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Shrestha S, Goswami S, Banerjee D, Garcia V, Zhou E, Olmsted CN, Majumder ELW, Kumar D, Awasthi D, Mukhopadhyay A, Singer SW, Gladden JM, Simmons BA, Choudhary H. Perspective on Lignin Conversion Strategies That Enable Next Generation Biorefineries. CHEMSUSCHEM 2024:e202301460. [PMID: 38669480 DOI: 10.1002/cssc.202301460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 03/14/2024] [Indexed: 04/28/2024]
Abstract
The valorization of lignin, a currently underutilized component of lignocellulosic biomass, has attracted attention to promote a stable and circular bioeconomy. Successful approaches including thermochemical, biological, and catalytic lignin depolymerization have been demonstrated, enabling opportunities for lignino-refineries and lignocellulosic biorefineries. Although significant progress in lignin valorization has been made, this review describes unexplored opportunities in chemical and biological routes for lignin depolymerization and thereby contributes to economically and environmentally sustainable lignin-utilizing biorefineries. This review also highlights the integration of chemical and biological lignin depolymerization and identifies research gaps while also recommending future directions for scaling processes to establish a lignino-chemical industry.
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Affiliation(s)
- Shilva Shrestha
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD 21205, United States
| | - Shubhasish Goswami
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Deepanwita Banerjee
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Valentina Garcia
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Biomanufacturing and Biomaterials, Sandia National Laboratories, Livermore, CA 94550, United States
| | - Elizabeth Zhou
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
| | - Charles N Olmsted
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Erica L-W Majumder
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Deepak Kumar
- Department of Chemical Engineering, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, United States
| | - Deepika Awasthi
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - John M Gladden
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Biomanufacturing and Biomaterials, Sandia National Laboratories, Livermore, CA 94550, United States
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Hemant Choudhary
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Bioresource and Environmental Security, Sandia National Laboratories, Livermore, CA 94550, United States
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Li K, Jia W, Xu L, Zhang M, Huang Y. The plastisphere of biodegradable and conventional microplastics from residues exhibit distinct microbial structure, network and function in plastic-mulching farmland. JOURNAL OF HAZARDOUS MATERIALS 2023; 442:130011. [PMID: 36155295 DOI: 10.1016/j.jhazmat.2022.130011] [Citation(s) in RCA: 57] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
The inhomogeneity of plastisphere and soil may result in different microbial communities, thus potentially affecting soil functions. Biodegradable plastics offer an alternative to conventional plastics, nevertheless, the inadequate end-of-life treatment of biodegradable plastics may release more microplastics. Herein, we collected PE and PBAT/PLA microplastics in plastic-mulching farmland in Hebei, China. The bacterial communities of soil, PE and PBAT/PLA plastisphere were investigated using 16 S high-throughput sequencing. We found that the structure of bacterial communities in PBAT/PLA plastisphere were significantly distinct from PE plastisphere and soil. The alpha diversities in PBAT/PLA plastisphere were significantly lower than PE plastisphere and soil. Statistical analysis of differentially ASVs suggested that PBAT/PLA microplastics act as a filter, enriching taxa with the capability to degrade plastic polymers such as Proteobacteria and Actinobacteria. Compared to PE plastisphere, PBAT/PLA plastisphere has networks of less complexity, lower modularity, and more competitive interactions. Predicted metabolic pathways involved in human diseases, carbohydrate metabolism, amino acid metabolism, and xenobiotic biodegradation and metabolism were promoted in PBAT/PLA plastisphere, along with the facilitation in abundance of genes associated with carbon and nitrogen cycling. Our results highlighted the uniqueness of plastisphere of biodegradable microplastics from conventional microplastics and their potential impact on soil functions.
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Affiliation(s)
- Kang Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
| | - Weiqian Jia
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
| | - Libo Xu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
| | - Mengjun Zhang
- Marine Institute for Bioresources and Environment, Peking University Shenzhen Institute, Shenzhen, Guangdong 518057, China.
| | - Yi Huang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Marine Institute for Bioresources and Environment, Peking University Shenzhen Institute, Shenzhen, Guangdong 518057, China.
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Jiang X, Guo Y, Li H, Li X, Liu J. Ecological evolution during the three-year restoration using rhizosphere soil cover method at a Lead-Zinc tailing pond in Karst areas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 853:158291. [PMID: 36030848 DOI: 10.1016/j.scitotenv.2022.158291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 08/21/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
A major challenge for the restoration of the Lead-Zinc tailing pond in Karst areas lies in how to establish vegetation with less soil and restore the ecological functions of the substrate. In this study, a novel method, rhizosphere soil cover method (RSC), was applied to recover the vegetation at a Pb-Zn tailing pond in Karst areas. Two local tolerate plants, Miscanthus sinensis and Pueraria phaseoloides, were planted as pioneer species. Although 68 % of the tailing pond was not covered with soil, the vegetation coverage has reached over 90 % after restoration for three years. Compared with the natural revegetation process (vegetation coverage was <5 % after 20 years of natural succession), the revegetation in the tailing pond was accelerated by RSC and planting pioneer species. Both the plant's diversity and richness have significantly increased in the tailings pond during the restoration (p < 0.05). The important value indicators of M. sinensis and P. phaseoloides were the highest in the plant community, indicating the dominant role of these two plants in revegetation. Moreover, the total organic carbon, total nitrogen, total phosphorus, and total potassium in the tailings increased annually (p < 0.05), which demonstrated that the revegetation has improved the chemical properties in the substrate. In addition, the Shannon diversity index of bacteria in the tailings increased significantly from 4.11 to 5.51. The relative abundance of microbial genes related to carbon fixation and nitrogen fixation in the tailings increased by 17 % and 43 %, respectively. Meanwhile, the physicochemical properties, microbial community structure, and nutrient cycling function in the tailings without topsoil were improved more obviously than those in soils. It is thereby concluded that RSC is an efficient means for ecological restoration of the tailing ponds in Karst areas to improve the ecosystem structure and function of Pb-Zn tailings.
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Affiliation(s)
- Xusheng Jiang
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin 541004, China
| | - Yu Guo
- Technical Innovation Center of Mine Geological Environmental Restoration Engineering in Southern Karst Area, MNR, Guilin 541004, China
| | - Haixiang Li
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin 541004, China
| | - Xiangmin Li
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin 541004, China
| | - Jie Liu
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin 541004, China; Technical Innovation Center of Mine Geological Environmental Restoration Engineering in Southern Karst Area, MNR, Guilin 541004, China.
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Singh R, Pal DB, Alkhanani MF, Almalki AH, Areeshi MY, Haque S, Srivastava N. Prospects of soil microbiome application for lignocellulosic biomass degradation: An overview. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:155966. [PMID: 35584752 DOI: 10.1016/j.scitotenv.2022.155966] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/04/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Sustainable and practically viable biofuels production technology using lignocellulosic biomass is still seeking its way of implementation owing to some major issues involved therein. Unavailability of efficient microbial sources for the degradation of cellulosic biomass is one of the major roadblocks in biomass to biofuels production technology. In this context, utilization of microbiomes to degrade lignocellulaosic biomass is emerging as a rapid and effective approach that can fulfill the requirements of biomass based biofuels production technology. Therefore, the present review is targeted to explore soil metagenomic approach to improve the lignocellulosic biomass degradation processing for the cost-effective and eco-friendly application. Soil microbiomes consist of rich microbial community along with high probability of cellulolytic microbes, and can be identified by culture independent metagenomics method which can be structurally and functionally explored via genomic library. Therefore, in depth analysis and discussion have also been made via structural & functional metagenomics tools along with their contribution to genomic library. Additionally, the present review highlights currently existing bottlenecks along with their feasible solutions. This review will help to understand the basic research as well as industrial concept for the process improvement based on soil microbiome mediated lignocellulosic biomass degradation, and this may likely to implement for the low-cost commercial biofuels production technology.
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Affiliation(s)
- Rajeev Singh
- Department of Environmental Studies, Satyawati College, University of Delhi, Delhi, 110052, India
| | - Dan Bahadur Pal
- Department of Chemical Engineering, Birla Institute of Technology, Mesra, Ranchi 835215, Jharkhand, India
| | - Mustfa F Alkhanani
- Emergency Service Department, College of Applied Sciences, AlMaarefa University, Riyadh 11597, Saudi Arabia
| | - Atiah H Almalki
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia; Addiction and Neuroscience Research Unit, College of Pharmacy, Taif University, Al-Hawiah, Taif 21944, Saudi Arabia
| | - Mohammed Yahya Areeshi
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia; Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia; Bursa Uludağ University, Faculty of Medicine, Görükle Campus, 16059 Nilüfer, Bursa, Turkey
| | - Neha Srivastava
- Department of Chemical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi 221005, India.
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Discovery of lignin-transforming bacteria and enzymes in thermophilic environments using stable isotope probing. THE ISME JOURNAL 2022; 16:1944-1956. [PMID: 35501417 PMCID: PMC9296663 DOI: 10.1038/s41396-022-01241-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/04/2022] [Accepted: 04/06/2022] [Indexed: 12/14/2022]
Abstract
Characterizing microorganisms and enzymes involved in lignin biodegradation in thermal ecosystems can identify thermostable biocatalysts. We integrated stable isotope probing (SIP), genome-resolved metagenomics, and enzyme characterization to investigate the degradation of high-molecular weight, 13C-ring-labeled synthetic lignin by microbial communities from moderately thermophilic hot spring sediment (52 °C) and a woody "hog fuel" pile (53 and 62 °C zones). 13C-Lignin degradation was monitored using IR-GCMS of 13CO2, and isotopic enrichment of DNA was measured with UHLPC-MS/MS. Assembly of 42 metagenomic libraries (72 Gb) yielded 344 contig bins, from which 125 draft genomes were produced. Fourteen genomes were significantly enriched with 13C from lignin, including genomes of Actinomycetes (Thermoleophilaceae, Solirubrobacteraceae, Rubrobacter sp.), Firmicutes (Kyrpidia sp., Alicyclobacillus sp.) and Gammaproteobacteria (Steroidobacteraceae). We employed multiple approaches to screen genomes for genes encoding putative ligninases and pathways for aromatic compound degradation. Our analysis identified several novel laccase-like multi-copper oxidase (LMCO) genes in 13C-enriched genomes. One of these LMCOs was heterologously expressed and shown to oxidize lignin model compounds and minimally transformed lignin. This study elucidated bacterial lignin depolymerization and mineralization in thermal ecosystems, establishing new possibilities for the efficient valorization of lignin at elevated temperature.
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Shi S, Lin Z, Zhou J, Fan X, Huang Y, Zhou J. Enhanced thermophilic denitrification performance and potential microbial mechanism in denitrifying granular sludge system. BIORESOURCE TECHNOLOGY 2022; 344:126190. [PMID: 34710607 DOI: 10.1016/j.biortech.2021.126190] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
Thermophilic biological nitrogen removal will provide low-cost strategies for the treatment of high-temperature nitrogenous wastewater (greater than 45 ℃). In this study, a thermophilic denitrifying granular sludge system was established at 50 ℃ and compared with mesophilic systems (30 ℃ and 40 ℃). The results showed a significant increase in COD and nitrate removal rate with the elevating temperature. Besides, the microbial community analysis indicated an obvious succession of key functional bacteria at different temperatures. Enriched thermophiles including Truepera, Azoarcus, and Elioraea were the dominant denitrifiers in the thermophilic denitrifying granular sludge system, which ensured the high nitrate removal at 50 ℃. Moreover, the functional gene prediction also denoted an enrichment of nitrate reduction genes and carbon metabolism pathways at 50 ℃, which could explain the enhancement of thermophilic denitrification. These findings could provide new insight into the application of denitrifying granular sludge in thermophilic wastewater treatment.
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Affiliation(s)
- Shuohui Shi
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Ziyuan Lin
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Jiong Zhou
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Xing Fan
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Yangyang Huang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Jian Zhou
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China.
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Haidar R, Yacoub A, Vallance J, Compant S, Antonielli L, Saad A, Habenstein B, Kauffmann B, Grélard A, Loquet A, Attard E, Guyoneaud R, Rey P. Bacteria associated with wood tissues of Esca-diseased grapevines: functional diversity and synergy with Fomitiporia mediterranea to degrade wood components. Environ Microbiol 2021; 23:6104-6121. [PMID: 34288352 PMCID: PMC9291561 DOI: 10.1111/1462-2920.15676] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 07/18/2021] [Indexed: 11/30/2022]
Abstract
Fungi are considered to cause grapevine trunk diseases such as esca that result in wood degradation. For instance, the basidiomycete Fomitiporia mediterranea (Fmed) is overabundant in white rot, a key type of wood‐necrosis associated with esca. However, many bacteria colonize the grapevine wood too, including the white rot. In this study, we hypothesized that bacteria colonizing grapevine wood interact, possibly synergistically, with Fmed and enhance the fungal ability to degrade wood. We isolated 237 bacterial strains from esca‐affected grapevine wood. Most of them belonged to the families Xanthomonadaceae and Pseudomonadaceae. Some bacterial strains that degrade grapevine‐wood components such as cellulose and hemicellulose did not inhibit Fmed growth in vitro. We proved that the fungal ability to degrade wood can be strongly influenced by bacteria inhabiting the wood. This was shown with a cellulolytic and xylanolytic strain of the Paenibacillus genus, which displays synergistic interaction with Fmed by enhancing the degradation of wood structures. Genome analysis of this Paenibacillus strain revealed several gene clusters such as those involved in the expression of carbohydrate‐active enzymes, xylose utilization and vitamin metabolism. In addition, certain other genetic characteristics of the strain allow it to thrive as an endophyte in grapevine and influence the wood degradation by Fmed. This suggests that there might exist a synergistic interaction between the fungus Fmed and the bacterial strain mentioned above, enhancing grapevine wood degradation. Further step would be to point out its occurrence in mature grapevines to promote esca disease development.
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Affiliation(s)
- Rana Haidar
- INRAE, UMR SAVE, Bordeaux Science Agro, ISVV, University of Bordeaux, Villenave d'Ornon, 33882, France.,Biology Department, Faculty of Science, Tishreen University, Latakia, Syria
| | - Amira Yacoub
- INRAE, UMR SAVE, Bordeaux Science Agro, ISVV, University of Bordeaux, Villenave d'Ornon, 33882, France
| | - Jessica Vallance
- INRAE, UMR SAVE, Bordeaux Science Agro, ISVV, University of Bordeaux, Villenave d'Ornon, 33882, France
| | - Stéphane Compant
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Center for Health and Bioresources, Konrad Lorenz Straße 24, Tulln, 3430, Austria
| | - Livio Antonielli
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Center for Health and Bioresources, Konrad Lorenz Straße 24, Tulln, 3430, Austria
| | - Ahmad Saad
- Institut de Chimie et Biologie des Membranes et des Nanoobjets, IECB, CNRS, Université de Bordeaux, Pessac, 33607, France
| | - Birgit Habenstein
- Institut de Chimie et Biologie des Membranes et des Nanoobjets, IECB, CNRS, Université de Bordeaux, Pessac, 33607, France
| | - Brice Kauffmann
- IECB, UMS 3033, US001, CNRS, Université de Bordeaux, Pessac, 33607, France
| | - Axelle Grélard
- Institut de Chimie et Biologie des Membranes et des Nanoobjets, IECB, CNRS, Université de Bordeaux, Pessac, 33607, France
| | - Antoine Loquet
- Institut de Chimie et Biologie des Membranes et des Nanoobjets, IECB, CNRS, Université de Bordeaux, Pessac, 33607, France
| | - Eléonore Attard
- Université de Pau et des Pays de l'Adour/E2S UPPA/CNRS, Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux - UMR 5254, IBEAS Avenue de l'Université, Pau, 64013, France
| | - Rémy Guyoneaud
- Université de Pau et des Pays de l'Adour/E2S UPPA/CNRS, Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux - UMR 5254, IBEAS Avenue de l'Université, Pau, 64013, France
| | - Patrice Rey
- INRAE, UMR SAVE, Bordeaux Science Agro, ISVV, University of Bordeaux, Villenave d'Ornon, 33882, France
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Pérez-Hernández V, Hernández-Guzmán M, Luna-Guido M, Navarro-Noya YE, Romero-Tepal EM, Dendooven L. Bacterial Communities in Alkaline Saline Soils Amended with Young Maize Plants or Its (Hemi)Cellulose Fraction. Microorganisms 2021; 9:1297. [PMID: 34203640 PMCID: PMC8232260 DOI: 10.3390/microorganisms9061297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 11/28/2022] Open
Abstract
We studied three soils of the former lake Texcoco with different electrolytic conductivity (1.9 dS m-1, 17.3 dS m-1, and 33.4 dS m-1) and pH (9.3, 10.4, and 10.3) amended with young maize plants and their neutral detergent fibre (NDF) fraction and aerobically incubated in the laboratory for 14 days while the soil bacterial community structure was monitored by means of 454-pyrosequencing of their 16S rRNA marker gene. We identified specific bacterial groups that showed adaptability to soil salinity, i.e., Prauseria in soil amended with young maize plants and Marinobacter in soil amended with NDF. An increase in soil salinity (17.3 dS m-1, 33.4 dS m-1) showed more bacterial genera enriched than soil with low salinity (1.9 dS m-1). Functional prediction showed that members of Alfa-, Gamma-, and Deltaproteobacteria, which are known to adapt to extreme conditions, such as salinity and low nutrient soil content, were involved in the lignocellulose degradation, e.g., Marinimicrobium and Pseudomonas as cellulose degraders, and Halomonas and Methylobacterium as lignin degraders. This research showed that the taxonomic annotation and their functional prediction both highlighted keystone bacterial groups with the ability to degrade complex C-compounds, such as lignin and (hemi)cellulose, in the extreme saline-alkaline soil of the former Lake of Texcoco.
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Affiliation(s)
- Valentín Pérez-Hernández
- Laboratory of Soil Ecology, Department of Chemistry and Biochemistry, Instituto Tecnológico de Tuxtla-Gutiérrez, Tecnológico Nacional de México, Tuxtla Gutiérrez, Chiapas 29050, Mexico;
- Laboratory of Soil Ecology, Cinvestav, Mexico City 07360, Mexico; (M.H.-G.); (M.L.-G.); (E.M.R.-T.)
| | - Mario Hernández-Guzmán
- Laboratory of Soil Ecology, Cinvestav, Mexico City 07360, Mexico; (M.H.-G.); (M.L.-G.); (E.M.R.-T.)
| | - Marco Luna-Guido
- Laboratory of Soil Ecology, Cinvestav, Mexico City 07360, Mexico; (M.H.-G.); (M.L.-G.); (E.M.R.-T.)
| | - Yendi E. Navarro-Noya
- Centro de Investigación en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, Tlaxcala 90070, Mexico;
| | - Elda M. Romero-Tepal
- Laboratory of Soil Ecology, Cinvestav, Mexico City 07360, Mexico; (M.H.-G.); (M.L.-G.); (E.M.R.-T.)
| | - Luc Dendooven
- Laboratory of Soil Ecology, Cinvestav, Mexico City 07360, Mexico; (M.H.-G.); (M.L.-G.); (E.M.R.-T.)
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Gallo G, Puopolo R, Carbonaro M, Maresca E, Fiorentino G. Extremophiles, a Nifty Tool to Face Environmental Pollution: From Exploitation of Metabolism to Genome Engineering. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:5228. [PMID: 34069056 PMCID: PMC8157027 DOI: 10.3390/ijerph18105228] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/06/2021] [Accepted: 05/09/2021] [Indexed: 12/13/2022]
Abstract
Extremophiles are microorganisms that populate habitats considered inhospitable from an anthropocentric point of view and are able to tolerate harsh conditions such as high temperatures, extreme pHs, high concentrations of salts, toxic organic substances, and/or heavy metals. These microorganisms have been broadly studied in the last 30 years and represent precious sources of biomolecules and bioprocesses for many biotechnological applications; in this context, scientific efforts have been focused on the employment of extremophilic microbes and their metabolic pathways to develop biomonitoring and bioremediation strategies to face environmental pollution, as well as to improve biorefineries for the conversion of biomasses into various chemical compounds. This review gives an overview on the peculiar metabolic features of certain extremophilic microorganisms, with a main focus on thermophiles, which make them attractive for biotechnological applications in the field of environmental remediation; moreover, it sheds light on updated genetic systems (also those based on the CRISPR-Cas tool), which expand the potentialities of these microorganisms to be genetically manipulated for various biotechnological purposes.
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Affiliation(s)
- Giovanni Gallo
- Department of Biology, University of Naples Federico II, Via Cinthia 21, 80126 Napoli, Italy; (G.G.); (R.P.); (M.C.); (E.M.)
- Consiglio Nazionale delle Ricerche CNR, Institute of Polymers, Composites and Biomaterials (IPCB), Via Campi Flegrei, 34, 80078 Pozzuoli, Italy
| | - Rosanna Puopolo
- Department of Biology, University of Naples Federico II, Via Cinthia 21, 80126 Napoli, Italy; (G.G.); (R.P.); (M.C.); (E.M.)
| | - Miriam Carbonaro
- Department of Biology, University of Naples Federico II, Via Cinthia 21, 80126 Napoli, Italy; (G.G.); (R.P.); (M.C.); (E.M.)
| | - Emanuela Maresca
- Department of Biology, University of Naples Federico II, Via Cinthia 21, 80126 Napoli, Italy; (G.G.); (R.P.); (M.C.); (E.M.)
| | - Gabriella Fiorentino
- Department of Biology, University of Naples Federico II, Via Cinthia 21, 80126 Napoli, Italy; (G.G.); (R.P.); (M.C.); (E.M.)
- Consiglio Nazionale delle Ricerche CNR, Institute of Polymers, Composites and Biomaterials (IPCB), Via Campi Flegrei, 34, 80078 Pozzuoli, Italy
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10
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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.
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Díaz-García L, Bugg TDH, Jiménez DJ. Exploring the Lignin Catabolism Potential of Soil-Derived Lignocellulolytic Microbial Consortia by a Gene-Centric Metagenomic Approach. MICROBIAL ECOLOGY 2020; 80:885-896. [PMID: 32572536 DOI: 10.1007/s00248-020-01546-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/15/2020] [Indexed: 05/25/2023]
Abstract
An exploration of the ligninolytic potential of lignocellulolytic microbial consortia can improve our understanding of the eco-enzymology of lignin conversion in nature. In this study, we aimed to detect enriched lignin-transforming enzymes on metagenomes from three soil-derived microbial consortia that were cultivated on "pre-digested" plant biomass (wheat straw, WS1-M; switchgrass, SG-M; and corn stover, CS-M). Of 60 selected enzyme-encoding genes putatively involved in lignin catabolism, 20 genes were significantly abundant in WS1-M, CS-M, and/or SG-M consortia compared with the initial forest soil inoculum metagenome (FS1). These genes could be involved in lignin oxidation (e.g., superoxide dismutases), oxidative stress responses (e.g., catalase/peroxidases), generation of protocatechuate (e.g., vanAB genes), catabolism of gentisate, catechol and 3-phenylpropionic acid (e.g., gentisate 1,2-dioxygenases, muconate cycloisomerases, and hcaAB genes), the beta-ketoadipate pathway (e.g., pcaIJ genes), and tolerance to lignocellulose-derived inhibitors (e.g., thymidylate synthases). The taxonomic affiliation of 22 selected lignin-transforming enzymes from WS1-M and CS-M consortia metagenomes revealed that Pseudomonadaceae, Alcaligenaceae, Sphingomonadaceae, Caulobacteraceae, Comamonadaceae, and Xanthomonadaceae are the key bacterial families in the catabolism of lignin. A predictive "model" was sketched out, where each microbial population has the potential to metabolize an array of aromatic compounds through different pathways, suggesting that lignin catabolism can follow a "task division" strategy. Here, we have established an association between functions and taxonomy, allowing a better understanding of lignin transformations in soil-derived lignocellulolytic microbial consortia, and pinpointing some bacterial taxa and catabolic genes as ligninolytic trait-markers.
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Affiliation(s)
- Laura Díaz-García
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | | | - Diego Javier Jiménez
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia.
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Rodríguez-Berbel N, Ortega R, Lucas-Borja ME, Solé-Benet A, Miralles I. Long-term effects of two organic amendments on bacterial communities of calcareous mediterranean soils degraded by mining. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 271:110920. [PMID: 32579515 DOI: 10.1016/j.jenvman.2020.110920] [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: 02/18/2020] [Revised: 06/02/2020] [Accepted: 06/03/2020] [Indexed: 06/11/2023]
Abstract
The application of organic amendments to improve the chemical and biological properties of degraded soils from calcareous quarries is necessary to accelerate restoration processes. The aim of this study is to assess the success of different restoration treatments in the long-term using two organic amendments (sewage sludge from urban waste water (SS) and compost from domestic solid waste (CW)). The chemical properties and bacterial communities of restored soils were compared with unamended soils (NA) and surrounding natural soils (NS) from a limestone quarry in a semi-arid ecosystem. After 10 years of the addition of organic amendments, the abundance of soil bacteria, diversity, and taxonomic composition at the phylum and genus level in each soil type was analysed by rRNA 16 S amplification (PCR), sequencing using Illumina, and comparison with the SILVA database using QIIME2 software. The relationships between soil bacterial taxa and chemical soil properties (pH, electrical conductivity (EC), total organic carbon (TOC), and total nitrogen content (TN)) were also studied, as well as the interrelations between soil bacterial taxa at the genus level or the next upper taxonomic level identified. The organic amendments changed the chemical properties of the restored soils, influencing the microbial communities of the restored soils. CW treatment was the organic amendment that most resembled NS, favouring in the long-term a greater diversity and proliferation of bacteria. Several bacterial communities, more abundant in NA and CW soils, were strongly correlated with each other (Craurococcus, Phaselicystis, Crossiella, etc.), forming a bacterial co-occurrence pattern (Co-occurrence pattern 1). Those bacteria showed high significant positive correlations with TOC, TN, and EC and negative correlations with the soil pH. In contrast, NA soils presented other groups of bacterial communities (Co-occurrence pattern 2) represented by Sphingomonas, Rubellimicrobium, Noviherbaspirillum, Psychroglaciecola and Caenimonas, which showed high significant positive correlations with soil pH and negative correlations with TOC, TN, and EC. The distance-based redundancy analysis indicated that SS soils remained in an intermediate stage of chemical and biological quality between NS and NA soils. Our results demonstrate that soil chemical properties and soil bacterial communities significantly changed with organic amendments in calcareous Mediterranean soils degraded by mining.
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Affiliation(s)
- N Rodríguez-Berbel
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120, Almería, Spain
| | - R Ortega
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120, Almería, Spain
| | - M E Lucas-Borja
- Escuela Técnica Superior Ingenieros Agrónomos y Montes, Universidad de Castilla-La Mancha, Campus Universitario, 02071, Albacete, Spain
| | - A Solé-Benet
- EEZA-CSIC, Estación Experimental de Zonas Áridas, Consejo Superior de Investigaciones Científicas, Carretera de Sacramento S/n, 04120, La Cañada de San Urbano, Almería, Spain
| | - I Miralles
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120, Almería, Spain.
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Liu H, Chen L, Wang ET, Liu Y, Zhang L, Zhao K, Gu Y, Yu X, Ma M, Penttinen P, Zhang X, Huang M, Deng L, Chen Q. Combined Microbial Consortium Inoculation and Black Locust Planting Is Effective in the Bioremediation of Waste Drill Cuttings. Front Microbiol 2020; 11:536787. [PMID: 33101222 PMCID: PMC7555700 DOI: 10.3389/fmicb.2020.536787] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 09/04/2020] [Indexed: 12/02/2022] Open
Abstract
Waste drill cuttings (WDCs), produced during gas and oil drilling consisting of 80% rock cuttings and 20% drilling muds, are an increasingly potent source of environmental pollution. We studied the efficiency of bioaugmentation and phytoremediation to remediate WDCs in an experiment where WDCs were incubated in a greenhouse for 120 days with and without black locust (Robinia pseudoacacia) plant and with or without bacterial and fungal consortium inoculant. The pollutant removal rates were highest in inoculated and planted treatment, followed by inoculated treatment and planted treatment. The small decrease in contaminant level in the control treatment suggested that indigenous microorganisms in WDCs had little pollutant degradation capability. In the inoculated and planted treatments, after 120 days, the germination rate of red clover seeds was on the same level as in the natural soil, showing a marked decrease in the ecotoxicity of WDC. Both the bacterial and fungal richness and bacterial diversity increased in all the treatments over time, whereas fungal diversity increased only in the not-inoculated treatments. The activity of laccase enzyme played a key role in the bioremediation process. The enzyme activities were mostly governed by inoculated consortium and soil bacterial community, and black locust affected the bioremediation mainly through its effect on N content that further affected bacterial and fungal communities.
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Affiliation(s)
- Hanjun Liu
- College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, China.,Safety and Environmental Protection Quality Supervision and Testing Research Institute, CNPC Chuanqing Drilling Engineering Co. Ltd., Guanghan, China
| | - Lirong Chen
- Safety and Environmental Protection Quality Supervision and Testing Research Institute, CNPC Chuanqing Drilling Engineering Co. Ltd., Guanghan, China
| | - En T Wang
- Departamento de Microbiologia, Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional, Mexico City, Mexico
| | - Yihao Liu
- College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Lingzi Zhang
- College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Ke Zhao
- College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yunfu Gu
- College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xiumei Yu
- College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Menggen Ma
- College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Petri Penttinen
- College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xiaoping Zhang
- College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Min Huang
- Safety and Environmental Protection Quality Supervision and Testing Research Institute, CNPC Chuanqing Drilling Engineering Co. Ltd., Guanghan, China
| | - Liangji Deng
- College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qiang Chen
- College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, China
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Microbiological evaluation of nano-Fe3O4/GO enhanced the micro-aerobic activate sludge system for the treatment of mid-stage pulping effluent. APPLIED NANOSCIENCE 2020. [DOI: 10.1007/s13204-020-01314-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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15
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Domański J, Marchut-Mikołajczyk O, Cieciura-Włoch W, Patelski P, Dziekońska-Kubczak U, Januszewicz B, Zhang B, Dziugan P. Production of Methane, Hydrogen and Ethanol from Secale cereale L. Straw Pretreated with Sulfuric Acid. Molecules 2020; 25:molecules25041013. [PMID: 32102411 PMCID: PMC7070859 DOI: 10.3390/molecules25041013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/16/2020] [Accepted: 02/18/2020] [Indexed: 01/15/2023] Open
Abstract
The study describes sulfuric acid pretreatment of straw from Secale cereale L. (rye straw) to evaluate the effect of acid concentration and treatment time on the efficiency of biofuel production. The highest ethanol yield occurred after the enzyme treatment at a dose of 15 filter paper unit (FPU) per gram of rye straw (subjected to chemical hydrolysis with 2% sulfuric acid (SA) at 121 °C for 1 h) during 120 h. Anaerobic digestion of rye straw treated with 10% SA at 121 °C during 1 h allowed to obtain 347.42 L methane/kg volatile solids (VS). Most hydrogen was released during dark fermentation of rye straw after pretreatment of 2% SA, 121 °C, 1 h and 1% SA, 121 °C, 2 h—131.99 and 134.71 L hydrogen/kg VS, respectively. If the rye straw produced in the European Union were processed into methane, hydrogen, ethanol, the annual electricity production in 2018 could reach 9.87 TWh (terawatt-hours), 1.16 TWh, and 0.60 TWh, respectively.
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Affiliation(s)
- Jarosław Domański
- Department of Environmental Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, 90-924 Lodz, Poland; (W.C.-W.); (P.D.)
- Correspondence: ; Tel.: +48-42-631-34-84
| | - Olga Marchut-Mikołajczyk
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, 90-924 Lodz, Poland;
| | - Weronika Cieciura-Włoch
- Department of Environmental Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, 90-924 Lodz, Poland; (W.C.-W.); (P.D.)
| | - Piotr Patelski
- Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, 90-924 Lodz, Poland; (P.P.); (U.D.-K.)
| | - Urszula Dziekońska-Kubczak
- Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, 90-924 Lodz, Poland; (P.P.); (U.D.-K.)
| | - Bartłomiej Januszewicz
- Institute of Material Science and Engineering, Faculty of Mechanical Engineering, Lodz University of Technology, 90-924 Lodz, Poland;
| | - Bolin Zhang
- College of Biological Science and Biotechnology, Beijing Forestry University, Beijing 100083, China;
| | - Piotr Dziugan
- Department of Environmental Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, 90-924 Lodz, Poland; (W.C.-W.); (P.D.)
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16
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Yang J, Wang Y, Cui X, Xue K, Zhang Y, Yu Z. Habitat filtering shapes the differential structure of microbial communities in the Xilingol grassland. Sci Rep 2019; 9:19326. [PMID: 31852979 PMCID: PMC6920139 DOI: 10.1038/s41598-019-55940-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 12/04/2019] [Indexed: 02/07/2023] Open
Abstract
The spatial variability of microorganisms in grasslands can provide important insights regarding the biogeographic patterns of microbial communities. However, information regarding the degree of overlap and partitions of microbial communities across different habitats in grasslands is limited. This study investigated the microbial communities in three distinct habitats from Xilingol steppe grassland, i.e. animal excrement, phyllosphere, and soil samples, by Illumina MiSeq sequencing. All microbial community structures, i.e. for bacteria, archaea, and fungi, were significantly distinguished according to habitat. A high number of unique microorganisms but few coexisting microorganisms were detected, suggesting that the structure of microbial communities was mainly regulated by species selection and niche differentiation. However, the sequences of those limited coexisting microorganisms among the three different habitats accounted for over 60% of the total sequences, indicating their ability to adapt to variable environments. In addition, the biotic interactions among microorganisms based on a co-occurrence network analysis highlighted the importance of Microvirga, Blastococcus, RB41, Nitrospira, and four norank members of bacteria in connecting the different microbiomes. Collectively, the microbial communities in the Xilingol steppe grassland presented strong habitat preferences with a certain degree of dispersal and colonization potential to new habitats along the animal excrement- phyllosphere-soil gradient. This study provides the first detailed comparison of microbial communities in different habitats in a single grassland, and offers new insights into the biogeographic patterns of the microbial assemblages in grasslands.
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Affiliation(s)
- Jie Yang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanfen Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoyong Cui
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kai Xue
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiming Zhang
- Beijing Municipal Ecological Environment Bureau, Beijing, 100048, China
| | - Zhisheng Yu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
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17
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Planý M, Czolderová M, Kraková L, Puškárová A, Bučková M, Šoltys K, Budiš J, Szemes T, Mackulak T, Wu JH, Pangallo D. Biogas production: evaluation of the influence of K2FeO4 pretreatment of maple leaves (Acer platanoides) on microbial consortia composition. Bioprocess Biosyst Eng 2019; 42:1151-1163. [DOI: 10.1007/s00449-019-02112-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/20/2019] [Indexed: 10/27/2022]
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18
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Guo H, Wang XD, Lee DJ. Proteomic researches for lignocellulose-degrading enzymes: A mini-review. BIORESOURCE TECHNOLOGY 2018; 265:532-541. [PMID: 29884341 DOI: 10.1016/j.biortech.2018.05.101] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 05/29/2018] [Accepted: 05/30/2018] [Indexed: 05/14/2023]
Abstract
Protective action of lignin/hemicellulose networks and crystalline structures of embedded cellulose render lignocellulose material resistant to external enzymatic attack. To eliminate this bottleneck, research has been conducted in which advanced proteomic techniques are applied to identify effective commercial hydrolytic enzymes. This mini-review summarizes researches on lignocellulose-degrading enzymes, the mechanisms of the responses of various lignocellulose-degrading strains and microbial communities to various carbon sources and various biomass substrates, post-translational modifications of lignocellulose-degrading enzymes, new lignocellulose-degrading strains, new lignocellulose-degrading enzymes and a new method of secretome analysis. The challenges in the practical use of enzymatic hydrolysis process to realize lignocellulose biorefineries are discussed, along with the prospects for the same.
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Affiliation(s)
- Hongliang Guo
- College of Food Engineering, Harbin University of Commerce, Harbin 150076, China
| | - Xiao-Dong Wang
- Research Center of Engineering Thermophysics, North China Electric Power University, Beijing 102206, China; School of Energy Power and Mechanical Engineering, North China Electric Power University, Beijing 102206, China
| | - Duu-Jong Lee
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan; Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan.
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19
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Carlos C, Fan H, Currie CR. Substrate Shift Reveals Roles for Members of Bacterial Consortia in Degradation of Plant Cell Wall Polymers. Front Microbiol 2018; 9:364. [PMID: 29545786 PMCID: PMC5839234 DOI: 10.3389/fmicb.2018.00364] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 02/15/2018] [Indexed: 01/05/2023] Open
Abstract
Deconstructing the intricate matrix of cellulose, hemicellulose, and lignin poses a major challenge in biofuel production. In diverse environments in nature, some microbial communities, are able to overcome plant biomass recalcitrance. Identifying key degraders of each component of plant cell wall can help improve biological degradation of plant feedstock. Here, we sequenced the metagenome of lignocellulose-adapted microbial consortia sub-cultured on xylan and alkali lignin media. We observed a drastic shift on community composition after sub-culturing, independently of the original consortia. Proteobacteria relative abundance increased after growth in alkali lignin medium, while Bacteroidetes abundance increased after growth in xylan medium. At the genus level, Pseudomonas was more abundant in the communities growing on alkali lignin, Sphingobacterium in the communities growing on xylan and Cellulomonas abundance was the highest in the original microbial consortia. We also observed functional convergence of microbial communities after incubation in alkali lignin, due to an enrichment of genes involved in benzoate degradation and catechol ortho-cleavage pathways. Our results represent an important step toward the elucidation of key members of microbial communities on lignocellulose degradation and may aide the design of novel lignocellulolytic microbial consortia that are able to efficiently degrade plant cell wall polymers.
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Affiliation(s)
- Camila Carlos
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States.,U.S. Department of Energy, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Huan Fan
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States.,U.S. Department of Energy, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
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