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Di Capua I, Luise F, Zampicinini G, Roncalli V, Carotenuto Y, Piredda R. Integrative approach to monitoring metazoan diversity and distribution in two Mediterranean coastal sites through morphology and organismal eDNA. Sci Rep 2024; 14:19291. [PMID: 39164301 PMCID: PMC11336219 DOI: 10.1038/s41598-024-69520-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 08/06/2024] [Indexed: 08/22/2024] Open
Abstract
Marine and coastal ecosystems respond to climate change in various ways, such as the type of ecosystem, the species composition, interactions, and distribution, and the effect of local stressors. Metazoan organisms, particularly zooplankton, are important indicators for monitoring the effects climate-driven warming in marine coastal ecosystems over the long term. In this study, the diversity and distribution of zooplankton communities in the Mediterranean Sea (Canyon Dohrn and LTER-MareChiara, Gulf of Naples), a known biodiversity and climate changes hotspot, have been assessed using the integration of morphological-based identification and organismal eDNA. Our findings showed that the multi-locus strategy including the mitochondrial cytochrome c oxidase I (COI) gene and the hypervariable region V9 of the 18S rDNA (18S V9) as targets, improved the taxonomic overview, with the COI gene being more effective than the 18S V9 region for metazoans at the species level. However, appendicularians were detected only with the 18S V9 region. Overall, organismal eDNA is a powerful approach for revealing hidden biodiversity, especially for gelatinous and meroplankton components, and provided new insights into biodiversity patterns. The ecological importance of calanoid copepods in coastal ecosystems has been confirmed. In contrast, the discovery of 13 new metazoan records in the Mediterranean Sea, including two non-indigenous copepod species, suggested that local stressors affect zooplankton community structure and resilience, highlighting the importance of biomonitoring and protecting marine coastal ecosystems.
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Affiliation(s)
- Iole Di Capua
- Marine Organism Taxonomy Core Facility - MOTax, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
- NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133, Palermo, Italy.
| | | | | | - Vittoria Roncalli
- Marine Organism Taxonomy Core Facility - MOTax, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Ylenia Carotenuto
- Marine Organism Taxonomy Core Facility - MOTax, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Roberta Piredda
- NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133, Palermo, Italy
- Department of Veterinary Medicine, University of Bari Aldo Moro, Bari, Italy
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2
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Banchi E, Manna V, Muggia L, Celussi M. Marine Fungal Diversity and Dynamics in the Gulf of Trieste (Northern Adriatic Sea). MICROBIAL ECOLOGY 2024; 87:78. [PMID: 38806848 PMCID: PMC11133070 DOI: 10.1007/s00248-024-02394-z] [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: 02/12/2024] [Accepted: 05/20/2024] [Indexed: 05/30/2024]
Abstract
Fungi contribute to different important ecological processes, including decomposition of organic matter and nutrient cycling, but in the marine environment the main factors influencing their diversity and dynamics at the spatial and temporal levels are still largely unclear. In this study, we performed DNA metabarcoding on seawater sampled monthly over a year and a half in the Gulf of Trieste (northern Adriatic Sea), targeting the internal transcribed spacer (ITS) and the 18S rRNA gene regions. The fungal communities were diverse, very dynamic, and belonged predominantly to marine taxa. Samples could be clustered in two groups, mainly based on the high (> 30%) or low relative proportion of the ascomycetes Parengyodontium album, which emerged as a key taxon in this area. Dissolved and particulate organic C:N ratio played important roles in shaping the mycoplankton assemblages, suggesting that differently bioavailable organic matter pools may be utilized by different consortia. The proportion of fungal over total reads was 31% for ITS and 0.7% for 18S. ITS had the highest taxonomic resolution but low power to detect early divergent fungal lineages. Our results on composition, distribution, and environmental drivers extended our knowledge of the structure and function of the mycobiome of coastal waters.
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Affiliation(s)
- Elisa Banchi
- National Institute of Oceanography and Applied Geophysics (OGS), Trieste, Italy.
- NBFC, National Biodiversity Future Center, Palermo, Italy.
| | - Vincenzo Manna
- National Institute of Oceanography and Applied Geophysics (OGS), Trieste, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Mauro Celussi
- National Institute of Oceanography and Applied Geophysics (OGS), Trieste, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
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3
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Pernice MC, Forn I, Logares R, Massana R. A fungi hotspot deep in the ocean: explaining the presence of Gjaerumia minor in equatorial Pacific bathypelagic waters. Sci Rep 2024; 14:10601. [PMID: 38719921 PMCID: PMC11079054 DOI: 10.1038/s41598-024-61422-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 05/06/2024] [Indexed: 05/12/2024] Open
Abstract
A plant parasite associated with the white haze disease in apples, the Basidiomycota Gjaerumia minor, has been found in most samples of the global bathypelagic ocean. An analysis of environmental 18S rDNA sequences on 12 vertical profiles of the Malaspina 2010 expedition shows that the relative abundance of this cultured species increases with depth while its distribution is remarkably different between the deep waters of the Pacific and Atlantic oceans, being present in higher concentrations in the former. This is evident from sequence analysis and a microscopic survey with a species-specific newly designed TSA-FISH probe. Several hints point to the hypothesis that G. minor is transported to the deep ocean attached to particles, and the absence of G. minor in bathypelagic Atlantic waters could then be explained by the absence of this organism in surface waters of the equatorial Atlantic. The good correlation of G. minor biomass with Apparent Oxygen Utilization, recalcitrant carbon and free-living prokaryotic biomass in South Pacific waters, together with the identification of the observed cells as yeasts and not as resting spores (teliospores), point to the possibility that once arrived at deep layers this species keeps on growing and thriving.
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Affiliation(s)
- Massimo C Pernice
- Departament de Biologia Marina I Oceanografia, Institut de Ciències del Mar-CSIC, Barcelona, Spain.
| | - Irene Forn
- Departament de Biologia Marina I Oceanografia, Institut de Ciències del Mar-CSIC, Barcelona, Spain
| | - Ramiro Logares
- Departament de Biologia Marina I Oceanografia, Institut de Ciències del Mar-CSIC, Barcelona, Spain
| | - Ramon Massana
- Departament de Biologia Marina I Oceanografia, Institut de Ciències del Mar-CSIC, Barcelona, Spain
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Fernández-Valero AD, Karpov SA, Sampedro N, Gordi J, Timoneda N, Garcés E, Reñé A. Newly identified diversity of Dinomycetaceae (Rhizophydiales, Chytridiomycota), a family of fungal parasites of marine dinoflagellates. Eur J Protistol 2024; 93:126053. [PMID: 38350179 DOI: 10.1016/j.ejop.2024.126053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/15/2024]
Abstract
We identified two new parasite species of Chytridiomycota isolated during blooms of the dinoflagellate Alexandrium minutum in the coastal Mediterranean Sea. Light and electron microscopy together with molecular characterization of the nuclear 18S, ITS, and 28S rDNA regions led to their identification as two new species, Dinomyces gilberthii and Paradinomyces evelyniae, both belonging to the family Dinomycetaceae, order Rhizophydiales. Dinomyces gilberthii differs from the previously described D. arenysensis by the presence of discharge papillae and the development of a drop-shaped sporangium. Paradinomyces evelyniae differs from the previously described P. triforaminorum by the prominent lipid globule present in early sporangia and by the pointed end producing a rhizoid. The two chytrids differed in their geographical distribution. Dinomyces gilberthii was detected in several Mediterranean habitats, including harbours and beaches, and was particularly prevalent during summer dinoflagellate blooms. Its widespread occurrence in coastal ecosystems suggested a high level of adaptability to this environment. Paradinomyces evelyniae had a more restricted distribution in the coastal-marine environment, occurring in harbour sediments and only occasionally in the water column during winter and early spring. Paradinomyces evelyniae has previously been detected in the Baltic Sea, suggesting that its distribution encompasses contrasting coastal environments, although its presence is rare.
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Affiliation(s)
- Alan Denis Fernández-Valero
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC), Pg. Marítim de la Barceloneta, 37-49, 08003 Barcelona, Catalonia, Spain.
| | - Sergey A Karpov
- Department of Invertebrate Zoology, Biological Faculty, St Petersburg State University, Universitetskaya nab. 7/9, St Petersburg 199034, Russia; Zoological Institute of Russian Academy of Sciences, Universitetskaya nab. 1, St Petersburg 199034, Russia; North-Western State Medical University named after I.I. Mechnikov, Kirochnaya st. 41, St Petersburg 191015, Russia
| | - Nagore Sampedro
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC), Pg. Marítim de la Barceloneta, 37-49, 08003 Barcelona, Catalonia, Spain
| | - Jordina Gordi
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC), Pg. Marítim de la Barceloneta, 37-49, 08003 Barcelona, Catalonia, Spain
| | - Natàlia Timoneda
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC), Pg. Marítim de la Barceloneta, 37-49, 08003 Barcelona, Catalonia, Spain
| | - Esther Garcés
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC), Pg. Marítim de la Barceloneta, 37-49, 08003 Barcelona, Catalonia, Spain
| | - Albert Reñé
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC), Pg. Marítim de la Barceloneta, 37-49, 08003 Barcelona, Catalonia, Spain
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Nakagiri A, Hakotani A, Shino R, Miyazaki K, Endo N, Sotome K, Maekawa N. Taxonomic and life cycle reappraisals of the marine basidiomycete Nia vibrissa complex, with descriptions of three new Nia species. Mycologia 2024; 116:59-91. [PMID: 38109665 DOI: 10.1080/00275514.2023.2276028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 10/24/2023] [Indexed: 12/20/2023]
Abstract
The marine basidiomycete Nia vibrissa has been regarded as a species complex, possibly including several species, because morphological variations in fruitbody, spore, and spore appendage have been observed in materials from worldwide collections. Using more than 50 monosporic isolates of N. vibrissa-like fungi mainly obtained from Japanese beach coasts, we investigated their molecular phylogeny, morphological characteristics, mating compatibility, nuclear behavior during spore formation, and life cycles. Molecular phylogenetic analyses separated the examined strains into seven clades. Each clade of fungi exhibited distinctive characteristics in fruitbodies and spores produced by culturing monokaryotic strains and mated dikaryotic strains; these characteristics included the color of fruitbodies, apical structure of peridial hair hyphae, spore shape, and apical structure of spore appendages. Mating tests of monokaryotic strains demonstrated mating compatibility between strains within a clade and incompatibility among clades. Therefore, each clade of fungi was phylogenetically, morphologically, and biologically recognized as a different Nia species. Observation of the type specimen of N. vibrissa revealed a tiny T-shaped apical structure of spore appendages-not mentioned in the original description-that is unique to the species. This finding, together with the original description, suggests that our studied strains include N. aff. vibrissa, whose morphology is mostly identical to N. vibrissa sensu stricto, and three new species. Thus, we describe three new Nia species and propose emendation of the descriptions of the genus Nia. Culture-based studies have demonstrated that Nia species have both sexual and asexual morphs that produce morphologically similar fruitbodies (basidiomata and conidiomata) and spores (basidiospores and conidia). Because it has both morphs forming appendaged waterborne basidiospores and conidia, Nia must be the most well-adapted marine basidiomycete, ensuring the continuation of new generations by two morphs, while distributing in and inhabiting numerous marine environments.
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Affiliation(s)
- A Nakagiri
- Fungus/Mushroom Resource and Research Center, Faculty of Agriculture, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8553, Japan
| | - A Hakotani
- Graduate School of Sustainability Science, Department of Agricultural Sciences, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8553, Japan
| | - R Shino
- The United Graduate School of Agricultural Sciences, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8553, Japan
| | - K Miyazaki
- Graduate School of Sustainability Science, Department of Agricultural Sciences, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8553, Japan
| | - N Endo
- Fungus/Mushroom Resource and Research Center, Faculty of Agriculture, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8553, Japan
| | - K Sotome
- Fungus/Mushroom Resource and Research Center, Faculty of Agriculture, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8553, Japan
| | - N Maekawa
- Fungus/Mushroom Resource and Research Center, Faculty of Agriculture, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8553, Japan
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Nakbi A, Banaoues RC, Ben Dhiab R, Ghozzi K, Belgacem S, Challouf R, Haouas N, Babba H. Marine fungal community composition and diversity across a polluted site in the south Mediterranean coast: the Monastir Bay, Tunisia. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2024; 89:319-332. [PMID: 39219132 PMCID: wst_2023_415 DOI: 10.2166/wst.2023.415] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Marine fungi communities play a crucial role in the recycling of nutrients, restoration of biological systems, and the overall functioning of ecosystems. While aquatic fungal communities do react to pollution, there is a significant lack of information regarding the changes in the fungal community's structure, caused by marine pollution. In this study, we aim to address this gap in knowledge by investigating the range and makeup of fungal species present in marine environments in a polluted bay in Tunisia, spanning a biodiversity hotspot (Monastir Bay). Sequence analysis of the internal transcribed spacer region from culturable mycobiome and physicochemical parameters were investigated at seven sites in the bay. A total of 32 fungal taxa were identified at the genus and/or species levels and were assigned to four major groups (Aspergillacae 37.5%, Dothiomyceta 21.87%, Sordariamyceta 28.12%, and Yeasts 12.5%) with a remarkable predominance of Aspergillus genus. Assessment of the Shannon-Wiener diversity index and the Simpson dominance index revealed that the highest species diversity index (0.84) was recorded at the Kheniss site. Our results suggest the existence of diverse fungal communities, can be considered a useful community model for further ecological and evolutionary study of fungi in the bay.
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Affiliation(s)
- Amel Nakbi
- Marine Biodiversity Laboratory (BIOMAR) Code: LR16INSTM02, National Institute of Marine Sciences and Technologies (Annex Monastir) (INSTM), Monastir, Tunisia E-mail:
| | - Raja Chaâbane Banaoues
- Laboratory of Medical and Molecular Parasitology-Mycology LP3M (code LR12ES08), Department of Clinical Biology B, Faculty of Pharmacy, Monastir University, Monastir, Tunisia
| | - Rym Ben Dhiab
- Marine Biodiversity Laboratory (BIOMAR) Code: LR16INSTM02, National Institute of Marine Sciences and Technologies (Annex Monastir) (INSTM), Monastir, Tunisia
| | - Khemissa Ghozzi
- Marine Biodiversity Laboratory (BIOMAR) Code: LR16INSTM02, National Institute of Marine Sciences and Technologies (Annex Monastir) (INSTM), Monastir, Tunisia
| | - Sameh Belgacem
- Laboratory of Medical and Molecular Parasitology-Mycology LP3M (code LR12ES08), Department of Clinical Biology B, Faculty of Pharmacy, Monastir University, Monastir, Tunisia
| | - Rafika Challouf
- Marine Biodiversity Laboratory (BIOMAR) Code: LR16INSTM02, National Institute of Marine Sciences and Technologies (Annex Monastir) (INSTM), Monastir, Tunisia
| | - Najoua Haouas
- Laboratory of Medical and Molecular Parasitology-Mycology LP3M (code LR12ES08), Department of Clinical Biology B, Faculty of Pharmacy, Monastir University, Monastir, Tunisia
| | - Hamouda Babba
- Laboratory of Medical and Molecular Parasitology-Mycology LP3M (code LR12ES08), Department of Clinical Biology B, Faculty of Pharmacy, Monastir University, Monastir, Tunisia
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7
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Danz A, Quandt CA. A review of the taxonomic diversity, host-parasite interactions, and experimental research on chytrids that parasitize diatoms. Front Microbiol 2023; 14:1281648. [PMID: 38029223 PMCID: PMC10643281 DOI: 10.3389/fmicb.2023.1281648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/05/2023] [Indexed: 12/01/2023] Open
Abstract
Diatoms (Bacillariophyta) are a major source of primary production on Earth, generating between 1/4 to 1/2 of all oxygen. They are found in almost all bodies of water, the ice of mountains, the arctic and the antarctic, and soils. Diatoms are also a major source of food in aquatic systems, a key component of the silica cycle, and are carbon capturers in oceans. Recently, diatoms have been examined as sources of biofuels, food, and other economic boons. Chytrids are members of the Kingdom fungi comprising, at a minimum, Chytridiomycota, Blastocladiomycota, and Neocallimastigales. Most chytrids are saprobes, plant pathogens, or parasites, and play an important role in aquatic ecosystems. Chytrid parasitism of diatoms has been reported to cause epidemics of over 90% fatality, though most of the information regarding these epidemics is limited to interactions between just a few hosts and parasites. Given the ubiquity of diatoms, their importance in natural and economic systems, and the massive impact epidemics can have on populations, the relative lack of knowledge regarding parasitism by chytrids is alarming. Here we present a list of the firsthand accounts of diatoms reported parasitized by chytrids. The list includes 162 named parasitic chytrid-diatom interactions, with 63 unique chytrid taxa from 11 genera, and 74 unique diatom taxa from 28 genera. Prior to this review, no list of all documented diatom-chytrid interactions existed. We also synthesize the currently known methods of infection, defense, and experiments examining diatoms and chytrids, and we document the great need for work examining both a greater breadth of taxonomic diversity of parasites and hosts, and a greater depth of experiments probing their interactions. This resource is intended to serve as a building block for future researchers studying diatom-parasite interactions and global planktonic communities in both fresh and marine systems.
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Affiliation(s)
- August Danz
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, United States
- University of Colorado Museum of Natural History, Boulder, CO, United States
| | - C. Alisha Quandt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, United States
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Pagani DM, Ventura SPR, Vu D, Mendes-Pereira T, Ribeiro Tomé LM, de Carvalho DS, Costa-Rezende DH, Kato RB, García GJY, Geml J, Robert V, They NH, Brenig B, Azevedo V, Scroferneker ML, Valente P, Góes-Neto A. Unveiling Fungal Community Structure along Different Levels of Anthropic Disturbance in a South American Subtropical Lagoon. J Fungi (Basel) 2023; 9:890. [PMID: 37754998 PMCID: PMC10532596 DOI: 10.3390/jof9090890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/19/2023] [Accepted: 08/29/2023] [Indexed: 09/28/2023] Open
Abstract
Studies of fungal communities through amplicon metagenomics in aquatic environments, particularly in freshwater ecosystems, are still relatively recent. Unfortunately, many of these water bodies are facing growing threats from human expansion, such as effluent discharge from various human activities. As a result, these effluents have the potential to significantly alter the characteristics of water bodies and, subsequently, impact the diversity of their resident microorganisms. In this context, our objective was to investigate whether the fungal community structure varies according to the presence of different anthropic disturbances. We expect (i) the diversity of fungi will be greater and (ii) more specific unique operational taxonomic units (OTUs) related to each ecotonal system will be found compared to other sites of a lagoon. The study was conducted in the Tramandaí Lagoon (subtropical southern Brazil) at four distinct sampling points (estuary, middle of the lagoon, crop field area, and near a residential area where the Tramandaí River flows into the lagoon). As expected, the estuary and residential zones, which are ecotones, exhibited greater fungal diversity and more specific OTUs compared to the middle of the lagoon and crop field area. Moreover, a substantial proportion of fungal taxa could not be identified at the genus level, with many only classified at the phylum level, indicating potential new lineages. These findings underscore our limited understanding of the subtropical freshwater mycobiota.
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Affiliation(s)
- Danielle Machado Pagani
- Programa de Pós-Graduação em Microbiologia Agrícola e do Ambiente, Universidade Federal do Rio Grande do Sul, Porto Alegre 90010-150, RS, Brazil; (D.M.P.); (P.V.)
| | - Stefânia P. R. Ventura
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (S.P.R.V.); (R.B.K.); (G.J.Y.G.); (V.A.)
| | - Duong Vu
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (D.V.); (V.R.)
| | - Thairine Mendes-Pereira
- Programa de Pós-Graduação em Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (T.M.-P.); (L.M.R.T.); (D.S.d.C.)
| | - Luiz Marcelo Ribeiro Tomé
- Programa de Pós-Graduação em Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (T.M.-P.); (L.M.R.T.); (D.S.d.C.)
| | - Daniel Santana de Carvalho
- Programa de Pós-Graduação em Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (T.M.-P.); (L.M.R.T.); (D.S.d.C.)
| | - Diogo Henrique Costa-Rezende
- Departamento de Ciências Biológicas, Programa de Pós-Graduação em Botânica, Universidade Estadual de Feira de Santana, Feira de Santana 44036-900, BA, Brazil;
| | - Rodrigo Bentes Kato
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (S.P.R.V.); (R.B.K.); (G.J.Y.G.); (V.A.)
| | - Glen Jasper Yupanqui García
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (S.P.R.V.); (R.B.K.); (G.J.Y.G.); (V.A.)
| | - József Geml
- ELKH-EKKE Lendület Environmental Microbiome Research Group, Eszterházy Károly Catholic University, Leányka U. 6, 3300 Eger, Hungary;
| | - Vincent Robert
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (D.V.); (V.R.)
| | - Ng Haig They
- Laboratório de Ecologia Aquática Microbiana, Programa de Pós-Graduação em Biologia de Ambientes Aquáticos Continentais, Departamento Interdisciplinar, Centro de Estudos Costeiros, Limnológicos e Marinhos, Universidade Federal do Rio Grande do Sul, Campus Litoral Norte, Tramandaí 95590-000, RS, Brazil;
| | - Bertram Brenig
- Institute of Veterinary Medicine, Georg-August-University Goettingen, 37073 Göttingen, Germany;
| | - Vasco Azevedo
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (S.P.R.V.); (R.B.K.); (G.J.Y.G.); (V.A.)
- Laboratory of Cellular and Molecular Genetics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
| | - Maria Lúcia Scroferneker
- Programa de Pós-Graduação em Ciências Médicas, Universidade Federal do Rio Grande do Sul, Porto Alegre 90010-150, RS, Brazil;
| | - Patricia Valente
- Programa de Pós-Graduação em Microbiologia Agrícola e do Ambiente, Universidade Federal do Rio Grande do Sul, Porto Alegre 90010-150, RS, Brazil; (D.M.P.); (P.V.)
| | - Aristóteles Góes-Neto
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (S.P.R.V.); (R.B.K.); (G.J.Y.G.); (V.A.)
- Programa de Pós-Graduação em Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (T.M.-P.); (L.M.R.T.); (D.S.d.C.)
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Seto K, Simmons DR, Quandt CA, Frenken T, Dirks AC, Clemons RA, McKindles KM, McKay RML, James TY. A combined microscopy and single-cell sequencing approach reveals the ecology, morphology, and phylogeny of uncultured lineages of zoosporic fungi. mBio 2023; 14:e0131323. [PMID: 37486265 PMCID: PMC10470594 DOI: 10.1128/mbio.01313-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 07/25/2023] Open
Abstract
Environmental DNA analyses of fungal communities typically reveal a much larger diversity than can be ascribed to known species. Much of this hidden diversity lies within undescribed fungal lineages, especially the early diverging fungi (EDF). Although these EDF often represent new lineages even at the phylum level, they have never been cultured, making their morphology and ecology uncertain. One of the methods to characterize these uncultured fungi is a single-cell DNA sequencing approach. In this study, we established a large data set of single-cell sequences of EDF by manually isolating and photographing parasitic fungi on various hosts such as algae, protists, and micro-invertebrates, combined with subsequent long-read sequencing of the ribosomal DNA locus (rDNA). We successfully obtained rDNA sequences of 127 parasitic fungal cells, which clustered into 71 phylogenetic lineages belonging to seven phylum-level clades of EDF: Blastocladiomycota, Chytridiomycota, Aphelidiomycota, Rozellomycota, and three unknown phylum-level clades. Most of our single cells yielded novel sequences distinguished from both described taxa and existing metabarcoding data, indicating an expansive and hidden diversity of parasitic taxa of EDF. We also revealed an unexpected diversity of endobiotic Olpidium-like chytrids and hyper-parasitic lineages. Overall, by combining photographs of parasitic fungi with phylogenetic analyses, we were able to better understand the ecological function and morphology of many of the branches on the fungal tree of life known only from DNA sequences. IMPORTANCE Much of the diversity of microbes from natural habitats, such as soil and freshwater, comprise species and lineages that have never been isolated into pure culture. In part, this stems from a bias of culturing in favor of saprotrophic microbes over the myriad symbiotic ones that include parasitic and mutualistic relationships with other taxa. In the present study, we aimed to shed light on the ecological function and morphology of the many undescribed lineages of aquatic fungi by individually isolating and sequencing molecular barcodes from 127 cells of host-associated fungi using single-cell sequencing. By adding these sequences and their photographs into the fungal tree, we were able to understand the morphology of reproductive and vegetative structures of these novel fungi and to provide a hypothesized ecological function for them. These individual host-fungal cells revealed themselves to be complex environments despite their small size; numerous samples were hyper-parasitized with other zoosporic fungal lineages such as Rozellomycota.
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Affiliation(s)
- Kensuke Seto
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
- Faculty of Environment and Information Sciences, Yokohama National University, Yokohama, Kanagawa, Japan
| | - D. Rabern Simmons
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA
| | - C. Alisha Quandt
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Thijs Frenken
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
- Cluster Nature and Society, HAS University of Applied Sciences, 's-Hertogenbosch, the Netherlands
| | - Alden C. Dirks
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Rebecca A. Clemons
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Katelyn M. McKindles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
| | - R. Michael L. McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
- Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, Ohio, USA
| | - Timothy Y. James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
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10
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Yang J, Yun J, Liu X, Du W, Xiang M. Niche and ecosystem preference of earliest diverging fungi in soils. Mycology 2023; 14:239-255. [PMID: 37583459 PMCID: PMC10424602 DOI: 10.1080/21501203.2023.2237047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 07/11/2023] [Indexed: 08/17/2023] Open
Abstract
Within the supergroup Rotosphaeromycetes, or "Holomycota"/"Nucletmycea", there are several well-recognised unicellular clades in the earliest diverging fungi (EDF). However, we know little about their occurrence. Here, we investigated EDF in the rhizosphere and bulk soils from cropland, forest, orchard, and wetland ecosystems around the Beijing-Hebei area, China, to illustrate their niche and ecosystem preference. More than 500 new operational taxonomic units (OTUs) of EDF were detected based on the 18S rRNA genes. Microsporida and Aphelida constitute dominant groups, whereas Rozellosporida was quite rare. Although the EDF community was site-specific, the soil chemical characteristics, vegetation, and other eukaryotic microorganisms were the key factors driving the occurrence of EDF. Moreover, the stochastic process consisted the most of the EDF community assembly.
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Affiliation(s)
- Jiarui Yang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, China
| | - Juanli Yun
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- School of Environmental Science and Engineering, Shaanxi University of Science and Technology, Xi’an, China
| | - Xingzhong Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, China
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- School of Environmental Science and Engineering, Shaanxi University of Science and Technology, Xi’an, China
| | - Meichun Xiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, China
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11
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Wang M, Mara P, Burgaud G, Edgcomb V, Long X, Yang H, Cai L, Li W. Metatranscriptomics and metabarcoding reveal spatiotemporal shifts in fungal communities and their activities in Chinese coastal waters. Mol Ecol 2023; 32:2750-2765. [PMID: 36852430 DOI: 10.1111/mec.16905] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 03/01/2023]
Abstract
Fungal communities are diverse and abundant in coastal waters, yet, their ecological roles and adaptations remain largely unknown. To address these gaps, ITS2 metabarcoding and metatranscriptomic analyses were used to capture the whole suite of fungal diversity and their metabolic potential in water column and sediments in the Yellow Sea during August and October 2019. ITS2 metabarcoding described successfully the abundance of Dikarya during August and October at the different examined habitats, but strongly underrepresented or failed to identify other fungal taxa, including zoosporic and early-diverging lineages, that were abundant in the mycobiome as uncovered by metatranscriptomes. Metatranscriptomics also revealed enriched expression of genes annotated to zoosporic fungi (e.g., chytrids) mainly in the surface water column in October. This enriched expression was correlated with the two-fold increase in chlorophyll-a intensity attributed to phytoplanktonic species which are known to be parasitized by chytrids. The concurrent high expression of genes related to calcium signalling and GTPase activity suggested that these metabolic traits facilitate the parasitic lifestyle of chytrids. Similarly, elevated expression of phagosome genes annotated to Rozellomycota, an early-diverging fungal phylum not fully detected with ITS2 metabarcoding, suggested that this taxon utilizes a suite of feeding modes, including phagotrophy in this coastal setting. Our data highlight the necessity of using combined approaches to accurately describe the community structure of coastal mycobiome. We also provide in-depth insights into the fungal ecological roles in coastal waters, and report potential metabolic mechanisms utilized by fungi to cope with environmental stresses that occur during distinct seasonal months in coastal ecosystems.
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Affiliation(s)
- Mengmeng Wang
- College of Science, Shantou University, Shantou, China.,State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Paraskevi Mara
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Gaëtan Burgaud
- University of Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, Plouzané, France
| | - Virginia Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Xuedan Long
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Haiping Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wei Li
- College of Science, Shantou University, Shantou, China
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12
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Klawonn I, Van den Wyngaert S, Iversen MH, Walles TJW, Flintrop CM, Cisternas-Novoa C, Nejstgaard JC, Kagami M, Grossart HP. Fungal parasitism on diatoms alters formation and bio-physical properties of sinking aggregates. Commun Biol 2023; 6:206. [PMID: 36810576 PMCID: PMC9944279 DOI: 10.1038/s42003-023-04453-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 01/10/2023] [Indexed: 02/24/2023] Open
Abstract
Phytoplankton forms the base of aquatic food webs and element cycling in diverse aquatic systems. The fate of phytoplankton-derived organic matter, however, often remains unresolved as it is controlled by complex, interlinked remineralization and sedimentation processes. We here investigate a rarely considered control mechanism on sinking organic matter fluxes: fungal parasites infecting phytoplankton. We demonstrate that bacterial colonization is promoted 3.5-fold on fungal-infected phytoplankton cells in comparison to non-infected cells in a cultured model pathosystem (diatom Synedra, fungal microparasite Zygophlyctis, and co-growing bacteria), and even ≥17-fold in field-sampled populations (Planktothrix, Synedra, and Fragilaria). Additional data obtained using the Synedra-Zygophlyctis model system reveals that fungal infections reduce the formation of aggregates. Moreover, carbon respiration is 2-fold higher and settling velocities are 11-48% lower for similar-sized fungal-infected vs. non-infected aggregates. Our data imply that parasites can effectively control the fate of phytoplankton-derived organic matter on a single-cell to single-aggregate scale, potentially enhancing remineralization and reducing sedimentation in freshwater and coastal systems.
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Affiliation(s)
- Isabell Klawonn
- Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 16775, Stechlin, Germany.
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde (IOW), 18119, Rostock, Germany.
| | - Silke Van den Wyngaert
- Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 16775, Stechlin, Germany
- Department of Biology, University of Turku, 20014, Turku, Finland
| | - Morten H Iversen
- Alfred Wegener Institute (AWI), Helmholtz Centre for Polar and Marine Research, 27570, Bremerhaven, Germany
- Centre for Marine Environmental Sciences (MARUM) and University of Bremen, 28359, Bremen, Germany
| | - Tim J W Walles
- Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 16775, Stechlin, Germany
| | - Clara M Flintrop
- Alfred Wegener Institute (AWI), Helmholtz Centre for Polar and Marine Research, 27570, Bremerhaven, Germany
- Centre for Marine Environmental Sciences (MARUM) and University of Bremen, 28359, Bremen, Germany
- The Inter-University Institute for Marine Sciences in Eilat, Eilat, 8810302, Israel
| | - Carolina Cisternas-Novoa
- Helmholtz Centre for Ocean Research (GEOMAR), 24148, Kiel, Germany
- Ocean Sciences Centre, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada
| | - Jens C Nejstgaard
- Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 16775, Stechlin, Germany
| | - Maiko Kagami
- Faculty of Science, Toho University, Funabashi, Chiba, 274‑8510, Japan
- Faculty of Environment and Information Sciences, Yokohama National University, Yokohama, Kanagawa, 240‑8502, Japan
| | - Hans-Peter Grossart
- Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 16775, Stechlin, Germany
- Institute of Biochemistry and Biology, Potsdam University, 14469, Potsdam, Germany
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13
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Munusamy M, Tan K, Nge CE, Gakuubi MM, Crasta S, Kanagasundaram Y, Ng SB. Diversity and Biosynthetic Potential of Fungi Isolated from St. John's Island, Singapore. Int J Mol Sci 2023; 24:1033. [PMID: 36674548 PMCID: PMC9861175 DOI: 10.3390/ijms24021033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/01/2022] [Accepted: 12/13/2022] [Indexed: 01/06/2023] Open
Abstract
Adaptation to a wide variety of habitats allows fungi to develop unique abilities to produce diverse secondary metabolites with diverse bioactivities. In this study, 30 Ascomycetes fungi isolated from St. John's Island, Singapore were investigated for their general biosynthetic potential and their ability to produce antimicrobial secondary metabolites (SMs). All the 30 fungal isolates belong to the Phylum Ascomycota and are distributed into 6 orders and 18 genera with Order Hypocreales having the highest number of representative (37%). Screening for polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) genes using degenerate PCR led to the identification of 23 polyketide synthases (PKSs) and 5 nonribosomal peptide synthetases (NRPSs) grouped into nine distinct clades based on their reduction capabilities. Some of the identified PKSs genes share high similarities between species and known reference genes, suggesting the possibility of conserved biosynthesis of closely related compounds from different fungi. Fungal extracts were tested for their antimicrobial activity against S. aureus, Methicillin-resistant S. aureus (MRSA), and Candida albicans. Bioassay-guided fractionation of the active constituents from two promising isolates resulted in the isolation of seven compounds: Penilumamides A, D, and E from strain F4335 and xanthomegnin, viomellein, pretrichodermamide C and vioxanthin from strain F7180. Vioxanthin exhibited the best antibacterial activity with IC50 values of 3.0 μM and 1.6 μM against S. aureus and MRSA respectively. Viomellein revealed weak antiproliferative activity against A549 cells with an IC50 of 42 μM. The results from this study give valuable insights into the diversity and biosynthetic potential of fungi from this unique habitat and forms a background for an in-depth analysis of the biosynthetic capability of selected strains of interest with the aim of discovering novel fungal natural products.
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Affiliation(s)
- Madhaiyan Munusamy
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore
| | - Kenneth Tan
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore
| | - Choy Eng Nge
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore
| | - Martin Muthee Gakuubi
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Sharon Crasta
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore
| | - Yoganathan Kanagasundaram
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore
| | - Siew Bee Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore
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14
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Klawonn I, Dunker S, Kagami M, Grossart HP, Van den Wyngaert S. Intercomparison of Two Fluorescent Dyes to Visualize Parasitic Fungi (Chytridiomycota) on Phytoplankton. MICROBIAL ECOLOGY 2023; 85:9-23. [PMID: 34854932 PMCID: PMC9849195 DOI: 10.1007/s00248-021-01893-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
Fungal microparasites (here chytrids) are widely distributed and yet, they are often overlooked in aquatic environments. To facilitate the detection of microparasites, we revisited the applicability of two fungal cell wall markers, Calcofluor White (CFW) and wheat germ agglutinin (WGA), for the direct visualization of chytrid infections on phytoplankton in laboratory-maintained isolates and field-sampled communities. Using a comprehensive set of chytrid-phytoplankton model pathosystems, we verified the staining pattern on diverse morphological structures of chytrids via fluorescence microscopy. Empty sporangia were stained most effectively, followed by encysted zoospores and im-/mature sporangia, while the staining success was more variable for rhizoids, stalks, and resting spores. In a few instances, the staining was unsuccessful (mostly with WGA), presumably due to insufficient cell fixation, gelatinous cell coatings, and multilayered cell walls. CFW and WGA staining could be done in Utermöhl chambers or on polycarbonate filters, but CFW staining on filters seemed less advisable due to high background fluorescence. To visualize chytrids, 1 µg dye mL-1 was sufficient (but 5 µg mL-1 are recommended). Using a dual CFW-WGA staining protocol, we detected multiple, mostly undescribed chytrids in two natural systems (freshwater and coastal), while falsely positive or negative stained cells were well detectable. As a proof-of-concept, we moreover conducted imaging flow cytometry, as a potential high-throughput technology for quantifying chytrid infections. Our guidelines and recommendations are expected to facilitate the detection of chytrid epidemics and to unveil their ecological and economical imprint in natural and engineered aquatic systems.
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Affiliation(s)
- Isabell Klawonn
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587, Berlin, Germany.
- Leibniz Institute for Baltic Sea Research (IOW), Seestrasse 15, 18119, Rostock, Germany.
| | - Susanne Dunker
- Department for Physiological Diversity, Helmholtz Centre for Environmental Research (UFZ), 04318, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv), 04103, Leipzig, Germany
| | - Maiko Kagami
- Faculty of Science, Toho University, Funabashi, Chiba, 274-8510, Japan
- Faculty of Environment and Information Sciences, Yokohama National University, Yokohama, Kanagawa, 240-8502, Japan
| | - Hans-Peter Grossart
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587, Berlin, Germany
- Institute of Biochemistry and Biology, Potsdam University, 14476, Potsdam, Germany
| | - Silke Van den Wyngaert
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587, Berlin, Germany.
- WasserCluster Lunz, Biologische Station, Dr. Carl Kupelwieser Promenade 5, 3293, Lunz am See, Austria.
- Department of Biology, University of Turku, Vesilinnantie 5, 20014, Turku, Finland.
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15
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Fernández-Valero AD, Reñé A, Timoneda N, Sampedro N, Garcés E. Dinoflagellate hosts determine the community structure of marine Chytridiomycota: Demonstration of their prominent interactions. Environ Microbiol 2022; 24:5951-5965. [PMID: 36057937 PMCID: PMC10087856 DOI: 10.1111/1462-2920.16182] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/26/2022] [Indexed: 01/12/2023]
Abstract
The interactions of parasitic fungi with their phytoplankton hosts in the marine environment are mostly unknown. In this study, we evaluated the diversity of Chytridiomycota in phytoplankton communities dominated by dinoflagellates at several coastal locations in the NW Mediterranean Sea and demonstrated the most prominent interactions of these parasites with their hosts. The protist community in seawater differed from that in sediment, with the latter characterized by a greater heterogeneity of putative hosts, such as dinoflagellates and diatoms, as well as a chytrid community more diverse in its composition and with a higher relative abundance. Chytrids accounted for 77 amplicon sequence variants, of which 70 were found exclusively among different blooming host species. The relative abundance of chytrids was highest in samples dominated by the dinoflagellate genera Ostreopsis and Alexandrium, clearly indicating the presence of specific chytrid communities. The establishment of parasitoid-host co-cultures of chytrids and dinoflagellates allowed the morphological identification and molecular characterization of three species of Chytridiomycota, including Dinomyces arenysensis, as one of the most abundant environmental sequences, and the discovery of two other species not yet described.
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Affiliation(s)
- Alan Denis Fernández-Valero
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC), Barcelona, Catalonia, Spain
| | - Albert Reñé
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC), Barcelona, Catalonia, Spain
| | - Natàlia Timoneda
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC), Barcelona, Catalonia, Spain
| | - Nagore Sampedro
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC), Barcelona, Catalonia, Spain
| | - Esther Garcés
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC), Barcelona, Catalonia, Spain
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16
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Navvabi A, Homaei A, Pletschke BI, Navvabi N, Kim SK. Marine Cellulases and their Biotechnological Significance from Industrial Perspectives. Curr Pharm Des 2022; 28:3325-3336. [PMID: 35388747 DOI: 10.2174/1381612828666220406125132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 11/03/2021] [Accepted: 01/18/2022] [Indexed: 01/28/2023]
Abstract
Marine microorganisms represent virtually unlimited sources of novel biological compounds and can survive extreme conditions. Cellulases, a group of enzymes that are able to degrade cellulosic materials, are in high demand in various industrial and biotechnological applications, such as in the medical and pharmaceutical industries, food, fuel, agriculture, and single-cell protein, and as probiotics in aquaculture. The cellulosic biopolymer is a renewable resource and is a linearly arranged polysaccharide of glucose, with repeating units of disaccharide connected via β-1,4-glycosidic bonds, which are broken down by cellulase. A great deal of biodiversity resides in the ocean, and marine systems produce a wide range of distinct, new bioactive compounds that remain available but dormant for many years. The marine environment is filled with biomass from known and unknown vertebrates and invertebrate microorganisms, with much potential for use in medicine and biotechnology. Hence, complex polysaccharides derived from marine sources are a rich resource of microorganisms equipped with enzymes for polysaccharides degradation. Marine cellulases' extracts from the isolates are tested for their functional role in degrading seaweed and modifying wastes to low molecular fragments. They purify and renew environments by eliminating possible feedstocks of pollution. This review aims to examine the various types of marine cellulase producers and assess the ability of these microorganisms to produce these enzymes and their subsequent biotechnological applications.
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Affiliation(s)
- Azita Navvabi
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran
| | - Ahmad Homaei
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran
| | - Brett I Pletschke
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa
| | - Nazila Navvabi
- Department of Tumor Biology and Immunotherapy, Molecular Biology of Cancer, Institute of Experimental Medicine, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Prague, Czech Republic
| | - Se-Kwon Kim
- Department of Marine Sciences and Convergent Technology, Hanyang University, Ansan, Seoul 426-791, Republic of Korea
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17
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Vass M, Eriksson K, Carlsson-Graner U, Wikner J, Andersson A. Co-occurrences enhance our understanding of aquatic fungal metacommunity assembly and reveal potential host-parasite interactions. FEMS Microbiol Ecol 2022; 98:fiac120. [PMID: 36202390 PMCID: PMC9621394 DOI: 10.1093/femsec/fiac120] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/30/2022] [Accepted: 10/03/2022] [Indexed: 01/21/2023] Open
Abstract
Our knowledge of aquatic fungal communities, their assembly, distributions and ecological roles in marine ecosystems is scarce. Hence, we aimed to investigate fungal metacommunities of coastal habitats in a subarctic zone (northern Baltic Sea, Sweden). Using a novel joint species distribution model and network approach, we quantified the importance of biotic associations contributing to the assembly of mycoplankton, further, detected potential biotic interactions between fungi-algae pairs, respectively. Our long-read metabarcoding approach identified 493 fungal taxa, of which a dominant fraction (44.4%) was assigned as early-diverging fungi (i.e. Cryptomycota and Chytridiomycota). Alpha diversity of mycoplankton declined and community compositions changed along inlet-bay-offshore transects. The distributions of most fungi were rather influenced by environmental factors than by spatial drivers, and the influence of biotic associations was pronounced when environmental filtering was weak. We found great number of co-occurrences (120) among the dominant fungal groups, and the 25 associations between fungal and algal OTUs suggested potential host-parasite and/or saprotroph links, supporting a Cryptomycota-based mycoloop pathway. We emphasize that the contribution of biotic associations to mycoplankton assembly are important to consider in future studies as it helps to improve predictions of species distributions in aquatic ecosystems.
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Affiliation(s)
- Máté Vass
- Department of Ecology and Environmental Science, Umeå University, SE-901 87, Umeå, Sweden
| | - Karolina Eriksson
- Department of Ecology and Environmental Science, Umeå University, SE-901 87, Umeå, Sweden
| | - Ulla Carlsson-Graner
- Department of Ecology and Environmental Science, Umeå University, SE-901 87, Umeå, Sweden
| | - Johan Wikner
- Department of Ecology and Environmental Science, Umeå University, SE-901 87, Umeå, Sweden
- Sweden Umeå Marine Sciences Centre, Umeå University, SE-905 71, Hörnefors, Sweden
| | - Agneta Andersson
- Department of Ecology and Environmental Science, Umeå University, SE-901 87, Umeå, Sweden
- Sweden Umeå Marine Sciences Centre, Umeå University, SE-905 71, Hörnefors, Sweden
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18
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Wijayawardene NN, Dai DQ, Jayasinghe PK, Gunasekara SS, Nagano Y, Tibpromma S, Suwannarach N, Boonyuen N. Ecological and Oceanographic Perspectives in Future Marine Fungal Taxonomy. J Fungi (Basel) 2022; 8:1141. [PMID: 36354908 PMCID: PMC9696965 DOI: 10.3390/jof8111141] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/21/2022] [Accepted: 10/22/2022] [Indexed: 11/07/2023] Open
Abstract
Marine fungi are an ecological rather than a taxonomic group that has been widely researched. Significant progress has been made in documenting their phylogeny, biodiversity, ultrastructure, ecology, physiology, and capacity for degradation of lignocellulosic compounds. This review (concept paper) summarizes the current knowledge of marine fungal diversity and provides an integrated and comprehensive view of their ecological roles in the world's oceans. Novel terms for 'semi marine fungi' and 'marine fungi' are proposed based on the existence of fungi in various oceanic environments. The major maritime currents and upwelling that affect species diversity are discussed. This paper also forecasts under-explored regions with a greater diversity of marine taxa based on oceanic currents. The prospects for marine and semi-marine mycology are highlighted, notably, technological developments in culture-independent sequencing approaches for strengthening our present understanding of marine fungi's ecological roles.
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Affiliation(s)
- Nalin N. Wijayawardene
- Centre for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
- Section of Genetics, Institute for Research and Development in Health and Social Care, No: 393/3, Lily Avenue, Off Robert Gunawardane Mawatha, Battaramulla 10120, Sri Lanka
- National Institute of Fundamental Studies, Hantana Road, Kandy 20000, Sri Lanka
| | - Don-Qin Dai
- Centre for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
| | - Prabath K. Jayasinghe
- National Aquatic Resources Research and Development Agency (NARA), Crow Island, Colombo 00150, Sri Lanka
| | - Sudheera S. Gunasekara
- National Aquatic Resources Research and Development Agency (NARA), Crow Island, Colombo 00150, Sri Lanka
| | - Yuriko Nagano
- Deep-Sea Biodiversity Research Group, Marine Biodiversity and Environmental Assessment Research Center, Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Saowaluck Tibpromma
- Centre for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
| | - Nakarin Suwannarach
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Nattawut Boonyuen
- Plant Microbe Interaction Research Team (APMT), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
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19
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The Culturable Mycobiota of Sediments and Associated Microplastics: From a Harbor to a Marine Protected Area, a Comparative Study. J Fungi (Basel) 2022; 8:jof8090927. [PMID: 36135652 PMCID: PMC9501098 DOI: 10.3390/jof8090927] [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: 08/09/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
Fungi are an essential component of marine ecosystems, although little is known about their global distribution and underwater diversity, especially in sediments. Microplastics (MPs) are widespread contaminants worldwide and threaten the organisms present in the oceans. In this study, we investigated the fungal abundance and diversity in sediments, as well as the MPs, of three sites with different anthropogenic impacts in the Mediterranean Sea: the harbor of Livorno, the marine protected area “Secche della Meloria”; and an intermediate point, respectively. A total of 1526 isolates were cultured and identified using a polyphasic approach. For many of the fungal species this is the first record in a marine environment. A comparison with the mycobiota associated with the sediments and MPs underlined a “substrate specificity”, highlighting the complexity of MP-associated fungal assemblages, potentially leading to altered microbial activities and hence changes in ecosystem functions. A further driving force that acts on the fungal communities associated with sediments and MPs is sampling sites with different anthropogenic impacts.
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20
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Sen K, Sen B, Wang G. Diversity, Abundance, and Ecological Roles of Planktonic Fungi in Marine Environments. J Fungi (Basel) 2022; 8:jof8050491. [PMID: 35628747 PMCID: PMC9147564 DOI: 10.3390/jof8050491] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 02/07/2023] Open
Abstract
Fungi are considered terrestrial and oceans are a “fungal desert”. However, with the considerable progress made over past decades, fungi have emerged as morphologically, phylogenetically, and functionally diverse components of the marine water column. Although their communities are influenced by a plethora of environmental factors, the most influential include salinity, temperature, nutrients, and dissolved oxygen, suggesting that fungi respond to local environmental gradients. The biomass carbon of planktonic fungi exhibits spatiotemporal dynamics and can reach up to 1 μg CL−1 of seawater, rivaling bacteria on some occasions, which suggests their active and important role in the water column. In the nutrient-rich coastal water column, there is increasing evidence for their contribution to biogeochemical cycling and food web dynamics on account of their saprotrophic, parasitic, hyper-parasitic, and pathogenic attributes. Conversely, relatively little is known about their function in the open-ocean water column. Interestingly, methodological advances in sequencing and omics approach, the standardization of sequence data analysis tools, and integration of data through network analyses are enhancing our current understanding of the ecological roles of these multifarious and enigmatic members of the marine water column. This review summarizes the current knowledge of the diversity and abundance of planktonic fungi in the world’s oceans and provides an integrated and holistic view of their ecological roles.
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Affiliation(s)
- Kalyani Sen
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Biswarup Sen
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Guangyi Wang
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin 300072, China
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21
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Li J, Cui L, Delgado-Baquerizo M, Wang J, Zhu Y, Wang R, Li W, Lei Y, Zhai X, Zhao X, Singh BK. Fungi drive soil multifunctionality in the coastal salt marsh ecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 818:151673. [PMID: 34793796 DOI: 10.1016/j.scitotenv.2021.151673] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 10/14/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
Salt marshes are highly productive intertidal wetlands located in temperate climatic zones, in which marine-to-terrestrial transition significantly influences microbial life. Numerous studies revealed the important coupling relationship between microbial diversity and ecosystem functions in terrestrial ecosystems, however, the importance of microbial diversity in maintaining soil functions in coastal ecosystems remains poorly understood. Here, we studied the shifts of microbial communities and soil multifunctionality (SMF; nine functions related with C, N and P cycling) along a vegetation gradient in a salt marsh ecosystem and investigated the microbial diversity - ecosystem function relationship. The aboveground vegetation shifted from mud flat (MF) to Scirpus triqueter (SM) and then Phragmites australis (PA) with increasing distance away from the sea. Average approach showed that the SMF was much higher in halophytes covered zones including SM and PA than in MF. Structural equation model (SEM) analysis confirmed that vegetation was an important predictor on SMF besides moisture and organic carbon. Linear regression and multiple threshold methods showed that in MF and SM zones, fungal rather than bacterial richness was significantly and positively correlated with SMF, while in the PA zone microbial diversity did not relate with SMF. Random forest analysis identified several Ascomycota taxa with preference over marine environment as strong predictors of SMF. Taken together, our study lays the basis for a better understanding on the relationships between belowground microbial diversity and soil functions in coastal ecosystems.
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Affiliation(s)
- Jing Li
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing Key Laboratory of Wetland Ecological Function and Restoration, Beijing 100091, China; Beijing Hanshiqiao National Wetland Ecosystem Research Station, Beijing 101399, China
| | - Lijuan Cui
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing Key Laboratory of Wetland Ecological Function and Restoration, Beijing 100091, China; Beijing Hanshiqiao National Wetland Ecosystem Research Station, Beijing 101399, China.
| | - Manuel Delgado-Baquerizo
- Departamento de Ecología and Instituto Multidisciplinar para el Estudio del Medio "Ramón Margalef", Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, 03690 San Vicente del Raspeig, Alicante, Spain
| | - Juntao Wang
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales 2751, Australia; Global Centre for Land-Based Innovation, Western Sydney University, Penrith South DC, NSW 2751, Australia
| | - Yinuo Zhu
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing Key Laboratory of Wetland Ecological Function and Restoration, Beijing 100091, China; Beijing Hanshiqiao National Wetland Ecosystem Research Station, Beijing 101399, China
| | - Rumiao Wang
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing Key Laboratory of Wetland Ecological Function and Restoration, Beijing 100091, China; Beijing Hanshiqiao National Wetland Ecosystem Research Station, Beijing 101399, China
| | - Wei Li
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing Key Laboratory of Wetland Ecological Function and Restoration, Beijing 100091, China; Beijing Hanshiqiao National Wetland Ecosystem Research Station, Beijing 101399, China
| | - Yinru Lei
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing Key Laboratory of Wetland Ecological Function and Restoration, Beijing 100091, China; Beijing Hanshiqiao National Wetland Ecosystem Research Station, Beijing 101399, China
| | - Xiajie Zhai
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing Key Laboratory of Wetland Ecological Function and Restoration, Beijing 100091, China; Beijing Hanshiqiao National Wetland Ecosystem Research Station, Beijing 101399, China
| | - Xinsheng Zhao
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing Key Laboratory of Wetland Ecological Function and Restoration, Beijing 100091, China; Beijing Hanshiqiao National Wetland Ecosystem Research Station, Beijing 101399, China
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales 2751, Australia; Global Centre for Land-Based Innovation, Western Sydney University, Penrith South DC, NSW 2751, Australia
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Can Aggregate-Associated Organisms Influence the Fouling in a SWRO Desalination Plant? Microorganisms 2022; 10:microorganisms10040682. [PMID: 35456734 PMCID: PMC9032733 DOI: 10.3390/microorganisms10040682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/17/2022] [Accepted: 03/17/2022] [Indexed: 12/10/2022] Open
Abstract
This pilot study investigates the formation of aggregates within a desalination plant, before and after pre-treatment, as well as their potential impact on fouling. The objective is to provide an understanding of the biofouling potential of the feed water within a seawater reverse osmosis (SWRO) desalination plant, due to the limited removal of fouling precursors. The 16S and 18S rRNA was extracted from the water samples, and the aggregates and sequenced. Pre-treatment systems, within the plant remove < 5 µm precursors and organisms; however, smaller size particles progress through the plant, allowing for the formation of aggregates. These become hot spots for microbes, due to their nutrient gradients, facilitating the formation of niche environments, supporting the proliferation of those organisms. Aggregate-associated organisms are consistent with those identified on fouled SWRO membranes. This study examines, for the first time, the factors supporting the formation of aggregates within a desalination system, as well as their microbial communities and biofouling potential.
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Jones EBG, Ramakrishna S, Vikineswary S, Das D, Bahkali AH, Guo SY, Pang KL. How Do Fungi Survive in the Sea and Respond to Climate Change? J Fungi (Basel) 2022; 8:jof8030291. [PMID: 35330293 PMCID: PMC8949214 DOI: 10.3390/jof8030291] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/08/2022] [Accepted: 03/10/2022] [Indexed: 02/05/2023] Open
Abstract
With the over 2000 marine fungi and fungal-like organisms documented so far, some have adapted fully to life in the sea, while some have the ability to tolerate environmental conditions in the marine milieu. These organisms have evolved various mechanisms for growth in the marine environment, especially against salinity gradients. This review highlights the response of marine fungi, fungal-like organisms and terrestrial fungi (for comparison) towards salinity variations in terms of their growth, spore germination, sporulation, physiology, and genetic adaptability. Marine, freshwater and terrestrial fungi and fungal-like organisms vary greatly in their response to salinity. Generally, terrestrial and freshwater fungi grow, germinate and sporulate better at lower salinities, while marine fungi do so over a wide range of salinities. Zoosporic fungal-like organisms are more sensitive to salinity than true fungi, especially Ascomycota and Basidiomycota. Labyrinthulomycota and marine Oomycota are more salinity tolerant than saprolegniaceous organisms in terms of growth and reproduction. Wide adaptability to saline conditions in marine or marine-related habitats requires mechanisms for maintaining accumulation of ions in the vacuoles, the exclusion of high levels of sodium chloride, the maintenance of turgor in the mycelium, optimal growth at alkaline pH, a broad temperature growth range from polar to tropical waters, and growth at depths and often under anoxic conditions, and these properties may allow marine fungi to positively respond to the challenges that climate change will bring. Other related topics will also be discussed in this article, such as the effect of salinity on secondary metabolite production by marine fungi, their evolution in the sea, and marine endophytes.
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Affiliation(s)
- E. B. Gareth Jones
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (E.B.G.J.); (A.H.B.)
| | - Sundari Ramakrishna
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia; (S.R.); (S.V.); (D.D.)
| | - Sabaratnam Vikineswary
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia; (S.R.); (S.V.); (D.D.)
| | - Diptosh Das
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia; (S.R.); (S.V.); (D.D.)
| | - Ali H. Bahkali
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (E.B.G.J.); (A.H.B.)
| | - Sheng-Yu Guo
- Institute of Marine Biology and Centre of Excellence for the Oceans, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung 202301, Taiwan;
| | - Ka-Lai Pang
- Institute of Marine Biology and Centre of Excellence for the Oceans, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung 202301, Taiwan;
- Correspondence:
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25
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Ilicic D, Woodhouse J, Karsten U, Zimmermann J, Wichard T, Quartino ML, Campana GL, Livenets A, Van den Wyngaert S, Grossart HP. Antarctic Glacial Meltwater Impacts the Diversity of Fungal Parasites Associated With Benthic Diatoms in Shallow Coastal Zones. Front Microbiol 2022; 13:805694. [PMID: 35308360 PMCID: PMC8931407 DOI: 10.3389/fmicb.2022.805694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/12/2022] [Indexed: 01/04/2023] Open
Abstract
Aquatic ecosystems are frequently overlooked as fungal habitats, although there is increasing evidence that their diversity and ecological importance are greater than previously considered. Aquatic fungi are critical and abundant components of nutrient cycling and food web dynamics, e.g., exerting top-down control on phytoplankton communities and forming symbioses with many marine microorganisms. However, their relevance for microphytobenthic communities is almost unexplored. In the light of global warming, polar regions face extreme changes in abiotic factors with a severe impact on biodiversity and ecosystem functioning. Therefore, this study aimed to describe, for the first time, fungal diversity in Antarctic benthic habitats along the salinity gradient and to determine the co-occurrence of fungal parasites with their algal hosts, which were dominated by benthic diatoms. Our results reveal that Ascomycota and Chytridiomycota are the most abundant fungal taxa in these habitats. We show that also in Antarctic waters, salinity has a major impact on shaping not just fungal but rather the whole eukaryotic community composition, with a diversity of aquatic fungi increasing as salinity decreases. Moreover, we determined correlations between putative fungal parasites and potential benthic diatom hosts, highlighting the need for further systematic analysis of fungal diversity along with studies on taxonomy and ecological roles of Chytridiomycota.
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Affiliation(s)
- Doris Ilicic
- Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Neuglobsow, Germany
| | - Jason Woodhouse
- Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Neuglobsow, Germany
| | - Ulf Karsten
- Institute of Biological Sciences, Applied Ecology and Phycology, University of Rostock, Rostock, Germany
| | - Jonas Zimmermann
- Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Berlin, Germany
| | - Thomas Wichard
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Jena, Germany
| | | | - Gabriela Laura Campana
- Department of Coastal Biology, Argentinean Antarctic Institute, Buenos Aires, Argentina
- Department of Basic Sciences, National University of Luján, Luján, Buenos Aires, Argentina
| | - Alexandra Livenets
- Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Neuglobsow, Germany
| | | | - Hans-Peter Grossart
- Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Neuglobsow, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- *Correspondence: Hans-Peter Grossart,
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26
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Ilicic D, Grossart HP. Basal Parasitic Fungi in Marine Food Webs-A Mystery Yet to Unravel. J Fungi (Basel) 2022; 8:114. [PMID: 35205868 PMCID: PMC8874645 DOI: 10.3390/jof8020114] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/20/2022] [Accepted: 01/25/2022] [Indexed: 02/01/2023] Open
Abstract
Although aquatic and parasitic fungi have been well known for more than 100 years, they have only recently received increased awareness due to their key roles in microbial food webs and biogeochemical cycles. There is growing evidence indicating that fungi inhabit a wide range of marine habitats, from the deep sea all the way to surface waters, and recent advances in molecular tools, in particular metagenome approaches, reveal that their diversity is much greater and their ecological roles more important than previously considered. Parasitism constitutes one of the most widespread ecological interactions in nature, occurring in almost all environments. Despite that, the diversity of fungal parasites, their ecological functions, and, in particular their interactions with other microorganisms remain largely speculative, unexplored and are often missing from current theoretical concepts in marine ecology and biogeochemistry. In this review, we summarize and discuss recent research avenues on parasitic fungi and their ecological potential in marine ecosystems, e.g., the fungal shunt, and emphasize the need for further research.
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Affiliation(s)
- Doris Ilicic
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, 16775 Stechlin, Germany;
| | - Hans-Peter Grossart
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, 16775 Stechlin, Germany;
- Institute of Biochemistry and Biology, Potsdam University, Maulbeerallee 2, 14469 Potsdam, Germany
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27
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Local Environmental Conditions Promote High Turnover Diversity of Benthic Deep-Sea Fungi in the Ross Sea (Antarctica). J Fungi (Basel) 2022; 8:jof8010065. [PMID: 35050005 PMCID: PMC8781733 DOI: 10.3390/jof8010065] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 11/16/2022] Open
Abstract
Fungi are a ubiquitous component of marine systems, but their quantitative relevance, biodiversity and ecological role in benthic deep-sea ecosystems remain largely unexplored. In this study, we investigated fungal abundance, diversity and assemblage composition in two benthic deep-sea sites of the Ross Sea (Southern Ocean, Antarctica), characterized by different environmental conditions (i.e., temperature, salinity, trophic availability). Our results indicate that fungal abundance (estimated as the number of 18S rDNA copies g−1) varied by almost one order of magnitude between the two benthic sites, consistently with changes in sediment characteristics and trophic availability. The highest fungal richness (in terms of Amplicon Sequence Variants−ASVs) was encountered in the sediments characterized by the highest organic matter content, indicating potential control of trophic availability on fungal diversity. The composition of fungal assemblages was highly diverse between sites and within each site (similarity less than 10%), suggesting that differences in environmental and ecological characteristics occurring even at a small spatial scale can promote high turnover diversity. Overall, this study provides new insights on the factors influencing the abundance and diversity of benthic deep-sea fungi inhabiting the Ross Sea, and also paves the way for a better understanding of the potential responses of benthic deep-sea fungi inhabiting Antarctic ecosystems in light of current and future climate changes.
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28
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Han Y, Guo C, Guan X, McMinn A, Liu L, Zheng G, Jiang Y, Liang Y, Shao H, Tian J, Wang M. Comparison of Deep-Sea Picoeukaryotic Composition Estimated from the V4 and V9 Regions of 18S rRNA Gene with a Focus on the Hadal Zone of the Mariana Trench. MICROBIAL ECOLOGY 2022; 83:34-47. [PMID: 33811505 DOI: 10.1007/s00248-021-01747-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/25/2021] [Indexed: 06/12/2023]
Abstract
Diversity of microbial eukaryotes is estimated largely based on sequencing analysis of the hypervariable regions of 18S rRNA genes. But the use of different regions of 18S rRNA genes as molecular markers may generate bias in diversity estimation. Here, we compared the differences between the two most widely used markers, V4 and V9 regions of the 18S rRNA gene, in describing the diversity of epipelagic, bathypelagic, and hadal picoeukaryotes in the Challenger Deep of the Mariana Trench, which is a unique and little explored environment. Generally, the V9 region identified more OTUs in deeper waters than V4, while the V4 region provided greater Shannon diversity than V9. In the epipelagic zone, where Alveolata was the dominant group, picoeukaryotic community compositions identified by V4 and V9 markers are similar at different taxonomic levels. However, in the deep waters, the results of the two datasets show clear differences. These differences were mainly contributed by Retaria, Fungi, and Bicosoecida. The primer targeting the V9 region has an advantage in amplifying Bicosoecids in the bathypelagic and hadal zone of the Mariana Trench, and its high abundance in V9 dataset pointed out the possibility of Bicosoecids as a dominant group in this environment. Chrysophyceae, Fungi, MALV-I, and Retaria were identified as the dominant picoeukaryotes in the bathypelagic and hadal zone and potentially play important roles in deep-sea microbial food webs and biogeochemical cycling by their phagotrophic, saprotrophic, and parasitic life styles. Overall, the use of different markers of 18S rRNA gene allows a better assessment and understanding of the picoeukaryotic diversity in deep-sea environments.
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Affiliation(s)
- Yuye Han
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Cui Guo
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.
| | - Xuran Guan
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Andrew McMinn
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Lu Liu
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Guiliang Zheng
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Yong Jiang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Yantao Liang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Hongbing Shao
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Jiwei Tian
- Key Laboratory of Physical Oceanography, Ministry of Education, Ocean University of China, Qingdao, China
- Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.
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29
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Pham TT, Dinh KV, Nguyen VD. Biodiversity and Enzyme Activity of Marine Fungi with 28 New Records from the Tropical Coastal Ecosystems in Vietnam. MYCOBIOLOGY 2021; 49:559-581. [PMID: 35035248 PMCID: PMC8725946 DOI: 10.1080/12298093.2021.2008103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 11/09/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
The coastal marine ecosystems of Vietnam are one of the global biodiversity hotspots, but the biodiversity of marine fungi is not well known. To fill this major gap of knowledge, we assessed the genetic diversity (ITS sequence) of 75 fungal strains isolated from 11 surface coastal marine and deeper waters in Nha Trang Bay and Van Phong Bay using a culture-dependent approach and 5 OTUs (Operational Taxonomic Units) of fungi in three representative sampling sites using next-generation sequencing. The results from both approaches shared similar fungal taxonomy to the most abundant phylum (Ascomycota), genera (Candida and Aspergillus) and species (Candida blankii) but were different at less common taxa. Culturable fungal strains in this study belong to 3 phyla, 5 subdivisions, 7 classes, 12 orders, 17 families, 22 genera and at least 40 species, of which 29 species have been identified and several species are likely novel. Among identified species, 12 and 28 are new records in global and Vietnamese marine areas, respectively. The analysis of enzyme activity and the checklist of trophic mode and guild assignment provided valuable additional biological information and suggested the ecological function of planktonic fungi in the marine food web. This is the largest dataset of marine fungal biodiversity on morphology, phylogeny and enzyme activity in the tropical coastal ecosystems of Vietnam and Southeast Asia. Biogeographic aspects, ecological factors and human impact may structure mycoplankton communities in such aquatic habitats.
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Affiliation(s)
- Thu Thuy Pham
- Institute of Biotechnology and Environment, Nha Trang University, Nha Trang, Vietnam
| | - Khuong V. Dinh
- Institute of Aquaculture, Nha Trang University, Nha Trang, Vietnam
| | - Van Duy Nguyen
- Institute of Biotechnology and Environment, Nha Trang University, Nha Trang, Vietnam
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30
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Ríos-Castro R, Romero A, Aranguren R, Pallavicini A, Banchi E, Novoa B, Figueras A. High-Throughput Sequencing of Environmental DNA as a Tool for Monitoring Eukaryotic Communities and Potential Pathogens in a Coastal Upwelling Ecosystem. Front Vet Sci 2021; 8:765606. [PMID: 34805343 PMCID: PMC8595318 DOI: 10.3389/fvets.2021.765606] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/08/2021] [Indexed: 12/04/2022] Open
Abstract
The marine environment includes diverse microeukaryotic organisms that play important functional roles in the ecosystem. With molecular approaches, eukaryotic taxonomy has been improved, complementing classical analysis. In this study, DNA metabarcoding was performed to describe putative pathogenic eukaryotic microorganisms in sediment and marine water fractions collected in Galicia (NW Spain) from 2016 to 2018. The composition of eukaryotic communities was distinct between sediment and water fractions. Protists were the most diverse group, with the clade TSAR (Stramenopiles, Alveolata, Rhizaria, and Telonemida) as the primary representative organisms in the environment. Harmful algae and invasive species were frequently detected. Potential pathogens, invasive pathogenic organisms as well as the causative agents of harmful phytoplanktonic blooms were identified in this marine ecosystem. Most of the identified pathogens have a crucial impact on the aquacultural sector or affect to relevant species in the marine ecosystem, such as diatoms. Moreover, pathogens with medical and veterinary importance worldwide were also found, as well as pathogens that affect diatoms. The evaluation of the health of a marine ecosystem that directly affects the aquacultural sector with a zoonotic concern was performed with the metabarcoding assay.
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Affiliation(s)
- Raquel Ríos-Castro
- Inmunology and Genomics, Marine Research Institute (IIM-CSIC), Vigo, Spain
| | - Alejandro Romero
- Inmunology and Genomics, Marine Research Institute (IIM-CSIC), Vigo, Spain
| | - Raquel Aranguren
- Inmunology and Genomics, Marine Research Institute (IIM-CSIC), Vigo, Spain
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Trieste, Italy
- Division of Oceanography, National Institute of Oceanography and Applied Geophysics, Trieste, Italy
| | - Elisa Banchi
- Department of Life Sciences, University of Trieste, Trieste, Italy
- Division of Oceanography, National Institute of Oceanography and Applied Geophysics, Trieste, Italy
| | - Beatriz Novoa
- Inmunology and Genomics, Marine Research Institute (IIM-CSIC), Vigo, Spain
| | - Antonio Figueras
- Inmunology and Genomics, Marine Research Institute (IIM-CSIC), Vigo, Spain
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31
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High-throughput amplicon sequencing of fungi and microbial eukaryotes associated with the seagrass Halophila stipulacea (Forssk.) Asch. from Al-Leith mangroves, Saudi Arabia. Mycol Prog 2021. [DOI: 10.1007/s11557-021-01744-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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32
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The Presence of Marine Filamentous Fungi on a Copper-Based Antifouling Paint. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11188277] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Marine biofouling is undesirable growth on submerged substances, which causes a major problem for maritime industries. Antifouling paints containing toxic compounds such as copper are used to prevent marine biofouling. However, bacteria and diatoms are usually found in biofilms developed on such paints. In this study, plastic panels painted with a copper-based self-polishing antifouling paint were exposed to biofouling for 6 months in the Marina Bandar Rowdha, Sea of Oman. Clean panels were used as a control substratum. Marine filamentous fungi from protected and unprotected substrate were isolated on a potato dextrose agar. Pure isolates were identified using sequences of the ITS region of rDNA. Six fungal isolates (Alternaria sp., Aspergillus niger, A. terreus, A. tubingensis, Cladosporium halotolerans, and C. omanense) were obtained from the antifouling paint. Four isolates (Aspergillus pseudodeflectus, C. omanense, and Parengyodontium album) were isolated from clean panels and nylon ropes. This is the first evidence of the presence of marine fungi on antifouling paints. In comparison with isolates from the unprotected substrate, fungi from the antifouling paint were highly resistant to copper, which suggests that filamentous fungi can grow on marine antifouling paints.
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33
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Genitsaris S, Stefanidou N, Beeri-Shlevin Y, Viner-Mozzini Y, Moustaka-Gouni M, Ninio S, Sukenik A. Air-dispersed aquatic microorganisms show establishment and growth preferences in different freshwater colonisation habitats. FEMS Microbiol Ecol 2021; 97:6356561. [PMID: 34424315 DOI: 10.1093/femsec/fiab122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/19/2021] [Indexed: 11/12/2022] Open
Abstract
We attempted to mimic aeolian ecosystems to examine how filters posed by regional characteristics can influence the establishment and growth of airborne microcolonisers of a common air source. Using a natural single source of aerosols we applied a combined microscopy and high-throughput sequencing approach to examine the diversity, settling and growth potential of air-dispersed microbes in water containers representing newly formed aquatic colonisation habitats of different trophic states and salinity. Heterotrophic microeukaryotes were favoured as initial settlers when nutrients were low, while autotrophs rapidly proliferated in the high-nutrient containers, possibly due to favourable germinating conditions for their preferred mode of dispersal with resting spores. Following settling of colonisers, we investigated two contrasting hypotheses: if the different water colonisation habitats harboured the same microbial communities after establishment and growth periods, this would point towards a selection of best-fit cosmopolitan colonisers, regardless of habitat-specific characteristics. Alternatively, community dissimilarities after the growth period would suggest a selection of settlers due to bottom-up controls combined with priority effects. Both analyses suggested that the structure of the microbial communities in the different colonisation habitats were driven by nutrient content and salinity, showing clustering to similar bottom-up forces and dissimilarities in significantly different colonisation habitats.
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Affiliation(s)
- Savvas Genitsaris
- Section of Ecology and Taxonomy, School of Biology, National and Kapodistrian University of Athens, Zografou Campus, 15784 Athens, Greece.,Department of Botany, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Natassa Stefanidou
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Yaron Beeri-Shlevin
- The Yigal Allon Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal 14950, Israel
| | - Yehudit Viner-Mozzini
- The Yigal Allon Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal 14950, Israel
| | - Maria Moustaka-Gouni
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Shira Ninio
- The Yigal Allon Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal 14950, Israel
| | - Assaf Sukenik
- The Yigal Allon Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal 14950, Israel
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34
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El Baidouri F, Zalar P, James TY, Gladfelter AS, Amend A. Evolution and Physiology of Amphibious Yeasts. Annu Rev Microbiol 2021; 75:337-357. [PMID: 34351793 DOI: 10.1146/annurev-micro-051421-121352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Since the emergence of the first fungi some 700 million years ago, unicellular yeast-like forms have emerged multiple times in independent lineages via convergent evolution. While tens to hundreds of millions of years separate the independent evolution of these unicellular organisms, they share remarkable phenotypic and metabolic similarities, and all have streamlined genomes. Yeasts occur in every aquatic environment yet examined. Many species are aquatic; perhaps most are amphibious. How these species have evolved to thrive in aquatic habitats is fundamental to understanding functions and evolutionary mechanisms in this unique group of fungi. Here we review the state of knowledge of the physiological and ecological diversity of amphibious yeasts and their key evolutionary adaptations enabling survival in aquatic habitats. We emphasize some genera previously thought to be exclusively terrestrial. Finally, we discuss the ability of many yeasts to survive in extreme habitats and how this might lend insight into ecological plasticity, including amphibious lifestyles. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Fouad El Baidouri
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, Hawaii 96822, USA; , .,Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - Polona Zalar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Amy S Gladfelter
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.,Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA
| | - Anthony Amend
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, Hawaii 96822, USA; ,
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35
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Laundon D, Cunliffe M. A Call for a Better Understanding of Aquatic Chytrid Biology. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:708813. [PMID: 37744140 PMCID: PMC10512372 DOI: 10.3389/ffunb.2021.708813] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/09/2021] [Indexed: 09/26/2023]
Abstract
The phylum Chytridiomycota (the "chytrids") is an early-diverging, mostly unicellular, lineage of fungi that consists of significant aquatic saprotrophs, parasites, and pathogens, and is of evolutionary interest because its members retain biological traits considered ancestral in the fungal kingdom. While the existence of aquatic chytrids has long been known, their fundamental biology has received relatively little attention. We are beginning to establish a detailed understanding of aquatic chytrid diversity and insights into their ecological functions and prominence. However, the underpinning biology governing their aquatic ecological activities and associated core processes remain largely understudied and therefore unresolved. Many biological questions are outstanding for aquatic chytrids. What are the mechanisms that control their development and life cycle? Which core processes underpin their aquatic influence? What can their biology tell us about the evolution of fungi and the wider eukaryotic tree of life? We propose that the field of aquatic chytrid ecology could be further advanced through the improved understanding of chytrid biology, including the development of model aquatic chytrids and targeted studies using culture-independent approaches.
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Affiliation(s)
- Davis Laundon
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, United Kingdom
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| | - Michael Cunliffe
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, United Kingdom
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, United Kingdom
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36
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Wang M, Ma Y, Cai L, Tedersoo L, Bahram M, Burgaud G, Long X, Zhang S, Li W. Seasonal dynamics of mycoplankton in the Yellow Sea reflect the combined effect of riverine inputs and hydrographic conditions. Mol Ecol 2021; 30:3624-3637. [PMID: 34002437 DOI: 10.1111/mec.15986] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 05/06/2021] [Accepted: 05/11/2021] [Indexed: 11/28/2022]
Abstract
Little is known about how multiple factors including land-based inputs and ocean currents affect the spatiotemporal distribution of the mycoplankton in coastal regions. To explore the seasonal changes of mycoplanktonic communities and potential environmental drivers, we collected water samples from the Yellow Sea, used here as a model for subtropical sea habitats, in different seasons over two years. Compared with winter and spring, summer exhibited higher levels of fungal richness and community heterogeneity in the water column. The seasonal shifts in mycoplankton diversity and community composition were mainly ascribed to freshwater inputs, the Cold Water Mass and invasion of the Yellow Sea Warm Current. Among the physicochemical variables tested, temperature was the primary determinant of fungal diversity and showed contrasting influences on fungal richness in the surface and bottom waters during summer. In addition, we provide evidence for the community similarity and dissolved nutrients of different water bodies to highlight the potential origin of the Cold Water Mass. Our findings bring new understanding on the factors determining the dynamics of mycoplankton communities by modelling the influence of physicochemical variables and tracking the geographical distribution of certain fungal taxa.
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Affiliation(s)
- Mengmeng Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.,State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yiyuan Ma
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Leho Tedersoo
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia.,College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Bahram
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia.,Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Gaëtan Burgaud
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, ESIAB, Technopôle Brest-Iroise, Université de Brest, Plouzané, France
| | - Xuedan Long
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Shoumei Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Wei Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
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37
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Lebreton A, Bonnardel F, Dai YC, Imberty A, Martin FM, Lisacek F. A Comprehensive Phylogenetic and Bioinformatics Survey of Lectins in the Fungal Kingdom. J Fungi (Basel) 2021; 7:453. [PMID: 34200153 PMCID: PMC8227253 DOI: 10.3390/jof7060453] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 12/28/2022] Open
Abstract
Fungal lectins are a large family of carbohydrate-binding proteins with no enzymatic activity. They play fundamental biological roles in the interactions of fungi with their environment and are found in many different species across the fungal kingdom. In particular, their contribution to defense against feeders has been emphasized, and when secreted, lectins may be involved in the recognition of bacteria, fungal competitors and specific host plants. Carbohydrate specificities and quaternary structures vary widely, but evidence for an evolutionary relationship within the different classes of fungal lectins is supported by a high degree of amino acid sequence identity. The UniLectin3D database contains 194 fungal lectin 3D structures, of which 129 are characterized with a carbohydrate ligand. Using the UniLectin3D lectin classification system, 109 lectin sequence motifs were defined to screen 1223 species deposited in the genomic portal MycoCosm of the Joint Genome Institute. The resulting 33,485 putative lectin sequences are organized in MycoLec, a publicly available and searchable database. These results shed light on the evolution of the lectin gene families in fungi.
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Affiliation(s)
- Annie Lebreton
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (A.L.); (Y.-C.D.)
| | - François Bonnardel
- University of Grenoble-Alpes, CNRS, CERMAV, 38000 Grenoble, France;
- Swiss Institute of Bioinformatics, CH-1227 Geneva, Switzerland
- Computer Science Department, UniGe, CH-1227 Geneva, Switzerland
| | - Yu-Cheng Dai
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (A.L.); (Y.-C.D.)
| | - Anne Imberty
- University of Grenoble-Alpes, CNRS, CERMAV, 38000 Grenoble, France;
| | - Francis M. Martin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (A.L.); (Y.-C.D.)
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes (IAM), Laboratoire d’Excellence ARBRE, Centre INRAE GrandEst-Nancy, 54280 Champenoux, France
| | - Frédérique Lisacek
- Swiss Institute of Bioinformatics, CH-1227 Geneva, Switzerland
- Computer Science Department, UniGe, CH-1227 Geneva, Switzerland
- Section of Biology, UniGe, CH-1205 Geneva, Switzerland
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38
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Frolova EV, Paskerova GG, Smirnov AV, Nassonova ES. Molecular phylogeny and new light microscopic data of Metchnikovella spiralis (Microsporidia: Metchnikovellidae), a hyperparasite of eugregarine Polyrhabdina sp. from the polychaete Pygospio elegans. Parasitology 2021; 148:779-786. [PMID: 33843504 PMCID: PMC11010189 DOI: 10.1017/s0031182021000603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 03/19/2021] [Accepted: 03/29/2021] [Indexed: 11/07/2022]
Abstract
Metchnikovellids are a deep-branching group of microsporidia, parasites of gregarines inhabiting the alimentary tract of polychaetes and some other invertebrates. The diversity and phylogeny of these hyperparasites remain poorly studied. Modern descriptions and molecular data are still lacking for many species. The results of a light microscopy study and molecular data for Metchnikovella spiralis Sokolova et al., 2014, a hyperparasite of the eugregarine Polyrhabdina sp., isolated from the polychaete Pygospio elegans, were obtained. The original description of M. spiralis was based primarily on the analysis of stained preparations and transmission electron microscopy images. Here, the species description was complemented with the results of in vivo observations and phylogenetic analysis based on the SSU rRNA gene. It was shown that in this species, free sporogony precedes sac-bound sporogony, as it occurs in the life cycle of most other metchnikovellids. Spore sacs are entwined with spirally wound cords, and possess only one polar plug. Phylogenetic analyses did not group M. spiralis with M. incurvata, another metchnikovellid from the same gregarine species, but placed it as a sister branch to Amphiacantha. The paraphyletic nature of the genus Metchnikovella was discussed. The taxonomic summary for M. spiralis was emended.
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Affiliation(s)
- Ekaterina V. Frolova
- Laboratory of Cytology of Unicellular Organisms, Institute of Cytology RAS, Tikhoretsky ave. 4, Saint Petersburg194064, Russian Federation
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaya emb. 7/9, Saint Petersburg199034, Russian Federation
| | - Gita G. Paskerova
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaya emb. 7/9, Saint Petersburg199034, Russian Federation
| | - Alexey V. Smirnov
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaya emb. 7/9, Saint Petersburg199034, Russian Federation
| | - Elena S. Nassonova
- Laboratory of Cytology of Unicellular Organisms, Institute of Cytology RAS, Tikhoretsky ave. 4, Saint Petersburg194064, Russian Federation
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaya emb. 7/9, Saint Petersburg199034, Russian Federation
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39
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Sen K, Bai M, Sen B, Wang G. Disentangling the structure and function of mycoplankton communities in the context of marine environmental heterogeneity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 766:142635. [PMID: 33071110 DOI: 10.1016/j.scitotenv.2020.142635] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/23/2020] [Accepted: 09/26/2020] [Indexed: 06/11/2023]
Abstract
Mycoplankton are a diverse and ubiquitous component of marine environments with a suggested role in ocean biogeochemical cycling. Thus far, the patterns of their abundance, structure, and function against spatial environmental heterogeneity remains poorly understood. Based on in silico and experimental evaluation of multiple markers, we adopted the ITS1 region to determine the composition, guilds, and metabolic potential of mycoplankton communities in contrasting marine environments. The trophic status of estuarine (SB1 and SB2) and coastal (DB1 and DB2) sites, but not oceanic (OS) site, was the major factor that determined their abundances. While ascomycetous fungi dominated the estuarine and coastal sites, basidiomycetous fungi were found to dominate the oceanic site. The zoosporic fungi were relatively more abundant in SB1 and DB2 sites compared to the other sites. The relative abundances of the core fungi, namely Cystobasidium, Phlebia, Rhodotorula, Trichoderma, Alternaria, Penicillium, Malassezia, and Aspergillus varied widely across the sites. Additionally, several fungal genera unique to each site were also identified. DB2 site exhibited the lowest fungal richness while the OS site the highest. Conversely, the diversity and evenness were the lowest for the OS site but highest for the SB1 site. Temperature, pH, and chlorophyll-a were strongly associated with spatial diversity patterns. Of the 11 assigned guilds, some guilds particularly were not detected, including plant pathogen-wood saprotroph in DB2, the endophyte-plant pathogen in OS, the animal pathogen in SB1, and fungal parasite in DB1 and SB2. Within core functions-metabolism of amino acids, carbohydrates and energy, fatty acids and lipids, nitrogen, sulfur, and other compounds-several pathways showed spatial variations. Overall, this study not just broadens the taxonomic and metabolic repertoire of marine mycoplankton but also provides the first evidence of how these are shaped by site-scale environmental heterogeneity.
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Affiliation(s)
- Kalyani Sen
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Mohan Bai
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Biswarup Sen
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Guangyi Wang
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Qingdao Institute Ocean Engineering of Tianjin University, Qingdao 266237, China.
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40
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David GM, López-García P, Moreira D, Alric B, Deschamps P, Bertolino P, Restoux G, Rochelle-Newall E, Thébault E, Simon M, Jardillier L. Small freshwater ecosystems with dissimilar microbial communities exhibit similar temporal patterns. Mol Ecol 2021; 30:2162-2177. [PMID: 33639035 DOI: 10.1111/mec.15864] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 11/27/2022]
Abstract
Despite small freshwater ecosystems being biodiversity reservoirs and contributing significantly to greenhouse fluxes, their microbial communities remain largely understudied. Yet, microorganisms intervene in biogeochemical cycling and impact water quality. Because of their small size, these ecosystems are in principle more sensitive to disturbances, seasonal variation and pluri-annual climate change. However, how microbial community composition varies over space and time, and whether archaeal, bacterial and microbial eukaryote communities behave similarly remain unanswered. Here, we aim to unravel the composition and intra/interannual temporal dynamic patterns for archaea, bacteria and microbial eukaryotes in a set of small freshwater ecosystems. We monitored archaeal and bacterial community composition during 24 consecutive months in four ponds and one brook from northwestern France by 16S rRNA gene amplicon sequencing (microbial eukaryotes were previously investigated for the same systems). Unexpectedly for oxic environments, bacterial Candidate Phyla Radiation (CPR) were highly diverse and locally abundant. Our results suggest that microbial community structure is mainly driven by environmental conditions acting over space (ecosystems) and time (seasons). A low proportion of operational taxonomic units (OTUs) (<1%) was shared by the five ecosystems despite their geographical proximity (2-9 km away), making microbial communities almost unique in each ecosystem and highlighting the strong selective influence of local environmental conditions. Marked and similar seasonality patterns were observed for archaea, bacteria and microbial eukaryotes in all ecosystems despite strong turnovers of rare OTUs. Over the 2-year survey, microbial community composition varied despite relatively stable environmental parameters. This suggests that biotic associations play an important role in interannual community assembly.
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Affiliation(s)
- Gwendoline M David
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | | | - David Moreira
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | - Benjamin Alric
- Irstea, UR RiverLy, Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, Villeurbanne, France
| | - Philippe Deschamps
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | - Paola Bertolino
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | - Gwendal Restoux
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Emma Rochelle-Newall
- Sorbonne Université, UPEC, CNRS, IRD, INRAE, Institute d'Ecologie de des Sciences de l'Environnement de Paris, iEES-Paris, Paris, France
| | - Elisa Thébault
- Sorbonne Université, UPEC, CNRS, IRD, INRAE, Institute d'Ecologie de des Sciences de l'Environnement de Paris, iEES-Paris, Paris, France
| | - Marianne Simon
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | - Ludwig Jardillier
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
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41
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Hyde KD, Bao DF, Hongsanan S, Chethana KWT, Yang J, Suwannarach N. Evolution of freshwater Diaporthomycetidae (Sordariomycetes) provides evidence for five new orders and six new families. FUNGAL DIVERS 2021. [DOI: 10.1007/s13225-021-00469-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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42
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Parasitoid chytridiomycete Ericiomyces syringoforeus gen. et sp. nov. has unique cellular structures to infect the host. Mycol Prog 2021. [DOI: 10.1007/s11557-020-01652-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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43
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Genitsaris S, Stefanidou N, Leontidou K, Matsi T, Karamanoli K, Mellidou I. Bacterial Communities in the Rhizosphere and Phyllosphere of Halophytes and Drought-Tolerant Plants in Mediterranean Ecosystems. Microorganisms 2020; 8:E1708. [PMID: 33142812 PMCID: PMC7692439 DOI: 10.3390/microorganisms8111708] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 12/23/2022] Open
Abstract
The aim of the study was to investigate the bacterial community diversity and structure by means of 16S rRNA gene high-throughput amplicon sequencing, in the rhizosphere and phyllosphere of halophytes and drought-tolerant plants in Mediterranean ecosystems with different soil properties. The locations of the sampled plants included alkaline, saline-sodic soils, acidic soils, and the volcanic soils of Santorini Island, differing in soil fertility. Our results showed high bacterial richness overall with Proteobacteria and Actinobacteria dominating in terms of OTUs number and indicated that variable bacterial communities differed depending on the plant's compartment (rhizosphere and phyllosphere), the soil properties and location of sampling. Furthermore, a shared pool of generalist bacterial taxa was detected independently of sampling location, plant species, or plant compartment. We conclude that the rhizosphere and phyllosphere of native plants in stressed Mediterranean ecosystems consist of common bacterial assemblages contributing to the survival of the plant, while at the same time the discrete soil properties and environmental pressures of each habitat drive the development of a complementary bacterial community with a distinct structure for each plant and location. We suggest that this trade-off between generalist and specialist bacterial community is tailored to benefit the symbiosis with the plant.
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Affiliation(s)
- Savvas Genitsaris
- Department of Ecology, School of Biology, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
| | - Natassa Stefanidou
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
| | - Kleopatra Leontidou
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
| | - Theodora Matsi
- Soil Science Laboratory, School of Agriculture, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
| | - Katerina Karamanoli
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
| | - Ifigeneia Mellidou
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
- Institute of Plant Breeding and Genetic Resources, HAO ELGO-DEMETER, 57 001 Thermi, Greece
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Gonçalves MFM, Esteves AC, Alves A. Revealing the hidden diversity of marine fungi in Portugal with the description of two novel species, Neoascochyta fuci sp. nov. and Paraconiothyrium salinum sp. nov. Int J Syst Evol Microbiol 2020; 70:5337-5354. [PMID: 32845832 DOI: 10.1099/ijsem.0.004410] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fungi are ubiquitous organisms with a wide distribution in almost all ecosystems, including marine environments. Coastal and estuarine ecosystems remain poorly unexplored as fungal habitats, potentially harbouring a hidden diversity with important ecological roles. During an extensive survey of marine fungi in coastal and estuarine Portuguese environments, a collection of 612 isolates was obtained from water, algae, sponges and driftwood. From these, 282 representative isolates were selected through microsatellite-primed PCR (MSP-PCR) fingerprinting analysis, which were identified based on DNA sequence data. The collection yielded 117 taxa from 38 distinct genera, which were identified using DNA sequence analysis. Overall, fungal community composition varied with host/substrate, but the most abundant taxa in the collection were Cladosporium cladosporioides, Penicillium terrigenum, Penicillium brevicompactum and Fusarium equiseti/incarnatum complex. The occurrence of a high fungal diversity harbouring novel species was disclosed. Through a multilocus phylogeny based on ITS, tub2 and tef1-α sequences, in conjunction with morphological and physiological data, we propose Neoascochyta fuci sp. nov. and Paraconiothyrium salinum sp. nov.
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Affiliation(s)
| | - Ana C Esteves
- Present address: Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Investigation (CIIS), Viseu, Portugal.,CESAM, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Artur Alves
- CESAM, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal
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Nagano Y, Miura T, Tsubouchi T, Lima AO, Kawato M, Fujiwara Y, Fujikura K. Cryptic fungal diversity revealed in deep-sea sediments associated with whale-fall chemosynthetic ecosystems. Mycology 2020; 11:263-278. [PMID: 33062387 PMCID: PMC7534350 DOI: 10.1080/21501203.2020.1799879] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
In this study, sediments from whale-fall chemosynthetic ecosystems (two different sites, one naturally occurring at 4200 m water depth in South Atlantic Ocean and one artificially immersed at 100 m water depth in Kagoshima Bay, Japan) were investigated by Ion Torrent PGM sequencing of the ITS region of ribosomal RNA to reveal fungal communities in these unique marine environments. As a result, a total of 107 (897 including singletons) Operational Taxonomic Units (OTUs) were obtained from the samples explored. Composition of the 107 OTUs at the phylum level among the five samples from two different whale-fall sites was assigned to Ascomycota (46%), Basidiomycota (7%), unidentified fungi (21%), non-fungi (10%), and sequences with no affiliation to any organisms in the public database (No-match) (16%). The high detection of the unidentified fungi and unassigned fungi was revealed in the whale-fall environments in this study. Some of these unidentified fungi are allied to early diverging fungi and they were more abundant in the sediments not directly in contact with whalebone. This study suggests that a cryptic fungal community exists in unique whale-fall ecosystems.
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Affiliation(s)
- Yuriko Nagano
- Deep-Sea Biodiversity Research Group, Marine Biodiversity and Environmental Assessment Research Center, Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Toshiko Miura
- Research Institute of Environment, Agriculture and Fisheries, Osaka, Japan
| | - Taishi Tsubouchi
- Department of Bacteriology, Graduate School of Medicine, Public University Corporation Osaka City University (OCU), Osaka, Japan
| | - Andre O Lima
- Department of Biological Sciences, University of Vale do Itajaí (UNIVALI), Itajaí, Brazil
| | - Masaru Kawato
- Deep-Sea Biodiversity Research Group, Marine Biodiversity and Environmental Assessment Research Center, Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yoshihiro Fujiwara
- Deep-Sea Biodiversity Research Group, Marine Biodiversity and Environmental Assessment Research Center, Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Katsunori Fujikura
- Deep-Sea Biodiversity Research Group, Marine Biodiversity and Environmental Assessment Research Center, Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
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Abstract
In this review, we discuss the current status and future challenges for fully elucidating the fungal tree of life. In the last 15 years, advances in genomic technologies have revolutionized fungal systematics, ushering the field into the phylogenomic era. This has made the unthinkable possible, namely access to the entire genetic record of all known extant taxa. We first review the current status of the fungal tree and highlight areas where additional effort will be required. We then review the analytical challenges imposed by the volume of data and discuss methods to recover the most accurate species tree given the sea of gene trees. Highly resolved and deeply sampled trees are being leveraged in novel ways to study fungal radiations, species delimitation, and metabolic evolution. Finally, we discuss the critical issue of incorporating the unnamed and uncultured dark matter taxa that represent the vast majority of fungal diversity.
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Affiliation(s)
- Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA;
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, California 92521, USA;
| | - Chris Todd Hittinger
- Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Center for Genomic Science and Innovation, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin 53726, USA;
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235, USA;
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Lacerda ALDF, Proietti MC, Secchi ER, Taylor JD. Diverse groups of fungi are associated with plastics in the surface waters of the Western South Atlantic and the Antarctic Peninsula. Mol Ecol 2020; 29:1903-1918. [DOI: 10.1111/mec.15444] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/30/2020] [Accepted: 04/02/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Ana L. d. F. Lacerda
- Instituto de Oceanografia Universidade Federal do Rio Grande-FURG Rio Grande Brazil
| | - Maíra C. Proietti
- Instituto de Oceanografia Universidade Federal do Rio Grande-FURG Rio Grande Brazil
| | - Eduardo R. Secchi
- Instituto de Oceanografia Universidade Federal do Rio Grande-FURG Rio Grande Brazil
| | - Joe D. Taylor
- School of Science, Engineering and Environment University of Salford Manchester UK
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Kilias ES, Junges L, Šupraha L, Leonard G, Metfies K, Richards TA. Chytrid fungi distribution and co-occurrence with diatoms correlate with sea ice melt in the Arctic Ocean. Commun Biol 2020; 3:183. [PMID: 32317738 PMCID: PMC7174370 DOI: 10.1038/s42003-020-0891-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 03/09/2020] [Indexed: 11/09/2022] Open
Abstract
Global warming is rapidly altering physicochemical attributes of Arctic waters. These changes are predicted to alter microbial networks, potentially perturbing wider community functions including parasite infections and saprotrophic recycling of biogeochemical compounds. Specifically, the interaction between autotrophic phytoplankton and heterotrophic fungi e.g. chytrids (fungi with swimming tails) requires further analysis. Here, we investigate the diversity and distribution patterns of fungi in relation to abiotic variables during one record sea ice minimum in 2012 and explore co-occurrence of chytrids with diatoms, key primary producers in these changing environments. We show that chytrid fungi are primarily encountered at sites influenced by sea ice melt. Furthermore, chytrid representation positively correlates with sea ice-associated diatoms such as Fragilariopsis or Nitzschia. Our findings identify a potential future scenario where chytrid representation within these communities increases as a consequence of ice retreat, further altering community structure through perturbation of parasitic or saprotrophic interaction networks. Estelle. S. Kilias et al. show that chytrid fungi exhibiting swimming tales are primarily encountered at sites influenced by sea ice melt and that its representation positively correlates with sea ice-associated diatoms. This study predicts that chytrid representation within its Arctic communities may increase as ice retreats further.
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Affiliation(s)
- Estelle S Kilias
- University of Exeter, Bioscience, Living System Institute, Exeter, UK. .,University of Oxford, Department of Zoology, Oxford, UK.
| | - Leandro Junges
- Centre for Systems Modelling and Quantitative Biomedicine, University of Birmingham, Birmingham, UK.,Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | - Luka Šupraha
- University of Oslo, Department of Biosciences, Oslo, Norway
| | - Guy Leonard
- University of Oxford, Department of Zoology, Oxford, UK
| | - Katja Metfies
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany.,Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
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Variability and Community Composition of Marine Unicellular Eukaryote Assemblages in a Eutrophic Mediterranean Urban Coastal Area with Marked Plankton Blooms and Red Tides. DIVERSITY-BASEL 2020. [DOI: 10.3390/d12030114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The Thessaloniki Bay is a eutrophic coastal area which has been characterized in recent years by frequent and intense phytoplankton blooms and red tides. The aim of the study was to investigate the underexplored diversity of marine unicellular eukaryotes in four different sampling sites in Thessaloniki Bay during a year of plankton blooms, red tides, and mucilage aggregates. High-Throughput Sequencing (HTS) was applied in extracted DNA from weekly water samples targeting the 18S rRNA gene. In almost all samples, phytoplankton blooms and/or red tides and mucilage aggregates were observed. The metabarcoding analysis has detected the known unicellular eukaryotic groups frequently observed in the Bay, dominated by Bacillariophyta and Dinoflagellata, and revealed taxonomic groups previously undetected in the study area (MALVs, MAST, and Cercozoa). The dominant OTUs were closely related to species known to participate in red tides, harmful blooms, and mucilage aggregates. Other OTUs, present also during the blooms in low abundance (number of reads), were closely related to known harmful species, suggesting the occurrence of rare taxa with potential negative impacts on human health not detectable with classical microscopy. Overall, the unicellular eukaryote assemblages showed temporal patterns rather than small-scale spatial separation responding to the variability of physical and chemical factors.
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Abstract
Fungi are phylogenetically and functionally diverse ubiquitous components of almost all ecosystems on Earth, including aquatic environments stretching from high montane lakes down to the deep ocean. Aquatic ecosystems, however, remain frequently overlooked as fungal habitats, although fungi potentially hold important roles for organic matter cycling and food web dynamics. Recent methodological improvements have facilitated a greater appreciation of the importance of fungi in many aquatic systems, yet a conceptual framework is still missing. In this Review, we conceptualize the spatiotemporal dimensions, diversity, functions and organismic interactions of fungi in structuring aquatic food webs. We focus on currently unexplored fungal diversity, highlighting poorly understood ecosystems, including emerging artificial aquatic habitats.
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