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Masawa J, Winters G, Kaminer M, Szitenberg A, Gruntman M, Ashckenazi-Polivoda S. A matter of choice: Understanding the interactions between epiphytic foraminifera and their seagrass host Halophila stipulacea. Mar Environ Res 2024; 196:106437. [PMID: 38479296 DOI: 10.1016/j.marenvres.2024.106437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 01/28/2024] [Accepted: 03/05/2024] [Indexed: 03/23/2024]
Abstract
In sub/tropical waters, benthic foraminifera are among the most abundant epiphytic organisms inhabiting seagrass meadows. This study explored the nature of the association between foraminifera and the tropical seagrass species H. stipulacea, aiming to determine whether these interactions are facilitative or random. For this, we performed a "choice" experiment, where foraminifera could colonize H. stipulacea plants or plastic "seagrasses" plants. At the end of the experiment, a microbiome analysis was performed to identify possible variances in the microbial community and diversity of the substrates. Results show that foraminifera prefer to colonize H. stipulacea, which had a higher abundance and diversity of foraminifera than plastic seagrass plants, which increased over time and with shoot age. Moreover, H. stipulacea leaves have higher epiphytic microbial community abundance and diversity. These results demonstrate that seagrass meadows are important hosts of the foraminifera community and suggest the potential facilitative effect of H. stipulacea on epiphytic foraminifera, which might be attributed to a greater diversity of the microbial community inhabiting H. stipulacea.
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Affiliation(s)
- Jenipher Masawa
- Dead Sea and Arava Science Center, Masada National Park, Mount Masada, 869100, Israel; School of Plant Sciences and Food Security, Porter School of the Environment and Earth Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Gidon Winters
- Dead Sea and Arava Science Center, Masada National Park, Mount Masada, 869100, Israel; Ben-Gurion University of the Negev, Eilat Campus, Eilat, 881000, Israel.
| | - Moran Kaminer
- Dead Sea and Arava Science Center, Masada National Park, Mount Masada, 869100, Israel
| | - Amir Szitenberg
- Dead Sea and Arava Science Center, Masada National Park, Mount Masada, 869100, Israel
| | - Michal Gruntman
- School of Plant Sciences and Food Security, Porter School of the Environment and Earth Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Sarit Ashckenazi-Polivoda
- Dead Sea and Arava Science Center, Masada National Park, Mount Masada, 869100, Israel; Ben-Gurion University of the Negev, Eilat Campus, Eilat, 881000, Israel.
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2
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Szitenberg A, Beca-Carretero P, Azcárate-García T, Yergaliyev T, Alexander-Shani R, Winters G. Teasing apart the host-related, nutrient-related and temperature-related effects shaping the phenology and microbiome of the tropical seagrass Halophila stipulacea. Environ Microbiome 2022; 17:18. [PMID: 35428367 PMCID: PMC9013022 DOI: 10.1186/s40793-022-00412-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 03/24/2022] [Indexed: 06/02/2023]
Abstract
BACKGROUND Halophila stipulacea seagrass meadows are an ecologically important and threatened component of the ecosystem in the Gulf of Aqaba. Recent studies have demonstrated correlated geographic patterns for leaf epiphytic community composition and leaf morphology, also coinciding with different levels of water turbidity and nutrient concentrations. Based on these observations, workers have suggested an environmental microbial fingerprint, which may reflect various environmental stress factors seagrasses have experienced, and may add a holobiont level of plasticity to seagrasses, assisting their acclimation to changing environments and through range expansion. However, it is difficult to tease apart environmental effects from host-diversity dependent effects, which have covaried in field studies, although this is required in order to establish that differences in microbial community compositions among sites are driven by environmental conditions rather than by features governed by the host. RESULTS In this study we carried out a mesocosm experiment, in which we studied the effects of warming and nutrient stress on the composition of epiphytic bacterial communities and on some phenological traits. We studied H. stipulacea collected from two different meadows in the Gulf of Aqaba, representing differences in the host and the environment alike. We found that the source site from which seagrasses were collected was the major factor governing seagrass phenology, although heat increased shoot mortality and nutrient loading delayed new shoot emergence. Bacterial diversity, however, mostly depended on the environmental conditions. The most prominent pattern was the increase in Rhodobacteraceae under nutrient stress without heat stress, along with an increase in Microtrichaceae. Together, the two taxa have the potential to maintain nitrate reduction followed by an anammox process, which can together buffer the increase in nutrient concentrations across the leaf surface. CONCLUSIONS Our results thus corroborate the existence of environmental microbial fingerprints, which are independent from the host diversity, and support the notion of a holobiont level plasticity, both important to understand and monitor H. stipulacea ecology under the changing climate.
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Affiliation(s)
- Amir Szitenberg
- Dead Sea and Arava Science Center, Dead Sea Branch, 8693500, Masada, Israel.
- Ben-Gurion University of the Negev, 8858537, Eilat, Israel.
| | - Pedro Beca-Carretero
- Department of Theoretical Ecology and Modelling, Leibniz Centre for Tropical Marine Research, Fahrenheitstrasse 6, 28359, Bremen, Germany
- Department of Oceanography, Instituto de Investigacións Mariñas (IIM-CSIC), Vigo, Spain
- Departamento de Biología, Área de Ecología, Facultad de Ciencias del Mar Y Ambientales, Universidad de Cádiz, 11510, Puerto Real, Cádiz, Spain
| | - Tomás Azcárate-García
- Department of Theoretical Ecology and Modelling, Leibniz Centre for Tropical Marine Research, Fahrenheitstrasse 6, 28359, Bremen, Germany
- Departamento de Biología, Área de Ecología, Facultad de Ciencias del Mar Y Ambientales, Universidad de Cádiz, 11510, Puerto Real, Cádiz, Spain
- Dead Sea and Arava Science Center, Central Arava Branch, 8682500, Sapir, Israel
| | - Timur Yergaliyev
- Dead Sea and Arava Science Center, Dead Sea Branch, 8693500, Masada, Israel
- Hohenheim Center for Livestock Microbiome Research (HoLMiR), Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | | | - Gidon Winters
- Ben-Gurion University of the Negev, 8858537, Eilat, Israel
- Dead Sea and Arava Science Center, Central Arava Branch, 8682500, Sapir, Israel
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3
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Brandwein M, Fuks G, Israel A, Sabbah F, Hodak E, Szitenberg A, Harari M, Steinberg D, Bentwich Z, Shental N, Meshner S. Skin Microbiome Compositional Changes in Atopic Dermatitis Accompany Dead Sea Climatotherapy. Photochem Photobiol 2020; 96:450. [PMID: 32249480 DOI: 10.1111/php.13218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michael Brandwein
- Biofilm Research Laboratory, Faculty of Dental Medicine, Institute of Dental Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.,Cutaneous Microbiology Laboratory, The Skin Research Institute, The Dead Sea and Arava Science Center, Masada, Israel
| | - Garold Fuks
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Avigail Israel
- Cutaneous Microbiology Laboratory, The Skin Research Institute, The Dead Sea and Arava Science Center, Masada, Israel
| | - Fareed Sabbah
- Department of Dermatology, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel
| | - Emmilia Hodak
- Department of Dermatology, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel
| | - Amir Szitenberg
- Cutaneous Microbiology Laboratory, The Skin Research Institute, The Dead Sea and Arava Science Center, Masada, Israel
| | - Marco Harari
- Cutaneous Microbiology Laboratory, The Skin Research Institute, The Dead Sea and Arava Science Center, Masada, Israel
| | - Droron Steinberg
- Biofilm Research Laboratory, Faculty of Dental Medicine, Institute of Dental Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Zvi Bentwich
- Cutaneous Microbiology Laboratory, The Skin Research Institute, The Dead Sea and Arava Science Center, Masada, Israel
| | - Noam Shental
- Department of Mathematics and Computer Science, The Open University of Israel, Raanana, Israel
| | - Shiri Meshner
- Cutaneous Microbiology Laboratory, The Skin Research Institute, The Dead Sea and Arava Science Center, Masada, Israel
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4
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Krotman Y, Yergaliyev TM, Alexander Shani R, Avrahami Y, Szitenberg A. Dissecting the factors shaping fish skin microbiomes in a heterogeneous inland water system. Microbiome 2020; 8:9. [PMID: 32005134 PMCID: PMC6995075 DOI: 10.1186/s40168-020-0784-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 01/05/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND Fish skin microbiomes are rarely studied in inland water systems, in spite of their importance for fish health and ecology. This is mainly because fish species distribution often covaries with other biotic and abiotic factors, complicating the study design. We tackled this issue in the northern part of the Jordan River system, in which a few fish species geographically overlap, across steep gradients of water temperature and salinity. RESULTS Using 16S rRNA metabarcoding, we studied the water properties that shape the skin bacterial communities, and their interaction with fish taxonomy. To better characterise the indigenous skin community, we excluded bacteria that were equally abundant in the skin samples and in the water samples, from our analysis of the skin samples. With this in mind, we found alpha diversity of the skin communities to be stable across sites, but higher in benthic loaches, compared to other fish. Beta diversity was found to be different among sites and to weakly covary with the dissolved oxygen, when treated skin communities were considered. In contrast, water temperature and conductivity were strong factors explaining beta diversity in the untreated skin communities. Beta diversity differences between co-occurring fish species emerged only for the treated skin communities. Metagenomics predictions highlighted the microbiome functional implications of excluding the water community contamination from the fish skin communities. Finally, we found that human-induced eutrophication promotes dysbiosis of the fish skin community, with signatures relating to fish health. CONCLUSIONS Consideration of the background water microbiome when studying fish skin microbiomes, across varying fish species and water properties, exposes patterns otherwise undetected and highlight among-fish-species differences. We suggest that sporadic nutrient pollution events, otherwise undetected, drive fish skin communities to dysbiosis. This finding is in line with a recent study, showing that biofilms capture sporadic pollution events, undetectable by interspersed water monitoring. Video abstract.
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Affiliation(s)
| | - Timur M Yergaliyev
- Dead Sea and Arava Science Center, Dead Sea Branch, 8693500, Masada, Israel
| | | | - Yosef Avrahami
- Dead Sea and Arava Science Center, Dead Sea Branch, 8693500, Masada, Israel
| | - Amir Szitenberg
- Dead Sea and Arava Science Center, Dead Sea Branch, 8693500, Masada, Israel.
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5
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Aouizerat T, Maeir AM, Paz Y, Gadot Y, Szitenberg A, Alkalay-Oren S, Coppenhagen-Glazer S, Klutstein M, Hazan R. Isolation and Characterization of Live Yeast Cells from Ancient Clay Vessels. Bio Protoc 2020; 10:e3473. [PMID: 33654708 DOI: 10.21769/bioprotoc.3473] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 11/23/2019] [Accepted: 11/24/2019] [Indexed: 11/02/2022] Open
Abstract
Ancient fermented food has been studied mainly based on residue analysis and recipes and reconstruction attempts were performed using modern domesticated yeast. Furthermore, microorganisms which participated in fermentation were studied using ancient-DNA techniques. In a recent paper, we presented a novel approach based on the hypothesis that enriched yeast populations in fermented beverages could have become the dominant species in storage vessels and their descendants could be isolated and studied today. Here we present a pipeline for isolation of yeast from clay vessels uncovered in archeological sites and transferred to the microbiology lab where they can be isolated and characterized. This method opens new avenues for experimental archeology and enables attempts to recreate ancient food and beverages using the original microorganisms.
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Affiliation(s)
- Tzemach Aouizerat
- Institute of Dental Sciences, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Aren M Maeir
- Tell es-Safi/Gath Archaeological Project, The Martin (Szusz) Department of Land of Israel and Archaeology, Bar-Ilan University, Ramat-Gan, Israel
| | - Yitzhak Paz
- Israel Antiquities Authority, Jerusalem, Israel
| | | | - Amir Szitenberg
- Microbial Metagenomics Division, Dead Sea and Arava Science Center, Masada, Israel
| | - Sivan Alkalay-Oren
- Institute of Dental Sciences, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shunit Coppenhagen-Glazer
- Institute of Dental Sciences, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Michael Klutstein
- Institute of Dental Sciences, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ronen Hazan
- Institute of Dental Sciences, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
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6
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Qing X, Bik H, Yergaliyev TM, Gu J, Fonderie P, Brown-Miyara S, Szitenberg A, Bert W. Widespread prevalence but contrasting patterns of intragenomic rRNA polymorphisms in nematodes: Implications for phylogeny, species delimitation and life history inference. Mol Ecol Resour 2019; 20:318-332. [PMID: 31721426 DOI: 10.1111/1755-0998.13118] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 10/26/2019] [Accepted: 11/07/2019] [Indexed: 01/15/2023]
Abstract
Ribosomal RNA genes have long been a favoured locus in phylogenetic and metabarcoding studies. Within a genome, rRNA loci are organized as tandem repeated arrays and the copies are homogenized through the process of concerted evolution. However, some level of rRNA variation (intragenomic polymorphism) is known to persist and be maintained in the genomes of many species. In nematode worms, the extent of rRNA polymorphism (RP) across species and the evolutionary and life history factors that contribute to the maintenance of intragenomic RP is largely unknown. Here, we present an extensive analysis across 30 terrestrial nematode species representing a range of free-living and parasitic taxa isolated worldwide. Our results indicate that RP is common and widespread, ribosome function appears to be maintained despite mutational changes, and intragenomic variants are stable in the genome and neutrally evolving. However, levels of variation were varied widely across rRNA locus and species, with some taxa observed to lack RP entirely. Higher levels of RP were significantly correlated with shorter generation time and high reproductive rates, and population-level factors may play a role in the geographic and phylogenetic structuring of rRNA variants observed in genera such as Rotylenchulus and Pratylenchus. Although RP did not dramatically impact the clustering and recovery of taxa in mock metabarcoding analyses, the present study has significant implications for global biodiversity estimates of nematode species derived from environmental rRNA amplicon studies, as well as our understanding of the evolutionary and ecological factors shaping genetic diversity across the nematode Tree of Life.
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Affiliation(s)
- Xue Qing
- Nematology Research Unit, Department of Biology, Ghent University, Ghent, Belgium.,Department of Entomology, Nematology and Chemistry Units, Agricultural Research Organization (ARO), Volcani Center, Rishon LeZion, Israel
| | - Holly Bik
- Department of Nematology, University of California-Riverside, Riverside, CA, USA
| | - Timur M Yergaliyev
- Dead Sea and Arava Science Center, Dead Sea Branch, Masada National Park, Tamar Regional Council, Tel Aviv, Israel.,A. Baitursynov Kostanay State University, Kostanay, Kazakhstan
| | - Jianfeng Gu
- Technical Center of Ningbo Customs (Ningbo Inspection and Quarantine Science Technology Academy), Ningbo, China
| | - Pamela Fonderie
- Nematology Research Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Sigal Brown-Miyara
- Department of Entomology, Nematology and Chemistry Units, Agricultural Research Organization (ARO), Volcani Center, Rishon LeZion, Israel
| | - Amir Szitenberg
- Dead Sea and Arava Science Center, Dead Sea Branch, Masada National Park, Tamar Regional Council, Tel Aviv, Israel
| | - Wim Bert
- Nematology Research Unit, Department of Biology, Ghent University, Ghent, Belgium
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7
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Aouizerat T, Gelman D, Szitenberg A, Gutman I, Glazer S, Reich E, Schoemann M, Kaplan R, Saragovi A, Hazan R, Klutstein M. Eukaryotic Adaptation to Years-Long Starvation Resembles that of Bacteria. iScience 2019; 19:545-558. [PMID: 31470363 PMCID: PMC6722386 DOI: 10.1016/j.isci.2019.08.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 02/12/2019] [Accepted: 08/01/2019] [Indexed: 12/18/2022] Open
Abstract
The Growth Advantage in Stationary Phase (GASP) phenomenon, described in bacteria, reflects the genetic adaptation of bacteria to stress, including starvation, for a long time. Unlike in stationary phase where no cell division occurs, GASP harbors active cell division, concurrent with genetic adaptation. Here we show that GASP occurs also in eukaryotes. Two strains of Saccharomyces cerevisiae (Sc404 and Sc424) have been isolated from 2-year-old sealed bottles of beer. These strains presented advantage in survival and growth over the parent during stress. The differences between the strains are irreversible and therefore genetic in origin rather than epigenetic. Direct competition assays show that Sc404 and Sc424 outcompete the parent in direct competition. DNA sequencing shows changes of the genome: the TOR complexes are mutated, and DNA repair gene mutations confer a mutator phenotype. The differences between the strains are reflected in a difference in taste between beers brewed from them. Yeast genetically adapts to long-term starvation in a similar way to bacteria Adaptation to long-term starvation in yeast includes multi-stress tolerance Adaptation to long-term starvation in yeast includes mutations in TORC Adaptation to long-term starvation in yeast includes a mutator phenotype
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Affiliation(s)
- Tzemach Aouizerat
- Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem 9112001, Israel
| | - Daniel Gelman
- Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem 9112001, Israel
| | - Amir Szitenberg
- Microbial and Metagenomics Division, Dead Sea and Arava Science Center, Masada 8698000, Israel
| | - Itay Gutman
- Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem 9112001, Israel
| | - Shunit Glazer
- Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem 9112001, Israel
| | - Eli Reich
- Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem 9112001, Israel
| | - Miriam Schoemann
- Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem 9112001, Israel
| | - Rachel Kaplan
- Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem 9112001, Israel
| | - Amijai Saragovi
- The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Ronen Hazan
- Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem 9112001, Israel.
| | - Michael Klutstein
- Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem 9112001, Israel.
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8
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Brandwein M, Fuks G, Israel A, Sabbah F, Hodak E, Szitenberg A, Harari M, Steinberg D, Bentwich Z, Shental N, Meshner S. Skin Microbiome Compositional Changes in Atopic Dermatitis Accompany Dead Sea Climatotherapy. Photochem Photobiol 2019; 95:1446-1453. [PMID: 31074874 DOI: 10.1111/php.13119] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/14/2019] [Accepted: 04/26/2019] [Indexed: 12/27/2022]
Abstract
Dead Sea climatotherapy (DSC) is a well-established therapeutic modality for the treatment of several diseases, including atopic dermatitis. Skin microbiome studies have shown that skin microbiome diversity is anticorrelated with both atopic dermatitis severity and concurrent Staphylococcus aureus overgrowth. This study aimed to determine whether DSC induces skin microbiome changes concurrent with clinical improvements in atopic dermatitis. We sampled 35 atopic dermatitis patients and ten healthy controls on both the antecubital and popliteal fossa. High-resolution microbial community profiling was attained by sequencing multiple regions of the 16S rRNA gene. Dysbiosis was observed in both lesional and nonlesional sites, which was partially attenuated following treatment. Severe AD skin underwent the most significant community shifts, and Staphylococcus epidermidis, Streptococcus mitis and Micrococcus luteus relative abundance were significantly affected by Dead Sea climatotherapy. Our study highlights the temporal shifts of the AD skin microbiome induced by Dead Sea climatotherapy and offers potential explanations for the success of climatotherapy on a variety of skin diseases, including AD.
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Affiliation(s)
- Michael Brandwein
- Biofilm Research Laboratory, Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.,Cutaneous Microbiology Laboratory, The Skin Research Institute, The Dead Sea and Arava Science Center, Masada, Israel
| | - Garold Fuks
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Avigail Israel
- Cutaneous Microbiology Laboratory, The Skin Research Institute, The Dead Sea and Arava Science Center, Masada, Israel
| | - Fareed Sabbah
- Department of Dermatology, Rabin Medical Center, Beilinson Hospital, Petach Tikva, Israel
| | - Emmilia Hodak
- Department of Dermatology, Rabin Medical Center, Beilinson Hospital, Petach Tikva, Israel
| | - Amir Szitenberg
- Cutaneous Microbiology Laboratory, The Skin Research Institute, The Dead Sea and Arava Science Center, Masada, Israel
| | - Marco Harari
- Cutaneous Microbiology Laboratory, The Skin Research Institute, The Dead Sea and Arava Science Center, Masada, Israel
| | - Droron Steinberg
- Biofilm Research Laboratory, Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Zvi Bentwich
- Cutaneous Microbiology Laboratory, The Skin Research Institute, The Dead Sea and Arava Science Center, Masada, Israel
| | - Noam Shental
- Department of Mathematics and Computer Science, The Open University of Israel, Raanana, Israel
| | - Shiri Meshner
- Cutaneous Microbiology Laboratory, The Skin Research Institute, The Dead Sea and Arava Science Center, Masada, Israel
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9
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Szitenberg A, Salazar-Jaramillo L, Blok VC, Laetsch DR, Joseph S, Williamson VM, Blaxter ML, Lunt DH. Comparative Genomics of Apomictic Root-Knot Nematodes: Hybridization, Ploidy, and Dynamic Genome Change. Genome Biol Evol 2018; 9:2844-2861. [PMID: 29036290 PMCID: PMC5737495 DOI: 10.1093/gbe/evx201] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2017] [Indexed: 12/22/2022] Open
Abstract
The root-knot nematodes (genus Meloidogyne) are important plant parasites causing substantial agricultural losses. The Meloidogyne incognita group (MIG) of species, most of which are obligatory apomicts (mitotic parthenogens), are extremely polyphagous and important problems for global agriculture. While understanding the genomic basis for their variable success on different crops could benefit future agriculture, analyses of their genomes are challenging due to complex evolutionary histories that may incorporate hybridization, ploidy changes, and chromosomal fragmentation. Here, we sequence 19 genomes, representing five species of key root-knot nematodes collected from different geographic origins. We show that a hybrid origin that predated speciation within the MIG has resulted in each species possessing two divergent genomic copies. Additionally, the apomictic MIG species are hypotriploids, with a proportion of one genome present in a second copy. The hypotriploid proportion varies among species. The evolutionary history of the MIG genomes is revealed to be very dynamic, with noncrossover recombination both homogenizing the genomic copies, and acting as a mechanism for generating divergence between species. Interestingly, the automictic MIG species M. floridensis differs from the apomict species in that it has become homozygous throughout much of its genome.
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Affiliation(s)
- Amir Szitenberg
- Evolutionary Biology Group, School of Environmental Sciences, University of Hull, United Kingdom.,Microbial Metagenomics Division, The Dead Sea and Arava Science Center, Mt. Masada, Israel
| | - Laura Salazar-Jaramillo
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, United Kingdom
| | - Vivian C Blok
- The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Dominik R Laetsch
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, United Kingdom.,The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Soumi Joseph
- Department of Entomology and Nematology, University of Florida
| | | | - Mark L Blaxter
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, United Kingdom
| | - David H Lunt
- Evolutionary Biology Group, School of Environmental Sciences, University of Hull, United Kingdom
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10
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Szitenberg A, Cha S, Opperman CH, Bird DM, Blaxter ML, Lunt DH. Genetic Drift, Not Life History or RNAi, Determine Long-Term Evolution of Transposable Elements. Genome Biol Evol 2016; 8:2964-2978. [PMID: 27566762 PMCID: PMC5635653 DOI: 10.1093/gbe/evw208] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2016] [Indexed: 12/11/2022] Open
Abstract
Transposable elements (TEs) are a major source of genome variation across the branches of life. Although TEs may play an adaptive role in their host's genome, they are more often deleterious, and purifying selection is an important factor controlling their genomic loads. In contrast, life history, mating system, GC content, and RNAi pathways have been suggested to account for the disparity of TE loads in different species. Previous studies of fungal, plant, and animal genomes have reported conflicting results regarding the direction in which these genomic features drive TE evolution. Many of these studies have had limited power, however, because they studied taxonomically narrow systems, comparing only a limited number of phylogenetically independent contrasts, and did not address long-term effects on TE evolution. Here, we test the long-term determinants of TE evolution by comparing 42 nematode genomes spanning over 500 million years of diversification. This analysis includes numerous transitions between life history states, and RNAi pathways, and evaluates if these forces are sufficiently persistent to affect the long-term evolution of TE loads in eukaryotic genomes. Although we demonstrate statistical power to detect selection, we find no evidence that variation in these factors influence genomic TE loads across extended periods of time. In contrast, the effects of genetic drift appear to persist and control TE variation among species. We suggest that variation in the tested factors are largely inconsequential to the large differences in TE content observed between genomes, and only by these large-scale comparisons can we distinguish long-term and persistent effects from transient or random changes.
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Affiliation(s)
- Amir Szitenberg
- Evolutionary Biology Group, School of Environmental Sciences, University of Hull, England, United Kingdom The Dead Sea and Arava Science Center, Israel
| | - Soyeon Cha
- Department of Plant Pathology, North Carolina State University
| | | | - David M Bird
- Department of Plant Pathology, North Carolina State University
| | - Mark L Blaxter
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Scotland
| | - David H Lunt
- Evolutionary Biology Group, School of Environmental Sciences, University of Hull, England, United Kingdom
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Eves-van den Akker S, Laetsch DR, Thorpe P, Lilley CJ, Danchin EGJ, Da Rocha M, Rancurel C, Holroyd NE, Cotton JA, Szitenberg A, Grenier E, Montarry J, Mimee B, Duceppe MO, Boyes I, Marvin JMC, Jones LM, Yusup HB, Lafond-Lapalme J, Esquibet M, Sabeh M, Rott M, Overmars H, Finkers-Tomczak A, Smant G, Koutsovoulos G, Blok V, Mantelin S, Cock PJA, Phillips W, Henrissat B, Urwin PE, Blaxter M, Jones JT. The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. Genome Biol 2016; 17:124. [PMID: 27286965 PMCID: PMC4901422 DOI: 10.1186/s13059-016-0985-1] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 05/12/2016] [Indexed: 11/23/2022] Open
Abstract
Background The yellow potato cyst nematode, Globodera rostochiensis, is a devastating plant pathogen of global economic importance. This biotrophic parasite secretes effectors from pharyngeal glands, some of which were acquired by horizontal gene transfer, to manipulate host processes and promote parasitism. G. rostochiensis is classified into pathotypes with different plant resistance-breaking phenotypes. Results We generate a high quality genome assembly for G. rostochiensis pathotype Ro1, identify putative effectors and horizontal gene transfer events, map gene expression through the life cycle focusing on key parasitic transitions and sequence the genomes of eight populations including four additional pathotypes to identify variation. Horizontal gene transfer contributes 3.5 % of the predicted genes, of which approximately 8.5 % are deployed as effectors. Over one-third of all effector genes are clustered in 21 putative ‘effector islands’ in the genome. We identify a dorsal gland promoter element motif (termed DOG Box) present upstream in representatives from 26 out of 28 dorsal gland effector families, and predict a putative effector superset associated with this motif. We validate gland cell expression in two novel genes by in situ hybridisation and catalogue dorsal gland promoter element-containing effectors from available cyst nematode genomes. Comparison of effector diversity between pathotypes highlights correlation with plant resistance-breaking. Conclusions These G. rostochiensis genome resources will facilitate major advances in understanding nematode plant-parasitism. Dorsal gland promoter element-containing effectors are at the front line of the evolutionary arms race between plant and parasite and the ability to predict gland cell expression a priori promises rapid advances in understanding their roles and mechanisms of action. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-0985-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Dominik R Laetsch
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Peter Thorpe
- Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Dundee, DD2 5DA, UK
| | | | - Etienne G J Danchin
- INRA, University Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, 06900, Sophia Antipolis, France
| | - Martine Da Rocha
- INRA, University Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, 06900, Sophia Antipolis, France
| | - Corinne Rancurel
- INRA, University Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, 06900, Sophia Antipolis, France
| | - Nancy E Holroyd
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
| | - James A Cotton
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
| | - Amir Szitenberg
- School of Biological, Biomedical and Environmental Sciences, University of Hull, Hull, HU6 7RX, UK
| | - Eric Grenier
- INRA, UMR1349 IGEPP (Institute for Genetics, Environment and Plant Protection), 35653, Le Rheu, France
| | - Josselin Montarry
- INRA, UMR1349 IGEPP (Institute for Genetics, Environment and Plant Protection), 35653, Le Rheu, France
| | - Benjamin Mimee
- Agriculture and Agri-food Canada, Horticulture Research and Development Centre, 430 Bboul. Gouin, St-Jean-sur-Richelieu, Quebec, J3B 3E6, Canada
| | - Marc-Olivier Duceppe
- Agriculture and Agri-food Canada, Horticulture Research and Development Centre, 430 Bboul. Gouin, St-Jean-sur-Richelieu, Quebec, J3B 3E6, Canada
| | - Ian Boyes
- Sidney Laboratory, Canadian Food Inspection Agency (CFIA), 8801 East Saanich Rd, Sidney, BC, V8L 1H3, Canada
| | | | - Laura M Jones
- Centre for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Hazijah B Yusup
- Centre for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Joël Lafond-Lapalme
- Agriculture and Agri-food Canada, Horticulture Research and Development Centre, 430 Bboul. Gouin, St-Jean-sur-Richelieu, Quebec, J3B 3E6, Canada
| | - Magali Esquibet
- INRA, UMR1349 IGEPP (Institute for Genetics, Environment and Plant Protection), 35653, Le Rheu, France
| | - Michael Sabeh
- Agriculture and Agri-food Canada, Horticulture Research and Development Centre, 430 Bboul. Gouin, St-Jean-sur-Richelieu, Quebec, J3B 3E6, Canada
| | - Michael Rott
- Sidney Laboratory, Canadian Food Inspection Agency (CFIA), 8801 East Saanich Rd, Sidney, BC, V8L 1H3, Canada
| | - Hein Overmars
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
| | - Anna Finkers-Tomczak
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
| | - Geert Smant
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
| | | | - Vivian Blok
- Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Dundee, DD2 5DA, UK
| | - Sophie Mantelin
- Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Dundee, DD2 5DA, UK
| | - Peter J A Cock
- Information and Computational Sciences Group, James Hutton Institute, Dundee, UK
| | - Wendy Phillips
- USDA-ARS Horticultural Crops Research Laboratory, Corvallis, OR, USA
| | - Bernard Henrissat
- CNRS UMR 7257, INRA, USC 1408, Aix-Marseille University, AFMB, 13288, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Peter E Urwin
- Centre for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Mark Blaxter
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - John T Jones
- Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Dundee, DD2 5DA, UK.,School of Biology, University of St Andrews, North Haugh, St Andrews, KY16 9TZ, UK
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12
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Huchon D, Szitenberg A, Shefer S, Ilan M, Feldstein T. Mitochondrial group I and group II introns in the sponge orders Agelasida and Axinellida. BMC Evol Biol 2015; 15:278. [PMID: 26653218 PMCID: PMC4676843 DOI: 10.1186/s12862-015-0556-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 12/03/2015] [Indexed: 11/21/2022] Open
Abstract
Background Self-splicing introns are present in the mitochondria of members of most eukaryotic lineages. They are divided into Group I and Group II introns, according to their secondary structure and splicing mechanism. Being rare in animals, self-splicing introns were only described in a few sponges, cnidarians, placozoans and one annelid species. In sponges, three types of mitochondrial Group I introns were previously described in two demosponge families (Tetillidae, and Aplysinellidae) and in the homoscleromorph family Plakinidae. These three introns differ in their insertion site, secondary structure and in the sequence of the LAGLIDADG gene they encode. Notably, no group II introns have been previously described in sponges. Results We report here the presence of mitochondrial introns in the cytochrome oxidase subunit 1 (COI) gene of three additional sponge species from three different families: Agelas oroides (Agelasidae, Agelasida), Cymbaxinellapverrucosa (Hymerhabdiidae, Agelasida) and Axinella polypoides (Axinellidae, Axinellida). We show, for the first time, that sponges can also harbour Group II introns in their COI gene, whose presence in animals’ mitochondria has so far been described in only two phyla, Placozoa and Annelida. Surprisingly, two different Group II introns were discovered in the COI gene of C. verrucosa. Phylogenetic analysis indicates that the Group II introns present in C. verrucosa are related to red algae (Rhodophyta) introns. Conclusions The differences found among intron secondary structures and the phylogenetic inferences support the hypothesis that the introns originated from independent horizontal gene transfer events. Our results thus suggest that self-splicing introns are more diverse in the mitochondrial genome of sponges than previously anticipated. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0556-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dorothée Huchon
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel. .,The Steinhardt Museum of Natural History, Israel National Center for Biodiversity Studies, Tel Aviv University, Tel Aviv, 6997801, Israel.
| | - Amir Szitenberg
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel. .,Current address: School of Biological, Biomedical and Environmental Sciences, University of Hull, Hull, HU6 7RX, UK.
| | - Sigal Shefer
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel. .,The Steinhardt Museum of Natural History, Israel National Center for Biodiversity Studies, Tel Aviv University, Tel Aviv, 6997801, Israel.
| | - Micha Ilan
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel.
| | - Tamar Feldstein
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel. .,The Steinhardt Museum of Natural History, Israel National Center for Biodiversity Studies, Tel Aviv University, Tel Aviv, 6997801, Israel.
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13
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Diamant A, Rothman SBS, Goren M, Galil BS, Yokes MB, Szitenberg A, Huchon D. Biology of a new xenoma-forming gonadotropic microsporidium in the invasive blotchfin dragonet Callionymus filamentosus. Dis Aquat Organ 2014; 109:35-54. [PMID: 24781795 DOI: 10.3354/dao02718] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
A gonadotropic microsporidian parasite, Obruspora papernae gen. et sp. nov. (Microsporidia: Enterocytozoonidae), is described from Callionymus filamentosus (Teleostei: Callionymidae) in the Mediterranean Sea. The host, a Red Sea invasive species which entered the Mediterranean through the Suez Canal, was first collected in the Levant Basin in 1953, whereas its parasite went unobserved until 2008. Analysis of partial small subunit ribosomal gene sequences (SSU rDNA) placed the new species within the Nucleospora, Desmozoon, and Paranucleospora clade, and as it differs from each of them, it is assigned to a new genus. The development of the parasite is described, and the biological mechanisms underlying this parasite-host system are analyzed. Prevalence of infection approached 80% in female samples throughout most of the year. Males showed no signs of infection, but parasite rDNA was detected in male internal organs. The parasite-induced xenomas progressively occupied and eventually replaced much of the ovary, in some cases producing effective castration. Despite high levels of parasite infection, current trawl fishery statistics indicate that the abundance of Mediterranean populations of the host remains high. The parasite impact on the host population dynamics is unclear. Possible effects of the new microsporidian parasite on the reproductive effort of C. filamentosus and the potential role of another parasite, the ectoparasitic copepod Lernanthropus callionymicola, as an additional host in the life cycle of O. papernae, require further investigation.
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Affiliation(s)
- Arik Diamant
- National Center for Mariculture, Israel Oceanographic and Limnological Research, PO Box 1212, Eilat 88112, Israel
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14
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Szitenberg A, Becking LE, Vargas S, Fernandez JCC, Santodomingo N, Wörheide G, Ilan M, Kelly M, Huchon D. Phylogeny of Tetillidae (Porifera, Demospongiae, Spirophorida) based on three molecular markers. Mol Phylogenet Evol 2013; 67:509-19. [PMID: 23485919 DOI: 10.1016/j.ympev.2013.02.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 12/29/2012] [Accepted: 02/15/2013] [Indexed: 10/27/2022]
Abstract
Tetillidae are spherical to elliptical cosmopolitan demosponges. The family comprises eight genera: namely, Acanthotetilla Burton, 1959, Amphitethya Lendenfeld, 1907, CinachyraSollas, 1886, CinachyrellaWilson, 1925, Craniella Schmidt, 1870, Fangophilina Schmidt, 1880, Paratetilla Dendy, 1905, and Tetilla Schmidt, 1868. These genera are characterized by few conflicting morphological characters, resulting in an ambiguity of phylogenetic relationships. The phylogeny of tetillid genera was investigated using the cox1, 18S rRNA and 28S rRNA (C1-D2 domains) genes in 88 specimens (8 genera, 28 species). Five clades were identified: (i) Cinachyrella, Paratetilla and Amphitethya species, (ii) Cinachyrella levantinensis, (iii) Tetilla, (iv) Craniella, Cinachyra and Fangophilina and (v) Acanthotetilla. Consequently, the phylogenetic analysis supports the monophyly of Tetilla, a genus lacking any known morphological synapomorphy. Acanthotetilla is also recovered. In contrast, within the first clade, species of the genera Paratetilla and Amphitethya were nested within Cinachyrella. Similarly, within the fourth clade, species of the genera Cinachyra and Fangophilina were nested within Craniella. As previously postulated by taxonomists, the loss of ectodermal specialization (i.e., a cortex) has occurred several times independently. Nevertheless, the presence or absence of a cortex and its features carry a phylogenetic signal. Surprisingly, the common view that assumes close relationships among sponges with porocalices (i.e., surface depressions) is refuted.
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Affiliation(s)
- Amir Szitenberg
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel
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15
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Belinky F, Szitenberg A, Goldfarb I, Feldstein T, Wörheide G, Ilan M, Huchon D. ALG11 – A new variable DNA marker for sponge phylogeny: Comparison of phylogenetic performances with the 18S rDNA and the COI gene. Mol Phylogenet Evol 2012; 63:702-13. [DOI: 10.1016/j.ympev.2012.02.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 02/13/2012] [Accepted: 02/14/2012] [Indexed: 11/30/2022]
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Szitenberg A, Goren M, Huchon D. Mitochondrial and morphological variation of Tilapia zillii in Israel. BMC Res Notes 2012; 5:172. [PMID: 22469095 PMCID: PMC3412729 DOI: 10.1186/1756-0500-5-172] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 04/02/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tilapia zillii is widespread in the East Levant inland aquatic systems as well as in artificial water reservoirs. In this study we explore the genetic and morphological variation of this widespread species, using mitochondrial control region sequences and meristic characters. We examine the hypothesis that T. zillii's population structure corresponds to the four Israeli aquatic systems. RESULTS Out of seven natural water bodies, only two were found to possess genetically divergent populations of T. zillii. In addition to its presence in fish farms, the species was found in two artificial recreational ponds which were supposed to have been stocked only with other fish species. In these two artificial habitats, the haplotype frequencies diverged significantly from those of natural populations. Finally, fish from the Dead Sea springs of Ne'ot HaKikar appear to differ both genetically and morphologically from fish of the same aquatic system but not from fish of other water systems. CONCLUSIONS Our results show that the population structure of T. zillii does not match the geography of the Israeli water-basins, with the exception of the Dead Sea and Kishon River, when considering natural populations only. The absence of a significant divergence between basins is discussed. Our results and observations suggest that the Ne'ot HaKikar Dead Sea population and those of artificial ponds could have originated from the "hitchhiking" of T. zillii, at the expense of some other cultivated tilapiine species.
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Affiliation(s)
- Amir Szitenberg
- Department of Zoology, Tel-Aviv University, Tel Aviv, Israel
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17
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Szitenberg A, Rot C, Ilan M, Huchon D. Diversity of sponge mitochondrial introns revealed by cox 1 sequences of Tetillidae. BMC Evol Biol 2010; 10:288. [PMID: 20849667 PMCID: PMC2955029 DOI: 10.1186/1471-2148-10-288] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Accepted: 09/20/2010] [Indexed: 01/31/2023] Open
Abstract
Background Animal mitochondrial introns are rare. In sponges and cnidarians they have been found in the cox 1 gene of some spirophorid and homosclerophorid sponges, as well as in the cox 1 and nad 5 genes of some Hexacorallia. Their sporadic distribution has raised a debate as to whether these mobile elements have been vertically or horizontally transmitted among their hosts. The first sponge found to possess a mitochondrial intron was a spirophorid sponge from the Tetillidae family. To better understand the mode of transmission of mitochondrial introns in sponges, we studied cox 1 intron distribution among representatives of this family. Results Seventeen tetillid cox 1 sequences were examined. Among these sequences only six were found to possess group I introns. Remarkably, three different forms of introns were found, named introns 714, 723 and 870 based on their different positions in the cox 1 alignment. These introns had distinct secondary structures and encoded LAGLIDADG ORFs belonging to three different lineages. Interestingly, sponges harboring the same intron form did not always form monophyletic groups, suggesting that their introns might have been transferred horizontally. To evaluate whether the introns were vertically or horizontally transmitted in sponges and cnidarians we used a host parasite approach. We tested for co-speciation between introns 723 (the introns with the highest number of sponge representatives) and their nesting cox 1 sequences. Reciprocal AU tests indicated that the intron and cox 1 tree are significantly different, while a likelihood ratio test was not significant. A global test of co-phylogeny had significant results; however, when cnidarian sequences were analyzed separately the results were not significant. Conclusions The co-speciation analyses thus suggest that a vertical transmission of introns in the ancestor of sponges and cnidarians, followed by numerous independent losses, cannot solely explain the current distribution of metazoan group I introns. An alternative scenario that includes horizontal gene transfer events appears to be more suitable to explain the incongruence between the intron 723 and the cox 1 topologies. In addition, our results suggest that three different intron forms independently colonized the cox 1 gene of tetillids. Among sponges, the Tetillidae family seems to be experiencing an unusual number of intron insertions.
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Affiliation(s)
- Amir Szitenberg
- Department of Zoology, Tel-Aviv University, Tel Aviv 69978, Israel
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Diamant A, Goren M, Yokeş MB, Galil BS, Klopman Y, Huchon D, Szitenberg A, Karhan SU. Dasyatispora levantinae gen. et sp. nov., a new microsporidian parasite from the common stingray Dasyatis pastinaca in the eastern Mediterranean. Dis Aquat Organ 2010; 91:137-150. [PMID: 21387993 DOI: 10.3354/dao02256] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A new microsporidian infecting the Mediterranean common stingray Dasyatis pastinaca (Linnaeus, 1758) is described from Iskenderun Bay, Turkey. The parasite invades the disc muscles, producing slender, spindle-shaped subcutaneous swellings that develop into massive, elongated, tumor-like protuberances measuring up to 11 x 4 cm. Severity of the infection may vary from light (1 or 2 small lesions) to intense, with large parts of the dorsal surface covered with lumps and protrusions. These masses contained a yellowish-white caseous substance consisting of degraded host tissue and microsporidian sporophorous vesicles, which in turn contained developing sporonts, sporoblasts and spores. The ripe spore contained a uni-nucleate sporoplasm and large posterior vacuole, and measured 3.8-4.3 x 2.6-2.8 microm. Infection prevalence was 21% in a sample of 143 host individuals examined. All the infected stingray individuals were within the weight class of 300 to 800 g (200 to 305 mm disc width). Phylogenetic analyses of rDNA sequences indicate that this microsporidian belongs to the Pleistophoridae and clusters with species of the genera Ovipleistophora Pekkarinen, Lom & Nilsen, 2002 and Heterosporis Schubert, 1969. However, the morphology, development and host differ distinctly from all reported species, including those belonging to these 2 genera, and it is thus assigned to a newly erected genus and named Dasyatispora levantinae gen. et sp. nov. This is the first record of a microsporidian infection in a batoid. It is also the first microsporidian species to be formally described from an elasmobranch.
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Affiliation(s)
- Ariel Diamant
- National Center for Mariculture, Israel Oceanographic and Limnological Research, P.O.B. 1212, Eilat 88112, Israel.
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