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Cabrera FP, Paiano MO, Fumo JT, Allsopp KR, Smith CM, Spalding HL, Kosaki RK, Sherwood AR. Organellar genomic characterization of Anunuuluaehu liula representing a new genus and species of Phyllophoraceae (Gigartinales, Rhodophyta) from the mesophotic zone of Hawai'i. JOURNAL OF PHYCOLOGY 2024; 60:116-132. [PMID: 38289653 DOI: 10.1111/jpy.13427] [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: 08/22/2023] [Revised: 11/22/2023] [Accepted: 12/15/2023] [Indexed: 02/17/2024]
Abstract
Over the last 2 decades, routine collections in the Hawaiian Archipelago have expanded to mesophotic reefs, leading to the discovery of a new red algal genus and species, here described as Anunuuluaehu liula gen. et sp. nov. This study provides a detailed genus and species description and characterizes chloroplast and mitochondrial organellar genomes. The new genus, Anunuuluaehu, shares many characteristics with the family Phyllophoraceae and shows close similarities to Archestennogramma and Stenogramma, including habit morphology, nemathecia forming proliferations at the outer cortex with terminal chains of tetrasporangia, and carposporophytes with multi-layered pericarps. The single species in this genus exhibits distinctive features within the Phyllophoraceae: the presence of single-layer construction of large medullary cells and the development of long, tubular gonimoblastic filaments. Multi-gene phylogenetic analyses confirmed it as a unique, monophyletic lineage within the family. Cis-splicing genes, interrupted by intron-encoded proteins within group II introns, are present in both the chloroplast and mitochondrial genomes of A. liula. Notably, a specific region of the coxI group II intron exhibits similarity to fungal introns. Anunuuluaehu liula is presumed to be endemic to the Hawaiian Archipelago and thus far is known to live solely at mesophotic depths from Hōlanikū to Kaho'olawe ranging from 54 to 201 m, which is the deepest collection record of any representative in the family. Overall, this study enhances our understanding of the genomic and taxonomic complexities of red algae in mesophotic habitats, emphasizing the significance of continued research in this area to uncover further insights into evolutionary processes and biogeographic patterns.
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Affiliation(s)
- Feresa P Cabrera
- School of Life Sciences, University of Hawai'i, Honolulu, Hawai'i, USA
| | - Monica O Paiano
- School of Life Sciences, University of Hawai'i, Honolulu, Hawai'i, USA
| | - James T Fumo
- School of Life Sciences, University of Hawai'i, Honolulu, Hawai'i, USA
| | - Kazumi R Allsopp
- School of Life Sciences, University of Hawai'i, Honolulu, Hawai'i, USA
| | - Celia M Smith
- School of Life Sciences, University of Hawai'i, Honolulu, Hawai'i, USA
| | - Heather L Spalding
- Department of Biology, College of Charleston, Charleston, South Carolina, USA
| | - Randall K Kosaki
- Papahānaumokuākea Marine National Monument, NOAA, Honolulu, Hawai'i, USA
| | - Alison R Sherwood
- School of Life Sciences, University of Hawai'i, Honolulu, Hawai'i, USA
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2
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Rawson C, Zahn G. Inclusion of database outgroups reduces false positives in fungal metabarcoding taxonomic assignments. Mycologia 2023:1-7. [PMID: 37196170 DOI: 10.1080/00275514.2023.2206931] [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: 12/06/2022] [Accepted: 04/14/2023] [Indexed: 05/19/2023]
Abstract
Metabarcoding studies of fungal communities rely on curated databases for assigning taxonomy. Any host or other nonfungal environmental sequences that are amplified during polymerase chain reaction (PCR) are inherently assigned taxonomy by these same databases, possibly leading to ambiguous nonfungal amplicons being assigned to fungal taxa. Here, we investigated the effects of including nonfungal outgroups in a fungal taxonomic database to aid in detecting and removing these nontarget amplicons. We processed 15 publicly available fungal metabarcode data sets and discovered that roughly 40% of the reads from these studies were not fungal, although they were assigned as Fungus sp. when using a database without nonfungal outgroups. We discuss implications for metabarcoding studies and recommend assigning taxonomy using a database with outgroups to better detect these nonfungal amplicons.
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Affiliation(s)
- Clayton Rawson
- Department of Biology, Utah Valley University, 800 W University Parkway, SB243, Orem, Utah 84058
| | - Geoffrey Zahn
- Department of Biology, Utah Valley University, 800 W University Parkway, SB243, Orem, Utah 84058
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3
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Marzougui Z, Le Hegarat L, Hogeveen K, Huet S, Kharrat R, Marrouchi R, Fessard V. An Evaluation of the Cytotoxic and Genotoxic Effects of the Marine Toxin C17-SAMT in Human TK6 and HepaRG Cell Lines. Int J Mol Sci 2023; 24:ijms24097805. [PMID: 37175512 PMCID: PMC10177896 DOI: 10.3390/ijms24097805] [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: 03/23/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
This study investigates the genotoxicity and cytotoxicity of C17-sphinganine analog mycotoxin (C17-SAMT) using in vitro assays. C17-SAMT was previously identified as the cause of unusual toxicity in cultured mussels from the Bizerte Lagoon in northern Tunisia. While a previous in vivo genotoxicity study was inconclusive, in vitro results demonstrated that C17-SAMT induced an increase in micronucleus formation in human lymphoblastoid TK6 cells at concentrations of 0.87 µM and 1.74 µM. In addition, multiparametric cytotoxicity assays were performed in the human hepatoma HepaRG cell line, which showed that C17-SAMT induced mitochondrial dysfunction, decreased cellular ATP levels, and altered the expression of various proteins, including superoxide dismutase SOD2, heme oxygenase HO-1, and NF-κB. These results suggest that C17-SAMT is mutagenic in vitro and can induce mitochondrial dysfunction in HepaRG cells. However, the exact mode of action of this toxin requires further investigation. Overall, this study highlights the potential toxicity of C17-SAMT and the need for further research to better understand its effects.
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Affiliation(s)
- Zeineb Marzougui
- Laboratoire des Venins et Biomolécules Thérapeutiques, Institut Pasteur de Tunis, Université Tunis El Manar, 13 Place Pasteur, B.P. 74, Tunis-Belvédère 1002, Tunisia
- Institut National Agronomique de Tunisie, Université de Carthage, Tunis 1082, Tunisia
| | - Ludovic Le Hegarat
- Unité de Toxicologie des Contaminants, Agence Nationale de Sécurité Sanitaire (ANSES), 10 B rue Claude Bourgelat, 35306 Fougères, France
| | - Kevin Hogeveen
- Unité de Toxicologie des Contaminants, Agence Nationale de Sécurité Sanitaire (ANSES), 10 B rue Claude Bourgelat, 35306 Fougères, France
| | - Sylvie Huet
- Unité de Toxicologie des Contaminants, Agence Nationale de Sécurité Sanitaire (ANSES), 10 B rue Claude Bourgelat, 35306 Fougères, France
| | - Riadh Kharrat
- Laboratoire des Venins et Biomolécules Thérapeutiques, Institut Pasteur de Tunis, Université Tunis El Manar, 13 Place Pasteur, B.P. 74, Tunis-Belvédère 1002, Tunisia
| | - Riadh Marrouchi
- Laboratoire des Venins et Biomolécules Thérapeutiques, Institut Pasteur de Tunis, Université Tunis El Manar, 13 Place Pasteur, B.P. 74, Tunis-Belvédère 1002, Tunisia
| | - Valérie Fessard
- Unité de Toxicologie des Contaminants, Agence Nationale de Sécurité Sanitaire (ANSES), 10 B rue Claude Bourgelat, 35306 Fougères, France
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4
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Bonthond G, Barilo A, Allen RJ, Cunliffe M, Krueger-Hadfield SA. Fungal endophytes vary by species, tissue type, and life cycle stage in intertidal macroalgae. JOURNAL OF PHYCOLOGY 2022; 58:330-342. [PMID: 35090190 DOI: 10.1111/jpy.13237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
Fungal symbionts of terrestrial plants are among the most widespread and well-studied symbioses, relatively little is known about fungi that are associated with macroalgae. To fill the gap in marine fungal taxonomy, we combined simple culture methods with amplicon sequencing to characterize the fungal communities associated with three brown (Sargassum muticum, Pelvetia canaliculata, and Himanthalia elongata) and two red (Mastocarpus stellatus and Chondrus crispus) macroalgae from one intertidal zone. In addition to characterizing novel fungal diversity, we tested three hypotheses: fungal diversity and community composition vary (i) among species distributed at different tidal heights, (ii) among tissue types (apices, mid-thallus, and stipe), and (iii) among "isomorphic" C. crispus life cycle stages. Almost 70% of our reads were classified as Ascomycota, 29% as Basidiomycota, and 1% that could not be classified to a phylum. Thirty fungal isolates were obtained, 18 of which were also detected with amplicon sequencing. Fungal communities differed by host and tissue type. Interestingly, P. canaliculata, a fucoid at the extreme high intertidal, did not show differences in fungal diversity across the thallus. As found in filamentous algal endophytes, fungal diversity varied among the three life cycle stages in C. crispus. Female gametophytes were also compositionally more dispersed as compared to the fewer variable tetrasporophytes and male gametophytes. We demonstrate the utility of combining relatively simple cultivation and sequencing approaches to characterize and study macroalgal-fungal associations and highlight the need to understand the role of fungi in near-shore marine ecosystems.
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Affiliation(s)
- Guido Bonthond
- Institute for Chemistry and Biology of the Marine environment (ICBM), Carl-von-Ossietzky University Oldenburg, Schleusenstrasse 1, Wilhelmshaven, 26382, Germany
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, Kiel, 24105, Germany
| | - Anastasiia Barilo
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, UK
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
| | - Ro J Allen
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, UK
| | - Michael Cunliffe
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, UK
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
| | - Stacy A Krueger-Hadfield
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, Alabama, 35294, USA
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5
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Tipton L, Zahn GL, Darcy JL, Amend AS, Hynson NA. Hawaiian Fungal Amplicon Sequence Variants Reveal Otherwise Hidden Biogeography. MICROBIAL ECOLOGY 2022; 83:48-57. [PMID: 33742230 DOI: 10.1007/s00248-021-01730-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/07/2021] [Indexed: 06/12/2023]
Abstract
To study biogeography and other ecological patterns of microorganisms, including fungi, scientists have been using operational taxonomic units (OTUs) as representations of species or species hypotheses. However, when defined by 97% sequence similarity cutoff at an accepted barcode locus such as 16S in bacteria or ITS in fungi, these OTUs can obscure biogeographic patterns, mask taxonomic diversity, and hinder meta-analyses. Amplicon sequence variants (ASVs) have been proposed to alleviate all of these issues and have been shown to do so in bacteria. Analyzing ASVs is just emerging as a common practice among fungal studies, and it is unclear whether the benefits found in bacterial studies of using such an approach carryover to fungi. Here, we conducted a meta-analysis of Hawaiian fungi by analyzing ITS1 amplicon sequencing data as ASVs and exploring ecological patterns. These surveys spanned three island groups and five ecosystems combined into the first comprehensive Hawaiian Mycobiome ASV Database. Our results show that ASVs can be used to combine fungal ITS surveys, increase reproducibility, and maintain the broad ecological patterns observed with OTUs, including diversity orderings. Additionally, the ASVs that comprise some of the most common OTUs in our database reveals some island specialists, indicating that traditional OTU clustering can obscure important biogeographic patterns. We recommend that future fungal studies, especially those aimed at assessing biogeography, analyze ASVs rather than OTUs. We conclude that similar to bacterial studies, ASVs improve reproducibility and data sharing for fungal studies.
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Affiliation(s)
- Laura Tipton
- School of Natural Science and Mathematics, Chaminade University of Honolulu, Honolulu, HI, USA
| | | | - John L Darcy
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Anthony S Amend
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Nicole A Hynson
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, USA.
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6
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Oh RM, Bollati E, Maithani P, Huang D, Wainwright BJ. The Microbiome of the Reef Macroalga Sargassum ilicifolium in Singapore. Microorganisms 2021; 9:microorganisms9050898. [PMID: 33922357 PMCID: PMC8145558 DOI: 10.3390/microorganisms9050898] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/01/2021] [Accepted: 04/19/2021] [Indexed: 01/04/2023] Open
Abstract
The large canopy-forming macroalga, Sargassum ilicifolium, provides shelter and food for numerous coral reef species, but it can also be detrimental at high abundances where it outcompetes other benthic organisms for light and space. Here, we investigate the microbial communities associated with S. ilicifolium in Singapore, where it is an abundant and important member of coral reef communities. We collected eight complete S. ilicifolium thalli from eight island locations along an approximate 14 km east-to-west transect. Each thallus was dissected into three separate parts: holdfast, vesicles, and leaves. We then characterized the bacterial communities associated with each part via polymerase chain reaction (PCR) amplification of the 16S rRNA gene V4 region. We then inferred predicted metagenome functions using METAGENassist. Despite the comparatively short distances between sample sites, we show significant differences in microbial community composition, with communities further differentiated by part sampled. Holdfast, vesicles and leaves all harbor distinct microbial communities. Functional predictions reveal some separation between holdfast and leaf communities, with higher representation of sulphur cycling taxa in the holdfast and higher representation of nitrogen cycling taxa in the leaves. This study provides valuable baseline data that can be used to monitor microbial change, and helps lay the foundation upon which we can begin to understand the complexities of reef-associated microbial communities and the roles they play in the functioning and diversity of marine ecosystems.
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Affiliation(s)
- Ren Min Oh
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (R.M.O.); (E.B.); (P.M.); (D.H.)
| | - Elena Bollati
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (R.M.O.); (E.B.); (P.M.); (D.H.)
| | - Prasha Maithani
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (R.M.O.); (E.B.); (P.M.); (D.H.)
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (R.M.O.); (E.B.); (P.M.); (D.H.)
- Centre for Nature-Based Climate Solutions, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
- Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore 119227, Singapore
| | - Benjamin J. Wainwright
- Yale-NUS College, National University of Singapore, 16 College Avenue West, Singapore 138527, Singapore
- Correspondence:
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7
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Lee NLY, Huang D, Quek ZBR, Lee JN, Wainwright BJ. Distinct fungal communities associated with different organs of the mangrove Sonneratia alba in the Malay Peninsula. IMA Fungus 2020; 11:17. [PMID: 32974121 PMCID: PMC7493156 DOI: 10.1186/s43008-020-00042-y] [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: 01/28/2020] [Accepted: 08/31/2020] [Indexed: 12/14/2022] Open
Abstract
Mangrove forests are key tropical marine ecosystems that are rich in fungi, but our understanding of fungal communities associated with mangrove trees and their various organs remains limited because much of the diversity lies within the microbiome. In this study, we investigated the fungal communities associated with the mangrove tree Sonneratia alba throughout Peninsular Malaysia and Singapore. At each sampling location, we collected leaves, fruits, pneumatophores and sediment samples and performed amplicon sequencing of the ribosomal internal transcribed spacer 1 to characterise the associated communities. Results show distinct fungal communities at each sampled location with further differentiation according to the plant part. We find a significant distance decay of similarity, particularly for sediment samples due to the greater variability of sediment environments relative to the more stable fungal habitats provided by living plant organs. We are able to assign taxonomy to the majority of sequences from leaves and fruits, but a much larger portion of the sequences recovered from pneumatophores and sediment samples could not be identified. This pattern underscores the limited mycological research performed in marine environments and demonstrates the need for a concerted research effort on multiple species to fully characterise the coastal microbiome and its role in the functioning of marine ecosystems.
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Affiliation(s)
- Nicole Li Ying Lee
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558 Singapore
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558 Singapore.,Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore, 119227 Singapore
| | - Zheng Bin Randolph Quek
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558 Singapore
| | - Jen Nie Lee
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Malaysia
| | - Benjamin J Wainwright
- Yale-NUS College, National University of Singapore, 16 College Avenue West, Singapore, 138527 Singapore
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Lee NLY, Huang D, Quek ZBR, Lee JN, Wainwright BJ. Mangrove-Associated Fungal Communities Are Differentiated by Geographic Location and Host Structure. Front Microbiol 2019; 10:2456. [PMID: 31736902 PMCID: PMC6831645 DOI: 10.3389/fmicb.2019.02456] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 10/14/2019] [Indexed: 11/13/2022] Open
Abstract
Marine fungi on the whole remain understudied, especially in the highly diverse Southeast Asian region. We investigated the fungal communities associated with the mangrove tree Avicennia alba throughout Singapore and Peninsular Malaysia. At each sampling location, we examined ten individual trees, collecting leaves, fruits, pneumatophores, and an adjacent sediment sample from each plant. Amplicon sequencing of the fungal internal transcribed spacer 1 and subsequent analyses reveal significant differences in fungal communities collected from different locations and host structures. Mantel tests and multiple regression on distance matrices show a significant pattern of distance decay with samples collected close to one another having more similar fungal communities than those farther away. Submergence appears to drive part of the variation as host structures that are never submerged (leaves and fruits) have more similar fungal communities relative to those that are covered by water during high tide (pneumatophores and sediment). We suggest that fungi of terrestrial origins dominate structures that are not inundated by tidal regimes, while marine fungi dominate mangrove parts and sediments that are submerged by the incoming tide. Given the critical functions fungi play in all plants, and the important role they can have in determining the success of restoration schemes, we advocate that fungal community composition should be a key consideration in any mangrove restoration or rehabilitation project.
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Affiliation(s)
- Nicole Li Ying Lee
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.,Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | | | - Jen Nie Lee
- School of Marine and Environmental Sciences, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia
| | - Benjamin J Wainwright
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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9
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Wainwright BJ, Zahn GL, Zushi J, Lee NLY, Ooi JLS, Lee JN, Huang D. Seagrass-associated fungal communities show distance decay of similarity that has implications for seagrass management and restoration. Ecol Evol 2019; 9:11288-11297. [PMID: 31641473 PMCID: PMC6802368 DOI: 10.1002/ece3.5631] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 08/13/2019] [Accepted: 08/16/2019] [Indexed: 01/18/2023] Open
Abstract
Marine fungal biodiversity remains vastly understudied, and even less is known of their biogeography and the processes responsible for driving these distributions in marine environments. We investigated the fungal communities associated with the seagrass Enhalus acoroides collected from Singapore and Peninsular Malaysia to test the hypothesis that fungal communities are homogeneous throughout the study area. Seagrass samples were separated into different structures (leaves, roots, and rhizomes), and a sediment sample was collected next to each plant. Amplicon sequencing of the fungal internal transcribed spacer 1 and subsequent analysis revealed significant differences in fungal communities collected from different locations and different structures. We show a significant pattern of distance decay, with samples collected close to each other having more similar fungal communities in comparison with those that are more distant, indicating dispersal limitations and/or differences in habitat type are contributing to the observed biogeographic patterns. These results add to our understanding of the seagrass ecosystem in an understudied region of the world that is also the global epicenter of seagrass diversity. This work has implications for seagrass management and conservation initiatives, and we recommend that fungal community composition be a consideration for any seagrass transplant or restoration programme.
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Affiliation(s)
- Benjamin J. Wainwright
- Department of Biological SciencesNational University of SingaporeSingapore CitySingapore
| | | | - Joshua Zushi
- Biology DepartmentUtah Valley UniversityOremUTUSA
| | - Nicole Li Ying Lee
- Department of Biological SciencesNational University of SingaporeSingapore CitySingapore
| | - Jillian Lean Sim Ooi
- Department of GeographyFaculty of Arts and Social SciencesUniversity of MalayaKuala LumpurMalaysia
| | - Jen Nie Lee
- Faculty of Science and Marine EnvironmentUniversity Malaysia TerengganuTerengganuMalaysia
| | - Danwei Huang
- Department of Biological SciencesNational University of SingaporeSingapore CitySingapore
- Tropical Marine Science InstituteNational University of SingaporeSingapore CitySingapore
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Amend A, Burgaud G, Cunliffe M, Edgcomb VP, Ettinger CL, Gutiérrez MH, Heitman J, Hom EFY, Ianiri G, Jones AC, Kagami M, Picard KT, Quandt CA, Raghukumar S, Riquelme M, Stajich J, Vargas-Muñiz J, Walker AK, Yarden O, Gladfelter AS. Fungi in the Marine Environment: Open Questions and Unsolved Problems. mBio 2019; 10:e01189-18. [PMID: 30837337 PMCID: PMC6401481 DOI: 10.1128/mbio.01189-18] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Terrestrial fungi play critical roles in nutrient cycling and food webs and can shape macroorganism communities as parasites and mutualists. Although estimates for the number of fungal species on the planet range from 1.5 to over 5 million, likely fewer than 10% of fungi have been identified so far. To date, a relatively small percentage of described species are associated with marine environments, with ∼1,100 species retrieved exclusively from the marine environment. Nevertheless, fungi have been found in nearly every marine habitat explored, from the surface of the ocean to kilometers below ocean sediments. Fungi are hypothesized to contribute to phytoplankton population cycles and the biological carbon pump and are active in the chemistry of marine sediments. Many fungi have been identified as commensals or pathogens of marine animals (e.g., corals and sponges), plants, and algae. Despite their varied roles, remarkably little is known about the diversity of this major branch of eukaryotic life in marine ecosystems or their ecological functions. This perspective emerges from a Marine Fungi Workshop held in May 2018 at the Marine Biological Laboratory in Woods Hole, MA. We present the state of knowledge as well as the multitude of open questions regarding the diversity and function of fungi in the marine biosphere and geochemical cycles.
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Affiliation(s)
- Anthony Amend
- Department of Botany, University of Hawai'i at Manoa, Honolulu, Hawaii, USA
| | - Gaetan Burgaud
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, ESIAB, Technopôle Brest-Iroise, Plouzané, France
| | - Michael Cunliffe
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, United Kingdom
| | - Virginia P Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | | | - M H Gutiérrez
- Departamento de Oceanografía, Centro de Investigación Oceanográfica COPAS Sur-Austral, Universidad de Concepción, Concepción, Chile
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Erik F Y Hom
- Department of Biology, University of Mississippi, Oxford, Mississippi, USA
| | - Giuseppe Ianiri
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Adam C Jones
- Gordon and Betty Moore Foundation, Palo Alto, California, USA
| | - Maiko Kagami
- Graduate School of Environment and Information Sciences, Yokohama National University, Yokohama, Japan
| | - Kathryn T Picard
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - C Alisha Quandt
- Ecology and Evolutionary Biology Department, University of Colorado, Boulder, Colorado, USA
| | | | - Mertixell Riquelme
- Department of Microbiology, Centro de Investigación Científica y Educación Superior de Ensenada (CICESE), Ensenada, Baja California, Mexico
| | - Jason Stajich
- Department of Microbiology & Plant Pathology and Institute for Integrative Genome Biology, University of California-Riverside, Riverside, California, USA
| | - José Vargas-Muñiz
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Allison K Walker
- Department of Biology, Acadia University, Wolfville, Nova Scotia, Canada
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Amy S Gladfelter
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Marine Biological Laboratory, Woods Hole, Massachusetts, USA
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11
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12
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Savidov N, Gloriozova TA, Poroikov VV, Dembitsky VM. Highly oxygenated isoprenoid lipids derived from fungi and fungal endophytes: Origin and biological activities. Steroids 2018; 140:114-124. [PMID: 30326211 DOI: 10.1016/j.steroids.2018.10.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/19/2018] [Accepted: 10/09/2018] [Indexed: 02/07/2023]
Abstract
This mini review is devoted to highly oxygenated isoprenoid lipids (HOIL) that are produced by fungi and fungal endophytes from various ecological niches, both terrestrial and aquatic. Steroids were distributed as from edible cultivated fungi, as well as fungi collected in forests. Fungal endophytes were generally isolated from plants and cultured to obtain sufficient biomass. Marine fungi were obtained from marine brown and red algae and marine invertebrates such as sponges, corals, worms, crustacea or from marine sediments. HOIL isolated from the terrestrial ecosystem have the pharmacological potential on anti-hypercholesterolemic, anti-neoplastic, anti-eczematic and anti-inflammatory activity estimated with a confidence of 84-90%. HOIL that produced by marine fungal species are predicted as having anti-inflammatory and anti-hypercholesterolemic activity with a confidence of 82-91%. In addition, they may have potential acetylcholinesterase and cell adhesion molecule inhibitors estimated with a confidence of 86-88%.
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Affiliation(s)
- Nick Savidov
- Centre for Applied Research and Innovation, Lethbridge College, 3000 College Drive South, Lethbridge AB T1K 1L6, Canada
| | | | | | - Valery M Dembitsky
- Centre for Applied Research and Innovation, Lethbridge College, 3000 College Drive South, Lethbridge AB T1K 1L6, Canada; N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation; National Scientific Center of Marine Biology, Vladivostok 690041, Russian Federation.
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13
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Qian X, Chen L, Guo X, He D, Shi M, Zhang D. Shifts in community composition and co-occurrence patterns of phyllosphere fungi inhabiting Mussaenda shikokiana along an elevation gradient. PeerJ 2018; 6:e5767. [PMID: 30345176 PMCID: PMC6187995 DOI: 10.7717/peerj.5767] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 09/17/2018] [Indexed: 02/03/2023] Open
Abstract
The altitudinal effects on the distributions of phyllosphere fungal assemblages in conspecific plants remain poorly elucidated. To address this, phyllosphere fungal communities associated with Mussaenda shikokiana were investigated at four sites across a 350 m elevation gradient in a subtropical forest by employing Illumina metabarcoding of the fungal internal transcribed spacer 2 (ITS2) region. Our results demonstrated that phyllosphere fungal assemblages with a single host possessed high taxonomic diversity and multiple trophic guilds. OTU richness was significantly influenced by elevation. The elevation gradient also entailed distinct shifts in the community composition of phyllosphere fungi, which was significantly related to geographical distance and mean annual temperature (MAT). Additionally, comparison of phyllosphere fungal networks showed reduced connectivity with increasing elevation. Our data provide insights on the distribution and interactions of the phyllosphere fungal community associated with a single host along a short elevation gradient.
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Affiliation(s)
- Xin Qian
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Liang Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoming Guo
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dan He
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Miaomiao Shi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Dianxiang Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
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14
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Synergy among Microbiota and Their Hosts: Leveraging the Hawaiian Archipelago and Local Collaborative Networks To Address Pressing Questions in Microbiome Research. mSystems 2018; 3:mSystems00159-17. [PMID: 29556540 PMCID: PMC5850080 DOI: 10.1128/msystems.00159-17] [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: 10/30/2017] [Accepted: 11/28/2017] [Indexed: 11/29/2022] Open
Abstract
Despite increasing acknowledgment that microorganisms underpin the healthy functioning of basically all multicellular life, few cross-disciplinary teams address the diversity and function of microbiota across organisms and ecosystems. Our newly formed consortium of junior faculty spanning fields such as ecology and geoscience to mathematics and molecular biology from the University of Hawai‘i at Mānoa aims to fill this gap. Despite increasing acknowledgment that microorganisms underpin the healthy functioning of basically all multicellular life, few cross-disciplinary teams address the diversity and function of microbiota across organisms and ecosystems. Our newly formed consortium of junior faculty spanning fields such as ecology and geoscience to mathematics and molecular biology from the University of Hawai‘i at Mānoa aims to fill this gap. We are united in our mutual interest in advancing a new paradigm for biology that incorporates our modern understanding of the importance of microorganisms. As our first concerted research effort, we will assess the diversity and function of microbes across an entire watershed on the island of Oahu, Hawai‘i. Due to its high ecological diversity across tractable areas of land and sea, Hawai‘i provides a model system for the study of complex microbial communities and the processes they mediate. Owing to our diverse expertise, we will leverage this study system to advance the field of biology.
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15
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Bonthond G, Merselis DG, Dougan KE, Graff T, Todd W, Fourqurean JW, Rodriguez-Lanetty M. Inter-domain microbial diversity within the coral holobiont Siderastrea siderea from two depth habitats. PeerJ 2018; 6:e4323. [PMID: 29441234 PMCID: PMC5808317 DOI: 10.7717/peerj.4323] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 01/13/2018] [Indexed: 12/31/2022] Open
Abstract
Corals host diverse microbial communities that are involved in acclimatization, pathogen defense, and nutrient cycling. Surveys of coral-associated microbes have been particularly directed toward Symbiodinium and bacteria. However, a holistic understanding of the total microbiome has been hindered by a lack of analyses bridging taxonomically disparate groups. Using high-throughput amplicon sequencing, we simultaneously characterized the Symbiodinium, bacterial, and fungal communities associated with the Caribbean coral Siderastrea siderea collected from two depths (17 and 27 m) on Conch reef in the Florida Keys. S. siderea hosted an exceptionally diverse Symbiodinium community, structured differently between sampled depth habitats. While dominated at 27 m by a Symbiodinium belonging to clade C, at 17 m S. siderea primarily hosted a mixture of clade B types. Most fungal operational taxonomic units were distantly related to available reference sequences, indicating the presence of a high degree of fungal novelty within the S. siderea holobiont and a lack of knowledge on the diversity of fungi on coral reefs. Network analysis showed that co-occurrence patterns in the S. siderea holobiont were prevalent among bacteria, however, also detected between fungi and bacteria. Overall, our data show a drastic shift in the associated Symbiodinium community between depths on Conch Reef, which might indicate that alteration in this community is an important mechanism facilitating local physiological adaptation of the S. siderea holobiont. In contrast, bacterial and fungal communities were not structured differently between depth habitats.
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Affiliation(s)
- Guido Bonthond
- Department of Biological Sciences, Florida International University, Miami, FL, USA.,Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Daniel G Merselis
- Department of Biological Sciences, Florida International University, Miami, FL, USA
| | - Katherine E Dougan
- Department of Biological Sciences, Florida International University, Miami, FL, USA
| | | | | | - James W Fourqurean
- Department of Biological Sciences, Florida International University, Miami, FL, USA
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16
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Sun JY, Song Y, Ma ZP, Zhang HJ, Yang ZD, Cai ZH, Zhou J. Fungal community dynamics during a marine dinoflagellate (Noctiluca scintillans) bloom. MARINE ENVIRONMENTAL RESEARCH 2017; 131:183-194. [PMID: 29017729 DOI: 10.1016/j.marenvres.2017.10.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 09/27/2017] [Accepted: 10/02/2017] [Indexed: 06/07/2023]
Abstract
Contamination and eutrophication have caused serious ecological events (such as algal bloom) in coastal area. During this ecological process, microbial community structure is critical for algal bloom succession. The diversity and composition of bacteria and archaea communities in algal blooms have been widely investigated; however, those of fungi are poorly understood. To fill this gap, we used pyrosequencing and correlation approaches to assess fungal patterns and associations during a dinoflagellate (Noctiluca scintillans) bloom. Phylum level fungal types were predominated by Ascomycota, Chytridiomycota, Mucoromycotina, and Basidiomycota. At the genus level drastic changes were observed with Hysteropatella, Malassezia and Saitoella dominating during the initial bloom stage, while Malassezia was most abundant (>50%) during onset and peak-bloom stages. Saitoella and Lipomyces gradually became more abundant and, in the decline stage, contributed almost 70% of sequences. In the terminal stage of the bloom, Rozella increased rapidly to a maximum of 50-60%. Fungal population structure was significantly influenced by temperature and substrate (N and P) availability (P < 0.05). Inter-specific network analyses demonstrated that Rozella and Saitoella fungi strongly impacted the ecological trajectory of N. scintillans. The functional prediction show that symbiotrophic fungi was dominated in the onset stage; saprotroph type was the primary member present during the exponential growth period; whereas pathogentroph type fungi enriched in decline phase. Overall, fungal communities and functions correlated significantly with N. scintillans processes, suggesting that they may regulate dinoflagellate bloom fates. Our results will facilitate deeper understanding of the ecological importance of marine fungi and their roles in algal bloom formation and collapse.
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Affiliation(s)
- Jing-Yun Sun
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China; School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, Gansu Province, PR China
| | - Yu Song
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China
| | - Zhi-Ping Ma
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China
| | - Huai-Jing Zhang
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China
| | - Zhong-Duo Yang
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, Gansu Province, PR China; The Provincial Education Key Laboratory of Screening, Evaluation and Advanced Processing of Traditional Chinese Medicine and Tibetan Medicine, School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730050, Gansu Province, PR China
| | - Zhong-Hua Cai
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China.
| | - Jin Zhou
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China.
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