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Grellier M, Moreau C, Beaugrand J, Grisel S, Berrin JG, Cathala B, Villares A. Action of AA9 lytic polysaccharide monooxygenase enzymes on different cellulose allomorphs. Int J Biol Macromol 2024; 275:133429. [PMID: 38944074 DOI: 10.1016/j.ijbiomac.2024.133429] [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: 04/15/2024] [Revised: 06/04/2024] [Accepted: 06/24/2024] [Indexed: 07/01/2024]
Abstract
Lytic polysaccharide monooxygenase (LPMO)-catalyzed oxidative processes play a major role in natural biomass conversion. Despite their oxidative cleavage at the surface of polysaccharides, understanding of their mode of action, and the impact of structural patterns of the cellulose fiber on LPMO activity is still not fully understood. In this work, we investigated the action of two different LPMOs from Podospora anserina on celluloses showing different structural patterns. For this purpose, we prepared cellulose II and cellulose III allomorphs from cellulose I cotton linters, as well as amorphous cellulose. LPMO action was monitored in terms of surface morphology, molar mass changes and monosaccharide profile. Both PaLPMO9E and PaLPMO9H were active on the different cellulose allomorphs (I, II and III), and on amorphous cellulose (PASC) whereas they displayed a different behavior, with a higher molar mass decrease observed for cellulose I. Overall, the pretreatment with LPMO enzymes clearly increased the accessibility of all types of cellulose, which was quantified by the higher carboxylate content after carboxymethylation reaction on LPMO-pretreated celluloses. This work gives more insight into the action of LPMOs as a tool for deconstructing lignocellulosic biomass to obtain new bio-based building blocks.
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Affiliation(s)
| | | | | | - Sacha Grisel
- INRAE, Aix Marseille Univ., UMR BBF, F-13009 Marseille, France; INRAE, Aix Marseille Univ., 3PE Platform, F-13009 Marseille, France
| | - Jean-Guy Berrin
- INRAE, Aix Marseille Univ., UMR BBF, F-13009 Marseille, France; INRAE, Aix Marseille Univ., 3PE Platform, F-13009 Marseille, France
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2
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Li X, Ren X, Ibrahim E, Kong H, Wang M, Xia J, Wang H, Shou L, Zhou T, Li B, Yan J. Response of Chinese cabbage ( Brassica rapa subsp. pekinensis) to bacterial soft rot infection by change of soil microbial community in root zone. Front Microbiol 2024; 15:1401896. [PMID: 38784798 PMCID: PMC11111923 DOI: 10.3389/fmicb.2024.1401896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 04/18/2024] [Indexed: 05/25/2024] Open
Abstract
Chinese cabbage, scientifically known as Brassica rapa subsp. pekinensis, is a highly popular vegetable in China for its delectable taste. However, the occurrence of bacterial soft rot disease poses a significant threat to its growth and overall development. Consequently, this study aimed to explore the defense mechanisms employed by Chinese cabbage against bacterial soft rot disease. Specifically, the investigation focused on understanding the relationship between the disease and the microbial communities present in the soil surrounding the roots of Chinese cabbage. Significant disparities were observed in the composition of microbial communities present in the root-zone soil of healthy Chinese cabbage plants compared to those affected by Pectobacterium brasiliense-caused soft rot disease. The analysis of 16S rRNA gene high-throughput sequencing results revealed a lower abundance of Proteobacteria (8.39%), Acidobacteriot (0.85), Sphingomonas (3.51%), and Vicinamibacteraceae (1.48%), whereas Firmicutes (113.76%), Bacteroidota (8.71%), Chloroflexi (4.89%), Actinobacteriota (1.71%), A4b (15.52%), Vicinamibacterales (1.62%), and Gemmatimonadaceae (1.35%) were more prevalent in healthy plant soils. Similarly, the analysis of ITS gene high-throughput sequencing results indicated a reduced occurrence of Chytridiomycota (23.58%), Basidiomycota (21.80%), Plectosphaerella (86.22%), and Agaricomycetes (22.57%) in healthy soils. In comparison, Mortierellomycota (50.72%), Ascomycota (31.22%), Podospora (485.08%), and Mortierella (51.59%) were more abundant in healthy plant soils. In addition, a total of 15 bacterial strains were isolated from the root-zone soil of diseased Chinese cabbage plants. These isolated strains demonstrated the ability to fix nitrogen (with the exception of ZT20, ZT26, ZT41, ZT45, and ZT61), produce siderophores and indole acetic acid (IAA), and solubilize phosphate. Notably, ZT14 (Citrobacter freundii), ZT33 (Enterobacter cloacae), ZT41 (Myroides odoratimimus), ZT52 (Bacillus paramycoides), ZT58 (Klebsiella pasteurii), ZT45 (Klebsiella aerogenes), and ZT32 (Pseudomonas putida) exhibited significant growth-promoting effects as determined by the plant growth promotion (PGP) tests. Consequently, this investigation not only confirmed the presence of the soft rot pathogen in Chinese cabbage plants in Hangzhou, China, but also advanced our understanding of the defense mechanisms employed by Chinese cabbage to combat soft rot-induced stress. Additionally, it identified promising plant-growth-promoting microbes (PGPMs) that could be utilized in the future to enhance the Chinese cabbage industry.
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Affiliation(s)
- Xuqing Li
- Institute of Vegetable, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaoxu Ren
- Institute of Vegetable, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Ezzeldin Ibrahim
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Haimin Kong
- Zhejiang Management Station of Cropland Quality and Fertilizer, Hangzhou, China
| | - Maofeng Wang
- Agricultural Office of Daciyan Town, Jiande, China
| | - Jiaojiao Xia
- Soil Fertilizer and Plant Protection Station in Qingtian County, Qingtian, Zhejiang, China
| | - Hong Wang
- Institute of Vegetable, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Linfei Shou
- Station for the Plant Protection and Quarantine and Control of Agrochemicals of Zhejiang Province, Hangzhou, China
| | - Tiefeng Zhou
- Institute of Vegetable, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Bin Li
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Jianli Yan
- Institute of Vegetable, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
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3
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Tang X, Zhang L, Ren S, Zhao Y, Liu K, Zhang Y. Stochastic Processes Derive Gut Fungi Community Assembly of Plateau Pikas ( Ochotona curzoniae) along Altitudinal Gradients across Warm and Cold Seasons. J Fungi (Basel) 2023; 9:1032. [PMID: 37888290 PMCID: PMC10607853 DOI: 10.3390/jof9101032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 10/05/2023] [Accepted: 10/18/2023] [Indexed: 10/28/2023] Open
Abstract
Although fungi occupy only a small proportion of the microbial community in the intestinal tract of mammals, they play important roles in host fat accumulation, nutrition metabolism, metabolic health, and immune development. Here, we investigated the dynamics and assembly of gut fungal communities in plateau pikas inhabiting six altitudinal gradients across warm and cold seasons. We found that the relative abundances of Podospora and Sporormiella significantly decreased with altitudinal gradients in the warm season, whereas the relative abundance of Sarocladium significantly increased. Alpha diversity significantly decreased with increasing altitudinal gradient in the warm and cold seasons. Distance-decay analysis showed that fungal community similarities were significantly and negatively correlated with elevation. The co-occurrence network complexity significantly decreased along the altitudinal gradients as the total number of nodes, number of edges, and degree of nodes significantly decreased. Both the null and neutral model analyses showed that stochastic or neutral processes dominated the gut fungal community assembly in both seasons and that ecological drift was the main ecological process explaining the variation in the gut fungal community across different plateau pikas. Homogeneous selection played a weak role in structuring gut fungal community assembly during the warm season. Collectively, these results expand our understanding of the distribution patterns of gut fungal communities and elucidate the mechanisms that maintain fungal diversity in the gut ecosystems of small mammals.
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Affiliation(s)
- Xianjiang Tang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liangzhi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
| | - Shien Ren
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaqi Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Liu
- Qinghai Provincial Grassland Station, Xining 810008, China
| | - Yanming Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
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4
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Degradation activity of fungal communities on avocado peel (Persea americana Mill.) in a solid-state process: mycobiota successions and trophic guild shifts. Arch Microbiol 2021; 204:2. [PMID: 34870719 DOI: 10.1007/s00203-021-02600-3] [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: 07/15/2020] [Revised: 11/19/2021] [Accepted: 11/21/2021] [Indexed: 10/19/2022]
Abstract
To explore the capability of soil mycobiota to degrade avocado peel waste and identify relevant successions and trophic guild shifts, fungal communities from three environments with different land uses were evaluated in a solid-state process. Soil samples used as inoculum were collected from a pristine mature tropical forest, a traditionally managed Mayan land, and an intensively managed monospecific avocado plantation. Soil-substrate mixes were evaluated for 52 weeks to evaluate organic matter decay and the carbon-to-nitrogen ratio. Amplicon-based high-throughput sequencing from internally transcribed spacer (ITS) analysis revealed significant differences in fungal communities widely dominated by Fusarium sp. and Clonostachys sp.; however, less represented taxa showed relevant shifts concomitantly with organic matter content drops. Trophic guild assignment revealed different behaviors in fungal communities between treatments over the 52 weeks, suggesting distinct preconditioning of fungal communities in these environments. Overall, the results lead to the identification of promising degradation moments and inoculum sources for further consortia enrichment or bioprospecting efforts.
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Nagel JH, Wingfield MJ, Slippers B. Increased abundance of secreted hydrolytic enzymes and secondary metabolite gene clusters define the genomes of latent plant pathogens in the Botryosphaeriaceae. BMC Genomics 2021; 22:589. [PMID: 34348651 PMCID: PMC8336260 DOI: 10.1186/s12864-021-07902-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 06/30/2021] [Indexed: 01/11/2023] Open
Abstract
Background The Botryosphaeriaceae are important plant pathogens, but also have the ability to establish asymptomatic infections that persist for extended periods in a latent state. In this study, we used comparative genome analyses to shed light on the genetic basis of the interactions of these fungi with their plant hosts. For this purpose, we characterised secreted hydrolytic enzymes, secondary metabolite biosynthetic gene clusters and general trends in genomic architecture using all available Botryosphaeriaceae genomes, and selected Dothideomycetes genomes. Results The Botryosphaeriaceae genomes were rich in carbohydrate-active enzymes (CAZymes), proteases, lipases and secondary metabolic biosynthetic gene clusters (BGCs) compared to other Dothideomycete genomes. The genomes of Botryosphaeria, Macrophomina, Lasiodiplodia and Neofusicoccum, in particular, had gene expansions of the major constituents of the secretome, notably CAZymes involved in plant cell wall degradation. The Botryosphaeriaceae genomes were shown to have moderate to high GC contents and most had low levels of repetitive DNA. The genomes were not compartmentalized based on gene and repeat densities, but genes of secreted enzymes were slightly more abundant in gene-sparse regions. Conclusion The abundance of secreted hydrolytic enzymes and secondary metabolite BGCs in the genomes of Botryosphaeria, Macrophomina, Lasiodiplodia, and Neofusicoccum were similar to those in necrotrophic plant pathogens and some endophytes of woody plants. The results provide a foundation for comparative genomic analyses and hypotheses to explore the mechanisms underlying Botryosphaeriaceae host-plant interactions. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07902-w.
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Affiliation(s)
- Jan H Nagel
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0001, South Africa.
| | - Michael J Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0001, South Africa
| | - Bernard Slippers
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0001, South Africa
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6
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Liang Y, Wei G, Ning K, Li M, Zhang G, Luo L, Zhao G, Wei J, Liu Y, Dong L, Chen S. Increase in carbohydrate content and variation in microbiome are related to the drought tolerance of Codonopsis pilosula. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 165:19-35. [PMID: 34034158 DOI: 10.1016/j.plaphy.2021.05.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
Drought stress is one of the main limiting factors in geographical distribution and production of Codonopsis pilosula. Understanding the biochemical and genetic information of the response of C. pilosula to drought stress is urgently needed for breeding tolerant varieties. Here, carbohydrates, namely trehalose, raffinose, maltotetraose, sucrose, and melezitose, significantly accumulated in C. pilosula roots under drought stress and thus served as biomarkers for drought stress response. Compared with those in the control group, the expression levels of key genes such as adenosine diphosphate glucose pyrophosphorylase, starch branching enzyme, granule-bound starch synthase, soluble starch synthase, galacturonate transferase, cellulose synthase A catalytic subunit, cellulase Korrigan in the carbohydrate biosynthesis pathway were markedly up-regulated in C. pilosula roots in the drought treatment group, some of them even exceeded 70%. Notably, and that of key genes including trehalose-6-phosphatase, trehalose-6-phosphate phosphatase, galactinol synthase, and raffinose synthase in the trehalose and raffinose biosynthesis pathways was improved by 12.6%-462.2% in C. pilosula roots treated by drought stress. The accumulation of carbohydrates in C. pilosula root or rhizosphere soil was correlated with microbiome variations. Analysis of exogenous trehalose and raffinose confirmed that increased carbohydrate content improved the drought tolerance of C. pilosula in a dose-dependent manner. This study provided solid foundation for breeding drought-tolerant C. pilosula varieties and developing drought-resistant microbial fertilizers.
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Affiliation(s)
- Yichuan Liang
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China; Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Guangfei Wei
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Kang Ning
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Mengzhi Li
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Guozhuang Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Lu Luo
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Guanghui Zhao
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Jianhe Wei
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou, 570311, China.
| | - Youping Liu
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| | - Linlin Dong
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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7
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Wang Y, Fu Y, He Y, Kulyar MFEA, Iqbal M, Li K, Liu J. Longitudinal Characterization of the Gut Bacterial and Fungal Communities in Yaks. J Fungi (Basel) 2021; 7:jof7070559. [PMID: 34356938 PMCID: PMC8304987 DOI: 10.3390/jof7070559] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/28/2021] [Accepted: 07/08/2021] [Indexed: 12/12/2022] Open
Abstract
Development phases are important in maturing immune systems, intestinal functions, and metabolism for the construction, structure, and diversity of microbiome in the intestine during the entire life. Characterizing the gut microbiota colonization and succession based on age-dependent effects might be crucial if a microbiota-based therapeutic or disease prevention strategy is adopted. The purpose of this study was to reveal the dynamic distribution of intestinal bacterial and fungal communities across all development stages in yaks. Dynamic changes (a substantial difference) in the structure and composition ratio of the microbial community were observed in yaks that matched the natural aging process from juvenile to natural aging. This study included a significant shift in the abundance and proportion of bacterial phyla (Planctomycetes, Firmicutes, Bacteroidetes, Spirochaetes, Tenericutes, Proteobacteria, and Cyanobacteria) and fungal phyla (Chytridiomycota, Mortierellomycota, Neocallimastigomycota, Ascomycota, and Basidiomycota) across all development stages in yaks. As yaks grew older, variation reduced, and diversity increased as compared to young yaks. In addition, the intestine was colonized by a succession of microbiomes that coalesced into a more mature adult, including Ruminococcaceae_UCG-005, Romboutsia, Prevotellaceae_UCG-004, Blautia, Clostridium_sensu_stricto_1, Ruminococcus_1, Ruminiclostridium_5, Rikenellaceae_RC9_gut_group, Alloprevotella, Acetitomaculum, Lachnospiraceae_NK3A20_group, Bacteroides, Treponema_2, Olsenella, Escherichia-Shigella, Candidatus_Saccharimonas, and fungal communities Mortierella, Lomentospora, Orpinomyces, and Saccharomyces. In addition, microorganisms that threaten health, such as Escherichia-Shigella, Mortierella, Lomentospora and Hydrogenoanaerobacterium, Corynebacterium_1, Trichosporon, and Coprinellus, were enriched in young and old yaks, respectively, although all yaks were healthy. The significant shifts in microflora composition and structure might reflect adaptation of gut microbiome, which is associated with physicochemical conditions changes and substrate availability in the gut across all development periods of yaks.
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Affiliation(s)
- Yaping Wang
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China;
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.H.); (M.F.-e.-A.K.); (M.I.)
| | - Yuhang Fu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.H.); (M.F.-e.-A.K.); (M.I.)
| | - Yuanyuan He
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.H.); (M.F.-e.-A.K.); (M.I.)
| | - Muhammad Fakhar-e-Alam Kulyar
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.H.); (M.F.-e.-A.K.); (M.I.)
| | - Mudassar Iqbal
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.H.); (M.F.-e.-A.K.); (M.I.)
- Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Kun Li
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China;
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (K.L.); (J.L.)
| | - Jiaguo Liu
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China;
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (K.L.); (J.L.)
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8
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Moreira EA, Persinoti GF, Menezes LR, Paixão DAA, Alvarez TM, Cairo JPLF, Squina FM, Costa-Leonardo AM, Rodrigues A, Sillam-Dussès D, Arab A. Complementary Contribution of Fungi and Bacteria to Lignocellulose Digestion in the Food Stored by a Neotropical Higher Termite. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.632590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Lignocellulose digestion in termites is achieved through the functional synergy between gut symbionts and host enzymes. However, some species have evolved additional associations with nest microorganisms that collaborate in the decomposition of plant biomass. In a previous study, we determined that plant material packed with feces inside the nests of Cornitermes cumulans (Syntermitinae) harbors a distinct microbial assemblage. These food nodules also showed a high hemicellulolytic activity, possibly acting as an external place for complementary lignocellulose digestion. In this study, we used a combination of ITS sequence analysis, metagenomics, and metatranscriptomics to investigate the presence and differential expression of genes coding for carbohydrate-active enzymes (CAZy) in the food nodules and the gut of workers and soldiers. Our results confirm that food nodules express a distinct set of CAZy genes suggesting that stored plant material is initially decomposed by enzymes that target the lignin and complex polysaccharides from fungi and bacteria before the passage through the gut, where it is further targeted by a complementary set of cellulases, xylanases, and esterases produced by the gut microbiota and the termite host. We also showed that the expression of CAZy transcripts associated to endoglucanases and xylanases was higher in the gut of termites than in the food nodules. An additional finding in this study was the presence of fungi in the termite gut that expressed CAZy genes. This study highlights the importance of externalization of digestion by nest microbes and provides new evidence of complementary digestion in the context of higher termite evolution.
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9
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Ament-Velásquez SL, Johannesson H, Giraud T, Debuchy R, Saupe SJ, Debets AJ, Bastiaans E, Malagnac F, Grognet P, Peraza-Reyes L, Gladieux P, Kruys Å, Silar P, Huhndorf SM, Miller AN, Vogan AA. The taxonomy of the model filamentous fungus Podospora anserina. MycoKeys 2020; 75:51-69. [PMID: 33281477 PMCID: PMC7710671 DOI: 10.3897/mycokeys.75.55968] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/11/2020] [Indexed: 11/17/2022] Open
Abstract
The filamentous fungus Podospora anserina has been used as a model organism for more than 100 years and has proved to be an invaluable resource in numerous areas of research. Throughout this period, P. anserina has been embroiled in a number of taxonomic controversies regarding the proper name under which it should be called. The most recent taxonomic treatment proposed to change the name of this important species to Triangularia anserina. The results of past name changes of this species indicate that the broader research community is unlikely to accept this change, which will lead to nomenclatural instability and confusion in literature. Here, we review the phylogeny of the species closely related to P. anserina and provide evidence that currently available marker information is insufficient to resolve the relationships amongst many of the lineages. We argue that it is not only premature to propose a new name for P. anserina based on current data, but also that every effort should be made to retain P. anserina as the current name to ensure stability and to minimise confusion in scientific literature. Therefore, we synonymise Triangularia with Podospora and suggest that either the type species of Podospora be moved to P. anserina from P. fimiseda or that all species within the Podosporaceae be placed in the genus Podospora.
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Affiliation(s)
- S. Lorena Ament-Velásquez
- Systematic Biology, Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, SwedenUppsala UniveristyUppsalaSweden
| | - Hanna Johannesson
- Systematic Biology, Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, SwedenUppsala UniveristyUppsalaSweden
| | - Tatiana Giraud
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, 91400, Orsay, FranceUniversité Paris-SaclayOrsayFrance
| | - Robert Debuchy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, FranceUniversité Paris-SaclayGif-sur-YvetteFrance
| | - Sven J. Saupe
- IBGC, UMR 5095, CNRS Université de Bordeaux, 1 rue Camille Saint Saëns, 33077, Bordeaux, FranceUniversité de BordeauxBordeauxFrance
| | - Alfons J.M. Debets
- Laboratory of Genetics, Wageningen University, Arboretumlaan 4, 6703 BD, Wageningen, NetherlandsWageningen UniversityWageningenNetherlands
| | - Eric Bastiaans
- Laboratory of Genetics, Wageningen University, Arboretumlaan 4, 6703 BD, Wageningen, NetherlandsWageningen UniversityWageningenNetherlands
| | - Fabienne Malagnac
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, FranceUniversité Paris-SaclayGif-sur-YvetteFrance
| | - Pierre Grognet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, FranceUniversité Paris-SaclayGif-sur-YvetteFrance
| | - Leonardo Peraza-Reyes
- Instituto de Fisiología Celular, Departamento de Bioquímica y Biología Estructural, Universidad Nacional Autónoma de México, Mexico City, MexicoUniversidad Nacional Autónoma de MéxicoMexico CityMexico
| | - Pierre Gladieux
- UMR BGPI, Université de Montpellier, INRAE, CIRAD, Institut Agro, F-34398, Montpellier, FranceUniversité de MontpellierMontpellierFrance
| | - Åsa Kruys
- Museum of Evolution, Botany, Uppsala University, Norbyvägen 18, 752 36, Uppsala, SwedenUppsala UniversityUppsalaSweden
| | - Philippe Silar
- Université de Paris, Laboratoire Interdisciplinaire des Energies de Demain (LIED), F-75006, Paris, FranceUniversité de ParisParisFrance
| | - Sabine M. Huhndorf
- Botany Department, The Field Museum, Chicago, Illinois 60605, USAThe Field MuseumChicagoUnited States of America
| | - Andrew N. Miller
- Illinois Natural History Survey, University of Illinois, Champaign, IL 61820, USAUniversity of IllinoisChampaignUnited States of America
| | - Aaron A. Vogan
- Systematic Biology, Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, SwedenUppsala UniveristyUppsalaSweden
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10
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Dicko M, Ferrari R, Tangthirasunun N, Gautier V, Lalanne C, Lamari F, Silar P. Lignin Degradation and Its Use in Signaling Development by the Coprophilous Ascomycete Podospora anserina. J Fungi (Basel) 2020; 6:E278. [PMID: 33187140 PMCID: PMC7712204 DOI: 10.3390/jof6040278] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 01/06/2023] Open
Abstract
The filamentous fungus Podospora anserina is a good model to study the breakdown of lignocellulose, owing to its ease of culture and genetical analysis. Here, we show that the fungus is able to use a wide range of lignocellulosic materials as food sources. Using color assays, spectroscopy and pyrolysis-gas chromatography mass spectrometry, we confirm that this ascomycete is able to degrade lignin, primarily by hydrolyzing β-O-4 linkages, which facilitates its nutrient uptake. We show that the limited weight loss that is promoted when attacking Miscanthus giganteus is due to a developmental blockage rather than an inefficiency of its enzymes. Finally, we show that lignin, and, more generally, phenolics, including degradation products of lignin, greatly stimulate the growth and fertility of the fungus in liquid cultures. Analyses of the CATΔΔΔΔΔ mutant lacking all its catalases, pro-oxidants and antioxidants indicate that improved growth and fertility of the fungus is likely caused by augmented reactive oxygen species levels triggered by the presence of phenolics.
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Affiliation(s)
- Moussa Dicko
- Université Sorbonne Paris Nord, CNRS LSPM UPR 3407, 93430 Villetaneuse, France; (M.D.); (F.L.)
| | - Roselyne Ferrari
- Université de Paris, Laboratoire Interdisciplinaire des Energies de Demain (LIED), F-75006 Paris, France; (R.F.); (N.T.); (V.G.); (C.L.)
| | - Narumon Tangthirasunun
- Université de Paris, Laboratoire Interdisciplinaire des Energies de Demain (LIED), F-75006 Paris, France; (R.F.); (N.T.); (V.G.); (C.L.)
| | - Valérie Gautier
- Université de Paris, Laboratoire Interdisciplinaire des Energies de Demain (LIED), F-75006 Paris, France; (R.F.); (N.T.); (V.G.); (C.L.)
| | - Christophe Lalanne
- Université de Paris, Laboratoire Interdisciplinaire des Energies de Demain (LIED), F-75006 Paris, France; (R.F.); (N.T.); (V.G.); (C.L.)
| | - Farida Lamari
- Université Sorbonne Paris Nord, CNRS LSPM UPR 3407, 93430 Villetaneuse, France; (M.D.); (F.L.)
| | - Philippe Silar
- Université de Paris, Laboratoire Interdisciplinaire des Energies de Demain (LIED), F-75006 Paris, France; (R.F.); (N.T.); (V.G.); (C.L.)
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11
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Christensen SJ, Badino SF, Cavaleiro AM, Borch K, Westh P. Functional analysis of chimeric TrCel6A enzymes with different carbohydrate binding modules. Protein Eng Des Sel 2020; 32:401-409. [PMID: 32100026 DOI: 10.1093/protein/gzaa003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 01/10/2019] [Accepted: 01/13/2019] [Indexed: 11/14/2022] Open
Abstract
The glycoside hydrolase (GH) family 6 is an important group of enzymes that constitute an essential part of industrial enzyme cocktails used to convert lignocellulose into fermentable sugars. In nature, enzymes from this family often have a carbohydrate binding module (CBM) from the CBM family 1. These modules are known to promote adsorption to the cellulose surface and influence enzymatic activity. Here, we have investigated the functional diversity of CBMs found within the GH6 family. This was done by constructing five chimeric enzymes based on the model enzyme, TrCel6A, from the soft-rot fungus Trichoderma reesei. The natural CBM of this enzyme was exchanged with CBMs from other GH6 enzymes originating from different cellulose degrading fungi. The chimeric enzymes were expressed in the same host and investigated in adsorption and quasi-steady-state kinetic experiments. Our results quantified functional differences of these phylogenetically distant binding modules. Thus, the partitioning coefficient for substrate binding varied 4-fold, while the maximal turnover (kcat) showed a 2-fold difference. The wild-type enzyme showed the highest cellulose affinity on all tested substrates and the highest catalytic turnover. The CBM from Serendipita indica strongly promoted the enzyme's ability to form productive complexes with sites on the substrate surface but showed lower turnover of the complex. We conclude that the CBM plays an important role for the functional differences between GH6 wild-type enzymes.
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Affiliation(s)
- Stefan Jarl Christensen
- Research Unit for Functional Biomaterials, Department of Science and Environment, Roskilde University, building 28B, DK-4000, Roskilde, Denmark
| | - Silke Flindt Badino
- Research Unit for Functional Biomaterials, Department of Science and Environment, Roskilde University, building 28B, DK-4000, Roskilde, Denmark
| | - Ana Mafalda Cavaleiro
- Research Unit for Functional Biomaterials, Department of Science and Environment, Roskilde University, building 28B, DK-4000, Roskilde, Denmark.,Novozymes A/S, Department of Enzyme Discovery, Rævehøjvej 32A, DK-2800 Kgs. Lyngby, Denmark
| | - Kim Borch
- Novozymes A/S, Department of Enzyme Discovery, Rævehøjvej 32A, DK-2800 Kgs. Lyngby, Denmark
| | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, building 224, DK-2800, Kgs. Lyngby, Denmark
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12
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Li Y, Yan P, Lu X, Qiu Y, Liang S, Liu G, Li S, Mou L, Xie N. Involvement of PaSNF1 in Fungal Development, Sterigmatocystin Biosynthesis, and Lignocellulosic Degradation in the Filamentous Fungus Podospora anserina. Front Microbiol 2020; 11:1038. [PMID: 32587577 PMCID: PMC7299030 DOI: 10.3389/fmicb.2020.01038] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 04/27/2020] [Indexed: 02/05/2023] Open
Abstract
The sucrose non-fermenting 1/AMP-activated protein kinase (SNF1/AMPK) is a central regulator of carbon metabolism and energy production in the eukaryotes. In this study, the functions of the Podospora anserina SNF1 (PaSNF1) ortholog were investigated. The ΔPaSNF1 mutant displays a delayed development of mycelium and fruiting bodies and fails to form ascospores. The expression of the PaSNF1 gene in the strain providing female organs in a cross is sufficient to ensure fertility, indicating a maternal effect. Results of environmental stress showed that ΔPaSNF1 was hypersensitive to stress, such as osmotic pressure and heat shock, and resistant to fluconazole. Interestingly, the knockout of PaSNF1 significantly promoted sterigmatocystin (ST) synthesis but suppressed cellulase [filter paperase (FPA), endoglucanase (EG), and β-glucosidase (BG)] activity. Further, transcriptome analysis indicated that PaSNF1 made positive regulatory effects on the expression of genes encoding cellulolytic enzymes. These results suggested that PaSNF1 may function in balancing the operation of primary and secondary metabolism. This study suggested that SNF1 was a key regulator concerting vegetative growth, sexual development, and stress tolerance. Our study provided the first genetic evidence that SNF1 was involved in the ST biosynthesis and that it may also be a major actor of lignocellulose degradation in P. anserina.
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Affiliation(s)
- Yuanjing Li
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Pengfei Yan
- Key Laboratory of Functional Inorganic Material Chemistry (MOE), School of Chemistry and Materials Science, Heilongjiang University, Harbin, China
| | - Xiaojie Lu
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Yanling Qiu
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Shang Liang
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Gang Liu
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Shuangfei Li
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Lin Mou
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Ning Xie
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
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13
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van Erven G, Kleijn AF, Patyshakuliyeva A, Di Falco M, Tsang A, de Vries RP, van Berkel WJH, Kabel MA. Evidence for ligninolytic activity of the ascomycete fungus Podospora anserina. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:75. [PMID: 32322305 PMCID: PMC7161253 DOI: 10.1186/s13068-020-01713-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 04/09/2020] [Indexed: 05/25/2023]
Abstract
BACKGROUND The ascomycete fungus Podospora anserina has been appreciated for its targeted carbohydrate-active enzymatic arsenal. As a late colonizer of herbivorous dung, the fungus acts specifically on the more recalcitrant fraction of lignocellulose and this lignin-rich biotope might have resulted in the evolution of ligninolytic activities. However, the lignin-degrading abilities of the fungus have not been demonstrated by chemical analyses at the molecular level and are, thus far, solely based on genome and secretome predictions. To evaluate whether P. anserina might provide a novel source of lignin-active enzymes to tap into for potential biotechnological applications, we comprehensively mapped wheat straw lignin during fungal growth and characterized the fungal secretome. RESULTS Quantitative 13C lignin internal standard py-GC-MS analysis showed substantial lignin removal during the 7 days of fungal growth (24% w/w), though carbohydrates were preferably targeted (58% w/w removal). Structural characterization of residual lignin by using py-GC-MS and HSQC NMR analyses demonstrated that Cα-oxidized substructures significantly increased through fungal action, while intact β-O-4' aryl ether linkages, p-coumarate and ferulate moieties decreased, albeit to lesser extents than observed for the action of basidiomycetes. Proteomic analysis indicated that the presence of lignin induced considerable changes in the secretome of P. anserina. This was particularly reflected in a strong reduction of cellulases and galactomannanases, while H2O2-producing enzymes clearly increased. The latter enzymes, together with laccases, were likely involved in the observed ligninolysis. CONCLUSIONS For the first time, we provide unambiguous evidence for the ligninolytic activity of the ascomycete fungus P. anserina and expand the view on its enzymatic repertoire beyond carbohydrate degradation. Our results can be of significance for the development of biological lignin conversion technologies by contributing to the quest for novel lignin-active enzymes and organisms.
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Affiliation(s)
- Gijs van Erven
- Laboratory of Food Chemistry, Wageningen University and Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Anne F. Kleijn
- Laboratory of Food Chemistry, Wageningen University and Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Aleksandrina Patyshakuliyeva
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Marcos Di Falco
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6 Canada
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6 Canada
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Willem J. H. van Berkel
- Laboratory of Food Chemistry, Wageningen University and Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Mirjam A. Kabel
- Laboratory of Food Chemistry, Wageningen University and Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
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14
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Demoor A, Silar P, Brun S. Appressorium: The Breakthrough in Dikarya. J Fungi (Basel) 2019; 5:jof5030072. [PMID: 31382649 PMCID: PMC6787622 DOI: 10.3390/jof5030072] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/24/2019] [Accepted: 07/30/2019] [Indexed: 11/23/2022] Open
Abstract
Phytopathogenic and mycorrhizal fungi often penetrate living hosts by using appressoria and related structures. The differentiation of similar structures in saprotrophic fungi to penetrate dead plant biomass has seldom been investigated and has been reported only in the model fungus Podospora anserina. Here, we report on the ability of many saprotrophs from a large range of taxa to produce appressoria on cellophane. Most Ascomycota and Basidiomycota were able to form appressoria. In contrast, none of the three investigated Mucoromycotina was able to differentiate such structures. The ability of filamentous fungi to differentiate appressoria no longer belongs solely to pathogenic or mutualistic fungi, and this raises the question of the evolutionary origin of the appressorium in Eumycetes.
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Affiliation(s)
- Alexander Demoor
- Laboratoire Interdisciplinaire des Energies de Demain, LIED-UMR 8236, Université de Paris, 5 rue Marie-Andree Lagroua, 75205 Paris, France
| | - Philippe Silar
- Laboratoire Interdisciplinaire des Energies de Demain, LIED-UMR 8236, Université de Paris, 5 rue Marie-Andree Lagroua, 75205 Paris, France
| | - Sylvain Brun
- Laboratoire Interdisciplinaire des Energies de Demain, LIED-UMR 8236, Université de Paris, 5 rue Marie-Andree Lagroua, 75205 Paris, France.
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15
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Benocci T, Daly P, Aguilar-Pontes MV, Lail K, Wang M, Lipzen A, Ng V, Grigoriev IV, de Vries RP. Enzymatic Adaptation of Podospora anserina to Different Plant Biomass Provides Leads to Optimized Commercial Enzyme Cocktails. Biotechnol J 2019; 14:e1800185. [PMID: 30221832 DOI: 10.1002/biot.201800185] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 09/10/2018] [Indexed: 12/17/2023]
Abstract
As a late colonizer of herbivore dung, Podospora anserina has evolved an enzymatic machinery to degrade the more recalcitrant fraction of plant biomass, suggesting a great potential for biotechnology applications. The authors investigated its transcriptome during growth on two industrial feedstocks, soybean hulls (SBH) and corn stover (CS). Initially, CS and SBH results in the expression of hemicellulolytic and amylolytic genes, respectively, while at later time points a more diverse gene set is induced, especially for SBH. Substrate adaptation is also observed for carbon catabolism. Overall, SBH resulted in a larger diversity of expressed genes, confirming previous proteomics studies. The results not only provide an in depth view on the transcriptomic adaptation of P. anserina to substrate composition, but also point out strategies to improve saccharification of plant biomass at the industrial level.
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Affiliation(s)
- Tiziano Benocci
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands
| | - Paul Daly
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands
| | - Maria Victoria Aguilar-Pontes
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands
| | - Kathleen Lail
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Mei Wang
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Vivian Ng
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94598, USA
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands
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16
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Maurício da Fonseca MJ, Jurak E, Kataja K, Master ER, Berrin JG, Stals I, Desmet T, Van Landschoot A, Briers Y. Analysis of the substrate specificity of α-L-arabinofuranosidases by DNA sequencer-aided fluorophore-assisted carbohydrate electrophoresis. Appl Microbiol Biotechnol 2018; 102:10091-10102. [PMID: 30267127 DOI: 10.1007/s00253-018-9389-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/04/2018] [Accepted: 09/09/2018] [Indexed: 01/11/2023]
Abstract
Carbohydrate-active enzyme discovery is often not accompanied by experimental validation, demonstrating the need for techniques to analyze substrate specificities of carbohydrate-active enzymes in an efficient manner. DNA sequencer-aided fluorophore-assisted carbohydrate electrophoresis (DSA-FACE) is utmost appropriate for the analysis of glycoside hydrolases that have complex substrate specificities. DSA-FACE is demonstrated here to be a highly convenient method for the precise identification of the specificity of different α-L-arabinofuranosidases for (arabino)xylo-oligosaccharides ((A)XOS). The method was validated with two α-L-arabinofuranosidases (EC 3.2.1.55) with well-known specificity, specifically a GH62 α-L-arabinofuranosidase from Aspergillus nidulans (AnAbf62A-m2,3) and a GH43 α-L-arabinofuranosidase from Bifidobacterium adolescentis (BaAXH-d3). Subsequently, application of DSA-FACE revealed the AXOS specificity of two α-L-arabinofuranosidases with previously unknown AXOS specificities. PaAbf62A, a GH62 α-L-arabinofuranosidase from Podospora anserina strain S mat+, was shown to target the O-2 and the O-3 arabinofuranosyl monomers as side chain from mono-substituted β-D-xylosyl residues, whereas a GH43 α-L-arabinofuranosidase from a metagenomic sample (AGphAbf43) only removes an arabinofuranosyl monomer from the smallest AXOS tested. DSA-FACE excels ionic chromatography in terms of detection limit for (A)XOS (picomolar sensitivity), hands-on and analysis time, and the analysis of the degree of polymerization and binding site of the arabinofuranosyl substituent.
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Affiliation(s)
| | - Edita Jurak
- Department of Biotechnology and Chemical Technology, Aalto University, Espoo, Finland
| | - Kim Kataja
- Department of Biotechnology and Chemical Technology, Aalto University, Espoo, Finland
| | - Emma R Master
- Department of Biotechnology and Chemical Technology, Aalto University, Espoo, Finland
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Jean-Guy Berrin
- INRA, Aix Marseille Université, UMR1163 BBF, Marseille, France
| | - Ingeborg Stals
- Department of Materials, Textiles and Chemical Engineering, Ghent University, Ghent, Belgium
| | - Tom Desmet
- Department of Biotechnology, Ghent University, Ghent, Belgium
| | | | - Yves Briers
- Department of Biotechnology, Ghent University, Ghent, Belgium.
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17
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Characterization of fungus microbial diversity in healthy and diarrheal yaks in Gannan region of Tibet Autonomous Prefecture. Acta Trop 2018; 182:14-26. [PMID: 29454733 DOI: 10.1016/j.actatropica.2018.02.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 02/12/2018] [Accepted: 02/12/2018] [Indexed: 12/27/2022]
Abstract
Diarrhea is a serious epidemic in yaks on Qinghai Tibet plateau, but the exact pathogen is not confirmed. Diarrhea is related to the changes in diversity of intestinal flora. The current study herein is performed for high-throughput sequencing of fungus microbial diversity in healthy adult yaks, diarrheal adult yaks and diarrheal yak calves in Gannan Tibetan Autonomous Prefecture. A total 446726 optimized sequences were achieved. Over 250 OTUs in species level have been indentified for each sample. The Shannon and Simpson index revealed that there was no visible difference in the flora between different yak groups (p > 0.05). However, obvious difference was watched in the principal component of microbial community structure in different yak groups by PCA analysis, especially between healthy adult yak group and diarrheal adult yak groups. There were 248 fungus species shared in three groups. Interestingly, there were 97 fungus species shared in the diarrheal groups (calves and adult yaks), which were not found in the healthy yaks, while there were 212 fungus species only found in the healthy yaks. In the Phylum level, 1 phylum (Neocallimastigomycota) was discovered to have significant difference between healthy yaks and diarrheal yak calves (p < 0.05). In the genus level, 23 genus were found obvious difference between healthy adult yaks and diarrheal adults yaks (p < 0.05); 28 genus were found significant difference between healthy adult yaks and diarrheal yak calves (p < 0.05); 23 genus were found obvious difference between diarrheal adult yaks and diarrheal yak calves (p < 0.05). The present study herein first reported an insight of the change of microbial diversity of fungus in diarrhea yaks at altitude regions, which contributed towards the solid prevention of diarrhea in yaks.
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18
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Benocci T, de Vries RP, Daly P. A senescence-delaying pre-culture medium for transcriptomics of Podospora anserina. J Microbiol Methods 2018; 146:33-36. [DOI: 10.1016/j.mimet.2018.01.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 01/18/2018] [Accepted: 01/18/2018] [Indexed: 01/15/2023]
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19
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Yim B, Nitt H, Wrede A, Jacquiod S, Sørensen SJ, Winkelmann T, Smalla K. Effects of Soil Pre-Treatment with Basamid® Granules, Brassica juncea, Raphanus sativus, and Tagetes patula on Bacterial and Fungal Communities at Two Apple Replant Disease Sites. Front Microbiol 2017; 8:1604. [PMID: 28919882 PMCID: PMC5586068 DOI: 10.3389/fmicb.2017.01604] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 08/07/2017] [Indexed: 12/04/2022] Open
Abstract
Nurseries producing apple and rose rootstock plants, apple orchards as well as rose production often experience replanting problems after several cultivations at the same site when a chemical soil disinfectant is not applied. The etiology of apple and rose replanting problems is most likely caused by soil-borne pathogen complex, defined as "replant disease (RD)". Symptoms typical of RD are reduced shoot and root growth, a smaller leaf area, a significant decrease in plant biomass, yield and fruit quality and a shorter life span. In our previous study, we showed that RD symptoms were reduced when apple rootstock M106 were grown in RD soils treated either with the soil fumigant Basamid or after biofumigation by incorporating Brassica juncea or Raphanus sativus or by growing Tagetes under field conditions compared to untreated control soil. The present study aimed at identifying potential bacterial and fungal taxa that were affected by different soil treatments and linking bacterial and fungal responders to plant performance. Miseq® Illumina® sequencing of 16S rRNA gene fragments (bacteria) and ITS regions (fungi) amplified from total community DNA extracted from soil samples taken 4 weeks after treatments were performed. Soil properties and culture history of the two RD sites greatly influenced soil microbiomes. Several bacterial genera were identified that significantly increased in treated soils such as Arthrobacter (R. sativus, both sites), Curtobacterium (Basamid, both sites), Terrimonas (Basamid and R. sativus, site A) and Ferruginibacter (B. juncea, site K and R. sativus, site A) that were also significantly and positively correlated with growth of apple M106 plants. Only few fungal genera, such as Podospora, Monographella and Mucor, were significantly promoted in soils treated with B. juncea and R. sativus (both sites). The least pronounced changes were recorded for bacterial as well as fungal communities in the RD soils planted with Tagetes. The detection of bacterial and fungal genera that were significantly increased in relative abundance in response to the treatments and that were positively correlated with plant growth suggests that management of the soil microbial community could contribute to overcome the apple RD encountered at affected sites.
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Affiliation(s)
- Bunlong Yim
- Institute of Horticultural Production Systems, Leibniz Universität HannoverHannover, Germany
- Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen DiagnosticsBraunschweig, Germany
| | - Heike Nitt
- Department of Plant Production, Plant Protection, Environment, Landwirtschaftskammer Schleswig-HolsteinEllerhoop, Germany
| | - Andreas Wrede
- Department of Horticulture, Landwirtschaftskammer Schleswig-HolsteinEllerhoop, Germany
| | - Samuel Jacquiod
- Section of Microbiology, Department of Biology, University of CopenhagenCopenhagen, Denmark
| | - Søren J. Sørensen
- Section of Microbiology, Department of Biology, University of CopenhagenCopenhagen, Denmark
| | - Traud Winkelmann
- Institute of Horticultural Production Systems, Leibniz Universität HannoverHannover, Germany
| | - Kornelia Smalla
- Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen DiagnosticsBraunschweig, Germany
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20
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Mäkelä MR, Bouzid O, Robl D, Post H, Peng M, Heck A, Altelaar M, de Vries RP. Cultivation of Podospora anserina on soybean hulls results in an efficient enzyme cocktail for plant biomass hydrolysis. N Biotechnol 2017; 37:162-171. [PMID: 28188936 DOI: 10.1016/j.nbt.2017.02.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/06/2017] [Accepted: 02/06/2017] [Indexed: 11/25/2022]
Abstract
The coprophilic ascomycete fungus Podospora anserina was cultivated on three different plant biomasses, i.e. cotton seed hulls (CSH), soybean hulls (SBH) and acid-pretreated wheat straw (WS) for four days, and the potential of the produced enzyme mixtures was compared in the enzymatic saccharification of the corresponding lignocellulose feedstocks. The enzyme cocktail P. anserina produced after three days of growth on SBH showed superior capacity to release reducing sugars from all tested plant biomass feedstocks compared to the enzyme mixtures from CSH and WS cultures. Detailed proteomics analysis of the culture supernatants revealed that SBH contained the most diverse set of enzymes targeted on plant cell wall polymers and was particularly abundant in xylan, mannan and pectin acting enzymes. The importance of lytic polysaccharide monooxygenases (LPMOs) in plant biomass deconstruction was supported by identification of 20 out of 33 AA9 LPMOs in the SBH cultures. The results highlight the suitability of P. anserina as a source of plant cell wall degrading enzymes for biotechnological applications and the importance of selecting the most optimal substrate for the production of enzyme mixtures.
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Affiliation(s)
- Miia R Mäkelä
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands; Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, P.O. Box 56, Viikinkaari 9, University of Helsinki, Helsinki, Finland, Finland
| | - Ourdia Bouzid
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands; Microbiology, Utrecht University, Padualaan 8, 3584 Ch Utrecht, The Netherlands
| | - Diogo Robl
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands; Brazilian Laboratory of Science and Technology of Bioethanol, Giuseppe Maximo Scolfaro 10.000, Campinas, Brazil
| | - Harm Post
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecules Research and Utrecht Institute for Pharmaceutical Sciences, Padualaan 8, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Albert Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecules Research and Utrecht Institute for Pharmaceutical Sciences, Padualaan 8, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecules Research and Utrecht Institute for Pharmaceutical Sciences, Padualaan 8, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands; Microbiology, Utrecht University, Padualaan 8, 3584 Ch Utrecht, The Netherlands.
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Fanuel M, Garajova S, Ropartz D, McGregor N, Brumer H, Rogniaux H, Berrin JG. The Podospora anserina lytic polysaccharide monooxygenase PaLPMO9H catalyzes oxidative cleavage of diverse plant cell wall matrix glycans. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:63. [PMID: 28293293 PMCID: PMC5346257 DOI: 10.1186/s13068-017-0749-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 03/02/2017] [Indexed: 05/08/2023]
Abstract
BACKGROUND The enzymatic conversion of plant biomass has been recently revolutionized by the discovery of lytic polysaccharide monooxygenases (LPMO) that catalyze oxidative cleavage of polysaccharides. These powerful enzymes are secreted by a large number of fungal saprotrophs and are important components of commercial enzyme cocktails used for industrial biomass conversion. Among the 33 AA9 LPMOs encoded by the genome of Podospora anserina, the PaLPMO9H enzyme catalyzes mixed C1/C4 oxidative cleavage of cellulose and cello-oligosaccharides. Activity of PaLPMO9H on several hemicelluloses has been suggested, but the regioselectivity of the cleavage remained to be determined. RESULTS In this study, we investigated the activity of PaLPMO9H on mixed-linkage glucans, xyloglucan and glucomannan using tandem mass spectrometry and ion mobility-mass spectrometry. Structural analysis of the released products revealed that PaLPMO9H catalyzes C4 oxidative cleavage of mixed-linkage glucans and mixed C1/C4 oxidative cleavage of glucomannan and xyloglucan. Gem-diols and ketones were produced at the non-reducing end, while aldonic acids were produced at the reducing extremity of the products. CONCLUSION The ability of PaLPMO9H to target polysaccharides, differing from cellulose by their linkages, glycosidic composition and/or presence of sidechains, could be advantageous for this coprophilous fungus when catabolizing highly variable polysaccharides and for the development of optimized enzyme cocktails in biorefineries.
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Affiliation(s)
- Mathieu Fanuel
- Unité de Recherche Biopolymères, Interactions, Assemblages, INRA, 44316 Nantes, France
| | - Sona Garajova
- Polytech Marseille, UMR1163 Biodiversité et Biotechnologie Fongiques, INRA, Aix-Marseille Université, Avenue de Luminy, 13288 Marseille, France
| | - David Ropartz
- Unité de Recherche Biopolymères, Interactions, Assemblages, INRA, 44316 Nantes, France
| | - Nicholas McGregor
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4 Canada
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1 Canada
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4 Canada
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1 Canada
- Department of Biochemistry, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3 Canada
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4 Canada
| | - Hélène Rogniaux
- Unité de Recherche Biopolymères, Interactions, Assemblages, INRA, 44316 Nantes, France
| | - Jean-Guy Berrin
- Polytech Marseille, UMR1163 Biodiversité et Biotechnologie Fongiques, INRA, Aix-Marseille Université, Avenue de Luminy, 13288 Marseille, France
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Inactivation of Cellobiose Dehydrogenases Modifies the Cellulose Degradation Mechanism of Podospora anserina. Appl Environ Microbiol 2016; 83:AEM.02716-16. [PMID: 27836848 DOI: 10.1128/aem.02716-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 11/04/2016] [Indexed: 12/24/2022] Open
Abstract
Conversion of biomass into high-value products, including biofuels, is of great interest to developing sustainable biorefineries. Fungi are an inexhaustible source of enzymes to degrade plant biomass. Cellobiose dehydrogenases (CDHs) play an important role in the breakdown through synergistic action with fungal lytic polysaccharide monooxygenases (LPMOs). The three CDH genes of the model fungus Podospora anserina were inactivated, resulting in single and multiple CDH mutants. We detected almost no difference in growth and fertility of the mutants on various lignocellulose sources, except on crystalline cellulose, on which a 2-fold decrease in fertility of the mutants lacking P. anserina CDH1 (PaCDH1) and PaCDH2 was observed. A striking difference between wild-type and mutant secretomes was observed. The secretome of the mutant lacking all CDHs contained five beta-glucosidases, whereas the wild type had only one. P. anserina seems to compensate for the lack of CDH with secretion of beta-glucosidases. The addition of P. anserina LPMO to either the wild-type or mutant secretome resulted in improvement of cellulose degradation in both cases, suggesting that other redox partners present in the mutant secretome provided electrons to LPMOs. Overall, the data showed that oxidative degradation of cellulosic biomass relies on different types of mechanisms in fungi. IMPORTANCE Plant biomass degradation by fungi is a complex process involving dozens of enzymes. The roles of each enzyme or enzyme class are not fully understood, and utilization of a model amenable to genetic analysis should increase the comprehension of how fungi cope with highly recalcitrant biomass. Here, we report that the cellobiose dehydrogenases of the model fungus Podospora anserina enable it to consume crystalline cellulose yet seem to play a minor role on actual substrates, such as wood shavings or miscanthus. Analysis of secreted proteins suggests that Podospora anserina compensates for the lack of cellobiose dehydrogenase by increasing beta-glucosidase expression and using an alternate electron donor for LPMO.
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Lalucque H, Malagnac F, Green K, Gautier V, Grognet P, Chan Ho Tong L, Scott B, Silar P. IDC2 and IDC3, two genes involved in cell non-autonomous signaling of fruiting body development in the model fungus Podospora anserina. Dev Biol 2016; 421:126-138. [PMID: 27979655 DOI: 10.1016/j.ydbio.2016.12.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 11/07/2016] [Accepted: 12/10/2016] [Indexed: 12/14/2022]
Abstract
Filamentous ascomycetes produce complex multicellular structures during sexual reproduction. Little is known about the genetic pathways enabling the construction of such structures. Here, with a combination of classical and reverse genetic methods, as well as genetic mosaic and graft analyses, we identify and provide evidence for key roles for two genes during the formation of perithecia, the sexual fruiting bodies, of the filamentous fungus Podospora anserina. Data indicate that the proteins coded by these two genes function cell-non-autonomously and that their activity depends upon conserved cysteines, making them good candidate for being involved in the transmission of a reactive oxygen species (ROS) signal generated by the PaNox1 NADPH oxidase inside the maturing fruiting body towards the PaMpk1 MAP kinase, which is located inside the underlying mycelium, in which nutrients are stored. These data provide important new insights to our understanding of how fungi build multicellular structures.
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Affiliation(s)
- Hervé Lalucque
- Univ. Paris Diderot, Sorbonne Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain (LIED), 75205 Paris, France
| | - Fabienne Malagnac
- Univ. Paris Diderot, Sorbonne Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain (LIED), 75205 Paris, France
| | - Kimberly Green
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Valérie Gautier
- Univ. Paris Diderot, Sorbonne Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain (LIED), 75205 Paris, France
| | - Pierre Grognet
- Univ. Paris Diderot, Sorbonne Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain (LIED), 75205 Paris, France
| | - Laetitia Chan Ho Tong
- Univ. Paris Diderot, Sorbonne Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain (LIED), 75205 Paris, France
| | - Barry Scott
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Philippe Silar
- Univ. Paris Diderot, Sorbonne Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain (LIED), 75205 Paris, France.
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