally, sorted-MAGs expanded the rare biosphere not captured through MAGs from bulk sequences, exemplified through phylogenetic and functional analyses of members of the phylum Bacteroidetes Analysis of 67 Bacteroidetes sorted-MAGs showed conserved patterns of carbon metabolism across four clades. These results indicate that mini-metagenomics enables genome-resolved investigation of predicted metabolism and demonstrates the utility of combining metagenomics methods to tap into the diversity of heterogeneous microbial assemblages.IMPORTANCE Microbial ecologists have historically used cultivation-based approaches as well as amplicon sequencing and shotgun metagenomics to characterize microbial diversity in soil. However, challenges persist in the study of microbial diversity, including the recalcitrance of the majority of microorganisms to laboratory cultivation and limited sequence assembly from highly complex samples. The uncultivated majority thus remains a reservoir of untapped genetic diversity. To address some of the challenges associated with bulk metagenomics as well as low throughput of single-cell genomics, we applied flow cytometry-enabled mini-metagenomics to capture expanded microbial diversity from forest soil and compare it to soil bulk metagenomics. Our resulting data from this pooled-cell sorting approach combined with bulk metagenomics revealed increased phylogenetic diversity through novel soil taxa and rare biosphere members. In-depth analysis of genomes within the highly represented Bacteroidetes phylum provided insights into conserved and clade-specific patterns of carbon metabolism.
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Samba-Louaka A, Delafont V, Rodier MH, Cateau E, Héchard Y. Free-living amoebae and squatters in the wild: ecological and molecular features. FEMS Microbiol Rev 2019; 43:415-434. [DOI: 10.1093/femsre/fuz011] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/30/2019] [Indexed: 02/06/2023] Open
Abstract
ABSTRACT
Free-living amoebae are protists frequently found in water and soils. They feed on other microorganisms, mainly bacteria, and digest them through phagocytosis. It is accepted that these amoebae play an important role in the microbial ecology of these environments. There is a renewed interest for the free-living amoebae since the discovery of pathogenic bacteria that can resist phagocytosis and of giant viruses, underlying that amoebae might play a role in the evolution of other microorganisms, including several human pathogens. Recent advances, using molecular methods, allow to bring together new information about free-living amoebae. This review aims to provide a comprehensive overview of the newly gathered insights into (1) the free-living amoeba diversity, assessed with molecular tools, (2) the gene functions described to decipher the biology of the amoebae and (3) their interactions with other microorganisms in the environment.
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Affiliation(s)
- Ascel Samba-Louaka
- Laboratoire Ecologie et Biologie des Interactions (EBI), Equipe Microbiologie de l'Eau, Université de Poitiers, UMR CNRS 7267, 1 rue Georges Bonnet, TSA51106, 86073 POITIERS Cedex 9, France
| | - Vincent Delafont
- Laboratoire Ecologie et Biologie des Interactions (EBI), Equipe Microbiologie de l'Eau, Université de Poitiers, UMR CNRS 7267, 1 rue Georges Bonnet, TSA51106, 86073 POITIERS Cedex 9, France
| | - Marie-Hélène Rodier
- Laboratoire Ecologie et Biologie des Interactions (EBI), Equipe Microbiologie de l'Eau, Université de Poitiers, UMR CNRS 7267, 1 rue Georges Bonnet, TSA51106, 86073 POITIERS Cedex 9, France
- Laboratoire de Parasitologie et Mycologie, CHU La Milétrie, 2 rue de la Milétrie, 86021 Poitiers Cedex, France
| | - Estelle Cateau
- Laboratoire Ecologie et Biologie des Interactions (EBI), Equipe Microbiologie de l'Eau, Université de Poitiers, UMR CNRS 7267, 1 rue Georges Bonnet, TSA51106, 86073 POITIERS Cedex 9, France
- Laboratoire de Parasitologie et Mycologie, CHU La Milétrie, 2 rue de la Milétrie, 86021 Poitiers Cedex, France
| | - Yann Héchard
- Laboratoire Ecologie et Biologie des Interactions (EBI), Equipe Microbiologie de l'Eau, Université de Poitiers, UMR CNRS 7267, 1 rue Georges Bonnet, TSA51106, 86073 POITIERS Cedex 9, France
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Cobaviruses - a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems. ISME JOURNAL 2019; 13:1404-1421. [PMID: 30718806 PMCID: PMC6775973 DOI: 10.1038/s41396-019-0362-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 01/15/2019] [Accepted: 01/22/2019] [Indexed: 11/13/2022]
Abstract
Bacteriophages are widely considered to influence bacterial communities, however most phages are still unknown or not studied well enough to understand their ecological roles. We have isolated two phages infecting Lentibacter sp. SH36, affiliated with the marine Roseobacter group, and retrieved similar phage genomes from publicly available metagenomics databases. Phylogenetic analysis placed the new phages within the Cobavirus group, in the here newly proposed genus Siovirus and subfamily Riovirinae of the Podoviridae. Gene composition and presence of direct terminal repeats in cultivated cobaviruses point toward a genome replication and packaging strategy similar to the T7 phage. Investigation of the genomes suggests that viral lysis of the cell proceeds via the canonical holin-endolysin pathway. Cobaviral hosts include members of the genera Lentibacter, Sulfitobacter and Celeribacter of the Roseobacter group within the family Rhodobacteraceae (Alphaproteobacteria). Screening more than 5,000 marine metagenomes, we found cobaviruses worldwide from temperate to tropical waters, in the euphotic zone, mainly in bays and estuaries, but also in the open ocean. The presence of cobaviruses in protist metagenomes as well as the phylogenetic neighborhood of cobaviruses in glutaredoxin and ribonucleotide reductase trees suggest that cobaviruses could infect bacteria associated with phototrophic or grazing protists. With this study, we expand the understanding of the phylogeny, classification, genomic organization, biogeography and ecology of this phage group infecting marine Rhodobacteraceae.
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Woyke T, Schulz F. Entities inside one another - a matryoshka doll in biology? ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:26-28. [PMID: 30588764 PMCID: PMC7379638 DOI: 10.1111/1758-2229.12716] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- Tanja Woyke
- U.S. Department of Energy Joint Genome InstituteWalnut Creek, CA94598USA
| | - Frederik Schulz
- U.S. Department of Energy Joint Genome InstituteWalnut Creek, CA94598USA
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Identification and characterization of a large family of superbinding bacterial SH2 domains. Nat Commun 2018; 9:4549. [PMID: 30382091 PMCID: PMC6208348 DOI: 10.1038/s41467-018-06943-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 10/02/2018] [Indexed: 11/27/2022] Open
Abstract
Src homology 2 (SH2) domains play a critical role in signal transduction in mammalian cells by binding to phosphorylated Tyr (pTyr). Apart from a few isolated cases in viruses, no functional SH2 domain has been identified to date in prokaryotes. Here we identify 93 SH2 domains from Legionella that are distinct in sequence and specificity from mammalian SH2 domains. The bacterial SH2 domains are not only capable of binding proteins or peptides in a Tyr phosphorylation-dependent manner, some bind pTyr itself with micromolar affinities, a property not observed for mammalian SH2 domains. The Legionella SH2 domains feature the SH2 fold and a pTyr-binding pocket, but lack a specificity pocket found in a typical mammalian SH2 domain for recognition of sequences flanking the pTyr residue. Our work expands the boundary of phosphotyrosine signalling to prokaryotes, suggesting that some bacterial effector proteins have acquired pTyr-superbinding characteristics to facilitate bacterium-host interactions. SH2 domains bind to tyrosine-phosphorylated proteins and play crucial roles in signal transduction in mammalian cells. Here, Kaneko et al. identify a large family of SH2 domains in the bacterial pathogen Legionella that bind to mammalian phosphorylated proteins, in some cases with very high affinity.
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17
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Duron O, Doublet P, Vavre F, Bouchon D. The Importance of Revisiting Legionellales Diversity. Trends Parasitol 2018; 34:1027-1037. [PMID: 30322750 DOI: 10.1016/j.pt.2018.09.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 09/19/2018] [Accepted: 09/24/2018] [Indexed: 12/15/2022]
Abstract
Bacteria of the order Legionellales, such as Legionella pneumophila, the agent of Legionnaires' disease, and Coxiella burnetii, the agent of Q fever, are widely recognized as human pathogens. While our view of the Legionellales is often limited to clinical isolates, ecological surveys are continually uncovering new members of the Legionellales that do not fall into the recognized pathogenic species. Here we emphasize that most of these Legionellales are nonpathogenic forms that have evolved symbiotic lifestyles with nonvertebrate hosts. The diversity of nonpathogenic forms remains, however, largely underexplored. We conjecture that its characterization, once contrasted with the data on pathogenic species, will reveal novel highlights on the mechanisms underlying lifestyle transitions of intracellular bacteria, including the emergence of pathogenesis and mutualism, transmission routes, and host specificity.
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Affiliation(s)
- Olivier Duron
- Laboratoire Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), Centre National de la Recherche Scientifique (CNRS) - Institut pour la Recherche et le Développement (IRD) - Université de Montpellier (UM), 911 Avenue Agropolis, F-34394 Montpellier, France.
| | - Patricia Doublet
- CIRI, Centre International de Recherche en Infectiologie, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Université Lyon, F-69100 Villeurbanne, France
| | - Fabrice Vavre
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, 43 Boulevard du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Didier Bouchon
- Université de Poitiers, Laboratoire Ecologie et Biologie des Interactions - UMR CNRS 7267, F-86073 Poitiers, France
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18
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Diversity of free-living amoebae in soils and their associated human opportunistic bacteria. Parasitol Res 2017; 116:3151-3162. [DOI: 10.1007/s00436-017-5632-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/21/2017] [Indexed: 02/06/2023]
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19
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Maciver SK, De Obeso Fernandez Del Valle A, Koutsogiannis Z. Vannella pentlandii n. sp., (Amoebozoa, Discosea, Vannellida) a small, cyst-forming soil amoeba. Exp Parasitol 2017; 183:109-116. [PMID: 28778744 DOI: 10.1016/j.exppara.2017.07.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 07/04/2017] [Accepted: 07/30/2017] [Indexed: 11/28/2022]
Abstract
We describe a new species of cyst-producing soil amoeba Vannella pentlandii from course pasture in the Pentland Hills, Scotland. Analysis of the 18S rDNA gene reveals that it belongs to the sub-group within the genus, presently composed of V. placida, V. epipetala and V. fimicola (the PEF group). This group share features such as longitudinal folds/ridges on the lamella (the anterior hyaline region of the trophozoite), stubby floating forms and cyst production. While each PEF species contain cyst producing strains, not all strains within these species do so. V. fimicola produces cysts on stalks leading to its former classification as a slime mould, however no such stalks were evident in the V. pentlandii, instead groups of cysts become piled on top of each other forming clumps. The encysting amoebae crawl toward each other, pushing some off the surface to form these mounds. The V. pentlandii trophozoites are of typical size for the genus but the cysts at 6.9 μm in diameter, are the smallest so far described in genus Vannella. Other cyst producing species are found in various branches within the Vannella phylogenetic tree, probably meaning that this ability was ancestral but lost in many branches (particularly in marine species), and perhaps re-gained in others.
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Affiliation(s)
- Sutherland K Maciver
- Centre for Integrative Physiology, Biomedical Sciences, Edinburgh Medical School, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh, EH8 9XD, Scotland, UK.
| | - Alvaro De Obeso Fernandez Del Valle
- Centre for Integrative Physiology, Biomedical Sciences, Edinburgh Medical School, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh, EH8 9XD, Scotland, UK
| | - Zisis Koutsogiannis
- Centre for Integrative Physiology, Biomedical Sciences, Edinburgh Medical School, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh, EH8 9XD, Scotland, UK
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20
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Viana F, Buchrieser C. Environmental treasures: co-isolation of the first marine Chlamydiae and its protozoan host. Environ Microbiol 2016; 18:2295-7. [PMID: 26996407 DOI: 10.1111/1462-2920.13264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 02/12/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Flávia Viana
- Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris, France.,CNRS UMR 3525, 75724, Paris, France
| | - Carmen Buchrieser
- Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris, France.,CNRS UMR 3525, 75724, Paris, France
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Pizzetti I, Schulz F, Tyml T, Fuchs BM, Amann R, Horn M, Fazi S. Chlamydial seasonal dynamics and isolation of 'Candidatus Neptunochlamydia vexilliferae' from a Tyrrhenian coastal lake. Environ Microbiol 2015; 18:2405-17. [PMID: 26530333 DOI: 10.1111/1462-2920.13111] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/27/2015] [Accepted: 10/28/2015] [Indexed: 12/01/2022]
Abstract
The Chlamydiae are a phylum of obligate intracellular bacteria comprising important human and animal pathogens, yet their occurrence in the environment, their phylogenetic diversity and their host range has been largely underestimated. We investigated the seasonality of environmental chlamydiae in a Tyrrhenian coastal lake. By catalysed reporter deposition fluorescence in situ hybridization, we quantified the small planktonic cells and detected a peak in the abundance of environmental chlamydiae in early autumn with up to 5.9 × 10(4) cells ml(-1) . Super-resolution microscopy improved the visualization and quantification of these bacteria and enabled the detection of pleomorphic chlamydial cells in their protist host directly in an environmental sample. To isolate environmental chlamydiae together with their host, we applied a high-throughput limited dilution approach and successfully recovered a Vexillifera sp., strain harbouring chlamydiae (93% 16S rRNA sequence identity to Simkania negevensis), tentatively named 'Candidatus Neptunochlamydia vexilliferae'. Transmission electron microscopy in combination with fluorescence in situ hybridization was used to prove the intracellular location of these bacteria representing the first strain of marine chlamydiae stably maintained alongside with their host in a laboratory culture. Taken together, this study contributes to a better understanding of the distribution and diversity of environmental chlamydiae in previously neglected marine environments.
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Affiliation(s)
- Ilaria Pizzetti
- Water Research Institute, IRSA-CNR, via Salaria km 29,300, 00015 Monterotondo, Roma, Italy
| | - Frederik Schulz
- University of Vienna, Department of Microbiology and Ecosystem Science, Althanstrasse 14, A-1090, Vienna, Austria
| | - Tomáš Tyml
- University of South Bohemia, Faculty of Science, Branišovská 31, 370 05, České Budějovice, Czech Republic.,Masaryk University, Department of Botany and Zoology, Faculty of Science, Kotlářská 2, 61137, Brno, Czech Republic
| | - Bernhard M Fuchs
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Matthias Horn
- University of Vienna, Department of Microbiology and Ecosystem Science, Althanstrasse 14, A-1090, Vienna, Austria
| | - Stefano Fazi
- Water Research Institute, IRSA-CNR, via Salaria km 29,300, 00015 Monterotondo, Roma, Italy
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