1
|
Sumranwanich T, Amosu E, Chankhamhaengdecha S, Phetruen T, Loktumraks W, Ounjai P, Harnvoravongchai P. Evaluating lignin degradation under limited oxygen conditions by bacterial isolates from forest soil. Sci Rep 2024; 14:13350. [PMID: 38858437 PMCID: PMC11164938 DOI: 10.1038/s41598-024-64237-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 06/06/2024] [Indexed: 06/12/2024] Open
Abstract
Lignin, a heterogeneous aromatic polymer present in plant biomass, is intertwined with cellulose and hemicellulose fibrils, posing challenges to its effective utilization due to its phenolic nature and recalcitrance to degradation. In this study, three lignin utilizing bacteria, Klebsiella sp. LEA1, Pseudomonas sp. LEA2, and Burkholderia sp. LEA3, were isolated from deciduous forest soil samples in Nan province, Thailand. These isolates were capable of growing on alkali lignin and various lignin-associated monomers at 40 °C under microaerobic conditions. The presence of Cu2+ significantly enhanced guaiacol oxidation in Klebsiella sp. LEA1 and Pseudomonas sp. LEA2. Lignin-related monomers and intermediates such as 2,6-dimethoxyphenol, 4-vinyl guaiacol, 4-hydroxybenzoic acid, benzoic acid, catechol, and succinic acid were detected mostly during the late stage of incubation of Klebsiella sp. LEA1 and Pseudomonas sp. LEA2 in lignin minimal salt media via GC-MS analysis. The intermediates identified from Klebsiella sp. LEA1 degradation suggested that conversion and utilization occurred through the β-ketoadipate (ortho-cleavage) pathway under limited oxygen conditions. The ability of these bacteria to thrive on alkaline lignin and produce various lignin-related intermediates under limited oxygen conditions suggests their potential utility in oxygen-limited processes and the production of renewable chemicals from plant biomass.
Collapse
Affiliation(s)
- Thitinun Sumranwanich
- Department of Biology, Faculty of Science, Mahidol University, Thung Phaya Thai, Ratchathewi, Bangkok, 10400, Thailand
| | - Esther Amosu
- Department of Biology, Faculty of Science, Mahidol University, Thung Phaya Thai, Ratchathewi, Bangkok, 10400, Thailand
| | - Surang Chankhamhaengdecha
- Department of Biology, Faculty of Science, Mahidol University, Thung Phaya Thai, Ratchathewi, Bangkok, 10400, Thailand
| | - Tanaporn Phetruen
- Department of Biochemistry, Faculty of Science, Mahidol University, Thung Phaya Thai, Ratchathewi, Bangkok, 10400, Thailand
| | - Wethaka Loktumraks
- Department of Biology, Faculty of Science, Mahidol University, Thung Phaya Thai, Ratchathewi, Bangkok, 10400, Thailand
| | - Puey Ounjai
- Department of Biology, Faculty of Science, Mahidol University, Thung Phaya Thai, Ratchathewi, Bangkok, 10400, Thailand
| | - Phurt Harnvoravongchai
- Department of Biology, Faculty of Science, Mahidol University, Thung Phaya Thai, Ratchathewi, Bangkok, 10400, Thailand.
| |
Collapse
|
2
|
Fernández-Guisuraga JM, Ansola G, Pinto R, Marcos E, Calvo L, Sáenz de Miera LE. Resistance of soil bacterial communities from montane heathland ecosystems in the Cantabrian mountains (NW Spain) to a gradient of experimental nitrogen deposition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 920:171079. [PMID: 38373460 DOI: 10.1016/j.scitotenv.2024.171079] [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: 11/28/2023] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 02/21/2024]
Abstract
Elevated atmospheric nitrogen (N) deposition on terrestrial ecosystems has become one of the most important drivers of microbial diversity loss on a global scale, and has been reported to alter the soil function of nutrient-poor, montane Calluna vulgaris heathlands in the context of global change. In this work we analyze for the first time the shifts of bacterial communities in response to experimental addition of N in Calluna heathlands as a simulation of atmospheric deposition. Specifically, we evaluated the effects of five N addition treatments (0, 10, 20, and 50 kg N ha-1 yr-1 for 3-years; and 56 kg N ha-1 yr-1 for 10-years) on the resistance of soil bacterial communities as determined by changes in their composition and alpha and beta diversities. The study was conducted in montane Calluna heathlands at different development stages (young and mature phases) in the southern side of the Cantabrian Mountains (NW Spain). Our results evidenced a substantial increase of long-term (10-years) N inputs on soil extractable N-NH4+, particularly in young Calluna stands. The alpha diversity of soil bacterial communities in mature Calluna stands did not show a significant response to experimental N addition, whereas it was significantly higher under long-term chronic N addition (56 kg N ha-1 yr-1 for 10-years) in young Calluna stands. These bacterial community shifts are mainly attributable to a decrease in the dominance of Acidobacteria phylum, the most representative in montane Calluna ecosystems, in favor of copiotrophic taxa such as Actinobacteria or Proteobacteria phyla, favored under increased N availability. Future research should investigate what specific ecosystem functions performed by soil bacterial communities may be sensitive to increased nitrogen depositions, which may have substantial implications for the understanding of montane Calluna ecosystems' stability.
Collapse
Affiliation(s)
- José Manuel Fernández-Guisuraga
- Departamento de Biodiversidad y Gestión Ambiental, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain; Centro de Investigação e de Tecnologias Agroambientais e Biológicas, Universidade de Trás-os-Montes e Alto Douro, 5000-801 Vila Real, Portugal.
| | - Gemma Ansola
- Departamento de Biodiversidad y Gestión Ambiental, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain
| | - Rayo Pinto
- Departamento de Biodiversidad y Gestión Ambiental, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain
| | - Elena Marcos
- Departamento de Biodiversidad y Gestión Ambiental, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain
| | - Leonor Calvo
- Departamento de Biodiversidad y Gestión Ambiental, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain
| | - Luis E Sáenz de Miera
- Departamento de Biología Molecular, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain
| |
Collapse
|
3
|
Czerwiec Q, Chabbert B, Crônier D, Kurek B, Rakotoarivonina H. Combined hemicellulolytic and phenoloxidase activities of Thermobacillus xylanilyticus enable growth on lignin-rich substrates and the release of phenolic molecules. BIORESOURCE TECHNOLOGY 2024; 397:130507. [PMID: 38423483 DOI: 10.1016/j.biortech.2024.130507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024]
Abstract
Major challenge in biorefineries is the use of all lignocellulosic components, particularly lignins. In this study, Thermobacillus xylanilyliticus grew on kraft lignin, steam-exploded and native wheat straws produced different sets of phenoloxidases and xylanases, according to the substrate. After growth, limited lignin structural modifications, mainly accompanied by a decrease in phenolic acids was observed by Nuclear Magnetic Resonance spectroscopy. The depletion of p-coumaric acid, vanillin and p-hydroxybenzaldehyde combined to vanillin production in the culture media indicated that the bacterium can transform some phenolic compounds. Proteomic approaches allowed the identification of 29 to 33 different hemicellulases according to the substrates. Twenty oxidoreductases were differentially expressed between kraft lignin and steam-exploded wheat straw. These oxidoreductases may be involved in lignin and aromatic compound utilization and detoxification. This study highlights the potential value of Thermobacillus xylanilyticus and its enzymes in the simultaneous valorization of hemicellulose and phenolic compounds from lignocelluloses.
Collapse
Affiliation(s)
- Quentin Czerwiec
- Université de Reims Champagne-Ardenne, INRAE, FARE, UMR A 614, Reims, France; Université de Reims Champagne-Ardenne, INRAE, FARE, UMR A 614, AFERE, Reims, France.
| | - Brigitte Chabbert
- Université de Reims Champagne-Ardenne, INRAE, FARE, UMR A 614, Reims, France.
| | - David Crônier
- Université de Reims Champagne-Ardenne, INRAE, FARE, UMR A 614, Reims, France.
| | - Bernard Kurek
- Université de Reims Champagne-Ardenne, INRAE, FARE, UMR A 614, Reims, France.
| | - Harivony Rakotoarivonina
- Université de Reims Champagne-Ardenne, INRAE, FARE, UMR A 614, Reims, France; Université de Reims Champagne-Ardenne, INRAE, FARE, UMR A 614, AFERE, Reims, France.
| |
Collapse
|
4
|
Kumagawa E, Katsumata M, Nishimura H, Watanabe T, Ishii S, Ohta Y. The etherase system of Novosphingobium sp. MBES04 functions as a sensor of lignin fragments through phenylpropanone production to induce specific transcriptional responses. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13210. [PMID: 37950419 PMCID: PMC10866074 DOI: 10.1111/1758-2229.13210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 10/20/2023] [Indexed: 11/12/2023]
Abstract
The MBES04 strain of Novosphingobium accumulates phenylpropanone monomers as end-products of the etherase system, which specifically and reductively cleaves the β-O-4 ether bond (a major bond in lignin molecules). However, it does not utilise phenylpropanone monomers as an energy source. Here, we studied the response to the lignin-related perturbation to clarify the physiological significance of its etherase system. Transcriptome analysis revealed two gene clusters, each consisting of four tandemly linked genes, specifically induced by a lignin preparation extracted from hardwood (Eucalyptus globulus) and a β-O-4-type lignin model biaryl compound, but not by vanillin. The most strongly induced gene was a 2,4'-dihydroxyacetophenone dioxygenase-like protein, which leads to energy production through oxidative degradation. The other cluster was related to multidrug resistance. The former cluster was transcriptionally regulated by a common promoter, where a phenylpropanone monomer acted as one of the effectors responsible for gene induction. These results indicate that the physiological significance of the etherase system of the strain lies in its function as a sensor for lignin fragments. This may be a survival strategy to detect nutrients and gain tolerance to recalcitrant toxic compounds, while the strain preferentially utilises easily degradable aromatic compounds with lower energy demands for catabolism.
Collapse
Affiliation(s)
- Eri Kumagawa
- Gunma University Center for Food Science and Wellness, Gunma UniversityMaebashiGunmaJapan
| | - Madoka Katsumata
- Gunma University Center for Food Science and Wellness, Gunma UniversityMaebashiGunmaJapan
| | - Hiroshi Nishimura
- Research Institute for Sustainable HumanosphereKyoto UniversityUjiKyotoJapan
| | - Takashi Watanabe
- Research Institute for Sustainable HumanosphereKyoto UniversityUjiKyotoJapan
| | - Shun'ichi Ishii
- Institute for Extra‐cutting‐edge Science and Technology Avant‐garde Research (X‐star)Japan Agency for Marine‐Earth Science and Technology (JAMSTEC)YokosukaKanagawaJapan
| | - Yukari Ohta
- Gunma University Center for Food Science and Wellness, Gunma UniversityMaebashiGunmaJapan
| |
Collapse
|
5
|
Grenier V, Laur J, Gonzalez E, Pitre FE. Glyphosate has a negligible impact on bacterial diversity and dynamics during composting. Environ Microbiol 2023; 25:2897-2912. [PMID: 36975075 DOI: 10.1111/1462-2920.16374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/15/2023] [Indexed: 03/29/2023]
Abstract
The herbicide glyphosate has several potential entry points into composting sites and its impact on composting processes has not yet been evaluated. To assess its impact on bacterial diversity and abundance as well as on community composition and dynamics, we conducted a mesocosm experiment at the Montreal Botanical Garden. Glyphosate had no effect on physicochemical property evolution during composting, while it was completely dissipated by the end of the experiment. Sampling at Days 0, 2, 28 and 112 of the process followed by 16S rRNA amplicon sequencing also found no effect of glyphosate on species richness and community composition. Differential abundance analyses revealed an increase of a few taxa in the presence of glyphosate, namely TRA3-20 (order Polyangiales), Pedosphaeraceae and BIrii41 (order Burkholderiales) after 28 days. In addition, five amplicon sequence variants (ASVs) had lower relative abundance in the glyphosate treatment compared to the control on Day 2, namely Comamonadaceae, Pseudomonas sp., Streptomyces sp., Thermoclostridium sp. and Actinomadura keratinilytica, while two ASVs were less abundant on Day 112, namely Pedomicrobium sp. and Pseudorhodoplanes sp. Most differences in abundance were measured between the different sampling points within each treatment. These results present glyphosate as a poor determinant of species recruitment during composting.
Collapse
Affiliation(s)
- Vanessa Grenier
- Department of Biological Sciences, Université de Montréal, Montréal, Québec, Canada
- Institut de recherche en biologie végétale, Montréal, Québec, Canada
| | - Joan Laur
- Department of Biological Sciences, Université de Montréal, Montréal, Québec, Canada
- Institut de recherche en biologie végétale, Montréal, Québec, Canada
- Montreal Botanical Garden, Montreal, Québec, Canada
| | - Emmanuel Gonzalez
- Canadian Centre for Computational Genomics, McGill Genome Centre, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montreal, Québec, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montréal, Québec, Canada
| | - Frederic E Pitre
- Department of Biological Sciences, Université de Montréal, Montréal, Québec, Canada
- Institut de recherche en biologie végétale, Montréal, Québec, Canada
- Montreal Botanical Garden, Montreal, Québec, Canada
| |
Collapse
|
6
|
Lourenço KS, Cantarella H, Kuramae EE. Carbon and Nutrients from Organic Residues Modulate the Dynamics of Prokaryotic and Fungal Communities. Microorganisms 2023; 11:2905. [PMID: 38138049 PMCID: PMC10745876 DOI: 10.3390/microorganisms11122905] [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: 11/01/2023] [Revised: 11/23/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Inputs of carbon (C) and nutrients from organic residues may select specific microbes and shape the soil microbial community. However, little is known about the abiotic filtering of the same residues with different nutrient concentrations applied to the soil. In our study, we explored how applying organic residue, vinasse, as fertilizer in its natural state (V) versus its concentrated form (CV) impacts soil microbiota. We conducted two field experiments, evaluating soil prokaryotic and fungal communities over 24 and 45 days with vinasse (V or CV) plus N fertilizer. We used 16S rRNA gene and ITS amplicon sequencing. Inorganic N had no significant impact on bacterial and fungal diversity compared to the control. However, the varying concentrations of organic C and nutrients in vinasse significantly influenced the soil microbiome structure, with smaller effects observed for V compared to CV. Prokaryotic and fungal communities were not correlated (co-inertia: RV coefficient = 0.1517, p = 0.9708). Vinasse did not change the total bacterial but increased the total fungal abundance. A higher C input enhanced the prokaryotic but reduced the fungal diversity. Our findings highlight vinasse's role as an abiotic filter shaping soil microbial communities, with distinct effects on prokaryotic and fungal communities. Vinasse primarily selects fast-growing microorganisms, shedding light on the intricate dynamics between organic residues, nutrient concentrations, and soil microbes.
Collapse
Affiliation(s)
- Késia Silva Lourenço
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands;
- Soils and Environmental Resources Center, Agronomic Institute of Campinas (IAC), Av. Barão de Itapura 1481, Campinas 13020-902, SP, Brazil;
| | - Heitor Cantarella
- Soils and Environmental Resources Center, Agronomic Institute of Campinas (IAC), Av. Barão de Itapura 1481, Campinas 13020-902, SP, Brazil;
| | - Eiko Eurya Kuramae
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands;
- Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
7
|
Min K, Zheng T, Zhu X, Bao X, Lynch L, Liang C. Bacterial community structure and assembly dynamics hinge on plant litter quality. FEMS Microbiol Ecol 2023; 99:fiad118. [PMID: 37771081 DOI: 10.1093/femsec/fiad118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 06/29/2023] [Accepted: 09/28/2023] [Indexed: 09/30/2023] Open
Abstract
Litter decomposition is a fundamental ecosystem process controlling the biogeochemical cycling of energy and nutrients. Using a 360-day lab incubation experiment to control for environmental factors, we tested how litter quality (low C/N deciduous vs. high C/N coniferous litter) governed the assembly and taxonomic composition of bacterial communities and rates of litter decomposition. Overall, litter mass loss was significantly faster in soils amended with deciduous (DL) rather than coniferous (CL) litter. Communities degrading DL were also more taxonomically diverse and exhibited stochastic assembly throughout the experiment. By contrast, alpha-diversity rapidly declined in communities exposed to CL. Strong environmental selection and competitive biological interactions induced by molecularly complex, nutrient poor CL were reflected in a transition from stochastic to deterministic assembly after 180 days. Constraining how the diversity and assembly of microbial populations modulates core ecosystem processes, such as litter decomposition, will become increasingly important under novel climate conditions, and as policymakers and land managers emphasize soil carbon sequestration as a key natural climate solution.
Collapse
Affiliation(s)
- Kaikai Min
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Tiantian Zheng
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, People's Republic of China
| | - Xuefeng Zhu
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, People's Republic of China
| | - Xuelian Bao
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, People's Republic of China
| | - Laurel Lynch
- Department of Soil and Water Systems, University of Idaho, Moscow, ID 83844, USA
| | - Chao Liang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, People's Republic of China
| |
Collapse
|
8
|
Dube SL, Osunsanmi FO, Ngcobo BP, Mkhwanazi LB, Jobe ZZ, Aruleba RT, Mosa RA, Opoku AR. Isolation and Characterization of Potential Lignin Peroxidase-Producing Bacteria from Compost Samples at Richards Bay (South Africa). Pol J Microbiol 2023:pjm-2023-003. [PMID: 37218281 DOI: 10.33073/pjm-2023-003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/27/2023] [Indexed: 05/24/2023] Open
Abstract
Lignin recalcitrance is a key issue in producing value-added products from lignocellulose biomass. In situ biodegradable lignin-modifying enzymes-producing bacteria are considered a suitable solution to lignin biodegradation problems, but exploitation of ligninolytic bacteria is still limited to date. Hence, this study aimed to isolate and characterize potential lignin peroxidase ligninolytic bacteria from decomposing soil, sawdust, and cow dung at Richard Bay, South Africa. The samples were collected and cultured in the lignin-enriched medium. Pure isolated colonies were characterized through 16S rRNA gene sequencing. The ability of the isolates to grow and utilize aromatic monomers (veratryl and guaiacol alcohol) and decolorize lignin-like dyes (Azure B, Congo Red, Remazol Brilliant Blue R) was evaluated. Of the twenty-six (26) bacteria isolates 10 isolates, including Pseudomonas spp. (88%), Enterobacter spp. (8%), and Escherichia coli (4%) were identified as true lignin peroxidase producers. Pseudomonas aeruginosa (CP031449.2) and E. coli (LR025096.1) exhibited the highest ligninolytic activities. These isolates could potentially be exploited in the industry and wastewater treatment as effective lignin degrading agents.
Collapse
|
9
|
Du Y, Yao C, Dou M, Wu J, Su L, Xia W. Oxidative degradation of pre-oxidated polystyrene plastics by dye decolorizing peroxidases from Thermomonospora curvata and Nostocaceae. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129265. [PMID: 35739782 DOI: 10.1016/j.jhazmat.2022.129265] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 05/27/2022] [Accepted: 05/28/2022] [Indexed: 06/15/2023]
Abstract
Biodegradation of PS has attracted lots of public attentions due to its environmental friendliness. However, no specific PS degrading enzyme has been identified yet. Dye decolorizing peroxidases (DyPs) are heme-containing peroxidases named for the ability to degrade a variety of organic dyes. Herein, the abilities of two DyPs from Thermomonospora curvata (TcDyP) and Nostocaceae (AnaPX) to degrade PS were evaluated. Preoxidation methods by ultraviolet (UV) irradiation and chemical oxidants were developed to initially activate C-C bonds in the PS skeleton. DyPs degradation caused obvious etching and enhanced hydrophilicity of UV-PS films, and also generated new CO and C-OH groups. The cleavage of activated C-C bonds by DyPs was experimentally proven by analyzing the degradation products of UV-PS and model substrates. Furthermore, better pre-oxidation was obtained by using chemical oxidants KMnO4/H2SO4 and mCPBA to oxidize PS materials in dissolved state. And AnaPX exhibited stronger degradation effects on KMnO4/H2SO4-PS and mCPBA-PS by causing greater changes in functional groups CO, C-O, -OH groups and substituted benzenes and higher molecular weight reductions of 19.7% and 31.0%, respectively. To our knowledge, this is the first report on the identification of PS-degrading enzymes that provides experimental evidence.
Collapse
Affiliation(s)
- Yanyi Du
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Congyu Yao
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Mingde Dou
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Jing Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Lingqia Su
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Wei Xia
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China.
| |
Collapse
|
10
|
Rammala B, Zhou N. Looking into the world's largest elephant population in search of ligninolytic microorganisms for biorefineries: a mini-review. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:64. [PMID: 35689287 PMCID: PMC9188235 DOI: 10.1186/s13068-022-02159-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 05/12/2022] [Indexed: 11/24/2022]
Abstract
Gastrointestinal tracts (GIT) of herbivores are lignin-rich environments with the potential to find ligninolytic microorganisms. The occurrence of the microorganisms in herbivore GIT is a well-documented mutualistic relationship where the former benefits from the provision of nutrients and the latter benefits from the microorganism-assisted digestion of their recalcitrant lignin diets. Elephants are one of the largest herbivores that rely on the microbial anaerobic fermentation of their bulky recalcitrant low-quality forage lignocellulosic diet given their inability to break down major components of plant cells. Tapping the potential of these mutualistic associations in the biggest population of elephants in the whole world found in Botswana is attractive in the valorisation of the bulky recalcitrant lignin waste stream generated from the pulp and paper, biofuel, and agro-industries. Despite the massive potential as a feedstock for industrial fermentations, few microorganisms have been commercialised. This review focuses on the potential of microbiota from the gastrointestinal tract and excreta of the worlds' largest population of elephants of Botswana as a potential source of extremophilic ligninolytic microorganisms. The review further discusses the recalcitrance of lignin, achievements, limitations, and challenges with its biological depolymerisation. Methods of isolation of microorganisms from elephant dung and their improvement as industrial strains are further highlighted.
Collapse
Affiliation(s)
- Bame Rammala
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Palapye, Botswana.
| | - Nerve Zhou
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Palapye, Botswana.
| |
Collapse
|
11
|
Liu Y, Wang Q, Pan Q, Zhou X, Peng Z, Jahng D, Yang B, Pan X. Ventilation induced evolution pattern of archaea, fungi, bacteria and their potential roles during co-bioevaporation treatment of concentrated landfill leachate and food waste. CHEMOSPHERE 2022; 289:133122. [PMID: 34871608 DOI: 10.1016/j.chemosphere.2021.133122] [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: 07/13/2021] [Revised: 10/27/2021] [Accepted: 11/28/2021] [Indexed: 06/13/2023]
Abstract
To obtain a favorable aeration type in co-bioevaporation treatment of concentrated landfill leachate and food waste, and to deeply understand the co-bioevaporation mechanisms, the temporal evolution differences of archaea, fungi and bacteria as well as the related microbial metabolism genes and functional enzymes under intermittent ventilation (IV) and continuous ventilation (CV) were investigated. Results through metagenomics analysis showed that the less sufficient oxygen and longer thermophilic phase in IV stimulated the vigorous growth of archaea, while CV was beneficial for fungal growth. Even genes of carbohydrates and lipids metabolism and ATP-associated enzymes (enzyme 2.7.13.3 and 3.6.4.12), as well as peptidoglycan biosynthesis enzyme (enzyme 3.4.16.4), were more abundant in CV, IV hold better DNA repair ability, higher microbial viability, and less dehydrogenase sensitivity to temperatures due to the critical contribution of Pseudomonas (3.1-45.9%). Furthermore, IV consumed a similar amount of heat for water evaporation with nearly half of the ventilation of CV and was a favorable aeration type in the practical application of co-bioevaporation.
Collapse
Affiliation(s)
- Yanmei Liu
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China; College of Environmental Science and Engineering, China West Normal University, Nanchong, 637009, China
| | - Qingzuo Wang
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China
| | - Qian Pan
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China
| | - Xiandong Zhou
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China
| | - Zhenghua Peng
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China
| | - Deokjin Jahng
- Department of Environmental Engineering & Energy, Myongji University, San 38-2, Namdong, Cheoingu, Yonginshi, Gyeonggido, 449-728, Republic of Korea
| | - Benqin Yang
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Xuejun Pan
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China.
| |
Collapse
|
12
|
Elframawy A, El-Hanafy A, Sharamant M, Ghozlan H. Molecular identification of native Egyptian Actinobacteria: Screening for lignin utilization and degradation of lignin model compounds. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
13
|
Reshmy R, Athiyaman Balakumaran P, Divakar K, Philip E, Madhavan A, Pugazhendhi A, Sirohi R, Binod P, Kumar Awasthi M, Sindhu R. Microbial valorization of lignin: Prospects and challenges. BIORESOURCE TECHNOLOGY 2022; 344:126240. [PMID: 34737164 DOI: 10.1016/j.biortech.2021.126240] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/22/2021] [Accepted: 10/23/2021] [Indexed: 06/13/2023]
Abstract
Lignin is the world's second most prevalent biomaterial, but its effective value-added product valorization methods are still being developed. The most common preparation processes for converting lignin to platform chemicals and biofuels are fragmentation and depolymerization. Due to its structural diversity, fragmentation generally produces a variety of products, necessitating tedious separation and purifying methods to isolate the desired products. Bacterial-based techniques are commonly utilized for lignin fragmentation due to their high metabolitic activity. Recent advancements in lignin valorization utilizing bacteria, such as lignin decomposing microbes and major pathways involved that can breakdown lignin into various valuable products namely lipids, furfural, vanillin, polyhydroxybutyrate, poly lactic acid blends were discussed in this review. This review also covers the genetic and fermentation methodologies to enhance lignin decomposition, challenges and future trends of microbe based lignin valorization.
Collapse
Affiliation(s)
- R Reshmy
- Post Graduate and Research Department of Chemistry, Bishop Moore College, Mavelikara 690 110, Kerala, India
| | - Palanisamy Athiyaman Balakumaran
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - K Divakar
- Department of Biotechnology, Sri Venkateswara College of Engineering, Sriperumbudur 602 117, Tamil Nadu, India
| | - Eapen Philip
- Post Graduate and Research Department of Chemistry, Bishop Moore College, Mavelikara 690 110, Kerala, India
| | - Aravind Madhavan
- Rajiv Gandhi Centre for Biotechnology, Jagathy, Thiruvananthapuram 695 014, Kerala, India
| | - Arivalagan Pugazhendhi
- School of Renewable Energy, Maejo University, Chiang Mai 50290, Thailand; College of Medical and Health Science, Asia University, Taichung, Taiwan
| | - Ranjna Sirohi
- Department of Chemical & Biological Engineering, Korea University, Seoul 136713, Republic of Korea; Centre for Energy and Environmental Sustainability, Lucknow 226 029, Uttar Pradesh, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi 712 100, China
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, Kerala, India.
| |
Collapse
|
14
|
Li X, Li M, Pu Y, Ragauskas AJ, Tharayil N, Huang J, Zheng Y. Degradation of aromatic compounds and lignin by marine protist Thraustochytrium striatum. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
15
|
Qualitative and Molecular Screening of Potential Ligninolytic Microbes from Termite (Coptotermes curvignathus) Gut. BORNEO JOURNAL OF RESOURCE SCIENCE AND TECHNOLOGY 2021. [DOI: 10.33736/bjrst.2879.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Ligninolytic microbes have great potential in converting high lignin by-products to more utilisable products by decomposing the lignin-rich agricultural and industrial wastes. Thus, the aim of this study are to screen and identify the potential ligninolytic microbes from the termite (Coptotermes curvignathus) gut. The study was conducted at Universiti Putra Malaysia Bintulu Sarawak Campus, Malaysia. Twenty-seven microbes isolated from termite gut obtained from the Microbiology Laboratory, Faculty of Agricultural Science and Forestry, were used for the ligninolytic activity screening. Media with four different ligninolytic indicator dyes (Azure B, phenol red, methylene blue, and Remazol Brilliant Blue) were streaked with microbial isolates and incubated at 37 °C for 48 h. Out of twenty-seven microbe isolates, only three (CH2, CH5, and CH9) isolates showed decolourisation zone indicating the positive presence of ligninolytic activity. The 16S rRNA gene sequence data indicated the isolates are highly homologous to Bacillus spp.
Collapse
|
16
|
Georgiadou DN, Avramidis P, Ioannou E, Hatzinikolaou DG. Microbial bioprospecting for lignocellulose degradation at a unique Greek environment. Heliyon 2021; 7:e07122. [PMID: 34141913 PMCID: PMC8187967 DOI: 10.1016/j.heliyon.2021.e07122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/24/2021] [Accepted: 05/18/2021] [Indexed: 11/30/2022] Open
Abstract
Bacterial systems have gained wide attention for depolymerization of lignocellulosic biomass, due to their high functional diversity and adaptability. To achieve the full microbial exploitation of lignocellulosic residues and the cost-effective production of bioproducts within a biorefinery, multiple metabolic pathways and enzymes of various specificities are required. In this work, highly diverse aerobic, mesophilic bacteria enriched from Keri Lake, a pristine marsh of increased biomass degradation and natural underground oil leaks, were explored for their metabolic versatility and enzymatic potential towards lignocellulosic substrates. A high number of Pseudomonas species, obtained from enrichment cultures where organosolv lignin served as the sole carbon and energy source, were able to assimilate a range of lignin-associated aromatic compounds. Comparatively more complex bacterial consortia, including members of Actinobacteria, Proteobacteria, Bacilli, Sphingobacteria, and Flavobacteria, were also enriched from cultures with xylan or carboxymethyl cellulose as sole carbon sources. Numerous individual isolates could target diverse structural lignocellulose polysaccharides by expressing hydrolytic activities on crystalline or amorphous cellulose and xylan. Specific isolates showed increased potential for growth in lignin hydrolysates prepared from alkali pretreated agricultural wastes. The results suggest that Keri isolates represent a pool of effective lignocellulose degraders with significant potential for industrial applications in a lignocellulose biorefinery.
Collapse
Affiliation(s)
- Daphne N. Georgiadou
- Enzyme and Microbial Biotechnology Unit, Department of Biology, National and Kapodistrian University of Athens, Zografou Campus, 15784, Athens, Greece
| | - Pavlos Avramidis
- Laboratory of Sedimentology, Department of Geology, University of Patras, 26504, Rio-Patra, Greece
| | - Efstathia Ioannou
- Section of Pharmacognosy and Chemistry of Natural Products, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771, Athens, Greece
| | - Dimitris G. Hatzinikolaou
- Enzyme and Microbial Biotechnology Unit, Department of Biology, National and Kapodistrian University of Athens, Zografou Campus, 15784, Athens, Greece
- Corresponding author.
| |
Collapse
|
17
|
Singh AK, Katari SK, Umamaheswari A, Raj A. In silico exploration of lignin peroxidase for unraveling the degradation mechanism employing lignin model compounds. RSC Adv 2021; 11:14632-14653. [PMID: 35423962 PMCID: PMC8697836 DOI: 10.1039/d0ra10840e] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 03/10/2021] [Indexed: 12/16/2022] Open
Abstract
Lignin peroxidase is a heme-containing biocatalyst, well-known for its diverse applications in the fields from environmental chemistry to biotechnology. LiP-mediated oxidative catalysis is H2O2-dependent, and can oxidize phenolic, and non-phenolic substrates by oxidative cleavage of the C-C and C-O bonds of lignin. In contrast to fungi-derived LiP, the binding affinity of bacterial-derived LiP to lignin at the molecular level is poorly known to date. Tremendous wet-lab studies have been unveiled that provide degradation and biotransformation information on kraft lignin, whilst studies on the completely transformed compounds and the degradation of each transformed compounds simultaneously during degradation are scarce. To gain an understanding of the degradation process using docking, and MDS based studies, we assessed the binding affinity of selected lignin model compounds with bacterial origin LiP and validated such docked complexes exploiting 30 ns molecular dynamics simulations. We selected and picked a total of 12 lignin model compounds for molecular modeling analysis, namely two chlorinated lignin model compounds (monomer) (2-chlorosyringaldehyde and 5-chlorovanillin), eight standard lignin model compounds (veratryl alcohol, syringyl alcohol, sinapyl alcohol, methyl hydroquinone, guaiacol, coniferyl alcohol, catechol, and 4-methoxy phenol), while, two 4-O-5, and β-O-4 linkage-based multimeric model compounds (dimer: 2-methoxy-6-(2-methoxy-4-methylphenoxy)-4-methylphenol; trimer: syringyl β-O-4 syringyl β-O-4 sinapyl alcohol). Far more specific binding residues were observed from XP-Glide docking, as TYR, HIP (protonated histidine), PHE, VAL, ASP, THR, LYS and GLN. The binding affinity was confirmed by the Gibbs free energy or binding energy (ΔG) score; furthermore, it is found that the maximum binding energy seems to be observed for 4-methoxyphenol with a Glide score of -3.438 with Pi-Pi stacking and H-bond type bonding interactions, whilst the lowest XP Gscore as -8.136 with Pi-Pi stacking and H-bond (side chain) type bonding interactions were found for the trimer model compound. The docked complexes were further evaluated for deep rigorous structural and functional fluctuation analyses through high-performance molecular dynamics simulations-DESMOND, after a post simulation run of 30 ns. The RMSD trajectory analyses of the protein-ligands were found to be in the equilibrium state at the end of simulation run for multimeric lignin model compounds. In addition, ionic ligand-protein interaction occurs among chlorinated compounds, while hydrophobic and H-bond contacts have frequently been observed in all lignin-model compounds. The findings herein demonstrate that bacterial LiP can effectively catalyze multiple lignin model compounds, and it might further be used as an effective tool for sustainable mitigation of diverse environmental contaminants.
Collapse
Affiliation(s)
- Anil Kumar Singh
- Environmental Microbiology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR) Vishvigyan Bhawan, 31, Mahatma Gandhi Marg Lucknow 226001 Uttar Pradesh India .,Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Sudheer Kumar Katari
- Department of Bioinformatics, Sri Venkateswara Institute of Medical Sciences (SVIMS) University Tirupati 517507 Andhra Pradesh India
| | - Amineni Umamaheswari
- Department of Bioinformatics, Sri Venkateswara Institute of Medical Sciences (SVIMS) University Tirupati 517507 Andhra Pradesh India
| | - Abhay Raj
- Environmental Microbiology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR) Vishvigyan Bhawan, 31, Mahatma Gandhi Marg Lucknow 226001 Uttar Pradesh India .,Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| |
Collapse
|
18
|
Weng C, Peng X, Han Y. Depolymerization and conversion of lignin to value-added bioproducts by microbial and enzymatic catalysis. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:84. [PMID: 33812391 PMCID: PMC8019502 DOI: 10.1186/s13068-021-01934-w] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/19/2021] [Indexed: 05/23/2023]
Abstract
Lignin, the most abundant renewable aromatic compound in nature, is an excellent feedstock for value-added bioproducts manufacturing; while the intrinsic heterogeneity and recalcitrance of which hindered the efficient lignin biorefinery and utilization. Compared with chemical processing, bioprocessing with microbial and enzymatic catalysis is a clean and efficient method for lignin depolymerization and conversion. Generally, lignin bioprocessing involves lignin decomposition to lignin-based aromatics via extracellular microbial enzymes and further converted to value-added bioproducts through microbial metabolism. In the review, the most recent advances in degradation and conversion of lignin to value-added bioproducts catalyzed by microbes and enzymes were summarized. The lignin-degrading microorganisms of white-rot fungi, brown-rot fungi, soft-rot fungi, and bacteria under aerobic and anaerobic conditions were comparatively analyzed. The catalytic metabolism of the microbial lignin-degrading enzymes of laccase, lignin peroxidase, manganese peroxidase, biphenyl bond cleavage enzyme, versatile peroxidase, and β-etherize was discussed. The microbial metabolic process of H-lignin, G-lignin, S-lignin based derivatives, protocatechuic acid, and catechol was reviewed. Lignin was depolymerized to lignin-derived aromatic compounds by the secreted enzymes of fungi and bacteria, and the aromatics were converted to value-added compounds through microbial catalysis and metabolic engineering. The review also proposes new insights for future work to overcome the recalcitrance of lignin and convert it to value-added bioproducts by microbial and enzymatic catalysis.
Collapse
Affiliation(s)
- Caihong Weng
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
- School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaowei Peng
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
- School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yejun Han
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China.
- School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
19
|
Merino C, Kuzyakov Y, Godoy K, Jofré I, Nájera F, Matus F. Iron-reducing bacteria decompose lignin by electron transfer from soil organic matter. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 761:143194. [PMID: 33183799 DOI: 10.1016/j.scitotenv.2020.143194] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 10/11/2020] [Accepted: 10/17/2020] [Indexed: 06/11/2023]
Abstract
Iron-reducing bacteria (IRB) are crucial for electron transfer in anaerobic soil microsites. The utilization of the energy gathered by this mechanism by decomposers of organic matter is a challenging and fascinating issue. We hypothesized that bacteria reducing Fe(III) (oxyhydr)oxides to soluble Fe(II) obtain electrons from reduced soil organic matter (SOMr) involving lignin oxidation. Iron-reducing bacteria were isolated from topsoils of various climates (humid temperate, cold temperate, subpolar), vegetation types (mostly grasslands and forests), and derived from various parent materials treatments assigned as Granitic, Volcanic-allophanic, Fluvio-glacial, Basaltic-Antarctic and Metamorphic. After the screening of IRB by phospholipid fatty acid (PLFA) analysis and PCR identification (full-length 16S rDNA), the IRB were inoculated to 20 samples (five soils and 4 replicates) and a broad range of parallel processes were traced. Geobacter metallireducens and Geobacter lovleyi were the main Geobacteraceae-strains present in all soils and strongly increased the activity of ligninolytic enzymes: lignin peroxidase and manganese peroxidase. Carbon dioxide (CO2) released from IRB-inoculated soils was 140% higher than that produced by Fenton reactions (induced by H2O2 and Fe(II) addition) but 40% lower than in non-sterile soils. CO2 release was closely correlated with the produced Fe (II) and H2O2 consumption. The highest CO2 was released from Basaltic-Antarctic soils with the highest Fe content and was closely correlated with lignin depolymerization (detection by fluorescence images). All IRB oxidized the lignin contained in the SOM within a wide pH range and in soils from all parent materials. We present a conceptual model showing electron shuttling from SOM containing lignin (as a C and energy source) to IRB to produce energy and promote Fe(III) (oxyhydr)oxides reduction was proposed and discussed.
Collapse
Affiliation(s)
- Carolina Merino
- Center of Plant, Soil Interaction and Natural Resources Biotechnology Scientific and Technological Bioresource Nucleus (BIOREN), Temuco, Chile; Laboratory of Conservation and Dynamics of Volcanic Soils, Department of Chemical Sciences and Natural Resources, Universidad de La Frontera, Temuco, Chile; Network for Extreme Environmental Research, Universidad de la Frontera, Temuco, Chile
| | - Yakov Kuzyakov
- Network for Extreme Environmental Research, Universidad de la Frontera, Temuco, Chile; Soil Science of Temperate Ecosystems, Büsgen Institute, Georg-August-Universität Göttingen, Germany; Institute of Environmental Sciences, Kazan Federal University, Kazan, Russia; RUDN, Moscow, Russia
| | - Karina Godoy
- Center of Plant, Soil Interaction and Natural Resources Biotechnology Scientific and Technological Bioresource Nucleus (BIOREN), Temuco, Chile
| | - Ignacio Jofré
- Laboratory of Conservation and Dynamics of Volcanic Soils, Department of Chemical Sciences and Natural Resources, Universidad de La Frontera, Temuco, Chile
| | - Francisco Nájera
- PhD Program in Science of Natural Resource Sciences, Universidad de La Frontera, Chile
| | - Francisco Matus
- Laboratory of Conservation and Dynamics of Volcanic Soils, Department of Chemical Sciences and Natural Resources, Universidad de La Frontera, Temuco, Chile; Network for Extreme Environmental Research, Universidad de la Frontera, Temuco, Chile.
| |
Collapse
|
20
|
Genomics and metatranscriptomics of biogeochemical cycling and degradation of lignin-derived aromatic compounds in thermal swamp sediment. THE ISME JOURNAL 2021; 15:879-893. [PMID: 33139871 PMCID: PMC8027834 DOI: 10.1038/s41396-020-00820-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/13/2020] [Accepted: 10/21/2020] [Indexed: 01/30/2023]
Abstract
Thermal swamps are unique ecosystems where geothermally warmed waters mix with decomposing woody biomass, hosting novel biogeochemical-cycling and lignin-degrading microbial consortia. Assembly of shotgun metagenome libraries resolved 351 distinct genomes from hot-spring (30-45 °C) and mesophilic (17 °C) sediments. Annotation of 39 refined draft genomes revealed metabolism consistent with oligotrophy, including pathways for degradation of aromatic compounds, such as syringate, vanillate, p-hydroxybenzoate, and phenol. Thermotolerant Burkholderiales, including Rubrivivax ssp., were implicated in diverse biogeochemical and aromatic transformations, highlighting their broad metabolic capacity. Lignin catabolism was further investigated using metatranscriptomics of sediment incubated with milled or Kraft lignin at 45 °C. Aromatic compounds were depleted from lignin-amended sediment over 148 h. The metatranscriptomic data revealed upregulation of des/lig genes predicted to specify the catabolism of syringate, vanillate, and phenolic oligomers in the sphingomonads Altererythrobacter ssp. and Novosphingobium ssp., as well as in the Burkholderiales genus, Rubrivivax. This study demonstrates how temperature structures biogeochemical cycling populations in a unique ecosystem, and combines community-level metagenomics with targeted metatranscriptomics to identify pathways with potential for bio-refinement of lignin-derived aromatic compounds. In addition, the diverse aromatic catabolic pathways of Altererythrobacter ssp. may serve as a source of thermotolerant enzymes for lignin valorization.
Collapse
|
21
|
Jia T, Wang Y, Chai B. Bacterial Community Characteristics and Enzyme Activities in Bothriochloa ischaemum Litter Over Progressive Phytoremediation Years in a Copper Tailings Dam. Front Microbiol 2020; 11:565806. [PMID: 33408700 PMCID: PMC7779404 DOI: 10.3389/fmicb.2020.565806] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 12/03/2020] [Indexed: 11/13/2022] Open
Abstract
Litter decomposition is the key link between material circulation and energy flow in ecosystems, resulting from the activity of resident microbes and various enzymes. This study investigated enzyme activity in litter and associated microbial community characteristics to help clarify the internal mechanisms associated with litter decomposition, while also providing researchers a scientific basis for soil remediation in mining areas. Results confirmed that the nutrient content of Bothriochloa ischaemum litter significantly increased as phytoremediation years progressed, while enzyme activities in litter varied over different phytoremediation years. During the litter decomposition process, cellulase predominated in the early phytoremediation stage and catalase predominated in the intermediate phytoremediation stage. Obvious differences were found in bacterial community structure and diversity over progressive phytoremediation years. Predominant bacterial genera mainly included Massilia, Sphingomonas, Curtobacterium, Amnibacterium, and Methylobacterium. Moreover, Methylorosula and Jatrophihabitans had relatively higher betweenness centrality, and played important roles in bacterial community positive interactions. Additionally, total nitrogen (TN) and total zinc in soil, sucrase and catalase activity in litter were the main environmental factors that affected the structural framework of bacteria in B. ischaemum litter. However, TN had the greatest overall effect on the structural framework of bacteria in litter. Results from this study can help our understanding of the role that litter plays in degraded ecosystems. Our results also provide a scientific basis for improving poor quality soil in areas affected by copper tailings while also amending ecological restoration efficiency.
Collapse
Affiliation(s)
- Tong Jia
- Shanxi Key Laboratory of Ecological Restoration on Loess Plateau, Institute of Loess Plateau, Shanxi University, Taiyuan, China
| | - Yuwen Wang
- Shanxi Key Laboratory of Ecological Restoration on Loess Plateau, Institute of Loess Plateau, Shanxi University, Taiyuan, China
| | - Baofeng Chai
- Shanxi Key Laboratory of Ecological Restoration on Loess Plateau, Institute of Loess Plateau, Shanxi University, Taiyuan, China
| |
Collapse
|
22
|
Falade AO, Mabinya LV, Okoh AI, Nwodo UU. Agroresidues enhanced peroxidase activity expression by Bacillus sp. MABINYA-1 under submerged fermentation. BIORESOUR BIOPROCESS 2020. [DOI: 10.1186/s40643-020-00345-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractAgroresidues have continued to gain preference over conventional carbon sources for microbial enzyme production due to the low price and abundance in the environment. Therefore, this study aimed at improving peroxidase yield by Bacillus sp. MABINYA-1 (BMAB-1) using agroresidues under submerged fermentation. The culture parameters that support maximum peroxidase yield by BMAB-1 was initially determined and the results showed that peroxidase activity expression was optimum at pH 5, 30 °C and 150 rpm while veratryl alcohol and ammonium sulphate served as the best peroxidase-inducer and inorganic nitrogen source, respectively. BMAB-1 exhibited maximum peroxidase expression (17.50 ± 0.10 U/mg) at 72 h using kraft lignin liquid medium (KLLM) under the optimized culture conditions. Upon utilization of selected agroresidues (sawdust, wheat straw and maize stover) as sole carbon sources by BMAB-1 in the fermentation process, peroxidase activity was significantly enhanced when compared with glucose (14.91 ± 0.31 U/mg) and kraft lignin (17.50 ± 0.10 U/mg). Sawdust produced the highest peroxidase yield (47.14 ± 0.41 U/mg), followed by maize stover (37.09 ± 0.00 U/mg) while wheat straw yielded the lowest peroxidase specific activity (21.65 ± 0.35 U/mg). This indicates that utilization of sawdust by BMAB-1 resulted in 3.2- and 2.7-fold increase in peroxidase activity expression as compared to glucose and kraft lignin, respectively. The aptitude of BMAB-1 to utilize agroresidues would reduce the cost of peroxidase production by the bacteria since the substrates are cheaper than the conventional carbon sources and are, as well, more readily available.
Collapse
|
23
|
Microbial community dynamics in phyto-thermotherapy baths viewed through next generation sequencing and metabolomics approach. Sci Rep 2020; 10:17931. [PMID: 33087817 PMCID: PMC7578836 DOI: 10.1038/s41598-020-74586-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 07/28/2020] [Indexed: 01/04/2023] Open
Abstract
Phyto-thermotherapy is a treatment consisting in immersing oneself in baths of self-heating alpine grass, to benefit of the heat and rich aromatic components released by the process. The aim of this study was to characterize the bacterial and fungal diversity of three phyto-thermal baths (PTB) performed in three different months, and to compare the data with the profile of the volatile organic compounds (VOCs) of the process. All the data collected showed that PTBs were structured in two stages: the first three days were characterised by an exponential rise of the temperature, a fast bacterial development, higher microbial diversity and higher concentrations of plant aliphatic hydrocarbons. The second stage was characterised by a stable high temperature, shrinkage of the microbial diversity with a predominance of few bacterial and fungi species and higher concentrations of volatiles of microbial origin. Erwinia was the dominant microbial species during the first stage and probably responsible of the self-heating process. In conclusion, PTBs has shown both similarities with common self-heating processes and important peculiarities such as the absence of pathogenic bacteria and the dominance of plant terpenoids with health characteristics among the VOCs confirming the evidence of beneficial effects in particular in the first three days.
Collapse
|
24
|
Liang J, Jin Y, Wen X, Mi J, Wu Y. Adding a complex microbial agent twice to the composting of laying-hen manure promoted doxycycline degradation with a low risk on spreading tetracycline resistance genes. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 265:114202. [PMID: 32806409 DOI: 10.1016/j.envpol.2020.114202] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 02/14/2020] [Accepted: 02/15/2020] [Indexed: 06/11/2023]
Abstract
Poultry manure is a reservoir for antibiotics and antibiotic resistance genes and composting is an effective biological treatment for manure. This study explored the effect of using two methods of adding a complex microbial agent to the composting of laying-hen manure on doxycycline degradation and tetracycline resistance genes elimination. The results showed that incorporating a complex microbial agent at 0.8% (w/w) on the 0th and 11th day (group MT2) effectively degraded doxycycline with a final degradation rate of 46.83 ± 0.55%. The half-life of doxycycline in this group was 21.90 ± 0.00 days and was significantly lower than that of group MT1 (1.6% (w/w) complex microbial agent added on the 0th day) and group DT (compost without complex microbial agent). But there was no significant difference in the final degradation rate of doxycycline between group DT and group MT1. The addictive with the complex microbial agent changed the microbial community structure. Bacteroidetes, Firmicutes and Proteobacteria were the dominant phyla during composting. Aerococcus, Desemzia, Facklamia, Lactobacillus, Streptococcus, and Trichococcus were the bacteria related to the degradation of doxycycline. Moreover, the incorporation of a complex microbial agent could decrease the risk on spreading tetracycline resistance genes. The single addition promoted the elimination of tetM, whose possible hosts were Enterococcus, Lactobacillus, Staphylococcus, and Trichococcus. Adding the complex microbial agent twice promoted the elimination of tetX, which was related to the low abundance of Chryseobacterium, Flavobacterium and Neptunomonas in group MT2. Redundancy analysis showed that the bacterial community, residual doxycycline and physiochemical properties have a potential effect on the variation in tetracycline resistance genes levels. Overall, adding the complex microbial agent twice is an effective measure to degrade doxycycline.
Collapse
Affiliation(s)
- Jiadi Liang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Yiman Jin
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Xin Wen
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Jiandui Mi
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, 510642, Guangdong, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou, 510642, China; Guangdong Engineering Research Center for Disposal and Resource Utilization of Animal Wastes, Yunfu, Xinxing, 527400, China
| | - Yinbao Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, 510642, Guangdong, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China; Ministry of Agriculture Key Laboratory of Tropical Agricultural Environment, South China Agricultural University, Guangzhou, 510642, China; Guangdong Engineering Research Center for Disposal and Resource Utilization of Animal Wastes, Yunfu, Xinxing, 527400, China.
| |
Collapse
|
25
|
Muaaz-Us-Salam S, Cleall PJ, Harbottle MJ. Application of enzymatic and bacterial biodelignification systems for enhanced breakdown of model lignocellulosic wastes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 728:138741. [PMID: 32339836 DOI: 10.1016/j.scitotenv.2020.138741] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/14/2020] [Accepted: 04/14/2020] [Indexed: 06/11/2023]
Abstract
This paper explores the extent to which enzymatic and bacterial biodelignification systems can breakdown lignocellulose in model wastes to potentially enhance biogas generation. Two representative lignocellulosic wastes (newspaper and softwood) commonly found largely undegraded in old landfills were used. A fungal peroxidase (lignin peroxidase) enzyme and a recently isolated lignin-degrading bacterial strain (Agrobacterium sp.) were used. Tests were conducted in stirred bioreactors with methanogens from sewage sludge added to produce biogas from breakdown products. Addition of lignin peroxidase resulted in ~20% enhancement in cumulative methane produced in newspaper reactors. It had a negative effect on wood. Agrobacterium sp. strain enhanced biodegradation of both wood (~20% higher release of soluble organic carbon and enhanced breakdown) and newspaper (~2-fold biogas yield). The findings of this paper have important implications for enhanced breakdown in old landfills that are rich in these wastes, and anaerobic operations utilising lignocellulosic wastes for higher degradation efficiencies and biogas production.
Collapse
|
26
|
Gonçalves CC, Bruce T, Silva CDOG, Fillho EXF, Noronha EF, Carlquist M, Parachin NS. Bioprospecting Microbial Diversity for Lignin Valorization: Dry and Wet Screening Methods. Front Microbiol 2020; 11:1081. [PMID: 32582068 PMCID: PMC7295907 DOI: 10.3389/fmicb.2020.01081] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/30/2020] [Indexed: 01/02/2023] Open
Abstract
Lignin is an abundant cell wall component, and it has been used mainly for generating steam and electricity. Nevertheless, lignin valorization, i.e. the conversion of lignin into high value-added fuels, chemicals, or materials, is crucial for the full implementation of cost-effective lignocellulosic biorefineries. From this perspective, rapid screening methods are crucial for time- and resource-efficient development of novel microbial strains and enzymes with applications in the lignin biorefinery. The present review gives an overview of recent developments and applications of a vast arsenal of activity and sequence-based methodologies for uncovering novel microbial strains with ligninolytic potential, novel enzymes for lignin depolymerization and for unraveling the main metabolic routes during growth on lignin. Finally, perspectives on the use of each of the presented methods and their respective advantages and disadvantages are discussed.
Collapse
Affiliation(s)
- Carolyne Caetano Gonçalves
- Department of Genomic Science and Biotechnology, Universidade Católica de Brasília - UCB, Brasília, Brazil
| | - Thiago Bruce
- Department of Genomic Science and Biotechnology, Universidade Católica de Brasília - UCB, Brasília, Brazil
| | | | | | - Eliane Ferreira Noronha
- Laboratory of Enzymology, Department of Cellular Biology, University of Brasília, Brasília, Brazil
| | - Magnus Carlquist
- Division of Applied Microbiology, Department of Chemistry, Faculty of Engineering, Lund University, Lund, Sweden
| | - Nádia Skorupa Parachin
- Department of Genomic Science and Biotechnology, Universidade Católica de Brasília - UCB, Brasília, Brazil
| |
Collapse
|
27
|
Tao X, Feng J, Yang Y, Wang G, Tian R, Fan F, Ning D, Bates CT, Hale L, Yuan MM, Wu L, Gao Q, Lei J, Schuur EAG, Yu J, Bracho R, Luo Y, Konstantinidis KT, Johnston ER, Cole JR, Penton CR, Tiedje JM, Zhou J. Winter warming in Alaska accelerates lignin decomposition contributed by Proteobacteria. MICROBIOME 2020; 8:84. [PMID: 32503635 PMCID: PMC7275452 DOI: 10.1186/s40168-020-00838-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 04/15/2020] [Indexed: 06/01/2023]
Abstract
BACKGROUND In a warmer world, microbial decomposition of previously frozen organic carbon (C) is one of the most likely positive climate feedbacks of permafrost regions to the atmosphere. However, mechanistic understanding of microbial mediation on chemically recalcitrant C instability is limited; thus, it is crucial to identify and evaluate active decomposers of chemically recalcitrant C, which is essential for predicting C-cycle feedbacks and their relative strength of influence on climate change. Using stable isotope probing of the active layer of Arctic tundra soils after depleting soil labile C through a 975-day laboratory incubation, the identity of microbial decomposers of lignin and, their responses to warming were revealed. RESULTS The β-Proteobacteria genus Burkholderia accounted for 95.1% of total abundance of potential lignin decomposers. Consistently, Burkholderia isolated from our tundra soils could grow with lignin as the sole C source. A 2.2 °C increase of warming considerably increased total abundance and functional capacities of all potential lignin decomposers. In addition to Burkholderia, α-Proteobacteria capable of lignin decomposition (e.g. Bradyrhizobium and Methylobacterium genera) were stimulated by warming by 82-fold. Those community changes collectively doubled the priming effect, i.e., decomposition of existing C after fresh C input to soil. Consequently, warming aggravates soil C instability, as verified by microbially enabled climate-C modeling. CONCLUSIONS Our findings are alarming, which demonstrate that accelerated C decomposition under warming conditions will make tundra soils a larger biospheric C source than anticipated. Video Abstract.
Collapse
Affiliation(s)
- Xuanyu Tao
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Jiajie Feng
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
| | - Gangsheng Wang
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Renmao Tian
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Fenliang Fan
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Daliang Ning
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Colin T Bates
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Lauren Hale
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Mengting M Yuan
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Linwei Wu
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Qun Gao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Jiesi Lei
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Edward A G Schuur
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Julian Yu
- College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ, 85212, USA
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA
| | - Rosvel Bracho
- School of Forest Resources and Conservation, Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Yiqi Luo
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, School of Biology, and Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Eric R Johnston
- School of Civil and Environmental Engineering, School of Biology, and Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - James R Cole
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
| | - C Ryan Penton
- College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ, 85212, USA
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA.
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA.
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| |
Collapse
|
28
|
|
29
|
Granja-Travez RS, Persinoti GF, Squina FM, Bugg TDH. Functional genomic analysis of bacterial lignin degraders: diversity in mechanisms of lignin oxidation and metabolism. Appl Microbiol Biotechnol 2020; 104:3305-3320. [PMID: 32088760 DOI: 10.1007/s00253-019-10318-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 12/06/2019] [Accepted: 12/13/2019] [Indexed: 02/07/2023]
Abstract
Although several bacterial lignin-oxidising enzymes have been discovered in recent years, it is not yet clear whether different lignin-degrading bacteria use similar mechanisms for lignin oxidation and degradation of lignin fragments. Genome sequences of 13 bacterial lignin-oxidising bacteria, including new genome sequences for Microbacterium phyllosphaerae and Agrobacterium sp., were analysed for the presence of lignin-oxidising enzymes and aromatic degradation gene clusters that could be used to metabolise the products of lignin degradation. Ten bacterial genomes contain DyP-type peroxidases, and ten bacterial strains contain putative multi-copper oxidases (MCOs), both known to have activity for lignin oxidation. Only one strain lacks both MCOs and DyP-type peroxidase genes. Eleven bacterial genomes contain aromatic degradation gene clusters, of which ten contain the central β-ketoadipate pathway, with variable numbers and types of degradation clusters for other aromatic substrates. Hence, there appear to be diverse metabolic strategies used for lignin oxidation in bacteria, while the β-ketoadipate pathway appears to be the most common route for aromatic metabolism in lignin-degrading bacteria.
Collapse
Affiliation(s)
- Rommel Santiago Granja-Travez
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.,Facultad de Ciencias de la Ingeniería e Industrias, Universidad UTE, Quito, Ecuador
| | | | - Fabio M Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, Brazil
| | - Timothy D H Bugg
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
| |
Collapse
|
30
|
Bacterial enzymes for lignin depolymerisation: new biocatalysts for generation of renewable chemicals from biomass. Curr Opin Chem Biol 2020; 55:26-33. [PMID: 31918394 DOI: 10.1016/j.cbpa.2019.11.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/17/2019] [Accepted: 11/19/2019] [Indexed: 11/20/2022]
Abstract
The conversion of polymeric lignin from plant biomass into renewable chemicals is an important unsolved problem in the biorefinery concept. This article summarises recent developments in the discovery of bacterial enzymes for lignin degradation, our current understanding of their molecular mechanism of action, and their use to convert lignin or lignocellulose into aromatic chemicals. The review also discusses the recent developments in screening of metagenomic libraries for new biocatalysts, and the use of protein engineering to enhance lignin degradation activity.
Collapse
|
31
|
Larsbrink J, McKee LS. Bacteroidetes bacteria in the soil: Glycan acquisition, enzyme secretion, and gliding motility. ADVANCES IN APPLIED MICROBIOLOGY 2020; 110:63-98. [PMID: 32386606 DOI: 10.1016/bs.aambs.2019.11.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The secretion of extracellular enzymes by soil microbes is rate-limiting in the recycling of biomass. Fungi and bacteria compete and collaborate for nutrients in the soil, with wide ranging ecological impacts. Within soil microbiota, the Bacteroidetes tend to be a dominant phylum, just like in human and animal intestines. The Bacteroidetes thrive because of their ability to secrete diverse arrays of carbohydrate-active enzymes (CAZymes) that target the highly varied glycans in the soil. Bacteroidetes use an energy-saving system of genomic organization, whereby most of their CAZymes are grouped into Polysaccharide Utilization Loci (PULs). These loci enable high level production of specific CAZymes only when their substrate glycans are abundant in the local environment. This gives the Bacteroidetes a clear advantage over other species in the competitive soil environment, further enhanced by the phylum-specific Type IX Secretion System (T9SS). The T9SS is highly effective at secreting CAZymes and/or tethering them to the cell surface, and is tightly coupled to the ability to rapidly glide over solid surfaces, a connection that promotes an active hunt for nutrition. Although the soil Bacteroidetes are less well studied than human gut symbionts, research is uncovering important biochemical and physiological phenomena. In this review, we summarize the state of the art on research into the CAZymes secreted by soil Bacteroidetes in the contexts of microbial soil ecology and the discovery of novel CAZymes for use in industrial biotechnology. We hope that this review will stimulate further investigations into the somewhat neglected enzymology of non-gut Bacteroidetes.
Collapse
Affiliation(s)
- Johan Larsbrink
- Wallenberg Wood Science Center, Gothenburg and Stockholm, Sweden; Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Lauren Sara McKee
- Wallenberg Wood Science Center, Gothenburg and Stockholm, Sweden; Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden.
| |
Collapse
|
32
|
Argiroff WA, Zak DR, Upchurch RA, Salley SO, Grandy AS. Anthropogenic N deposition alters soil organic matter biochemistry and microbial communities on decaying fine roots. GLOBAL CHANGE BIOLOGY 2019; 25:4369-4382. [PMID: 31314956 DOI: 10.1111/gcb.14770] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 07/06/2019] [Indexed: 06/10/2023]
Abstract
Fine root litter is a primary source of soil organic matter (SOM), which is a globally important pool of C that is responsive to climate change. We previously established that ~20 years of experimental nitrogen (N) deposition has slowed fine root decay and increased the storage of soil carbon (C; +18%) across a widespread northern hardwood forest ecosystem. However, the microbial mechanisms that have directly slowed fine root decay are unknown. Here, we show that experimental N deposition has decreased the relative abundance of Agaricales fungi (-31%) and increased that of partially ligninolytic Actinobacteria (+24%) on decaying fine roots. Moreover, experimental N deposition has increased the relative abundance of lignin-derived compounds residing in SOM (+53%), and this biochemical response is significantly related to shifts in both fungal and bacterial community composition. Specifically, the accumulation of lignin-derived compounds in SOM is negatively related to the relative abundance of ligninolytic Mycena and Kuehneromyces fungi, and positively related to Microbacteriaceae. Our findings suggest that by altering the composition of microbial communities on decaying fine roots such that their capacity for lignin degradation is reduced, experimental N deposition has slowed fine root litter decay, and increased the contribution of lignin-derived compounds from fine roots to SOM. The microbial responses we observed may explain widespread findings that anthropogenic N deposition increases soil C storage in terrestrial ecosystems. More broadly, our findings directly link composition to function in soil microbial communities, and implicate compositional shifts in mediating biogeochemical processes of global significance.
Collapse
Affiliation(s)
- William A Argiroff
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, USA
| | - Donald R Zak
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Rima A Upchurch
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, USA
| | - Sydney O Salley
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, USA
| | - A Stuart Grandy
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, USA
| |
Collapse
|
33
|
Sant' Anna D, Sampaio JLM, Sommaggio LRD, Mazzeo DEC, Marin-Morales MA, Marson FAL, Levy CE. The applicability of gene sequencing and MALDI-TOF to identify less common gram-negative rods (Advenella, Castellaniella, Kaistia, Pusillimonas and Sphingobacterium) from environmental isolates. Antonie van Leeuwenhoek 2019; 113:233-252. [PMID: 31560092 DOI: 10.1007/s10482-019-01333-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 09/13/2019] [Indexed: 11/26/2022]
Abstract
Our aim was to identify less common non-fermenting gram-negative rods during the bioremediation process. Five genera were found: Advenella, Castellaniella, Kaistia, Pusillimonas and Sphingobacterium, for a total of 15 isolates. Therefore, we evaluated the applicability of four methods currently available for bacteria identification: (1) conventional biochemical methods, (2) the VITEK®-2 system, (3) MALDI-TOF mass spectrometry and (4) 16S rRNA gene sequencing. The biochemical methods and the VITEK®-2 system were reliable only for the Sphingobacterium isolate and solely at the genus level. Both MALDI-TOF mass spectrometry platforms (Bruker and VITEK® MS) did not achieve reliable identification results for any of these genera. 16S rRNA gene sequencing identified eight isolates to the species level but not to the subspecies level, when applicable. The remaining seven isolates were reliably identified through 16S rRNA gene sequencing to the genus level only. Our findings suggest that the detection and identification of less common genera (and species) that appeared at certain moments during the bioremediation process can be a challenge to microbiologists considering the most used techniques. In addition, more studies are required to confirm our results.
Collapse
Affiliation(s)
- Débora Sant' Anna
- Microbiology Laboratory, Department of Clinical Pathology, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Villela, 1331, Barretos, São Paulo, Brazil.
| | - Jorge Luiz Mello Sampaio
- Microbiology Section, Fleury-Centers for Diagnostic Medicine, Av. General Waldomiro de Lima 508, São Paulo, 04344-070, Brazil
- Clinical Analysis and Toxicology Department, School of Pharmacy, University of São Paulo, Av. Professor Lineu Prestes, 580, Butantã, São Paulo, 05508-000, Brazil
| | - Lais Roberta Deroldo Sommaggio
- Department of Biology, Institute of Biosciences, São Paulo State University - Rio Claro, Av. 24 A, 1515, Bela Vista, Rio Claro, São Paulo, 13506-900, Brazil
| | - Dânia Elisa Christofoletti Mazzeo
- Department of Analytical Chemistry, Institute of Chemistry, São Paulo State University - Araraquara, Rua Professor Francisco Degni, 55, Araraquara, São Paulo, 14800-060, Brazil
| | - Maria Aparecida Marin-Morales
- Department of Biology, Institute of Biosciences, São Paulo State University - Rio Claro, Av. 24 A, 1515, Bela Vista, Rio Claro, São Paulo, 13506-900, Brazil
| | - Fernando Augusto Lima Marson
- Department of Pediatrics, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
- Laboratory of Pulmonary Physiology, Center for Pediatrics Investigation, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
- Department of Medical Genetics and Genomic Medicine, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
- Post-Graduate Program in Health Science, São Francisco University, Avenida São Francisco de Assis, 218, Cidade Universitária, Bragança Paulista, São Paulo, 12916-400, Brazil.
| | - Carlos Emílio Levy
- Microbiology Laboratory, Department of Clinical Pathology, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
- Department of Pediatrics, Faculty of Medical Sciences, University of Campinas, Rua Tessália Vieira de Camargo, 126, Cidade Universitária, Campinas, São Paulo, 13083-887, Brazil.
| |
Collapse
|
34
|
Lee S, Kang M, Bae JH, Sohn JH, Sung BH. Bacterial Valorization of Lignin: Strains, Enzymes, Conversion Pathways, Biosensors, and Perspectives. Front Bioeng Biotechnol 2019; 7:209. [PMID: 31552235 PMCID: PMC6733911 DOI: 10.3389/fbioe.2019.00209] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 08/19/2019] [Indexed: 12/17/2022] Open
Abstract
Lignin, an aromatic polymer found in plants, has been studied for years in many biological fields. Initially, when biofuel was produced from lignocellulosic biomass, lignin was regarded as waste generated by the biorefinery and had to be removed, because of its inhibitory effects on fermentative bacteria. Although it has since proven to be a natural resource for bio-products with considerable potential, its utilization is confined by its complex structure. Hence, the microbial degradation of lignin has attracted researchers' interest to overcome this problem. From this perspective, the studies have primarily focused on fungal systems, such as extracellular peroxidase and laccase from white- and brown-rot fungi. However, recent reports have suggested that bacteria play an increasing role in breaking down lignin. This paper, therefore, reviews the role of bacteria in lignin and lignin-related research. Several reports on bacterial species in soil that can degrade lignin and their enzymes are included. In addition, a cellulolytic anaerobic bacterium capable of solubilizing lignin and carbohydrate simultaneously has recently been identified, even though the enzyme involved has not been discovered yet. The assimilation of lignin-derived small molecules and their conversion to renewable chemicals by bacteria, such as muconic acid and polyhydroxyalkanoates, including genetic modification to enhance their capability was discussed. This review also covers the indirect use of bacteria for lignin degradation, which is concerned with whole-cell biosensors designed to detect the aromatic chemicals released from lignin transformation.
Collapse
Affiliation(s)
- Siseon Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Minsik Kang
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- Department of Biosystems and Bioengineering, Korea University of Science and Technology, Daejeon, South Korea
| | - Jung-Hoon Bae
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Jung-Hoon Sohn
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- Department of Biosystems and Bioengineering, Korea University of Science and Technology, Daejeon, South Korea
| | - Bong Hyun Sung
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- Department of Biosystems and Bioengineering, Korea University of Science and Technology, Daejeon, South Korea
| |
Collapse
|
35
|
Exoproduction and Molecular Characterization of Peroxidase from Ensifer adhaerens. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9153121] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The increased industrial application potentials of peroxidase have led to high market demand, which has outweighed the commercially available peroxidases. Hence, the need for alternative and efficient peroxidase-producers is imperative. This study reported the process parameters for enhanced exoperoxidase production by Ensifer adhaerens NWODO-2 (accession number: KX640918) for the first time, and characterized the enzyme using molecular methods. Peroxidase production by the bacteria was optimal at 48 h, with specific productivity of 12.76 U mg−1 at pH 7, 30 °C and 100 rpm in an alkali lignin fermentation medium supplemented with guaiacol as the most effective inducer and ammonium sulphate as the best inorganic nitrogen source. Upon assessment of some agricultural residues as sources of carbon for the enzyme production, sawdust gave the highest peroxidase productivity (37.50 U mg−1) under solid-state fermentation. A search of the polymerase chain reaction (PCR)-amplified peroxidase gene in UniProtKB using blastx showed 70.5% similarity to an uncharacterized protein in Ensifer adhaerens but phylogenetic analysis suggests that the gene may encode a catalase-peroxidase with an estimated molecular weight of approximately 31 kDa and isoelectric point of about 11. The nucleotide sequence of the detected gene was deposited in the GenBank under the accession number MF374336. In conclusion, the ability of the strain to utilize lignocellulosic materials for peroxidase production augurs well for biotechnological application as this would greatly reduce cost, which is a major challenge in industrial enzyme production.
Collapse
|
36
|
Ravi K, García-Hidalgo J, Brink DP, Skyvell M, Gorwa-Grauslund MF, Lidén G. Physiological characterization and sequence analysis of a syringate-consuming Actinobacterium. BIORESOURCE TECHNOLOGY 2019; 285:121327. [PMID: 30991184 DOI: 10.1016/j.biortech.2019.121327] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/05/2019] [Accepted: 04/06/2019] [Indexed: 06/09/2023]
Abstract
Hardwood lignin is made of up to 75% syringyl-units and the bioconversion of syringate and syringaldehyde is therefore of considerable interest for biological valorization of lignin. In the current study, we have isolated a syringate-consuming bacterium identified as Microbacterium sp. RG1 and characterized its growth on several lignin model compounds. Growth was observed on syringate, 3-O-methylgallate, vanillate, 4-hydroxybenzoate, ferulate and p-coumarate. Toxic aromatic aldehydes such as vanillin and syringaldehyde were converted to their respective alcohols/acids which were eventually consumed with a maximum specific uptake rate of 0.02 and 0.1 mmol (gCDW h)-1 respectively. The isolate was further subjected to whole genome sequencing and putative genes related to the metabolism of syringyl-compounds were mapped for the first time in a Gram-positive bacterium. These findings will be of high significance when designing future host microorganisms and bioprocesses for the efficient valorization of pre-treated lignin feedstocks.
Collapse
Affiliation(s)
- Krithika Ravi
- Department of Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Javier García-Hidalgo
- Division of Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Daniel P Brink
- Division of Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Martin Skyvell
- Department of Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Marie F Gorwa-Grauslund
- Division of Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Gunnar Lidén
- Department of Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden.
| |
Collapse
|
37
|
Zhu L, Zhao Y, Zhang W, Zhou H, Chen X, Li Y, Wei D, Wei Z. Roles of bacterial community in the transformation of organic nitrogen toward enhanced bioavailability during composting with different wastes. BIORESOURCE TECHNOLOGY 2019; 285:121326. [PMID: 30986627 DOI: 10.1016/j.biortech.2019.121326] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/03/2019] [Accepted: 04/05/2019] [Indexed: 06/09/2023]
Abstract
This study aimed to explore the roles of bacterial community in the transformation of bioavailable organic-N (BON) during different wastes composting. BON fractions with different forms and molecular weights were identified in this study. Results indicated that core bacterial communities improved the availability of BON by degrading high molecular weights BON into low molecular weights BON during different wastes composting. A total of fifty-two core bacterial genera involved in BON transformation were identified by network analysis. Three types of high molecular weights BON fractions (amino acid-N, amine-N and amino sugar-N) were degraded by bacteria during chicken manure and garden waste composting, while only amine-N was degraded during municipal solid waste composting. Finally, moisture, C/N and pH were identified as the key operational parameters affecting BON transformation mediated by microorganisms, which can be used to improve bioavailability of organic-N and reduce N loss during composting.
Collapse
Affiliation(s)
- Longji Zhu
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Yue Zhao
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Wenshuai Zhang
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Haixuan Zhou
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Xiaomeng Chen
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Yingjun Li
- Beijing Vocational College of Agriculture, Beijing 100012, China
| | - Dan Wei
- Institute of Plant Nutrition and Resources, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Zimin Wei
- College of Life Science, Northeast Agricultural University, Harbin 150030, China.
| |
Collapse
|
38
|
Li M, Eskridge K, Liu E, Wilkins M. Enhancement of polyhydroxybutyrate (PHB) production by 10-fold from alkaline pretreatment liquor with an oxidative enzyme-mediator-surfactant system under Plackett-Burman and central composite designs. BIORESOURCE TECHNOLOGY 2019; 281:99-106. [PMID: 30807996 DOI: 10.1016/j.biortech.2019.02.045] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/06/2019] [Accepted: 02/08/2019] [Indexed: 06/09/2023]
Abstract
In this study, Plackett-Burman and central composite designs were applied to improve polyhydroxybutyrate (PHB) production from alkaline pretreatment liquor (APL) by Cupriavidus necator DSM 545 using a supplement system consisting of oxidative enzymes (laccase, aryl alcohol oxidase (AAO)), mediators (ABTS, HOBT), DMSO, silica nanoparticle Aerosol R816 and surfactant Tween 80. First, screening experiments under Plackett-Burman design showed R816, ABTS and Tween 80 could significantly enhance PHB production. Additional experiments showed that HOBT and DMSO could be removed, and laccase and AAO were needed to remain in the system. Second, a central composite design was applied to obtain the optimum supplemental levels of R816, ABTS and Tween 80. Under optimum conditions, theoretical maximum PHB production (1.9 g/L) was close to experimental PHB production (2.1 g/L). With the supplement system, a 10-fold increase was achieved compared to PHB production (0.2 g/L) without any supplements.
Collapse
Affiliation(s)
- Mengxing Li
- Department of Biological Systems Engineering, The University of Nebraska-Lincoln, Lincoln 68583, USA; Department of Statistics, The University of Nebraska-Lincoln, Lincoln 68583, USA
| | - Kent Eskridge
- Department of Statistics, The University of Nebraska-Lincoln, Lincoln 68583, USA
| | - Enshi Liu
- Department of Biological Systems Engineering, The University of Nebraska-Lincoln, Lincoln 68583, USA
| | - Mark Wilkins
- Department of Biological Systems Engineering, The University of Nebraska-Lincoln, Lincoln 68583, USA; Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln 68588, USA; Industrial Agricultural Products Center, University of Nebraska-Lincoln, Lincoln 68583, USA.
| |
Collapse
|
39
|
Wei Z, Wilkinson RC, Rashid GMM, Brown D, Fülöp V, Bugg TDH. Characterization of Thiamine Diphosphate-Dependent 4-Hydroxybenzoylformate Decarboxylase Enzymes from Rhodococcus jostii RHA1 and Pseudomonas fluorescens Pf-5 Involved in Degradation of Aryl C 2 Lignin Degradation Fragments. Biochemistry 2019; 58:5281-5293. [PMID: 30946572 DOI: 10.1021/acs.biochem.9b00177] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A thiamine diphosphate-dependent enzyme annotated as a benzoylformate decarboxylase is encoded by gene cluster ro02984-ro02986 in Rhodococcus jostii RHA1 previously shown to generate vanillin and 4-hydroxybenzaldehyde from lignin oxidation, and a closely related gene cluster is also found in the genome of Pseudomonas fluorescens Pf-5. Two hypotheses for possible pathways involving a thiamine diphosphate-dependent cleavage, either C-C cleavage of a ketol or diketone aryl C3 substrate or decarboxylation of an aryl C2 substrate, were investigated by expression and purification of the recombinant enzymes and expression of dehydrogenase and oxidase enzymes also found in the gene clusters. The ThDP-dependent enzymes showed no activity for cleavage of aryl C3 ketol or diketone substrates but showed activity for decarboxylation of benzoylformate and 4-hydroxybenzoylformate. A flavin-dependent oxidase encoded by gene ro02984 was found to oxidize either mandelic acid or phenylglyoxal. The crystal structure of the P. fluorescens decarboxylase enzyme was determined at 1.69 Å resolution, showing similarity to structures of known benzoylformate decarboxylase enzymes. The P. fluorescens decarboxylase enzyme showed enhanced carboligase activity between vanillin and acetaldehyde, rationalized by the presence of alanine versus serine at residue 73 in the enzyme active site, which was investigated further by site-directed mutagenesis of this residue. A hypothesis for a pathway for degradation of aryl C2 fragments arising from oxidative cleavage of phenylcoumaran and diarylpropane structures in lignin is proposed.
Collapse
Affiliation(s)
- Zhen Wei
- Department of Chemistry , University of Warwick , Coventry CV4 7AL , U.K
| | | | - Goran M M Rashid
- Department of Chemistry , University of Warwick , Coventry CV4 7AL , U.K
| | - David Brown
- Department of Chemistry , University of Warwick , Coventry CV4 7AL , U.K
| | - Vilmos Fülöp
- School of Life Sciences , University of Warwick , Coventry CV4 7AL , U.K
| | - Timothy D H Bugg
- Department of Chemistry , University of Warwick , Coventry CV4 7AL , U.K
| |
Collapse
|
40
|
Brink DP, Ravi K, Lidén G, Gorwa-Grauslund MF. Mapping the diversity of microbial lignin catabolism: experiences from the eLignin database. Appl Microbiol Biotechnol 2019; 103:3979-4002. [PMID: 30963208 PMCID: PMC6486533 DOI: 10.1007/s00253-019-09692-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 02/06/2019] [Accepted: 02/09/2019] [Indexed: 12/18/2022]
Abstract
Lignin is a heterogeneous aromatic biopolymer and a major constituent of lignocellulosic biomass, such as wood and agricultural residues. Despite the high amount of aromatic carbon present, the severe recalcitrance of the lignin macromolecule makes it difficult to convert into value-added products. In nature, lignin and lignin-derived aromatic compounds are catabolized by a consortia of microbes specialized at breaking down the natural lignin and its constituents. In an attempt to bridge the gap between the fundamental knowledge on microbial lignin catabolism, and the recently emerging field of applied biotechnology for lignin biovalorization, we have developed the eLignin Microbial Database ( www.elignindatabase.com ), an openly available database that indexes data from the lignin bibliome, such as microorganisms, aromatic substrates, and metabolic pathways. In the present contribution, we introduce the eLignin database, use its dataset to map the reported ecological and biochemical diversity of the lignin microbial niches, and discuss the findings.
Collapse
Affiliation(s)
- Daniel P Brink
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00, Lund, Sweden.
| | - Krithika Ravi
- Department of Chemical Engineering, Lund University, Lund, Sweden
| | - Gunnar Lidén
- Department of Chemical Engineering, Lund University, Lund, Sweden
| | - Marie F Gorwa-Grauslund
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00, Lund, Sweden
| |
Collapse
|
41
|
Ravi K, Abdelaziz OY, Nöbel M, García-Hidalgo J, Gorwa-Grauslund MF, Hulteberg CP, Lidén G. Bacterial conversion of depolymerized Kraft lignin. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:56. [PMID: 30923564 PMCID: PMC6420747 DOI: 10.1186/s13068-019-1397-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/08/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND Lignin is a potential feedstock for microbial conversion into various chemicals. However, the microbial degradation rate of native or technical lignin is low, and chemical depolymerization is needed to obtain reasonable conversion rates. In the current study, nine bacterial strains belonging to the Pseudomonas and Rhodococcus genera were evaluated for their ability to grow on alkaline-treated softwood lignin as a sole carbon source. RESULTS Pseudomonas fluorescens DSM 50090 and Rhodococcus opacus DSM1069 showed the best growth of the tested species on plates with lignin. Further evaluation of P. fluorescens and R. opacus was made in liquid cultivations with depolymerized softwood Kraft lignin (DL) at a concentration of 1 g/L. Size-exclusion chromatography (SEC) showed that R. opacus consumed most of the available lower-molecular weight compounds (approximately 0.1-0.4 kDa) in the DL, but the weight distribution of larger fractions was almost unaffected. Importantly, the consumed compounds included guaiacol-one of the main monomers in the DL. SEC analysis of P. fluorescens culture broth, in contrast, did not show a large conversion of low-molecular weight compounds, and guaiacol remained unconsumed. However, a significant shift in molecular weight distribution towards lower average weights was seen after cultivation with P. fluorescens. CONCLUSIONS Rhodococcus opacus and P. fluorescens were identified as two potential microbial candidates for the conversion/consumption of base-catalyzed depolymerized lignin, acting on low- and high-molecular weight lignin fragments, respectively. These findings will be of relevance for designing bioconversion of softwood Kraft lignin.
Collapse
Affiliation(s)
- Krithika Ravi
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - Omar Y. Abdelaziz
- Department of Chemical Engineering, 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
- Present Address: Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072 Australia
| | - Javier García-Hidalgo
- Department of Chemistry, Applied Microbiology, 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
|
42
|
Characterization of multicopper oxidase CopA from Pseudomonas putida KT2440 and Pseudomonas fluorescens Pf-5: Involvement in bacterial lignin oxidation. Arch Biochem Biophys 2018; 660:97-107. [DOI: 10.1016/j.abb.2018.10.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 10/15/2018] [Accepted: 10/16/2018] [Indexed: 12/23/2022]
|
43
|
Xu R, Zhang K, Liu P, Han H, Zhao S, Kakade A, Khan A, Du D, Li X. Lignin depolymerization and utilization by bacteria. BIORESOURCE TECHNOLOGY 2018; 269:557-566. [PMID: 30219494 DOI: 10.1016/j.biortech.2018.08.118] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/28/2018] [Accepted: 08/29/2018] [Indexed: 05/21/2023]
Abstract
Lignin compound wastes are generated as a result of agricultural and industrial practices. Microorganism-mediated bio-catalytic processes can depolymerize and utilize lignin eco-friendly. Although fungi have been studied since several decades for their ability to depolymerize lignin, strict growth conditions of fungus limit it's industrial application. Compared with fungi, bacteria can tolerate wider pH, temperature, oxygen ranges and are easy to manipulate. Several studies have focused on bacteria involved in the process of lignin depolymerization and utilization. Pseudomonas have been used for paper mill wastewater treatment while Rhodococcus are widely reported to accumulate lipid. In this review, the recent studies on bacterial utilization in paper wastewater treatment, lignin conversion to biofuels, bioplastic, biofertilizers and other value-added chemicals are summarized. As bacteria possess remarkable advantages in industrial production, they may play a promising role in the future commercial lignin utilization.
Collapse
Affiliation(s)
- Rong Xu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu 730000, People's Republic of China
| | - Kai Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu 730000, People's Republic of China
| | - Pu Liu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu 730000, People's Republic of China
| | - Huawen Han
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu 730000, People's Republic of China
| | - Shuai Zhao
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu 730000, People's Republic of China
| | - Apurva Kakade
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu 730000, People's Republic of China
| | - Aman Khan
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu 730000, People's Republic of China
| | - Daolin Du
- Institute for Energy Research, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, People's Republic of China
| | - Xiangkai Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu 730000, People's Republic of China.
| |
Collapse
|
44
|
Saito Y, Tsuchida H, Matsumoto T, Makita Y, Kawashima M, Kikuchi J, Matsui M. Screening of fungi for decomposition of lignin-derived products from Japanese cedar. J Biosci Bioeng 2018; 126:573-579. [DOI: 10.1016/j.jbiosc.2018.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 04/23/2018] [Accepted: 05/04/2018] [Indexed: 11/24/2022]
|
45
|
Rashid GMM, Zhang X, Wilkinson RC, Fülöp V, Cottyn B, Baumberger S, Bugg TDH. Sphingobacterium sp. T2 Manganese Superoxide Dismutase Catalyzes the Oxidative Demethylation of Polymeric Lignin via Generation of Hydroxyl Radical. ACS Chem Biol 2018; 13:2920-2929. [PMID: 30247873 DOI: 10.1021/acschembio.8b00557] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sphingobacterium sp. T2 contains two extracellular manganese superoxide dismutase enzymes which exhibit unprecedented activity for lignin oxidation but via an unknown mechanism. Enzymatic treatment of lignin model compounds gave products whose structures were indicative of aryl-Cα oxidative cleavage and demethylation, as well as alkene dihydroxylation and alcohol oxidation. 18O labeling studies on the SpMnSOD-catalyzed oxidation of lignin model compound guiaiacylglycerol-β-guaiacyl ether indicated that the an oxygen atom inserted by the enzyme is derived from superoxide or peroxide. Analysis of an alkali lignin treated by SpMnSOD1 by quantitative 31P NMR spectroscopy demonstrated 20-40% increases in phenolic and aliphatic OH content, consistent with lignin demethylation and some internal oxidative cleavage reactions. Assay for hydroxyl radical generation using a fluorometric hydroxyphenylfluorescein assay revealed the release of 4.1 molar equivalents of hydroxyl radical by SpMnSOD1. Four amino acid replacements in SpMnSOD1 were investigated, and A31H or Y27H site-directed mutant enzymes were found to show no lignin demethylation activity according to 31P NMR analysis. Structure determination of the A31H and Y27H mutant enzymes reveals the repositioning of an N-terminal protein loop, leading to widening of a solvent channel at the dimer interface, which would provide increased solvent access to the Mn center for hydroxyl radical generation.
Collapse
Affiliation(s)
| | | | | | | | - Betty Cottyn
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS,
Université Paris-Saclay, 78000 Versailles, France
| | - Stéphanie Baumberger
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS,
Université Paris-Saclay, 78000 Versailles, France
| | | |
Collapse
|
46
|
Falade AO, Mabinya LV, Okoh AI, Nwodo UU. Agrowastes utilization by Raoultella ornithinolytica for optimal extracellular peroxidase activity. Biotechnol Appl Biochem 2018; 66:60-67. [PMID: 30303255 DOI: 10.1002/bab.1696] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 10/04/2018] [Indexed: 11/12/2022]
Abstract
The industrial applications and prospects of microbial peroxidase are on the upwards trend, thus necessitating the search for sources with high turnaround time. Actinobacterial species have been a major source of peroxidase for the obvious reasons of having robust metabolite expression capabilities. However, other bacteria species have been underexplored for peroxidase production, hence the motivation for the investigation into the peroxidase production potential of Raoultella ornithinolytica OKOH-1 (KX640917). The bacteria expressed optimum specific peroxidase activity of 16.48 ± 0.89 U mg-1 , which is higher than those previously reported. The optimal fermentation conditions were pH 5 (3.44 ± 0.64 U mL-1 ), incubation temperature of 35 °C (5.25 ± 0.00 U mL-1 ), and agitation speed of 150 rpm (9.45 ± 2.57 U mL-1 ), with guaiacol and ammonium chloride as the best inducer and nitrogen supplement, respectively. On valorization of agrowastes as a sole carbon source for the secretion of peroxidase, sawdust gave the best peroxidase yield (15.21 ± 2.48 U mg-1 ) under solid-state fermentation. Also, a nonperoxide-dependent enzyme activity, which suggests probable laccase activity, was observed. The ability of the bacteria to utilize agrowastes is highly economical and as well a suitable waste management strategy. Consequently, R. ornithinolytica OKOH-1 is a promising industrial strain with dexterity for enhanced peroxidase production.
Collapse
Affiliation(s)
- Ayodeji O Falade
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa.,Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa
| | - Leonard V Mabinya
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa.,Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa
| | - Anthony I Okoh
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa.,Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa
| | - Uchechukwu U Nwodo
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa.,Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa
| |
Collapse
|
47
|
Wilhelm RC, Singh R, Eltis LD, Mohn WW. Bacterial contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing. ISME JOURNAL 2018; 13:413-429. [PMID: 30258172 PMCID: PMC6331573 DOI: 10.1038/s41396-018-0279-6] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 05/20/2018] [Accepted: 08/11/2018] [Indexed: 11/19/2022]
Abstract
Delignification, or lignin-modification, facilitates the decomposition of lignocellulose in woody plant biomass. The extant diversity of lignin-degrading bacteria and fungi is underestimated by culture-dependent methods, limiting our understanding of the functional and ecological traits of decomposers populations. Here, we describe the use of stable isotope probing (SIP) coupled with amplicon and shotgun metagenomics to identify and characterize the functional attributes of lignin, cellulose and hemicellulose-degrading fungi and bacteria in coniferous forest soils from across North America. We tested the extent to which catabolic genes partitioned among different decomposer taxa; the relative roles of bacteria and fungi, and whether taxa or catabolic genes correlated with variation in lignocellulolytic activity, measured as the total assimilation of 13C-label into DNA and phospholipid fatty acids. We found high overall bacterial degradation of our model lignin substrate, particularly by gram-negative bacteria (Comamonadaceae and Caulobacteraceae), while fungi were more prominent in cellulose-degradation. Very few taxa incorporated 13C-label from more than one lignocellulosic polymer, suggesting specialization among decomposers. Collectively, members of Caulobacteraceae could degrade all three lignocellulosic polymers, providing new evidence for their importance in lignocellulose degradation. Variation in lignin-degrading activity was better explained by microbial community properties, such as catabolic gene content and community structure, than cellulose-degrading activity. SIP significantly improved shotgun metagenome assembly resulting in the recovery of several high-quality draft metagenome-assembled genomes and over 7500 contigs containing unique clusters of carbohydrate-active genes. These results improve understanding of which organisms, conditions and corresponding functional genes contribute to lignocellulose decomposition.
Collapse
Affiliation(s)
- Roland C Wilhelm
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Rahul Singh
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Lindsay D Eltis
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - William W Mohn
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
| |
Collapse
|
48
|
Ravi K, Abdelaziz OY, Nöbel M, García-Hidalgo J, Gorwa-Grauslund MF, Hulteberg CP, Lidén G. Bacterial conversion of depolymerized Kraft lignin. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:240. [PMID: 30202435 PMCID: PMC6123935 DOI: 10.1186/s13068-018-1240-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 08/27/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Lignin is a potential feedstock for microbial conversion into various chemicals. However, the degradation rate of native or technical lignin is low, and depolymerization is needed to obtain reasonable conversion rates. In the current study, base-catalyzed depolymerization-using NaOH (5 wt%)-of softwood Kraft lignin was conducted in a continuous-flow reactor system at temperatures in the range 190-240 °C and residence times of 1 or 2 min. The ability of growth of nine bacterial strains belonging to the genera Pseudomonas and Rhodococcus was tested using the alkaline-treated lignin as a sole carbon source. RESULTS Pseudomonas fluorescens and Rhodococcus opacus showed the best growth of the tested species on plates with lignin. Further evaluation of P. fluorescens and R. opacus was made in liquid cultivations with depolymerized lignin (DL) at a concentration of 1 g/L. Size exclusion chromatography (SEC) showed that R. opacus consumed most of the available lower molecular weight compounds (approximately 0.1-0.4 kDa) in the DL, but the weight distribution of larger fractions was almost unaffected. Importantly, the consumed compounds included guaiacol-one of the main monomers in the DL. SEC analysis of P. fluorescens culture broth, in contrast, did not show a large conversion of low molecular weight compounds, and guaiacol remained unconsumed. However, a significant shift in molecular weight distribution towards lower average weights was seen. CONCLUSIONS Rhodococcus opacus and P. fluorescens were identified as two potential microbial candidates for the conversion/consumption of base-catalyzed depolymerized lignin, acting on low and high molecular weight lignin fragments, respectively. These findings will be of relevance for designing bioconversion of softwood Kraft lignin.
Collapse
Affiliation(s)
- Krithika Ravi
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - Omar Y. Abdelaziz
- Department of Chemical Engineering, 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
- Present Address: Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072 Australia
| | - Javier García-Hidalgo
- Department of Chemistry, Applied Microbiology, 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
|
49
|
Puentes-Téllez PE, Falcao Salles J. Construction of Effective Minimal Active Microbial Consortia for Lignocellulose Degradation. MICROBIAL ECOLOGY 2018; 76:419-429. [PMID: 29392382 PMCID: PMC6061470 DOI: 10.1007/s00248-017-1141-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/29/2017] [Indexed: 06/02/2023]
Abstract
Enriched microbial communities, obtained from environmental samples through selective processes, can effectively contribute to lignocellulose degradation. Unfortunately, fully controlled industrial degradation processes are difficult to reach given the intrinsically dynamic nature and complexity of the microbial communities, composed of a large number of culturable and unculturable species. The use of less complex but equally effective microbial consortia could improve their applications by allowing for more controlled industrial processes. Here, we combined ecological theory and enrichment principles to develop an effective lignocellulose-degrading minimal active microbial Consortia (MAMC). Following an enrichment of soil bacteria capable of degrading lignocellulose material from sugarcane origin, we applied a reductive-screening approach based on molecular phenotyping, identification, and metabolic characterization to obtain a selection of 18 lignocellulose-degrading strains representing four metabolic functional groups. We then generated 65 compositional replicates of MAMC containing five species each, which vary in the number of functional groups, metabolic potential, and degradation capacity. The characterization of the MAMC according to their degradation capacities and functional diversity measurements revealed that functional diversity positively correlated with the degradation of the most complex lignocellulosic fraction (lignin), indicating the importance of metabolic complementarity, whereas cellulose and hemicellulose degradation were either negatively or not affected by functional diversity. The screening method described here successfully led to the selection of effective MAMC, whose degradation potential reached up 96.5% of the degradation rates when all 18 species were present. A total of seven assembled synthetic communities were identified as the most effective MAMC. A consortium containing Stenotrophomonas maltophilia, Paenibacillus sp., Microbacterium sp., Chryseobacterium taiwanense, and Brevundimonas sp. was found to be the most effective degrading synthetic community.
Collapse
Affiliation(s)
- Pilar Eliana Puentes-Téllez
- Microbial Community Ecology, GELIFES - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
- Department of Biology, Institute of Environmental Biology, Ecology and Biodiversity Group, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Joana Falcao Salles
- Microbial Community Ecology, GELIFES - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
| |
Collapse
|
50
|
Yang C, Yue F, Cui Y, Xu Y, Shan Y, Liu B, Zhou Y, Lü X. Biodegradation of lignin by Pseudomonas sp. Q18 and the characterization of a novel bacterial DyP-type peroxidase. J Ind Microbiol Biotechnol 2018; 45:913-927. [PMID: 30051274 DOI: 10.1007/s10295-018-2064-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 07/23/2018] [Indexed: 11/25/2022]
Abstract
Lignin valorization can be obtained through cleavage of selected bonds by microbial enzymes, in which lignin is segregated from cellulose and hemicellulose and abundant phenolic compounds can be provided. In this study, Pseudomonas sp. Q18, previously isolated from rotten wood in China, was used to degrade alkali lignin and raw lignocellulosic material. Gel-permeation chromatography, field-emission scanning electron microscope, and GC-MS were combined to investigate the degradation process. The GC-MS results revealed that the quantities of aromatic compounds with phenol ring from lignin increased significantly after incubation with Pseudomonas sp. Q18, which indicated the degradation of lignin. According to the lignin-derived metabolite analysis, it was proposed that a DyP-type peroxidase (PmDyP) might exist in strain Q18. Thereafter, the gene of PmDyP was cloned and expressed, after which the recombinant PmDyP was purified and the enzymatic kinetics of PmDyP were assayed. According to results, PmDyP showed promising characteristics for lignocellulosic biodegradation in biorefinery.
Collapse
Affiliation(s)
- Chenxian Yang
- College of Food Science and Engineering, Northwest A&F University, Yangling District, Xianyang, 712100, Shaanxi Province, China
| | - Fangfang Yue
- College of Food Science and Engineering, Northwest A&F University, Yangling District, Xianyang, 712100, Shaanxi Province, China
| | - Yanlong Cui
- College of Food Science and Engineering, Northwest A&F University, Yangling District, Xianyang, 712100, Shaanxi Province, China
| | - Yuanmei Xu
- College of Food Science and Engineering, Northwest A&F University, Yangling District, Xianyang, 712100, Shaanxi Province, China
| | - Yuanyuan Shan
- College of Food Science and Engineering, Northwest A&F University, Yangling District, Xianyang, 712100, Shaanxi Province, China
| | - Bianfang Liu
- College of Food Science and Engineering, Northwest A&F University, Yangling District, Xianyang, 712100, Shaanxi Province, China
| | - Yuan Zhou
- College of Food Science and Engineering, Northwest A&F University, Yangling District, Xianyang, 712100, Shaanxi Province, China
| | - Xin Lü
- College of Food Science and Engineering, Northwest A&F University, Yangling District, Xianyang, 712100, Shaanxi Province, China.
| |
Collapse
|