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Posadas J, Velez P, Pajares S, Gasca-Pineda J, Espinosa-Asuar L. Fungal diversity in sediments of the eastern tropical Pacific oxygen minimum zone revealed by metabarcoding. PLoS One 2024; 19:e0301605. [PMID: 38739592 PMCID: PMC11090300 DOI: 10.1371/journal.pone.0301605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 03/19/2024] [Indexed: 05/16/2024] Open
Abstract
Oxygen minimum zones (OMZ) represent ~8% of the ocean, with the Pacific as the largest and top expanding area. These regions influence marine ecosystems, promoting anaerobic microbial communities. Nevertheless, only a fraction of microbial diversity has been studied, with fungi being the less explored component. So, herein we analyzed fungal diversity patterns in surface and subsurface sediments along a bathymetric transect using metabarcoding of the ITS1 region in the OMZ of the Mexican Pacific off Mazatlán. We identified 353 amplicon sequence variants (ASV), within the Ascomycota, Basidiomycota, and Rozellomycota. Spatial patterns evidenced higher alpha diversity in nearshore and subsurface subsamples, probably due to temporal fluctuations in organic matter inputs. Small-scale heterogeneity characterized the community with the majority of ASV (269 ASV) occurring in a single subsample, hinting at the influence of local biogeochemical conditions. This baseline data evidenced a remarkable fungal diversity presenting high variation along a bathymetric and vertical transects.
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Affiliation(s)
- Judith Posadas
- Posgrado en Ciencias del Mar y Limnología, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Patricia Velez
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Silvia Pajares
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Jaime Gasca-Pineda
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Laura Espinosa-Asuar
- Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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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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3
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Guerra-Mateo D, Cano-Lira JF, Fernández-Bravo A, Gené J. Sunken Riches: Ascomycete Diversity in the Western Mediterranean Coast through Direct Plating and Flocculation, and Description of Four New Taxa. J Fungi (Basel) 2024; 10:281. [PMID: 38667952 PMCID: PMC11051201 DOI: 10.3390/jof10040281] [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: 02/15/2024] [Revised: 03/23/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
The Mediterranean Sea stands out as a hotspot of biodiversity, whose fungal composition remains underexplored. Marine sediments represent the most diverse substrate; however, the challenge of recovering fungi in culture hinders the precise identification of this diversity. Concentration techniques like skimmed milk flocculation (SMF) could represent a suitable solution. Here, we compare the effectiveness in recovering filamentous ascomycetes of direct plating and SMF in combination with three culture media and two incubation temperatures, and we describe the fungal diversity detected in marine sediments. Sediments were collected at different depths on two beaches (Miracle and Arrabassada) on the Spanish western Mediterranean coast between 2021 and 2022. We recovered 362 strains, and after a morphological selection, 188 were identified primarily with the LSU and ITS barcodes, representing 54 genera and 94 species. Aspergillus, Penicillium, and Scedosporium were the most common genera, with different percentages of abundance between both beaches. Arrabassada Beach was more heterogeneous, with 42 genera representing 60 species (Miracle Beach, 28 genera and 54 species). Although most species were recovered with direct plating (70 species), 20 species were exclusively obtained using SMF as a sample pre-treatment, improving our ability to detect fungi in culture. In addition, we propose three new species in the genera Exophiala, Nigrocephalum, and Queenslandipenidiella, and a fourth representing the novel genus Schizochlamydosporiella. We concluded that SMF is a useful technique that, in combination with direct plating, including different culture media and incubation temperatures, improves the chance of recovering marine fungal communities in culture-dependent studies.
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Affiliation(s)
| | | | | | - Josepa Gené
- Unitat de Micologia i Microbiologia Ambiental, Facultat de Medicina i Ciències de la Salut and Institut Universitari de Recerca en Sostenibilitat, Canvi Climàtic i Transició Energètica (IU-RESCAT), Universitat Rovira i Virgili, 43201 Reus, Spain; (D.G.-M.); (J.F.C.-L.); (A.F.-B.)
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Qu W, Zuo Y, Zhang Y, Wang J. Structure and assembly process of fungal communities in the Yangtze River Estuary. Front Microbiol 2024; 14:1220239. [PMID: 38260888 PMCID: PMC10800840 DOI: 10.3389/fmicb.2023.1220239] [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: 05/10/2023] [Accepted: 12/11/2023] [Indexed: 01/24/2024] Open
Abstract
Marine fungi are essential for the ecological function of estuarine ecosystems. However, limited studies have reported on the structure and assembly pattern of the fungal communities in estuaries. The purpose of this study is to reveal the structure and the ecological process of the fungal community in the Yangtze River Estuary (YRE) by using the amplicon sequencing method. Phyla of Ascomycota, Basidiomycota, and Chytridiomycota were dominant in the seawater and sediment samples from YRE. The null model analysis, community-neutral community model (NCM), and phylogenetic normalized stochasticity ratio (pNST) showed that the stochastic process dominated the assembly of fungal communities in YRE. Drift and homogeneous dispersal were the predominant stochastic processes for the fungal community assembly in seawater and sediment samples, respectively. The co-occurrence network analysis showed that fungal communities were more complex and closely connected in the sediment than in the seawater samples. Phyla Ascomycota, Basidiomycota, and Mucoromycota were the potential keystone taxa in the network. These findings demonstrated the importance of stochastic processes for the fungal community assembly, thereby widening our knowledge of the community structure and dynamics of fungi for future study and utilization in the YRE ecosystem.
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Affiliation(s)
| | | | | | - Jianxin Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
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Wang MM, Yang SY, Li Q, Zheng Y, Ma HH, Tu YH, Li W, Cai L. Microascaceae from the Marine Environment, with Descriptions of Six New Species. J Fungi (Basel) 2024; 10:45. [PMID: 38248952 PMCID: PMC10821522 DOI: 10.3390/jof10010045] [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: 11/03/2023] [Revised: 12/20/2023] [Accepted: 12/23/2023] [Indexed: 01/23/2024] Open
Abstract
Most reported members of Microascaceae that have been reported originate from the terrestrial environment, where they act as saprobes or plant pathogens. However, our understanding of their species diversity and distribution in the marine environment remains vastly limited, with only 22 species in nine genera having been reported so far. A survey of the fungal diversity in intertidal areas of China's mainland has revealed the discovery of several Microascaceae strains from 14 marine algae and 15 sediment samples. Based on morphological characteristics and LSU-ITS-tef1-tub2 multilocus phylogeny using Bayesian inference and maximum likelihood methods, 48 strains were identified as 18 species belonging to six genera. Among these, six new species were discovered: Gamsia sedimenticola, Microascus algicola, M. gennadii, Scedosporium ellipsosporium, S. shenzhenensis, and S. sphaerospermum. Additionally, the worldwide distribution of the species within this family across various marine habitats was briefly reviewed and discussed. Our study expands the knowledge of species diversity and distribution of Microascaceae in the marine environment.
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Affiliation(s)
- Meng-Meng Wang
- College of Science, Shantou University, Shantou 515063, China; (M.-M.W.); (S.-Y.Y.); (Q.L.); (Y.-H.T.)
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou 515063, China
| | - Shi-Yu Yang
- College of Science, Shantou University, Shantou 515063, China; (M.-M.W.); (S.-Y.Y.); (Q.L.); (Y.-H.T.)
| | - Qi Li
- College of Science, Shantou University, Shantou 515063, China; (M.-M.W.); (S.-Y.Y.); (Q.L.); (Y.-H.T.)
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou 515063, China
| | - Yao Zheng
- College of Marine Life Sciences, Ocean University of China, Qingdao 266005, China (H.-H.M.)
| | - He-He Ma
- College of Marine Life Sciences, Ocean University of China, Qingdao 266005, China (H.-H.M.)
| | - Ye-Hui Tu
- College of Science, Shantou University, Shantou 515063, China; (M.-M.W.); (S.-Y.Y.); (Q.L.); (Y.-H.T.)
| | - Wei Li
- College of Science, Shantou University, Shantou 515063, China; (M.-M.W.); (S.-Y.Y.); (Q.L.); (Y.-H.T.)
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou 515063, China
- College of Marine Life Sciences, Ocean University of China, Qingdao 266005, China (H.-H.M.)
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Li W, Li Q, Pan Z, Burgaud G, Ma H, Zheng Y, Wang M, Cai L. Seasonal and Spatial Dynamics of Fungal Diversity and Communities in the Intertidal Zones of Qingdao, China. J Fungi (Basel) 2023; 9:1015. [PMID: 37888271 PMCID: PMC10607781 DOI: 10.3390/jof9101015] [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: 08/23/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/28/2023] Open
Abstract
Intertidal zones comprise diverse habitats and directly suffer from the influences of human activities. Nevertheless, the seasonal fluctuations in fungal diversity and community structure in these areas are not well comprehended. To address this gap, samples of seawater and sediment were collected seasonally from the estuary and swimming beaches of Qingdao's intertidal areas in China and were analyzed using a metabarcoding approach targeting ITS2 rDNA regions. Compared to the seawater community dominated by Ciliophora and Agaricomycetes, the sediment community was rather dominated by Dothideomycetes and Eurotiomycetes. Furthermore, the seawater community shifted with the seasons but not with the locations, while the sediment community shifted seasonally and spatially, with a specific trend showing that Cladosporium, Alternaria, and Aureobasidium occurred predominantly in the estuarine habitats during winter and in the beach habitats during spring. These spatiotemporal shifts in fungal communities' composition were supported by the PERMANOVA test and could be explained partially by the environmental variables checked, including temperature, salinity, and total organic carbon. Unexpectedly, the lowest fungal richness was observed in the summer sediments from two swimming beaches which were attracting a high influx of tourists during summer, leading to a significant anthropogenic influence. Predicted trophic modes of fungal taxa exhibited a seasonal pattern with an abundance of saprotrophic fungi in the summer sediments, positively correlating to the temperature, while the taxa affiliated with symbiotroph and pathotroph-saprotroph occurred abundantly in the winter and spring sediments, respectively. Our results demonstrate the space-time shifts in terms of the fungal community, as well as the trophic modes in the intertidal region, providing in-depth insights into the potential influence of environmental factors and human activity on intertidal mycobiomes.
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Affiliation(s)
- Wei Li
- College of Science, Shantou University, Shantou 515063, China; (Q.L.); (M.W.)
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China; (Z.P.); (H.M.); (Y.Z.)
| | - Qi Li
- College of Science, Shantou University, Shantou 515063, China; (Q.L.); (M.W.)
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China
| | - Zhihui Pan
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China; (Z.P.); (H.M.); (Y.Z.)
| | - Gaëtan Burgaud
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, Frech National Research Institute for Agriculture, Food and Environment (INRAE), Université de Bretagne Occidentale, F-29280 Plouzané, France;
| | - Hehe Ma
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China; (Z.P.); (H.M.); (Y.Z.)
| | - Yao Zheng
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China; (Z.P.); (H.M.); (Y.Z.)
| | - Mengmeng Wang
- College of Science, Shantou University, Shantou 515063, China; (Q.L.); (M.W.)
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Fernández-Valero AD, Reñé A, Timoneda N, Pou-Solà N, Gordi J, Sampedro N, Garcés E. The succession of epiphytic microalgae conditions fungal community composition: how chytrids respond to blooms of dinoflagellates. ISME COMMUNICATIONS 2023; 3:103. [PMID: 37752353 PMCID: PMC10522651 DOI: 10.1038/s43705-023-00304-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/28/2023]
Abstract
This study aims to investigate the temporal dynamics of the epiphytic protist community on macroalgae, during the summer months, with a specific focus on fungi, and the interactions between zoosporic chytrid parasites and the proliferation of the dinoflagellates. We employed a combination of environmental sequencing techniques, incubation of natural samples, isolation of target organisms and laboratory experiments. Metabarcoding sequencing revealed changes in the dominant members of the epiphytic fungal community. Initially, fungi comprised < 1% of the protist community, mostly accounted for by Basidiomycota and Ascomycota, but with the emergence of Chytridiomycota during the mature phase of the biofilm, the fungal contribution increased to almost 30%. Chytridiomycota became dominant in parallel with an increase in the relative abundance of dinoflagellates in the community. Microscopy observations showed a general presence of chytrids following the peak proliferation of the dinoflagellate Ostreopsis sp., with the parasite, D. arenysensis as the dominant chytrid. The maximum infection prevalence was 2% indicating host-parasite coexistence. To further understand the in-situ prevalence of chytrids, we characterised the dynamics of the host abundance and prevalence of chytrids through co-culture. These laboratory experiments revealed intraspecific variability of D. arenysensis in its interaction with Ostreopsis, exhibiting a range from stable coexistence to the near-extinction of the host population. Moreover, while chytrids preferentially parasitized dinoflagellate cells, one of the strains examined displayed the ability to utilize pollen as a resource to maintain its viability, thus illustrating a facultative parasitic lifestyle. Our findings not only enrich our understanding of the diversity, ecology, and progression of epiphytic microalgal and fungal communities on Mediterranean coastal macroalgae, but they also shed light on the presence of zoosporic parasites in less-explored benthic habitats.
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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.
| | - 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
| | - 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
| | - Núria Pou-Solà
- 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
| | - 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
| | - 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
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8
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Breyer E, Baltar F. The largely neglected ecological role of oceanic pelagic fungi. Trends Ecol Evol 2023; 38:870-888. [PMID: 37246083 DOI: 10.1016/j.tree.2023.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/25/2023] [Accepted: 05/02/2023] [Indexed: 05/30/2023]
Abstract
Most investigations into ocean ecology and biogeochemistry have tended to focus on marine bacteria, archaea, and protists, while pelagic fungi (mycoplankton) have traditionally been neglected and considered to reside only in association with benthic solid substrates. Nevertheless, recent studies have revealed that pelagic fungi are distributed ubiquitously throughout the water column in every ocean basin and play an active role in the degradation of organic matter and the cycling of nutrients. We review the current status of knowledge on the ecology of mycoplankton and highlight knowledge gaps and challenges. These findings underscore the need to recognize this neglected kingdom as significant contributors to the organic matter cycling and ecology of the oceans.
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Affiliation(s)
- Eva Breyer
- Fungal and Biogeochemical Oceanography Group, Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria.
| | - Federico Baltar
- Fungal and Biogeochemical Oceanography Group, Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria.
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Sen K, Bai M, Li J, Ding X, Sen B, Wang G. Spatial Patterns of Planktonic Fungi Indicate Their Potential Contributions to Biological Carbon Pump and Organic Matter Remineralization in the Water Column of South China Sea. J Fungi (Basel) 2023; 9:640. [PMID: 37367576 DOI: 10.3390/jof9060640] [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: 04/22/2023] [Revised: 05/25/2023] [Accepted: 05/29/2023] [Indexed: 06/28/2023] Open
Abstract
Fungi have long been known to be dynamic in coastal water columns with multiple trophic modes. However, little is known about their interactions with abiotic and biotic components, contribution to the biological carbon pump (BCP), and organic matter remineralization in the oceanic water column. In this study, we investigated how fungi vary spatially and how their variations relate to that of bacteria in the water column of the South China Sea (SCS). Fungi were about three orders less prevalent than bacteria, and the main factors influencing their distribution were depth, temperature, and distance from the sites of riverine inputs. The decline in the abundance of fungi with depth was less steep than that of bacteria. Correlation tests revealed a strong positive association between the abundance of fungi and bacteria, especially in the twilight (r = 0.62) and aphotic (r = 0.70) zones. However, the co-occurrence network revealed mutual exclusion between certain members of fungi and bacteria. The majority of fungi in the water column were saprotrophs, which indicated that they were generally involved in the degradation of organic matter, particularly in twilight and aphotic zones. Similar to bacteria, the involvement of fungi in the metabolism of carbohydrates, proteins, and lipids was predicted, pointing to their participation in the turnover of organic carbon and the biogeochemical cycling of carbon, nitrogen, and sulfur. These findings suggest that fungi play a role in BCP and support their inclusion in marine microbial ecosystem models.
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Affiliation(s)
- Kalyani Sen
- Centre for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Mohan Bai
- Centre for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Jiaqian Li
- Centre for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Xueyan Ding
- Centre for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Biswarup Sen
- Centre for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Guangyi Wang
- Centre 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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10
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Baeshen NN, Baz L, Shami AY, Ashy RA, Jalal RS, Abulfaraj AA, Refai M, Majeed MA, Abuzahrah SS, Abdelkader H, Baeshen NA, Baeshen MN. Composition, Abundance, and Diversity of the Soil Microbiome Associated with the Halophytic Plants Tamarix aphylla and Halopeplis perfoliata on Jeddah Seacoast, Saudi Arabia. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112176. [PMID: 37299153 DOI: 10.3390/plants12112176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023]
Abstract
The coast of the Red Sea in Jeddah City is home to a unique microbial community that has adapted to extreme environmental conditions. Therefore, it is essential to characterize the microbial community in this unique microbiome to predict how environmental changes will affect it. The aim of this study was to conduct metagenomic sequencing of 16S rRNA and ITS rRNA genes for the taxonomic classification of the microbial community in soil samples associated with the halophytic plants Tamarix aphylla and Halopeplis perfoliata. Fifteen soil samples were collected in triplicate to enhance robustness and minimize sampling bias. Firstly, to identify novel microbial candidates, the gDNAs were isolated from the saline soil samples surrounding each plant, and then bacterial 16S (V3-V4) and fungal ITS1 regions were sequenced utilizing a high-throughput approach (next-generation sequencing; NGS) on an Illumina MiSeq platform. Quality assessment of the constructed amplicon libraries was conducted using Agilent Bioanalyzer and fluorometric quantification methods. The raw data were processed and analyzed using the Pipeline (Nova Lifetech, Singapore) for bioinformatics analysis. Based on the total number of readings, it was determined that the phylum Actinobacteriota was the most prevalent in the soil samples examined, followed by the phylum Proteobacteria. Based on ITS rRNA gene analysis, the alpha and beta fungal diversity in the studied soil samples revealed that the fungal population is structured into various groups according to the crust (c) and/or rhizosphere (r) plant parts. Fungal communities in the soil samples indicated that Ascomycota and Basidiomycota were the two most abundant phyla based on the total amount of sequence reads. Secondly, heat-map analysis of the diversity indices showed that the bacterial alpha diversity, as measured by Shannon, Simpson, and InvSimpson, was associated with soil crust (Hc and Tc enclosing H. perfoliata and T. aphylla, respectively) and that the soil rhizosphere (Hr and Tr) was strongly correlated with bacterial beta diversity. Finally, fungal-associated Tc and Hc samples clustered together, according to observations made using the Fisher and Chao1 methods, and Hr and Tr samples clustered together according to Shannon, Simpson, and InvSimpson analyses. As a result of the soil investigation, potential agents that have been identified could lead to innovative agricultural, medical, and industrial applications.
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Affiliation(s)
- Naseebh N Baeshen
- Department of Biology, College of Sciences and Arts at Khulais, University of Jeddah, Jeddah 21959, Saudi Arabia
| | - Lina Baz
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ashwag Y Shami
- Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh 11617, Saudi Arabia
| | - Ruba A Ashy
- Department of Biology, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
| | - Rewaa S Jalal
- Department of Biology, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
| | - Aala A Abulfaraj
- Biological Sciences Department, College of Science & Arts, King Abdulaziz University, Rabigh 21911, Saudi Arabia
| | - Mohammed Refai
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
| | - Mazen A Majeed
- Department of Biology, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
| | - Samah S Abuzahrah
- Department of Biology, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
| | - Hayam Abdelkader
- Virus Research Department, Molecular Biology Laboratory, PPRI, ARC, Giza 12613, Egypt
| | - Nabih A Baeshen
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mohammed N Baeshen
- Department of Biology, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
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11
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Debeljak P, Baltar F. Fungal Diversity and Community Composition across Ecosystems. J Fungi (Basel) 2023; 9:jof9050510. [PMID: 37233221 DOI: 10.3390/jof9050510] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/13/2023] [Accepted: 04/21/2023] [Indexed: 05/27/2023] Open
Abstract
Fungi have shaped the biosphere since the development of life on Earth. Despite fungi being present in all environments, most of the available fungal research has focused on soils. As a result, the role and composition of fungal communities in aquatic (marine and freshwater) environments remain largely unexplored. The use of different primers to characterise fungal communities has additionally complicated intercomparisons among studies. Consequently, we lack a basic global assessment of fungal diversity across major ecosystems. Here, we took advantage of a recently published 18S rRNA dataset comprising samples from major ecosystems (terrestrial, freshwater, and marine) to attempt a global assessment of fungal diversity and community composition. We found the highest fungal diversities for terrestrial > freshwater > marine environments, and pronounced gradients of fungal diversity along temperature, salinity, and latitude in all ecosystems. We also identified the most abundant taxa in each of these ecosystems, mostly dominated by Ascomycota and Basidiomycota, except in freshwater rivers where Chytridiomycota dominated. Collectively, our analysis provides a global analysis of fungal diversity across all major environmental ecosystems, highlighting the most distinct order and ASVs (amplicon sequencing variants) by ecosystem, and thus filling a critical gap in the study of the Earth's mycobiome.
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Affiliation(s)
- Pavla Debeljak
- Fungal & Biogeochemical Oceanography, Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Vienna, Austria
- SupBiotech, 94800 Villejuif, France
| | - Federico Baltar
- Fungal & Biogeochemical Oceanography, Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Vienna, Austria
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12
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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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13
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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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14
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Zhao R, Zhao F, Zheng S, Li X, Wang J, Xu K. Bacteria, Protists, and Fungi May Hold Clues of Seamount Impact on Diversity and Connectivity of Deep-Sea Pelagic Communities. Front Microbiol 2022; 13:773487. [PMID: 35464911 PMCID: PMC9024416 DOI: 10.3389/fmicb.2022.773487] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 03/22/2022] [Indexed: 12/22/2022] Open
Abstract
The topography and hydrography around seamounts have a strong influence on plankton biogeography. The intrinsic properties of various biological taxa inherently also shape their distribution. Therefore, it is hypothesized that different pelagic groups respond differently to effects of seamounts regarding their distribution and connectivity patterns. Herein, bacterial, protist, and fungal diversity was investigated across the water column around the Kocebu Guyot in the western Pacific Ocean. A higher connectivity was detected for bacteria than for protists and an extremely low connectivity for fungi, which might be attributed to parasitic and commensal interactions of many fungal taxa. The seamount enhanced the vertical connectivity of bacterial and protist communities, but significantly reduced protist connectivity along horizontal dimension. Such effects provide ecological opportunities for eukaryotic adaption and diversification. All the bacterial, protist, and fungal communities were more strongly affected by deterministic than stochastic processes. Drift appeared to have a more significant role in influencing the fungal community than other groups. Our study indicates the impact of seamounts on the pelagic community distribution and connectivity and highlights the mechanism of horizontally restricted dispersal combined with vertical mixing, which promotes the diversification of eukaryotic life.
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Affiliation(s)
- Rongjie Zhao
- Laboratory of Marine Organism Taxonomy and Phylogeny, Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Feng Zhao
- Laboratory of Marine Organism Taxonomy and Phylogeny, Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Shan Zheng
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Xuegang Li
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Jianing Wang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Kuidong Xu
- Laboratory of Marine Organism Taxonomy and Phylogeny, Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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15
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Sun Y, Lyu H, Cheng Z, Wang Y, Tang J. Insight into the mechanisms of ball-milled biochar addition on soil tetracycline degradation enhancement: Physicochemical properties and microbial community structure. CHEMOSPHERE 2022; 291:132691. [PMID: 34755608 DOI: 10.1016/j.chemosphere.2021.132691] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/18/2021] [Accepted: 10/23/2021] [Indexed: 06/13/2023]
Abstract
A set of soil under the addition of ball-milled biochar (BM-biochar) from different feedstocks (wheat straw (WS) and rice husk (RH)) and pyrolysis temperature (300 °C, 500 °C, and 700 °C) was established to analyze the tetracycline (TC) degradation performance enhancement and greenhouse gas carbon dioxide (CO2), and nitrous oxide (N2O) emission reduction from various angles, including physicochemical properties of soil and microbial community structure. After 45 days' incubation, the pH value decreased slightly from 7.34 to 7.22 for WS biochar-treated soil, while slightly increased from 7.34 to 7.50 for RH biochar-treated soil. The lowest KCl-leachable TC concentrations of BMWS700 and RH700 was about 0.0037 mg/L. Ball-milled 500 °C and 700 °C biochars enhanced the removal rate of TC significantly. The maximum reduction of TC was from 2.17 to 0.079 mg/kg, equivalent to 96% removal after ball-milled 500 °C wheat straw biochar (BMWS500) addition, suggesting the promoting effect of biochars on microorganisms for adsorption and degradation of TC. Biochars' addition reduced CO2 and N2O emissions, BM-biochar enlarged this effect under the pyrolysis temperature 500 °C for both feedstock types. Ball milled rice husk biochar pyrolyzed under 500 °C (BMRH500) presented the maximum inhibitory effect CO2 emission. The addition of BM-biochar changed the microbial community and diversity. The relative abundance of bacterium and fungus such as Proteobacteria, Acidobacteria, Chlorofexi, Mortierella, and Chaetomium increased due to BM-biochar addition, which promoted the degradation of TC and gave rise to more healthy soil environment for plant or microbes. The larger specific surface area, π-π interactions, hydrophobic interaction, and hydrogen bonding are account for better adsorption and degradation of TC by BM-biochars. This work elucidated the management of organic contaminants in real soil by BM-biochar.
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Affiliation(s)
- Yanfang Sun
- Tianjin Key Laboratory of Clean Energy and Pollution Control, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, 300401, China
| | - Honghong Lyu
- Tianjin Key Laboratory of Clean Energy and Pollution Control, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, 300401, China; School of Civil and Transportation Engineering, Hebei University of Technology, Tianjin, 300401, China.
| | - Zi Cheng
- Tianjin Key Laboratory of Clean Energy and Pollution Control, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, 300401, China
| | - Yizhi Wang
- Tianjin Tianmai Energy-saving Equipment Co., Ltd., Tianjin, 300112, China
| | - Jingchun Tang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Engineering Center of Environmental Diagnosis and Contamination Remediation, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China.
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16
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Noorjahan A, Mahesh S, Aiyamperumal B, Anantharaman P. Exploring Marine Fungal Diversity and Their Applications in Agriculture. Fungal Biol 2022. [DOI: 10.1007/978-981-16-8877-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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17
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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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18
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Marchese P, Garzoli L, Young R, Allcock L, Barry F, Tuohy M, Murphy M. Fungi populate deep-sea coral gardens as well as marine sediments in the Irish Atlantic Ocean. Environ Microbiol 2021; 23:4168-4184. [PMID: 33939869 DOI: 10.1111/1462-2920.15560] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 04/06/2021] [Accepted: 05/02/2021] [Indexed: 02/06/2023]
Abstract
Fungi populate deep Oceans in extreme habitats characterized by high hydrostatic pressure, low temperature and absence of sunlight. Marine fungi are potential major contributors to biogeochemical events, critical for marine communities and food web equilibrium under climate change conditions and a valuable source of novel extremozymes and small molecules. Despite their ecophysiological and biotechnological relevance, fungal deep-sea biodiversity has not yet been thoroughly characterized. In this study, we describe the culturable mycobiota associated with the deepest margin of the European Western Continental Shelf: sediments sampled at the Porcupine Bank and deep-water corals and sponges sampled in the Whittard Canyon. Eighty-seven strains were isolated, belonging to 43 taxa and mainly Ascomycota. Ten species and four genera were detected for the first time in the marine environment and a possible new species of Arachnomyces was isolated from sediments. The genera Cladosporium and Penicillium were the most frequent and detected on both substrates, followed by Candida and Emericellopsis. Our results showed two different fungal communities: sediment-associated taxa which were predominantly saprotrophic and animal-associated taxa which were predominantly symbiotic. This survey supports selective fungal biodiversity in the deep North Atlantic, encouraging further mycological studies on cold water coral gardens, often overexploited marine habitats.
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Affiliation(s)
- Pietro Marchese
- Regenerative Medicine Institute, School of Medicine, National University of Ireland Galway, Galway, H91TK33, Ireland
| | - Laura Garzoli
- MEG-Molecular Ecology Group, Water Research Institute, National Research Council of Italy (CNR-IRSA), Verbania, 28922, Italy
| | - Ryan Young
- Martin Ryan Institute, School of Natural Sciences, National University of Ireland Galway, Galway, H91TK33, Ireland
| | - Louise Allcock
- Martin Ryan Institute, School of Natural Sciences, National University of Ireland Galway, Galway, H91TK33, Ireland
| | - Frank Barry
- Regenerative Medicine Institute, School of Medicine, National University of Ireland Galway, Galway, H91TK33, Ireland
| | - Maria Tuohy
- Molecular Glycobiotechnology, School of Natural Sciences, National University of Ireland Galway, Galway, H91TK33, Ireland
| | - Mary Murphy
- Regenerative Medicine Institute, School of Medicine, National University of Ireland Galway, Galway, H91TK33, Ireland
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19
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Vargas-Gastélum L, Riquelme M. The Mycobiota of the Deep Sea: What Omics Can Offer. Life (Basel) 2020; 10:E292. [PMID: 33228036 PMCID: PMC7699357 DOI: 10.3390/life10110292] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/14/2020] [Accepted: 11/18/2020] [Indexed: 01/23/2023] Open
Abstract
The deep sea (>1000 m below sea level) represents one of the most extreme environments of the ocean. Despite exhibiting harsh abiotic conditions such as low temperatures, high hydrostatic pressure, high salinity concentrations, a low input of organic matter, and absence of light, the deep sea encompasses a great fungal diversity. For decades, most knowledge on the fungal diversity of the deep sea was obtained through culture-dependent techniques. More recently, with the latest advances of high-throughput next generation sequencing platforms, there has been a rapid increment in the number of studies using culture-independent techniques. This review brings into the spotlight the progress of the techniques used to assess the diversity and ecological role of the deep-sea mycobiota and provides an overview on how the omics technologies have contributed to gaining knowledge about fungi and their activity in poorly explored marine environments. Finally, current challenges and suggested coordinated efforts to overcome them are discussed.
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Affiliation(s)
| | - Meritxell Riquelme
- Department of Microbiology, Centro de Investigación Científica y Educación Superior de Ensenada (CICESE), Ctra.Ensenada-Tijuana No. 3918, Ensenada 22860, Baja California, Mexico;
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20
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Rojas-Jimenez K, Grossart HP, Cordes E, Cortés J. Fungal Communities in Sediments Along a Depth Gradient in the Eastern Tropical Pacific. Front Microbiol 2020; 11:575207. [PMID: 33240232 PMCID: PMC7681244 DOI: 10.3389/fmicb.2020.575207] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/21/2020] [Indexed: 01/04/2023] Open
Abstract
Deep waters represent the largest biome on Earth and the largest ecosystem of Costa Rica. Fungi play a fundamental role in global biogeochemical cycling in marine sediments, yet, they remain little explored. We studied fungal diversity and community composition in several marine sediments from 16 locations sampled along a bathymetric gradient (from a depth of 380 to 3,474 m) in two transects of about 1,500 km length in the Eastern Tropical Pacific (ETP) of Costa Rica. Sequence analysis of the V7-V8 region of the 18S rRNA gene obtained from sediment cores revealed the presence of 787 fungal amplicon sequence variants (ASVs). On average, we detected a richness of 75 fungal ASVs per sample. Ascomycota represented the most abundant phylum with Saccharomycetes constituting the dominant class. Three ASVs accounted for ca. 63% of all fungal sequences: the yeast Metschnikowia (49.4%), Rhizophydium (6.9%), and Cladosporium (6.7%). We distinguished a cluster composed mainly by yeasts, and a second cluster by filamentous fungi, but we were unable to detect a strong effect of depth and the overlying water temperature, salinity, dissolved oxygen (DO), and pH on the composition of fungal communities. We highlight the need to understand further the ecological role of fungi in deep-sea ecosystems.
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Affiliation(s)
| | - Hans-Peter Grossart
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
| | - Erik Cordes
- Department of Biology, Temple University, Philadelphia, PA, United States
| | - Jorge Cortés
- Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
- Centro de Investigación en Ciencias del Mar y Limnología, Universidad de Costa Rica, San José, Costa Rica
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21
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Yang S, Xu W, Gao Y, Chen X, Luo ZH. Fungal diversity in deep-sea sediments from Magellan seamounts environment of the western Pacific revealed by high-throughput Illumina sequencing. J Microbiol 2020; 58:841-852. [PMID: 32876913 DOI: 10.1007/s12275-020-0198-x] [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] [Received: 04/13/2020] [Revised: 07/14/2020] [Accepted: 07/21/2020] [Indexed: 12/12/2022]
Abstract
There are lots of seamounts globally whose primary production is disproportionally greater than the surrounding areas. Compared to other deep-sea environments, however, the seamounts environment is relatively less explored for fungal diversity. In the present study, we explored the fungal community structure in deep-sea sediments from four different stations of the Magellan seamounts environment by using high-throughput sequencing of the ITS1 region. A total of 1,897,618 ITS1 sequences were obtained. Among these sequences, fungal ITS1 sequences could be clustered into 1,662 OTUs. The majority of these sequences belonged to Ascomycota. In the genera level, the most abundant genus was Mortierella (4.79%), which was reported as a common fungal genus in soil and marine sediments, followed by Umbelopsis (3.80%), Cladosporium (2.98%), Saccharomycopsis (2.53%), Aspergillus (2.42%), Hortaea (2.36%), Saitozyma (2.20%), Trichoderma (2.12%), Penicillium (2.11%), Russula (1.86%), and Verticillium (1.40%). Most of these recovered genera belong to Ascomycota. The Bray-Curtis analysis showed that there was 37 to 85% dissimilarity of fungal communities between each two sediment samples. The Principal coordinates analysis clearly showed variations in the fungal community among different sediment samples. These results suggested that there was a difference in fungal community structures not only among four different sampling stations but also for different layers at the same station. The depth and geographical distance significantly affect the fungal community, and the effect of depth and geographical distance on the structure of the fungal community in the Magellan seamounts is basically same. Most of the fungi were more or less related to plants, these plant parasitic/symbiotic/endophytic fungi constitute a unique type of seamounts environmental fungal ecology, different from other marine ecosystems.
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Affiliation(s)
- Shuai Yang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen, 361005, P. R. China
| | - Wei Xu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen, 361005, P. R. China
| | - Yuanhao Gao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen, 361005, P. R. China
| | - Xiaoyao Chen
- Monotoring Center of Fishery Resources, Fujian Province, Fuzhou, 350003, P. R. China
| | - Zhu-Hua Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen, 361005, P. R. China. .,Co-Innovation Center of Jiangsu Marine Bioindustry Technology, Jiangsu Ocean University, Lianyungang, 222005, P. R. China. .,School of Marine Sciences, Nanjing University of Information Science & Technology, Nanjing, 210044, P. R. China.
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22
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Quemener M, Mara P, Schubotz F, Beaudoin D, Li W, Pachiadaki M, Sehein TR, Sylvan JB, Li J, Barbier G, Edgcomb V, Burgaud G. Meta-omics highlights the diversity, activity and adaptations of fungi in deep oceanic crust. Environ Microbiol 2020; 22:3950-3967. [PMID: 32743889 DOI: 10.1111/1462-2920.15181] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/23/2020] [Accepted: 07/31/2020] [Indexed: 02/03/2023]
Abstract
The lithified oceanic crust, lower crust gabbros in particular, has remained largely unexplored by microbiologists. Recently, evidence for heterogeneously distributed viable and transcriptionally active autotrophic and heterotrophic microbial populations within low-biomass communities was found down to 750 m below the seafloor at the Atlantis Bank Gabbro Massif, Indian Ocean. Here, we report on the diversity, activity and adaptations of fungal communities in the deep oceanic crust from ~10 to 780 mbsf by combining metabarcoding analyses with mid/high-throughput culturing approaches. Metabarcoding along with culturing indicate a low diversity of viable fungi, mostly affiliated to ubiquitous (terrestrial and aquatic environments) taxa. Ecophysiological analyses coupled with metatranscriptomics point to viable and transcriptionally active fungal populations engaged in cell division, translation, protein modifications and other vital cellular processes. Transcript data suggest possible adaptations for surviving in the nutrient-poor, lithified deep biosphere that include the recycling of organic matter. These active communities appear strongly influenced by the presence of cracks and veins in the rocks where fluids and resulting rock alteration create micro-niches.
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Affiliation(s)
- Maxence Quemener
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Technopôle Brest-Iroise, Plouzané, France
| | - Paraskevi Mara
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA.,Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Florence Schubotz
- MARUM-Center for Marine Environmental Sciences, University Bremen, Leobener Strasse 8, Bremen, 28359, Germany
| | - David Beaudoin
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA.,Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Wei Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Maria Pachiadaki
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA.,Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Taylor R Sehein
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA.,Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Jason B Sylvan
- Department of Oceanography, Texas A&M University, College Station, TX, 77845, USA
| | - Jiangtao Li
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China
| | - Georges Barbier
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Technopôle Brest-Iroise, Plouzané, France
| | - Virginia Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA.,Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Gaëtan Burgaud
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Technopôle Brest-Iroise, Plouzané, France
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Luo Y, Wei X, Yang S, Gao YH, Luo ZH. Fungal diversity in deep-sea sediments from the Magellan seamounts as revealed by a metabarcoding approach targeting the ITS2 regions. Mycology 2020; 11:214-229. [PMID: 33062383 PMCID: PMC7534268 DOI: 10.1080/21501203.2020.1799878] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 07/03/2020] [Indexed: 12/11/2022] Open
Abstract
Recent reports have revealed diverse and abundant fungal communities in the deep-sea biosphere, while their composition, distribution, and variations in seamount zones are poorly understood. Using a metabarcoding approach targeting the ITS2 regions, we present the structure of the fungal community in 18 sediment samples from the Magellan seamount area of the northwest Pacific. A total of 1,979 fungal OTUs was obtained, which were taxonomically assigned to seven phyla, 17 classes, 43 orders, 7 families, and 98 genera. The majority of these OTUs were affiliated to Basidiomycota (873 OTUs, 44.11% of total OTUs) and Ascomycota (486 OTUs, 24.56% of total OTUs), followed by other five minor phyla (Mortierellomycota, Chytridiomycota, Mucoromycota, Glomeromycota, and Monoblepharidomycota). Sordriomycetes is the most abundant class, followed by Eurotiomycetes, and Dothideomycetes. Five genera were common in most of the samples, including worldwide reported genera Aspergillus, Cladosporium, Fusarium, Chaetomium, and Penicillium. The environmental data we collected (sampling depth, sampling location latitude and longitude, organic carbon content, and organic nitrogen content in the sediment) had no significant influence on the composition and distribution of fungal communities. Our findings provide valuable information for understanding the distribution and potential ecological functions of fungi in the deep-sea sediments of the Magellan seamounts.
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Affiliation(s)
- Ye Luo
- Key Laboratory of Marine Biogenetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, PR China
| | - Xu Wei
- Key Laboratory of Marine Biogenetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, PR China
| | - Shuai Yang
- Key Laboratory of Marine Biogenetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, PR China
| | - Yuan-Hao Gao
- Key Laboratory of Marine Biogenetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, PR China
| | - Zhu-Hua Luo
- Key Laboratory of Marine Biogenetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, PR China
- School of Marine Sciences, Nanjing University of Information Science & Technology, Nanjing, PR China
- Co-Innovation Center of Jiangsu Marine Bioindustry Technology, Jiangsu Ocean University, Lianyungang, PR China
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