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Thomé PC, Wolinska J, Van Den Wyngaert S, Reñé A, Ilicic D, Agha R, Grossart HP, Garcés E, Monaghan MT, Strassert JFH. Phylogenomics including new sequence data of phytoplankton-infecting chytrids reveals multiple independent lifestyle transitions across the phylum. Mol Phylogenet Evol 2024; 197:108103. [PMID: 38754710 DOI: 10.1016/j.ympev.2024.108103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 12/01/2023] [Accepted: 05/11/2024] [Indexed: 05/18/2024]
Abstract
Parasitism is the most common lifestyle on Earth and has emerged many times independently across the eukaryotic tree of life. It is frequently found among chytrids (Chytridiomycota), which are early-branching unicellular fungi that feed osmotrophically via rhizoids as saprotrophs or parasites. Chytrids are abundant in most aquatic and terrestrial environments and fulfil important ecosystem functions. As parasites, they can have significant impacts on host populations. They cause global amphibian declines and influence the Earth's carbon cycle by terminating algal blooms. To date, the evolution of parasitism within the chytrid phylum remains unclear due to the low phylogenetic resolution of rRNA genes for the early diversification of fungi, and because few parasitic lineages have been cultured and genomic data for parasites is scarce. Here, we combine transcriptomics, culture-independent single-cell genomics and a phylogenomic approach to overcome these limitations. We newly sequenced 29 parasitic taxa and combined these with existing data to provide a robust backbone topology for the diversification of Chytridiomycota. Our analyses reveal multiple independent lifestyle transitions between parasitism and saprotrophy among chytrids and multiple host shifts by parasites. Based on these results and the parasitic lifestyle of other early-branching holomycotan lineages, we hypothesise that the chytrid last common ancestor was a parasite of phytoplankton.
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Affiliation(s)
- Pauline C Thomé
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Justyna Wolinska
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany; Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Silke Van Den Wyngaert
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany; Department of Biology, University of Turku, Turku, Finland
| | - Albert Reñé
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Barcelona, Spain
| | - Doris Ilicic
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
| | - Ramsy Agha
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Hans-Peter Grossart
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany; Institute for Biochemistry and Biology, Potsdam University, Potsdam, Germany
| | - Esther Garcés
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Barcelona, Spain
| | - Michael T Monaghan
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany; Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Jürgen F H Strassert
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.
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Wan B, Lei Y, Yuan Z, Wang W. Metagenomic dissection of the intestinal microbiome in the giant river prawn Macrobrachium rosenbergii infected with Decapod iridescent virus 1. FISH & SHELLFISH IMMUNOLOGY 2024; 149:109617. [PMID: 38723876 DOI: 10.1016/j.fsi.2024.109617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/26/2024] [Accepted: 05/07/2024] [Indexed: 05/12/2024]
Abstract
Microbiome in the intestines of aquatic invertebrates plays pivotal roles in maintaining intestinal homeostasis, especially when the host is exposed to pathogen invasion. Decapod iridescent virus 1 (DIV1) is a devastating virus seriously affecting the productivity and success of crustacean aquaculture. In this study, a metagenomic analysis was conducted to investigate the genomic sequences, community structure and functional characteristics of the intestinal microbiome in the giant river prawn Macrobrachiumrosenbergii infected with DIV1. The results showed that DIV1 infection could significantly reduce the diversity and richness of intestinal microbiome. Proteobacteria represented the largest taxon at the phylum level, and at the species level, the abundance of Gonapodya prolifera and Solemya velum gill symbiont increased significantly following DIV1 infection. In the infected prawns, four metabolic pathways related to purine metabolism, pyrimidine metabolism, glycerophospholipid metabolism, and pentose phosphate pathway, and five pathways related to nucleotide excision repair, homologous recombination, mismatch repair, base excision repair, and DNA replication were significantly enriched. Moreover, several immune response related pathways, such as shigellosis, bacterial invasion of epithelial cells, Salmonella infection, and Vibrio cholerae infection were repressed, indicating that secondary infection in M. rosenbergii may be inhibited via the suppression of these immune related pathways. DIV1 infection led to the induction of microbial carbohydrate enzymes such as the glycoside hydrolases (GHs), and reduced the abundance and number of antibiotic-resistant ontologies (AROs). A variety of AROs were identified from the microbiota, and mdtF and lrfA appeared as the dominant genes in the detected AROs. In addition, antibiotic efflux, antibiotic inactivation, and antibiotic target alteration were the main antibiotic resistance mechanisms. Collectively, the data would enable a deeper understanding of the molecular response of intestinal microbiota to DIV1, and offer more insights into its roles in prawn resistance to DIVI infection.
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Affiliation(s)
- Boquan Wan
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Yiguo Lei
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Zhixiang Yuan
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Wei Wang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang, 524088, China.
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3
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Jones AL, Pratt CJ, Meili CH, Soo RM, Hugenholtz P, Elshahed MS, Youssef NH. Anaerobic gut fungal communities in marsupial hosts. mBio 2024; 15:e0337023. [PMID: 38259066 PMCID: PMC10865811 DOI: 10.1128/mbio.03370-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
The anaerobic gut fungi (AGF) inhabit the alimentary tracts of herbivores. In contrast to placental mammals, information regarding the identity, diversity, and community structure of AGF in marsupials is extremely sparse. Here, we characterized AGF communities in 61 fecal samples from 10 marsupial species belonging to four families in the order Diprotodontia: Vombatidae (wombats), Phascolarctidae (koalas), Phalangeridae (possums), and Macropodidae (kangaroos, wallabies, and pademelons). An amplicon-based diversity survey using the D2 region of the large ribosomal subunit as a phylogenetic marker indicated that marsupial AGF communities were dominated by eight genera commonly encountered in placental herbivores (Neocallimastix, Caecomyces, Cyllamyces, Anaeromyces, Orpinomyces, Piromyces, Pecoramyces, and Khoyollomyces). Community structure analysis revealed a high level of stochasticity, and ordination approaches did not reveal a significant role for the animal host, gut type, dietary preferences, or lifestyle in structuring marsupial AGF communities. Marsupial foregut and hindgut communities displayed diversity and community structure patterns comparable to AGF communities typically encountered in placental foregut hosts while exhibiting a higher level of diversity and a distinct community structure compared to placental hindgut communities. Quantification of AGF load using quantitative PCR indicated a significantly smaller load in marsupial hosts compared to their placental counterparts. Isolation efforts were only successful from a single red kangaroo fecal sample and yielded a Khoyollomyces ramosus isolate closely related to strains previously isolated from placental hosts. Our results suggest that AGF communities in marsupials are in low abundance and show little signs of selection based on ecological and evolutionary factors.IMPORTANCEThe AGF are integral part of the microbiome of herbivores. They play a crucial role in breaking down plant biomass in hindgut and foregut fermenters. The majority of research has been conducted on the AGF community in placental mammalian hosts. However, it is important to note that many marsupial mammals are also herbivores and employ a hindgut or foregut fermentation strategy for breaking down plant biomass. So far, very little is known regarding the AGF diversity and community structure in marsupial mammals. To fill this knowledge gap, we conducted an amplicon-based diversity survey targeting AGF in 61 fecal samples from 10 marsupial species. We hypothesize that, given the distinct evolutionary history and alimentary tract architecture, novel and unique AGF communities would be encountered in marsupials. Our results indicate that marsupial AGF communities are highly stochastic, present in relatively low loads, and display community structure patterns comparable to AGF communities typically encountered in placental foregut hosts. Our results indicate that marsupial hosts harbor AGF communities; however, in contrast to the strong pattern of phylosymbiosis typically observed between AGF and placental herbivores, the identity and gut architecture appear to play a minor role in structuring AGF communities in marsupials.
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Affiliation(s)
- Adrienne L. Jones
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Carrie J. Pratt
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Casey H. Meili
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Rochelle M. Soo
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Queensland, Australia
| | - Philip Hugenholtz
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Queensland, Australia
| | - Mostafa S. Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Noha H. Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
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4
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Dos Santos VL, Silva UC, Santos EH, Resende AA, Dias MF, Cuadros-Orellana S, Marques AR. Exploring the mycobiota of bromeliads phytotelmata in Brazilian Campos Rupestres. Braz J Microbiol 2023; 54:1885-1897. [PMID: 37322328 PMCID: PMC10485200 DOI: 10.1007/s42770-023-00977-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 03/10/2023] [Indexed: 06/17/2023] Open
Abstract
The phytotelmata is a water-filled tank on a terrestrial plant, and it plays an important role in bromeliad growth and ecosystem functioning. Even though previous studies have contributed to elucidate the composition of the prokaryotic component of this aquatic ecosystem, its mycobiota (fungal community) is still poorly known. In the present work, ITS2 amplicon deep sequencing was used to examine the fungal communities inhabiting the phytotelmata of two bromeliads species that coexist in a sun-exposed rupestrian field of Southeastern Brazil, namely Aechmea nudicaulis (AN) and Vriesea minarum (VM). Ascomycota was the most abundant phylum in both bromeliads (57.1 and 89.1% in AN and VM respectively, on average), while the others were present in low abundance (< 2%). Mortierellomycota and Glomeromycota were exclusively observed in AN. Beta-diversity analysis showed that samples from each bromeliad significantly clustered together. In conclusion, despite the considerable within-group variation, the results suggested that each bromeliad harbor a distinct fungi community, what could be associated with the physicochemical characteristics of the phytotelmata (mainly total nitrogen, total organic carbon, and total carbon) and plant morphological features.
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Affiliation(s)
- Vera Lúcia Dos Santos
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil.
| | - Ubiana Cássia Silva
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Eduardo Horta Santos
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Alessandra Abrão Resende
- Expertise Center Botany and Biodiversity, Museu de História Natural e Jardim Botânico, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31080-010, Brazil
| | - Marcela França Dias
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Sara Cuadros-Orellana
- Universidad Católica del Maule, Facultad de Ciencias Agrarias y Forestales, Centro de Biotecnología de los Recursos Naturales, 3480112, Talca, Chile
| | - Andréa Rodrigues Marques
- Department of Biological Sciences, Centro Federal de Educação Tecnológica de Minas Gerais - CEFET/MG, Av. Amazonas, 5253, Nova Suíça, 30.421-169, Belo Horizonte, MG, 30421-169, Brazil
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5
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Meili CH, Jones AL, Arreola AX, Habel J, Pratt CJ, Hanafy RA, Wang Y, Yassin AS, TagElDein MA, Moon CD, Janssen PH, Shrestha M, Rajbhandari P, Nagler M, Vinzelj JM, Podmirseg SM, Stajich JE, Goetsch AL, Hayes J, Young D, Fliegerova K, Grilli DJ, Vodička R, Moniello G, Mattiello S, Kashef MT, Nagy YI, Edwards JA, Dagar SS, Foote AP, Youssef NH, Elshahed MS. Patterns and determinants of the global herbivorous mycobiome. Nat Commun 2023; 14:3798. [PMID: 37365172 PMCID: PMC10293281 DOI: 10.1038/s41467-023-39508-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 06/14/2023] [Indexed: 06/28/2023] Open
Abstract
Despite their role in host nutrition, the anaerobic gut fungal (AGF) component of the herbivorous gut microbiome remains poorly characterized. Here, to examine global patterns and determinants of AGF diversity, we generate and analyze an amplicon dataset from 661 fecal samples from 34 mammalian species, 9 families, and 6 continents. We identify 56 novel genera, greatly expanding AGF diversity beyond current estimates (31 genera and candidate genera). Community structure analysis indicates that host phylogenetic affiliation, not domestication status and biogeography, shapes the community rather than. Fungal-host associations are stronger and more specific in hindgut fermenters than in foregut fermenters. Transcriptomics-enabled phylogenomic and molecular clock analyses of 52 strains from 14 genera indicate that most genera with preferences for hindgut hosts evolved earlier (44-58 Mya) than those with preferences for foregut hosts (22-32 Mya). Our results greatly expand the documented scope of AGF diversity and provide an ecologically and evolutionary-grounded model to explain the observed patterns of AGF diversity in extant animal hosts.
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Affiliation(s)
- Casey H Meili
- Oklahoma State University, Department of Microbiology and Molecular Genetics, Stillwater, OK, USA
| | - Adrienne L Jones
- Oklahoma State University, Department of Microbiology and Molecular Genetics, Stillwater, OK, USA
| | - Alex X Arreola
- Oklahoma State University, Department of Microbiology and Molecular Genetics, Stillwater, OK, USA
| | - Jeffrey Habel
- Oklahoma State University, Department of Microbiology and Molecular Genetics, Stillwater, OK, USA
| | - Carrie J Pratt
- Oklahoma State University, Department of Microbiology and Molecular Genetics, Stillwater, OK, USA
| | - Radwa A Hanafy
- Oklahoma State University, Department of Microbiology and Molecular Genetics, Stillwater, OK, USA
| | - Yan Wang
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada
| | - Aymen S Yassin
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Moustafa A TagElDein
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Christina D Moon
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
| | - Peter H Janssen
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
| | - Mitesh Shrestha
- Department of Applied Microbiology and Food Technology, Research Institute for Bioscience and Biotechnology (RIBB), Kathmandu, Nepal
| | - Prajwal Rajbhandari
- Department of Applied Microbiology and Food Technology, Research Institute for Bioscience and Biotechnology (RIBB), Kathmandu, Nepal
| | - Magdalena Nagler
- Universität Innsbruck, Faculty of Biology, Department of Microbiology, Innsbruck, Austria
| | - Julia M Vinzelj
- Universität Innsbruck, Faculty of Biology, Department of Microbiology, Innsbruck, Austria
| | - Sabine M Podmirseg
- Universität Innsbruck, Faculty of Biology, Department of Microbiology, Innsbruck, Austria
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, USA
| | | | | | - Diana Young
- Bavarian State Research Center for Agriculture, Freising, Germany
| | - Katerina Fliegerova
- Institute of Animal Physiology and Genetics Czech Academy of Sciences, Prague, Czechia
| | - Diego Javier Grilli
- Área de Microbiología, Facultad de Ciencias Médicas, Universidad Nacional de Cuyo, Mendoza, Argentina
| | | | - Giuseppe Moniello
- Department of Veterinary Medicine, University of Sassari, Sardinia, Italy
| | - Silvana Mattiello
- University of Milan, Dept. of Agricultural and Environmental Sciences, Milan, Italy
| | - Mona T Kashef
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Yosra I Nagy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | | | | | - Andrew P Foote
- Oklahoma State University, Department of Animal and Food Sciences, Stillwater, OK, USA
| | - Noha H Youssef
- Oklahoma State University, Department of Microbiology and Molecular Genetics, Stillwater, OK, USA.
| | - Mostafa S Elshahed
- Oklahoma State University, Department of Microbiology and Molecular Genetics, Stillwater, OK, USA.
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6
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Reynolds NK, Stajich JE, Benny GL, Barry K, Mondo S, LaButti K, Lipzen A, Daum C, Grigoriev IV, Ho HM, Crous PW, Spatafora JW, Smith ME. Mycoparasites, Gut Dwellers, and Saprotrophs: Phylogenomic Reconstructions and Comparative Analyses of Kickxellomycotina Fungi. Genome Biol Evol 2023; 15:6974727. [PMID: 36617272 PMCID: PMC9866270 DOI: 10.1093/gbe/evac185] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 01/09/2023] Open
Abstract
Improved sequencing technologies have profoundly altered global views of fungal diversity and evolution. High-throughput sequencing methods are critical for studying fungi due to the cryptic, symbiotic nature of many species, particularly those that are difficult to culture. However, the low coverage genome sequencing (LCGS) approach to phylogenomic inference has not been widely applied to fungi. Here we analyzed 171 Kickxellomycotina fungi using LCGS methods to obtain hundreds of marker genes for robust phylogenomic reconstruction. Additionally, we mined our LCGS data for a set of nine rDNA and protein coding genes to enable analyses across species for which no LCGS data were obtained. The main goals of this study were to: 1) evaluate the quality and utility of LCGS data for both phylogenetic reconstruction and functional annotation, 2) test relationships among clades of Kickxellomycotina, and 3) perform comparative functional analyses between clades to gain insight into putative trophic modes. In opposition to previous studies, our nine-gene analyses support two clades of arthropod gut dwelling species and suggest a possible single evolutionary event leading to this symbiotic lifestyle. Furthermore, we resolve the mycoparasitic Dimargaritales as the earliest diverging clade in the subphylum and find four major clades of Coemansia species. Finally, functional analyses illustrate clear variation in predicted carbohydrate active enzymes and secondary metabolites (SM) based on ecology, that is biotroph versus saprotroph. Saprotrophic Kickxellales broadly lack many known pectinase families compared with saprotrophic Mucoromycota and are depauperate for SM but have similar numbers of predicted chitinases as mycoparasitic.
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Affiliation(s)
| | - Jason E Stajich
- Department of Microbiology & Plant Pathology and Institute for Integrative Genome Biology, University of California–Riverside
| | | | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory
| | - Stephen Mondo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory
| | - Chris Daum
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory,Department of Plant and Microbial Biology, University of California Berkeley
| | - Hsiao-Man Ho
- Department of Science Education, University of Education, 134, Section 2, Heping E. Road, National Taipei, Taipei 106, Taiwan
| | - Pedro W Crous
- Department of Evolutionary Phytopathology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
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7
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Vasantha Raman N, Gsell AS, Voulgarellis T, van den Brink NW, de Senerpont Domis LN. Moving beyond standard toxicological metrics: The effect of diclofenac on planktonic host-parasite interactions. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 254:106370. [PMID: 36516501 DOI: 10.1016/j.aquatox.2022.106370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 12/01/2022] [Accepted: 12/04/2022] [Indexed: 06/17/2023]
Abstract
Pharmaceuticals are increasingly released into surface waters and therefore ubiquitous in aquatic systems. While pharmaceuticals are known to influence species interactions, their effect on host-parasite interactions is still underexplored despite potential ecosystem-level consequences. Here, we ask whether diclofenac, a widely used non-steroid anti-inflammatory drug, affects the interaction between a phytoplankton host (Staurastrum sp.; green alga) and its obligate fungal parasite (Staurastromyces oculus; chytrid fungus). We hypothesized that the effect of increasing diclofenac concentration on the host-parasite system depends on parasite exposure. We assessed acute and chronic effects of a wide range of diclofenac concentrations (0-150 mg/L) on host and parasite performance using a replicated long gradient design in batch cultures. Overall system response summarizing parameters related to all biotic components in an experimental unit i.e., number of bacteria and phytoplankton host cells along with photosynthetic yield (a measure of algal cell fitness), depended on diclofenac concentration and presence/absence of parasite. While host standing biomass decreased at diclofenac concentrations >10 mg/L in non-parasite-exposed treatments, it increased at ≥10 mg/L in parasite-exposed treatments since losses due to infection declined. During acute phase (0-48 h), diclofenac concentrations <0.1 mg/L had no effect on host net-production neither in parasite-exposed nor non-parasite-exposed treatments, but parasite infection ceased at 10 mg/L. During chronic phase (0-216 h), host net-production declined only at concentrations >10 mg/L in non-parasite-exposed cultures, while it was overall close to zero in parasite-exposed cultures. Our results suggest that chytrid parasites are more sensitive to diclofenac than their host, allowing a window of opportunity for growth of phytoplankton hosts, despite exposure to a parasite. Our work provides a first understanding about effects of a pharmaceutical on a host-parasite interaction beyond those defined by standard toxicological metrics.
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Affiliation(s)
- Nandini Vasantha Raman
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, PB 6708, the Netherlands.
| | - Alena S Gsell
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, PB 6708, the Netherlands
| | - Themistoklis Voulgarellis
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, PB 6708, the Netherlands
| | - Nico W van den Brink
- Division of Toxicology, Wageningen University & Research, Stippeneng 4, Wageningen, WE 6708, the Netherlands
| | - Lisette N de Senerpont Domis
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, PB 6708, the Netherlands; Aquatic Ecology and Water Quality Management Group, Wageningen University & Research, Wageningen, the Netherlands; Pervasive Systems Research Group, Faculty of Electrical Engineering, Mathematics and Computer Science, University of Twente, the Netherlands; Department of Water Resources, Faculty of Geo-Information Science and Earth Observation, University of Twente, the Netherlands
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8
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Van Den Wyngaert S, Kainz MJ, Ptacnik R. Mucilage protects the planktonic desmid Staurodesmus sp. against parasite attack by a chytrid fungus. JOURNAL OF PLANKTON RESEARCH 2023; 45:3-14. [PMID: 36751484 PMCID: PMC9896892 DOI: 10.1093/plankt/fbac071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/23/2022] [Indexed: 06/18/2023]
Abstract
Zoosporic fungi of the phylum Chytridiomycota are ubiquitous parasites of phytoplankton in aquatic ecosystems, but little is known about phytoplankton defense strategies against parasitic chytrid attacks. Using a model chytrid-phytoplankton pathosystem, we experimentally tested the hypothesis that the mucilage envelope of a mucilage-forming desmid species provides protection against the parasitic chytrid Staurastromyces oculus. Mucilage-forming Staurodesmus cells were not accessible to the chytrid, whereas physical removal of the mucilage envelope rendered the same Staurodesmus sp. strain equally susceptible to chytrid infections as the original non-mucilage-forming host Staurastrum sp. Epidemic spread of the parasite only occurred in Staurastrum sp., whereas non-mucilage-bearing Staurodesmus sp. allowed for co-existence of host and parasite, and mucilage-bearing Staurodesmus sp. caused parasite extinction. In addition to the mucilage defense barrier, we also demonstrate the ability of both Staurastrum sp. and Staurodesmus sp. to resist infection by preventing chytrid development while still remaining viable and being able to reproduce and thus recover from an infection. This study extends our knowledge on phytoplankton defense traits and the functional role of mucilage in phytoplankton as a physical barrier against fungal parasites.
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Affiliation(s)
| | - Martin J Kainz
- Wassercluster – Biologische Station Lunz, Dr Carl Kupelwieser Promenade 5, 3293 Lunz Am See, Austria
- Department of Biomedical Research, Danube University, Dr Karl Dorrek Strasse 20, 3500 Krems, Austria
| | - Robert Ptacnik
- Wassercluster – Biologische Station Lunz, Dr Carl Kupelwieser Promenade 5, 3293 Lunz Am See, Austria
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9
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YÜCEL H, EKİNCİ K. Carbohydrate active enzyme system in rumen fungi: a review. INTERNATIONAL JOURNAL OF SECONDARY METABOLITE 2022. [DOI: 10.21448/ijsm.1075030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Hydrolysis and dehydration reactions of carbohydrates, which are used as energy raw materials by all living things in nature, are controlled by Carbohydrate Active Enzyme (CAZy) systems. These enzymes are also used in different industrial areas today. There are different types of microorganisms that have the CAZy system and are used in the industrial sector. Apart from current organisms, there are also rumen fungi within the group of candidate microorganisms with the CAZy system. It has been reported that xylanase (EC3.2.1.8 and EC3.2.1.37) enzyme, a member of the glycoside hydrolase enzyme family obtained from Trichoderma sp. and used especially in areas such as bread, paper, and feed industry, is more synthesized in rumen fungi such as Orpinomyces sp. and Neocallimastix sp. Therefore, this study reviews Neocallimastixsp., Orpinomyces sp., Caecomyces sp., Piromyces sp., and Anaeromyces sp., registered in the CAZy and Mycocosm database for rumen fungi to have both CAZy enzyme activity and to be an alternative microorganism in the industry. Furthermore the CAZy enzyme activities of the strains are investigated. The review shows thatNeocallimax sp. and Orpinomyces sp. areconsidered as candidate microorganisms.
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Affiliation(s)
- Halit YÜCEL
- KAHRAMANMARAŞ SÜTÇÜ İMAM ÜNİVERSİTESİ, ZİRAAT FAKÜLTESİ
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10
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Roik A, Reverter M, Pogoreutz C. A roadmap to understanding diversity and function of coral reef-associated fungi. FEMS Microbiol Rev 2022; 46:6615459. [PMID: 35746877 PMCID: PMC9629503 DOI: 10.1093/femsre/fuac028] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/01/2022] [Accepted: 06/14/2022] [Indexed: 01/09/2023] Open
Abstract
Tropical coral reefs are hotspots of marine productivity, owing to the association of reef-building corals with endosymbiotic algae and metabolically diverse bacterial communities. However, the functional importance of fungi, well-known for their contribution to shaping terrestrial ecosystems and global nutrient cycles, remains underexplored on coral reefs. We here conceptualize how fungal functional traits may have facilitated the spread, diversification, and ecological adaptation of marine fungi on coral reefs. We propose that functions of reef-associated fungi may be diverse and go beyond their hitherto described roles of pathogens and bioeroders, including but not limited to reef-scale biogeochemical cycles and the structuring of coral-associated and environmental microbiomes via chemical mediation. Recent technological and conceptual advances will allow the elucidation of the physiological, ecological, and chemical contributions of understudied marine fungi to coral holobiont and reef ecosystem functioning and health and may help provide an outlook for reef management actions.
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Affiliation(s)
- Anna Roik
- Corresponding author: Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heerstrasse 231, D-26129 Oldenburg, Germany. E-mail:
| | - Miriam Reverter
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Wilhelmshaven, 26046, Germany,School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, United Kingdom
| | - Claudia Pogoreutz
- Corresponding author: Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Federale de Lausanne (EPFL), 1015 Lausanne, Switzerland.,
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11
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Xu SS, Zhang XL, Liu SS, Feng ST, Xiang GM, Xu CJ, Fan ZY, Xu K, Wang N, Wang Y, Che JJ, Liu ZG, Mu YL, Li K. Multi-Omic Analysis in a Metabolic Syndrome Porcine Model Implicates Arachidonic Acid Metabolism Disorder as a Risk Factor for Atherosclerosis. Front Nutr 2022; 9:807118. [PMID: 35284467 PMCID: PMC8906569 DOI: 10.3389/fnut.2022.807118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/10/2022] [Indexed: 11/25/2022] Open
Abstract
Background The diet-induced gut microbiota dysbiosis has been suggested as a major risk factor for atherothrombosis, however, the detailed mechanism linking these conditions is yet to be fully understood. Methods We established a long-term excessive-energy diet-induced metabolic syndrome (MetS) inbred Wuzhishan minipig model, which is characterized by its genetic stability, small size, and human-like physiology. The metabolic parameters, atherosclerotic lesions, gut microbiome, and host transcriptome were analyzed. Metabolomics profiling revealed a linkage between gut microbiota and atherothrombosis. Results We showed that white atheromatous plaque was clearly visible on abdominal aorta in the MetS model. Furthermore, using metagenome and metatranscriptome sequencing, we discovered that the long-term excessive energy intake altered the local intestinal microbiota composition and transcriptional profile, which was most dramatically illustrated by the reduced abundance of SCFAs-producing bacteria including Bacteroides, Lachnospiraceae, and Ruminococcaceae in the MetS model. Liver and abdominal aorta transcriptomes in the MetS model indicate that the diet-induced gut microbiota dysbiosis activated host chronic inflammatory responses and significantly upregulated the expression of genes related to arachidonic acid-dependent signaling pathways. Notably, metabolomics profiling further revealed an intimate linkage between arachidonic acid metabolism and atherothrombosis in the host-gut microbial metabolism axis. Conclusions These findings provide new insights into the relationship between atherothrombosis and regulation of gut microbiota via host metabolomes and will be of potential value for the treatment of cardiovascular diseases in MetS.
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Affiliation(s)
- Song-Song Xu
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiu-Ling Zhang
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Sha-Sha Liu
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Animal Husbandry and Veterinary Department, Beijing Vocational College of Agriculture, Beijing, China
| | - Shu-Tang Feng
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guang-Ming Xiang
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chang-Jiang Xu
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zi-Yao Fan
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kui Xu
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Nan Wang
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yue Wang
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing-Jing Che
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhi-Guo Liu
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu-Lian Mu
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Yu-Lian Mu
| | - Kui Li
- State Key Laboratory of Animal Nutrition and Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kui Li
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12
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Kelly M, Pasmans F, Muñoz JF, Shea TP, Carranza S, Cuomo CA, Martel A. Diversity, multifaceted evolution, and facultative saprotrophism in the European Batrachochytrium salamandrivorans epidemic. Nat Commun 2021; 12:6688. [PMID: 34795258 PMCID: PMC8602665 DOI: 10.1038/s41467-021-27005-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 10/28/2021] [Indexed: 01/06/2023] Open
Abstract
While emerging fungi threaten global biodiversity, the paucity of fungal genome assemblies impedes thoroughly characterizing epidemics and developing effective mitigation strategies. Here, we generate de novo genomic assemblies for six outbreaks of the emerging pathogen Batrachochytrium salamandrivorans (Bsal). We reveal the European epidemic currently damaging amphibian populations to comprise multiple, highly divergent lineages demonstrating isolate-specific adaptations and metabolic capacities. In particular, we show extensive gene family expansions and acquisitions, through a variety of evolutionary mechanisms, and an isolate-specific saprotrophic lifecycle. This finding both explains the chytrid's ability to divorce transmission from host density, producing Bsal's enigmatic host population declines, and is a key consideration in developing successful mitigation measures.
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Affiliation(s)
- Moira Kelly
- Wildlife Health Ghent, Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, 9820, Merelbeke, Belgium.
| | - Frank Pasmans
- grid.5342.00000 0001 2069 7798Wildlife Health Ghent, Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | - Jose F. Muñoz
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, 02142 MA USA
| | - Terrance P. Shea
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, 02142 MA USA
| | - Salvador Carranza
- grid.507636.10000 0004 0424 5398Institute of Evolutionary Biology (CSIC-UPF), 08003 Barcelona, Spain
| | - Christina A. Cuomo
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, 02142 MA USA
| | - An Martel
- Wildlife Health Ghent, Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, 9820, Merelbeke, Belgium.
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13
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Laundon D, Cunliffe M. A Call for a Better Understanding of Aquatic Chytrid Biology. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:708813. [PMID: 37744140 PMCID: PMC10512372 DOI: 10.3389/ffunb.2021.708813] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/09/2021] [Indexed: 09/26/2023]
Abstract
The phylum Chytridiomycota (the "chytrids") is an early-diverging, mostly unicellular, lineage of fungi that consists of significant aquatic saprotrophs, parasites, and pathogens, and is of evolutionary interest because its members retain biological traits considered ancestral in the fungal kingdom. While the existence of aquatic chytrids has long been known, their fundamental biology has received relatively little attention. We are beginning to establish a detailed understanding of aquatic chytrid diversity and insights into their ecological functions and prominence. However, the underpinning biology governing their aquatic ecological activities and associated core processes remain largely understudied and therefore unresolved. Many biological questions are outstanding for aquatic chytrids. What are the mechanisms that control their development and life cycle? Which core processes underpin their aquatic influence? What can their biology tell us about the evolution of fungi and the wider eukaryotic tree of life? We propose that the field of aquatic chytrid ecology could be further advanced through the improved understanding of chytrid biology, including the development of model aquatic chytrids and targeted studies using culture-independent approaches.
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Affiliation(s)
- Davis Laundon
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, United Kingdom
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| | - Michael Cunliffe
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, United Kingdom
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, United Kingdom
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14
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Tan MH, Loke S, Croft LJ, Gleason FH, Lange L, Pilgaard B, Trevathan-Tackett SM. First Genome of Labyrinthula sp., an Opportunistic Seagrass Pathogen, Reveals Novel Insight into Marine Protist Phylogeny, Ecology and CAZyme Cell-Wall Degradation. MICROBIAL ECOLOGY 2021; 82:498-511. [PMID: 33410934 DOI: 10.1007/s00248-020-01647-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/15/2020] [Indexed: 06/12/2023]
Abstract
Labyrinthula spp. are saprobic, marine protists that also act as opportunistic pathogens and are the causative agents of seagrass wasting disease (SWD). Despite the threat of local- and large-scale SWD outbreaks, there are currently gaps in our understanding of the drivers of SWD, particularly surrounding Labyrinthula spp. virulence and ecology. Given these uncertainties, we investigated the Labyrinthula genus from a novel genomic perspective by presenting the first draft genome and predicted proteome of a pathogenic isolate Labyrinthula SR_Ha_C, generated from a hybrid assembly of Nanopore and Illumina sequences. Phylogenetic and cross-phyla comparisons revealed insights into the evolutionary history of Stramenopiles. Genome annotation showed evidence of glideosome-type machinery and an apicoplast protein typically found in protist pathogens and parasites. Proteins involved in Labyrinthula SR_Ha_C's actin-myosin mode of transport, as well as carbohydrate degradation were also prevalent. Further, CAZyme functional predictions revealed a repertoire of enzymes involved in breakdown of cell-wall and carbohydrate storage compounds common to seagrasses. The relatively low number of CAZymes annotated from the genome of Labyrinthula SR_Ha_C compared to other Labyrinthulea species may reflect the conservative annotation parameters, a specialized substrate affinity and the scarcity of characterized protist enzymes. Inherently, there is high probability for finding both unique and novel enzymes from Labyrinthula spp. This study provides resources for further exploration of Labyrinthula spp. ecology and evolution, and will hopefully be the catalyst for new hypothesis-driven SWD research revealing more details of molecular interactions between the Labyrinthula genus and its host substrate.
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Affiliation(s)
- Mun Hua Tan
- Centre of Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
- Department of Microbiology and Immunology, University of Melbourne, Bio21 Institute, Melbourne, Victoria, Australia
| | - Stella Loke
- Centre of Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia
| | - Laurence J Croft
- Centre of Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia
| | - Frank H Gleason
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Lene Lange
- BioEconomy, Research & Advisory, Valby, Copenhagen, Denmark
| | - Bo Pilgaard
- Protein Chemistry and Enzyme Technology, Department of Bioengineering, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Stacey M Trevathan-Tackett
- Centre of Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia.
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15
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Neubauer D, Kolmakova O, Woodhouse J, Taube R, Mangelsdorf K, Gladyshev M, Premke K, Grossart HP. Zooplankton carcasses stimulate microbial turnover of allochthonous particulate organic matter. THE ISME JOURNAL 2021; 15:1735-1750. [PMID: 33462364 PMCID: PMC8163850 DOI: 10.1038/s41396-020-00883-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 12/07/2020] [Accepted: 12/11/2020] [Indexed: 01/04/2023]
Abstract
Carbon turnover in aquatic environments is dependent on biochemical properties of organic matter (OM) and its degradability by the surrounding microbial community. Non-additive interactive effects represent a mechanism where the degradation of biochemically persistent OM is stimulated by the provision of bioavailable OM to the degrading microbial community. Whilst this is well established in terrestrial systems, whether it occurs in aquatic ecosystems remains subject to debate. We hypothesised that OM from zooplankton carcasses can stimulate the degradation of biochemically persistent leaf material, and that this effect is influenced by the daphnia:leaf OM ratio and the complexity of the degrading microbial community. Fresh Daphnia magna carcasses and 13C-labelled maize leaves (Zea mays) were incubated at different ratios (1:1, 1:3 and 1:5) alongside either a complex microbial community (<50 µm) or solely bacteria (<0.8 µm). 13C stable-isotope measurements of CO2 analyses were combined with phospholipid fatty acids (PLFA) analysis and DNA sequencing to link metabolic activities, biomass and taxonomic composition of the microbial community. Our experiments indicated a significantly higher respiration of leaf-derived C when daphnia-derived OM was most abundant (i.e. daphnia:leaf OM ratio of 1:1). This process was stronger in a complex microbial community, including eukaryotic microorganisms, than a solely bacterial community. We concluded that non-additive interactive effects were a function of increased C-N chemodiversity and microbial complexity, with the highest net respiration to be expected when chemodiversity is high and the degrading community complex. This study indicates that identifying the interactions and processes of OM degradation is one important key for a deeper understanding of aquatic and thus global carbon cycle.
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Affiliation(s)
- Darshan Neubauer
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Experimental Limnology, 16775, Stechlin, Germany.
- Institute of Biochemistry and Biology, Potsdam University, 14476, Potsdam, Germany.
| | - Olesya Kolmakova
- Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, Russia
- Siberian Federal University, Institute of Fundamental Biology and Biotechnology, Krasnoyarsk, Russia
| | - Jason Woodhouse
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Experimental Limnology, 16775, Stechlin, Germany
| | - Robert Taube
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Experimental Limnology, 16775, Stechlin, Germany
- Institute of Biochemistry and Biology, Potsdam University, 14476, Potsdam, Germany
| | - Kai Mangelsdorf
- GFZ German Research Centre -for Geosciences, Helmholtz Centre Potsdam, Section 3.2 Organic Geochemistry, 14473, Potsdam, Germany
| | - Michail Gladyshev
- Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, Russia
- Siberian Federal University, Institute of Fundamental Biology and Biotechnology, Krasnoyarsk, Russia
| | - Katrin Premke
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Chemical Analytics and Biogeochemistry, Müggelseedamm 310, 12587, Berlin, Germany
| | - Hans-Peter Grossart
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Experimental Limnology, 16775, Stechlin, Germany.
- Institute of Biochemistry and Biology, Potsdam University, 14476, Potsdam, Germany.
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16
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Lange L, Barrett K, Meyer AS. New Method for Identifying Fungal Kingdom Enzyme Hotspots from Genome Sequences. J Fungi (Basel) 2021; 7:jof7030207. [PMID: 33799907 PMCID: PMC8000046 DOI: 10.3390/jof7030207] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/05/2021] [Accepted: 03/07/2021] [Indexed: 11/23/2022] Open
Abstract
Fungal genome sequencing data represent an enormous pool of information for enzyme discovery. Here, we report a new approach to identify and quantitatively compare biomass-degrading capacity and diversity of fungal genomes via integrated function-family annotation of carbohydrate-active enzymes (CAZymes) encoded by the genomes. Based on analyses of 1932 fungal genomes the most potent hotspots of fungal biomass processing CAZymes are identified and ranked according to substrate degradation capacity. The analysis is achieved by a new bioinformatics approach, Conserved Unique Peptide Patterns (CUPP), providing for CAZyme-family annotation and robust prediction of molecular function followed by conversion of the CUPP output to lists of integrated “Function;Family” (e.g., EC 3.2.1.4;GH5) enzyme observations. An EC-function found in several protein families counts as different observations. Summing up such observations allows for ranking of all analyzed genome sequenced fungal species according to richness in CAZyme function diversity and degrading capacity. Identifying fungal CAZyme hotspots provides for identification of fungal species richest in cellulolytic, xylanolytic, pectinolytic, and lignin modifying enzymes. The fungal enzyme hotspots are found in fungi having very different lifestyle, ecology, physiology and substrate/host affinity. Surprisingly, most CAZyme hotspots are found in enzymatically understudied and unexploited species. In contrast, the most well-known fungal enzyme producers, from where many industrially exploited enzymes are derived, are ranking unexpectedly low. The results contribute to elucidating the evolution of fungal substrate-digestive CAZyme profiles, ecophysiology, and habitat adaptations, and expand the knowledge base for novel and improved biomass resource utilization.
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Affiliation(s)
- Lene Lange
- BioEconomy, Research & Advisory, Copenhagen, 2500 Valby, Denmark;
| | - Kristian Barrett
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Building 221, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark;
| | - Anne S. Meyer
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Building 221, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark;
- Correspondence: ; Tel.: +45-4525-2600
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Evolution of Fungal Carbohydrate-Active Enzyme Portfolios and Adaptation to Plant Cell-Wall Polymers. J Fungi (Basel) 2021; 7:jof7030185. [PMID: 33807546 PMCID: PMC7998857 DOI: 10.3390/jof7030185] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/25/2021] [Accepted: 02/25/2021] [Indexed: 12/21/2022] Open
Abstract
The postindustrial era is currently facing two ecological challenges. First, the rise in global temperature, mostly caused by the accumulation of carbon dioxide (CO2) in the atmosphere, and second, the inability of the environment to absorb the waste of human activities. Fungi are valuable levers for both a reduction in CO2 emissions, and the improvement of a circular economy with the optimized valorization of plant waste and biomass. Soil fungi may promote plant growth and thereby increase CO2 assimilation via photosynthesis or, conversely, they may prompt the decomposition of dead organic matter, and thereby contribute to CO2 emissions. The strategies that fungi use to cope with plant-cell-wall polymers and access the saccharides that they use as a carbon source largely rely on the secretion of carbohydrate-active enzymes (CAZymes). In the past few years, comparative genomics and phylogenomics coupled with the functional characterization of CAZymes significantly improved the understanding of their evolution in fungal genomes, providing a framework for the design of nature-inspired enzymatic catalysts. Here, we provide an overview of the diversity of CAZyme enzymatic systems employed by fungi that exhibit different substrate preferences, different ecologies, or belong to different taxonomical groups for lignocellulose degradation.
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18
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Roberts C, Allen R, Bird KE, Cunliffe M. Chytrid fungi shape bacterial communities on model particulate organic matter. Biol Lett 2020; 16:20200368. [PMID: 32991826 PMCID: PMC7532721 DOI: 10.1098/rsbl.2020.0368] [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] [Indexed: 12/22/2022] Open
Abstract
Microbial colonization and degradation of particulate organic matter (POM) are important processes that influence the structure and function of aquatic ecosystems. Although POM is readily used by aquatic fungi and bacteria, there is a limited understanding of POM-associated interactions between these taxa, particularly for early-diverging fungal lineages. Using a model ecological system with the chitin-degrading freshwater chytrid fungus Rhizoclosmatium globosum and chitin microbeads, we assessed the impacts of chytrid fungi on POM-associated bacteria. We show that the presence of chytrids on POM alters concomitant bacterial community diversity and structure, including differing responses between chytrid life stages. We propose that chytrids can act as ecosystem facilitators through saprotrophic feeding by producing ‘public goods’ from POM degradation that modify bacterial POM communities. This study suggests that chytrid fungi have complex ecological roles in aquatic POM degradation not previously considered, including the regulation of bacterial colonization, community succession and subsequent biogeochemical potential.
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Affiliation(s)
- Cordelia Roberts
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, UK.,School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
| | - Ro Allen
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, UK
| | - Kimberley E Bird
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, UK
| | - Michael Cunliffe
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, UK.,School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
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19
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Genomic and fossil windows into the secret lives of the most ancient fungi. Nat Rev Microbiol 2020; 18:717-730. [PMID: 32908302 DOI: 10.1038/s41579-020-0426-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2020] [Indexed: 12/26/2022]
Abstract
Fungi have crucial roles in modern ecosystems as decomposers and pathogens, and they engage in various mutualistic associations with other organisms, especially plants. They have a lengthy geological history, and there is an emerging understanding of their impact on the evolution of Earth systems on a large scale. In this Review, we focus on the roles of fungi in the establishment and early evolution of land and freshwater ecosystems. Today, questions of evolution over deep time are informed by discoveries of new fossils and evolutionary analysis of new genomes. Inferences can be drawn from evolutionary analysis by comparing the genes and genomes of fungi with the biochemistry and development of their plant and algal hosts. We then contrast this emerging picture against evidence from the fossil record to develop a new, integrated perspective on the origin and early evolution of fungi.
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20
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van Munster JM, Daly P, Blythe MJ, Ibbett R, Kokolski M, Gaddipati S, Lindquist E, Singan VR, Barry KW, Lipzen A, Ngan CY, Petzold CJ, Chan LJG, Arvas M, Raulo R, Pullan ST, Delmas S, Grigoriev IV, Tucker GA, Simmons BA, Archer DB. Succession of physiological stages hallmarks the transcriptomic response of the fungus Aspergillus niger to lignocellulose. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:69. [PMID: 32313551 PMCID: PMC7155255 DOI: 10.1186/s13068-020-01702-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/24/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Understanding how fungi degrade lignocellulose is a cornerstone of improving renewables-based biotechnology, in particular for the production of hydrolytic enzymes. Considerable progress has been made in investigating fungal degradation during time-points where CAZyme expression peaks. However, a robust understanding of the fungal survival strategies over its life time on lignocellulose is thereby missed. Here we aimed to uncover the physiological responses of the biotechnological workhorse and enzyme producer Aspergillus niger over its life time to six substrates important for biofuel production. RESULTS We analysed the response of A. niger to the feedstock Miscanthus and compared it with our previous study on wheat straw, alone or in combination with hydrothermal or ionic liquid feedstock pretreatments. Conserved (substrate-independent) metabolic responses as well as those affected by pretreatment and feedstock were identified via multivariate analysis of genome-wide transcriptomics combined with targeted transcript and protein analyses and mapping to a metabolic model. Initial exposure to all substrates increased fatty acid beta-oxidation and lipid metabolism transcripts. In a strain carrying a deletion of the ortholog of the Aspergillus nidulans fatty acid beta-oxidation transcriptional regulator farA, there was a reduction in expression of selected lignocellulose degradative CAZyme-encoding genes suggesting that beta-oxidation contributes to adaptation to lignocellulose. Mannan degradation expression was wheat straw feedstock-dependent and pectin degradation was higher on the untreated substrates. In the later life stages, known and novel secondary metabolite gene clusters were activated, which are of high interest due to their potential to synthesize bioactive compounds. CONCLUSION In this study, which includes the first transcriptional response of Aspergilli to Miscanthus, we highlighted that life time as well as substrate composition and structure (via variations in pretreatment and feedstock) influence the fungal responses to lignocellulose. We also demonstrated that the fungal response contains physiological stages that are conserved across substrates and are typically found outside of the conditions with high CAZyme expression, as exemplified by the stages that are dominated by lipid and secondary metabolism.
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Affiliation(s)
- Jolanda M. van Munster
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Manchester Institute of Biotechnology (MIB) & School of Chemistry, The University of Manchester, Manchester, M1 7DN UK
| | - Paul Daly
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Present Address: Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, People’s Republic of China
| | - Martin J. Blythe
- Deep Seq, Faculty of Medicine and Health Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham, NG7 2UH UK
| | - Roger Ibbett
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Matt Kokolski
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Sanyasi Gaddipati
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Erika Lindquist
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA
| | - Vasanth R. Singan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA
| | - Kerrie W. Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA
| | - Chew Yee Ngan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA
| | | | | | - Mikko Arvas
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 VTT Espoo, Finland
| | - Roxane Raulo
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Steven T. Pullan
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Present Address: Public Health England, National Infection Service, Salisbury, UK
| | - Stéphane Delmas
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Present Address: Laboratory of Computational and Quantitative Biology, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, 75005 Paris, France
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA
| | - Gregory A. Tucker
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | | | - David B. Archer
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
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