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Chen J, Cui Y, Xiao Q, Lin K, Wang B, Zhou J, Li X. Difference in microbial community structure along a gradient of crater altitude: insights from the Nushan volcano. Appl Environ Microbiol 2024; 90:e0075324. [PMID: 39028194 PMCID: PMC11337807 DOI: 10.1128/aem.00753-24] [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: 04/16/2024] [Accepted: 06/20/2024] [Indexed: 07/20/2024] Open
Abstract
The variation in the soil microbial community along the altitude gradient has been widely documented. However, the structure and function of the microbial communities distributed along the altitude gradient in the crater still need to be determined. We gathered soil specimens from different elevations within the Nushan volcano crater to bridge this knowledge gap. We investigated the microbial communities of bacteria and fungi in the soil. It is noteworthy that the microbial alpha diversity peaks in the middle of the crater. However, network analysis shows that bacterial (nodes 760 vs 613 vs 601) and fungal (nodes 328 vs 224 vs 400) communities are most stable at the bottom and top of the crater, respectively. Furthermore, the soil microbial network exhibited a decline, followed by an increase across varying altitudes. The core microorganisms displayed the highest correlation with pH and alkaline phosphatase (AP, as determined through redundancy analysis (RDA) and Mantel tests for correlation analysis. The fungal community has a higher number of core microorganisms, while the bacterial core microorganisms demonstrate greater susceptibility to environmental factors. In conclusion, we utilized Illumina sequencing techniques to assess the disparities in the structure and function of bacteria and fungi in the soil.IMPORTANCEThese findings serve as a foundation for future investigations on microbial communities present in volcanic soil.
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Affiliation(s)
- Jin Chen
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China
- Key Laboratory of Crop Stress Resistance and High-Quality Biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Ye Cui
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China
- Key Laboratory of Crop Stress Resistance and High-Quality Biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Qingchen Xiao
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China
- Key Laboratory of Crop Stress Resistance and High-Quality Biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Keqin Lin
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China
- Key Laboratory of Crop Stress Resistance and High-Quality Biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Boyan Wang
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China
- Key Laboratory of Crop Stress Resistance and High-Quality Biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Jing Zhou
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China
- Key Laboratory of Crop Stress Resistance and High-Quality Biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Xiaoyu Li
- School of Life Sciences, Anhui Agricultural University, Hefei, China
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei, China
- Key Laboratory of Crop Stress Resistance and High-Quality Biology of Anhui Province, Anhui Agricultural University, Hefei, China
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Xu ZX, Zeng B, Chen S, Xiao S, Jiang LG, Li X, Wu YF, You LX. Soil microbial community composition and nitrogen enrichment responses to the operation of electric power substation. Front Microbiol 2024; 15:1453162. [PMID: 39228385 PMCID: PMC11368844 DOI: 10.3389/fmicb.2024.1453162] [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: 06/22/2024] [Accepted: 07/30/2024] [Indexed: 09/05/2024] Open
Abstract
The surge in global energy demand mandates a significant expansion of electric power substations. Nevertheless, the ecological consequences of electric power substation operation, particularly concerning the electromagnetic field, on soil microbial communities and nitrogen enrichment remain unexplored. In this study, we collected soil samples from six distinct sites at varying distances from an electric power substation in Xintang village, southeastern China, and investigated the impacts of electromagnetic field on the microbial diversity and community structures employing metagenomic sequencing technique. Our results showed discernible dissimilarities in the fungal community across the six distinct sites, each characterized by unique magnetic and electric intensities, whereas comparable variations were not evident within bacterial communities. Correlation analysis revealed a diminished nitrogen fixation capacity at the site nearest to the substation, characterized by low moisture content, elevated pH, and robust magnetic induction intensity and electric field intensity. Conversely, heightened nitrification processes were observed at this location compared to others. These findings were substantiated by the relative abundance of key genes associated with ammonium nitrogen and nitrate nitrogen production. This study provides insights into the relationships between soil microbial communities and the enduring operation of electric power substations, thereby contributing fundamental information essential for the rigorous environmental impact assessments of these facilities.
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Affiliation(s)
- Zhi-Xin Xu
- High Voltage Branch of State Grid Fujian Electric Power Co., Ltd., Fuzhou, China
| | - Bo Zeng
- High Voltage Branch of State Grid Fujian Electric Power Co., Ltd., Fuzhou, China
| | - Sheng Chen
- High Voltage Branch of State Grid Fujian Electric Power Co., Ltd., Fuzhou, China
| | - Sa Xiao
- High Voltage Branch of State Grid Fujian Electric Power Co., Ltd., Fuzhou, China
| | - Lin-Gao Jiang
- High Voltage Branch of State Grid Fujian Electric Power Co., Ltd., Fuzhou, China
| | - Xiang Li
- High Voltage Branch of State Grid Fujian Electric Power Co., Ltd., Fuzhou, China
| | - Yun-Fang Wu
- High Voltage Branch of State Grid Fujian Electric Power Co., Ltd., Fuzhou, China
| | - Le-Xing You
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, China
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Fang M, Sun X, Yao F, Lu L, Ma X, Shao K, Kaimoyo E. A Combination of Transcriptome and Enzyme Activity Analysis Unveils Key Genes and Patterns of Corncob Lignocellulose Degradation by Auricularia heimuer under Cultivation Conditions. J Fungi (Basel) 2024; 10:545. [PMID: 39194871 DOI: 10.3390/jof10080545] [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: 06/25/2024] [Revised: 07/25/2024] [Accepted: 07/26/2024] [Indexed: 08/29/2024] Open
Abstract
The cultivation of Auricularia heimuer, a species of edible mushroom, heavily relies on the availability of wood resources serving as substrate for the growth of the species. To ensure the sustainable development of the A. heimuer industry and optimize the utilization of corncob as a substrate, this study sought to investigate the potential use of corncob as a substrate for the cultivation of A. heimuer. The purpose of this study was to explore the utilization of corncob lignocellulose by A. heimuer at the mycelium, primordium, and fruiting stages, by specifically examining the expression profiles of both carbohydrate-active enzymes (CAZymes) and the transcriptome of differentially expressed genes (DEGs) relevant to corncob biomass degradation. The results revealed 10,979, 10,630, and 11,061 DEGs at the mycelium, primordium, and fruiting stages, respectively, while 639 DGEs were identified as carbohydrate-active enzymes. Of particular interest were 46 differentially expressed CAZymes genes that were associated directly with lignocellulose degradation. Furthermore, the study found that A. heimuer exhibited adaptive changes that enabled it to effectively utilize the cellulose present in the corncob. These changes were observed primarily at the primordium and fruiting stages. Key genes involved in lignocellulose degradation were also identified, including g6952, g8349, g12487, and g2976 at the mycelium stage, g5775, g2857, g3018, and g11016 at the primordium stage, and g10290, g2857, g12385, g7656, and g8953 at the fruiting stage. This study found that lytic polysaccharide monooxygenase (LPMO) played a crucial role in the degradation of corncob cellulose, further highlighting the complexity of the molecular mechanisms involved in the degradation of lignocellulose biomass by A. heimuer. The study sheds light on the molecular mechanisms underlying the ability of A. heimuer to degrade corncob biomass, with implications for the efficient utilization of lignocellulose resources. The findings from this study may facilitate the development of innovative biotechnologies for the transformation of corncob biomass into useful products.
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Affiliation(s)
- Ming Fang
- Lab of the Genetic Breeding of Edible Mushroom, College of Horticulture, Jilin Agricultural University, Changchun 130118, China
| | - Xu Sun
- Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Fangjie Yao
- Lab of the Genetic Breeding of Edible Mushroom, College of Horticulture, Jilin Agricultural University, Changchun 130118, China
- Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Lixin Lu
- Lab of the Genetic Breeding of Edible Mushroom, College of Horticulture, Jilin Agricultural University, Changchun 130118, China
| | - Xiaoxu Ma
- Lab of the Genetic Breeding of Edible Mushroom, College of Horticulture, Jilin Agricultural University, Changchun 130118, China
| | - Kaisheng Shao
- Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Evans Kaimoyo
- Great East Road Campus, University of Zambia, Lusaka 32379, Zambia
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Zheng J, Shi J, Wang D. Diversity of soil fungi and entomopathogenic fungi in subtropical mountain forest in southwest China. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13267. [PMID: 38943366 PMCID: PMC11213981 DOI: 10.1111/1758-2229.13267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 04/06/2024] [Indexed: 07/01/2024]
Abstract
Till now, the diversity of entomopathogenic fungi in subtropical mountain forest was less studied. Here, the vertical distribution of forest soil fungi, entomopathogenic fungi, and their environmental influencing factors in a subtropical mountain in western China were investigated. Soil samples were collected from four elevations in a subtropical forest in Shaanxi. The results indicated a greater richness of soil fungi at middle elevations and soil fungi were more even at low elevation. Soil pH, available iron, available potassium, total potassium, and available zinc were the most important influencing factors affecting this vertical distribution of fungi. Interestingly, the Isaria genus was predominant while Metarhizium and Beauveria showed decreasing abundance. The presence of Isaria showed a significant positive correlation with both total phosphorus and available iron, while, available zinc was negatively correlated. Metarhizium was influenced by elevation, pH, available phosphorus, and available copper and Beauveria was influenced by soil organic carbon, total nitrogen, total potassium, available potassium, and available zinc. Overall, as environmental factors affecting soil fungi, elevation, and plant species diversity were less important than soil physical and chemical properties. The virulence of isolated entomopathogenic fungi were tested against larvae of Tenebrio molitor, with mortality ranging from 31.11% to 100%. The above findings provide valuable data to deepen our understanding of the diversity of entomopathogenic fungi in subtropical mountain forests.
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Affiliation(s)
- Jiyang Zheng
- Key Laboratory of Crop Stress Biology for Arid AreasNorthwest A&F UniversityYanglingShaanxiChina
| | - Jinduo Shi
- Forest Bureau of Ankang CityAnkangShaanxiChina
| | - Dun Wang
- Key Laboratory of Crop Stress Biology for Arid AreasNorthwest A&F UniversityYanglingShaanxiChina
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Samim AR, Singh VK, Singh MP, Vaseem H. An ecofriendly approach to bioremediate nickel oxide nanoparticles using a macrofungus, Pleurotus fossulatus. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:45776-45792. [PMID: 38977547 DOI: 10.1007/s11356-024-34210-z] [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: 01/19/2024] [Accepted: 06/29/2024] [Indexed: 07/10/2024]
Abstract
Nowadays, nickel oxide nanoparticles are in great demands owing to their use in many sectors. These nanoparticles may release into aquatic environment from different industries and cause negative effect on aquatic flora and fauna. Therefore, an effective and efficient method is required to remove these nanoparticles from contaminated water. Hence, the aim of this study was to bioremediate nickel oxide nanoparticles using a macrofungus, Pleurotus fossulatus, and to analyze its impact on fungal physiology. For this purpose, fungal spawns were inoculated in malt dextrose agar media containing different concentrations of nickel oxide nanoparticles (24 mg/l, 48 mg/l, and 100 mg/l) as well as control group (having no nickel oxide nanoparticles) and allowed to grow for a period of 20 days. Fungal mycelia as well as media were collected at different time intervals (5th day, 10th day, 15th day, and 20th day) for evaluation of Ni concentration and different biochemical parameters. Ni removal efficiency of P. fossulatus from media was found to be highest in 48 mg/l (66.98%) followed by 24 mg/l (60.83%) and 100 mg/l (18.03%), respectively. Increased level of metallothionein, lipid peroxidation, activity of different antioxidant enzymes (superoxide dismutase, catalase, glutathione s transferase, glutathione reductase), activity of ligninolytic enzymes (laccase, lignin peroxidase, manganese peroxidase), and shift in FTIR spectra were also reported in mycelia cultured in malt dextrose agar media containing nickel oxide nanoparticles. This study suggests that P. fossulatus has great efficiency to remediate nanoparticles from contaminated water and it can be utilized as potential agent in wastewater treatment plants by different industries.
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Affiliation(s)
- Abdur Rouf Samim
- Department of Zoology, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, India
| | - Vinay Kumar Singh
- Department of Zoology, CMP Degree College, University of Allahabad, Prayagraj, 211002, India
| | - Mohan Prasad Singh
- Centre of Biotechnology, University of Allahabad, Prayagraj, 211002, India
| | - Huma Vaseem
- Department of Zoology, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, India.
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Loffredo E, Carnimeo C, De Chirico N, Traversa A, Cocozza C. The liquid by-product of biogas production: characterisation and impact on soil fungi. ENVIRONMENTAL TECHNOLOGY 2024; 45:3570-3585. [PMID: 37254968 DOI: 10.1080/09593330.2023.2220888] [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: 02/12/2023] [Accepted: 05/25/2023] [Indexed: 06/01/2023]
Abstract
ABSTRACTA liquid digestate (LD) obtained from the anaerobic digestion of mixed organic waste was characterised and tested on the fungi Pleurotus eryngii, Irpex lacteus and Trametes versicolor. Aqueous mixtures of LD at doses of 0.5, 1 and 2% (v/v) were tested directly or after interaction with 5% (w/v) biochar (BC-LD) and/or 100 mg L-1 soil humic acid (HA-BC-LD and HA-LD). Total luminescence (TL) analysis of LD showed the presence of fluorophores typical of scarcely aromatic matter, while the Fourier transform infrared (FTIR) spectrum evidenced absorption bands typical of labile and non-condensed material. Some spectroscopic variations of the LD sample were observed after its interaction with the other materials. All LD treatments markedly promoted hyphal extension of P. eryngii whose growth rate increased up to 38% at the highest LD dose. The LD alone had no influence on the other fungi, whose growth was stimulated by some combinations of LD with the other materials. In facts, the growth rate of I. lacteus increased in BC-LD 1 and BC-LD 2 (P ≤ 0.05) and in all treatments with HA (up to 6% in HA-LD 2, P ≤ 0.01), while the growth of T. versicolor was promoted by HA-BC-LD 2 treatment (P ≤ 0.05) and slightly inhibited by all BC-LD combinations (up to 7% by BC-LD 1, P ≤ 0.05). The overall results obtained encourage the addition of LD to the soil and suggest a possible use of this material as substrate ingredient for the cultivation of edible mushrooms such as P. eryngii.
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Affiliation(s)
- Elisabetta Loffredo
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Claudia Carnimeo
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Nicoletta De Chirico
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Andreina Traversa
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Claudio Cocozza
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Bari, Italy
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Flores-Almaraz VS, Truong C, Hernández-Oaxaca D, Reyes-Galindo V, Mastretta-Yanes A, Jaramillo-Correa JP, Salas-Lizana R. Foliar mycobiome remains unaltered under urban air-pollution but differentially express stress-related genes. MICROBIAL ECOLOGY 2024; 87:72. [PMID: 38755460 PMCID: PMC11098924 DOI: 10.1007/s00248-024-02387-y] [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: 12/15/2023] [Accepted: 04/29/2024] [Indexed: 05/18/2024]
Abstract
Air pollution caused by tropospheric ozone contributes to the decline of forest ecosystems; for instance, sacred fir, Abies religiosa (Kunth) Schltdl. & Cham. forests in the peri-urban region of Mexico City. Individual trees within these forests exhibit variation in their response to ozone exposure, including the severity of visible symptoms in needles. Using RNA-Seq metatranscriptomic data and ITS2 metabarcoding, we investigated whether symptom variation correlates with the taxonomic and functional composition of fungal mycobiomes from needles collected in this highly polluted area in the surroundings of Mexico City. Our findings indicate that ozone-related symptoms do not significantly correlate with changes in the taxonomic composition of fungal mycobiomes. However, genes coding for 30 putative proteins were differentially expressed in the mycobiome of asymptomatic needles, including eight genes previously associated with resistance to oxidative stress. These results suggest that fungal communities likely play a role in mitigating the oxidative burst caused by tropospheric ozone in sacred fir. Our study illustrates the feasibility of using RNA-Seq data, accessible from global sequence repositories, for the characterization of fungal communities associated with plant tissues, including their gene expression.
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Affiliation(s)
- Valeria Stephany Flores-Almaraz
- Posgrado en Ciencias Biológicas, Unidad de Posgrado, Edificio A, 1° Piso, Circuito de Posgrados, Ciudad Universitaria, Coyoacán, C.P. 04510, Distrito Federal, México
- Instituto de Biología, Universidad Nacional Autónoma de México, Av. Universidad 3000, 04510, Coyoacán, Ciudad de México, Mexico
| | - Camille Truong
- Royal Botanic Gardens Victoria, Birdwood Ave, Melbourne, VIC 3004, Australia.
| | - Diana Hernández-Oaxaca
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad S/N, 62210, Cuernavaca, Morelos, México
| | - Verónica Reyes-Galindo
- Depto. de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Av. Universidad 3000, 04510, Coyoacán, Ciudad de México, Mexico
| | - Alicia Mastretta-Yanes
- Consejo Nacional de Humanidades Ciencias y Tecnología (CONAHCYT), Avenida Insurgentes Sur 1582, Crédito Constructor, Benito Juárez, Ciudad de México, 03940, México.
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Av. Universidad 3000, 04510, Coyoacán, Ciudad de México, Mexico.
| | - Juan Pablo Jaramillo-Correa
- Depto. de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Av. Universidad 3000, 04510, Coyoacán, Ciudad de México, Mexico
| | - Rodolfo Salas-Lizana
- Laboratorios de Micología. Depto. de Biología Comparada, Facultad de Ciencias., Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, 04510, Ciudad de México, México.
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Kapich AN, Suzuki H, Hirth KC, Fernández-Fueyo E, Martínez AT, Houtman CJ, Hammel KE. The white rot basidiomycete Gelatoporia subvermispora produces fatty aldehydes that enable fungal manganese peroxidases to degrade recalcitrant lignin structures. Appl Environ Microbiol 2024; 90:e0204423. [PMID: 38483171 PMCID: PMC11022559 DOI: 10.1128/aem.02044-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/26/2024] [Indexed: 04/18/2024] Open
Abstract
The ability of some white rot basidiomycetes to remove lignin selectively from wood indicates that low molecular weight oxidants have a role in ligninolysis. These oxidants are likely free radicals generated by fungal peroxidases from compounds in the biodegrading wood. Past work supports a role for manganese peroxidases (MnPs) in the production of ligninolytic oxidants from fungal membrane lipids. However, the fatty acid alkylperoxyl radicals initially formed during this process are not reactive enough to attack the major structures in lignin. Here, we evaluate the hypothesis that the peroxidation of fatty aldehydes might provide a source of more reactive acylperoxyl radicals. We found that Gelatoporia subvermispora produced trans-2-nonenal, trans-2-octenal, and n-hexanal (a likely metabolite of trans-2,4-decadienal) during the incipient decay of aspen wood. Fungal fatty aldehydes supported the in vitro oxidation by MnPs of a nonphenolic lignin model dimer, and also of the monomeric model veratryl alcohol. Experiments with the latter compound showed that the reactions were partially inhibited by oxalate, the chelator that white rot fungi employ to detach Mn3+ from the MnP active site, but nevertheless proceeded at its physiological concentration of 1 mM. The addition of catalase was inhibitory, which suggests that the standard MnP catalytic cycle is involved in the oxidation of aldehydes. MnP oxidized trans-2-nonenal quantitatively to trans-2-nonenoic acid with the consumption of one O2 equivalent. The data suggest that when Mn3+ remains associated with MnP, it can oxidize aldehydes to their acyl radicals, and the latter subsequently add O2 to become ligninolytic acylperoxyl radicals.IMPORTANCEThe biodegradation of lignin by white rot fungi is essential for the natural recycling of plant biomass and has useful applications in lignocellulose bioprocessing. Although fungal peroxidases have a key role in ligninolysis, past work indicates that biodegradation is initiated by smaller, as yet unidentified oxidants that can infiltrate the substrate. Here, we present evidence that the peroxidase-catalyzed oxidation of naturally occurring fungal aldehydes may provide a source of ligninolytic free radical oxidants.
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Affiliation(s)
| | - Hideki Suzuki
- US Forest Products Laboratory, Madison, Wisconsin, USA
| | | | - Elena Fernández-Fueyo
- Centro de Investigaciones Biológicas "Margarita Salas", Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Angel T. Martínez
- Centro de Investigaciones Biológicas "Margarita Salas", Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | | | - Kenneth E. Hammel
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, USA
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Vélez-Martínez GA, Reyes-Ardila WL, Duque-Zapata JD, Rugeles-Silva PA, Muñoz Flórez JE, López-Álvarez D. Soil bacteria and fungi communities are shaped by elevation influences in Colombian forest and páramo natural ecosystems. Int Microbiol 2024; 27:377-391. [PMID: 37458953 PMCID: PMC10991037 DOI: 10.1007/s10123-023-00392-8] [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: 04/27/2023] [Revised: 06/08/2023] [Accepted: 06/15/2023] [Indexed: 04/05/2024]
Abstract
The influence of elevation on natural terrestrial ecosystems determines the arrangements of microbial communities in soils to be associated with biotic and abiotic factors. To evaluate changes of fungi and bacteria at the community level along an elevational gradient (between 1000 and 3800 m.a.s.l.), physicochemical measurements of soils, taxonomic identifications of plants, and metabarcoding sequences of the 16S rRNA gene for bacteria and the ITS1 region for fungi were obtained. The bacterial taxonomic composition showed that Acidobacteriota increased in abundance with elevation, while Actinobacteriota and Verrucomicrobiota decreased. Furthermore, Firmicutes and Proteobacteria maintained maximum levels of abundance at intermediate elevations (1200 and 2400 m.a.s.l.). In fungi, Ascomycota was more abundant at higher elevations, Basidiomycota tended to dominate at lower elevations, and Mortierellomycota had a greater presence at intermediate sites. These results correlated with the edaphic parameters of decreasing pH and increasing organic carbon and available nitrogen with elevation. In addition, the Shannon index found a greater diversity in bacteria than fungi, but both showed a unimodal pattern with maximum values in the Andean Forest at 2400 m.a.s.l. Through the microbial characterization of the ecosystems, the elevational gradient, soil properties, and vegetation were found to exert significant effects on microbial communities and alpha diversity indices. We conclude that the most abundant soil microorganisms at the sampling points differed in abundance and diversity according to the variations in factors influencing ecological communities.
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Affiliation(s)
- Glever Alexander Vélez-Martínez
- Grupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia-Sede Palmira, Carrera, 32 No. 12-00, 763536, Palmira, Valle del Cauca, Colombia.
| | - Wendy Lorena Reyes-Ardila
- Grupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia-Sede Palmira, Carrera, 32 No. 12-00, 763536, Palmira, Valle del Cauca, Colombia
| | - Juan Diego Duque-Zapata
- Grupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia-Sede Palmira, Carrera, 32 No. 12-00, 763536, Palmira, Valle del Cauca, Colombia
| | - Paula Andrea Rugeles-Silva
- Grupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia-Sede Palmira, Carrera, 32 No. 12-00, 763536, Palmira, Valle del Cauca, Colombia
| | - Jaime Eduardo Muñoz Flórez
- Grupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia-Sede Palmira, Carrera, 32 No. 12-00, 763536, Palmira, Valle del Cauca, Colombia
| | - Diana López-Álvarez
- Grupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia-Sede Palmira, Carrera, 32 No. 12-00, 763536, Palmira, Valle del Cauca, Colombia.
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Cen Q, Fan J, Zhang R, Chen H, Hui F, Li J, Zeng X, Qin L. Impact of Ganoderma lucidum fermentation on the nutritional composition, structural characterization, metabolites, and antioxidant activity of Soybean, sweet potato and Zanthoxylum pericarpium residues. Food Chem X 2024; 21:101078. [PMID: 38205161 PMCID: PMC10776642 DOI: 10.1016/j.fochx.2023.101078] [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: 08/27/2023] [Revised: 12/04/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024] Open
Abstract
One of the major issues in the food sector is the lack of resource utilization and the contamination of the environment caused by by-products. This study aimed to investigate the effects of Ganoderma lucidum (GL) fermentation on the nutritional components, structural characterization, metabolites, and antioxidant activity of soybean residue (SR), sweet potato residue (SPR), and zanthoxylum pericarpium residue (ZPR). The results showed that the nutrient contents of SR, SPR and ZPR increased. The active substances, amino acids (umami, aromatic and basic), metabolites and antioxidant activity (DPPH, ABTS, FRAP) (SR and SPR increased by 11.43, 32.64, 40.19 μmol Trolox/100 g and 19.29, 17.7, 32.35 μmol Trolox/100 g, respectively) of SR and SPR were increased. However, the results of ZPR showed a decrease in the content of bioactive substances, amino acids, and antioxidant activity. The results show that using GL fermentation can provide novel ideas and theoretical basis for improving SR and SPR to obtain new raw materials for antioxidant products.
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Affiliation(s)
- Qin Cen
- School of Liquor and Food Engineering, Guizhou University, Guiyang 550000, China
- Guizhou Provincial Key Laboratory of Agricultural and Animal Products Storage and Processing, Guiyang 550000, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guiyang 550000, China
| | - Jin Fan
- School of Liquor and Food Engineering, Guizhou University, Guiyang 550000, China
- Guizhou Provincial Key Laboratory of Agricultural and Animal Products Storage and Processing, Guiyang 550000, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guiyang 550000, China
| | - Rui Zhang
- School of Liquor and Food Engineering, Guizhou University, Guiyang 550000, China
- Guizhou Provincial Key Laboratory of Agricultural and Animal Products Storage and Processing, Guiyang 550000, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guiyang 550000, China
| | - Hongyan Chen
- School of Liquor and Food Engineering, Guizhou University, Guiyang 550000, China
- Guizhou Provincial Key Laboratory of Agricultural and Animal Products Storage and Processing, Guiyang 550000, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guiyang 550000, China
| | - Fuyi Hui
- School of Liquor and Food Engineering, Guizhou University, Guiyang 550000, China
- Guizhou Provincial Key Laboratory of Agricultural and Animal Products Storage and Processing, Guiyang 550000, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guiyang 550000, China
| | - Jiamin Li
- School of Liquor and Food Engineering, Guizhou University, Guiyang 550000, China
- Guizhou Provincial Key Laboratory of Agricultural and Animal Products Storage and Processing, Guiyang 550000, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guiyang 550000, China
| | - Xuefeng Zeng
- School of Liquor and Food Engineering, Guizhou University, Guiyang 550000, China
- Guizhou Provincial Key Laboratory of Agricultural and Animal Products Storage and Processing, Guiyang 550000, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guiyang 550000, China
| | - Likang Qin
- School of Liquor and Food Engineering, Guizhou University, Guiyang 550000, China
- Guizhou Provincial Key Laboratory of Agricultural and Animal Products Storage and Processing, Guiyang 550000, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guiyang 550000, China
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11
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Zhao S, Deng D, Wan T, Feng J, Deng L, Tian Q, Wang J, Aiman UE, Mukhaddi B, Hu X, Chen S, Qiu L, Huang L, Wei Y. Lignin bioconversion based on genome mining for ligninolytic genes in Erwinia billingiae QL-Z3. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:25. [PMID: 38360683 PMCID: PMC10870720 DOI: 10.1186/s13068-024-02470-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/02/2024] [Indexed: 02/17/2024]
Abstract
BACKGROUND Bioconversion of plant biomass into biofuels and bio-products produces large amounts of lignin. The aromatic biopolymers need to be degraded before being converted into value-added bio-products. Microbes can be environment-friendly and efficiently degrade lignin. Compared to fungi, bacteria have some advantages in lignin degradation, including broad tolerance to pH, temperature, and oxygen and the toolkit for genetic manipulation. RESULTS Our previous study isolated a novel ligninolytic bacterial strain Erwinia billingiae QL-Z3. Under optimized conditions, its rate of lignin degradation was 25.24% at 1.5 g/L lignin as the sole carbon source. Whole genome sequencing revealed 4556 genes in the genome of QL-Z3. Among 4428 protein-coding genes are 139 CAZyme genes, including 54 glycoside hydrolase (GH) and 16 auxiliary activity (AA) genes. In addition, 74 genes encoding extracellular enzymes are potentially involved in lignin degradation. Real-time PCR quantification demonstrated that the expression of potential ligninolytic genes were significantly induced by lignin. 8 knock-out mutants and complementary strains were constructed. Disruption of the gene for ELAC_205 (laccase) as well as EDYP_48 (Dyp-type peroxidase), ESOD_1236 (superoxide dismutase), EDIO_858 (dioxygenase), EMON_3330 (monooxygenase), or EMCAT_3587 (manganese catalase) significantly reduced the lignin-degrading activity of QL-Z3 by 47-69%. Heterologously expressed and purified enzymes further confirmed their role in lignin degradation. Fourier transform infrared spectroscopy (FTIR) results indicated that the lignin structure was damaged, the benzene ring structure and groups of macromolecules were opened, and the chemical bond was broken under the action of six enzymes encoded by genes. The abundant enzymatic metabolic products by EDYP_48, ELAC_205 and ESOD_1236 were systematically analyzed via liquid chromatography-mass spectrometry (LC-MS) analysis, and then provide a speculative pathway for lignin biodegradation. Finally, The activities of ligninolytic enzymes from fermentation supernatant, namely, LiP, MnP and Lac were 367.50 U/L, 839.50 U/L, and 219.00 U/L by orthogonal optimization. CONCLUSIONS Our findings provide that QL-Z3 and its enzymes have the potential for industrial application and hold great promise for the bioconversion of lignin into bioproducts in lignin valorization.
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Affiliation(s)
- Shuting Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Dongtao Deng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Tianzheng Wan
- Vrije University Amsterdam, De Boelelaan 1105, 1081 HV, Amsterdam, Netherlands
| | - Jie Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Lei Deng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Qianyi Tian
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Jiayu Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Umm E Aiman
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Balym Mukhaddi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Xiaofeng Hu
- Shanghai Personal Biotechnology Co., Ltd, Shanghai, 20030, People's Republic of China
| | - Shaolin Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Ling Qiu
- College of Mechanical and Electronic Engineering, The West Scientific Observing and Experimental Station of Rural Renewable Energy Exploitation and Utilization of the Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
| | - Yahong Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
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12
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Gacura MD, Zak DR, Blackwood CB. From individual leaves to forest stands: importance of niche, distance decay, and stochasticity vary by ecosystem type and functional group for fungal community composition. FEMS Microbiol Ecol 2024; 100:fiae016. [PMID: 38373845 PMCID: PMC10913062 DOI: 10.1093/femsec/fiae016] [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: 09/01/2023] [Revised: 01/26/2024] [Accepted: 02/16/2024] [Indexed: 02/21/2024] Open
Abstract
Community assembly is influenced by environmental niche processes as well as stochastic processes that can be spatially dependent (e.g. dispersal limitation) or independent (e.g. priority effects). Here, we sampled senesced tree leaves as unit habitats to investigate fungal community assembly at two spatial scales: (i) small neighborhoods of overlapping leaves from differing tree species and (ii) forest stands of differing ecosystem types. Among forest stands, ecosystem type explained the most variation in community composition. Among adjacent leaves within stands, variability in fungal composition was surprisingly high. Leaf type was more important in stands with high soil fertility and dominated by differing tree mycorrhizal types (sugar maple vs. basswood or red oak), whereas distance decay was more important in oak-dominated forest stands with low soil fertility. Abundance of functional groups was explained by environmental factors, but predictors of taxonomic composition within differing functional groups were highly variable. These results suggest that fungal community assembly processes are clearest for functional group abundances and large spatial scales. Understanding fungal community assembly at smaller spatial scales will benefit from further study focusing on differences in drivers for different ecosystems and functional groups, as well as the importance of spatially independent factors such as priority effects.
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Affiliation(s)
- Matthew D Gacura
- Department of Biological Sciences, Kent State University, 800 E. Summit St., Kent, OH 44242, United States
- Biology Department, Gannon University, 109 University Square, Erie, PA 16541, United States
| | - Donald R Zak
- School for Environment and Sustainability, University of Michigan, 440 Church St., Ann Arbor, MI 48109, United States
| | - Christopher B Blackwood
- Department of Biological Sciences, Kent State University, 800 E. Summit St., Kent, OH 44242, United States
- Department of Plant, Soil, and Microbial Sciences and Department of Plant Biology, Michigan State University, 1066 Bogue St., East Lansing, MI 48842, United States
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13
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Leonardo-Silva L, Xavier-Santos S. Corticioid and poroid fungi from Brazilian Cerrado: a history of research and a checklist of species. AN ACAD BRAS CIENC 2023; 95:e20220165. [PMID: 38126430 DOI: 10.1590/0001-3765202320220165] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 11/22/2022] [Indexed: 12/23/2023] Open
Abstract
Corticioid and poroid fungi are widely known for wood decomposition which confers an important ecological role and biotechnological properties upon these species. Although being one of the most studied groups of fungi worldwide, data on diversity and geographic occurrence patterns in Brazil are insufficient, especially in poorly studied areas, including the Cerrado biome. Here we present an overview of the scientific literature concerning the corticioid and poroid fungi from Cerrado, along with a list of species found in the biome so far. The historic research at Cerrado comprised 47 articles published between 1876 and 2021, of which 55% were published in the last decade. We found 387 records and 223 species, while 94 species are new additions to the checklists published in the last decade. Six of the listed species are endemic to Cerrado. Furthermore, 29 species are only known from Cerrado in Brazil, although they occur in other regions of the world. The main research groups focused on these fungi in Brazil have already published at least one article with samples from Cerrado. Therefore, intensifying studies throughout Cerrado could help in a better understanding of its Funga, its evolutionary relationship, and its threatens status.
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Affiliation(s)
- Lucas Leonardo-Silva
- Universidade Estadual de Goiás, Laboratório de Micologia Básica, Aplicada e Divulgação Científica (FungiLab), Campus Anápolis de Ciências Exatas e Tecnológicas, Br 153, Km 99, Zona Rural, 75132-903 Anápolis, GO, Brazil
| | - Solange Xavier-Santos
- Universidade Estadual de Goiás, Laboratório de Micologia Básica, Aplicada e Divulgação Científica (FungiLab), Campus Anápolis de Ciências Exatas e Tecnológicas, Br 153, Km 99, Zona Rural, 75132-903 Anápolis, GO, Brazil
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14
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Sawada Y, Sato T, Fukushi R, Kohari Y, Takahashi Y, Tomii S, Yang L, Yamagishi T, Arai H. Fermentation of soybeans with Pleurotus cornucopiae and Pleurotus ostreatus increases isoflavone aglycones, total polyphenol content and antioxidant activity. MYCOSCIENCE 2023; 64:156-165. [PMID: 39229281 PMCID: PMC11367249 DOI: 10.47371/mycosci.2023.09.004] [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: 06/06/2023] [Revised: 09/30/2023] [Accepted: 09/30/2023] [Indexed: 09/05/2024]
Abstract
Edible basidiomycetes are highly active in the oxidative decomposition and polymerisation of polyphenols, and soybeans contain large amounts of isoflavones, which are polyphenol glycosides. Isoflavone aglycones exhibit weak estrogenic activities. In this study, we investigated the isoflavone content, polyphenol production, antioxidant activity and ergothioneine (EGT) content of soybeans fermented by Pleurotus cornucopiae and Pleurotus ostreatus. Isoflavone glycosides, which were abundant in unfermented soybeans, decreased, and aglycones increased on day 10 of culture in both edible basidiomycete-fermented soybeans. The total maximum polyphenol content in soybeans fermented by both mushrooms were approximately 4 times higher on day 30 to 40 of culture, than that of unfermented soybeans. P. cornucopiae-fermented soybeans showed maximum antioxidant activity on day 20 of culture, and this was approximately 6.1 times higher than that of unfermented soybeans. EGT was not detected in unfermented soybeans, whereas both fermented soybeans showed a maximum EGT content on day 20 of culture, which was especially high in P. cornucopiae-fermented soybeans. The antioxidant activity and EGT of P. cornucopiae-fermented soybeans were higher than those of P. ostreatus, suggesting that EGT was responsible for the increase in the antioxidant activity of P. cornucopiae-fermented soybeans.
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Affiliation(s)
- Yuta Sawada
- National University Corporation Hokkaido Higher Education and Research System, Kitami Institute of Technology
| | - Toshitsugu Sato
- National University Corporation Hokkaido Higher Education and Research System, Kitami Institute of Technology
| | - Ryosuke Fukushi
- National University Corporation Hokkaido Higher Education and Research System, Kitami Institute of Technology
| | - Yoshihito Kohari
- National University Corporation Hokkaido Higher Education and Research System, Kitami Institute of Technology
| | - Yuuki Takahashi
- National University Corporation Hokkaido Higher Education and Research System, Kitami Institute of Technology
| | - Sayaka Tomii
- National University Corporation Hokkaido Higher Education and Research System, Kitami Institute of Technology
| | - Lifeng Yang
- National University Corporation Hokkaido Higher Education and Research System, Kitami Institute of Technology
| | - Takashi Yamagishi
- National University Corporation Hokkaido Higher Education and Research System, Kitami Institute of Technology
| | - Hirofumi Arai
- National University Corporation Hokkaido Higher Education and Research System, Kitami Institute of Technology
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15
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Saha S, Huang L, Khoso MA, Wu H, Han D, Ma X, Poudel TR, Li B, Zhu M, Lan Q, Sakib N, Wei R, Islam MZ, Zhang P, Shen H. Fine root decomposition in forest ecosystems: an ecological perspective. FRONTIERS IN PLANT SCIENCE 2023; 14:1277510. [PMID: 38023858 PMCID: PMC10643187 DOI: 10.3389/fpls.2023.1277510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023]
Abstract
Fine root decomposition is a physio-biochemical activity that is critical to the global carbon cycle (C) in forest ecosystems. It is crucial to investigate the mechanisms and factors that control fine root decomposition in forest ecosystems to understand their system-level carbon balance. This process can be influenced by several abiotic (e.g., mean annual temperature, mean annual precipitation, site elevation, stand age, salinity, soil pH) and biotic (e.g., microorganism, substrate quality) variables. Comparing decomposition rates within sites reveals positive impacts of nitrogen and phosphorus concentrations and negative effects of lignin concentration. Nevertheless, estimating the actual fine root breakdown is difficult due to inadequate methods, anthropogenic activities, and the impact of climate change. Herein, we propose that how fine root substrate and soil physiochemical characteristics interact with soil microorganisms to influence fine root decomposition. This review summarized the elements that influence this process, as well as the research methods used to investigate it. There is also need to study the influence of annual and seasonal changes affecting fine root decomposition. This cumulative evidence will provide information on temporal and spatial dynamics of forest ecosystems, and will determine how logging and reforestation affect fine root decomposition.
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Affiliation(s)
- Sudipta Saha
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Lei Huang
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Muneer Ahmed Khoso
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Department of Life Science, Northeast Forestry University, Harbin, China
| | - Haibo Wu
- College of Forestry, Northeast Forestry University, Harbin, China
- Key Laboratory of Sustainable Forest Ecosystem Management, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Donghui Han
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Xiao Ma
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Tika Ram Poudel
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Bei Li
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Meiru Zhu
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Qiurui Lan
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Nazmus Sakib
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Ruxiao Wei
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Md. Zahirul Islam
- Key Laboratory of Sustainable Forest Ecosystem Management, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Peng Zhang
- College of Forestry, Northeast Forestry University, Harbin, China
- Key Laboratory of Sustainable Forest Ecosystem Management, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Hailong Shen
- College of Forestry, Northeast Forestry University, Harbin, China
- State Forestry and Grassland Administration Engineering Technology Research Center of Korean Pine, Harbin, China
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16
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Zhang J, Liu Q, Wang D, Zhang Z. Soil Microbial Community, Soil Quality, and Productivity along a Chronosequence of Larix principis-rupprechtii Forests. PLANTS (BASEL, SWITZERLAND) 2023; 12:2913. [PMID: 37631125 PMCID: PMC10458017 DOI: 10.3390/plants12162913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/27/2023] [Accepted: 08/06/2023] [Indexed: 08/27/2023]
Abstract
Elucidating the correlation between soil microbial communities and forest productivity is the focus of research in the field of forest ecology. Nonetheless, the relationship between stand age, soil quality, soil microorganisms, and their combined influence on productivity is still unclear. In this study, five development stages (14, 25, 31, 39, and >80 years) of larch (Larix principis-rupprechtii) forests were investigated in Inner Mongolia and Shanxi provinces of China. We evaluated soil quality using the Integrated Soil Quality Index (SQI) and analyzed changes in bacterial and fungal communities using high-throughput sequencing. Regression models were also established to examine the impacts of stand age, microbial diversity, and SQI on productivity. The findings revealed an ascending trend in soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), available potassium (AK), and SQI in 14, 25, 31, and 39-year-old stands. The abundance of oligotrophic bacteria Acidobacteria exhibited a gradual decline with increasing forest age, whereas copiotroph bacteria Proteobacteria displayed a progressive increase. Stands older than 80 years exhibited a higher abundance of both the saprophytic fungus Ascomycota and mycorrhizal fungus Basidiomycota. Forest age had a significant impact on microbial diversity, particularly in terms of bacterial diversity, impacting both α and β diversity. The soil bacterial community structure was influenced by AK, SOM, TN, TP, and pH. Conversely, the fungal community structure was regulated by crucial factors including SOM, TN, TP, TK, AK, and pH. Fungal diversity demonstrated a significant and positive correlation with the basal area increment (BAI) of larch. Furthermore, microbial diversity accounted for 23.6% of the variation in BAI. In summary, the findings implied a robust association between microbial composition, diversity, and soil chemical properties throughout the chronosequence of larch forests. These factors collectively played a crucial role in influencing the productivity of larch forest.
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Affiliation(s)
| | | | | | - Zhidong Zhang
- College of Forestry, Hebei Agricultural University, Baoding 071001, China; (J.Z.); (Q.L.); (D.W.)
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17
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Laothanachareon T, Kongtong K, Saeng-Kla K, Kanokratana P, Leetanasaksakul K, Champreda V. Evaluating the efficacy of wood decay fungi and synthetic fungal consortia for simultaneous decolorization of multiple textile dyes. World J Microbiol Biotechnol 2023; 39:226. [PMID: 37316623 DOI: 10.1007/s11274-023-03672-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/03/2023] [Indexed: 06/16/2023]
Abstract
Wastewater from the textile industry dyeing process containing high loads of synthetic dyes leads to pollution of water with these toxic and genotoxic dyes. Much effort has been put towards developing biological systems to resolve this issue. Mycoremediation is a well-known approach using fungi to remove, degrade, or remediate pollutants and can be applied to decolorize textile dyes in industrial effluent. Fungal strains from four genera of Polyporales, namely Coriolopsis sp. TBRC 2756, Fomitopsis pinicola TBRC-BCC 30881, Rigidoporus vinctus TBRC 6770, and Trametes pocas TBRC-BCC 18705, were studied for decolorization efficiency, and R. vinctus was found to exhibit the greatest activity in removing all seven tested reactive dyes and one acid dye with a decolorization efficiency of 80% or more within 7 days under limited oxygen. This fungus simultaneously degraded multiple dyes in synthetic wastewater as well as industrial effluent from the dyeing process. To enhance the decolorization rate, various fungal consortia were formulated for testing. However, these consortia only trivially improved efficiency compared with using R. vinctus TBRC 6770 alone. Evaluation of R. vinctus TBRC 6770 decolorization ability was further performed in a 15-L bioreactor to test its ability to eliminate multiple dyes from industrial effluent. The fungus took 45 days to adapt to growth in the bioreactor and subsequently reduced dye concentration to less than 10% of the initial concentration. The following six cycles required only 4-7 days to reduce dye concentrations to less than 25%, demonstrating that the system can run efficiently for multiple cycles without the need for extra medium or other carbon sources.
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Affiliation(s)
- Thanaporn Laothanachareon
- Enzyme Technology Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Khlong Luang, Pathumthani, 12120, Thailand.
| | - Kittima Kongtong
- Food Biotechnology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Khlong Luang, Pathumthani, 12120, Thailand
| | - Kanphorn Saeng-Kla
- Enzyme Technology Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Khlong Luang, Pathumthani, 12120, Thailand
| | - Pattanop Kanokratana
- Enzyme Technology Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Khlong Luang, Pathumthani, 12120, Thailand
| | - Kantinan Leetanasaksakul
- Functional Proteomics Technology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Khlong Luang, Pathumthani, 12120, Thailand
| | - Verawat Champreda
- Enzyme Technology Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Khlong Luang, Pathumthani, 12120, Thailand
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18
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Kang Y, Wu H, Zhang Y, Wu Q, Guan Q, Lu K, Lin Y. Differential distribution patterns and assembly processes of soil microbial communities under contrasting vegetation types at distinctive altitudes in the Changbai Mountain. Front Microbiol 2023; 14:1152818. [PMID: 37333641 PMCID: PMC10272400 DOI: 10.3389/fmicb.2023.1152818] [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: 01/28/2023] [Accepted: 03/29/2023] [Indexed: 06/20/2023] Open
Abstract
Diversity patterns and community assembly of soil microorganisms are essential for understanding soil biodiversity and ecosystem processes. Investigating the impacts of environmental factors on microbial community assembly is crucial for comprehending the functions of microbial biodiversity and ecosystem processes. However, these issues remain insufficiently investigated in related studies despite their fundamental significance. The present study aimed to assess the diversity and assembly of soil bacterial and fungal communities to altitude and soil depth variations in mountain ecosystems by using 16S and ITS rRNA gene sequence analyses. In addition, the major roles of environmental factors in determining soil microbial communities and assembly processes were further investigated. The results showed a U-shaped pattern of the soil bacterial diversity at 0-10 cm soil depth along altitudes, reaching a minimum value at 1800 m, while the fungal diversity exhibited a monotonically decreasing trend with increasing altitude. At 10-20 cm soil depth, the soil bacterial diversity showed no apparent changes along altitudinal gradients, while the fungal Chao1 and phylogenetic diversity (PD) indices exhibited hump-shaped patterns with increasing altitude, reaching a maximum value at 1200 m. Soil bacterial and fungal communities were distinctively distributed with altitude at the same depth of soil, and the spatial turnover rates in fungi was greater than in bacteria. Mantel tests suggested soil physiochemical and climate variables significantly correlated with the β diversity of microbial community at two soil depths, suggesting both soil and climate heterogeneity contributed to the variation of bacterial and fungal community. Correspondingly, a novel phylogenetic null model analysis demonstrated that the community assembly of soil bacterial and fungal communities were dominated by deterministic and stochastic processes, respectively. The assembly processes of bacterial community were significantly related to the soil DOC and C:N ratio, while the fungal community assembly processes were significantly related to the soil C:N ratio. Our results provide a new perspective to assess the responses of soil microbial communities to variations with altitude and soil depth.
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Affiliation(s)
- Yujuan Kang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Haitao Wu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Yifan Zhang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- College of Tourism and Geography Sciences, Jilin Normal University, Siping, China
| | - Qiong Wu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- College of Tourism and Geography Sciences, Jilin Normal University, Siping, China
| | - Qiang Guan
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Kangle Lu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Yiling Lin
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
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Yang C, Zhang H, Zhao X, Liu P, Wang L, Wang W. A functional metagenomics study of soil carbon and nitrogen degradation networks and limiting factors on the Tibetan plateau. Front Microbiol 2023; 14:1170806. [PMID: 37228377 PMCID: PMC10203874 DOI: 10.3389/fmicb.2023.1170806] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/10/2023] [Indexed: 05/27/2023] Open
Abstract
Introduction The Three-River Source Nature Reserve is located in the core area of the Qinghai-Tibetan Plateau, with the alpine swamp, meadow and steppe as the main ecosystem types. However, the microbial communities in these alpine ecosystems, and their carbon and nitrogen degrading metabolic networks and limiting factors remain unclear. Methods We sequenced the diversity of bacteria and fungi in alpine swamps, meadows, steppes, and their degraded and artificially restored ecosystems and analyzed soil environmental conditions. Results The results indicated that moisture content had a greater influence on soil microbial community structure compared to degradation and restoration. Proteobacteria dominated in high moisture alpine swamps and alpine meadows, while Actinobacteria dominated in low moisture alpine steppes and artificial grasslands. A metabolic network analysis of carbon and nitrogen degradation and transformation using metagenomic sequencing revealed that plateau microorganisms lacked comprehensive and efficient enzyme systems to degrade organic carbon, nitrogen, and other biological macromolecules, so that the short-term degradation of alpine vegetation had no effect on the basic composition of soil microbial community. Correlation analysis found that nitrogen fixation was strong in meadows with high moisture content, and their key nitrogen-fixing enzymes were significantly related to Sphingomonas. Denitrification metabolism was enhanced in water-deficient habitats, and the key enzyme, nitrous oxide reductase, was significantly related to Phycicoccus and accelerated the loss of nitrogen. Furthermore, Bacillus contained a large number of amylases (GH13 and GH15) and proteases (S8, S11, S26, and M24) which may promote the efficient degradation of organic carbon and nitrogen in artificially restored grasslands. Discussion This study illustrated the irrecoverability of meadow degradation and offered fundamental information for altering microbial communities to restore alpine ecosystems.
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Affiliation(s)
- Chong Yang
- School of Geographical Sciences, Qinghai Normal University, Xining, China
- School of Life Sciences, Qinghai Normal University, Xining, China
| | - Hong Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xinquan Zhao
- Northwest Plateau Institute of Biology, Chinese Academy of Sciences, Xining, China
| | - Pan Liu
- School of Geographical Sciences, Qinghai Normal University, Xining, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Wenying Wang
- School of Life Sciences, Qinghai Normal University, Xining, China
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20
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Silva D, Rodrigues F, Lorena C, Borges PT, Martins LO. Biocatalysis for biorefineries: The case of dye-decolorizing peroxidases. Biotechnol Adv 2023; 65:108153. [PMID: 37044267 DOI: 10.1016/j.biotechadv.2023.108153] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/06/2023] [Accepted: 04/09/2023] [Indexed: 04/14/2023]
Abstract
Dye-decolorizing Peroxidases (DyPs) are heme-containing enzymes in fungi and bacteria that catalyze the reduction of hydrogen peroxide to water with concomitant oxidation of various substrates, including anthraquinone dyes, lignin-related phenolic and non-phenolic compounds, and metal ions. Investigation of DyPs has shed new light on peroxidases, one of the most extensively studied families of oxidoreductases; still, details of their microbial physiological role and catalytic mechanisms remain to be fully disclosed. They display a distinctive ferredoxin-like fold encompassing anti-parallel β-sheets and α-helices, and long conserved loops surround the heme pocket with a role in catalysis and stability. A tunnel routes H2O2 to the heme pocket, whereas binding sites for the reducing substrates are in cavities near the heme or close to distal aromatic residues at the surface. Variations in reactions, the role of catalytic residues, and mechanisms were observed among different classes of DyP. They were hypothetically related to the presence or absence of distal H2O molecules in the heme pocket. The engineering of DyPs for improved properties directed their biotechnological applications, primarily centered on treating textile effluents and degradation of other hazardous pollutants, to fields such as biosensors and valorization of lignin, the most abundant renewable aromatic polymer. In this review, we track recent research contributions that furthered our understanding of the activity, stability, and structural properties of DyPs and their biotechnological applications. Overall, the study of DyP-type peroxidases has significant implications for environmental sustainability and the development of new bio-based products and materials with improved end-of-life options via biodegradation and chemical recyclability, fostering the transition to a sustainable bio-based industry in the circular economy realm.
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Affiliation(s)
- Diogo Silva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - F Rodrigues
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Constança Lorena
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Patrícia T Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Lígia O Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal.
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21
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Wang J, Yang J, Huang W, Huang W, Jia R. A mutant R70V/E166A of short manganese peroxidase showing Mn 2+-independent dye decolorization. Appl Microbiol Biotechnol 2023; 107:2303-2319. [PMID: 36843195 DOI: 10.1007/s00253-023-12438-y] [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: 11/09/2022] [Revised: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 02/28/2023]
Abstract
Il-MnP1, a short-type manganese peroxidase from Irpex lacteus F17, can oxidize some substrates in the absence of Mn2+, but the catalysis was much lower than in the presence of Mn2+. Here, we report a mutant R70V/E166A of Il-MnP1 with some unique properties, which possessed clearly higher catalysis for the decolorization of anthraquinone and azo dyes in the absence of Mn2+ than that of Il-MnP1. Importantly, the optimum pH of R70V/E166A for decolorization of anthraquinone dyes (Reactive Blue 19, RB19) was 6.5, and the mutant achieved high decolorization activities in the range of pH 4.0-7.0, whereas Il-MnP1 only showed decolorization for RB19 at pH 3.5-4.0. In addition, the optimum H2O2 concentration of R70V/E166A for RB19 decolorization was eight times that of Il-MnP1 and the H2O2 stability has improved 1.4 times compared with Il-MnP1. Furthermore, Mn2+ competitively inhibited the oxidation of RB19 by R70V/E166A, explaining the higher catalytic activity of the mutant R70V/E166A in the absence of Mn2+. Molecular docking results suggested that RB19 binds to the distal side of the heme plane in mutant R70V/E166A, which extended from the heme δ-side to the heme γ-side, and close to the mutated residues of R70V and E166A, whereas RB19 could not access the heme pocket of Il-MnP1 due to the steric hindrance of the side-chain group of Arg 70. Thus, this study constructed a useful mutant R70V/E166A and analyzed its higher Mn2+-independent activity, which is very important for better understanding the Mn2+-independent catalytic mechanism for short manganese peroxidases. KEY POINTS: • The mutant R70V/E166A of atypical MnP1 of I. lacteus F17 shows unique catalytic properties. • At pH 6.5, the R70V/E166A had a strong ability to decolorize anthraquinone dyes in the absence of Mn2+. • The binding sites of Reactive Blue 19 in mutant R70V/E166A were elucidated.
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Affiliation(s)
- Junli Wang
- School of Life Science, Anhui University, 111 Jiulong Road, Economic and Technology Development Zone, Hefei, Anhui Province, People's Republic of China, 230601
- Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, Anhui Province, China
| | - Jun Yang
- School of Life Science, Anhui University, 111 Jiulong Road, Economic and Technology Development Zone, Hefei, Anhui Province, People's Republic of China, 230601
- Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, Anhui Province, China
| | - Wenhan Huang
- School of Life Science, Anhui University, 111 Jiulong Road, Economic and Technology Development Zone, Hefei, Anhui Province, People's Republic of China, 230601
- Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, Anhui Province, China
| | - Wenting Huang
- School of Life Science, Anhui University, 111 Jiulong Road, Economic and Technology Development Zone, Hefei, Anhui Province, People's Republic of China, 230601
- Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, Anhui Province, China
| | - Rong Jia
- School of Life Science, Anhui University, 111 Jiulong Road, Economic and Technology Development Zone, Hefei, Anhui Province, People's Republic of China, 230601.
- Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, Anhui Province, China.
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22
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Motoda T, Chen FC, Tsuyama T, Tokumoto Y, Kijidani Y, Kamei I. Upregulation of MAP kinase HOG1 gene of white-rot fungus Phlebia sp. MG-60 inhibits the ethanol fermentation and mycelial growth. Biosci Biotechnol Biochem 2023; 87:217-227. [PMID: 36610726 DOI: 10.1093/bbb/zbac203] [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: 09/30/2022] [Accepted: 11/17/2022] [Indexed: 01/09/2023]
Abstract
Wood biomass conversion for fossil resource replacement could result in the sustainable production of chemicals, although lignin represents an obstacle to efficient polysaccharide use. White-rot fungus Phlebia sp. MG-60 reportedly selectively and aerobically degrades lignin in hardwood, then it begins cellulose saccharification from the delignified wood to produce ethanol. Environmental conditions might change white-rot fungi-driven biomass conversion. However, how the environmental response sensor affects ethanol fermentation in white-rot fungi remains elusive. In this study, we focused on MGHOG1, the yeast Hog1 homolog in Phlebia sp. MG-60, a presumably important player in osmoresponse. We generated MGHOG1 overexpressing (OE) transformants in Phlebia sp. MG-60, exhibiting slower mycelial growth compared with the wild-type under salinity stress. MGHOG1 overexpressing liquid cultures displayed suppressed mycelial growth and ethanol fermentation. Therefore, MGHOG1 potentially influences ethanol fermentation and mycelial growth in Phlebia sp. MG-60. This study provides novel insights into the regulation of white-rot fungi-mediated biomass conversion.
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Affiliation(s)
- Taichi Motoda
- Interdisciplinary Graduate School of Agriculture and Engineering, University of Miyazaki, Miyazaki, Japan
| | - Fu-Chia Chen
- Interdisciplinary Graduate School of Agriculture and Engineering, University of Miyazaki, Miyazaki, Japan
| | - Taku Tsuyama
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Yuji Tokumoto
- Institute for Tenure Track Promotion, University of Miyazaki, Miyazaki, Japan
| | - Yoshio Kijidani
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Ichiro Kamei
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
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23
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Wu G, Yu F, Yuan M, Wang J, Liu C, He W, Ge Z, Sun Y, Liu Y. Responses of Rhizosphere Bacterial and Fungal Communities to the Long-Term Continuous Monoculture of Water Oat. Microorganisms 2022; 10:2174. [PMID: 36363766 PMCID: PMC9695572 DOI: 10.3390/microorganisms10112174] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/21/2022] [Accepted: 10/25/2022] [Indexed: 08/13/2023] Open
Abstract
As an cultivated aquatic vegetable, the long-term continuous monocropping of water oat results in the frequent occurrence of diseases, the deterioration of ecological system and decreased quality of water oat. In this study, real-time quantitative PCR (qPCR) and Illumina high-throughput sequencing were used to determine the dynamic changes in bacterial and fungal communities in rhizosphere soil under continuous cropping of water oat for 1, 5, 10, 15 and 20 years (Y1, Y5, Y10, Y15 and Y20), and soil properties and enzyme activities were also determined. Results showed that the contents of soil organic carbon (SOC), total nitrogen (TN), alkali-hydrolyzable nitrogen (AN), available phosphorus (AP) and the activities of four soil enzymes increased in Y5 and Y10 and then decreased in Y15 and Y20. Spearman correlation analysis identified SOC, TN, AP and AN as the main factors that affect the four enzyme activities. The qPCR results showed that there was no significant difference in bacterial abundance between the different planting years, while the fungal abundance first increased and then decreased. The long-term continuous planting of water oat (Y15 and Y20) significantly reduced the operational taxonomic unit numbers and the Shannon, Chao1, and ACE indices of rhizosphere bacteria and fungi. The bacterial and fungal community compositions were markedly affected by the continuous planting year. The relative abundances of Bacteroidetes and Firmicutes decreased significantly in Y10 and Bacteroidetes increased significantly in Y15. Relative abundances of dominated Mortierellomycota and Ascomycota phyla increased with the continuous cropping years, while Rozellomycota presented the opposite trend. The AK, AN, and SOC were the main factors that changed the bacterial community, while AK and AP significantly shifted the fungal community. Thus, long-term continuous planting of water oat resulted in the deterioration of soil nutrients and microbial communities. The results provided a reference for the remediation of soil under continuous water oat planting and sustainable development of water oat industry.
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Affiliation(s)
- Gang Wu
- Institute of Soil and Fertilizer, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Key Laboratory of Nutrient Cyclling and Resources Environment of Anhui Province, Hefei 230031, China
| | - Feifei Yu
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Manman Yuan
- Institute of Soil and Fertilizer, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Key Laboratory of Nutrient Cyclling and Resources Environment of Anhui Province, Hefei 230031, China
| | - Jiabao Wang
- Institute of Soil and Fertilizer, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Key Laboratory of Nutrient Cyclling and Resources Environment of Anhui Province, Hefei 230031, China
| | - Chuang Liu
- Institute of Soil and Fertilizer, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Key Laboratory of Nutrient Cyclling and Resources Environment of Anhui Province, Hefei 230031, China
| | - Weizhu He
- Institute of Soil and Fertilizer, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Key Laboratory of Nutrient Cyclling and Resources Environment of Anhui Province, Hefei 230031, China
| | - Zhihuan Ge
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Yixiang Sun
- Institute of Soil and Fertilizer, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Key Laboratory of Nutrient Cyclling and Resources Environment of Anhui Province, Hefei 230031, China
| | - Yuan Liu
- College of Life Science, Huaibei Normal University, Huaibei 235000, China
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24
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Liu J, Li C, Ma W, Liu W, Wu W. Molecular Characterization of Distinct Fungal Communities in the Soil of a Rare Earth Mining Area. MICROBIAL ECOLOGY 2022; 84:1212-1223. [PMID: 34839384 DOI: 10.1007/s00248-021-01931-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/15/2021] [Indexed: 06/13/2023]
Abstract
The exploitation of ion-absorbed rare earth elements (REEs) has caused serious ecological destruction and environmental pollution. Effects on soil fungal structure and diversity exerted by mining activities are usually ignored, although fungus is one of the most important components in soil ecosystems. In the present research, quantitative polymerase chain reaction (qPCR) and high-throughput Illumina MiSeq sequencing were conducted to characterize fungal community composition and structure in soil of a rare earth mining area after in situ leaching. Statistical analyses, network, and FUNGuild were used to conduct in-depth analyses. Ascomycota, Basidiomycota, and Glomeromycota were the most abundant phyla in the mining soils. Fungal community structures were stable after leaching practice, but nutrition contents (organic matter, TC, and TN) significantly and positively contributed to fungal abundances and diversities. Saprotrophs in phyla Ascomycota and Basidiomycota were the dominant fungal trophic mode, and they played critical roles in nutrient cycling, transformation processes, and reducing REE toxicity. Symbiotrophs of phyla Glomeromycota contributed to soil aggregation and slowing down nutrient losses after in situ leaching practice. In addition, fungi could regulate the interactions between species to resist the harsh environment of REE toxicity or ammonium caused by in situ leaching practice.
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Affiliation(s)
- Jingjing Liu
- School of Energy and Machinery Engineering, Jiangxi University of Science and Technology, Nanchang, 330013, China.
- Jiangxi Key Laboratory of Mining & Metallurgy Environmental Pollution Control, Ganzhou, 341099, China.
| | - Chun Li
- School of Energy and Machinery Engineering, Jiangxi University of Science and Technology, Nanchang, 330013, China
| | - Wendan Ma
- School of Energy and Machinery Engineering, Jiangxi University of Science and Technology, Nanchang, 330013, China
| | - Wei Liu
- College of Chemistry and Environmental Science, Hebei University, Baoding, 071002, China
| | - Weixiang Wu
- Institute of Environmental Science and Technology, Zhejiang University, Hangzhou, 310030, People's Republic of China
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25
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Miao Y, Lin Y, Chen Z, Zheng H, Niu Y, Kuzyakov Y, Liu D, Ding W. Fungal key players of cellulose utilization: Microbial networks in aggregates of long-term fertilized soils disentangled using 13C-DNA-stable isotope probing. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 832:155051. [PMID: 35390367 DOI: 10.1016/j.scitotenv.2022.155051] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 03/07/2022] [Accepted: 04/01/2022] [Indexed: 06/14/2023]
Abstract
Long-term compost application accelerates organic carbon (C) accumulation and macroaggregate formation in soil. Stable aggregates and high soil organic C (SOC) content are supposed to increase microbiota activity and promote transformation of litter compounds (i.e., cellulose) into SOC. Here, we used 13C-DNA-stable isotope probing with subsequent high-throughput sequencing to characterize fungal succession and co-occurrence trends during 13C-cellulose decomposition in aggregate size classes in soils subjected to no fertilizer (control), nitrogen-phosphorus‑potassium (NPK) fertilizers, and compost (Compost) application for 27 years. Ascomycota (mostly saprotrophic fungi) were always highly competitive for cellulose in all aggregate size classes at the early stages of cellulose decomposition (20 days). Compost-treated soil was enriched with Ascomycota compared to the control soil, wherein Sordariomycetes, the majority, strongly dominated the cellulose utilization (13C incorporation in DNA). 13C-labeled fungal communities converged in the Compost soil, with lower abundance and diversity compared with the NPK and control soils. Such convergence led to greater cellulose decomposition, indicating that compost amendment increased the capacity of a few dominant fungal taxa to decompose litter. Compost soil had more 13C-labeled fungal decomposers in microaggregates and lower fungal decomposers in macroaggregates when compared with the levels in the NPK and control soils. This implies that compost application facilitates fungal colonization towards smaller aggregates. Fungal interactions were reinforced in microaggregates (<250 μm), with more positive associations than those in macroaggregates (>250 μm), indicating greater fungal synergism for recalcitrant resource utilization in microaggregates. The keystone taxa in the co-occurrence networks were not related to cellulose decomposition in microaggregates, but did in macroaggregates. The findings advance a process-based understanding of cellulose utilization by fungal key players based on C and energy availability and the regulation of microbial activity at the aggregate level.
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Affiliation(s)
- Yuncai Miao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongxin Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Zengming Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Huijie Zheng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhui Niu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Göttingen, Büsgenweg 2, Göttingen 37077, Germany; Agro-Technological Institute, RUDN University, 117198 Moscow, Russia
| | - Deyan Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Weixin Ding
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
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Community succession and straw degradation characteristics using a microbial decomposer at low temperature. PLoS One 2022; 17:e0270162. [PMID: 35802565 PMCID: PMC9269364 DOI: 10.1371/journal.pone.0270162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 06/03/2022] [Indexed: 11/19/2022] Open
Abstract
This study explored changes in the microbial community structure during straw degradation by a microbial decomposer, M44. The microbial community succession at different degradation periods was analyzed using MiSeq high-throughput sequencing. The results showed that 14 days after inoculation, the filter paper enzyme and endoglucanase activities increased to 2.55 U·mL-1 and 2.34 U·mL-1. The xylanase, laccase, and lignin peroxidase activities rose to 9.86 U·mL-1, 132.16 U·L-1, and 85.43 U·L-1 after 28 d, which was consistent with changes in the straw degradation rate. The degradation rates of straw, lignin, cellulose, and hemicellulose were 31.43%, 13.67%, 25.04%, and 21.69%, respectively, after 28 d of fermentation at 15°C. Proteobacteria, Firmicutes, and Bacteroidetes were the main bacterial species in samples at different degradation stages. The dominant genera included Pseudomonas, Delftia, and Paenibacillus during the initial stage (1 d, 7 d) and the mid-term stage (14 d). The key functional microbes during the late stage (21 d, 28 d) were Rhizobium, Chryseobacterium, Sphingobacterium, Brevundimonas, and Devosia. Changes in the bacterial consortium structure and straw degradation characteristics during different degradation periods were clarified to provide a theoretical basis for the rational utilization of microbial decomposer M44.
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Liu S, He F, Kuzyakov Y, Xiao H, Hoang DTT, Pu S, Razavi BS. Nutrients in the rhizosphere: A meta-analysis of content, availability, and influencing factors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 826:153908. [PMID: 35183641 DOI: 10.1016/j.scitotenv.2022.153908] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/11/2022] [Accepted: 02/12/2022] [Indexed: 06/14/2023]
Abstract
Nutrient deficiency in most terrestrial ecosystems constrains global primary productivity. Rhizosphere nutrient availability directly regulates plant growth and is influenced by many factors, including soil properties, plant characteristics and climate. A quantitatively comprehensive understanding of the role of these factors in modulating rhizosphere nutrient availability remains largely unknown. We reviewed 123 studies to assess nutrient availability in the rhizosphere compared to bulk soil depending on various factors. The increase in microbial nitrogen (N) content and N-cycling related enzyme activities in the rhizosphere led to a 10% increase in available N relative to bulk soil. The available phosphorus (P) in the rhizosphere decreased by 12% with a corresponding increase in phosphatase activities, indicating extreme demand and competition between plants and microorganisms for P. Greater organic carbon (C) content around taproots (+17%) confirmed their stronger ability to store more organic compounds than the fibrous roots. This corresponds to higher bacterial and fungal contents and slightly higher available nutrients in the rhizosphere of taproots. The maximal rhizosphere nutrient accumulation was common for low-fertile soils, which is confirmed by the negative correlation between most soil chemical properties and the effect sizes of available nutrients. Increases in rhizosphere bacterial and fungal population densities (205-254%) were much higher than microbial biomass increases (indicated as microbial C: +19%). Consequently, despite the higher microbial population densities in the rhizosphere, the biomass of individual microbial cells decreased, pointing on their younger age and faster turnover. This meta-analysis shows that, contrary to the common view, most nutrients are more available in the rhizosphere than in bulk soil because of higher microbial activities around roots.
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Affiliation(s)
- Shibin Liu
- College of Ecology and Environment, Chengdu University of Technology, 1# Dongsanlu, Erxianqiao, Chengdu 610059, Sichuan, PR China; State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, Chengdu University of Technology, 1# Dongsanlu, Erxianqiao, Chengdu 610059, Sichuan, PR China
| | - Fakun He
- College of Earth Sciences, Chengdu University of Technology, 1# Dongsanlu, Erxianqiao, Chengdu 610059, Sichuan, PR China
| | - Yakov Kuzyakov
- Peoples Friendship University of Russia (RUDN University), Moscow, Russia; Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
| | - Huxuan Xiao
- College of Earth Sciences, Chengdu University of Technology, 1# Dongsanlu, Erxianqiao, Chengdu 610059, Sichuan, PR China
| | - Duyen Thi Thu Hoang
- Climate Change and Development Program, VNU Vietnam-Japan University, Vietnam National University, Hanoi, Viet Nam
| | - Shengyan Pu
- College of Ecology and Environment, Chengdu University of Technology, 1# Dongsanlu, Erxianqiao, Chengdu 610059, Sichuan, PR China; State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, Chengdu University of Technology, 1# Dongsanlu, Erxianqiao, Chengdu 610059, Sichuan, PR China.
| | - Bahar S Razavi
- Department of Soil and Plant Microbiome, Institute of Phytopathology, Christian-Albrechts-University of Kiel, Kiel, Germany
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Changes in Soil Organic Carbon Fractions and Fungal Communities, Subsequent to Different Management Practices in Moso Bamboo Plantations. J Fungi (Basel) 2022; 8:jof8060640. [PMID: 35736123 PMCID: PMC9225535 DOI: 10.3390/jof8060640] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/11/2022] [Accepted: 06/15/2022] [Indexed: 12/03/2022] Open
Abstract
Moso bamboo (Phyllostachys pubescens) has an extremely fast growth rate and major carbon sequestration potential. However, little information is available on the dynamics of soil C accumulation and fungi communities related to different management practices. Here, we investigated changes in the soil organic carbon (SOC) fractions and fungal communities of a Moso bamboo plantation under three different management practices (M0: undisturbed; M1: extensively managed; and M2: intensively managed). Compared with M0, SOC levels were reduced by 41.2% and 71.5% in M1 and M2, respectively; furthermore, four SOC fractions (C1: very labile; C2: labile; C3: less labile; and C4: nonlabile) and the carbon management index (CMI) were also significantly reduced by plantation management. These practices further altered fungal communities, for example, by increasing Basidiomycota and Mortierellomycota, and by decreasing Ascomycota and Rozellomycota. Pyrenochaeta, Mortierella, Saitozyma, and Cladophialophora were identified as keystone taxa. Soil fungal communities were significantly related to the pH, NH4-N, AP, C3, and the C4 fractions of SOC. Random forest modeling identified soil C3 and Mortierella as the most important predictors of the CMI. Our results suggest that reducing human interference would be beneficial for fungal community improvement and C sequestration in Moso bamboo plantations.
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Idbella M, De Filippis F, Zotti M, Sequino G, Abd-ElGawad AM, Fechtali T, Mazzoleni S, Bonanomi G. Specific microbiome signatures under the canopy of Mediterranean shrubs. APPLIED SOIL ECOLOGY 2022; 173:104407. [DOI: 10.1016/j.apsoil.2022.104407] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Sánchez-Quitian ZA, Quitian-Romero JC, Moreno-Buitrago AT, Montoya Barreto S, Sanjuan T, Ortiz-Rosas JP. Isolation and characterization of wood-decomposing basidiomycetes from the Andean Forest in Boyacá, Colombia. Braz J Microbiol 2022; 53:1425-1437. [PMID: 35446011 PMCID: PMC9433503 DOI: 10.1007/s42770-022-00760-y] [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: 07/14/2021] [Accepted: 04/13/2022] [Indexed: 11/02/2022] Open
Abstract
This study explores the biotechnological potential of lignocellulolytic fungi collected in an oak forest. Fungal collections were obtained from natural reserves located in Boyacá-Colombia, ranging from 2700 to 3000 m.a.s.l. Twenty-three strains were isolated on malt agar, molecular characterization was performed, and ligninolytic and cellulolytic enzymatic activities were screened. Several white-rot fungi of biotechnological importance were identified as follows: Trametes sp., Trametes versicolor, Trametes villosa, Pycnoporus sanguineus, Bjerkandera adjusta, Lentinula boryana, Panus conchatus, Antrodia neotropica, Brunneoporus malicola, Laetiporus gilbertsonii, Stereum sp., Ganoderma sp., and Dichomitus sp. The strains T. versicolor 0554 and 0583, T. villosa 0562, and B. adusta 0556 showed the highest response in the qualitative enzymatic assays. These strains were used to determine their ability to decolorate the dyes aniline blue and Congo red, and it was found that T. villosa 0562 reached a level of decolorization close to 90% after 48 h of submerged culture. The fungal strains obtained here could offer alternatives to develop a process to accomplish sustainable development objectives.
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Zhang Y, Heal KV, Shi M, Chen W, Zhou C. Decreasing molecular diversity of soil dissolved organic matter related to microbial community along an alpine elevation gradient. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 818:151823. [PMID: 34808163 DOI: 10.1016/j.scitotenv.2021.151823] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
Characterization of soil dissolved organic matter (DOM) and understanding of the interactions between soil microbial communities and DOM molecules along elevation gradients in alpine ecosystems are still limited. To unravel these interactions and how they change along alpine elevation gradients, we sampled topsoil in the Sygera Mountains (Tibet, China) at elevations between 3800 and 4600 m. The molecular characteristics of soil DOM were determined using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and soil microbial composition was identified by high-throughput sequencing. Among the seven components of DOM, the lignins/CRAM (carboxyl-rich alicyclic molecules)-like structure dominated at all elevations, followed by tannins, while the relative abundance of unstable substances, including lipids, aliphatic/protein, and carbohydrates, was lower. As elevation increased, the molecular diversity, degree of oxidation, aromaticity, and unsaturation of soil DOM decreased. The abundance and diversity of soil bacteria and fungi also generally decreased with elevation. Both bacteria and fungi play an important role in the degradation of DOM molecules, but bacteria appear to have greater degradation ability. Among them, Proteobacteria and Bacteroidetes mainly promote the degradation of lignins/CRAM-like structure molecules, while Basidiomycota mainly degrade more unstable substrates. Co-occurrence network analysis revealed complex correlations between specific microbial groups and DOM molecules. Our results suggest that more active cycling of soil DOM could occur in alpine ecosystems due to climate warming, as the result of increased vegetation productivity and litter input in response to rising temperature promoting the relative abundance of microbial groups capable of degrading lignins/CRAM-like structures in soil DOM.
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Affiliation(s)
- Yanlin Zhang
- Forestry College, Fujian Agriculture and Forestry University, National Positioning Observation Research Station of Red Earth Hilly Ecosystem in Changting, Fujian, 350002, Fujian Province, China
| | - Kate V Heal
- School of GeoSciences, The University of Edinburgh, Crew Building, Alexander Crum Brown Road, Edinburgh EH9 3FF, UK
| | - Mengjie Shi
- Forestry College, Fujian Agriculture and Forestry University, National Positioning Observation Research Station of Red Earth Hilly Ecosystem in Changting, Fujian, 350002, Fujian Province, China
| | - Wenxin Chen
- Forestry College, Fujian Agriculture and Forestry University, National Positioning Observation Research Station of Red Earth Hilly Ecosystem in Changting, Fujian, 350002, Fujian Province, China
| | - Chuifan Zhou
- Forestry College, Fujian Agriculture and Forestry University, National Positioning Observation Research Station of Red Earth Hilly Ecosystem in Changting, Fujian, 350002, Fujian Province, China.
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32
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Sui X, Zeng X, Li M, Weng X, Frey B, Yang L, Li M. Influence of Different Vegetation Types on Soil Physicochemical Parameters and Fungal Communities. Microorganisms 2022; 10:microorganisms10040829. [PMID: 35456878 PMCID: PMC9026879 DOI: 10.3390/microorganisms10040829] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 04/05/2022] [Accepted: 04/14/2022] [Indexed: 12/18/2022] Open
Abstract
This study assessed the effects of Betula dahurica (BD), Betula platyphylla (BP), Larix gmelinii (LG), Quercus mongolica (QM), and a mixed conifer–broadleaf forest composed of LG and QM (LGQM) on the soil physicochemical parameters and community structure of fungi in the Zhongyangzhan Black-billed Capercaillie Nature Reserve. Fungal community structures were characterized via ITS rRNA sequencing. The effects of soil parameters on the community structure of soil fungi were assessed by Pearson correlation analysis and redundancy analysis (RDA). LGQM exhibited lower C/N, available nitrogen (AN), total phosphorus (TP), and available phosphorus (AP) compared with the QM broadleaf forest. The fungal Shannon and Simpson diversity indices were highest in BP, whereas LG exhibited the highest ACE index. The Basidiomycota, Ascomycota, Mortierellomycota, and Mucoromycota fungal phyla were dominant across all vegetation types. Each of the different vegetation types studied herein exhibited a unique fungal community structure. The RDA results indicated that fungal community structures were primarily shaped by the total N, available N, and available P of soil. Our findings thus indicated that forests restored with different species of trees may exhibit variations in soil quality and characteristics despite sharing the same climate. Furthermore, broadleaved and coniferous forests exhibited a unique fungal community diversity and composition.
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Affiliation(s)
- Xin Sui
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150080, China; (X.S.); (X.W.)
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin 150080, China
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland;
| | - Xiannan Zeng
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Harbin 150088, China;
| | - Mengsha Li
- Institute of Nature and Ecology, Heilongjiang Academy of Sciences, Harbin 150040, China
- Correspondence: (M.L.); (L.Y.); (M.L.)
| | - Xiaohong Weng
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150080, China; (X.S.); (X.W.)
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Beat Frey
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland;
| | - Libin Yang
- Institute of Nature and Ecology, Heilongjiang Academy of Sciences, Harbin 150040, China
- Correspondence: (M.L.); (L.Y.); (M.L.)
| | - Maihe Li
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland;
- Key Laboratory of Geographical Processes and Ecological Security in Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun 130024, China
- Erguna Forest-Steppe Ecotone Research Station, CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, China
- Correspondence: (M.L.); (L.Y.); (M.L.)
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Yang J, Han M, Zhao Z, Han J, Zhang X, Xie Z, Jiang H. Microbial response to multiple-level addition of grass organic matter in lake sediments with different salinity. FEMS Microbiol Ecol 2022; 98:6568899. [DOI: 10.1093/femsec/fiac046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/05/2022] [Accepted: 04/12/2022] [Indexed: 11/12/2022] Open
Abstract
ABSTRACT
Water surface expansion of saline lakes usually causes the inundation of surrounding grassland, leading to the increase of terrestrial grass organic matter (OM) input to the lakes and the decrease of lake salinity. However, the influence of terrestrial grass OM input increase and salinity decrease on organic carbon mineralization and microbial community composition remains unknown in saline lakes. Here, microbial mineralization of terrestrial grass (Achnatherum splendens) OM at different quantity levels in lake sediments with different salinity was investigated by performing microcosm experiments. The results showed that the CO2 production rates increased with the increase of grass OM supply in the studied sediments with different salinity, which may be driven by certain microbial groups (e.g., Bacteroidota, Firmicutes and Ascomycota). The increase of grass OM supply reduced the richness of prokaryotic community, which will decrease the size and complexity of the studied microbial networks, but increase the interaction between prokaryotic and fungal taxa. Taken together, our results suggest that the increase of terrestrial grass OM input caused by lake expansion would enhance the mineralization of organic carbon and affect the community composition and interactions of related microorganisms in lake sediments with different salinity.
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Affiliation(s)
- Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
| | - Mingxian Han
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
| | - Zhuoli Zhao
- School of Ocean Sciences, China University of Geosciences, Beijing, 100083, China
| | - Jinbin Han
- Qinghai Provincial Key Laboratory of Geology and Environment of Salt Lakes, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining 810008, China
| | - Xiying Zhang
- Qinghai Provincial Key Laboratory of Geology and Environment of Salt Lakes, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining 810008, China
| | - Zhanling Xie
- College of Ecology-Environment Engineering, Qinghai University, Xining, 810016, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
- Qinghai Provincial Key Laboratory of Geology and Environment of Salt Lakes, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining 810008, China
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Cobo-Díaz JF, Legrand F, Le Floch G, Picot A. Influence of Maize Residues in Shaping Soil Microbiota and Fusarium spp. Communities. MICROBIAL ECOLOGY 2022; 83:702-713. [PMID: 34169333 DOI: 10.1007/s00248-021-01797-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
Fusarium head blight (FHB) is a devastating fungal disease of small grain cereals including wheat. Causal fungal agents colonize various components of the field during their life cycle including previous crop residues, soil, and grains. Although soil and residues constitute the main inoculum source, these components have received much less attention than grains. This study aimed at disentangling the role of previous crop residues in shaping soil microbiota, including Fusarium spp. communities, in fields under wheat-maize rotation. Such knowledge may contribute to better understand the complex interactions between Fusarium spp. and soil microbiota. Dynamics of bacterial and fungal communities, with a special focus on Fusarium spp., were monitored in soils at 3 time points: during wheat cultivation (April 2015 and 2017) and after maize harvest (November 2016) and in maize residues taken from fields after harvest. Shifts in microbiota were also evaluated under mesocosm experiments using soils amended with maize residues. Fusarium graminearum and F. avenaceum were predominant on maize residues but did not remain in soils during wheat cultivation. Differences in soil bacterial diversity and compositions among years were much lower than variation between fields, suggesting that bacterial communities are field-specific and more conserved over time. In contrast, soil fungal diversity and compositions were more influenced by sampling time. Maize residues, left after harvest, led to a soil enrichment with several fungal genera, including Epicoccum, Fusarium, Vishniacozyma, Papiliotrema, Sarocladium, Xenobotryosphaeria, Ramularia, Cladosporium, Cryptococcus, and Bullera, but not with bacterial genera. Likewise, under mesocosm conditions, the addition of maize residues had a stronger influence on fungal communities than on bacterial communities. In particular, addition of maize significantly increased soil fungal richness, while bacteria were much less prone to changes. Based on co-occurrence networks, OTUs negatively correlated to Fusarium spp. were identified, such as those assigned to Epicoccum and Vishniacozyma. Altogether, our results allowed to gain a deeper insight into the complex microbiota interactions in soils, with bacteria and fungi responding differently to environmental disturbances.
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Affiliation(s)
- José F Cobo-Díaz
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, Université de Bretagne Occidentale, 29280, Plouzané, France.
- Department of Food Hygiene and Technology, Faculty of Veterinary, Universidad de León, León, Spain.
- Institute of Food Science and Technology, Universidad de León, León, Spain.
| | - Fabienne Legrand
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, Université de Bretagne Occidentale, 29280, Plouzané, France
- Agence Nationale de Sécurité Sanitaire de L'alimentation, de L'environnement Et du Travail (ANSES), 94701, Maisons-Alfort, France
| | - Gaétan Le Floch
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, Université de Bretagne Occidentale, 29280, Plouzané, France
| | - Adeline Picot
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, Université de Bretagne Occidentale, 29280, Plouzané, France
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Mattila H, Österman-Udd J, Mali T, Lundell T. Basidiomycota Fungi and ROS: Genomic Perspective on Key Enzymes Involved in Generation and Mitigation of Reactive Oxygen Species. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:837605. [PMID: 37746164 PMCID: PMC10512322 DOI: 10.3389/ffunb.2022.837605] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/21/2022] [Indexed: 09/26/2023]
Abstract
Our review includes a genomic survey of a multitude of reactive oxygen species (ROS) related intra- and extracellular enzymes and proteins among fungi of Basidiomycota, following their taxonomic classification within the systematic classes and orders, and focusing on different fungal lifestyles (saprobic, symbiotic, pathogenic). Intra- and extracellular ROS metabolism-involved enzymes (49 different protein families, summing 4170 protein models) were searched as protein encoding genes among 63 genomes selected according to current taxonomy. Extracellular and intracellular ROS metabolism and mechanisms in Basidiomycota are illustrated in detail. In brief, it may be concluded that differences between the set of extracellular enzymes activated by ROS, especially by H2O2, and involved in generation of H2O2, follow the differences in fungal lifestyles. The wood and plant biomass degrading white-rot fungi and the litter-decomposing species of Agaricomycetes contain the highest counts for genes encoding various extracellular peroxidases, mono- and peroxygenases, and oxidases. These findings further confirm the necessity of the multigene families of various extracellular oxidoreductases for efficient and complete degradation of wood lignocelluloses by fungi. High variations in the sizes of the extracellular ROS-involved gene families were found, however, among species with mycorrhizal symbiotic lifestyle. In addition, there are some differences among the sets of intracellular thiol-mediation involving proteins, and existence of enzyme mechanisms for quenching of intracellular H2O2 and ROS. In animal- and plant-pathogenic species, extracellular ROS enzymes are absent or rare. In these fungi, intracellular peroxidases are seemingly in minor role than in the independent saprobic, filamentous species of Basidiomycota. Noteworthy is that our genomic survey and review of the literature point to that there are differences both in generation of extracellular ROS as well as in mechanisms of response to oxidative stress and mitigation of ROS between fungi of Basidiomycota and Ascomycota.
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Affiliation(s)
| | | | | | - Taina Lundell
- Department of Microbiology, Faculty of Agriculture and Forestry, Viikki Campus, University of Helsinki, Helsinki, Finland
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Pacetti A, Moretti S, Perrin C, Gelhaye E, Bieler E, Kassemeyer HH, Mugnai L, Farine S, Bertsch C. Grapevine Wood-Degrading Activity of Fomitiporia mediterranea M. Fisch.: A Focus on the Enzymatic Pathway Regulation. Front Microbiol 2022; 13:844264. [PMID: 35369524 PMCID: PMC8971955 DOI: 10.3389/fmicb.2022.844264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 02/04/2022] [Indexed: 11/13/2022] Open
Abstract
Fomitiporia mediterranea is a Basidiomycetes fungus associated with some of the Esca complex diseases and responsible for decay in grapevine wood. Its role in the onset of foliar symptoms has recently been reconsidered, mainly after evidence showing a reduction in foliar symptom expression after removal of rotten wood. The study of its degradation pathways has already been approached by other authors, and with this study much information is consolidated. A microscopic observation of degraded wood provides a first approach to the characterization of F. mediterranea modalities of wood cellular structure degradation. The decay of grapevine wood was reproduced in vitro, and the measurement of each wood-forming polymer loss highlighted characteristics of F. mediterranea common to selective white rot and showed how fungal strain and vine variety are factors determining the wood degradation. All these observations were supported by the analysis of the laccase and manganese peroxidase enzyme activity, as well as by the expression of the genes coding 6 putative laccase isoforms and 3 manganese peroxidase isoforms, thereby highlighting substantial intraspecific variability.
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Affiliation(s)
- Andrea Pacetti
- Laboratoire Vigne Biotechnologies et Environnement UR-3991, Université de Haute Alsace, Colmar, France
- Department of Agricultural, Food, Environmental and Forestry Science and Technology (DAGRI), Plant Pathology and Entomology Section, University of Florence, Florence, Italy
| | - Samuele Moretti
- Laboratoire Vigne Biotechnologies et Environnement UR-3991, Université de Haute Alsace, Colmar, France
| | - Célia Perrin
- Laboratoire Vigne Biotechnologies et Environnement UR-3991, Université de Haute Alsace, Colmar, France
| | - Eric Gelhaye
- Faculté des Sciences et Technologies Boulevard des Aiguillettes, UMR IAM - Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Evi Bieler
- Swiss Nanoscience Institute (SNI) – Nano Imaging, University of Basel, Basel, Switzerland
| | - Hanns-Heinz Kassemeyer
- Swiss Nanoscience Institute (SNI) – Nano Imaging, University of Basel, Basel, Switzerland
- State Institute for Viticulture, Plant Pathology & Diagnostics, Freiburg, Germany
- Faculty of Biology, Plant Biomechanics Group and Botanic Garden, Albert-Ludwigs-Universität Freiburg, Freiburg im Breisgau, Germany
| | - Laura Mugnai
- Department of Agricultural, Food, Environmental and Forestry Science and Technology (DAGRI), Plant Pathology and Entomology Section, University of Florence, Florence, Italy
| | - Sibylle Farine
- Laboratoire Vigne Biotechnologies et Environnement UR-3991, Université de Haute Alsace, Colmar, France
| | - Christophe Bertsch
- Laboratoire Vigne Biotechnologies et Environnement UR-3991, Université de Haute Alsace, Colmar, France
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Gu D, Xiang X, Wu Y, Zeng J, Lin X. Synergy between fungi and bacteria promotes polycyclic aromatic hydrocarbon cometabolism in lignin-amended soil. JOURNAL OF HAZARDOUS MATERIALS 2022; 425:127958. [PMID: 34894508 DOI: 10.1016/j.jhazmat.2021.127958] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/29/2021] [Accepted: 11/28/2021] [Indexed: 06/14/2023]
Abstract
Lignin enhanced biodegradation of polycyclic aromatic hydrocarbons (PAHs) in soil, but collaboration among soil microorganisms during this process remains poorly understood. Here we explored the relations between microbial communities and PAH transformation in soil microcosms amended with lignin. Mineralization of the four-ring benzo(a)anthracene (BaA), which was selected as a model, was determined by using an isotope-labeled tracer. The eukaryotic inhibitor cycloheximide and redox mediator ABTS were used to validate the fungal role, while microbial communities were monitored by amplicon sequencing. The results demonstrated that lignin significantly promoted BaA mineralization to CO2, which was inhibited and enhanced by cycloheximide and ABTS, respectively. Together with the increased abundance of Basidiomycota, these observations suggested an essential contribution of fungi to BaA biodegradation, which possibly through a ligninolytic enzyme-mediated pathway. The enrichment of Methylophilaceae and Sphingomonadaceae supported bacterial utilization of methyl and aryl groups derived from lignin, implicating cometabolic BaA degradation. Co-occurrence network analysis revealed increased interactions between fungi and bacteria, suggesting they played synergistic roles in the transformation of lignin and BaA. Collectively, these findings demonstrate the importance of synergy between fungi and bacteria in PAH transformation, and further suggest that the modulation of microbial interplay may ameliorate soil bioremediation with natural materials such as lignin.
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Affiliation(s)
- Decheng Gu
- Anhui Province Key Laboratory of Wetland Ecological Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei 230031, China; Key laboratory of soil environment and pollution remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing 210008, China
| | - Xingjia Xiang
- Anhui Province Key Laboratory of Wetland Ecological Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei 230031, China
| | - Yucheng Wu
- Key laboratory of soil environment and pollution remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing 210008, China.
| | - Jun Zeng
- Key laboratory of soil environment and pollution remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing 210008, China
| | - Xiangui Lin
- Key laboratory of soil environment and pollution remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing 210008, China
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Kamei I, Tomitaka N, Taichi, Motoda, Yamasaki Y. Selective Homologous Expression of Recombinant Manganese Peroxidase Isozyme of Salt-Tolerant White-Rot Fungus Phlebia sp. MG-60, and Its Salt-Tolerance and Thermostability. J Microbiol Biotechnol 2022; 32:248-255. [PMID: 34949746 PMCID: PMC9628849 DOI: 10.4014/jmb.2108.08042] [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: 09/01/2021] [Revised: 12/02/2021] [Accepted: 12/09/2021] [Indexed: 12/15/2022]
Abstract
Phlebia sp. MG-60 is the salt-tolerant, white-rot fungus which was isolated from a mangrove forest. This fungus expresses three kinds of manganese peroxidase (MGMnP) isozymes, MGMnP1, MGMnP2 and MGMnP3 in low nitrogen medium (LNM) or LNM containing NaCl. To date, there have been no reports on the biochemical salt-tolerance of these MnP isozymes due to the difficulty of purification. In present study, we established forced expression transformants of these three types of MnP isozymes. In addition, the fact that this fungus hardly produces native MnP in a high-nitrogen medium (HNM) was used to perform isozyme-selective expression and simple purification in HNM. The resulting MGMnPs showed high tolerance for NaCl compared with the MnP of Phanerochaete chrysosporium. It was worth noting that high concentration of NaCl (over 200 mM to 1200 mM) can enhance the activity of MGMnP1. Additionally, MGMnP1 showed relatively high thermo tolerance compared with other isozymes. MGMnPs may have evolved to adapt to chloride-rich environments, mangrove forest.
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Affiliation(s)
- Ichiro Kamei
- Faculty of Agriculture, University of Miyazaki, 1-1, Gakuen-kibanadai-nishi, Miyazaki 889-2192, Japan,Graduate School of Agriculture and Engineering, University of Miyazaki, 1-1, Gakuen-kibanadai-nishi, Miyazaki 889-2192, Japan,Corresponding author Phone: +81-985-58-7181 Fax: +81-985-58-7181 E-mail:
| | - Nana Tomitaka
- Faculty of Agriculture, University of Miyazaki, 1-1, Gakuen-kibanadai-nishi, Miyazaki 889-2192, Japan
| | - Taichi
- Faculty of Agriculture, University of Miyazaki, 1-1, Gakuen-kibanadai-nishi, Miyazaki 889-2192, Japan
| | - Motoda
- Graduate School of Agriculture and Engineering, University of Miyazaki, 1-1, Gakuen-kibanadai-nishi, Miyazaki 889-2192, Japan
| | - Yumi Yamasaki
- Faculty of Regional Innovation, University of Miyazaki, 1-1, Gakuen-kibanadai-nishi, Miyazaki 889-2192, Japan
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Wang Y, Jiao P, Guo W, Du D, Hu Y, Tan X, Liu X. Changes in Bulk and Rhizosphere Soil Microbial Diversity and Composition Along an Age Gradient of Chinese Fir ( Cunninghamia lanceolate) Plantations in Subtropical China. Front Microbiol 2022; 12:777862. [PMID: 35281312 PMCID: PMC8904968 DOI: 10.3389/fmicb.2021.777862] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 12/13/2021] [Indexed: 11/13/2022] Open
Abstract
Soil microorganisms play key roles in biogeochemical cycling in forest ecosystems. However, whether the responses of microbial community with stand development differed in rhizosphere and bulk soils remains unknown. We collected rhizosphere and bulk soil in Chinese fir plantations with different stand ages (7a, 15a, 24a, and 34a) in subtropical China, and determined bacterial and fungal community variation via high-throughput sequencing. The results showed that soil bacterial, but not fungal, community diversity significantly differed among stand ages and between rhizosphere and bulk soils (p < 0.05). The differences in Shannon-Wiener and Simpson's indices between rhizosphere and bulk soil varied with stand age, with significant higher soil bacterial diversity in rhizosphere than bulk soils in 7a and 34a plantations (p < 0.05), but there were no significant difference in soil bacterial diversity between rhizosphere and bulk soils in 15a and 24a plantations (p > 0.05). Soil microbial community composition varied significantly with stand age but not between the rhizosphere and bulk soil. The dominant bacterial phyla at all ages were Acidobacteria and Proteobacteria, while the dominant fungal phyla were Ascomycota and Basidiomycota in both rhizosphere and bulk soil. They showed inconsistent distribution patterns along stand age gradient (7-34a) in the rhizosphere and bulk soil, suggesting distinct ecological strategy (r-strategist vs. k-strategist) of different microbial taxa, as well as changes in the microenvironment (i.e., nutrient stoichiometry and root exudates). Moreover, bacterial and fungal community composition in rhizosphere and bulk soil were governed by distinct driving factors. TP and NH4 +-N are the two most important factors regulating bacterial and fungal community structure in rhizosphere soil, while pH and NO3 --N, DON, and TN were driving factors for bacterial and fungal community structure in bulk soil, respectively. Collectively, our results demonstrated that the changes in microbial diversity and composition were more obvious along stand age gradients than between sampling locations (rhizosphere vs. bulk soil) in Chinese fir plantations.
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Affiliation(s)
- Yuzhe Wang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Pengyu Jiao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wen Guo
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dajun Du
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yalin Hu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiang Tan
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Xian Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
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40
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Leonardo-Silva L, Pereira-Silva G, Moreira IC, Silveira-Silva RB, Xavier-Santos S. Wood-inhabiting corticioid and poroid fungi (Basidiomycota) from Reserva Ecológica da Universidade Estadual de Goiás, a remnant of the Brazilian Cerrado. BIOTA NEOTROPICA 2022. [DOI: 10.1590/1676-0611-bn-2022-1359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Abstract Corticioid and poroid fungi are traditional morphological groups composed of ligninolytic species. Due to their efficiency in wood decomposition process, many species have great ecological importance, especially in nutrient cycling, as well as for their biotechnological properties. Nevertheless, knowledge about these fungi is scarce in many phytogeographic regions of Brazil, as is the case of the Cerrado, since mycodiversity studies in this biome are mainly focused on areas of the São Paulo state. Here we present the taxonomic inventory of corticioid and poroid fungi from the Reserva Ecológica da Universidade Estadual de Goiás (REC-UEG), a Cerrado remnant in Anápolis, Goiás, Brazil. The area is covered by three typical Cerrado landscapes (cerrado stricto sensu, mesophilic forest, and gallery forest), widely explored for scientific and educational purposes by the academic and regional community which seeks to learn about and preserve its biodiversity. Exsiccates deposited in the fungarium of the Universidade Estadual de Goiás (HUEG-Fungi) were analyzed. They are the result of collections made over 20 years, in approximately 103 ha of the reserve. Samples were characterized macro and microscopically and identified based on specialized literature. 51 species were recognized, which are distributed in 33 genera, 15 families, and five orders. Species were most frequent in forested areas and among them, six are new occurrence records for the Cerrado, nine for the Midwest region, and nine for the Goiás state. These results contribute to increase the knowledge of these fungi in the Cerrado, as well as geographic distribution, and show the relevance of preserving the reserve for the regional Funga representativity.
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41
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Illuri R, Kumar M, Eyini M, Veeramanikandan V, Almaary KS, Elbadawi YB, Biraqdar MA, Balaji P. Production, partial purification and characterization of ligninolytic enzymes from selected basidiomycetes mushroom fungi. Saudi J Biol Sci 2021; 28:7207-7218. [PMID: 34867024 PMCID: PMC8626257 DOI: 10.1016/j.sjbs.2021.08.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/05/2021] [Accepted: 08/08/2021] [Indexed: 11/26/2022] Open
Abstract
In recent years, many research on the quantity of lignocellulosic waste have been developed. The production, partial purification, and characterisation of ligninolytic enzymes from various fungi are described in this work. On the 21st day of incubation in Potato Dextrose (PD) broth, Hypsizygus ulmarius developed the most laccase (14.83 × 10−6 IU/ml) and manganese peroxidase (24.11 × 10−6 IU/ml), while Pleurotus florida produced the most lignin peroxidase (19.56 × −6 IU/ml). Laccase (Lac), lignin peroxidase (LiP), and manganese peroxidase (MnP), all generated by selected basidiomycetes mushroom fungi, were largely isolated using ammonium sulphate precipitation followed by dialysis. Laccase, lignin peroxidase, and manganese peroxidase purification findings indicated 1.83, 2.13, and 1.77 fold purity enhancements, respectively. Specific activity of purified laccase enzyme preparations ranged from 305.80 to 376.85 IU/mg, purified lignin peroxidase from 258.51 to 336.95 IU/mg, and purified manganese peroxidase from 253.45 to 529.34 IU/mg. H. ulmarius laccase (376.85 IU/mg) with 1.83 fold purification had the highest specific activity of all the ligninolytic enzymes studied, followed by 2.13 fold purification in lignin peroxidase (350.57 IU/mg) and manganese peroxidase (529.34 IU/mg) with 1.77-fold purification. Three notable bands with molecular weights ranging from 43 to 68 kDa and a single prominent band with a molecular weight of 97.4 kDa were identified on a Native PAGE gel from mycelial proteins of selected mushroom fungus. The SDS PAGE profiles of the mycelial proteins from the selected mushroom fungus were similar to the native PAGE. All three partially purified ligninolytic isozymes display three bands in native gel electrophoresis, with only one prominent band in enzyme activity staining. The 43 kDa, 55 kDa, and 68 kDa protein bands correspond to laccase, lignin peroxidase, and manganese peroxidase, respectively.
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Affiliation(s)
- Ramanaiah Illuri
- PG and Research Centre in Biotechnology, MGR College, Hosur, Tamil Nadu, India
| | - M Kumar
- Department of Plant Biology and Plant Biotechnology, Madras Christian College (Autonomous), Tambaram, Chennai, Tamil Nadu, India
| | - M Eyini
- Department of Botany, Thiagarajar College (Autonomous), Madurai, Tamil Nadu, India
| | - V Veeramanikandan
- PG and Research Centre in Microbiology, MGR College, Hosur, Tamil Nadu, India
| | - Khalid S Almaary
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. 2455, Riyadh 11451, Saudi Arabia
| | - Yahya B Elbadawi
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. 2455, Riyadh 11451, Saudi Arabia
| | - M A Biraqdar
- College of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009 Australia
| | - P Balaji
- PG and Research Centre in Biotechnology, MGR College, Hosur, Tamil Nadu, India
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42
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Vuong TV, Singh R, Eltis LD, Master ER. The Comparative Abilities of a Small Laccase and a Dye-Decoloring Peroxidase From the Same Bacterium to Transform Natural and Technical Lignins. Front Microbiol 2021; 12:723524. [PMID: 34733245 PMCID: PMC8559727 DOI: 10.3389/fmicb.2021.723524] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/23/2021] [Indexed: 11/29/2022] Open
Abstract
The relative ability of the small laccase (sLac) and dye-decoloring peroxidase (DyP2) from Amycolatopsis sp. 75iv2 to transform a variety of lignins was investigated using time-of-flight secondary ion mass spectrometry (ToF-SIMS). The enzymes modified organosolv hardwood lignin to different extents even in the absence of an added mediator. More particularly, sLac decreased the lignin modification metric S (S-lignin)/Ar (total aromatics) by 58% over 16h, while DyP2 lowered this ratio by 31% in the absence of exogenous H2O2. When used on their own, both sLac and DyP2 also modified native lignin present in aspen wood powder, albeit to lesser extents than in the organosolv lignin. The addition of ABTS for sLac and Mn2+ as well as H2O2 for DyP2 led to increased lignin modification in aspen wood powder as reflected by a decrease in the G/Ar metric by up to a further 13%. This highlights the importance of exogenous mediators for transforming lignin within its native matrix. Furthermore, the addition of ABTS reduced the selectivity of sLac for S-lignin over G-lignin, indicating that the mediator also altered the product profiles. Finally, when sLac was included in reactions containing DyP2, in part to generate H2O2in situ, the relative abundance of lignin products differed from individual enzymatic treatments. Overall, these results identify possible routes to tuning lignin modification or delignification through choice of enzyme and mediator. Moreover, the current study expands the application of ToF-SIMS to evaluating enzyme action on technical lignins, which can accelerate the discovery and engineering of industrially relevant enzymes for lignin valorization.
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Affiliation(s)
- Thu V Vuong
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Rahul Singh
- Department of Microbiology and Immunology, BioProducts Institute, The University of British Columbia, Vancouver, BC, Canada.,Genome British Columbia, Vancouver, BC, Canada
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, BioProducts Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Emma R Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada.,Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland
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Agustin MB, de Carvalho DM, Lahtinen MH, Hilden K, Lundell T, Mikkonen KS. Laccase as a Tool in Building Advanced Lignin-Based Materials. CHEMSUSCHEM 2021; 14:4615-4635. [PMID: 34399033 PMCID: PMC8597079 DOI: 10.1002/cssc.202101169] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/09/2021] [Indexed: 05/22/2023]
Abstract
Lignin is an abundant natural feedstock that offers great potential as a renewable substitute for fossil-based resources. Its polyaromatic structure and unique properties have attracted significant research efforts. The advantages of an enzymatic over chemical or thermal approach to construct or deconstruct lignins are that it operates in mild conditions, requires less energy, and usually uses non-toxic chemicals. Laccase is a widely investigated oxidative enzyme that can catalyze the polymerization and depolymerization of lignin. Its dual nature causes a challenge in controlling the overall direction of lignin-laccase catalysis. In this Review, the factors that affect laccase-catalyzed lignin polymerization were summarized, evaluated, and compared to identify key features that favor lignin polymerization. In addition, a critical assessment of the conditions that enable production of novel lignin hybrids via laccase-catalyzed grafting was presented. To assess the industrial relevance of laccase-assisted lignin valorization, patented applications were surveyed and industrial challenges and opportunities were analyzed. Finally, our perspective in realizing the full potential of laccase in building lignin-based materials for advanced applications was deduced from analysis of the limitations governing laccase-assisted lignin polymerization and grafting.
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Affiliation(s)
- Melissa B. Agustin
- Department of Food and NutritionFaculty of Agriculture and ForestryUniversity of Helsinki00014HelsinkiFinland
| | - Danila Morais de Carvalho
- Department of Food and NutritionFaculty of Agriculture and ForestryUniversity of Helsinki00014HelsinkiFinland
| | - Maarit H. Lahtinen
- Department of Food and NutritionFaculty of Agriculture and ForestryUniversity of Helsinki00014HelsinkiFinland
| | - Kristiina Hilden
- Department of MicrobiologyFaculty of Agriculture and ForestryUniversity of Helsinki00014HelsinkiFinland
- Helsinki Institute of Sustainability Science (HELSUS)University of HelsinkiP.O. Box 6500014HelsinkiFinland
| | - Taina Lundell
- Department of MicrobiologyFaculty of Agriculture and ForestryUniversity of Helsinki00014HelsinkiFinland
- Helsinki Institute of Sustainability Science (HELSUS)University of HelsinkiP.O. Box 6500014HelsinkiFinland
| | - Kirsi S. Mikkonen
- Department of Food and NutritionFaculty of Agriculture and ForestryUniversity of Helsinki00014HelsinkiFinland
- Helsinki Institute of Sustainability Science (HELSUS)University of HelsinkiP.O. Box 6500014HelsinkiFinland
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Coprinopsis cinerea uses laccase Lcc9 as a defense strategy to eliminate oxidative stress during fungal-fungal interactions. Appl Environ Microbiol 2021; 88:e0176021. [PMID: 34669425 DOI: 10.1128/aem.01760-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Frequently, laccases are triggered during fungal cocultivation for overexpression. The function of these activated laccases during coculture has not been clarified. Previously, we reported that Gongronella sp. w5 (w5) (Mucoromycota, Mucoromycetes) specifically triggered the laccase Lcc9 overexpression in Coprinopsis cinerea (Basidiomycota, Agaricomycetes). To systematically analyze the function of the overexpressed laccase during fungal interaction, C. cinerea mycelia before and after the initial Lcc9 overexpression were chosen for transcriptome analysis. Results showed that accompanied by specific utilization of fructose as carbohydrate substrate, oxidative stress derived from antagonistic compounds secreted by w5 appears to be a signal critical for laccase production in C. cinerea. Reactive oxygen species (ROS) decrease in the C. cinerea wild-type strain followed the increase in laccase production and then, lcc9 transcription and laccase activity stopped. By comparison, increased H2O2 content and mycelial ROS levels were observed during the entire cocultivation in lcc9 silenced C. cinerea strains. Moreover, lcc9 silencing slowed down the C. cinerea mycelial growth, affected hyphal morphology, and decreased the asexual sporulation in coculture. Our results showed that intracellular ROS acted as signal molecules to stimulate defense responses by C. cinerea with the expression of oxidative stress response regulator Skn7 and various detoxification proteins. Lcc9 takes part as a defense strategy to eliminate oxidative stress during the interspecific interaction with w5. Importance: The overproduction of laccase during interspecific fungal interactions is notoriously known. However, the exact role of the up-regulated laccases remains underexplored. Based on comparative transcriptomic analysis of C. cinerea and gene silencing of laccase Lcc9, here we show that oxidative stress derived from antagonistic compounds secreted by Gongronella sp. w5 was a signal critical for laccase Lcc9 production in Coprinopsis cinerea. Intracellular ROS acted as signal molecules to stimulate defense responses by C. cinerea with the expression of oxidative stress response regulator Skn7 and various detoxification proteins. Ultimately, Lcc9 takes part as a defense strategy to eliminate oxidative stress and help cell growth and development during the interspecific interaction with Gongronella sp. w5. These findings deepened our understanding of fungal interactions in their natural population and communities.
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Genomic Studies of White-Rot Fungus Cerrena unicolor SP02 Provide Insights into Food Safety Value-Added Utilization of Non-Food Lignocellulosic Biomass. J Fungi (Basel) 2021; 7:jof7100835. [PMID: 34682256 PMCID: PMC8541250 DOI: 10.3390/jof7100835] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/21/2021] [Accepted: 10/03/2021] [Indexed: 01/03/2023] Open
Abstract
Cerrena unicolor is an ecologically and biotechnologically important wood-degrading basidiomycete with high lignocellulose degrading ability. Biological and genetic investigations are limited in the Cerrena genus and, thus, hinder genetic modification and commercial use. The aim of the present study was to provide a global understanding through genomic and experimental research about lignocellulosic biomass utilization by Cerrena unicolor. In this study, we reported the genome sequence of C. unicolor SP02 by using the Illumina and PacBio 20 platforms to obtain trustworthy assembly and annotation. This is the combinational 2nd and 3rd genome sequencing and assembly of C. unicolor species. The generated genome was 42.79 Mb in size with an N50 contig size of 2.48 Mb, a G + C content of 47.43%, and encoding of 12,277 predicted genes. The genes encoding various lignocellulolytic enzymes including laccase, lignin peroxidase, manganese peroxidase, cytochromes P450, cellulase, xylanase, α-amylase, and pectinase involved in the degradation of lignin, cellulose, xylan, starch, pectin, and chitin that showed the C. unicolor SP02 potentially have a wide range of applications in lignocellulosic biomass conversion. Genome-scale metabolic analysis opened up a valuable resource for a better understanding of carbohydrate-active enzymes (CAZymes) and oxidoreductases that provide insights into the genetic basis and molecular mechanisms for lignocellulosic degradation. The C. unicolor SP02 model can be used for the development of efficient microbial cell factories in lignocellulosic industries. The understanding of the genetic material of C. unicolor SP02 coding for the lignocellulolytic enzymes will significantly benefit us in genetic manipulation, site-directed mutagenesis, and industrial biotechnology.
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Risueño Y, Petri C, Conesa HM. A critical assessment on the short-term response of microbial relative composition in a mine tailings soil amended with biochar and manure compost. JOURNAL OF HAZARDOUS MATERIALS 2021; 417:126080. [PMID: 33992925 DOI: 10.1016/j.jhazmat.2021.126080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/19/2021] [Accepted: 05/05/2021] [Indexed: 06/12/2023]
Abstract
Phytomanagement of tailings requires the use of soil conditioners to favour plant establishment, but their benefits on soil microbial composition need to be assessed. The goal of this work was to evaluate the effect of two organic amendments, manure compost and biochar, on soil bacterial and fungal composition at metallic mine tailings. The addition of compost caused stronger effects in most of soil parameters and microbial composition than biochar, especially at the initial stage of the experiment. However, the higher dependence on labile organic carbon for some bacterial groups at the treatments containing compost determined their decay along time (Flavobacteriales, Sphingobacteriales) and the appearance of other taxa more dependent on recalcitrant organic matter (Xanthomonadales, Myxococcales). Biochar favoured bacterial decomposers (Actinomycetales) specialised in high lignin and other recalcitrant carbon compounds. Unlike bacteria, only a few fungal orders increased their relative abundances in the treatments containing compost (Sordariales and Microascales) while the rest showed a decrease or remained unaltered. The mix biochar-compost may result the best option to support a more diverse microbial population in terms of soil functionality that is able to decompose both labile and recalcitrant carbon compounds. This may favour the resilience of the system against environmental stressors.
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Affiliation(s)
- Yolanda Risueño
- Universidad Politécnica de Cartagena, Escuela Técnica Superior de Ingeniería Agronómica, Departamento de Ingeniería Agronómica, Paseo Alfonso XIII, 48, 30203 Cartagena, Spain.
| | - César Petri
- IHSM-UMA-CSIC La Mayora, Departamento de Fruticultura Subtropical y Mediterránea, Avenida Dr. Wienberg, s/n, 29750 Algarrobo-Costa, Málaga, Spain.
| | - Héctor M Conesa
- Universidad Politécnica de Cartagena, Escuela Técnica Superior de Ingeniería Agronómica, Departamento de Ingeniería Agronómica, Paseo Alfonso XIII, 48, 30203 Cartagena, Spain.
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Wu B, Gaskell J, Held BW, Toapanta C, Vuong TV, Ahrendt S, Lipzen A, Zhang J, Schilling JS, Master E, Grigoriev IV, Blanchette RA, Cullen D, Hibbett DS. Retracted and Republished from: "Substrate-Specific Differential Gene Expression and RNA Editing in the Brown Rot Fungus Fomitopsis pinicola". Appl Environ Microbiol 2021; 87:e0032921. [PMID: 34313495 PMCID: PMC8353965 DOI: 10.1128/aem.00329-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 04/28/2021] [Indexed: 12/13/2022] Open
Abstract
Wood-decaying fungi tend to have characteristic substrate ranges that partly define their ecological niche. Fomitopsis pinicola is a brown rot species of Polyporales that is reported on 82 species of softwoods and 42 species of hardwoods. We analyzed gene expression levels of F. pinicola from submerged cultures with ground wood powder (sampled at 5 days) or solid wood wafers (sampled at 10 and 30 days), using aspen, pine, and spruce substrates (aspen was used only in submerged cultures). Fomitopsis pinicola expressed similar sets of wood-degrading enzymes typical of brown rot fungi across all culture conditions and time points. Nevertheless, differential gene expression was observed across all pairwise comparisons of substrates and time points. Genes exhibiting differential expression encode diverse enzymes with known or potential function in brown rot decay, including laccase, benzoquinone reductase, aryl alcohol oxidase, cytochrome P450s, and various glycoside hydrolases. Comparing transcriptomes from submerged cultures and wood wafers, we found that culture conditions had a greater impact on global expression profiles than substrate wood species. These findings highlight the need for standardization of culture conditions in studies of gene expression in wood-decaying fungi. IMPORTANCE All species of wood-decaying fungi occur on a characteristic range of substrates (host plants), which may be broad or narrow. Understanding the mechanisms that allow fungi to grow on particular substrates is important for both fungal ecology and applied uses of different feedstocks in industrial processes. We grew the wood-decaying polypore Fomitopsis pinicola on three different wood species—aspen, pine, and spruce—under various culture conditions. We found that F. pinicola is able to modify gene expression (transcription levels) across different substrate species and culture conditions. Many of the genes involved encode enzymes with known or predicted functions in wood decay. This study provides clues to how wood-decaying fungi may adjust their arsenal of decay enzymes to accommodate different host substrates.
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Affiliation(s)
- Baojun Wu
- Biology Department, Clark University, Worcester, Massachusetts, USA
| | - Jill Gaskell
- USDA Forest Products Laboratory, Madison, Wisconsin, USA
| | - Benjamin W. Held
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Cristina Toapanta
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Thu V. Vuong
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Steven Ahrendt
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Anna Lipzen
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | - Jiwei Zhang
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Jonathan S. Schilling
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Emma Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Igor V. Grigoriev
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Robert A. Blanchette
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Dan Cullen
- USDA Forest Products Laboratory, Madison, Wisconsin, USA
| | - David S. Hibbett
- Biology Department, Clark University, Worcester, Massachusetts, USA
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48
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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: 10] [Impact Index Per Article: 3.3] [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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Singh AK, Bilal M, Iqbal HMN, Meyer AS, Raj A. Bioremediation of lignin derivatives and phenolics in wastewater with lignin modifying enzymes: Status, opportunities and challenges. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 777:145988. [PMID: 33684751 DOI: 10.1016/j.scitotenv.2021.145988] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 02/14/2021] [Accepted: 02/15/2021] [Indexed: 02/08/2023]
Abstract
Lignin modifying enzymes from fungi and bacteria are potential biocatalysts for sustainable mitigation of different potentially toxic pollutants in wastewater. Notably, the paper and pulp industry generates enormous amounts of wastewater containing high amounts of complex lignin-derived chlorinated phenolics and sulfonated pollutants. The presence of these compounds in wastewater is a critical issue from environmental and toxicological perspectives. Some chloro-phenols are harmful to the environment and human health, as they exert carcinogenic, mutagenic, cytotoxic, and endocrine-disrupting effects. In order to address these most urgent concerns, the use of oxidative lignin modifying enzymes for bioremediation has come into focus. These enzymes catalyze modification of phenolic and non-phenolic lignin-derived substances, and include laccase and a range of peroxidases, specifically lignin peroxidase (LiP), manganese peroxidase (MnP), versatile peroxidase (VP), and dye-decolorizing peroxidase (DyP). In this review, we explore the key pollutant-generating steps in paper and pulp processing, summarize the most recently reported toxicological effects of industrial lignin-derived phenolic compounds, especially chlorinated phenolic pollutants, and outline bioremediation approaches for pollutant mitigation in wastewater from this industry, emphasizing the oxidative catalytic potential of oxidative lignin modifying enzymes in this regard. We highlight other emerging biotechnical approaches, including phytobioremediation, bioaugmentation, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based technology, protein engineering, and degradation pathways prediction, that are currently gathering momentum for the mitigation of wastewater pollutants. Finally, we address current research needs and options for maximizing sustainable biobased and biocatalytic degradation of toxic industrial wastewater pollutants.
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Affiliation(s)
- Anil Kumar Singh
- Environmental Microbiology Laboratory, Environmental Toxicology Group CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China.
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
| | - Anne S Meyer
- Department for Biotechnology and Biomedicine, Technical University of Denmark, Building 221, DK-2800 Lyngby, Denmark.
| | - Abhay Raj
- Environmental Microbiology Laboratory, Environmental Toxicology Group CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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50
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Xu W, Fan J, Wang Y, Wang Y, Zhu J, Ren A, Yu H, Shi L, Zhao M. Mitochondrial pyruvate carrier regulates the lignocellulosic decomposition rate through metabolism in Ganoderma lucidum. FEMS Microbiol Lett 2021; 368:6316105. [PMID: 34227669 DOI: 10.1093/femsle/fnab088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 07/02/2021] [Indexed: 11/14/2022] Open
Abstract
The activity of mitochondrial pyruvate carrier (MPC) can be modulated to regulate intracellular metabolism under different culture conditions. In Ganoderma lucidum, the role of MPC in regulating carbon sources remains unknown. By knocking down MPC genes (MPC1 and MPC2), this research found that the loss of MPC increased the growth rate of G. lucidum by ~30% in a medium with wood chips as a carbon source. Then cellulase and laccase activities were tested. Endoglucanase and laccase activity increased by ~50% and ~35%, respectively, in MPC knockdown mutants compared with that in the wild type strain. Finally, the expression levels of genes related to glycolysis were assayed, and the transcription levels of these enzymes were found to be increased by ~250% compared with the wild type strain. In conclusion, the regulation of intracellular metabolism by MPC provides a new way to improve the use of nondominant carbon sources such as lignocellulose.
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Affiliation(s)
- Wenzhao Xu
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, Jiangsu, P.R. China
| | - Junpei Fan
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, Jiangsu, P.R. China
| | - Yihong Wang
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, Jiangsu, P.R. China
| | - Yunxiao Wang
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, Jiangsu, P.R. China
| | - Jing Zhu
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, Jiangsu, P.R. China
| | - Ang Ren
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, Jiangsu, P.R. China
| | - Hanshou Yu
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, Jiangsu, P.R. China
| | - Liang Shi
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, Jiangsu, P.R. China
| | - Mingwen Zhao
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, Jiangsu, P.R. China
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