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Płachno BJ, Kapusta M. The Localization of Cell Wall Components in the Quadrifids of Whole-Mount Immunolabeled Utricularia dichotoma Traps. Int J Mol Sci 2023; 25:56. [PMID: 38203227 PMCID: PMC10778831 DOI: 10.3390/ijms25010056] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/13/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Utricularia (bladderworts) are carnivorous plants. They produce small hollow vesicles, which function as suction traps that work underwater and capture fine organisms. Inside the traps, there are numerous glandular trichomes (quadrifids), which take part in the secretion of digestive enzymes, the resorption of released nutrients, and likely the pumping out of water. Due to the extreme specialization of quadrifids, they are an interesting model for studying the cell walls. This aim of the study was to fill in the gap in the literature concerning the immunocytochemistry of quadrifids in the major cell wall polysaccharides and glycoproteins. To do this, the localization of the cell wall components in the quadrifids was performed using whole-mount immunolabeled Utricularia traps. It was observed that only parts (arms) of the terminal cells had enough discontinuous cuticle to be permeable to antibodies. There were different patterns of the cell wall components in the arms of the terminal cells of the quadrifids. The cell walls of the arms were especially rich in low-methyl-esterified homogalacturonan. Moreover, various arabinogalactan proteins also occurred. Cell walls in glandular cells of quadrifids were rich in low-methyl-esterified homogalacturonan; in contrast, in the aquatic carnivorous plant Aldrovanda vesiculosa, cell walls in the glandular cells of digestive glands were poor in low-methyl-esterified homogalacturonan. Arabinogalactan proteins were found in the cell walls of trap gland cells in all studied carnivorous plants: Utricularia, and members of Droseraceae and Drosophyllaceae.
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Affiliation(s)
- Bartosz J. Płachno
- Department of Plant Cytology and Embryology, Institute of Botany, Faculty of Biology, Jagiellonian University in Kraków, 9 Gronostajowa St., 30-387 Cracow, Poland
| | - Małgorzata Kapusta
- Laboratory of Bioimaging, Faculty of Biology, University of Gdańsk, 59 Wita Stwosza St., 80-308 Gdańsk, Poland;
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Castaldi V, Bellino A, Baldantoni D. The ecology of bladderworts: The unique hunting-gathering-farming strategy in plants. FOOD WEBS 2023. [DOI: 10.1016/j.fooweb.2023.e00273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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Yang H, Mai S, Liu W, Fu J, Yang Q, Zhang B, Huang B. Variations of arbuscular mycorrhizal fungi following succession stages in a tropical lowland rainforest ecosystem of South China. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1125749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
IntroductionThe grasslands in the Nature Reserve of Ganshenling, in the south of Hainan Island, were first formed after deforestation disturbance before a natural restoration of shrubs and secondary forests. However, the stages of grassland and shrubs in some parts of Ganshenling regions could not be naturally restored to secondary forests. In addition, the forest form of the secondary forest after 40 years (40a) of succession was similar to that of the secondary forest of 60 years (60a). However, it was not known whether the microorganisms recovered to the level of the secondary forest of 60a. Arbuscular mycorrhizal fungi (AMF) are plant root symbionts that can improve the nitrogen and phosphorus absorption of plants and play a key role in secondary forest succession. An understanding of the essential role of soil AMF in secondary forest succession of tropical rainforest in Ganshenling regions is still limited.MethodsTherefore, the soil of 0–10 cm was collected with the help of a 5-point sampling method in grassland, shrubs, and second tropical lowland rainforest of 40a and 60a. We studied community changes in AMF with the succession and explored the impacts of soil physicochemical properties on soil AMF.ResultsOur findings were as follows: (1) Different successional stages showed divergent effects on soil AMF communities. (2) After 40a recovery, the alpha-diversity indices of AMF recovered to the level of secondary forest of 60a, but the similarity of soil AMF communities only recovered to 25.3%. (3) Species richness of common species, rare species, and all the species of AMF showed a significantly positive correlation with soil nitrogen. (4) OTU10; OTU6, OTU9, and OTU141; OTU3 and OTU38; and OTU2, OTU15, OTU23, and OTU197 were significantly unique AMF for grasslands, shrubs, and secondary forests of 40a and 60a, respectively. (5) The phylogenetic tree and the heatmap of AMF showed that the OTUs in grasslands and shrubs were in contrast to the OTUs in secondary forests of 40a and 60a.DiscussionWe concluded that the succession of a secondary forest after deforestation disturbance was probably limited by its AMF community.
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Baharin A, Ting TY, Goh HH. Omics Approaches in Uncovering Molecular Evolution and Physiology of Botanical Carnivory. PLANTS (BASEL, SWITZERLAND) 2023; 12:408. [PMID: 36679121 PMCID: PMC9867145 DOI: 10.3390/plants12020408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/09/2023] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
Systems biology has been increasingly applied with multiple omics for a holistic comprehension of complex biological systems beyond the reductionist approach that focuses on individual molecules. Different high-throughput omics approaches, including genomics, transcriptomics, metagenomics, proteomics, and metabolomics have been implemented to study the molecular mechanisms of botanical carnivory. This covers almost all orders of carnivorous plants, namely Caryophyllales, Ericales, Lamiales, and Oxalidales, except Poales. Studies using single-omics or integrated multi-omics elucidate the compositional changes in nucleic acids, proteins, and metabolites. The omics studies on carnivorous plants have led to insights into the carnivory origin and evolution, such as prey capture and digestion as well as the physiological adaptations of trap organ formation. Our understandings of botanical carnivory are further enhanced by the discoveries of digestive enzymes and transporter proteins that aid in efficient nutrient sequestration alongside dynamic molecular responses to prey. Metagenomics studies revealed the mutualistic relationships between microbes and carnivorous plants. Lastly, in silico analysis accelerated the functional characterization of new molecules from carnivorous plants. These studies have provided invaluable molecular data for systems understanding of carnivorous plants. More studies are needed to cover the diverse species with convergent evolution of botanical carnivory.
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Pavlovič A, Jakšová J, Hrivňacký M, Adamec L. Alternative or cytochrome? Respiratory pathways in traps of aquatic carnivorous bladderwort Utricularia reflexa. PLANT SIGNALING & BEHAVIOR 2022; 17:2134967. [PMID: 36266991 PMCID: PMC9590445 DOI: 10.1080/15592324.2022.2134967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Carnivorous plants of the genus Utricularia (bladderwort) form modified leaves into suction bladder traps. The bladders are metabolically active plant tissue with high rates of mitochondrial respiration (RD). In general, plants possess two mitochondrial electron transport pathways to reduce oxygen to water: cytochrome and an alternative. Due to the high metabolic rate in the bladders, it is tempting to assume that the bladders prefer the cytochrome c oxidative pathway. Surprisingly, we revealed that alternative oxidase (AOX), which yields only a little ATP, is much more abundant in the bladders of Utricularia reflexa in comparison with the shoots. This pattern is similar to the carnivorous plants with passive pitcher traps (e.g. Sarracenia, Nepenthes) and seems to be widespread across many carnivorous taxa. The exact role of AOX in the traps of carnivorous plants remains to be investigated.
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Affiliation(s)
- Andrej Pavlovič
- Department of Biophysics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Jana Jakšová
- Department of Biophysics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Martin Hrivňacký
- Department of Biophysics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Lubomír Adamec
- Department of Experimental and Functional Morphology, Institute of Botany of the Czech Academy of Sciences, Třeboň, Czech Republic
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The effect of experimentally simulated climate warming on the microbiome of carnivorous plants – A microcosm experiment. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Miranda VFO, Silva SR, Reut MS, Dolsan H, Stolarczyk P, Rutishauser R, Płachno BJ. A Historical Perspective of Bladderworts ( Utricularia): Traps, Carnivory and Body Architecture. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122656. [PMID: 34961127 PMCID: PMC8707321 DOI: 10.3390/plants10122656] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/28/2021] [Accepted: 11/29/2021] [Indexed: 05/14/2023]
Abstract
The genus Utricularia includes around 250 species of carnivorous plants, commonly known as bladderworts. The generic name Utricularia was coined by Carolus Linnaeus in reference to the carnivorous organs (Utriculus in Latin) present in all species of the genus. Since the formal proposition by Linnaeus, many species of Utricularia were described, but only scarce information about the biology for most species is known. All Utricularia species are herbs with vegetative organs that do not follow traditional models of morphological classification. Since the formal description of Utricularia in the 18th century, the trap function has intrigued naturalists. Historically, the traps were regarded as floating organs, a common hypothesis that was maintained by different botanists. However, Charles Darwin was most likely the first naturalist to refute this idea, since even with the removal of all traps, the plants continued to float. More recently, due mainly to methodological advances, detailed studies on the trap function and mechanisms could be investigated. This review shows a historical perspective on Utricularia studies which focuses on the traps and body organization.
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Affiliation(s)
- Vitor F. O. Miranda
- Laboratory of Plant Systematics, Department of Applied Biology, School of Agricultural and Veterinarian Sciences, Campus Jaboticabal, UNESP—São Paulo State University, Jaboticabal CEP 14884-900, Brazil; (S.R.S.); (H.D.)
- Correspondence:
| | - Saura R. Silva
- Laboratory of Plant Systematics, Department of Applied Biology, School of Agricultural and Veterinarian Sciences, Campus Jaboticabal, UNESP—São Paulo State University, Jaboticabal CEP 14884-900, Brazil; (S.R.S.); (H.D.)
| | - Markus S. Reut
- Department of Plant Cytology and Embryology, Institute of Botany, Faculty of Biology, Jagiellonian University in Kraków, Gronostajowa 9 St., 30-387 Kraków, Poland; (M.S.R.); (B.J.P.)
| | - Hugo Dolsan
- Laboratory of Plant Systematics, Department of Applied Biology, School of Agricultural and Veterinarian Sciences, Campus Jaboticabal, UNESP—São Paulo State University, Jaboticabal CEP 14884-900, Brazil; (S.R.S.); (H.D.)
| | - Piotr Stolarczyk
- Department of Botany, Physiology and Plant Protection, Faculty of Biotechnology and Horticulture, University of Agriculture in Kraków, al. 29 Listopada 54, 31-425 Kraków, Poland;
| | - Rolf Rutishauser
- Department of Systematic and Evolutionary Botany, University of Zurich, CH-8008 Zurich, Switzerland;
| | - Bartosz J. Płachno
- Department of Plant Cytology and Embryology, Institute of Botany, Faculty of Biology, Jagiellonian University in Kraków, Gronostajowa 9 St., 30-387 Kraków, Poland; (M.S.R.); (B.J.P.)
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Jakšová J, Adamec L, Petřík I, Novák O, Šebela M, Pavlovič A. Contrasting effect of prey capture on jasmonate accumulation in two genera of aquatic carnivorous plants (Aldrovanda, Utricularia). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 166:459-465. [PMID: 34166972 DOI: 10.1016/j.plaphy.2021.06.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/08/2021] [Indexed: 06/13/2023]
Abstract
Terrestrial carnivorous plants of genera Drosera, Dionaea and Nepenthes within the order Caryophyllales employ jasmonates for the induction of digestive processes in their traps. Here, we focused on two aquatic carnivorous plant genera with different trapping mechanism from distinct families and orders: Aldrovanda (Droseraceae, Caryophyllales) with snap-traps and Utricularia (Lentibulariaceae, Lamiales) with suction traps. Using phytohormone analyses and simple biotest, we asked whether the jasmonates are involved in the activation of carnivorous response similar to that known in traps of terrestrial genera of Droseraceae (Drosera, Dionaea). The results showed that Utricularia, in contrast with Aldrovanda, does not use jasmonates for activation of carnivorous response and is the second genus in Lamiales, which has not co-opted jasmonate signalling for botanical carnivory. On the other hand, the nLC-MS/MS analyses revealed that both genera secreted digestive fluid containing cysteine protease homologous to dionain although the mode of its regulation may differ. Whereas in Utricularia the cysteine protease is present constitutively in digestive fluid, it is induced by prey and exogenous application of jasmonic acid in Aldrovanda.
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Affiliation(s)
- Jana Jakšová
- Department of Biophysics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | - Lubomír Adamec
- Institute of Botany of the Czech Academy of Sciences, Department of Experimental and Functional Morphology, Dukelská135, CZ-379 82, Třeboň, Czech Republic
| | - Ivan Petřík
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | - Marek Šebela
- Department of Biochemistry, Faculty of Science, and Centre of the Region Haná for Biotechnological and Agricultural Research, CATRIN, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | - Andrej Pavlovič
- Department of Biophysics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic.
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Adamec L, Matušíková I, Pavlovič A. Recent ecophysiological, biochemical and evolutional insights into plant carnivory. ANNALS OF BOTANY 2021; 128:241-259. [PMID: 34111238 PMCID: PMC8389183 DOI: 10.1093/aob/mcab071] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/07/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND Carnivorous plants are an ecological group of approx. 810 vascular species which capture and digest animal prey, absorb prey-derived nutrients and utilize them to enhance their growth and development. Extant carnivorous plants have evolved in at least ten independent lineages, and their adaptive traits represent an example of structural and functional convergence. Plant carnivory is a result of complex adaptations to mostly nutrient-poor, wet and sunny habitats when the benefits of carnivory exceed the costs. With a boost in interest and extensive research in recent years, many aspects of these adaptations have been clarified (at least partly), but many remain unknown. SCOPE We provide some of the most recent insights into substantial ecophysiological, biochemical and evolutional particulars of plant carnivory from the functional viewpoint. We focus on those processes and traits in carnivorous plants associated with their ecological characterization, mineral nutrition, cost-benefit relationships, functioning of digestive enzymes and regulation of the hunting cycle in traps. We elucidate mechanisms by which uptake of prey-derived nutrients leads to stimulation of photosynthesis and root nutrient uptake. CONCLUSIONS Utilization of prey-derived mineral (mainly N and P) and organic nutrients is highly beneficial for plants and increases the photosynthetic rate in leaves as a prerequisite for faster plant growth. Whole-genome and tandem gene duplications brought gene material for diversification into carnivorous functions and enabled recruitment of defence-related genes. Possible mechanisms for the evolution of digestive enzymes are summarized, and a comprehensive picture on the biochemistry and regulation of prey decomposition and prey-derived nutrient uptake is provided.
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Affiliation(s)
- Lubomír Adamec
- Institute of Botany of the Czech Academy of Sciences, Dukelská 135, CZ-379 01 Třeboň, Czech Republic
| | - Ildikó Matušíková
- University of Ss. Cyril and Methodius, Department of Ecochemistry and Radioecology, J. Herdu 2, SK-917 01 Trnava, Slovak Republic
| | - Andrej Pavlovič
- Department of Biophysics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic
- For correspondence. E-mail
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Arai N, Ohno Y, Jumyo S, Hamaji Y, Ohyama T. Organ-specific expression and epigenetic traits of genes encoding digestive enzymes in the lance-leaf sundew (Drosera adelae). JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1946-1961. [PMID: 33247920 PMCID: PMC7921302 DOI: 10.1093/jxb/eraa560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 11/25/2020] [Indexed: 05/16/2023]
Abstract
Over the last two decades, extensive studies have been performed at the molecular level to understand the evolution of carnivorous plants. As fruits, the repertoire of protein components in the digestive fluids of several carnivorous plants have gradually become clear. However, the quantitative aspects of these proteins and the expression mechanisms of the genes that encode them are still poorly understood. In this study, using the Australian sundew Drosera adelae, we identified and quantified the digestive fluid proteins. We examined the expression and methylation status of the genes corresponding to major hydrolytic enzymes in various organs; these included thaumatin-like protein, S-like RNase, cysteine protease, class I chitinase, β-1, 3-glucanase, and hevein-like protein. The genes encoding these proteins were exclusively expressed in the glandular tentacles. Furthermore, the promoters of the β-1, 3-glucanase and cysteine protease genes were demethylated only in the glandular tentacles, similar to the previously reported case of the S-like RNase gene da-I. This phenomenon correlated with high expression of the DNA demethylase DEMETER in the glandular tentacles, strongly suggesting that it performs glandular tentacle-specific demethylation of the genes. The current study strengthens and generalizes the relevance of epigenetics to trap organ-specific gene expression in D. adelae. We also suggest similarities between the trap organs of carnivorous plants and the roots of non-carnivorous plants.
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Affiliation(s)
- Naoki Arai
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Yusuke Ohno
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Shinya Jumyo
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Yusuke Hamaji
- Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Takashi Ohyama
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
- Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, Shinjuku-ku, Tokyo, Japan
- Correspondence:
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de Oliveira BFR, Freitas-Silva J, Sánchez-Robinet C, Laport MS. Transmission of the sponge microbiome: moving towards a unified model. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:619-638. [PMID: 33048474 DOI: 10.1111/1758-2229.12896] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/08/2020] [Accepted: 10/11/2020] [Indexed: 06/11/2023]
Abstract
Sponges have co-evolved for millions of years alongside several types of microorganisms, which aside from participating in the animal's diet, are mostly symbionts. Since most of the genetic repertoire in the holobiont genome is provided by microbes, it is expected that the host-associated microbiome will be at least partially heritable. Sponges can therefore acquire their symbionts in different ways. Both vertical transmission (VT) and horizontal transmission (HT) have different advantages and disadvantages in the life cycle of these invertebrates. However, a third mode of transmission, called leaky vertical transmission or mixed mode of transmission (MMT), which incorporates both VT and HT modes, has gained relevance and seems to be the most robust model. In that regard, the aim of this review is to present the evolving knowledge on these main modes of transmission of the sponge microbiome. Our conclusions lead us to suggest that MMT may be more common for all sponges, with its frequency varying across the transmission spectrum between species and the environment. This hybrid model supports the stable and specific transmission of these microbial partners and reinforces their assistance in the resilience of sponges over the years.
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Affiliation(s)
- Bruno Francesco Rodrigues de Oliveira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590, Rio de Janeiro, Brazil
| | - Jéssyca Freitas-Silva
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590, Rio de Janeiro, Brazil
| | - Claudia Sánchez-Robinet
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590, Rio de Janeiro, Brazil
| | - Marinella Silva Laport
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590, Rio de Janeiro, Brazil
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Phylogenomic Analyses of Non-Dikarya Fungi Supports Horizontal Gene Transfer Driving Diversification of Secondary Metabolism in the Amphibian Gastrointestinal Symbiont, Basidiobolus. G3-GENES GENOMES GENETICS 2020; 10:3417-3433. [PMID: 32727924 PMCID: PMC7466969 DOI: 10.1534/g3.120.401516] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Research into secondary metabolism (SM) production by fungi has resulted in the discovery of diverse, biologically active compounds with significant medicinal applications. The fungi rich in SM production are taxonomically concentrated in the subkingdom Dikarya, which comprises the phyla Ascomycota and Basidiomycota. Here, we explore the potential for SM production in Mucoromycota and Zoopagomycota, two phyla of nonflagellated fungi that are not members of Dikarya, by predicting and identifying core genes and gene clusters involved in SM. The majority of non-Dikarya have few genes and gene clusters involved in SM production except for the amphibian gut symbionts in the genus Basidiobolus. Basidiobolus genomes exhibit an enrichment of SM genes involved in siderophore, surfactin-like, and terpene cyclase production, all these with evidence of constitutive gene expression. Gene expression and chemical assays also confirm that Basidiobolus has significant siderophore activity. The expansion of SMs in Basidiobolus are partially due to horizontal gene transfer from bacteria, likely as a consequence of its ecology as an amphibian gut endosymbiont.
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Zhou J, Cao Y, Liu X, Jiang H, Li W. Bladder entrance of microplastic likely induces toxic effects in carnivorous macrophyte Utricularia aurea Lour. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:32124-32131. [PMID: 32564318 DOI: 10.1007/s11356-020-09529-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 05/29/2020] [Indexed: 06/11/2023]
Abstract
The global distribution of microplastic (particle size < 5 mm) is of growing concern, especially in aquatic environments where it may cause adverse effects on resident organisms. To date, however, few studies have focused on the impacts of microplastic on aquatic plants. Here, we conducted a microcosm study to investigate the toxic effects of microplastic on the carnivorous aquatic macrophyte Utricularia aurea Lour. Based on microscopic images and Raman spectrum analysis, we found that most polyvinyl chloride (PVC) particles were smaller than the valve of U. aurea bladders, thus allowing entrance into the plant, but this was not so for polyethylene (PE) particles. Furthermore, PVC (50 mg L-1) had significantly negative effects on growth and physiological parameters such as macrophyte length, chlorophyll content, and fluorescence, whereas, at the same concentration, PE had no such effects. Further analysis revealed that after bladder removal, the macrophytes did not respond to PVC particle toxicity. Thus, intake of microplastics (i.e., PVC) through bladders is likely responsible for inducing toxic effects to the growth and physiological parameters of U. aurea.
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Affiliation(s)
- Jingzhe Zhou
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Cao
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xiaoning Liu
- Institute of Hydroecology, State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan, 430072, China
| | - Hongsheng Jiang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Bacterial and Eukaryotic Small-Subunit Amplicon Data Do Not Provide a Quantitative Picture of Microbial Communities, but They Are Reliable in the Context of Ecological Interpretations. mSphere 2020; 5:5/2/e00052-20. [PMID: 32132159 PMCID: PMC7056804 DOI: 10.1128/msphere.00052-20] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
High-throughput sequencing (HTS) of amplified fragments of rRNA genes provides unprecedented insight into the diversity of prokaryotic and eukaryotic microorganisms. Unfortunately, HTS data are prone to quantitative biases, which may lead to an erroneous picture of microbial community composition and thwart efforts to advance its understanding. These concerns motivated us to investigate how accurately HTS data characterize the variability of microbial communities, the relative abundances of specific phylotypes, and their relationships with environmental factors in comparison to an established microscopy-based method. We compared results obtained by HTS and catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) from three independent aquatic time series for both prokaryotic and eukaryotic microorganisms (almost 900 data points, the largest obtained with both methods so far). HTS and CARD-FISH data disagree with regard to relative abundances of bacterial and eukaryotic phylotypes but identify similar environmental drivers shaping bacterial and eukaryotic communities. High-throughput sequencing (HTS) of gene amplicons is a preferred method of assessing microbial community composition, because it rapidly provides information from a large number of samples at high taxonomic resolution and low costs. However, mock community studies show that HTS data poorly reflect the actual relative abundances of individual phylotypes, casting doubt on the reliability of subsequent statistical analysis and data interpretation. We investigated how accurately HTS data reflect the variability of bacterial and eukaryotic community composition and their relationship with environmental factors in natural samples. For this, we compared results of HTS from three independent aquatic time series (n = 883) with those from an established, quantitative microscopic method (catalyzed reporter deposition-fluorescence in situ hybridization [CARD-FISH]). Relative abundances obtained by CARD-FISH and HTS disagreed for most bacterial and eukaryotic phylotypes. Nevertheless, the two methods identified the same environmental drivers to shape bacterial and eukaryotic communities. Our results show that amplicon data do provide reliable information for their ecological interpretations. Yet, when studying specific phylogenetic groups, it is advisable to combine HTS with quantification using microscopy and/or the addition of internal standards. IMPORTANCE High-throughput sequencing (HTS) of amplified fragments of rRNA genes provides unprecedented insight into the diversity of prokaryotic and eukaryotic microorganisms. Unfortunately, HTS data are prone to quantitative biases, which may lead to an erroneous picture of microbial community composition and thwart efforts to advance its understanding. These concerns motivated us to investigate how accurately HTS data characterize the variability of microbial communities, the relative abundances of specific phylotypes, and their relationships with environmental factors in comparison to an established microscopy-based method. We compared results obtained by HTS and catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) from three independent aquatic time series for both prokaryotic and eukaryotic microorganisms (almost 900 data points, the largest obtained with both methods so far). HTS and CARD-FISH data disagree with regard to relative abundances of bacterial and eukaryotic phylotypes but identify similar environmental drivers shaping bacterial and eukaryotic communities.
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Silva SR, Moraes AP, Penha HA, Julião MHM, Domingues DS, Michael TP, Miranda VFO, Varani AM. The Terrestrial Carnivorous Plant Utricularia reniformis Sheds Light on Environmental and Life-Form Genome Plasticity. Int J Mol Sci 2019; 21:E3. [PMID: 31861318 PMCID: PMC6982007 DOI: 10.3390/ijms21010003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/13/2019] [Accepted: 12/15/2019] [Indexed: 12/22/2022] Open
Abstract
Utricularia belongs to Lentibulariaceae, a widespread family of carnivorous plants that possess ultra-small and highly dynamic nuclear genomes. It has been shown that the Lentibulariaceae genomes have been shaped by transposable elements expansion and loss, and multiple rounds of whole-genome duplications (WGD), making the family a platform for evolutionary and comparative genomics studies. To explore the evolution of Utricularia, we estimated the chromosome number and genome size, as well as sequenced the terrestrial bladderwort Utricularia reniformis (2n = 40, 1C = 317.1-Mpb). Here, we report a high quality 304 Mb draft genome, with a scaffold NG50 of 466-Kb, a BUSCO completeness of 87.8%, and 42,582 predicted genes. Compared to the smaller and aquatic U. gibba genome (101 Mb) that has a 32% repetitive sequence, the U. reniformis genome is highly repetitive (56%). The structural differences between the two genomes are the result of distinct fractionation and rearrangements after WGD, and massive proliferation of LTR-retrotransposons. Moreover, GO enrichment analyses suggest an ongoing gene birth-death-innovation process occurring among the tandem duplicated genes, shaping the evolution of carnivory-associated functions. We also identified unique patterns of developmentally related genes that support the terrestrial life-form and body plan of U. reniformis. Collectively, our results provided additional insights into the evolution of the plastic and specialized Lentibulariaceae genomes.
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Affiliation(s)
- Saura R. Silva
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, UNESP—Universidade Estadual Paulista, Jaboticabal 14884-900, Brazil; (S.R.S.); (H.A.P.); (M.H.M.J.)
| | - Ana Paula Moraes
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo 09606-070, Brazil;
| | - Helen A. Penha
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, UNESP—Universidade Estadual Paulista, Jaboticabal 14884-900, Brazil; (S.R.S.); (H.A.P.); (M.H.M.J.)
| | - Maria H. M. Julião
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, UNESP—Universidade Estadual Paulista, Jaboticabal 14884-900, Brazil; (S.R.S.); (H.A.P.); (M.H.M.J.)
| | - Douglas S. Domingues
- Departamento de Botânica, Instituto de Biociências, UNESP—Universidade Estadual Paulista, Rio Claro 13506-900, Brazil;
| | | | - Vitor F. O. Miranda
- Departamento de Biologia Aplicada à Agropecuária, Faculdade de Ciências Agrárias e Veterinárias, UNESP—Universidade Estadual Paulista, Jaboticabal 14884-900, Brazil
| | - Alessandro M. Varani
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, UNESP—Universidade Estadual Paulista, Jaboticabal 14884-900, Brazil; (S.R.S.); (H.A.P.); (M.H.M.J.)
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Turon M, Cáliz J, Triadó-Margarit X, Casamayor EO, Uriz MJ. Sponges and Their Microbiomes Show Similar Community Metrics Across Impacted and Well-Preserved Reefs. Front Microbiol 2019; 10:1961. [PMID: 31507568 PMCID: PMC6713927 DOI: 10.3389/fmicb.2019.01961] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/09/2019] [Indexed: 11/13/2022] Open
Abstract
Sponge diversity has been reported to decrease from well-preserved to polluted environments, but whether diversity and intra-species variation of their associated microbiomes also change as function of environmental quality remains unknown. Our study aimed to assess whether microbiome composition and structure are related to the proliferation of some sponges and not others under degraded conditions. We characterized the most frequent sponges and their associated bacteria in two close areas (impacted and well-preserved) of Nha Trang Bay (Indo-Pacific). Sponge assemblages were richer and more diverse in the well-preserved reefs, but more abundant (individuals/m. transect) in the impacted environments, where two species (Clathria reinwardti and Amphimedon paraviridis) dominated. Sponge microbiomes from the polluted zones had, in general, lower bacterial diversity and core size and consequently, higher intra-species dispersion than microbiomes of sponges from the well-preserved environments. Microbial communities reflect the reduction of diversity and richness shown by their host sponges. In this sense, sponges with less complex and more variable microbiomes proliferate under degraded environmental conditions, following the ecological paradigm that negatively correlates community diversity and environmental degradation. Thereby, the diversity and structure of sponge microbiomes might indirectly determine the presence and proliferation of sponge species in certain habitats.
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Affiliation(s)
| | | | | | | | - Maria J. Uriz
- Centre d’Estudis Avançats de Blanes, CEAB-CSIC, Girona, Spain
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Sickel W, Van de Weyer AL, Bemm F, Schultz J, Keller A. Venus flytrap microbiotas withstand harsh conditions during prey digestion. FEMS Microbiol Ecol 2019; 95:5289860. [PMID: 30649283 DOI: 10.1093/femsec/fiz010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 01/15/2019] [Indexed: 11/13/2022] Open
Abstract
The carnivorous Venus flytrap (Dionaea muscipula) overcomes environmental nutrient limitation by capturing small animals. Such prey is digested with an acidic enzyme-containing mucilage that is secreted into the closed trap. However, surprisingly little is known about associations with microorganisms. Therefore, we assessed microbiotas of traps and petioles for the Venus flytrap by 16S amplicon meta-barcoding. We also performed time-series assessments of dynamics during digestion in traps and experimental acidification of petioles. We found that the traps hosted distinct microbiotas that differed from adjacent petioles. Further, they showed a significant taxonomic turnover during digestion. Following successful catches, prey-associated bacteria had strong effects on overall composition. With proceeding digestion, however, microbiotas were restored to compositions resembling pre-digestion stages. A comparable, yet less extensive shift was found when stimulating digestion with coronatine. Artificial acidification of petioles did not induce changes towards trap-like communities. Our results show that trap microbiota were maintained during digestion despite harsh conditions and recovered after short-term disturbances through prey microbiota. This indicates trap-specific and resilient associations. By mapping to known genomes, we predicted putative adaptations and functional implications for the system, yet direct mechanisms and quantification of host benefits, like the involvement in digestion, remain to be addressed.
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Affiliation(s)
- Wiebke Sickel
- Molecular Biodiversity Group, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | | | - Felix Bemm
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jörg Schultz
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.,Center for Computational and Theoretical Biology, University of Würzburg, Germany
| | - Alexander Keller
- Molecular Biodiversity Group, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany.,Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.,Center for Computational and Theoretical Biology, University of Würzburg, Germany
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Sirová D, Bárta J, Šimek K, Posch T, Pech J, Stone J, Borovec J, Adamec L, Vrba J. Correction to: Hunters or farmers? Microbiome characteristics help elucidate the diet composition in an aquatic carnivorous plant. MICROBIOME 2019; 7:4. [PMID: 30611307 PMCID: PMC6320574 DOI: 10.1186/s40168-018-0617-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
AbstractFollowing publication of the original article [1], the author reported an error in Fig. 3.
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Affiliation(s)
- Dagmara Sirová
- Biology Centre CAS, Institute of Hydrobiology, Na Sádkách 7, CZ-37005, České Budějovice, Czech Republic.
- Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-37005, České Budějovice, Czech Republic.
| | - Jiří Bárta
- Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-37005, České Budějovice, Czech Republic
| | - Karel Šimek
- Biology Centre CAS, Institute of Hydrobiology, Na Sádkách 7, CZ-37005, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-37005, České Budějovice, Czech Republic
| | - Thomas Posch
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, CH-8802, Kilchberg, Switzerland
| | - Jiří Pech
- Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-37005, České Budějovice, Czech Republic
| | - James Stone
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK-99775, USA
- Institute of Experimental Botany CAS, Rozvojová 263, CZ-16502, Praha 6-Lysolaje, Czech Republic
| | - Jakub Borovec
- Biology Centre CAS, Institute of Hydrobiology, Na Sádkách 7, CZ-37005, České Budějovice, Czech Republic
| | - Lubomír Adamec
- Institute of Botany CAS, Dukelská 135, CZ-37982, Třeboň, Czech Republic
| | - Jaroslav Vrba
- Biology Centre CAS, Institute of Hydrobiology, Na Sádkách 7, CZ-37005, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-37005, České Budějovice, Czech Republic
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