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Vasconcelos Rissi D, Ijaz M, Baschien C. Comparative genome analysis of the freshwater fungus Filosporella fistucella indicates potential for plant-litter degradation at cold temperatures. G3 (BETHESDA, MD.) 2023; 13:jkad190. [PMID: 37619983 PMCID: PMC10627260 DOI: 10.1093/g3journal/jkad190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 08/03/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023]
Abstract
Freshwater fungi play an important role in the decomposition of organic matter of leaf litter in rivers and streams. They also possess the necessary mechanisms to endure lower temperatures caused by habitat and weather variations. This includes the production of cold-active enzymes and antifreeze proteins. To better understand the physiological activities of freshwater fungi in their natural environment, different methods are being applied, and genome sequencing is one in the spotlight. In our study, we sequenced the first genome of the freshwater fungus Filosporella fistucella (45.7 Mb) and compared the genome with the evolutionary close-related species Tricladium varicosporioides (48.2 Mb). The genomes were annotated using the carbohydrate-active enzyme database where we then filtered for leaf-litter degradation-related enzymes (cellulase, hemicellulase, laccase, pectinase, cutinase, amylase, xylanase, and xyloglucanase). Those enzymes were analyzed for antifreeze properties using a machine-learning approach. We discovered that F. fistucella has more enzymes to participate in the breakdown of sugar, leaf, and wood than T. varicosporioides (855 and 719, respectively). Filosporella fistucella shows a larger set of enzymes capable of resisting cold temperatures than T. varicosporioides (75 and 66, respectively). Our findings indicate that in comparison with T. varicosporioides, F. fistucella has a greater capacity for aquatic growth, adaptability to freshwater environments, and resistance to low temperatures.
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Affiliation(s)
- Daniel Vasconcelos Rissi
- Leibniz - Institute DSMZ, German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Maham Ijaz
- Leibniz - Institute DSMZ, German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Christiane Baschien
- Leibniz - Institute DSMZ, German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
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ITS rDNA Barcodes Clarify Molecular Diversity of Aquatic Hyphomycetes. Microorganisms 2022; 10:microorganisms10081569. [PMID: 36013986 PMCID: PMC9415940 DOI: 10.3390/microorganisms10081569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 02/04/2023] Open
Abstract
Aquatic hyphomycetes are key microbial decomposers of allochthonous organic matter in freshwater ecosystems. Although their importance in carbon flow and food webs in streams is widely recognized, there are still gaps in our understanding of their molecular diversity and distribution patterns. Our study utilized the growing database of ITS rDNA barcodes of aquatic hyphomycetes (1252 sequences) and aimed to (i) produce new barcodes for some lesser-known taxa; (ii) clarify the taxonomic placement of some taxa at the class or order level, based on molecular data; and (iii) provide insights into the biogeographical origins of some taxa. This study increased the number of aquatic hyphomycete species with available ITS barcodes from 119 (out of ~300 species described) to 136. Phylogenetically, the 136 species were distributed between 2 phyla, 6 classes, and 10 orders of fungi. Future studies should strive to increase the database of ITS sequences, especially focusing on species with unclear phylogenetic relationships (incertae sedis) and with few sequences available. The geographical distribution of species with available ITS sequences included 50 countries from five continents, but 6 countries had more than 20 species associated, showing a bias toward the northern hemisphere, likely due to sampling bias.
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Tarda AS, Saparrat MCN, Gómez N. Studies on aquatic fungi in Dikarya: a review of the literature from Southern Cone of South America. AN ACAD BRAS CIENC 2022; 94:e20201210. [PMID: 35507977 DOI: 10.1590/0001-3765202220201210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 12/16/2020] [Indexed: 11/21/2022] Open
Abstract
A bibliographic analysis was carried out to update the state of knowledge about aquatic fungi belonging to the subkingdom Dikarya in the Southern Cone of South America. The exhaustive search resulted in 38 articles reported. These papers correspond to those on taxonomic, ecological and biogeographic topics and include studies from lotic environments of the temperate ecoregions of Chile and Argentina. A total of 325 aquatic fungal taxa were reported, of which 318 belong to the phylum Ascomycota and 7 to the phylum Basidiomycota. According to the subgroups of these aquatic fungi 17 taxa were aero-aquatic, 199 facultative and 109 Ingoldian fungi. Regarding the methodologies, in these studies the information was obtained mainly by using lignocellulosic substrates such as leaf litter and wood as fungal source and wet chamber traditional working technique. However, more studies are still needed using other few-reported perspectives for the region such as ecological and molecular approaches as well as analyses of water environments belonging to unexplored biomes. This information can contribute to a better understanding of aquatic fungal communities and their role in ecosystems of the Southern Cone of South America.
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Affiliation(s)
- Alan S Tarda
- UNLP-CONICET (CCT La Plata), Instituto de Limnología "Dr. Raúl Ringuelet", Bv. 120 y 62, n°1437, 1900 La Plata, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Rivadavia 1917 (C1033AAJ), Buenos Aires, Argentina
| | - Mario C N Saparrat
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Rivadavia 1917 (C1033AAJ), Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y técnicas (CONICET), Universidad Nacional de La Plata CCT-La Plata-Diag, Instituto de Fisiología Vegetal (INFIVE), 113 y 61, CC 327, 1900 La Plata, Buenos Aires, Argentina.,Universidad Nacional de La Plata, Facultad de Ciencias Naturales y Museo, Instituto de Botánica Carlos Spegazzini, 53 n° 477, 1900 La Plata, Buenos Aires, Argentina.,Universidad Nacional de La Plata, Facultad de Ciencias Agrarias y Forestales, Cátedra de Microbiología Agrícola, Departamento de Ciencias Biológicas, 60 y 119, 1900 La Plata, Buenos Aires, Argentina
| | - Nora Gómez
- UNLP-CONICET (CCT La Plata), Instituto de Limnología "Dr. Raúl Ringuelet", Bv. 120 y 62, n°1437, 1900 La Plata, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Rivadavia 1917 (C1033AAJ), Buenos Aires, Argentina
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Calabon MS, Hyde KD, Jones EBG, Luo ZL, Dong W, Hurdeal VG, Gentekaki E, Rossi W, Leonardi M, Thiyagaraja V, Lestari AS, Shen HW, Bao DF, Boonyuen N, Zeng M. Freshwater fungal numbers. FUNGAL DIVERS 2022. [DOI: 10.1007/s13225-022-00503-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Haelewaters D, Park D, Johnston PR. Multilocus phylogenetic analysis reveals that Cyttariales is a synonym of Helotiales. Mycol Prog 2021. [DOI: 10.1007/s11557-021-01736-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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