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Leroy A, Fanuel M, Alvarado C, Rogniaux H, Grisel S, Haon M, Berrin JG, Paës G, Guillon F. In situ imaging of LPMO action on plant tissues. Carbohydr Polym 2024; 343:122465. [PMID: 39174080 DOI: 10.1016/j.carbpol.2024.122465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/20/2024] [Accepted: 07/04/2024] [Indexed: 08/24/2024]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes that oxidatively cleave recalcitrant polysaccharides such as cellulose. Several studies have reported LPMO action in synergy with other carbohydrate-active enzymes (CAZymes) for the degradation of lignocellulosic biomass but direct LPMO action at the plant tissue level remains challenging to investigate. Here, we have developed a MALDI-MS imaging workflow to detect oxidised oligosaccharides released by a cellulose-active LPMO at cellular level on maize tissues. Using this workflow, we imaged LPMO action and gained insight into the spatial variation and relative abundance of oxidised and non-oxidised oligosaccharides. We reveal a targeted action of the LPMO related to the composition and organisation of plant cell walls.
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Affiliation(s)
- Amandine Leroy
- INRAE, UR 1268 BIA, 44316 Nantes, France; INRAE, Université de Reims Champagne Ardenne, FARE, UMR A 614, 51100 Reims, France.
| | - Mathieu Fanuel
- INRAE, UR 1268 BIA, 44316 Nantes, France; INRAE, BIBS Facility, 44316 Nantes, France.
| | | | - Hélène Rogniaux
- INRAE, UR 1268 BIA, 44316 Nantes, France; INRAE, BIBS Facility, 44316 Nantes, France.
| | - Sacha Grisel
- INRAE, Aix Marseille Université, Biodiversité et Biotechnologie Fongiques (BBF), 13009 Marseille, France; INRAE, Aix Marseille Université, 3PE platform, 13009 Marseille, France.
| | - Mireille Haon
- INRAE, Aix Marseille Université, Biodiversité et Biotechnologie Fongiques (BBF), 13009 Marseille, France; INRAE, Aix Marseille Université, 3PE platform, 13009 Marseille, France.
| | - Jean-Guy Berrin
- INRAE, Aix Marseille Université, Biodiversité et Biotechnologie Fongiques (BBF), 13009 Marseille, France.
| | - Gabriel Paës
- INRAE, Université de Reims Champagne Ardenne, FARE, UMR A 614, 51100 Reims, France.
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2
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Sarangi PK, Srivastava RK, Vivekanand V, Goksen G, Sahoo UK, Thakur TK, Debeaufort F, Uysal-Unalan I, Pugazhendhi A. Recovery of green phenolic compounds from lignin-based source: Role of ferulic acid esterase towards waste valorization and bioeconomic perspectives. ENVIRONMENTAL RESEARCH 2024; 256:119218. [PMID: 38782335 DOI: 10.1016/j.envres.2024.119218] [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: 02/05/2024] [Revised: 05/08/2024] [Accepted: 05/21/2024] [Indexed: 05/25/2024]
Abstract
The production of chemicals/products so far relies on fossil-based resources with the creation of several environmental problems at the global level. In this situation, a sustainable and circular economy model is necessitated to mitigate global environmental issues. Production of biowaste from various processing industries also creates environmental issues which would be valorized for the production of industrially important reactive and bioactive compounds. Lignin acts as a vital part in biowaste composition which can be converted into a wide range of phenolic compounds. The phenolic compounds have attracted much attention, owing to their influence on diverse not only organoleptic parameters, such as taste or color, but also active agents for active packaging systems. Crop residues of varied groups, which are an affluent source of lignocellulosic biomass could serve as a renewable resource for the biosynthesis of ferulic acid (FA). FA is obtained by the FA esterase enzyme action, and it can be further converted into various tail end phenolic flavor green compounds like vanillin, vanillic acid and hydroxycinnamic acid. Lignin being renewable in nature, processing and management of biowastes towards sustainability is the need as far as the global industrial point is concerned. This review explores all the approaches for conversion of lignin into value-added phenolic compounds that could be included to packaging applications. These valorized products can exhibit the antioxidant, antimicrobial, cardioprotective, anti-inflammatory and anticancer properties, and due to these features can emerge to incorporate them into production of functional foods and be utilization of them at active food packaging application. These approaches would be an important step for utilization of the recovered bioactive compounds at the nutraceutical and food industrial sectors.
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Affiliation(s)
| | - Rajesh Kumar Srivastava
- Department of Biotechnology, GST, Gandhi Institute of Technology and Management (GITAM), Visakhapatnam, 530045, A.P., India
| | - Vivekanand Vivekanand
- Center for Energy and Environment, Malaviya National Institute of Technology Jaipur, 302 017, Rajasthan, India
| | - Gulden Goksen
- Department of Food Technology, Vocational School of Technical Sciences, Mersin Tarsus Organized Industrial Zone, Tarsus University, 33100, Mersin, Turkey
| | | | | | - Frederic Debeaufort
- Department of BioEngineering, Institute of Technology Dijon Auxerre, University of Burgundy, 7 Blvd Docteur Petitjean, 20178 Dijon Cedex, France
| | - Ilke Uysal-Unalan
- Department of Food Science, Aarhus University, Agro Food Park 48, 8200, Aarhus N, Denmark; CiFOOD - Center for Innovative Food Research, Aarhus University, Agro Food Park 48, 8200, Aarhus N, Denmark
| | - Arivalagan Pugazhendhi
- School of Engineering, Lebanese American University, Byblos, Lebanon; Centre for Herbal Pharmacology and Environmental Sustainability, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam 603103, Tamil Nadu, India.
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Lu M, Hao Y, Lin B, Huang Z, Zhang Y, Chen L, Li K, Li J. The bioaugmentation effect of microbial inoculants on humic acid formation during co-composting of bagasse and cow manure. ENVIRONMENTAL RESEARCH 2024; 252:118604. [PMID: 38548254 DOI: 10.1016/j.envres.2024.118604] [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: 12/14/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 06/07/2024]
Abstract
The effective degradation of recalcitrant lignocellulose has emerged as a bottleneck for the humification of compost, and strategies are required to improve the efficiency of bagasse composting. Bioaugmentation is a promising method for promoting compost maturation and improving the quality of final compost. In this study, the bioaugmentation effects of microbial inoculants on humic acid (HA) formation during lignocellulosic composting were explored. In the inoculated group, the maximum temperature was increased to 72.5 °C, and the phenol-protein condensation and Maillard humification pathways were enhanced, thus increasing the HA content by 43.85%. After inoculation, the intensity of the microbial community interactions increased, particularly for fungi (1.4-fold). Macrogenomic analysis revealed that inoculation enriched thermophilic bacteria and lignocellulose-degrading fungi and increased the activity of carbohydrate-active enzymes and related metabolic functions, which effectively disrupted the recalcitrant structure of lignocellulose to achieve a high humification degree. Spearman correlation analysis indicated that Stappia of the Proteobacteria phylum, Ilumatobacter of the Actinomycetes phylum, and eleven genera of Ascomycota were the main HA producers. This study provides new ideas for bagasse treatment and recycling and realizing the comprehensive use of resources.
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Affiliation(s)
- Mengling Lu
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, Guangxi, China
| | - Yuhao Hao
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, Guangxi, China
| | - Binfeng Lin
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, Guangxi, China
| | - Zhi Huang
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, Guangxi, China
| | - Yu Zhang
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, Guangxi, China
| | - Liang Chen
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, Guangxi, China
| | - Kai Li
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, Guangxi, China
| | - Jianbin Li
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, Guangxi, China; Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning 530004, Guangxi, China.
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4
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Panneerselvam P, Senapati A, Mitra D, Priyadarshini A, Shadangi S, Behera S, Kumar U, Kumar A, Shahid M, Sharma S, Garhwal RS, Mani I, Kumar Nayak A. Enhancing soil quality and yield through microbial assisted in-situ residue management in rice-rice cropping system in Odisha, Eastern India. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 358:120916. [PMID: 38642486 DOI: 10.1016/j.jenvman.2024.120916] [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: 12/13/2023] [Revised: 03/21/2024] [Accepted: 04/13/2024] [Indexed: 04/22/2024]
Abstract
Crop residue management has become more challenging with intensive agricultural operations. Zero tillage and crop residue returns, along with the enhancement of in-situ residue decomposition through microbial intervention, are essential measures for preserving and enhancing soil quality. To address this problem in view of stubble burning, field experiments were conducted in rice-rice (variety Swarna) cropping systems under lowland conditions, wherein the following different residue management practices were adopted viz., conventional cultivation (CC), residue incorporation (RI @ 6 t paddy straw ha-1), residue retention (RR @6 t paddy straw ha-1), and zero tillage (ZT). In this experiment, two microbial products i.e. solid microbial consortium (SMC) at 2.0 kg ha-1) and capsule (10 numbers ha-1), were evaluated in both Rabi (dry) and Kharif (wet) seasons under different residue management practices. The results on soil microbial properties showed that application of either SMC or capsule based formulation could significantly improve the soil organic carbon (SOC) content in ZT (9.51 g/kg), followed by RI (9.36 g/kg), and RR (9.34 g/kg) as compared to CC (7.61 g/kg). There were significant differences in the soil functional properties (AcP, AkP, FDA, and DHA) with microbial interventions across all residue management practices. SOC was significantly positive correlated with cellulase (R2 = 0.64, p < 0.001), β-glucosidase (R2 = 0.61, p < 0.001), and laccase (R2 = 0.66, p < 0.001) activity; however, the regression coefficients varied significantly with microbial intervention. Moreover, the availability of N, P, and K in soil was significantly (p < 0.05) improved under microbial treatments with either RR or RI practices. Among the different methods of residues management practices, RI with microbial intervention registered a consistent yield improvement (8.4-17.8%) compared to conventional practices with microbial intervention. The present findings prove that the application of decomposing microbial consortia for in-situ rice residue management under field conditions significantly enhances soil quality and crop yield compared to conventional practices.
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Affiliation(s)
| | - Ansuman Senapati
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Debasis Mitra
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | | | - Smriti Shadangi
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Suchismita Behera
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Upendra Kumar
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Anjani Kumar
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Mohammad Shahid
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Sandeep Sharma
- Department of Soil Science, Punjab Agricultural University, Punjab, 141004, India
| | - Rajendra Singh Garhwal
- College of Agriculture, Chaudhary Charan Singh Haryana Agriculture University, Hisar, Haryana, 125004, India
| | - Indra Mani
- Division of Agricultural Engineering, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, 110012, India
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Sharma S, Kumawat KC, Kaur P, Kaur S, Gupta N. Crop residue heterogeneity: Decomposition by potential indigenous ligno-cellulolytic microbes and enzymatic profiling. CURRENT RESEARCH IN MICROBIAL SCIENCES 2024; 6:100227. [PMID: 38444877 PMCID: PMC10912851 DOI: 10.1016/j.crmicr.2024.100227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024] Open
Abstract
The continuous depletion of fossil resources, energy-crisis and environmental pollution has gained popularity for careful selection of suitable microbial consortium to efficiently decompose crop residue and facilitate nutrient cycling. While crop residue is commonly incorporated into soil, the impact of the heterogeneity of residue on decomposition and biological mechanisms involved in extracellular carbon (C) cycle related enzyme activities remain not fully understood. To address this problem, an incubation study was conducted on chemical heterogeneity of straw and root residue with indigenous ligno-cellulolytic microbial consortium on extracellular enzymes as their activity is crucial for making in-situ residue management decisions under field condition. The activity of extracellular enzymes in different substrates showed differential variation with the type of enzyme and ranged from 16.9 to 77.6 µg mL-1, 135.7 to 410.8 µg mL-1, 66.9 to 177.1 µg mL-1 and 42.1 to 160.9 µg mL-1 for cellulase, xylanase, laccase and lignin peroxidase, respectively. Extracellular enzyme activities were sensitive to heterogeneity of biochemical constituent's present in straw and root residues and enhanced the decomposition processes with indigenous ligno-cellulolytic microbial consortium (Bacillus altitudinis, Streptomyces flavomacrosporus and Aspergillus terreus). Correlation matrix elucidated A. terreus and B. altitudinis as potential indigenous ligno-cellulolytic microbial inoculant influencing soil enzymatic activity (p < 0.001). This research work demonstrates a substantial impact of chemically diverse crop residues on the decomposition of both straw and root. It also highlights the pivotal role played by key indigenous decomposers and interactions between different microorganisms in governing the decomposition of straw and root primarily through release of extracellular enzyme. Consequently, it is novel bio-emerging strategy suggested that incorporation of the crop residues under field conditions should be carried out in conjunction with the potential indigenous ligno-cellulolytic microbial consortium for efficient decomposition in the short period of time under sustainable agriculture system.
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Affiliation(s)
- Sandeep Sharma
- Department of Soil Science, Punjab Agricultural University, Ludhiana, Punjab 141004, India
| | - Kailash Chand Kumawat
- Department of Soil Science, Punjab Agricultural University, Ludhiana, Punjab 141004, India
- Department of Industrial Microbiology, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences (SHUATS), Prayagraj, Uttar Pradesh 211007, India
| | - Paawan Kaur
- Department of Soil Science, Punjab Agricultural University, Ludhiana, Punjab 141004, India
| | - Sukhjinder Kaur
- Department of Soil Science, Punjab Agricultural University, Ludhiana, Punjab 141004, India
| | - Nihar Gupta
- Department of Soil Science, Punjab Agricultural University, Ludhiana, Punjab 141004, India
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6
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Mitra D, Panneerselvam P, Mohapatra PK, Pellegrini M, Selvakumar G. Emerging frontiers in microbial-mediated utilization of crop residues for economically valuable biomaterials. CURRENT RESEARCH IN MICROBIAL SCIENCES 2024; 6:100225. [PMID: 38380107 PMCID: PMC10877099 DOI: 10.1016/j.crmicr.2024.100225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024] Open
Abstract
Agricultural crop residues include leftover and unmarketable materials, such as crop stover, weeds, leaf litter, sawdust, forest litter, and livestock manure originating from crop cultivation, and post-harvest activities. Such residues are a storehouse of plant nutrients and several other resources and therefore need to be managed in an environment- friendly manner with minimum loss of plant nutrients and other resources that can be recovered. Microbial starter consortia are a key component in the rapid recycling of farm residue wastes and the production of other valuable products, such as biogas, bioethanol/biofuel, enzymes, molecules, and metabolites. Recent advances in microbial biotechnology can also facilitate the conversion of farm residues into economically valuable materials, i.e. soil additives, adsorbents, energy, and enzymes, thereby contributing to a circular economy. This special issue attempts to compile the latest advancements in the field of agricultural crop residue management for enhanced nutrient recycling and resource recovery by the use of compost starters and inoculant formulations.
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Affiliation(s)
- Debasis Mitra
- Department of Microbiology, Raiganj University, Raiganj, 733134, West Bengal, India
- Department of Microbiology, Graphic Era (Deemed to be University), 566/6, Bell Road, Clement Town, Dehradun, 248002, Uttarakhand, India
| | - Periyasamy Panneerselvam
- Crop Production Division, ICAR - National Rice Research Institute, Cuttack, 753006, Odisha, India
| | | | - Marika Pellegrini
- Department of Life, Health and Environmental Sciences, University of L'Aquila, Coppito, L'Aquila, Italy
| | - G. Selvakumar
- Division of Natural Resources, ICAR-Indian Institute of Horticultural Research, Hesaraghatta Lake Post, Bengaluru, 560089, Karnataka, India
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Sun S, Li F, Li M, Zhang W, Jiang Z, Zhao H, Pu Y, Ragauskas AJ, Dai SY, Zhang X, Yu H, Yuan JS, Xie S. Lytic polysaccharide monooxygenase synergized with lignin-degrading enzymes for efficient lignin degradation. iScience 2023; 26:107870. [PMID: 37766973 PMCID: PMC10520884 DOI: 10.1016/j.isci.2023.107870] [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: 12/05/2022] [Revised: 05/09/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Even though the discovery of lytic polysaccharide monooxygenases (LPMOs) has fundamentally shifted our understanding of biomass degradation, most of the current studies focused on their roles in carbohydrate oxidation. However, no study demonstrated if LPMO could directly participate to the process of lignin degradation in lignin-degrading microbes. This study showed that LPMO could synergize with lignin-degrading enzymes for efficient lignin degradation in white-rot fungi. The transcriptomics analysis of fungi Irpex lacteus and Dichomitus squalens during their lignocellulosic biomass degradation processes surprisingly highlighted that LPMOs co-regulated with lignin-degrading enzymes, indicating their more versatile roles in the redox network. Biochemical analysis further confirmed that the purified LPMO from I. lacteus CD2 could use diverse electron donors to produce H2O2, drive Fenton reaction, and synergize with manganese peroxidase for lignin oxidation. The results thus indicated that LPMO might uniquely leverage the redox network toward dynamic and efficient degradation of different cell wall components.
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Affiliation(s)
- Su Sun
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- College of Urban Construction, Wuchang Shouyi University, Wuhan 430064, China
| | - Fei Li
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Department of Bioengineering, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, China
| | - Muzi Li
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Texas A&M Agrilife Synthetic, Systems Biology Innovation Hub, Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
| | - Wenqian Zhang
- Texas A&M Agrilife Synthetic, Systems Biology Innovation Hub, Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
| | - Zhenxiong Jiang
- Texas A&M Agrilife Synthetic, Systems Biology Innovation Hub, Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
| | - Honglu Zhao
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yunqiao Pu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Arthur J. Ragauskas
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Chemical and Biomolecular Engineering, Department of Forestry, Wildlife, and Fisheries, University of Tennessee, Knoxville, TN 37996, USA
| | - Susie Y. Dai
- Texas A&M Agrilife Synthetic, Systems Biology Innovation Hub, Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
| | - Xiaoyu Zhang
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Hongbo Yu
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Joshua S. Yuan
- Department of Energy, Environmental, and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Shangxian Xie
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
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8
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Raza T, Qadir MF, Khan KS, Eash NS, Yousuf M, Chatterjee S, Manzoor R, Rehman SU, Oetting JN. Unrevealing the potential of microbes in decomposition of organic matter and release of carbon in the ecosystem. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 344:118529. [PMID: 37418912 DOI: 10.1016/j.jenvman.2023.118529] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/13/2023] [Accepted: 06/25/2023] [Indexed: 07/09/2023]
Abstract
Organic matter decomposition is a biochemical process with consequences affecting climate change and ecosystem productivity. Once decomposition begins, C is lost as CO2 or sequestered into more recalcitrant carbon difficult to further degradation. As microbial respiration releases carbon dioxide into the atmosphere, microbes act as gatekeepers in the whole process. Microbial activities were found to be the second largest CO2 emission source in the environment after human activities (industrialization), and research investigations suggest that this may have affected climate change over the past few decades. It is crucial to note that microbes are major contributors in the whole C cycle (decomposition, transformation, and stabilization). Therefore, imbalances in the C cycle might be causing changes in the entire carbon content of the ecosystem. The significance of microbes, especially soil bacteria in the terrestrial carbon cycle requires more attention. This review focuses on the factors that affect microorganism behavior during the breakdown of organic materials. The key factors affecting the microbial degradation processes are the quality of the input material, nitrogen, temperature, and moisture content. In this review, we suggest that to address global climate change and its effects on agricultural systems and vice versa, there is a need to double-up on efforts and conduct new research studies to further evaluate the potential of microbial communities to reduce their contribution to terrestrial carbon emission.
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Affiliation(s)
- Taqi Raza
- The Biosystems Engineering & Soil Science, University of Tennessee, Knoxville, USA.
| | - Muhammad Farhan Qadir
- Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad 38040, Pakistan
| | - Khuram Shehzad Khan
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, China
| | - Neal S Eash
- The Biosystems Engineering & Soil Science, University of Tennessee, Knoxville, USA
| | - Muhammad Yousuf
- Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad 38040, Pakistan
| | - Sumanta Chatterjee
- USDA ARS, Hydrology and Remote Sensing Laboratory, 10300 Baltimore Avenue, Beltsville, MD 20705, USA; ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Rabia Manzoor
- Land Resources Research Institute, National Agricultural Research Centre, Islamabad, Pakistan
| | - Sana Ur Rehman
- National Research Center of Intercropping, The Islamia University of Bahawalpur, Pakistan
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9
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Panneerselvam P, Senapati A, Chidambaranathan P, Prabhukarthikeyan SR, Mitra D, Pandi Govindharaj GP, Nayak AK, Anandan A. Long-term impact of pulses crop rotation on soil fungal diversity in aerobic and wetland rice cultivation. Fungal Biol 2023; 127:1053-1066. [PMID: 37344007 DOI: 10.1016/j.funbio.2023.04.005] [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: 09/28/2022] [Revised: 03/17/2023] [Accepted: 04/17/2023] [Indexed: 06/23/2023]
Abstract
Pulse crop rotation in rice cultivation is a widely accepted agronomic practice. Depending upon the water regime, rice cultivation has been classified into wetland and aerobic practices. However, no studies have been conducted so far to understand the impact of pulse crop rotation and rice mono-cropping on fungal diversity, particularly in aerobic soil. A targeted metagenomic study was conducted to compare the effects of crop rotations (rice-rice and rice-pulse) on fungal diversity in wetland and aerobic rice soils. Out of 445 OTUs, 41.80% was unknown and 58.20% were assigned to six phyla, namely Ascomycota (56.57%), Basidiomycota (1.32%), Zygomycota (0.22%), Chytridiomycota (0.04%), Glomeromycota (0.03%), and Blastocladiomycota (0.02%). Functional trait analysis found wetland rice-pulse rotation increased symbiotrophs (36.7%) and saprotrophs (62.1%) population, whereas higher pathotrophs were found in aerobic rice-rice (62.8%) and rice-pulse (61.4%) cropping system. Certain soil nutrients played a major role in shaping the fungal community; Ca had significant (p < 0.05) positive impact on saprotroph, symbiotroph and endophytes, whereas Cu had significant (p < 0.05) negative impact on pathotrophs. This study showed that rice-pulse crop rotation could enhance the saprophytic and symbiotic fungal diversity in wetland and reduce the population of pathogens in aerobic rice cultivation.
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Affiliation(s)
- Periyasamy Panneerselvam
- Crop Production Division, ICAR - National Rice Research Institute, Cuttack, Odisha, 753006, India.
| | - Ansuman Senapati
- Crop Production Division, ICAR - National Rice Research Institute, Cuttack, Odisha, 753006, India
| | | | - S R Prabhukarthikeyan
- Crop Protection Division, ICAR - National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Debasis Mitra
- Crop Production Division, ICAR - National Rice Research Institute, Cuttack, Odisha, 753006, India
| | | | - Amaresh Kumar Nayak
- Crop Production Division, ICAR - National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Annamalai Anandan
- Crop Improvement Division, ICAR - National Rice Research Institute, Cuttack, Odisha, 753006, India; ICAR-Indian Institute of Seed Science, Regional Station, Bangalore, 560065, India.
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10
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Oelmüller R, Tseng YH, Gandhi A. Signals and Their Perception for Remodelling, Adjustment and Repair of the Plant Cell Wall. Int J Mol Sci 2023; 24:ijms24087417. [PMID: 37108585 PMCID: PMC10139151 DOI: 10.3390/ijms24087417] [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: 02/20/2023] [Revised: 04/04/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
The integrity of the cell wall is important for plant cells. Mechanical or chemical distortions, tension, pH changes in the apoplast, disturbance of the ion homeostasis, leakage of cell compounds into the apoplastic space or breakdown of cell wall polysaccharides activate cellular responses which often occur via plasma membrane-localized receptors. Breakdown products of the cell wall polysaccharides function as damage-associated molecular patterns and derive from cellulose (cello-oligomers), hemicelluloses (mainly xyloglucans and mixed-linkage glucans as well as glucuronoarabinoglucans in Poaceae) and pectins (oligogalacturonides). In addition, several types of channels participate in mechanosensing and convert physical into chemical signals. To establish a proper response, the cell has to integrate information about apoplastic alterations and disturbance of its wall with cell-internal programs which require modifications in the wall architecture due to growth, differentiation or cell division. We summarize recent progress in pattern recognition receptors for plant-derived oligosaccharides, with a focus on malectin domain-containing receptor kinases and their crosstalk with other perception systems and intracellular signaling events.
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Affiliation(s)
- Ralf Oelmüller
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Department of Plant Physiology, Friedrich-Schiller-University, 07743 Jena, Germany
| | - Yu-Heng Tseng
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Department of Plant Physiology, Friedrich-Schiller-University, 07743 Jena, Germany
| | - Akanksha Gandhi
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Department of Plant Physiology, Friedrich-Schiller-University, 07743 Jena, Germany
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11
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Zhang Y, Pan D, Xiao P, Xu Q, Geng F, Zhang X, Zhou X, Xu H. A novel lytic polysaccharide monooxygenase from enrichment microbiota and its application for shrimp shell powder biodegradation. Front Microbiol 2023; 14:1097492. [PMID: 37007517 PMCID: PMC10057547 DOI: 10.3389/fmicb.2023.1097492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/27/2023] [Indexed: 03/17/2023] Open
Abstract
Lytic polysaccharide monooxygenases (LPMO) are expected to change the current status of chitin resource utilization. This study reports that targeted enrichment of the microbiota was performed with chitin by the selective gradient culture technique, and a novel LPMO (M2822) was identified from the enrichment microbiota metagenome. First, soil samples were screened based on soil bacterial species and chitinase biodiversity. Then gradient enrichment culture with different chitin concentrations was carried out. The efficiency of chitin powder degradation was increased by 10.67 times through enrichment, and chitin degradation species Chitiniphilus and Chitinolyticbacter were enriched significantly. A novel LPMO (M2822) was found in the metagenome of the enriched microbiota. Phylogenetic analysis showed that M2822 had a unique phylogenetic position in auxiliary activity (AA) 10 family. The analysis of enzymatic hydrolysate showed that M2822 had chitin activity. When M2822 synergized with commercial chitinase to degrade chitin, the yield of N-acetyl glycosamine was 83.6% higher than chitinase alone. The optimum temperature and pH for M2822 activity were 35°C and 6.0. The synergistic action of M2822 and chitin-degrading enzymes secreted by Chitiniphilus sp. LZ32 could efficiently hydrolyze shrimp shell powder. After 12 h of enzymatic hydrolysis, chitin oligosaccharides (COS) yield reached 4,724 μg/mL. To our knowledge, this work is the first study to mine chitin activity LPMO in the metagenome of enriched microbiota. The obtained M2822 showed application prospects in the efficient production of COS.
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Affiliation(s)
- Yang Zhang
- School of Life Science, Liaocheng University, Liaocheng, Shandong, China
| | - Delong Pan
- School of Life Science, Liaocheng University, Liaocheng, Shandong, China
| | - Peiyao Xiao
- School of Life Science, Liaocheng University, Liaocheng, Shandong, China
| | - Qianqian Xu
- School of Life Science, Liaocheng University, Liaocheng, Shandong, China
| | - Fan Geng
- School of Life Science, Liaocheng University, Liaocheng, Shandong, China
| | - Xinyu Zhang
- School of Life Science, Liaocheng University, Liaocheng, Shandong, China
| | - Xiuling Zhou
- School of Life Science, Liaocheng University, Liaocheng, Shandong, China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
- *Correspondence: Xiuling Zhou,
| | - Hong Xu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
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12
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Fungal Assisted Valorisation of Polymeric Lignin: Mechanism, Enzymes and Perspectives. Catalysts 2023. [DOI: 10.3390/catal13010149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Lignocellulose is considered one of the significant recalcitrant materials and also is difficult to break down because of its complex structure. Different microbes such as bacteria and fungi are responsible for breaking down these complex lignin structures. This article discussed briefly the lignin-degrading bacteria and their critical steps involved in lignin depolymerization. In addition, fungi are regarded as the ideal microorganism for the degradation of lignin because of their highly effective hydrolytic and oxidative enzyme systems for the breakdown of lignocellulosic materials. The white rot fungi, mainly belonging to basidiomycetes, is the main degrader of lignin among various microorganisms. This could be achieved because of the presence of lignolytic enzymes such as laccases, lignin peroxidases, and manganese peroxidases. The significance of the fungi and lignolytic enzyme’s role in lignin depolymerization, along with its mechanism and chemical pathways, are emphasized in this article.
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13
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Tamburino R, Castiglia D, Marcolongo L, Sannino L, Ionata E, Scotti N. Tobacco Plastid Transformation as Production Platform of Lytic Polysaccharide MonoOxygenase Auxiliary Enzymes. Int J Mol Sci 2022; 24:ijms24010309. [PMID: 36613758 PMCID: PMC9820616 DOI: 10.3390/ijms24010309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
Plant biomass is the most abundant renewable resource in nature. In a circular economy perspective, the implementation of its bioconversion into fermentable sugars is of great relevance. Lytic Polysaccharide MonoOxygenases (LPMOs) are accessory enzymes able to break recalcitrant polysaccharides, boosting biomass conversion and subsequently reducing costs. Among them, auxiliary activity of family 9 (AA9) acts on cellulose in synergism with traditional cellulolytic enzymes. Here, we report for the first time, the production of the AA9 LPMOs from the mesophilic Trichoderma reesei (TrAA9B) and the thermophilic Thermoascus aurantiacus (TaAA9B) microorganisms in tobacco by plastid transformation with the aim to test this technology as cheap and sustainable manufacture platform. In order to optimize recombinant protein accumulation, two different N-terminal regulatory sequences were used: 5' untranslated region (5'-UTR) from T7g10 gene (DC41 and DC51 plants), and 5' translation control region (5'-TCR), containing the 5'-UTR and the first 14 amino acids (Downstream Box, DB) of the plastid atpB gene (DC40 and DC50 plants). Protein yields ranged between 0.5 and 5% of total soluble proteins (TSP). The phenotype was unaltered in all transplastomic plants, except for the DC50 line accumulating AA9 LPMO at the highest level, that showed retarded growth and a mild pale green phenotype. Oxidase activity was spectrophotometrically assayed and resulted higher for the recombinant proteins without the N-terminal fusion (DC41 and DC51), with a 3.9- and 3.4-fold increase compared to the fused proteins.
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Affiliation(s)
- Rachele Tamburino
- CNR-IBBR, Institute of Biosciences and BioResources, 80055 Portici, Italy
| | - Daniela Castiglia
- CNR-IBBR, Institute of Biosciences and BioResources, 80055 Portici, Italy
- CNR-ICB, Institute of Biomolecular Chemistry, 80078 Pozzuoli, Italy
| | | | - Lorenza Sannino
- CNR-IBBR, Institute of Biosciences and BioResources, 80055 Portici, Italy
| | - Elena Ionata
- CNR-IRET, Research Institute on Terrestrial Ecosystems, 80131 Naples, Italy
| | - Nunzia Scotti
- CNR-IBBR, Institute of Biosciences and BioResources, 80055 Portici, Italy
- Correspondence:
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14
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Jakhar AM, Aziz I, Kaleri AR, Hasnain M, Haider G, Ma J, Abideen Z. Nano-fertilizers: A sustainable technology for improving crop nutrition and food security. NANOIMPACT 2022; 27:100411. [PMID: 35803478 DOI: 10.1016/j.impact.2022.100411] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/19/2022] [Accepted: 06/26/2022] [Indexed: 05/21/2023]
Abstract
Excessive use of synthetic fertilizers cause economic burdens, increasing soil, water and atmospheric pollution. Nano-fertilizers have shown great potential for their sustainable uses in soil fertility, crop production and with minimum or no environmental tradeoffs. Nano-fertilizers are of submicroscopic sizes, have a large surface area to volume ratio, can have nutrient encapsulation, and greater mobility hence they may increase plant nutrient access and crop yield. Due to these properties, nano-fertilizers are regarded as deliverable 'smart system of nutrients'. However, the problems in the agroecosystem are broader than existing developments. For example, nutrient delivery in different physicochemical properties of soils, moisture, and other agro-ecological conditions is still a challenge. In this context, the present review provides an overview of various uses of nanotechnology in agriculture, preference of nano-fertilizers over the conventional fertilizers, nano particles formation, mobility, and role in heterogeneous soils, with special emphasis on the development and use of chitosan-based nano-fertilizers.
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Affiliation(s)
- Ali Murad Jakhar
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang Sichuan 621010, China; Institute of Plant Sciences, University of Sindh, Jamshoro, Pakistan
| | - Irfan Aziz
- Dr. Muhammad Ajmal Khan Institute of Sustainable Halophyte Utilization, University of Karachi, Karachi 75270, Pakistan
| | - Abdul Rasheed Kaleri
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang Sichuan 621010, China
| | - Maria Hasnain
- Department of Biotechnology, Lahore College for Women University, Lahore, Pakistan
| | - Ghulam Haider
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Jiahua Ma
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang Sichuan 621010, China.
| | - Zainul Abideen
- Dr. Muhammad Ajmal Khan Institute of Sustainable Halophyte Utilization, University of Karachi, Karachi 75270, Pakistan.
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Rouina H, Tseng YH, Nataraja KN, Uma Shaanker R, Krüger T, Kniemeyer O, Brakhage A, Oelmüller R. Comparative Secretome Analyses of Trichoderma/Arabidopsis Co-cultures Identify Proteins for Salt Stress, Plant Growth Promotion, and Root Colonization. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.808430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Numerous Trichoderma strains are beneficial for plants, promote their growth, and confer stress tolerance. A recently described novel Trichoderma strain strongly promotes the growth of Arabidopsis thaliana seedlings on media with 50 mM NaCl, while 150 mM NaCl strongly stimulated root colonization and induced salt-stress tolerance in the host without growth promotion. To understand the dynamics of plant-fungus interaction, we examined the secretome from both sides and revealed a substantial change under different salt regimes, and during co-cultivation. Stress-related proteins, such as a fungal cysteine-rich Kp4 domain-containing protein which inhibits plant cell growth, fungal WSC- and CFEM-domain-containing proteins, the plant calreticulin, and cell-wall modifying enzymes, disappear when the two symbionts are co-cultured under high salt concentrations. In contrast, the number of lytic polysaccharide monooxygenases increases, which indicates that the fungus degrades more plant lignocellulose under salt stress and its lifestyle becomes more saprophytic. Several plant proteins involved in plant and fungal cell wall modifications and root colonization are only found in the co-cultures under salt stress, while the number of plant antioxidant proteins decreased. We identified symbiosis- and salt concentration-specific proteins for both partners. The Arabidopsis PYK10 and a fungal prenylcysteine lyase are only found in the co-culture which promoted plant growth. The comparative analysis of the secretomes supports antioxidant enzyme assays and suggests that both partners profit from the interaction under salt stress but have to invest more in balancing the symbiosis. We discuss the role of the identified stage- and symbiosis-specific fungal and plant proteins for salt stress, and conditions promoting root colonization and plant growth.
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