51
|
Xu Z, Lei P, Zhai R, Wen Z, Jin M. Recent advances in lignin valorization with bacterial cultures: microorganisms, metabolic pathways, and bio-products. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:32. [PMID: 30815030 PMCID: PMC6376720 DOI: 10.1186/s13068-019-1376-0] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/08/2019] [Indexed: 05/09/2023]
Abstract
Lignin is the most abundant aromatic substrate on Earth and its valorization technologies are still under developed. Depolymerization and fragmentation are the predominant preparatory strategies for valorization of lignin to chemicals and fuels. However, due to the structural heterogeneity of lignin, depolymerization and fragmentation typically result in diverse product species, which require extensive separation and purification procedures to obtain target products. For lignin valorization, bacterial-based systems have attracted increasing attention because of their diverse metabolisms, which can be used to funnel multiple lignin-based compounds into specific target products. Here, recent advances in lignin valorization using bacteria are critically reviewed, including lignin-degrading bacteria that are able to degrade lignin and use lignin-associated aromatics, various associated metabolic pathways, and application of bacterial cultures for lignin valorization. This review will provide insight into the recent breakthroughs and future trends of lignin valorization based on bacterial systems.
Collapse
Affiliation(s)
- Zhaoxian Xu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094 China
| | - Peng Lei
- Nanjing Institute for Comprehensive Utilization of Wild Plants, Nanjing, 211111 China
| | - Rui Zhai
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094 China
| | - Zhiqiang Wen
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094 China
| | - Mingjie Jin
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094 China
| |
Collapse
|
52
|
Functional characterization of ligninolytic Klebsiella spp. strains associated with soil and freshwater. Arch Microbiol 2018; 200:1267-1278. [PMID: 29947838 DOI: 10.1007/s00203-018-1532-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 05/16/2018] [Accepted: 05/26/2018] [Indexed: 10/14/2022]
Abstract
Overcoming recalcitrance of lignin has motivated bioprospecting of high-yielding enzymes from environmental ligninolytic microorganisms associated with lignocellulose degrading-systems. Here, we performed isolation of 21 ligninolytic strains belonging to the genus Klebsiella spp., driven by the presence of lignin in the media. The fastest-growing strains (FP10-5.23, FP10-5.22 and P3TM1) reached the stationary phase in approximately 24 h, in the media containing lignin as the main carbon source. The strains showed biochemical evidence of ligninolytic potential in liquid- and solid media-converting dyes, which the molecular structures are similar to lignin fragments. In liquid medium, higher levels of dye decolorization was observed for P3TM.1 in the presence of methylene blue, reaching 98% decolorization in 48 h. The highest index values (1.25) were found for isolates P3TM.1 and FP10-5.23, in the presence of toluidine blue. The genomic analysis revealed the presence of more than 20 genes associated with known prokaryotic lignin-degrading systems. Identification of peroxidases (lignin peroxidase-LiP, dye-decolorizing peroxidase-DyP, manganese peroxidase-MnP) and auxiliary activities (AA2, AA3, AA6 and AA10 families) among the genetic repertoire suggest the ability to produce extracellular enzymes able to attack phenolic and non-phenolic lignin structures. Our results suggest that the Klebsiella spp. associated with fresh water and soil may play important role in the cycling of recalcitrant molecules in the Caatinga (desert-like Brazilian biome), and represent a potential source of lignin-degrading enzymes with biotechnological applications.
Collapse
|
53
|
Kumar M, Verma S, Gazara RK, Kumar M, Pandey A, Verma PK, Thakur IS. Genomic and proteomic analysis of lignin degrading and polyhydroxyalkanoate accumulating β-proteobacterium Pandoraea sp. ISTKB. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:154. [PMID: 29991962 PMCID: PMC5987411 DOI: 10.1186/s13068-018-1148-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 05/17/2018] [Indexed: 05/06/2023]
Abstract
BACKGROUND Lignin is a major component of plant biomass and is recalcitrant to degradation due to its complex and heterogeneous aromatic structure. The biomass-based research mainly focuses on polysaccharides component of biomass and lignin is discarded as waste with very limited usage. The sustainability and success of plant polysaccharide-based biorefinery can be possible if lignin is utilized in improved ways and with minimal waste generation. Discovering new microbial strains and understanding their enzyme system for lignin degradation are necessary for its conversion into fuel and chemicals. The Pandoraea sp. ISTKB was previously characterized for lignin degradation and successfully applied for pretreatment of sugarcane bagasse and polyhydroxyalkanoate (PHA) production. In this study, genomic analysis and proteomics on aromatic polymer kraft lignin and vanillic acid are performed to find the important enzymes for polymer utilization. RESULTS Genomic analysis of Pandoraea sp. ISTKB revealed the presence of strong lignin degradation machinery and identified various candidate genes responsible for lignin degradation and PHA production. We also applied label-free quantitative proteomic approach to identify the expression profile on monoaromatic compound vanillic acid (VA) and polyaromatic kraft lignin (KL). Genomic and proteomic analysis simultaneously discovered Dyp-type peroxidase, peroxidases, glycolate oxidase, aldehyde oxidase, GMC oxidoreductase, laccases, quinone oxidoreductase, dioxygenases, monooxygenases, glutathione-dependent etherases, dehydrogenases, reductases, and methyltransferases and various other recently reported enzyme systems such as superoxide dismutases or catalase-peroxidase for lignin degradation. A strong stress response and detoxification mechanism was discovered. The two important gene clusters for lignin degradation and three PHA polymerase spanning gene clusters were identified and all the clusters were functionally active on KL-VA. CONCLUSIONS The unusual aerobic '-CoA'-mediated degradation pathway of phenylacetate and benzoate (reported only in 16 and 4-5% of total sequenced bacterial genomes), peroxidase-accessory enzyme system, and fenton chemistry based are the major pathways observed for lignin degradation. Both ortho and meta ring cleavage pathways for aromatic compound degradation were observed in expression profile. Genomic and proteomic approaches provided validation to this strain's robust machinery for the metabolism of recalcitrant compounds and PHA production and provide an opportunity to target important enzymes for lignin valorization in future.
Collapse
Affiliation(s)
- Madan Kumar
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Sandhya Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Rajesh Kumar Gazara
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Manish Kumar
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Ashok Pandey
- CSIR-Indian Institute of Toxicology Research, 31 MG Marg, Lucknow, 226 001 India
| | - Praveen Kumar Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Indu Shekhar Thakur
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| |
Collapse
|
54
|
Liu D, Yan X, Zhuo S, Si M, Liu M, Wang S, Ren L, Chai L, Shi Y. Pandoraea sp. B-6 assists the deep eutectic solvent pretreatment of rice straw via promoting lignin depolymerization. BIORESOURCE TECHNOLOGY 2018; 257:62-68. [PMID: 29482167 DOI: 10.1016/j.biortech.2018.02.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 02/03/2018] [Accepted: 02/05/2018] [Indexed: 06/08/2023]
Abstract
Lignin depolymerization is a challenging process in biorefinery due to the recalcitrant and complex structure of lignin. This challenge was herein addressed via elaborating a new strategy of combining the bacterial strain Pandoraea sp. B-6 (hereafter B-6) with a deep eutectic solvent (DES) to pretreat rice straw (RS). In this approach, DES effectively depolymerized lignin yet easily caused sugar loss under severe conditions. B-6 not only overcame the obstacle of lignin droplets, but also significantly improved enzymatic digestibility. After B-6 assisted DES pretreatment, the reducing sugar yield increases by 0.3-1.5 times over DES pretreatment and 0.9-3.1 times over the untreated RS. Furthermore, a "cornhusking" mechanism explaining the improvement of the enzymatic digestibility by B-6 was suggested based on physicochemical characterizations of the untreated and pretreated RS. The findings provided a comprehensive perspective to establish a DES-microbial process for lignocellulose pretreatment.
Collapse
Affiliation(s)
- Dan Liu
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Xu Yan
- School of Metallurgy and Environment, Central South University, Changsha 410083, China; Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, Changsha 410083, China
| | - Shengnan Zhuo
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Mengying Si
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Mingren Liu
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Sheng Wang
- Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, Changsha 410083, China
| | - Lili Ren
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Liyuan Chai
- School of Metallurgy and Environment, Central South University, Changsha 410083, China; Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, Changsha 410083, China
| | - Yan Shi
- School of Metallurgy and Environment, Central South University, Changsha 410083, China; Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, Changsha 410083, China.
| |
Collapse
|
55
|
Xu Z, Qin L, Cai M, Hua W, Jin M. Biodegradation of kraft lignin by newly isolated Klebsiella pneumoniae, Pseudomonas putida, and Ochrobactrum tritici strains. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:14171-14181. [PMID: 29524172 DOI: 10.1007/s11356-018-1633-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 02/28/2018] [Indexed: 05/21/2023]
Abstract
Bacterial systems have drawn an increasing amount of attention on lignin valorization due to their rapid growth and powerful environmental adaptability. In this study, Klebsiella pneumoniae NX-1, Pseudomonas putida NX-1, and Ochrobactrum tritici NX-1 with ligninolytic potential were isolated from leaf mold samples. Their ligninolytic capabilities were determined by measuring (1) the cell growth on kraft lignin as the sole carbon source, (2) the decolorization of kraft lignin and lignin-mimicking dyes, (3) the micro-morphology changes and transformations of chemical groups in kraft lignin, and (4) the ligninolytic enzyme activities of these three isolates. To the best of our knowledge, this is the first report that Ochrobactrum tritici species can depolymerize and metabolize lignin. Moreover, laccase, lignin peroxidase, and Mn-peroxidase showed high activities in P. putida NX-1. Due to their excellent ligninolytic capabilities, these three bacteria are important supplements to ligninolytic bacteria library and could be valuable in lignin valorization.
Collapse
Affiliation(s)
- Zhaoxian Xu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Ling Qin
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Mufeng Cai
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Wenbo Hua
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Mingjie Jin
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
| |
Collapse
|
56
|
Ravi K, García-Hidalgo J, Nöbel M, Gorwa-Grauslund MF, Lidén G. Biological conversion of aromatic monolignol compounds by a Pseudomonas isolate from sediments of the Baltic Sea. AMB Express 2018; 8:32. [PMID: 29500726 PMCID: PMC5834416 DOI: 10.1186/s13568-018-0563-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 02/22/2018] [Indexed: 11/10/2022] Open
Abstract
Bacterial strains were isolated from the sediments of the Baltic Sea using ferulic acid, guaiacol or a lignin-rich softwood waste stream as substrate. In total nine isolates were obtained, five on ferulic acid, two on guaiacol and two on a lignin-rich softwood stream as a carbon source. Three of the isolates were found to be Pseudomonas sp. based on 16S rRNA sequencing. Among them, isolate 9.1, which showed the fastest growth in defined M9 medium, was tentatively identified as a Pseudomonas deceptionensis strain based on the gyrB sequencing. The growth of isolate 9.1 was further examined on six selected lignin model compounds (ferulate, p-coumarate, benzoate, syringate, vanillin and guaiacol) from different upper funneling aromatic pathways and was found able to grow on four out of these six compounds. No growth was detected on syringate and guaiacol. The highest specific growth and uptake rates were observed for benzoate (0.3 h-1 and 4.2 mmol g CDW-1 h-1) whereas the lowest were for the compounds from the coniferyl branch. Interestingly, several pathway intermediates were excreted during batch growth. Vanillyl alcohol was found to be excreted during growth on vanillin. Several other intermediates like cis,cis-muconate, catechol, vanillate and 4-hydroxybenzoate from the known bacterial catabolic pathways were excreted during growth on the model compounds.
Collapse
Affiliation(s)
- Krithika Ravi
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - Javier García-Hidalgo
- Department of Chemistry, Applied Microbiology, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - Matthias Nöbel
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - Marie F. Gorwa-Grauslund
- Department of Chemistry, Applied Microbiology, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - Gunnar Lidén
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| |
Collapse
|
57
|
Ceballos SJ, Yu C, Claypool JT, Singer SW, Simmons BA, Thelen MP, Simmons CW, VanderGheynst JS. Development and characterization of a thermophilic, lignin degrading microbiota. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.08.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
|
58
|
Janusz G, Pawlik A, Sulej J, Swiderska-Burek U, Jarosz-Wilkolazka A, Paszczynski A. Lignin degradation: microorganisms, enzymes involved, genomes analysis and evolution. FEMS Microbiol Rev 2017; 41:941-962. [PMID: 29088355 PMCID: PMC5812493 DOI: 10.1093/femsre/fux049] [Citation(s) in RCA: 345] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 10/12/2017] [Indexed: 12/11/2022] Open
Abstract
Extensive research efforts have been dedicated to describing degradation of wood, which is a complex process; hence, microorganisms have evolved different enzymatic and non-enzymatic strategies to utilize this plentiful plant material. This review describes a number of fungal and bacterial organisms which have developed both competitive and mutualistic strategies for the decomposition of wood and to thrive in different ecological niches. Through the analysis of the enzymatic machinery engaged in wood degradation, it was possible to elucidate different strategies of wood decomposition which often depend on ecological niches inhabited by given organism. Moreover, a detailed description of low molecular weight compounds is presented, which gives these organisms not only an advantage in wood degradation processes, but seems rather to be a new evolutionatory alternative to enzymatic combustion. Through analysis of genomics and secretomic data, it was possible to underline the probable importance of certain wood-degrading enzymes produced by different fungal organisms, potentially giving them advantage in their ecological niches. The paper highlights different fungal strategies of wood degradation, which possibly correlates to the number of genes coding for secretory enzymes. Furthermore, investigation of the evolution of wood-degrading organisms has been described.
Collapse
Affiliation(s)
- Grzegorz Janusz
- Department of Biochemistry, Maria Curie-Sklodowska University, Akademicka 19 St., 20-033 Lublin, Poland
| | - Anna Pawlik
- Department of Biochemistry, Maria Curie-Sklodowska University, Akademicka 19 St., 20-033 Lublin, Poland
| | - Justyna Sulej
- Department of Biochemistry, Maria Curie-Sklodowska University, Akademicka 19 St., 20-033 Lublin, Poland
| | - Urszula Swiderska-Burek
- Department of Botany and Mycology, Maria Curie-Sklodowska University, Akademicka 19 St., 20-033 Lublin, Poland
| | - Anna Jarosz-Wilkolazka
- Department of Biochemistry, Maria Curie-Sklodowska University, Akademicka 19 St., 20-033 Lublin, Poland
| | - Andrzej Paszczynski
- School of Food Science, Food Research Center, Room 103, University of Idaho, Moscow, ID 83844, USA
| |
Collapse
|
59
|
Tian JH, Pourcher AM, Bize A, Wazeri A, Peu P. Impact of wet aerobic pretreatments on cellulose accessibility and bacterial communities in rape straw. BIORESOURCE TECHNOLOGY 2017; 237:31-38. [PMID: 28411050 DOI: 10.1016/j.biortech.2017.03.142] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 03/21/2017] [Accepted: 03/22/2017] [Indexed: 06/07/2023]
Abstract
A new pretreatment method of lignocellulosic biomass was explored by using a wet aerobic process with an alkaline lignin and a mineral salt solution. This treatment significantly improved structural modification of rape straw used as substrate model in this study. Change in cellulose accessibility to cellulase of rape straw rose up to six fold within the first days of this pretreatment without generated significant modification of van Soest lignocellulose fractionation. The biological pretreatment apply to rape straw induced a high microbial activity revealed by quantitative PCR and sequencing techniques, suggesting that bacteria including Xanthomonadales and Sphingobacteriales may be involved in this lignocellulosic biomass transformation. Moreover, results of this work demonstrate that the endogenous microbial community associated with rape straw plays a key role in its alteration.
Collapse
Affiliation(s)
- Jiang-Hao Tian
- IRSTEA, UR OPAALE, 17 avenue de Cucillé, CS 64427, F-35044 Rennes, France; Université Bretagne Loire, France
| | - Anne-Marie Pourcher
- IRSTEA, UR OPAALE, 17 avenue de Cucillé, CS 64427, F-35044 Rennes, France; Université Bretagne Loire, France
| | - Ariane Bize
- IRSTEA, Hydrosystems and Bioprocesses Research Unit, 1 rue Pierre-Gilles de Gennes, CS 10030, F-92761 Antony, France
| | - Alaa Wazeri
- Egypt-Japan University of Science and Technology (E-JUST), Environmental Engineering Department, P.O. Box 179, New Borg El-Arab City 21934, Alexandria, Egypt
| | - Pascal Peu
- IRSTEA, UR OPAALE, 17 avenue de Cucillé, CS 64427, F-35044 Rennes, France; Université Bretagne Loire, France.
| |
Collapse
|
60
|
Delignification and enhanced gas release from soil containing lignocellulose by treatment with bacterial lignin degraders. J Appl Microbiol 2017; 123:159-171. [DOI: 10.1111/jam.13470] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/04/2017] [Accepted: 04/05/2017] [Indexed: 01/14/2023]
|
61
|
Forest Soil Bacteria: Diversity, Involvement in Ecosystem Processes, and Response to Global Change. Microbiol Mol Biol Rev 2017; 81:81/2/e00063-16. [PMID: 28404790 DOI: 10.1128/mmbr.00063-16] [Citation(s) in RCA: 212] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ecology of forest soils is an important field of research due to the role of forests as carbon sinks. Consequently, a significant amount of information has been accumulated concerning their ecology, especially for temperate and boreal forests. Although most studies have focused on fungi, forest soil bacteria also play important roles in this environment. In forest soils, bacteria inhabit multiple habitats with specific properties, including bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are shaped by nutrient availability and biotic interactions. Bacteria contribute to a range of essential soil processes involved in the cycling of carbon, nitrogen, and phosphorus. They take part in the decomposition of dead plant biomass and are highly important for the decomposition of dead fungal mycelia. In rhizospheres of forest trees, bacteria interact with plant roots and mycorrhizal fungi as commensalists or mycorrhiza helpers. Bacteria also mediate multiple critical steps in the nitrogen cycle, including N fixation. Bacterial communities in forest soils respond to the effects of global change, such as climate warming, increased levels of carbon dioxide, or anthropogenic nitrogen deposition. This response, however, often reflects the specificities of each studied forest ecosystem, and it is still impossible to fully incorporate bacteria into predictive models. The understanding of bacterial ecology in forest soils has advanced dramatically in recent years, but it is still incomplete. The exact extent of the contribution of bacteria to forest ecosystem processes will be recognized only in the future, when the activities of all soil community members are studied simultaneously.
Collapse
|
62
|
Jackson CA, Couger MB, Prabhakaran M, Ramachandriya KD, Canaan P, Fathepure BZ. Isolation and characterization of Rhizobium sp. strain YS-1r that degrades lignin in plant biomass. J Appl Microbiol 2017; 122:940-952. [PMID: 28092137 DOI: 10.1111/jam.13401] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/05/2017] [Accepted: 01/09/2017] [Indexed: 11/28/2022]
Abstract
AIMS The aim of this work was to isolate novel lignin-degrading organisms. METHODS AND RESULTS Several pure cultures of bacteria that degrade lignin were isolated from bacterial consortia developed from decaying biomass. Among the isolates, Rhizobium sp. strain YS-1r (closest relative of Rhizobium petrolearium strain SL-1) was explored for its lignin-degrading ability. Microcosm studies showed that strain YS-1r was able to degrade a variety of lignin monomers, dimers and also native lignin in switchgrass and alfalfa. The isolate demonstrated lignin peroxidase (LiP) activity when grown on alkali lignin, p-anisoin, switchgrass or alfalfa, and only negligible activity was measured in glucose-grown cells suggesting inducible nature of the LiP activity. Analysis of the strain YS-1r genome revealed the presence of a variety of genes that code for various lignin-oxidizing, H2 O2 -producing as well as polysaccharide-hydrolysing enzymes. CONCLUSIONS This study shows both the genomic and physiological capability of bacteria in the genus Rhizobium to metabolize lignin and lignin-like compounds. This is the first detailed report on the lignocellulose-degrading ability of a Rhizobium species and thus this study expands the role of alpha-proteobacteria in the degradation of lignin. SIGNIFICANCE AND IMPACT OF THE STUDY The organism's ability to degrade lignin is significant since Rhizobia are widespread in soil, water and plant rhizospheres and some fix atmospheric nitrogen and also have the ability to degrade aromatic hydrocarbons.
Collapse
Affiliation(s)
- C A Jackson
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - M B Couger
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - M Prabhakaran
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - K D Ramachandriya
- Department of Biosystems and Agricultural Engineering, Oklahoma State University, Stillwater, OK, USA
| | - P Canaan
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, USA
| | - B Z Fathepure
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| |
Collapse
|
63
|
Rais D, Zibek S. Biotechnological and Biochemical Utilization of Lignin. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017; 166:469-518. [PMID: 28540404 DOI: 10.1007/10_2017_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
This chapter provides an overview of the biosynthesis and structure of lignin. Moreover, examples of the commercial use of lignin and its promising future implementation are briefly described. Many applications are still hampered by the properties of technical lignins. Thus, the major challenge is the conversion of lignins into suitable building blocks or aromatics in order to open up new avenues for the usage of this renewable raw material. This chapter focuses on details about natural lignin degradation by fungi and bacteria, which harbor potential tools for lignin degradation and modification, which might help to develop eco-efficient processes for lignin utilization.
Collapse
Affiliation(s)
| | - Susanne Zibek
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany.
| |
Collapse
|
64
|
Tian JH, Pourcher AM, Bureau C, Peu P. Cellulose accessibility and microbial community in solid state anaerobic digestion of rape straw. BIORESOURCE TECHNOLOGY 2017; 223:192-201. [PMID: 27792929 DOI: 10.1016/j.biortech.2016.10.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/29/2016] [Accepted: 10/02/2016] [Indexed: 06/06/2023]
Abstract
Solid state anaerobic digestion (SSAD) with leachate recirculation is an appropriate method for the valorization of agriculture residues. Rape straw is a massively produced residue with considerable biochemical methane potential, but its degradation in SSAD remains poorly understood. A thorough study was conducted to understand the performance of rape straw as feedstock for laboratory solid state anaerobic digesters. We investigated the methane production kinetics of rape straw in relation to cellulose accessibility to cellulase and the microbial community. Improving cellulose accessibility through milling had a positive influence on both the methane production rate and methane yield. The SSAD of rape straw reached 60% of its BMP in a 40-day pilot-scale test. Distinct bacterial communities were observed in digested rape straw and leachate, with Bacteroidales and Sphingobacteriales as the most abundant orders, respectively. Archaeal populations showed no phase preference and increased chronologically.
Collapse
Affiliation(s)
- Jiang-Hao Tian
- IRSTEA, UR OPAALE, 17 Avenue de Cucillé, CS 64427, F-35044 Rennes, France; Université Bretagne Loire, France
| | - Anne-Marie Pourcher
- IRSTEA, UR OPAALE, 17 Avenue de Cucillé, CS 64427, F-35044 Rennes, France; Université Bretagne Loire, France
| | - Chrystelle Bureau
- IRSTEA, Hydrosystems and Bioprocesses Research Unit, 1 rue Pierre-Gilles de Gennes, CS 10030, 92761 Antony Cedex, France
| | - Pascal Peu
- IRSTEA, UR OPAALE, 17 Avenue de Cucillé, CS 64427, F-35044 Rennes, France; Université Bretagne Loire, France.
| |
Collapse
|
65
|
Biological valorization of low molecular weight lignin. Biotechnol Adv 2016; 34:1318-1346. [DOI: 10.1016/j.biotechadv.2016.10.001] [Citation(s) in RCA: 228] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 09/06/2016] [Accepted: 10/04/2016] [Indexed: 12/14/2022]
|
66
|
Pandit PD, Gulhane MK, Khardenavis AA, Purohit HJ. Mining of hemicellulose and lignin degrading genes from differentially enriched methane producing microbial community. BIORESOURCE TECHNOLOGY 2016; 216:923-930. [PMID: 27323244 DOI: 10.1016/j.biortech.2016.06.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 06/03/2016] [Accepted: 06/06/2016] [Indexed: 06/06/2023]
Abstract
Study creates a scenario for enrichment and selection of ligno-hemicellulose degrading genotypes with anaerobic bioreactor as a model using rice straw, vegetable waste and food waste as substrates. Relative discrimination analysis showed that the hydrolytic pathways and associated microbial communities for ligno-hemicellulose degradation were dominatingly colonized with rice straw as substrate. The dominating bacteria were Caldicellulosiruptor, Fervidobacterium, Cytophaga, Ruminococcus, Thermotoga associated with hemicellulose degradation and Burkholderia, Pandorea, Sphingomonas, Spirochaeta, Pseudomonas for lignocellulose hydrolysis. This was further supported by the abundance of anaerobic aromatic compound degrading genes along with genes for xylanase and xylosidase in rice straw enriched community. The metagenome analysis data was validated by evaluation of the biochemical methane potential for these substrates. Food waste being most amenable substrate yielded 1410mL of biogas/gVS added whereas, biogas yield of 1160mL/gVS and 1080mL/gVS was observed in presence of vegetable waste and rice straw respectively.
Collapse
Affiliation(s)
- Prabhakar D Pandit
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Environmental Genomics Division, National Environmental Engineering Research Institute, (CSIR-NEERI), Nehru Marg, Nagpur 440 020, India; CSIR-NEERI, Nagpur, India
| | | | | | - Hemant J Purohit
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Environmental Genomics Division, National Environmental Engineering Research Institute, (CSIR-NEERI), Nehru Marg, Nagpur 440 020, India; CSIR-NEERI, Nagpur, India.
| |
Collapse
|
67
|
Palazzolo MA, Kurina-Sanz M. Microbial utilization of lignin: available biotechnologies for its degradation and valorization. World J Microbiol Biotechnol 2016; 32:173. [PMID: 27565783 DOI: 10.1007/s11274-016-2128-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 08/12/2016] [Indexed: 10/21/2022]
Abstract
Lignocellulosic biomasses, either from non-edible plants or from agricultural residues, stock biomacromolecules that can be processed to produce both energy and bioproducts. Therefore, they become major candidates to replace petroleum as the main source of energy. However, to shift the fossil-based economy to a bio-based one, it is imperative to develop robust biotechnologies to efficiently convert lignocellulosic streams in power and platform chemicals. Although most of the biomass processing facilities use celluloses and hemicelluloses to produce bioethanol and paper, there is no consolidated bioprocess to produce valuable compounds out of lignin at industrial scale available currently. Usually, lignin is burned to provide heat or it remains as a by-product in different streams, thus arising environmental concerns. In this way, the biorefinery concept is not extended to completion. Due to Nature offers an arsenal of biotechnological tools through microorganisms to accomplish lignin valorization or degradation, an increasing number of projects dealing with these tasks have been described recently. In this review, outstanding reports over the last 6 years are described, comprising the microbial utilization of lignin to produce a variety of valuable compounds as well as to diminish its ecological impact. Furthermore, perspectives on these topics are given.
Collapse
Affiliation(s)
- Martín A Palazzolo
- Instituto de Investigaciones en Tecnología Química, Universidad Nacional de San Luis, CONICET, Area de Química Orgánica, FQByF, 5700, San Luis, Argentina.
| | - Marcela Kurina-Sanz
- Instituto de Investigaciones en Tecnología Química, Universidad Nacional de San Luis, CONICET, Area de Química Orgánica, FQByF, 5700, San Luis, Argentina
| |
Collapse
|
68
|
Gupta VK, Kubicek CP, Berrin JG, Wilson DW, Couturier M, Berlin A, Filho EXF, Ezeji T. Fungal Enzymes for Bio-Products from Sustainable and Waste Biomass. Trends Biochem Sci 2016; 41:633-645. [PMID: 27211037 DOI: 10.1016/j.tibs.2016.04.006] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 04/13/2016] [Accepted: 04/22/2016] [Indexed: 12/19/2022]
Abstract
Lignocellulose, the most abundant renewable carbon source on earth, is the logical candidate to replace fossil carbon as the major biofuel raw material. Nevertheless, the technologies needed to convert lignocellulose into soluble products that can then be utilized by the chemical or fuel industries face several challenges. Enzymatic hydrolysis is of major importance, and we review the progress made in fungal enzyme technology over the past few years with major emphasis on (i) the enzymes needed for the conversion of polysaccharides (cellulose and hemicellulose) into soluble products, (ii) the potential uses of lignin degradation products, and (iii) current progress and bottlenecks for the use of the soluble lignocellulose derivatives in emerging biorefineries.
Collapse
Affiliation(s)
- Vijai K Gupta
- Molecular Glycobiotechnology Group, Discipline of Biochemistry, National University of Ireland Galway, Galway City, Ireland.
| | - Christian P Kubicek
- Biotechnology and Microbiology, Institute of Chemical Engineering, Technische Universität Wien, Gumpendorferstrasse, 1060 Wien, Austria
| | - Jean-Guy Berrin
- Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche (UMR) 1163-Biodiversité et Biotechnologie Fongiques, Avenue de Luminy, 13288 Marseille, France; Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, Avenue de Luminy, 13288 Marseille, France
| | - David W Wilson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Marie Couturier
- Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche (UMR) 1163-Biodiversité et Biotechnologie Fongiques, Avenue de Luminy, 13288 Marseille, France; Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, Avenue de Luminy, 13288 Marseille, France
| | - Alex Berlin
- Novozymes, Inc., 1445 Drew Ave, Davis CA 95618 USA
| | - Edivaldo X F Filho
- Laboratory of Enzymology, Department of Cell Biology, University of Brasilia, Asa Norte, 70910-900 Brasilia, DF Brazil
| | - Thaddeus Ezeji
- Biotechnology and Fermentation Group, Department of Animal Sciences, Ohio State University and Ohio Agricultural Research and Development Center (OARDC), Madison Avenue, Wooster, OH 44691, USA
| |
Collapse
|
69
|
Linking pyrolysis and anaerobic digestion (Py-AD) for the conversion of lignocellulosic biomass. Curr Opin Biotechnol 2016; 38:167-73. [DOI: 10.1016/j.copbio.2016.02.004] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 02/07/2016] [Accepted: 02/09/2016] [Indexed: 11/20/2022]
|
70
|
Nelsen MP, DiMichele WA, Peters SE, Boyce CK. Delayed fungal evolution did not cause the Paleozoic peak in coal production. Proc Natl Acad Sci U S A 2016; 113:2442-7. [PMID: 26787881 PMCID: PMC4780611 DOI: 10.1073/pnas.1517943113] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Organic carbon burial plays a critical role in Earth systems, influencing atmospheric O2 and CO2 concentrations and, thereby, climate. The Carboniferous Period of the Paleozoic is so named for massive, widespread coal deposits. A widely accepted explanation for this peak in coal production is a temporal lag between the evolution of abundant lignin production in woody plants and the subsequent evolution of lignin-degrading Agaricomycetes fungi, resulting in a period when vast amounts of lignin-rich plant material accumulated. Here, we reject this evolutionary lag hypothesis, based on assessment of phylogenomic, geochemical, paleontological, and stratigraphic evidence. Lignin-degrading Agaricomycetes may have been present before the Carboniferous, and lignin degradation was likely never restricted to them and their class II peroxidases, because lignin modification is known to occur via other enzymatic mechanisms in other fungal and bacterial lineages. Furthermore, a large proportion of Carboniferous coal horizons are dominated by unlignified lycopsid periderm with equivalent coal accumulation rates continuing through several transitions between floral dominance by lignin-poor lycopsids and lignin-rich tree ferns and seed plants. Thus, biochemical composition had little relevance to coal accumulation. Throughout the fossil record, evidence of decay is pervasive in all organic matter exposed subaerially during deposition, and high coal accumulation rates have continued to the present wherever environmental conditions permit. Rather than a consequence of a temporal decoupling of evolutionary innovations between fungi and plants, Paleozoic coal abundance was likely the result of a unique combination of everwet tropical conditions and extensive depositional systems during the assembly of Pangea.
Collapse
Affiliation(s)
| | - William A DiMichele
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Shanan E Peters
- Department of Geoscience, University of Wisconsin-Madison, Madison, WI 53706
| | - C Kevin Boyce
- Geological Sciences, Stanford University, Stanford, CA 94305;
| |
Collapse
|
71
|
Lignin Biodegradation with Fungi, Bacteria and Enzymes for Producing Chemicals and Increasing Process Efficiency. PRODUCTION OF BIOFUELS AND CHEMICALS FROM LIGNIN 2016. [DOI: 10.1007/978-981-10-1965-4_6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
72
|
Bacterial Enzymes for Lignin Oxidation and Conversion to Renewable Chemicals. PRODUCTION OF BIOFUELS AND CHEMICALS FROM LIGNIN 2016. [DOI: 10.1007/978-981-10-1965-4_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
73
|
Cragg SM, Beckham GT, Bruce NC, Bugg TDH, Distel DL, Dupree P, Etxabe AG, Goodell BS, Jellison J, McGeehan JE, McQueen-Mason SJ, Schnorr K, Walton PH, Watts JEM, Zimmer M. Lignocellulose degradation mechanisms across the Tree of Life. Curr Opin Chem Biol 2015; 29:108-19. [PMID: 26583519 PMCID: PMC7571853 DOI: 10.1016/j.cbpa.2015.10.018] [Citation(s) in RCA: 296] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/11/2015] [Accepted: 10/14/2015] [Indexed: 12/13/2022]
Abstract
Organisms use diverse mechanisms involving multiple complementary enzymes, particularly glycoside hydrolases (GHs), to deconstruct lignocellulose. Lytic polysaccharide monooxygenases (LPMOs) produced by bacteria and fungi facilitate deconstruction as does the Fenton chemistry of brown-rot fungi. Lignin depolymerisation is achieved by white-rot fungi and certain bacteria, using peroxidases and laccases. Meta-omics is now revealing the complexity of prokaryotic degradative activity in lignocellulose-rich environments. Protists from termite guts and some oomycetes produce multiple lignocellulolytic enzymes. Lignocellulose-consuming animals secrete some GHs, but most harbour a diverse enzyme-secreting gut microflora in a mutualism that is particularly complex in termites. Shipworms however, house GH-secreting and LPMO-secreting bacteria separate from the site of digestion and the isopod Limnoria relies on endogenous enzymes alone. The omics revolution is identifying many novel enzymes and paradigms for biomass deconstruction, but more emphasis on function is required, particularly for enzyme cocktails, in which LPMOs may play an important role.
Collapse
Affiliation(s)
- Simon M Cragg
- School of Biological Sciences, University of Portsmouth, King Henry Building, King Henry 1st St., Portsmouth PO1 2DY, UK.
| | - Gregg T Beckham
- National Renewable Energy Laboratory, National Bioenergy Centre, Golden, CO 80401 USA
| | - Neil C Bruce
- University of York, Department of Biological Sciences, Centre for Novel Agricultural Products, York YO10 5DD, UK
| | - Timothy D H Bugg
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Daniel L Distel
- Ocean Genome Legacy, Marine Science Center, Northeastern University, Boston, MA, USA
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Amaia Green Etxabe
- School of Biological Sciences, University of Portsmouth, King Henry Building, King Henry 1st St., Portsmouth PO1 2DY, UK
| | - Barry S Goodell
- Department of Sustainable Biomaterials, 216 ICTAS II Bldg., Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA 24061, USA
| | - Jody Jellison
- Department of Plant Pathology, Physiology and Weed Science, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA 24061, USA
| | - John E McGeehan
- School of Biological Sciences, University of Portsmouth, King Henry Building, King Henry 1st St., Portsmouth PO1 2DY, UK
| | - Simon J McQueen-Mason
- University of York, Department of Biological Sciences, Centre for Novel Agricultural Products, York YO10 5DD, UK
| | | | - Paul H Walton
- Department of Chemistry, University of York, York YO10 5DD, UK
| | - Joy E M Watts
- School of Biological Sciences, University of Portsmouth, King Henry Building, King Henry 1st St., Portsmouth PO1 2DY, UK
| | - Martin Zimmer
- Leibniz-Center for Tropical Marine Ecology (ZMT) GmbH, Fahrenheitstrasse 6, 28359 Bremen, Germany
| |
Collapse
|
74
|
Enzymatic conversion of lignin into renewable chemicals. Curr Opin Chem Biol 2015; 29:10-7. [PMID: 26121945 DOI: 10.1016/j.cbpa.2015.06.009] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 05/29/2015] [Accepted: 06/08/2015] [Indexed: 11/22/2022]
Abstract
The aromatic heteropolymer lignin is a major component of plant cell walls, and is produced industrially from paper/pulp manufacture and cellulosic bioethanol production. Conversion of lignin into renewable chemicals is a major unsolved problem in the development of a biomass-based biorefinery. The review describes recent developments in the understanding of bacterial enzymes for lignin breakdown, such as DyP peroxidases, bacterial laccases, and beta-etherase enzymes. The use of pathway engineering methods to construct genetically modified microbes to convert lignin to renewable chemicals (e.g. vanillin, adipic acid) via fermentation is discussed, and the search for novel applications for lignin (e.g. carbon fibre).
Collapse
|
75
|
Microbial diversity observed during hemp retting. Appl Microbiol Biotechnol 2015; 99:4471-84. [DOI: 10.1007/s00253-014-6356-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 12/22/2014] [Accepted: 12/29/2014] [Indexed: 10/24/2022]
|
76
|
Lee S, J. Mitchell R. Perspectives on the use of transcriptomics to advance biofuels. AIMS BIOENGINEERING 2015. [DOI: 10.3934/bioeng.2015.4.487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|