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Martin FM, van der Heijden MGA. The mycorrhizal symbiosis: research frontiers in genomics, ecology, and agricultural application. THE NEW PHYTOLOGIST 2024; 242:1486-1506. [PMID: 38297461 DOI: 10.1111/nph.19541] [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: 08/14/2023] [Accepted: 12/07/2023] [Indexed: 02/02/2024]
Abstract
Mycorrhizal symbioses between plants and fungi are vital for the soil structure, nutrient cycling, plant diversity, and ecosystem sustainability. More than 250 000 plant species are associated with mycorrhizal fungi. Recent advances in genomics and related approaches have revolutionized our understanding of the biology and ecology of mycorrhizal associations. The genomes of 250+ mycorrhizal fungi have been released and hundreds of genes that play pivotal roles in regulating symbiosis development and metabolism have been characterized. rDNA metabarcoding and metatranscriptomics provide novel insights into the ecological cues driving mycorrhizal communities and functions expressed by these associations, linking genes to ecological traits such as nutrient acquisition and soil organic matter decomposition. Here, we review genomic studies that have revealed genes involved in nutrient uptake and symbiosis development, and discuss adaptations that are fundamental to the evolution of mycorrhizal lifestyles. We also evaluated the ecosystem services provided by mycorrhizal networks and discuss how mycorrhizal symbioses hold promise for sustainable agriculture and forestry by enhancing nutrient acquisition and stress tolerance. Overall, unraveling the intricate dynamics of mycorrhizal symbioses is paramount for promoting ecological sustainability and addressing current pressing environmental concerns. This review ends with major frontiers for further research.
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Affiliation(s)
- Francis M Martin
- Université de Lorraine, INRAE, UMR IAM, Champenoux, 54280, France
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Marcel G A van der Heijden
- Department of Agroecology & Environment, Plant-Soil Interactions, Agroscope, Zürich, 8046, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zürich, 8057, Switzerland
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2
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Leifheit EF, Camenzind T, Lehmann A, Andrade-Linares DR, Fussan M, Westhusen S, Wineberger TM, Rillig MC. Fungal traits help to understand the decomposition of simple and complex plant litter. FEMS Microbiol Ecol 2024; 100:fiae033. [PMID: 38486354 PMCID: PMC11022653 DOI: 10.1093/femsec/fiae033] [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: 12/12/2022] [Revised: 02/21/2024] [Accepted: 03/13/2024] [Indexed: 04/18/2024] Open
Abstract
Litter decomposition is a key ecosystem process, relevant for the release and storage of nutrients and carbon in soil. Soil fungi are one of the dominant drivers of organic matter decomposition, but fungal taxa differ substantially in their functional ability to decompose plant litter. Knowledge is mostly based on observational data and subsequent molecular analyses and in vitro studies have been limited to forest ecosystems. In order to better understand functional traits of saprotrophic soil fungi in grassland ecosystems, we isolated 31 fungi from a natural grassland and performed several in vitro studies testing for i) leaf and wood litter decomposition, ii) the ability to use carbon sources of differing complexity, iii) the enzyme repertoire. Decomposition strongly varied among phyla and isolates, with Ascomycota decomposing the most and Mucoromycota decomposing the least. The phylogeny of the fungi and their ability to use complex carbon were the most important predictors for decomposition. Our findings show that it is crucial to understand the role of individual members and functional groups within the microbial community. This is an important way forward to understand the role of microbial community composition for the prediction of litter decomposition and subsequent potential carbon storage in grassland soils.
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Affiliation(s)
- Eva F Leifheit
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin 14195, Germany
| | - Tessa Camenzind
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin 14195, Germany
| | - Anika Lehmann
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin 14195, Germany
| | - Diana R Andrade-Linares
- Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Research Unit for Comparative Microbiome Analyses – COMI, 85764 Neuherberg, Germany
| | - Max Fussan
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin 14195, Germany
| | - Sophia Westhusen
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
| | - Till M Wineberger
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
| | - Matthias C Rillig
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin 14195, Germany
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3
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Alshareef SA. Metabolic analysis of the CAZy class glycosyltransferases in rhizospheric soil fungiome of the plant species Moringa oleifera. Saudi J Biol Sci 2024; 31:103956. [PMID: 38404538 PMCID: PMC10891331 DOI: 10.1016/j.sjbs.2024.103956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 02/03/2024] [Accepted: 02/10/2024] [Indexed: 02/27/2024] Open
Abstract
The target of the present work is to study the most abundant carbohydrate-active enzymes (CAZymes) of glycosyltransferase (GT) class, which are encoded by fungiome genes present in the rhizospheric soil of the plant species Moringa oleifera. The datasets of this CAZy class were recovered using metagenomic whole shotgun genome sequencing approach, and the resultant CAZymes were searched against the KEGG pathway database to identify function. High emphasis was given to the two GT families, GT4 and GT2, which were the highest within GT class in the number and abundance of gene queries in this soil compartment. These two GT families harbor CAZymes playing crucial roles in cell membrane and cell wall processes. These CAZymes are responsible for synthesizing essential structural components such as cellulose and chitin, which contribute to the integrity of cell walls in plants and fungi. The CAZyme beta-1,3-glucan synthase of GT2 family accumulates 1,3-β-glucan, which provides elasticity as well as tensile strength to the fungal cell wall. Other GT CAZymes contribute to the biosynthesis of several compounds crucial for cell membrane and wall integrity, including lipopolysaccharide, e.g., lipopolysaccharide N-acetylglucosaminyltransferase, cell wall teichoic acid, e.g., alpha-glucosyltransferase, and cellulose, e.g., cellulose synthase. These compounds also play pivotal roles in ion homeostasis, organic carbon mineralization, and osmoprotection against abiotic stresses in plants. This study emphasizes the major roles of these two CAZy GT families in connecting the structure and function of cell membranes and cell walls of fungal and plant cells. The study also sheds light on the potential occurrence of tripartite symbiotic relationships involving the plant, rhizospheric bacteriome, and fungiome via the action of CAZymes of GT4 and GT2 families. These findings provide valuable insights towards the generation of innovative agricultural practices to enhance the performance of crop plants in the future.
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Affiliation(s)
- Sahar A. Alshareef
- Department of Biology, College of Science and Arts at Khulis, University of Jeddah, Jeddah, Saudi Arabia
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Shamshitov A, Kadžienė G, Supronienė S. The Role of Soil Microbial Consortia in Sustainable Cereal Crop Residue Management. PLANTS (BASEL, SWITZERLAND) 2024; 13:766. [PMID: 38592825 PMCID: PMC10974107 DOI: 10.3390/plants13060766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 04/11/2024]
Abstract
The global escalation in cereal production, essential to meet growing population demands, simultaneously augments the generation of cereal crop residues, estimated annually at approximately 3107 × 106 Mg/year. Among different crop residue management approaches, returning them to the soil can be essential for various ecological benefits, including nutrient recycling and soil carbon sequestration. However, the recalcitrant characteristics of cereal crop residues pose significant challenges in their management, particularly in the decomposition rate. Therefore, in this review, we aim to summarize the influence of different agricultural practices on enhancing soil microbial decomposer communities, thereby effectively managing cereal crop residues. Moreover, this manuscript provides indirect estimates of cereal crop residue production in Northern Europe and Lithuania, and highlights the diverse roles of lignocellulolytic microorganisms in the decomposition process, with a particular focus on enzymatic activities. This review bridges the knowledge gap and indicates future research directions concerning the influence of agricultural practices on cereal crop residue-associated microbial consortia.
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Affiliation(s)
- Arman Shamshitov
- Laboratory of Microbiology, Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Instituto al. 1, Akademija, LT-58344 Kedainiai, Lithuania;
| | - Gražina Kadžienė
- Department of Soil and Crop Management, Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Instituto al. 1, Akademija, LT-58344 Kedainiai, Lithuania
| | - Skaidrė Supronienė
- Laboratory of Microbiology, Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Instituto al. 1, Akademija, LT-58344 Kedainiai, Lithuania;
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Vizzini A, Alvarado P, Consiglio G, Marchetti M, Xu J. Family matters inside the order Agaricales: systematic reorganization and classification of incertae sedis clitocyboid, pleurotoid and tricholomatoid taxa based on an updated 6-gene phylogeny. Stud Mycol 2024; 107:67-148. [PMID: 38600959 PMCID: PMC11003440 DOI: 10.3114/sim.2024.107.02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 12/17/2023] [Indexed: 04/12/2024] Open
Abstract
The phylogenetic position of several clitocyboid/pleurotoid/tricholomatoid genera previously considered incertae sedis is here resolved using an updated 6-gene dataset of Agaricales including newly sequenced lineages and more complete data from those already analyzed before. Results allowed to infer new phylogenetic relationships, and propose taxonomic novelties to accommodate them, including up to ten new families and a new suborder. Giacomia (for which a new species from China is here described) forms a monophyletic clade with Melanoleuca (Melanoleucaceae) nested inside suborder Pluteineae, together with the families Pluteaceae, Amanitaceae (including Leucocortinarius), Limnoperdaceae and Volvariellaceae. The recently described family Asproinocybaceae is shown to be a later synonym of Lyophyllaceae (which includes also Omphaliaster and Trichocybe) within suborder Tricholomatineae. The families Biannulariaceae, Callistosporiaceae, Clitocybaceae, Fayodiaceae, Macrocystidiaceae (which includes Pseudoclitopilus), Entolomataceae, Pseudoclitocybaceae (which includes Aspropaxillus), Omphalinaceae (Infundibulicybe and Omphalina) and the new families Paralepistaceae and Pseudoomphalinaceae belong also to Tricholomatineae. The delimitation of the suborder Pleurotineae (= Schizophyllineae) is discussed and revised, accepting five distinct families within it, viz. Pleurotaceae, Cyphellopsidaceae, Fistulinaceae, Resupinataceae and Schizophyllaceae. The recently proposed suborder Phyllotopsidineae (= Sarcomyxineae) is found to encompass the families Aphroditeolaceae, Pterulaceae, Phyllotopsidaceae, Radulomycetaceae, Sarcomyxaceae (which includes Tectella), and Stephanosporaceae, all of them unrelated to Pleurotaceae (suborder Pleurotineae) or Typhulaceae (suborder Typhulineae). The new family Xeromphalinaceae, encompassing the genera Xeromphalina and Heimiomyces, is proposed within Marasmiineae. The suborder Hygrophorineae is here reorganized into the families Hygrophoraceae, Cantharellulaceae, Cuphophyllaceae, Hygrocybaceae and Lichenomphaliaceae, to homogenize the taxonomic rank of the main clades inside all suborders of Agaricales. Finally, the genus Hygrophorocybe is shown to represent a distinct clade inside Cuphophyllaceae, and the new combination H. carolinensis is proposed. Taxonomic novelties: New suborder: Typhulineae Vizzini, Consiglio & P. Alvarado. New families: Aphroditeolaceae Vizzini, Consiglio & P. Alvarado, Melanoleucaceae Locq. ex Vizzini, Consiglio & P. Alvarado, Paralepistaceae Vizzini, Consiglio & P. Alvarado, Pseudoomphalinaceae Vizzini, Consiglio & P. Alvarado, Volvariellaceae Vizzini, Consiglio & P. Alvarado, Xeromphalinaceae Vizzini, Consiglio & P. Alvarado. New species: Giacomia sinensis J.Z. Xu. Stat. nov.: Cantharellulaceae (Lodge, Redhead, Norvell & Desjardin) Vizzini, Consiglio & P. Alvarado, Cuphophyllaceae (Z.M. He & Zhu L. Yang) Vizzini, Consiglio & P. Alvarado, Hygrocybaceae (Padamsee & Lodge) Vizzini, Consiglio & P. Alvarado, Lichenomphaliaceae (Lücking & Redhead) Vizzini, Consiglio & P. Alvarado. New combination: Hygrophorocybe carolinensis (H.E. Bigelow & Hesler) Vizzini, Consiglio & P. Alvarado. New synonyms: Sarcomyxineae Zhu L. Yang & G.S. Wang, Schizophyllineae Aime, Dentinger & Gaya, Asproinocybaceae T. Bau & G.F. Mou. Incertae sedis taxa placed at family level: Aphroditeola Redhead & Manfr. Binder, Giacomia Vizzini & Contu, Hygrophorocybe Vizzini & Contu, Leucocortinarius (J.E. Lange) Singer, Omphaliaster Lamoure, Pseudoclitopilus Vizzini & Contu, Resupinatus Nees ex Gray, Tectella Earle, Trichocybe Vizzini. New delimitations of taxa: Hygrophorineae Aime, Dentinger & Gaya, Phyllotopsidineae Zhu L. Yang & G.S. Wang, Pleurotineae Aime, Dentinger & Gaya, Pluteineae Aime, Dentinger & Gaya, Tricholomatineae Aime, Dentinger & Gaya. Resurrected taxa: Fayodiaceae Jülich, Resupinataceae Jülich. Citation: Vizzini A, Alvarado P, Consiglio G, Marchetti M, Xu J (2024). Family matters inside the order Agaricales: systematic reorganization and classification of incertae sedis clitocyboid, pleurotoid and tricholomatoid taxa based on an updated 6-gene phylogeny. Studies in Mycology 107: 67-148. doi: 10.3114/sim.2024.107.02.
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Affiliation(s)
- A. Vizzini
- Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli 25, 10125 Turin, Italy
- Institute for Sustainable Plant Protection (IPSP-SS Turin), C.N.R., Viale P.A. Mattioli, 25, 10125 Turin, Italy
| | - P. Alvarado
- ALVALAB, Dr. Fernando Bongera st., Severo Ochoa bldg. S1.04, 33006 Oviedo, Spain
| | - G. Consiglio
- Via Ronzani 61, Casalecchio di Reno, 40033 Bologna, Italy
| | | | - J. Xu
- Agricultural College, Jilin Agriculture Science and Technology University, Jilin 132101, Jilin Province, P. R. China
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6
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Zhang C, de Pasquale S, Hartman K, Stanley CE, Berendsen RL, van der Heijden MGA. The microbial contribution to litter decomposition and plant growth. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13205. [PMID: 38018445 PMCID: PMC10866077 DOI: 10.1111/1758-2229.13205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/06/2023] [Indexed: 11/30/2023]
Abstract
Soil and plant roots are colonized by highly complex and diverse communities of microbes. It has been proposed that bacteria and fungi have synergistic effects on litter decomposition, but experimental evidence supporting this claim is weak. In this study, we manipulated the composition of two microbial kingdoms (Bacteria and Fungi) in experimental microcosms. In microcosms that were inoculated with fungi, litter loss was 47% higher than in microcosms that were not inoculated or only inoculated with bacteria. Combined inoculation with both bacteria and fungi did not significantly enhance decomposition compared with the fungi-only treatments, and, as such, we found no evidence for complementary effects using our experimental setup. Inoculation with fungi also had a positive impact on plant growth after 4 and 8 weeks (480% and 710% growth stimulation, respectively). After 16 weeks, plant biomass was highest in microcosms where both bacteria and fungi were present pointing to fungal-bacterial complementarity in stimulating plant growth. Overall, this study suggests that fungi are the main decomposers of plant litter and that the inoculated fungi contribute to plant growth in our experimental system.
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Affiliation(s)
- Changfeng Zhang
- Plant‐Microbe Interactions, Department of Biology, Faculty of ScienceUtrecht UniversityUtrechtthe Netherlands
- Plant Soil InteractionsDivision Agroecology and Environment, AgroscopeZürichSwitzerland
| | - Simone de Pasquale
- Plant Soil InteractionsDivision Agroecology and Environment, AgroscopeZürichSwitzerland
| | - Kyle Hartman
- Plant Soil InteractionsDivision Agroecology and Environment, AgroscopeZürichSwitzerland
| | - Claire E. Stanley
- Plant Soil InteractionsDivision Agroecology and Environment, AgroscopeZürichSwitzerland
| | - Roeland L. Berendsen
- Plant‐Microbe Interactions, Department of Biology, Faculty of ScienceUtrecht UniversityUtrechtthe Netherlands
| | - Marcel G. A. van der Heijden
- Plant‐Microbe Interactions, Department of Biology, Faculty of ScienceUtrecht UniversityUtrechtthe Netherlands
- Plant Soil InteractionsDivision Agroecology and Environment, AgroscopeZürichSwitzerland
- Department of Plant and Microbial BiologyUniversity of ZurichZurichSwitzerland
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7
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Defrenne CE, Moore JAM, Tucker CL, Lamit LJ, Kane ES, Kolka RK, Chimner RA, Keller JK, Lilleskov EA. Peat loss collocates with a threshold in plant-mycorrhizal associations in drained peatlands encroached by trees. THE NEW PHYTOLOGIST 2023; 240:412-425. [PMID: 37148190 DOI: 10.1111/nph.18954] [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: 02/23/2023] [Accepted: 04/14/2023] [Indexed: 05/08/2023]
Abstract
Drainage-induced encroachment by trees may have major effects on the carbon balance of northern peatlands, and responses of microbial communities are likely to play a central mechanistic role. We profiled the soil fungal community and estimated its genetic potential for the decay of lignin and phenolics (class II peroxidase potential) along peatland drainage gradients stretching from interior locations (undrained, open) to ditched locations (drained, forested). Mycorrhizal fungi dominated the community across the gradients. When moving towards ditches, the dominant type of mycorrhizal association abruptly shifted from ericoid mycorrhiza to ectomycorrhiza at c. 120 m from the ditches. This distance corresponded with increased peat loss, from which more than half may be attributed to oxidation. The ectomycorrhizal genus Cortinarius dominated at the drained end of the gradients and its relatively higher genetic potential to produce class II peroxidases (together with Mycena) was positively associated with peat humification and negatively with carbon-to-nitrogen ratio. Our study is consistent with a plant-soil feedback mechanism, driven by a shift in the mycorrhizal type of vegetation, that potentially mediates changes in aerobic decomposition during postdrainage succession. Such feedback may have long-term legacy effects upon postdrainage restoration efforts and implication for tree encroachment onto carbon-rich soils globally.
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Affiliation(s)
| | - Jessica A M Moore
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Colin L Tucker
- USDA Forest Service-Northern Research Station, Houghton, MI, 49931, USA
| | - Louis J Lamit
- Department of Biology, Syracuse University, Syracuse, NY, 13244, USA
| | - Evan S Kane
- Michigan Technological University, Houghton, MI, 49931, USA
- USDA Forest Service-Northern Research Station, Houghton, MI, 49931, USA
| | - Randall K Kolka
- U.S. Forest Service-Northern Research Station, Grand Rapids, MN, 55744, USA
| | | | - Jason K Keller
- Schmid College of Science and Technology, Chapman University, Orange, CA, 92866, USA
| | - Erik A Lilleskov
- USDA Forest Service-Northern Research Station, Houghton, MI, 49931, USA
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8
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Zhao H, Dai YC, Wu F, Liu XY, Maurice S, Krutovsky KV, Pavlov IN, Lindner DL, Martin FM, Yuan Y. Insights into the Ecological Diversification of the Hymenochaetales based on Comparative Genomics and Phylogenomics With an Emphasis on Coltricia. Genome Biol Evol 2023; 15:evad136. [PMID: 37498334 PMCID: PMC10410303 DOI: 10.1093/gbe/evad136] [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: 05/16/2023] [Revised: 07/01/2023] [Accepted: 07/16/2023] [Indexed: 07/28/2023] Open
Abstract
To elucidate the genomic traits of ecological diversification in the Hymenochaetales, we sequenced 15 new genomes, with attention to ectomycorrhizal (EcM) Coltricia species. Together with published data, 32 genomes, including 31 Hymenochaetales and one outgroup, were comparatively analyzed in total. Compared with those of parasitic and saprophytic members, EcM species have significantly reduced number of plant cell wall degrading enzyme genes, and expanded transposable elements, genome sizes, small secreted proteins, and secreted proteases. EcM species still retain some of secreted carbohydrate-active enzymes (CAZymes) and have lost the key secreted CAZymes to degrade lignin and cellulose, while possess a strong capacity to degrade a microbial cell wall containing chitin and peptidoglycan. There were no significant differences in secreted CAZymes between fungi growing on gymnosperms and angiosperms, suggesting that the secreted CAZymes in the Hymenochaetales evolved before differentiation of host trees into gymnosperms and angiosperms. Nevertheless, parasitic and saprophytic species of the Hymenochaetales are very similar in many genome features, which reflect their close phylogenetic relationships both being white rot fungi. Phylogenomic and molecular clock analyses showed that the EcM genus Coltricia formed a clade located at the base of the Hymenochaetaceae and divergence time later than saprophytic species. And Coltricia remains one to two genes of AA2 family. These indicate that the ancestors of Coltricia appear to have originated from saprophytic ancestor with the ability to cause a white rot. This study provides new genomic data for EcM species and insights into the ecological diversification within the Hymenochaetales based on comparative genomics and phylogenomics analyses.
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Affiliation(s)
- Heng Zhao
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yu-Cheng Dai
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Fang Wu
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Xiao-Yong Liu
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Sundy Maurice
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Konstantin V Krutovsky
- Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Göttingen, Germany
- Center for Integrated Breeding Research, George-August University of Göttingen, Göttingen, Germany
- Laboratory of Population Genetics, N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Laboratory of Forest Genomics, Department of Genomics and Bioinformatics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
- Scientific and Methodological Center, G. F. Morozov Voronezh State University of Forestry and Technologies, Voronezh, Russia
| | - Igor N Pavlov
- Mycology and Plant Pathology, V.N. Sukachev Institute of Forest SB RAS, Krasnoyarsk, Russia
- Department of Chemical Technology of Wood and Biotechnology, Reshetnev Siberian State University of Science and Technology, Krasnoyarsk, Russia
| | | | - Francis M Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE-GrandEst-Nancy, Champenoux, France
| | - Yuan Yuan
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
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9
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Schlatter DC, Gamble JD, Castle S, Rogers J, Wilson M. Abiotic and Biotic Drivers of Soil Fungal Communities in Response to Dairy Manure Amendment. Appl Environ Microbiol 2023; 89:e0193122. [PMID: 37212685 PMCID: PMC10304672 DOI: 10.1128/aem.01931-22] [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: 11/15/2022] [Accepted: 04/24/2023] [Indexed: 05/23/2023] Open
Abstract
Modern agriculture often relies on large inputs of synthetic fertilizers to maximize crop yield potential, yet their intensive use has led to nutrient losses and impaired soil health. Alternatively, manure amendments provide plant available nutrients, build organic carbon, and enhance soil health. However, we lack a clear understanding of how consistently manure impacts fungal communities, the mechanisms via which manure impacts soil fungi, and the fate of manure-borne fungi in soils. We assembled soil microcosms using five soils to investigate how manure amendments impact fungal communities over a 60-day incubation. Further, we used autoclaving treatments of soils and manure to determine if observed changes in soil fungal communities were due to abiotic or biotic properties, and if indigenous soil communities constrained colonization of manure-borne fungi. We found that manure amended soil fungal communities diverged from nonamended communities over time, often in concert with a reduction in diversity. Fungal communities responded to live and autoclaved manure in a similar manner, suggesting that abiotic forces are primarily responsible for the observed dynamics. Finally, manure-borne fungi declined quickly in both live and autoclaved soil, indicating that the soil environment is unsuitable for their survival. IMPORTANCE Manure amendments in agricultural systems can impact soil microbial communities via supplying growth substrates for indigenous microbes or by introducing manure-borne taxa. This study explores the consistency of these impacts on soil fungal communities and the relative importance of abiotic and biotic drivers across distinct soils. Different fungal taxa responded to manure among distinct soils, and shifts in soil fungal communities were driven largely by abiotic factors, rather than introduced microbes. This work demonstrates that manure may have inconsistent impacts on indigenous soil fungi, and that abiotic properties of soils render them largely resistant to invasion by manure-borne fungi.
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Affiliation(s)
| | - Joshua D. Gamble
- USDA-ARS Plant Science Research Unit, Saint Paul, Minnesota, USA
| | - Sarah Castle
- USDA-ARS Plant Science Research Unit, Saint Paul, Minnesota, USA
| | - Julia Rogers
- Department of Soil, Water, and Climate, University of Minnesota, Saint Paul, Minnesota, USA
| | - Melissa Wilson
- Department of Soil, Water, and Climate, University of Minnesota, Saint Paul, Minnesota, USA
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10
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Niego AGT, Rapior S, Thongklang N, Raspé O, Hyde KD, Mortimer P. Reviewing the contributions of macrofungi to forest ecosystem processes and services. FUNGAL BIOL REV 2023. [DOI: 10.1016/j.fbr.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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11
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Müller M, Kües U, Budde KB, Gailing O. Applying molecular and genetic methods to trees and their fungal communities. Appl Microbiol Biotechnol 2023; 107:2783-2830. [PMID: 36988668 PMCID: PMC10106355 DOI: 10.1007/s00253-023-12480-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/05/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023]
Abstract
Forests provide invaluable economic, ecological, and social services. At the same time, they are exposed to several threats, such as fragmentation, changing climatic conditions, or increasingly destructive pests and pathogens. Trees, the inherent species of forests, cannot be viewed as isolated organisms. Manifold (micro)organisms are associated with trees playing a pivotal role in forest ecosystems. Of these organisms, fungi may have the greatest impact on the life of trees. A multitude of molecular and genetic methods are now available to investigate tree species and their associated organisms. Due to their smaller genome sizes compared to tree species, whole genomes of different fungi are routinely compared. Such studies have only recently started in forest tree species. Here, we summarize the application of molecular and genetic methods in forest conservation genetics, tree breeding, and association genetics as well as for the investigation of fungal communities and their interrelated ecological functions. These techniques provide valuable insights into the molecular basis of adaptive traits, the impacts of forest management, and changing environmental conditions on tree species and fungal communities and can enhance tree-breeding cycles due to reduced time for field testing. It becomes clear that there are multifaceted interactions among microbial species as well as between these organisms and trees. We demonstrate the versatility of the different approaches based on case studies on trees and fungi. KEY POINTS: • Current knowledge of genetic methods applied to forest trees and associated fungi. • Genomic methods are essential in conservation, breeding, management, and research. • Important role of phytobiomes for trees and their ecosystems.
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Affiliation(s)
- Markus Müller
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany.
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, 37073, Göttingen, Germany.
| | - Ursula Kües
- Molecular Wood Biotechnology and Technical Mycology, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, 37077, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Katharina B Budde
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Oliver Gailing
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, 37073, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
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12
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Guo M, Ma X, Zhou Y, Bian Y, Liu G, Cai Y, Huang T, Dong H, Cai D, Wan X, Wang Z, Xiao Y, Kang H. Genome Sequencing Highlights the Plant Cell Wall Degrading Capacity of Edible Mushroom Stropharia rugosoannulata. J Microbiol 2023; 61:83-93. [PMID: 36723791 DOI: 10.1007/s12275-022-00003-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/04/2022] [Indexed: 02/02/2023]
Abstract
The basidiomycetous edible mushroom Stropharia rugosoannulata has excellent nutrition, medicine, bioremediation, and biocontrol properties. S. rugosoannulata has been widely and easily cultivated using agricultural by-products showing strong lignocellulose degradation capacity. However, the unavailable high-quality genome information has hindered the research on gene function and molecular breeding of S. rugosoannulata. This study provided a high-quality genome assembly and annotation from S. rugosoannulata monokaryotic strain QGU27 based on combined Illumina-Nanopore data. The genome size was about 47.97 Mb and consisted of 20 scaffolds, with an N50 of 3.73 Mb and a GC content of 47.9%. The repetitive sequences accounted for 17.41% of the genome, mostly long terminal repeats (LTRs). A total of 15,726 coding gene sequences were putatively identified with the BUSCO score of 98.7%. There are 142 genes encoding plant cell wall degrading enzymes (PCWDEs) in the genome, and 52, 39, 30, 11, 8, and 2 genes related to lignin, cellulose, hemicellulose, pectin, chitin, and cutin degradation, respectively. Comparative genomic analysis revealed that S. rugosoannulata is superior in utilizing aldehyde-containing lignins and is possible to utilize algae during the cultivation.
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Affiliation(s)
- Mengpei Guo
- Institute of Vegetable, Wuhan Academy of Agricultural Sciences, Wuhan, 430065, Hubei, People's Republic of China
| | - Xiaolong Ma
- Institute of Vegetable, Wuhan Academy of Agricultural Sciences, Wuhan, 430065, Hubei, People's Republic of China.
| | - Yan Zhou
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China.
| | - Yinbing Bian
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Gaolei Liu
- Institute of Vegetable, Wuhan Academy of Agricultural Sciences, Wuhan, 430065, Hubei, People's Republic of China
| | - Yingli Cai
- Institute of Vegetable, Wuhan Academy of Agricultural Sciences, Wuhan, 430065, Hubei, People's Republic of China
| | - Tianji Huang
- Hubei Changjiu Fungi Co. Ltd., Suizhou, 431525, Hubei, People's Republic of China
| | - Hongxia Dong
- Institute of Vegetable, Wuhan Academy of Agricultural Sciences, Wuhan, 430065, Hubei, People's Republic of China
| | - Dingjun Cai
- Institute of Vegetable, Wuhan Academy of Agricultural Sciences, Wuhan, 430065, Hubei, People's Republic of China
| | - Xueji Wan
- Institute of Vegetable, Wuhan Academy of Agricultural Sciences, Wuhan, 430065, Hubei, People's Republic of China
| | - Zhihong Wang
- Institute of Vegetable, Wuhan Academy of Agricultural Sciences, Wuhan, 430065, Hubei, People's Republic of China
| | - Yang Xiao
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Heng Kang
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
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13
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Cornelissen JHC, Cornwell WK, Freschet GT, Weedon JT, Berg MP, Zanne AE. Coevolutionary legacies for plant decomposition. Trends Ecol Evol 2023; 38:44-54. [PMID: 35945074 DOI: 10.1016/j.tree.2022.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 12/24/2022]
Abstract
Coevolution has driven speciation and evolutionary novelty in functional traits across the Tree of Life. Classic coevolutionary syndromes such as plant-pollinator, plant-herbivore, and host-parasite have focused strongly on the fitness consequences during the lifetime of the interacting partners. Less is known about the consequences of coevolved traits for ecosystem-level processes, in particular their 'afterlife' legacies for litter decomposition, nutrient cycling, and the functional ecology of decomposers. We review the mechanisms by which traits resulting from coevolution between plants and their consumers, microbial symbionts, or humans, and between microbial decomposers and invertebrates, drive plant litter decomposition pathways and rates. This supports the idea that much of current global variation in the decomposition of plant material is a legacy of coevolution.
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Affiliation(s)
- J Hans C Cornelissen
- Amsterdam Institute for Life and Environment (A-LIFE), Systems Ecology Section, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, The Netherlands.
| | - William K Cornwell
- Evolution and Ecology Research Centre, School of Biological, Earth, and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Grégoire T Freschet
- Station d'Ecologie Théorique et Expérimentale, Centre National de la Recherche Scientifique (CNRS), Moulis, France
| | - James T Weedon
- Amsterdam Institute for Life and Environment (A-LIFE), Systems Ecology Section, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, The Netherlands
| | - Matty P Berg
- A-LIFE, Ecology and Evolution Section, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands; Community and Conservation Ecology Group, Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Amy E Zanne
- Department of Biology, University of Miami, Miami, FL, USA
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14
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Kalntremtziou M, Papaioannou IA, Vangalis V, Polemis E, Pappas KM, Zervakis GI, Typas MA. Evaluation of the lignocellulose degradation potential of Mediterranean forests soil microbial communities through diversity and targeted functional metagenomics. Front Microbiol 2023; 14:1121993. [PMID: 36922966 PMCID: PMC10008878 DOI: 10.3389/fmicb.2023.1121993] [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: 12/12/2022] [Accepted: 01/31/2023] [Indexed: 02/28/2023] Open
Abstract
The enzymatic arsenal of several soil microorganisms renders them particularly suitable for the degradation of lignocellulose, a process of distinct ecological significance with promising biotechnological implications. In this study, we investigated the spatiotemporal diversity and distribution of bacteria and fungi with 16S and Internally Trascribed Spacer (ITS) ribosomal RNA next-generation-sequencing (NGS), focusing on forest mainland Abies cephalonica and insular Quercus ilex habitats of Greece. We analyzed samples during winter and summer periods, from different soil depths, and we applied optimized and combined targeted meta-omics approaches aiming at the peroxidase-catalase family enzymes to gain insights into the lignocellulose degradation process at the soil microbial community level. The microbial communities recorded showed distinct patterns of response to season, soil depth and vegetation type. Overall, in both forests Proteobacteria, Actinobacteria, Acidobacteria were the most abundant bacteria phyla, while the other phyla and the super-kingdom of Archaea were detected in very low numbers. Members of the orders Agaricales, Russulales, Sebacinales, Gomphales, Geastrales, Hysterangiales, Thelephorales, and Trechisporales (Basidiomycota), and Pezizales, Sordariales, Eurotiales, Pleosporales, Helotiales, and Diaporthales (Ascomycota) were the most abundant for Fungi. By using optimized "universal" PCR primers that targeted the peroxidase-catalase enzyme family, we identified several known and novel sequences from various Basidiomycota, even from taxa appearing at low abundance. The majority of the sequences recovered were manganese peroxidases from several genera of Agaricales, Hysterangiales, Gomphales, Geastrales, Russulales, Hymenochaetales, and Trechisporales, while lignin -and versatile-peroxidases were limited to two to eight species, respectively. Comparisons of the obtained sequences with publicly available data allowed a detailed structural analysis of polymorphisms and functionally relevant amino-acid residues at phylogenetic level. The targeted metagenomics applied here revealed an important role in lignocellulose degradation of hitherto understudied orders of Basidiomycota, such as the Hysterangiales and Gomphales, while it also suggested the auxiliary activity of particular members of Proteobacteria, Actinobacteria, Acidobacteria, Verrucomicrobia, and Gemmatimonadetes. The application of NGS-based metagenomics approaches allows a better understanding of the complex process of lignocellulolysis at the microbial community level as well as the identification of candidate taxa and genes for targeted functional investigations and genetic modifications.
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Affiliation(s)
- Maria Kalntremtziou
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Ioannis A Papaioannou
- Zentrum für Molekulare Biologie der Universität Heidelberg, ZMBH, University of Heidelberg, Heidelberg, Germany
| | - Vasileios Vangalis
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Elias Polemis
- Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens, Greece
| | - Katherine M Pappas
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgios I Zervakis
- Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens, Greece
| | - Milton A Typas
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
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15
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Pareek M, Hegedüs B, Hou Z, Csernetics Á, Wu H, Virágh M, Sahu N, Liu XB, Nagy L. Preassembled Cas9 Ribonucleoprotein-Mediated Gene Deletion Identifies the Carbon Catabolite Repressor and Its Target Genes in Coprinopsis cinerea. Appl Environ Microbiol 2022; 88:e0094022. [PMID: 36374019 PMCID: PMC9746306 DOI: 10.1128/aem.00940-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/11/2022] [Indexed: 11/16/2022] Open
Abstract
Cre1 is an important transcription factor that regulates carbon catabolite repression (CCR) and is widely conserved across fungi. The cre1 gene has been extensively studied in several Ascomycota species, whereas its role in gene expression regulation in the Basidiomycota species remains poorly understood. Here, we identified and investigated the role of cre1 in Coprinopsis cinerea, a basidiomycete model mushroom that can efficiently degrade lignocellulosic plant wastes. We used a rapid and efficient gene deletion approach based on PCR-amplified split-marker DNA cassettes together with in vitro assembled Cas9-guide RNA ribonucleoproteins (Cas9 RNPs) to generate C. cinerea cre1 gene deletion strains. Gene expression profiling of two independent C. cinerea cre1 mutants showed significant deregulation of carbohydrate metabolism, plant cell wall degrading enzymes (PCWDEs), plasma membrane transporter-related and several transcription factor-encoding genes, among others. Our results support the notion that, like reports in the ascomycetes, Cre1 of C. cinerea orchestrates CCR through a combined regulation of diverse genes, including PCWDEs, transcription factors that positively regulate PCWDEs, and membrane transporters which could import simple sugars that can induce the expression of PWCDEs. Somewhat paradoxically, though in accordance with other Agaricomycetes, genes related to lignin degradation were mostly downregulated in cre1 mutants, indicating they fall under different regulation than other PCWDEs. The gene deletion approach and the data presented here will expand our knowledge of CCR in the Basidiomycota and provide functional hypotheses on genes related to plant biomass degradation. IMPORTANCE Mushroom-forming fungi include some of the most efficient lignocellulosic plant biomass degraders. They degrade dead plant materials by a battery of lignin-, cellulose-, hemicellulose-, and pectin-degrading enzymes, the encoding genes of which are under tight transcriptional control. One of the highest-level regulations of these metabolic enzymes is known as carbon catabolite repression, which is orchestrated by the transcription factor Cre1, and ensures that costly lignocellulose-degrading enzyme genes are expressed only when simple carbon sources (e.g., glucose) are not available. Here, we identified the Cre1 ortholog in a litter decomposer Agaricomycete, Coprinopsis cinerea, knocked it out, and characterized transcriptional changes in the mutants. We identified several dozen lignocellulolytic enzyme genes as well as membrane transporters and other transcription factors as putative target genes of C. cinerea cre1. These results extend knowledge on carbon catabolite repression to litter decomposer Basidiomycota.
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Affiliation(s)
- Manish Pareek
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Botond Hegedüs
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Zhihao Hou
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Árpád Csernetics
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Hongli Wu
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Máté Virágh
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Neha Sahu
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Xiao-Bin Liu
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - László Nagy
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
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16
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Ghobad-Nejhad M, Antonín V, Moghaddam M, Langer E. Resources of Iranian agarics (Basidiomycota) with an outlook on their antioxidant potential. Front Microbiol 2022; 13:1015440. [DOI: 10.3389/fmicb.2022.1015440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Agaric fungi are an important group of macromycetes with diverse ecological and functional properties, yet are poorly studied in many parts of the world. Here, we comprehensively analyzed 558 agaric species in Iran to reveal their resources of edible and poisonous species as well as their ecological guilds and luminescence potential. We also made a thorough survey of the antioxidant activity of the species. Phylogenetic relationships were reconstructed based on nuclear ribosomal LSU and ITS sequences. Our results reveal that agarics of Iran comprise about 189 edible, 128 poisonous, 254 soil saprotrophic, 172 ectomycorrhizal, 146 wood-inhabiting, 18 leaf/litter-inhabiting, 9 parasitic, and 19 luminescent species. Twenty percent of the Iranian agaric species possess antioxidant activity, phylogenetically distributed in four orders and 21 agaric families. About 5% of the antioxidant species can be considered strong antioxidants, many of which are also edible and could be utilized to develop functional foods. This is the first study combining phylogeny and antioxidant potential of agaric mushrooms in a large scale, and the obtained results would guide the selection of agaric taxa to be examined in the future for taxonomic revisions, biotechnological applications, and applied phylogeny studies.
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17
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Recent Advancements and Challenges in Lignin Valorization: Green Routes towards Sustainable Bioproducts. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27186055. [PMID: 36144795 PMCID: PMC9500909 DOI: 10.3390/molecules27186055] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/10/2022] [Accepted: 09/13/2022] [Indexed: 11/27/2022]
Abstract
The aromatic hetero-polymer lignin is industrially processed in the paper/pulp and lignocellulose biorefinery, acting as a major energy source. It has been proven to be a natural resource for useful bioproducts; however, its depolymerization and conversion into high-value-added chemicals is the major challenge due to the complicated structure and heterogeneity. Conversely, the various pre-treatments techniques and valorization strategies offers a potential solution for developing a biomass-based biorefinery. Thus, the current review focus on the new isolation techniques for lignin, various pre-treatment approaches and biocatalytic methods for the synthesis of sustainable value-added products. Meanwhile, the challenges and prospective for the green synthesis of various biomolecules via utilizing the complicated hetero-polymer lignin are also discussed.
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18
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X-Ray Scattering Reveals Two Mechanisms of Cellulose Microfibril Degradation by Filamentous Fungi. Appl Environ Microbiol 2022; 88:e0099522. [PMID: 35997493 PMCID: PMC9469724 DOI: 10.1128/aem.00995-22] [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] [Indexed: 12/02/2022] Open
Abstract
Mushroom-forming fungi (Agaricomycetes) employ enzymatic and nonenzymatic cellulose degradation mechanisms, the latter presumably relying on Fenton-generated radicals. The effects of the two mechanisms on the cellulose microfibrils structure remain poorly understood. We examined cellulose degradation caused by litter decomposers and wood decomposers, including brown-rot and white-rot fungi and one fungus with uncertain wood decay type, by combining small- and wide-angle X-ray scattering. We also examined the effects of commercial enzymes and Fenton-generated radicals on cellulose using the same method. We detected two main degradation or modification mechanisms. The first characterized the mechanism used by most fungi and resembled enzymatic cellulose degradation, causing simultaneous microfibril thinning and decreased crystalline cellulose. The second mechanism was detected in one brown-rot fungus and one litter decomposer and was characterized by patchy amorphogenesis of crystalline cellulose without substantial thinning of the fibers. This pattern did not resemble the effect of Fenton-generated radicals, suggesting a more complex mechanism is involved in the destruction of cellulose crystallinity by fungi. Furthermore, our results showed a mismatch between decay classifications and cellulose degradation patterns and that even within litter decomposers two degradation mechanisms were found, suggesting higher functional diversity under current ecological classifications of fungi. IMPORTANCE Cellulose degradation by fungi plays a fundamental role in terrestrial carbon cycling, but the mechanisms by which fungi cope with the crystallinity of cellulose are not fully understood. We used X-ray scattering to analyze how fungi, a commercial enzyme mix, and a Fenton reaction-generated radical alter the crystalline structure of cellulose. Our data revealed two mechanisms involved in crystalline cellulose degradation by fungi: one that results in the thinning of the cellulose fibers, resembling the enzymatic degradation of cellulose, and one that involves amorphogenesis of crystalline cellulose by yet-unknown pathways, resulting in a patchy-like degradation pattern. These results pave the way to a deeper understanding of cellulose degradation and the development of novel ways to utilize crystalline cellulose.
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Duong HL, Paufler S, Harms H, Schlosser D, Maskow T. Fungal Lignocellulose Utilisation Strategies from a Bioenergetic Perspective: Quantification of Related Functional Traits Using Biocalorimetry. Microorganisms 2022; 10:microorganisms10081675. [PMID: 36014092 PMCID: PMC9415514 DOI: 10.3390/microorganisms10081675] [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: 07/14/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
In the present study, we investigated whether a non-invasive metabolic heat flux analysis could serve the determination of the functional traits in free-living saprotrophic decomposer fungi and aid the prediction of fungal influences on ecosystem processes. For this, seven fungi, including ascomycete, basidiomycete, and zygomycete species, were investigated in a standardised laboratory environment, employing wheat straw as a globally relevant lignocellulosic substrate. Our study demonstrates that biocalorimetry can be employed successfully to determine growth-related fungal activity parameters, such as apparent maximum growth rates (AMGR), cultivation times until the observable onset of fungal growth at AMGR (tAMGR), quotients formed from the AMGR and tAMGR (herein referred to as competitive growth potential, CGP), and heat yield coefficients (YQ/X), the latter indicating the degree of resource investment into fungal biomass versus other functional attributes. These parameters seem suitable to link fungal potentials for biomass production to corresponding ecological strategies employed during resource utilisation, and therefore may be considered as fungal life history traits. A close connection exists between the CGP and YQ/X values, which suggests an interpretation that relates to fungal life history strategies.
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Affiliation(s)
- Hieu Linh Duong
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraβe 15, 04318 Leipzig, Germany
- Faculty of Engineering, Vietnamese-German University (VGU), Le Lai Street, Hoa Phu Ward, Thủ Dầu Một 7500, Binh Duong, Vietnam
| | - Sven Paufler
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraβe 15, 04318 Leipzig, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraβe 15, 04318 Leipzig, Germany
| | - Dietmar Schlosser
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraβe 15, 04318 Leipzig, Germany
- Correspondence: (D.S.); (T.M.)
| | - Thomas Maskow
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraβe 15, 04318 Leipzig, Germany
- Correspondence: (D.S.); (T.M.)
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20
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Xiong BJ, Stanley CE, Dusny C, Schlosser D, Harms H, Wick LY. pH Distribution along Growing Fungal Hyphae at Microscale. J Fungi (Basel) 2022; 8:599. [PMID: 35736082 PMCID: PMC9224906 DOI: 10.3390/jof8060599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 02/06/2023] Open
Abstract
Creating unique microenvironments, hyphal surfaces and their surroundings allow for spatially distinct microbial interactions and functions at the microscale. Using a microfluidic system and pH-sensitive whole-cell bioreporters (Synechocystis sp. PCC6803) attached to hyphae, we spatially resolved the pH along surfaces of growing hyphae of the basidiomycete Coprinopsis cinerea. Time-lapse microscopy analysis of ratiometric fluorescence signals of >2400 individual bioreporters revealed an overall pH drop from 6.3 ± 0.4 (n = 2441) to 5.0 ± 0.3 (n = 2497) within 7 h after pH bioreporter loading to hyphal surfaces. The pH along hyphal surfaces varied significantly (p < 0.05), with pH at hyphal tips being on average ~0.8 pH units lower than at more mature hyphal parts near the entrance of the microfluidic observation chamber. Our data represent the first dynamic in vitro analysis of surface pH along growing hyphae at the micrometre scale. Such knowledge may improve our understanding of spatial, pH-dependent hyphal processes, such as the degradation of organic matter or mineral weathering.
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Affiliation(s)
- Bi-Jing Xiong
- Helmholtz Centre for Environmental Research-UFZ, Department of Environmental Microbiology, Permoserstraβe 15, 04318 Leipzig, Germany; (B.-J.X.); (D.S.); (H.H.)
| | - Claire E. Stanley
- Department of Bioengineering, Imperial College of London, South Kensington Campus, London SW7 2AZ, UK;
| | - Christian Dusny
- Helmholtz Centre for Environmental Research-UFZ, Department of Solar Materials, Permoserstraβe 15, 04318 Leipzig, Germany;
| | - Dietmar Schlosser
- Helmholtz Centre for Environmental Research-UFZ, Department of Environmental Microbiology, Permoserstraβe 15, 04318 Leipzig, Germany; (B.-J.X.); (D.S.); (H.H.)
| | - Hauke Harms
- Helmholtz Centre for Environmental Research-UFZ, Department of Environmental Microbiology, Permoserstraβe 15, 04318 Leipzig, Germany; (B.-J.X.); (D.S.); (H.H.)
| | - Lukas Y. Wick
- Helmholtz Centre for Environmental Research-UFZ, Department of Environmental Microbiology, Permoserstraβe 15, 04318 Leipzig, Germany; (B.-J.X.); (D.S.); (H.H.)
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21
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Litter Mixing Alters Microbial Decomposer Community to Accelerate Tomato Root Litter Decomposition. Microbiol Spectr 2022; 10:e0018622. [PMID: 35604181 PMCID: PMC9241821 DOI: 10.1128/spectrum.00186-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Mixing plant litters of multiple species can alter litter decomposition, a key driver of carbon and nutrient cycling in terrestrial ecosystems. Changes in microbial decomposer communities is proposed as one of the mechanisms explaining this litter-mixture effect, but the underlying mechanism is unclear. In a microcosm litterbag experiment, we found that, at the early stage of decomposition, litter mixing promoted tomato root litter decomposition, thus generating a synergistic nonadditive litter-mixture effect. The transplanting decomposer community experiment showed that changes in microbial decomposer communities contributed to the nonadditive litter-mixture effect on tomato root litter decomposition. Moreover, litter mixing altered the abundance and diversity of bacterial and fungal communities on tomato root litter. Litter mixing also stimulated several putative keystone operational taxonomic units (OTUs) in the microbial correlation network, such as Fusarium sp. fOTU761 and Microbacterium sp. bOTU6632. Then, we isolated and cultured representative isolates of these two taxa, named Fusarium sp. F13 and Microbacterium sp. B26. Subsequent in vitro tests found that F13, but not B26, had strong decomposing ability; moreover, these two isolates developed synergistic interaction, thus promoted litter decomposition in coculture. Addition of F13 or B26 both promoted the decomposing activity of the resident decomposer community on tomato root litter, confirming their importance for litter decomposition. Overall, litter mixing promoted tomato root litter decomposition through altering microbial decomposers, especially through stimulating certain putative keystone taxa. IMPORTANCE Microbial decomposer community plays a key role in litter decomposition, which is an important regulator of soil carbon and nutrient cycling. Though changes in decomposer communities has been proposed as one of the potential underlying mechanisms driving the litter-mixture effects, direct evidence is still lacking. Here, we demonstrated that litter mixing stimulated litter decomposition through altering microbial decomposers at the early stage of decomposition. Moreover, certain putative keystone taxa stimulated by litter mixing contributed to the nonadditive litter-mixture effect. In vitro culturing validated the role of these taxa in litter decomposition. This study also highlights the possibility of regulating litter decomposition through manipulating certain microbial taxa.
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Yang Y, Meng G, Ni S, Zhang H, Dong C. Genomic Analysis of Stropharia rugosoannulata Reveals Its Nutritional Strategy and Application Potential in Bioremediation. J Fungi (Basel) 2022; 8:jof8020162. [PMID: 35205916 PMCID: PMC8874372 DOI: 10.3390/jof8020162] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/01/2022] [Accepted: 02/04/2022] [Indexed: 11/16/2022] Open
Abstract
Stropharia rugosoannulata is not only a popular edible mushroom, but also has excellent potential in bioremediation. In this study, we present a high-quality genome of a monokaryotic strain of the S. rugosoannulata commercial cultivar in China. The assembly yielded an N50 length of 2.96 Mb and a total size of approximately 48.33 Mb, encoding 11,750 proteins. The number of heme peroxidase-encoding genes in the genome of S. rugosoannulata was twice the average of all of the tested Agaricales. The genes encoding lignin and xenobiotic degradation enzymes accounted for more than half of the genes encoding plant cell wall degradation enzymes. The expansion of genes encoding lignin and xenobiotic degradation enzymes, and cytochrome P450 involved in the xenobiotic metabolism, were responsible for its strong bioremediation and lignin degradation abilities. S. rugosoannulata was classified as a litter-decomposing (LD) fungus, based on the analysis of the cell wall degrading enzymes. Substrate selection for fruiting body cultivation should consider both the nutritional strategy of LD and a strong lignin degradation ability. Consistent with safe usage as an edible mushroom, the S. rugosoannulata genome does not contain genes for known psilocybin biosynthesis. Genome analysis will be helpful for understanding its nutritional strategy to guide fruiting body cultivation and for providing insight into its application in bioremediation.
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Affiliation(s)
- Ying Yang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Y.Y.); (G.M.)
| | - Guoliang Meng
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Y.Y.); (G.M.)
| | - Shujun Ni
- Institute of Animal Husbandry Research, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (S.N.); (H.Z.)
| | - Haifeng Zhang
- Institute of Animal Husbandry Research, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (S.N.); (H.Z.)
| | - Caihong Dong
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Y.Y.); (G.M.)
- Correspondence: ; Tel./Fax: +86-010-64806138
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23
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Wu G, Miyauchi S, Morin E, Kuo A, Drula E, Varga T, Kohler A, Feng B, Cao Y, Lipzen A, Daum C, Hundley H, Pangilinan J, Johnson J, Barry K, LaButti K, Ng V, Ahrendt S, Min B, Choi IG, Park H, Plett JM, Magnuson J, Spatafora JW, Nagy LG, Henrissat B, Grigoriev IV, Yang ZL, Xu J, Martin FM. Evolutionary innovations through gain and loss of genes in the ectomycorrhizal Boletales. THE NEW PHYTOLOGIST 2022; 233:1383-1400. [PMID: 34767630 DOI: 10.1111/nph.17858] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
We aimed to identify genomic traits of transitions to ectomycorrhizal ecology within the Boletales by comparing the genomes of 21 symbiotrophic species with their saprotrophic brown-rot relatives. Gene duplication rate is constant along the backbone of Boletales phylogeny with large loss events in several lineages, while gene family expansion sharply increased in the late Miocene, mostly in the Boletaceae. Ectomycorrhizal Boletales have a reduced set of plant cell-wall-degrading enzymes (PCWDEs) compared with their brown-rot relatives. However, the various lineages retain distinct sets of PCWDEs, suggesting that, over their evolutionary history, symbiotic Boletales have become functionally diverse. A smaller PCWDE repertoire was found in Sclerodermatineae. The gene repertoire of several lignocellulose oxidoreductases (e.g. laccases) is similar in brown-rot and ectomycorrhizal species, suggesting that symbiotic Boletales are capable of mild lignocellulose decomposition. Transposable element (TE) proliferation contributed to the higher evolutionary rate of genes encoding effector-like small secreted proteins, proteases, and lipases. On the other hand, we showed that the loss of secreted CAZymes was not related to TE activity but to DNA decay. This study provides novel insights on our understanding of the mechanisms influencing the evolutionary diversification of symbiotic boletes.
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Affiliation(s)
- Gang Wu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54 280, France
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming, Yunnan, 650201, China
| | - Shingo Miyauchi
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54 280, France
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54 280, France
| | - Alan Kuo
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques (USC1408), INRAE, Marseille, 13009, France
| | - Torda Varga
- Synthetic and Systems Biology Unit, Biological Research Centre, Szeged, 6726, Hungary
| | - Annegret Kohler
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54 280, France
| | - Bang Feng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming, Yunnan, 650201, China
| | - Yang Cao
- Yunnan Institute of Tropic Crops, Jinghong, Yunnan, 666100, China
| | - Anna Lipzen
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Christopher Daum
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Hope Hundley
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Jasmyn Pangilinan
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Jenifer Johnson
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Kerrie Barry
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Kurt LaButti
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Vivian Ng
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Steven Ahrendt
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
| | - Byoungnam Min
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 02841, Seoul, Korea
| | - In-Geol Choi
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 02841, Seoul, Korea
| | - Hongjae Park
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, 370 05, České Budějovice, Czech Republic
| | - Jonathan M Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Jon Magnuson
- Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Joseph W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - László G Nagy
- Synthetic and Systems Biology Unit, Biological Research Centre, Szeged, 6726, Hungary
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, 1117, Hungary
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (USC1408), INRAE, Marseille, 13009, France
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, 13009, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Igor V Grigoriev
- Lawrence Berkeley National Laboratory, US Department of Energy (DOE) Joint Genome Institute (JGI), Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Zhu-Liang Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming, Yunnan, 650201, China
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Francis M Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54 280, France
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
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Xiong BJ, Dusny C, Wang L, Appel J, Lindstaedt K, Schlosser D, Harms H, Wick LY. Illuminate the hidden: in vivo mapping of microscale pH in the mycosphere using a novel whole-cell biosensor. ISME COMMUNICATIONS 2021; 1:75. [PMID: 36765263 PMCID: PMC9723660 DOI: 10.1038/s43705-021-00075-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 11/02/2021] [Accepted: 11/15/2021] [Indexed: 01/07/2023]
Abstract
The pH of an environment is both a driver and the result of diversity and functioning of microbial habitats such as the area affected by fungal hyphae (mycosphere). Here we used a novel pH-sensitive bioreporter, Synechocystis sp. PCC6803_peripHlu, and ratiometric fluorescence microscopy, to spatially and temporally resolve the mycosphere pH at the micrometre scale. Hyphae of the basidiomycete Coprionopsis cinerea were allowed to overgrow immobilised and homogeneously embedded pH bioreporters in an agarose microcosm. Signals of >700 individual cells in an area of 0.4 × 0.8 mm were observed over time and used to create highly resolved (3 × 3 µm) pH maps using geostatistical approaches. C. cinerea changed the pH of the agarose from 6.9 to ca. 5.0 after 48 h with hyphal tips modifying pH in their vicinity up to 1.8 mm. pH mapping revealed distinct microscale spatial variability and temporally stable gradients between pH 4.4 and 5.8 over distances of ≈20 µm. This is the first in vivo mapping of a mycosphere pH landscape at the microscale. It underpins the previously hypothesised establishment of pH gradients serving to create spatially distinct mycosphere reaction zones.
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Affiliation(s)
- Bi-Jing Xiong
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraβe 15, 04318, Leipzig, Germany
| | - Christian Dusny
- Department of Solar Materials, Helmholtz Centre for Environmental Research-UFZ, Permoserstraβe 15, 04318, Leipzig, Germany
| | - Lin Wang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jens Appel
- Department of Biology, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 5, 24118, Kiel, Germany
| | - Kristin Lindstaedt
- Department of Solar Materials, Helmholtz Centre for Environmental Research-UFZ, Permoserstraβe 15, 04318, Leipzig, Germany
| | - Dietmar Schlosser
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraβe 15, 04318, Leipzig, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraβe 15, 04318, Leipzig, Germany
| | - Lukas Y Wick
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraβe 15, 04318, Leipzig, Germany.
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25
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Pellitier PT, Zak DR. Ectomycorrhizal fungal decay traits along a soil nitrogen gradient. THE NEW PHYTOLOGIST 2021; 232:2152-2164. [PMID: 34533216 DOI: 10.1111/nph.17734] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
The extent to which ectomycorrhizal (ECM) fungi decay soil organic matter (SOM) has implications for accurately predicting forest ecosystem response to climate change. Investigating the distribution of gene traits associated with SOM decay among ectomycorrhizal fungal communities could improve understanding of SOM dynamics and plant nutrition. We hypothesized that soil inorganic nitrogen (N) availability structures the distribution of ECM fungal genes associated with SOM decay and, specifically, that ECM fungal communities occurring in inorganic N-poor soils have greater SOM decay potential. To test this hypothesis, we paired amplicon and shotgun metagenomic sequencing of 60 ECM fungal communities associating with Quercus rubra along a natural soil inorganic N gradient. Ectomycorrhizal fungal communities occurring in low inorganic N soils were enriched in gene families involved in the decay of lignin, cellulose, and chitin. Ectomycorrhizal fungal community composition was the strongest driver of shifts in metagenomic estimates of fungal decay potential. Our study simultaneously illuminates the identity of key ECM fungal taxa and gene families potentially involved in the decay of SOM, and we link rhizomorphic and medium-distance hyphal morphologies with enhanced SOM decay potential. Coupled shifts in ECM fungal community composition and community-level decay gene frequencies are consistent with outcomes of trait-mediated community assembly processes.
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Affiliation(s)
- Peter T Pellitier
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Donald R Zak
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
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26
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Duong HL, Paufler S, Harms H, Maskow T, Schlosser D. Applicability and information value of biocalorimetry for the monitoring of fungal solid-state fermentation of lignocellulosic agricultural by-products. N Biotechnol 2021; 66:97-106. [PMID: 34767975 DOI: 10.1016/j.nbt.2021.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/02/2021] [Accepted: 11/07/2021] [Indexed: 11/30/2022]
Abstract
The applicability of biocalorimetry for monitoring fungal conversion of lignocellulosic agricultural by-products during solid-state fermentation (SSF) was substantiated through linking the non-invasive measurement of metabolic heat fluxes to conventional invasive determination of fungal activity (growth, substrate degradation, enzyme activity) parameters. For this, the fast-growing, cellulose-utilising ascomycete Stachybotrys chlorohalonata and the comparatively slow-growing litter-decay basidiomycete Stropharia rugosoannulata were investigated as model organisms during growth on solid wheat straw. Both biocalorimetric and non-calorimetric data may suggest R (ruderal)- and C (combative)-selected life history strategies in S. chlorohalonata and S. rugosoannulata, respectively. For both species, a strong linear correlation of the released metabolic heat with the corresponding fungal biomass was observed. Species-specific YQ/X values (metabolic heat released per fungal biomass unit) were obtained, which potentially enable use of biocalorimetric signals for the quantification of fungal biomass during single-species SSF processes. Moreover, YQ/X values may also indicate different fungal life history strategies and therefore be considered as useful parameters aiding fungal ecology research.
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Affiliation(s)
- Hieu Linh Duong
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research - UFZ, Permoserstraβe 15, 04318, Leipzig, Germany; Vietnamese-German University (VGU), Le Lai Street, Hoa Phu Ward, Thu Dau Mot City, Binh Duong Province, Viet Nam.
| | - Sven Paufler
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research - UFZ, Permoserstraβe 15, 04318, Leipzig, Germany.
| | - Hauke Harms
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research - UFZ, Permoserstraβe 15, 04318, Leipzig, Germany.
| | - Thomas Maskow
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research - UFZ, Permoserstraβe 15, 04318, Leipzig, Germany.
| | - Dietmar Schlosser
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research - UFZ, Permoserstraβe 15, 04318, Leipzig, Germany.
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27
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Lebreton A, Zeng Q, Miyauchi S, Kohler A, Dai YC, Martin FM. Evolution of the Mode of Nutrition in Symbiotic and Saprotrophic Fungi in Forest Ecosystems. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2021. [DOI: 10.1146/annurev-ecolsys-012021-114902] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In this review, we highlight the main insights that have been gathered from recent developments using large-scale genomics of fungal saprotrophs and symbiotrophs (including ectomycorrhizal and orchid and ericoid mycorrhizal fungi) inhabiting forest ecosystems. After assessing the goals and motivations underlying our approach, we explore our current understanding of the limits and future potential of using genomics to understand the ecological roles of these forest fungi. Comparative genomics unraveled the molecular machineries involved in lignocellulose decomposition in wood decayers, soil and litter saprotrophs, and mycorrhizal symbionts. They also showed that transitions from saprotrophy to mutualism entailed widespread losses of lignocellulose-degrading enzymes; diversification of novel, lineage-specific symbiosis-induced genes; and convergent evolution of genetic innovations that facilitate the accommodationof mutualistic symbionts within their plant hosts. We also identify the major questions that remain unanswered and propose new avenues of genome-based research to understand the role of soil fungi in sustainable forest ecosystems.
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Affiliation(s)
- Annie Lebreton
- Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design (BAIC-TBMD), Institute of Microbiology, Beijing Forestry University, Beijing, China 100083
- Université de Lorraine, Unité Mixte de Recherche (UMR) Interactions Arbres/Microorganismes, Centre INRAE (Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement) Grand Est-Nancy, INRAE, 54280 Champenoux, France
| | - Qingchao Zeng
- Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design (BAIC-TBMD), Institute of Microbiology, Beijing Forestry University, Beijing, China 100083
| | - Shingo Miyauchi
- Max Planck Institute for Plant Breeding Research, Department of Plant–Microbe Interactions, Köln, Germany, D-50829
| | - Annegret Kohler
- Université de Lorraine, Unité Mixte de Recherche (UMR) Interactions Arbres/Microorganismes, Centre INRAE (Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement) Grand Est-Nancy, INRAE, 54280 Champenoux, France
| | - Yu-Cheng Dai
- Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design (BAIC-TBMD), Institute of Microbiology, Beijing Forestry University, Beijing, China 100083
| | - Francis M. Martin
- Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design (BAIC-TBMD), Institute of Microbiology, Beijing Forestry University, Beijing, China 100083
- Université de Lorraine, Unité Mixte de Recherche (UMR) Interactions Arbres/Microorganismes, Centre INRAE (Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement) Grand Est-Nancy, INRAE, 54280 Champenoux, France
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Fungal Metagenome of Chernevaya Taiga Soils: Taxonomic Composition, Differential Abundance and Factors Related to Plant Gigantism. J Fungi (Basel) 2021; 7:jof7110908. [PMID: 34829197 PMCID: PMC8620766 DOI: 10.3390/jof7110908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 10/18/2021] [Accepted: 10/23/2021] [Indexed: 11/29/2022] Open
Abstract
The Chernevaya taiga of Western Siberia is a unique and complex ecosystem, distinguished by the unusually large sizes of herbaceous plants, the reasons for which are poorly understood. Here, we explored the fungal diversity of the Chernevaya taiga soils in the Tomsk regions of Western Siberia in comparison with other soil types. The soil biomes of Chernevaya taiga and the control regions were investigated using Illumina ITS rRNA sequencing, and taxonomic analysis revealed a predominance of fungal phyla in the different soils. These results demonstrate that the fungi of the Chernevaya taiga regions have a higher species diversity (Faith’s PD) vs. the control soils, and the diversity is due more to the sampling sites rather than to the seasons (Bray-Curtis distance). We studied most of the differentially abundant taxa among the soil types, and we annotated the taxa with their ecological guilds and trophic types. Some of the abundant fungal taxa in the summer- and fall-Chernevaya taiga samples belong to the phylum Glomeromycota—arbuscular mycorrhizal symbiotrophs, which are known to establish symbiotic relationships and enhance plant growth. Additionally, several OTUs were assigned to novel genera in the Glomeraceae and Claroideoglomeraceae families. Our findings add a potential explanation of the high productivity and plant gigantism in Chernevaya taiga and expand our knowledge of fungal biodiversity.
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Heeger F, Bourne EC, Wurzbacher C, Funke E, Lipzen A, He G, Ng V, Grigoriev IV, Schlosser D, Monaghan MT. Evidence for Lignocellulose-Decomposing Enzymes in the Genome and Transcriptome of the Aquatic Hyphomycete Clavariopsis aquatica. J Fungi (Basel) 2021; 7:jof7100854. [PMID: 34682274 PMCID: PMC8537685 DOI: 10.3390/jof7100854] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 12/13/2022] Open
Abstract
Fungi are ecologically outstanding decomposers of lignocellulose. Fungal lignocellulose degradation is prominent in saprotrophic Ascomycota and Basidiomycota of the subkingdom Dikarya. Despite ascomycetes dominating the Dikarya inventory of aquatic environments, genome and transcriptome data relating to enzymes involved in lignocellulose decay remain limited to terrestrial representatives of these phyla. We sequenced the genome of an exclusively aquatic ascomycete (the aquatic hyphomycete Clavariopsis aquatica), documented the presence of genes for the modification of lignocellulose and its constituents, and compared differential gene expression between C. aquatica cultivated on lignocellulosic and sugar-rich substrates. We identified potential peroxidases, laccases, and cytochrome P450 monooxygenases, several of which were differentially expressed when experimentally grown on different substrates. Additionally, we found indications for the regulation of pathways for cellulose and hemicellulose degradation. Our results suggest that C. aquatica is able to modify lignin to some extent, detoxify aromatic lignin constituents, or both. Such characteristics would be expected to facilitate the use of carbohydrate components of lignocellulose as carbon and energy sources.
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Affiliation(s)
- Felix Heeger
- Department Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587 Berlin, Germany; (E.C.B.); (E.F.); (M.T.M.)
- Department Materials and Environment, Federal Institute for Material Research and Testing, 12203 Berlin, Germany
- Berlin Center for Genomics in Biodiversity Research, 14195 Berlin, Germany
- Correspondence:
| | - Elizabeth C. Bourne
- Department Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587 Berlin, Germany; (E.C.B.); (E.F.); (M.T.M.)
- Berlin Center for Genomics in Biodiversity Research, 14195 Berlin, Germany
| | - Christian Wurzbacher
- Chair of Urban Water Systems Engineering, Technical University of Munich, 85748 Garching, Germany;
| | - Elisabeth Funke
- Department Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587 Berlin, Germany; (E.C.B.); (E.F.); (M.T.M.)
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.L.); (G.H.); (V.N.); (I.V.G.)
| | - Guifen He
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.L.); (G.H.); (V.N.); (I.V.G.)
| | - Vivian Ng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.L.); (G.H.); (V.N.); (I.V.G.)
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.L.); (G.H.); (V.N.); (I.V.G.)
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Dietmar Schlosser
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research—UFZ, 04318 Leipzig, Germany;
| | - Michael T. Monaghan
- Department Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587 Berlin, Germany; (E.C.B.); (E.F.); (M.T.M.)
- Berlin Center for Genomics in Biodiversity Research, 14195 Berlin, Germany
- Institut für Biologie, Freie Universität Berlin, 14195 Berlin, Germany
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30
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Pellitier PT, Ibáñez I, Zak DR, Argiroff WA, Acharya K. Ectomycorrhizal access to organic nitrogen mediates CO 2 fertilization response in a dominant temperate tree. Nat Commun 2021; 12:5403. [PMID: 34518539 PMCID: PMC8438073 DOI: 10.1038/s41467-021-25652-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 08/19/2021] [Indexed: 01/04/2023] Open
Abstract
Plant–mycorrhizal interactions mediate plant nitrogen (N) limitation and can inform model projections of the duration and strength of the effect of increasing CO2 on plant growth. We present dendrochronological evidence of a positive, but context-dependent fertilization response of Quercus rubra L. to increasing ambient CO2 (iCO2) along a natural soil nutrient gradient in a mature temperate forest. We investigated this heterogeneous response by linking metagenomic measurements of ectomycorrhizal (ECM) fungal N-foraging traits and dendrochronological models of plant uptake of inorganic N and N bound in soil organic matter (N-SOM). N-SOM putatively enhanced tree growth under conditions of low inorganic N availability, soil conditions where ECM fungal communities possessed greater genomic potential to decay SOM and obtain N-SOM. These trees were fertilized by 38 years of iCO2. In contrast, trees occupying inorganic N rich soils hosted ECM fungal communities with reduced SOM decay capacity and exhibited neutral growth responses to iCO2. This study elucidates how the distribution of N-foraging traits among ECM fungal communities govern tree access to N-SOM and subsequent growth responses to iCO2. Root-mycorrhizal interactions could help explain the heterogeneity of plant responses to CO2 fertilisation and nutrient availability. Here the authors combine tree-ring and metagenomic data to reveal that tree growth responses to increasing CO2 along a soil nutrient gradient depend on the nitrogen foraging traits of ectomycorrhizal fungi.
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Affiliation(s)
- Peter T Pellitier
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, USA. .,Department of Biology, Stanford University, Stanford, CA, USA.
| | - Inés Ibáñez
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, USA
| | - Donald R Zak
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, USA.
| | - William A Argiroff
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, USA
| | - Kirk Acharya
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, USA
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31
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Genomic and Experimental Investigations of Auriscalpium and Strobilurus Fungi Reveal New Insights into Pinecone Decomposition. J Fungi (Basel) 2021; 7:jof7080679. [PMID: 34436218 PMCID: PMC8401616 DOI: 10.3390/jof7080679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/16/2021] [Accepted: 08/19/2021] [Indexed: 11/16/2022] Open
Abstract
Saprophytic fungi (SPF) play vital roles in ecosystem dynamics and decomposition. However, because of the complexity of living systems, our understanding of how SPF interact with each other to decompose organic matter is very limited. Here we studied their roles and interactions in the decomposition of highly specialized substrates between the two genera Auriscalpium and Strobilurus fungi-colonized fallen pinecones of the same plant sequentially. We obtained the genome sequences from seven fungal species with three pairs: A. orientale-S. luchuensis, A. vulgare-S. stephanocystis and A. microsporum-S. pachcystidiatus/S. orientalis on cones of Pinus yunnanensis, P. sylvestris and P. armandii, respectively, and the organic profiles of substrate during decomposition. Our analyses revealed evidence for both competition and cooperation between the two groups of fungi during decomposition, enabling efficient utilization of substrates with complementary profiles of carbohydrate active enzymes (CAZymes). The Auriscalpium fungi are highly effective at utilizing the primary organic carbon, such as lignin, and hemicellulose in freshly fallen cones, facilitated the invasion and colonization by Strobilurus fungi. The Strobilurus fungi have genes coding for abundant CAZymes to utilize the remaining organic compounds and for producing an arsenal of secondary metabolites such as strobilurins that can inhibit other fungi from colonizing the pinecones.
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32
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Navarro D, Chaduli D, Taussac S, Lesage-Meessen L, Grisel S, Haon M, Callac P, Courtecuisse R, Decock C, Dupont J, Richard-Forget F, Fournier J, Guinberteau J, Lechat C, Moreau PA, Pinson-Gadais L, Rivoire B, Sage L, Welti S, Rosso MN, Berrin JG, Bissaro B, Favel A. Large-scale phenotyping of 1,000 fungal strains for the degradation of non-natural, industrial compounds. Commun Biol 2021; 4:871. [PMID: 34267314 PMCID: PMC8282864 DOI: 10.1038/s42003-021-02401-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/22/2021] [Indexed: 11/09/2022] Open
Abstract
Fungal biotechnology is set to play a keystone role in the emerging bioeconomy, notably to address pollution issues arising from human activities. Because they preserve biological diversity, Biological Resource Centres are considered as critical infrastructures to support the development of biotechnological solutions. Here, we report the first large-scale phenotyping of more than 1,000 fungal strains with evaluation of their growth and degradation potential towards five industrial, human-designed and recalcitrant compounds, including two synthetic dyes, two lignocellulose-derived compounds and a synthetic plastic polymer. We draw a functional map over the phylogenetic diversity of Basidiomycota and Ascomycota, to guide the selection of fungal taxa to be tested for dedicated biotechnological applications. We evidence a functional diversity at all taxonomic ranks, including between strains of a same species. Beyond demonstrating the tremendous potential of filamentous fungi, our results pave the avenue for further functional exploration to solve the ever-growing issue of ecosystems pollution.
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Affiliation(s)
- David Navarro
- INRAE, Aix Marseille Univ., BBF, UMR1163, Marseille, France. .,INRAE, Aix Marseille Univ., CIRM-CF, Marseille, France.
| | - Delphine Chaduli
- INRAE, Aix Marseille Univ., BBF, UMR1163, Marseille, France.,INRAE, Aix Marseille Univ., CIRM-CF, Marseille, France
| | - Sabine Taussac
- INRAE, Aix Marseille Univ., BBF, UMR1163, Marseille, France.,INRAE, Aix Marseille Univ., CIRM-CF, Marseille, France
| | - Laurence Lesage-Meessen
- INRAE, Aix Marseille Univ., BBF, UMR1163, Marseille, France.,INRAE, Aix Marseille Univ., CIRM-CF, Marseille, France
| | - Sacha Grisel
- INRAE, Aix Marseille Univ., BBF, UMR1163, Marseille, France
| | - Mireille Haon
- INRAE, Aix Marseille Univ., BBF, UMR1163, Marseille, France
| | | | - Régis Courtecuisse
- Faculté de Pharmacie Lille, Université de Lille, LGCgE, ER4, Lille, France
| | - Cony Decock
- Mycothèque de l'Université Catholique de Louvain (MUCL), Earth and Life Institute, Microbiology, Louvain-la-Neuve, Belgium
| | - Joëlle Dupont
- Institut de Systématique, Evolution et Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Muséum National d'Histoire Naturelle, Sorbonne Universités, Paris, France
| | | | | | | | | | | | | | | | - Lucile Sage
- Université Grenoble Alpes, LECA, UMR UGA-USMB-CNRS 5553, CS 40700, Grenoble, France
| | - Stéphane Welti
- Faculté de Pharmacie Lille, Université de Lille, LGCgE, ER4, Lille, France
| | | | | | - Bastien Bissaro
- INRAE, Aix Marseille Univ., BBF, UMR1163, Marseille, France.
| | - Anne Favel
- INRAE, Aix Marseille Univ., BBF, UMR1163, Marseille, France.,INRAE, Aix Marseille Univ., CIRM-CF, Marseille, France
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Ruiz-Dueñas FJ, Barrasa JM, Sánchez-García M, Camarero S, Miyauchi S, Serrano A, Linde D, Babiker R, Drula E, Ayuso-Fernández I, Pacheco R, Padilla G, Ferreira P, Barriuso J, Kellner H, Castanera R, Alfaro M, Ramírez L, Pisabarro AG, Riley R, Kuo A, Andreopoulos W, LaButti K, Pangilinan J, Tritt A, Lipzen A, He G, Yan M, Ng V, Grigoriev IV, Cullen D, Martin F, Rosso MN, Henrissat B, Hibbett D, Martínez AT. Genomic Analysis Enlightens Agaricales Lifestyle Evolution and Increasing Peroxidase Diversity. Mol Biol Evol 2021; 38:1428-1446. [PMID: 33211093 PMCID: PMC8480192 DOI: 10.1093/molbev/msaa301] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
As actors of global carbon cycle, Agaricomycetes (Basidiomycota) have developed complex enzymatic machineries that allow them to decompose all plant polymers, including lignin. Among them, saprotrophic Agaricales are characterized by an unparalleled diversity of habitats and lifestyles. Comparative analysis of 52 Agaricomycetes genomes (14 of them sequenced de novo) reveals that Agaricales possess a large diversity of hydrolytic and oxidative enzymes for lignocellulose decay. Based on the gene families with the predicted highest evolutionary rates—namely cellulose-binding CBM1, glycoside hydrolase GH43, lytic polysaccharide monooxygenase AA9, class-II peroxidases, glucose–methanol–choline oxidase/dehydrogenases, laccases, and unspecific peroxygenases—we reconstructed the lifestyles of the ancestors that led to the extant lignocellulose-decomposing Agaricomycetes. The changes in the enzymatic toolkit of ancestral Agaricales are correlated with the evolution of their ability to grow not only on wood but also on leaf litter and decayed wood, with grass-litter decomposers as the most recent eco-physiological group. In this context, the above families were analyzed in detail in connection with lifestyle diversity. Peroxidases appear as a central component of the enzymatic toolkit of saprotrophic Agaricomycetes, consistent with their essential role in lignin degradation and high evolutionary rates. This includes not only expansions/losses in peroxidase genes common to other basidiomycetes but also the widespread presence in Agaricales (and Russulales) of new peroxidases types not found in wood-rotting Polyporales, and other Agaricomycetes orders. Therefore, we analyzed the peroxidase evolution in Agaricomycetes by ancestral-sequence reconstruction revealing several major evolutionary pathways and mapped the appearance of the different enzyme types in a time-calibrated species tree.
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Affiliation(s)
| | - José M Barrasa
- Life Sciences Department, Alcalá University, Alcalá de Henares, Spain
| | | | - Susana Camarero
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | | | - Ana Serrano
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Dolores Linde
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Rashid Babiker
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques, CNRS/Aix-Marseille University, Marseille, France
| | | | - Remedios Pacheco
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Guillermo Padilla
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Patricia Ferreira
- Biochemistry and Molecular and Cellular Biology Department and BIFI, Zaragoza University, Zaragoza, Spain
| | - Jorge Barriuso
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Harald Kellner
- International Institute Zittau, Technische Universität Dresden, Zittau, Germany
| | - Raúl Castanera
- Institute for Multidisciplinary Research in Applied Biology, IMAB-UPNA, Pamplona, Spain
| | - Manuel Alfaro
- Institute for Multidisciplinary Research in Applied Biology, IMAB-UPNA, Pamplona, Spain
| | - Lucía Ramírez
- Institute for Multidisciplinary Research in Applied Biology, IMAB-UPNA, Pamplona, Spain
| | - Antonio G Pisabarro
- Institute for Multidisciplinary Research in Applied Biology, IMAB-UPNA, Pamplona, Spain
| | - Robert Riley
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Alan Kuo
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - William Andreopoulos
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Kurt LaButti
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Jasmyn Pangilinan
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Andrew Tritt
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Anna Lipzen
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Guifen He
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Mi Yan
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Vivian Ng
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Igor V Grigoriev
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Daniel Cullen
- Forest Products Laboratory, US Department of Agriculture, Madison, WI, USA
| | - Francis Martin
- INRAE, Laboratory of Excellence ARBRE, Champenoux, France
| | - Marie-Noëlle Rosso
- INRAE, Biodiversité et Biotechnologie Fongiques, Aix-Marseille University, Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS/Aix-Marseille University, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - David Hibbett
- Biology Department, Clark University, Worcester, MA, USA
| | - Angel T Martínez
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
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34
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Conlon BH, Gostinčar C, Fricke J, Kreuzenbeck NB, Daniel JM, Schlosser MS, Peereboom N, Aanen DK, de Beer ZW, Beemelmanns C, Gunde-Cimerman N, Poulsen M. Genome reduction and relaxed selection is associated with the transition to symbiosis in the basidiomycete genus Podaxis. iScience 2021; 24:102680. [PMID: 34189441 PMCID: PMC8220239 DOI: 10.1016/j.isci.2021.102680] [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: 03/31/2021] [Revised: 05/07/2021] [Accepted: 05/28/2021] [Indexed: 11/29/2022] Open
Abstract
Insights into the genomic consequences of symbiosis for basidiomycete fungi associated with social insects remain sparse. Capitalizing on viability of spores from centuries-old herbarium specimens of free-living, facultative, and specialist termite-associated Podaxis fungi, we obtained genomes of 10 specimens, including two type species described by Linnaeus >240 years ago. We document that the transition to termite association was accompanied by significant reductions in genome size and gene content, accelerated evolution in protein-coding genes, and reduced functional capacities for oxidative stress responses and lignin degradation. Functional testing confirmed that termite specialists perform worse under oxidative stress, while all lineages retained some capacity to cleave lignin. Mitochondrial genomes of termite associates were significantly larger; possibly driven by smaller population sizes or reduced competition, supported by apparent loss of certain biosynthetic gene clusters. Our findings point to relaxed selection that mirrors genome traits observed among obligate endosymbiotic bacteria of many insects.
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Affiliation(s)
- Benjamin H. Conlon
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
| | - Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Janis Fricke
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoll-Institute, Chemical Biology, 07745 Jena, Germany
| | - Nina B. Kreuzenbeck
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoll-Institute, Chemical Biology, 07745 Jena, Germany
| | - Jan-Martin Daniel
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoll-Institute, Chemical Biology, 07745 Jena, Germany
| | - Malte S.L. Schlosser
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
| | - Nils Peereboom
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
| | - Duur K. Aanen
- Department of Plant Sciences, Laboratory of Genetics, Wageningen University, 6708 PB Wageningen, the Netherlands
| | - Z. Wilhelm de Beer
- Department of Biochemistry, Genetics, and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa
| | - Christine Beemelmanns
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoll-Institute, Chemical Biology, 07745 Jena, Germany
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
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35
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36
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Vos AM, Bleichrodt R, Herman KC, Ohm RA, Scholtmeijer K, Schmitt H, Lugones LG, Wösten HAB. Cycling in degradation of organic polymers and uptake of nutrients by a litter-degrading fungus. Environ Microbiol 2021; 23:224-238. [PMID: 33140552 PMCID: PMC7894533 DOI: 10.1111/1462-2920.15297] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/25/2020] [Accepted: 10/26/2020] [Indexed: 11/30/2022]
Abstract
Wood and litter degrading fungi are the main decomposers of lignocellulose and thus play a key role in carbon cycling in nature. Here, we provide evidence for a novel lignocellulose degradation strategy employed by the litter degrading fungus Agaricus bisporus (known as the white button mushroom). Fusion of hyphae allows this fungus to synchronize the activity of its mycelium over large distances (50 cm). The synchronized activity has a 13-h interval that increases to 20 h before becoming irregular and it is associated with a 3.5-fold increase in respiration, while compost temperature increases up to 2°C. Transcriptomic analysis of this burst-like phenomenon supports a cyclic degradation of lignin, deconstruction of (hemi-) cellulose and microbial cell wall polymers, and uptake of degradation products during vegetative growth of A. bisporus. Cycling in expression of the ligninolytic system, of enzymes involved in saccharification, and of proteins involved in nutrient uptake is proposed to provide an efficient way for degradation of substrates such as litter.
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Affiliation(s)
- Aurin M. Vos
- Microbiology, Department of BiologyUtrecht UniversityUtrechtthe Netherlands
- Wageningen Plant ResearchWageningen URWageningenthe Netherlands
| | | | - Koen C. Herman
- Microbiology, Department of BiologyUtrecht UniversityUtrechtthe Netherlands
| | - Robin A. Ohm
- Microbiology, Department of BiologyUtrecht UniversityUtrechtthe Netherlands
| | - Karin Scholtmeijer
- Plant BreedingWageningen University and ResearchWageningenthe Netherlands
| | - Heike Schmitt
- Institute for Risk Assessment SciencesUtrecht UniversityUtrechtthe Netherlands
| | - Luis G. Lugones
- Microbiology, Department of BiologyUtrecht UniversityUtrechtthe Netherlands
| | - Han A. B. Wösten
- Microbiology, Department of BiologyUtrecht UniversityUtrechtthe Netherlands
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