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Li J, Zhao J, Liao X, Hu P, Wang W, Ling Q, Xie L, Xiao J, Zhang W, Wang K. Pathways of soil organic carbon accumulation are related to microbial life history strategies in fertilized agroecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172191. [PMID: 38588738 DOI: 10.1016/j.scitotenv.2024.172191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 04/10/2024]
Abstract
Although the formation, turnover, and accumulation of soil organic carbon (SOC) are driven by different fertilizer inputs and their subsequent microbial-mediated transformation, the relationship between changes in plant-derived and microbial-derived components and soil microbial life history strategies under different fertilization regimes has not been well explored. In this study, the changes in microbial necromass carbon (MNC), lignin phenols, and glomalin-related soil protein (GRSP), as well as soil microbial life history strategy were determined in a 16-year field experiment in response to different fertilization regimes, including a no-fertilizer control (C), conventional chemical NPK fertilization (NPK), and partial substitutions of the NPK in chemical fertilizers with a low (30 %) or high (60 %) level of straw (0.3S and 0.6S) or cattle manure (0.3M and 0.6M). The results showed that total lignin phenol content and its contribution to SOC were significantly increased by 88.7 % and 74.2 %, respectively, in high-level straw substitution treatment as compared to chemical fertilization. Both high-level straw and cattle manure substitution increased MNC and total GRSP contents, but did not alter their contributions to SOC compared to chemical fertilization. In fertilized treatments, the high-level cattle manure substitution had the lowest and highest bacterial and fungal K/r ratio, respectively. Bacterial K/r ratio was an important factor in predicting bacterial necromass carbon content and there was a significant negative correlation between them. The ratio of ectomycorrhizal to saprotrophic fungi and fungal diversity were important factors for predicting lignin phenol and GRSP contents, respectively. In addition, the SEMs modeling indicated that straw substitution directly affected lignin phenol and MNC accumulation, whereas cattle manure substitution indirectly affected MNC accumulation by affecting microbial life history strategies. In conclusions, agricultural residues inputs support the formation of a multiple carbon pool of SOC compared to chemical fertilization; and microbial life history strategy is an important driver of SOC formation and affects SOC accumulation and stability in agroecosystems.
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Affiliation(s)
- Jiangnan Li
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China; College of Environment and Ecology, Hunan Agricultural University, Changsha 410128, PR China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, PR China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, PR China
| | - Jie Zhao
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China; Guangxi Industrial Technology Research Institute for Karst Rocky Desertification Control, Nanning 530012, PR China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, PR China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, PR China.
| | - Xionghui Liao
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, PR China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, PR China
| | - Peilei Hu
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, PR China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, PR China
| | - Wenyu Wang
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, PR China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, PR China
| | - Qiumei Ling
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, PR China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, PR China
| | - Lei Xie
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, PR China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, PR China
| | - Jun Xiao
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, PR China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, PR China
| | - Wei Zhang
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China; Guangxi Industrial Technology Research Institute for Karst Rocky Desertification Control, Nanning 530012, PR China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, PR China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, PR China
| | - Kelin Wang
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, PR China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, PR China.
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Yang S, Sun J, Wang C, Li S, Li Z, Luo W, Wei G, Chen W. Residue quality drives SOC sequestration by altering microbial taxonomic composition and ecophysiological function in desert ecosystem. ENVIRONMENTAL RESEARCH 2024; 250:118518. [PMID: 38382662 DOI: 10.1016/j.envres.2024.118518] [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: 08/16/2023] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 02/23/2024]
Abstract
Plant residues are important sources of soil organic carbon in terrestrial ecosystems. The degradation of plant residue by microbes can influence the soil carbon cycle and sequestration. However, little is known about the microbial composition and function, as well as the accumulation of soil organic carbon (SOC) in response to the inputs of different quality plant residues in the desert environment. The present study evaluated the effects of plant residue addition from Pinus sylvestris var. mongolica (Pi), Artemisia desertorum (Ar) and Amorpha fruticosa (Am) on desert soil microbial community composition and function in a field experiment in the Mu Us Desert. The results showed that the addition of the three plant residues with different C/N ratios induced significant variation in soil microbial communities. The Am treatment (low C/N ratio) improved microbial diversity compared with the Ar and Pi treatments (medium and high C/N ratios). The variations in the taxonomic and functional compositions of the dominant phyla Actinobacteria and Proteobacteria were higher than those of the other phyla among the different treatments. Moreover, the network links between Proteobacteria and other phyla and the CAZyme genes abundances from Proteobacteria increased with increasing residue C/N, whereas those decreased for Actinobacteria. The SOC content of the Am, Ar and Pi treatments increased by 45.73%, 66.54% and 107.99%, respectively, as compared to the original soil. The net SOC accumulation was positively correlated with Proteobacteria abundance and negatively correlated with Actinobacteria abundance. These findings showed that changing the initial quality of plant residue from low C/N to high C/N can result in shifts in taxonomic and functional composition from Actinobacteria to Proteobacteria, which favors SOC accumulation. This study elucidates the ecophysiological roles of Actinobacteria and Proteobacteria in the desert carbon cycle, expands our understanding of the potential microbial-mediated mechanisms by which plant residue inputs affect SOC sequestration in desert soils, and provides valuable guidance for species selection in desert vegetation reconstruction.
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Affiliation(s)
- Shanshan Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Shaanxi, China
| | - Jieyu Sun
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Shaanxi, China
| | - Chang Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Shaanxi, China
| | - Shuyue Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Shaanxi, China
| | - Zubing Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Shaanxi, China
| | - Wen Luo
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Shaanxi, China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Shaanxi, China
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Shaanxi, China.
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Zhang K, Li J, Wang Z, Xie B, Xiong Z, Li H, Ahmed M, Fang F, Li J, Li X. Cloning, expression and application of a novel laccase derived from water buffalo ruminal lignin-degrading bacteria. Int J Biol Macromol 2024; 266:131109. [PMID: 38531520 DOI: 10.1016/j.ijbiomac.2024.131109] [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: 09/27/2023] [Revised: 01/05/2024] [Accepted: 03/21/2024] [Indexed: 03/28/2024]
Abstract
Water buffalo is the only mammal found to degrade lignin so far, and laccase plays an indispensable role in the degradation of lignin. In this study, multiple laccase genes were amplified based on the water buffalo rumen derived lignin-degrading bacteria Bacillus cereus and Ochrobactrum pseudintermedium. Subsequently, the corresponding recombinant plasmids were transformed into E. coli expression system BL21 (DE3) for induced expression by Isopropyl-β-D-thiogalactopyranoside (IPTG). After preliminary screening, protein purification and enzyme activity assays, Lac3833 with soluble expression and high enzyme activity was selected to test its characteristics, especially the ability of lignin degradation. The results showed that the optimum reaction temperature of Lac3833 was 40 °C for different substrates. The relative activity of Lac3833 reached the highest at pH 4.5 and pH 5.5 when the substrates were ABTS or 2,6-DMP and guaiacol, respectively. Additionally, Lac3833 could maintain high enzyme activity in different temperatures, pH and solutions containing Na+, K+, Mg2+, Ca2+ and Mn2+. Importantly, compared to negative treatment, recombinant laccase Lac3833 treatment showed that it had a significant function in degrading lignin. In conclusion, this is a pioneering study to produce recombinant laccase with lignin-degrading ability by bacteria from water buffalo rumen, which will provide new insights for the exploitation of more lignin-degrading enzymes.
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Affiliation(s)
- Kun Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jingfa Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhen Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Bohan Xie
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zixiang Xiong
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Hongyi Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Mehboob Ahmed
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Fang Fang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jiakui Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China.
| | - Xiang Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China; Shennongjia Science and Technology Innovation Center, Huazhong Agricultural University, Shennongjia, China.
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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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Pereira AR, Assis NVD, Paranhos AGDO, Lima DRS, Baeta BEL, Aquino SFD, Silva SDQ. Effect of inoculum composition on the microbial community involved in the anaerobic digestion of sugarcane bagasse. ENVIRONMENTAL TECHNOLOGY 2024; 45:2205-2217. [PMID: 36632771 DOI: 10.1080/09593330.2023.2166877] [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: 08/24/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
In anaerobic digestion (AD), the choice of inoculum type seems to be relevant for methane production for complex substrates, such as lignocellulosic material. Previous work demonstrated that the addition of fresh manure and ruminal fluid to anaerobic sludge improved methane productivity and kinetics of AD of crude sugarcane bagasse (CSB). Considering that the improvement of methane production could be a result of a more adapted microbial community, the present study performed the Next Generation Sequencing analysis to identify changes in the microbiome of anaerobic sludge inoculum, resulting from fresh manure and ruminal fluid addition. In comparison with AD performed only with anaerobic sludge inoculum (50:50, U), accumulated methane production was 15% higher with anaerobic sludge plus ruminal fluid inoculum (50:50, UR) and even higher (68%) with anaerobic sludge with fresh bovine manure inoculum (50:50, UFM), reaching the value of 143 NmLCH4.gVS-1. Clostridium species were highly abundant in all inocula, playing an important role during the hydrolysis and fermentation of CSB, and detoxifying potential inhibitors. Microbial composition also revealed the occurrence of Pseudomonas and Anaerobaculum at UFM inoculum that seem to have contributed to the higher methane production rate, mainly due to their hydrolytic and fermentative ability on lignocellulosic substrates. On the other hand, the presence of Alcaligenes might have had a negative effect on methane production due to their ability to perform methane oxidation.
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Affiliation(s)
- Andressa Rezende Pereira
- Graduate Program in Environmental Engineering, Federal University of Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, Brazil
| | - Nathália Vercelli de Assis
- Graduate Program in Biotechnology, Federal University of Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, Brazil
| | | | - Diego Roberto Sousa Lima
- Graduate Program in Environmental Engineering, Federal University of Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, Brazil
| | - Bruno Eduardo Lobo Baeta
- Department of Chemistry, Federal University of Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, Brazil
| | | | - Silvana de Queiroz Silva
- Department of Biological Sciences, Federal University of Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, Brazil
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Zhuang W, Li Y, Kang X, Yan L, Zhang X, Yan Z, Zhang K, Yang A, Niu Y, Yu X, Wang H, An M, Che R. Changes in soil oxidase activity induced by microbial life history strategies mediate the soil heterotrophic respiration response to drought and nitrogen enrichment. Front Microbiol 2024; 15:1375300. [PMID: 38559350 PMCID: PMC10978626 DOI: 10.3389/fmicb.2024.1375300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 02/29/2024] [Indexed: 04/04/2024] Open
Abstract
Drought and nitrogen deposition are two major climate challenges, which can change the soil microbial community composition and ecological strategy and affect soil heterotrophic respiration (Rh). However, the combined effects of microbial community composition, microbial life strategies, and extracellular enzymes on the dynamics of Rh under drought and nitrogen deposition conditions remain unclear. Here, we experimented with an alpine swamp meadow to simulate drought (50% reduction in precipitation) and multilevel addition of nitrogen to determine the interactive effects of microbial community composition, microbial life strategy, and extracellular enzymes on Rh. The results showed that drought significantly reduced the seasonal mean Rh by 40.07%, and increased the Rh to soil respiration ratio by 22.04%. Drought significantly altered microbial community composition. The ratio of K- to r-selected bacteria (BK:r) and fungi (FK:r) increased by 20 and 91.43%, respectively. Drought increased hydrolase activities but decreased oxidase activities. However, adding N had no significant effect on microbial community composition, BK:r, FK:r, extracellular enzymes, or Rh. A structural equation model showed that the effects of drought and adding nitrogen via microbial community composition, microbial life strategy, and extracellular enzymes explained 84% of the variation in Rh. Oxidase activities decreased with BK:r, but increased with FK:r. Our findings show that drought decreased Rh primarily by inhibiting oxidase activities, which is induced by bacterial shifts from the r-strategy to the K-strategy. Our results highlight that the indirect regulation of drought on the carbon cycle through the dynamic of bacterial and fungal life history strategy should be considered for a better understanding of how terrestrial ecosystems respond to future climate change.
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Affiliation(s)
- Weirong Zhuang
- Yunnan Key Laboratory of Soil Erosion Prevention and Green Development, Institute of International Rivers and Ecosecurity, Yunnan University, Kunming, China
- Ministry of Education Key Laboratory for Ecosecurity of Southwest China, Yunnan University, Kunming, China
| | - Yong Li
- Beijing Key Laboratory of Wetland Services and Restoration, Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Beijing, Sichuan, China
| | - Xiaoming Kang
- Beijing Key Laboratory of Wetland Services and Restoration, Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Beijing, Sichuan, China
| | - Liang Yan
- Beijing Key Laboratory of Wetland Services and Restoration, Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Beijing, Sichuan, China
| | - Xiaodong Zhang
- Beijing Key Laboratory of Wetland Services and Restoration, Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Beijing, Sichuan, China
| | - Zhongqing Yan
- Beijing Key Laboratory of Wetland Services and Restoration, Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Beijing, Sichuan, China
| | - Kerou Zhang
- Beijing Key Laboratory of Wetland Services and Restoration, Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Beijing, Sichuan, China
| | - Ao Yang
- Beijing Key Laboratory of Wetland Services and Restoration, Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Beijing, Sichuan, China
| | - Yuechuan Niu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoshun Yu
- Beijing Key Laboratory of Wetland Services and Restoration, Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Beijing, Sichuan, China
| | - Huan Wang
- Beijing Key Laboratory of Wetland Services and Restoration, Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Beijing, Sichuan, China
| | - Miaomiao An
- Beijing Key Laboratory of Wetland Services and Restoration, Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Beijing, Sichuan, China
| | - Rongxiao Che
- Yunnan Key Laboratory of Soil Erosion Prevention and Green Development, Institute of International Rivers and Ecosecurity, Yunnan University, Kunming, China
- Ministry of Education Key Laboratory for Ecosecurity of Southwest China, Yunnan University, Kunming, China
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7
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Cuebas‐Irizarry MF, Grunden AM. Streptomyces spp. as biocatalyst sources in pulp and paper and textile industries: Biodegradation, bioconversion and valorization of waste. Microb Biotechnol 2024; 17:e14258. [PMID: 37017414 PMCID: PMC10832569 DOI: 10.1111/1751-7915.14258] [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: 08/08/2022] [Revised: 03/14/2023] [Accepted: 03/21/2023] [Indexed: 04/06/2023] Open
Abstract
Complex polymers represent a challenge for remediating environmental pollution and an opportunity for microbial-catalysed conversion to generate valorized chemicals. Members of the genus Streptomyces are of interest because of their potential use in biotechnological applications. Their versatility makes them excellent sources of biocatalysts for environmentally responsible bioconversion, as they have a broad substrate range and are active over a wide range of pH and temperature. Most Streptomyces studies have focused on the isolation of strains, recombinant work and enzyme characterization for evaluating their potential for biotechnological application. This review discusses reports of Streptomyces-based technologies for use in the textile and pulp-milling industry and describes the challenges and recent advances aimed at achieving better biodegradation methods featuring these microbial catalysts. The principal points to be discussed are (1) Streptomyces' enzymes for use in dye decolorization and lignocellulosic biodegradation, (2) biotechnological processes for textile and pulp and paper waste treatment and (3) challenges and advances for textile and pulp and paper effluent treatment.
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Affiliation(s)
- Mara F. Cuebas‐Irizarry
- Department of Plant and Microbial BiologyNorth Carolina State UniversityPlant Sciences Building Rm 2323, 840 Oval DrRaleighNorth Carolina27606USA
| | - Amy M. Grunden
- Department of Plant and Microbial BiologyNorth Carolina State UniversityPlant Sciences Building Rm 2323, 840 Oval DrRaleighNorth Carolina27606USA
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Wang X, Li Z, Cheng Y, Yao H, Li H, You X, Zhang C, Li Y. Wheat straw hydrochar induced negative priming effect on carbon decomposition in a coastal soil. IMETA 2023; 2:e134. [PMID: 38868226 PMCID: PMC10989761 DOI: 10.1002/imt2.134] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 08/18/2023] [Indexed: 06/14/2024]
Abstract
The mechanisms underlying hydrochar-regulated soil organic carbon (SOC) decomposition in the coastal salt-affected soils were first investigated. Straw-derived hydrochar (SHC)-induced C-transformation bacterial modulation and soil aggregation enhancement primarily accounted for negative priming effects. Modification of soil properties (e.g., decreased pH and increased C/N ratios) by straw-derived pyrochar (SPC) was responsible for decreased SOC decomposition.
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Affiliation(s)
- Xiao Wang
- Marine Agriculture Research Center, Tobacco Research InstituteChinese Academy of Agricultural SciencesQingdaoChina
- National Center of Technology Innovation for Comprehensive Utilization of Saline‐Alkali LandDongyingChina
- Qingdao Key Laboratory of Coastal Saline‐alkali Land Resources Mining and Biological BreedingTobacco Research InstituteQingdaoChina
| | - Zhen Li
- Marine Agriculture Research Center, Tobacco Research InstituteChinese Academy of Agricultural SciencesQingdaoChina
| | - Yadong Cheng
- Marine Agriculture Research Center, Tobacco Research InstituteChinese Academy of Agricultural SciencesQingdaoChina
- National Center of Technology Innovation for Comprehensive Utilization of Saline‐Alkali LandDongyingChina
- Qingdao Key Laboratory of Coastal Saline‐alkali Land Resources Mining and Biological BreedingTobacco Research InstituteQingdaoChina
| | - Hui Yao
- Marine Agriculture Research Center, Tobacco Research InstituteChinese Academy of Agricultural SciencesQingdaoChina
- National Center of Technology Innovation for Comprehensive Utilization of Saline‐Alkali LandDongyingChina
- Qingdao Key Laboratory of Coastal Saline‐alkali Land Resources Mining and Biological BreedingTobacco Research InstituteQingdaoChina
| | - Hui Li
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNCUSA
| | - Xiangwei You
- Marine Agriculture Research Center, Tobacco Research InstituteChinese Academy of Agricultural SciencesQingdaoChina
- National Center of Technology Innovation for Comprehensive Utilization of Saline‐Alkali LandDongyingChina
- Qingdao Key Laboratory of Coastal Saline‐alkali Land Resources Mining and Biological BreedingTobacco Research InstituteQingdaoChina
| | - Chengsheng Zhang
- Marine Agriculture Research Center, Tobacco Research InstituteChinese Academy of Agricultural SciencesQingdaoChina
- National Center of Technology Innovation for Comprehensive Utilization of Saline‐Alkali LandDongyingChina
- Qingdao Key Laboratory of Coastal Saline‐alkali Land Resources Mining and Biological BreedingTobacco Research InstituteQingdaoChina
| | - Yiqiang Li
- Marine Agriculture Research Center, Tobacco Research InstituteChinese Academy of Agricultural SciencesQingdaoChina
- National Center of Technology Innovation for Comprehensive Utilization of Saline‐Alkali LandDongyingChina
- Qingdao Key Laboratory of Coastal Saline‐alkali Land Resources Mining and Biological BreedingTobacco Research InstituteQingdaoChina
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9
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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.
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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
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10
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Hartmann M, Herzog C, Brunner I, Stierli B, Meyer F, Buchmann N, Frey B. Long-term mitigation of drought changes the functional potential and life-strategies of the forest soil microbiome involved in organic matter decomposition. Front Microbiol 2023; 14:1267270. [PMID: 37840720 PMCID: PMC10570739 DOI: 10.3389/fmicb.2023.1267270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/14/2023] [Indexed: 10/17/2023] Open
Abstract
Climate change can alter the flow of nutrients and energy through terrestrial ecosystems. Using an inverse climate change field experiment in the central European Alps, we explored how long-term irrigation of a naturally drought-stressed pine forest altered the metabolic potential of the soil microbiome and its ability to decompose lignocellulolytic compounds as a critical ecosystem function. Drought mitigation by a decade of irrigation stimulated profound changes in the functional capacity encoded in the soil microbiome, revealing alterations in carbon and nitrogen metabolism as well as regulatory processes protecting microorganisms from starvation and desiccation. Despite the structural and functional shifts from oligotrophic to copiotrophic microbial lifestyles under irrigation and the observation that different microbial taxa were involved in the degradation of cellulose and lignin as determined by a time-series stable-isotope probing incubation experiment with 13C-labeled substrates, degradation rates of these compounds were not affected by different water availabilities. These findings provide new insights into the impact of precipitation changes on the soil microbiome and associated ecosystem functioning in a drought-prone pine forest and will help to improve our understanding of alterations in biogeochemical cycling under a changing climate.
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Affiliation(s)
- Martin Hartmann
- Department of Environmental Systems Science, Sustainable Agroecosystems, Institute of Agricultural Sciences, ETH Zürich, Zürich, Switzerland
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Claude Herzog
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Department of Environmental Systems Science, Grassland Sciences, Institute of Agricultural Sciences, ETH Zürich, Zürich, Switzerland
| | - Ivano Brunner
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Beat Stierli
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Folker Meyer
- Data Science, Institute for AI in Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Argonne National Laboratory, Argonne, IL, United States
- Computation Institute, University of Chicago, Chicago, IL, United States
- Department of Medicine, University of Chicago, Chicago, IL, United States
| | - Nina Buchmann
- Department of Environmental Systems Science, Grassland Sciences, Institute of Agricultural Sciences, ETH Zürich, Zürich, Switzerland
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
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11
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Janusz G, Mazur A, Pawlik A, Kołodyńska D, Jaroszewicz B, Marzec-Grządziel A, Koper P. Metagenomic Analysis of the Composition of Microbial Consortia Involved in Spruce Degradation over Time in Białowieża Natural Forest. Biomolecules 2023; 13:1466. [PMID: 37892148 PMCID: PMC10604581 DOI: 10.3390/biom13101466] [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: 09/05/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
Deadwood plays an important role in forest ecology; its degradation and, therefore, carbon assimilation is carried out by fungi and bacteria. To quantify the abundance and distribution of microbial taxa inhabiting dead spruce logs fallen over a span of 50 years and the soil beneath, we used taxonomic profiling with NGS sequencing of hypervariable DNA fragments of ITS1 and 16S V3-V4, respectively. The analysis of sequencing data revealed a high level of diversity in microbial communities participating in the degradation of spruce logs. Differences in the relative abundance of microbial taxa between the samples of the wood that died in 1974 and 2014, and of the soil in its immediate vicinity, were visible, especially at the genus level. Based on the Lefse analysis significantly higher numbers of classified bacterial taxa were observed in the wood and soil samples from 2014 (wood: 1974-18 and 2014-28 taxa; soil: 1974-8 and 2014-41 taxa) while the number of classified fungal taxa was significantly higher in the wood and soil samples from 1974 (wood: 1974-17 and 2014-9 taxa; soil: 1974-57 and 2014-28 taxa). Most of the bacterial and fungal amplicon sequence variants (ASVs) unique to wood were found in the samples from 1974, while those unique to soil were detected in the samples from 2014. The ATR-FTIR method supported by CHN analysis revealed physicochemical changes in deadwood induced by the activity of fungal and bacterial organisms.
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Affiliation(s)
- Grzegorz Janusz
- Department of Biochemistry and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland;
| | - Andrzej Mazur
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland; (A.M.); (P.K.)
| | - Anna Pawlik
- Department of Biochemistry and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland;
| | - Dorota Kołodyńska
- Faculty of Chemistry, Maria Curie Skłodowska University, M. Curie Skłodowska Sq. 2, 20-031 Lublin, Poland;
| | - Bogdan Jaroszewicz
- Białowieża Geobotanical Station, Faculty of Biology, University of Warsaw, Sportowa 19, 17-230 Białowieża, Poland;
| | - Anna Marzec-Grządziel
- Department of Agriculture Microbiology, Institute of Soil Science and Plant Cultivation, Czartoryskich 8 Str., 24-100 Puławy, Poland;
| | - Piotr Koper
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland; (A.M.); (P.K.)
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12
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More PP, Chavan AA, Sharma MB, Lali AM. Biobased volatile fatty acids (VFA) production via anaerobic acidogenesis of sugar processing industry effluent. ENVIRONMENTAL TECHNOLOGY 2023; 44:1179-1189. [PMID: 34669547 DOI: 10.1080/09593330.2021.1996472] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/09/2021] [Indexed: 06/13/2023]
Abstract
Rapid industrialization and unscientific disposal of industrial wastewaters have resulted in the pollution of water bodies and deterioration of water quality all over the globe. Valorization of industrial wastewaters will help in reducing the negative impact on the environment and will add value to the waste. The present study targets utilization of sugar processing industrial effluent for bio-based production of Volatile fatty acids (VFA) through anaerobic acidogenesis. Batch studies conducted to determine the VFA production potential of sugar processing industry effluent resulted in the VFA yield of 0.70 g/g COD utilized. Further continuous VFA production system was developed and optimization of Organic loading rate (OLR) (2-22 g COD/L·day) was carried out with constant Hydraulic retention time (HRT) of 1 day. The continuous reactors studies resulted in a maximum VFA yield of 0.72 g/g COD utilized and productivity of 11.04 g COD/L·day at OLR of 14 g COD/L·day and 22 g COD/L·day, respectively. The developed process will provide an environmentally safe and efficient method for the conversion of complex industrial wastes to valuable products such as VFA.
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Affiliation(s)
- Pooja P More
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Mumbai, India
| | - Aniket A Chavan
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Mumbai, India
| | - Manju B Sharma
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Mumbai, India
| | - Arvind M Lali
- Department of Chemical Engineering, Institute of Chemical Technology, Mumbai, India
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13
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Systems metabolic engineering upgrades Corynebacterium glutamicum to high-efficiency cis, cis-muconic acid production from lignin-based aromatics. Metab Eng 2023; 75:153-169. [PMID: 36563956 DOI: 10.1016/j.ymben.2022.12.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/14/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022]
Abstract
Lignin displays a highly challenging renewable. To date, massive amounts of lignin, generated in lignocellulosic processing facilities, are for the most part merely burned due to lacking value-added alternatives. Aromatic lignin monomers of recognized relevance are in particular vanillin, and to a lesser extent vanillate, because they are accessible at high yield from softwood-lignin using industrially operated alkaline oxidative depolymerization. Here, we metabolically engineered C. glutamicum towards cis, cis-muconate (MA) production from these key aromatics. Starting from the previously created catechol-based producer C. glutamicum MA-2, systems metabolic engineering first discovered an unspecific aromatic aldehyde reductase that formed aromatic alcohols from vanillin, protocatechualdehyde, and p- hydroxybenzaldehyde, and was responsible for the conversion up to 57% of vanillin into vanillyl alcohol. The alcohol was not re-consumed by the microbe later, posing a strong drawback on the producer. The identification and subsequent elimination of the encoding fudC gene completely abolished vanillyl alcohol formation. Second, the initially weak flux through the native vanillin and vanillate metabolism was enhanced up to 2.9-fold by implementing synthetic pathway modules. Third, the most efficient protocatechuate decarboxylase AroY for conversion of the midstream pathway intermediate protocatechuate into catechol was identified out of several variants in native and codon optimized form and expressed together with the respective helper proteins. Fourth, the streamlined modules were all genomically combined which yielded the final strain MA-9. MA-9 produced bio-based MA from vanillin, vanillate, and seven structurally related aromatics at maximum selectivity. In addition, MA production from softwood-based vanillin, obtained through alkaline depolymerization, was demonstrated.
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14
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Activity of cellulase and ligninase enzymes in a local bioactivator from cattle and buffalo rumen contents. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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15
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Potential of Using Dual-Media Biofilm Reactors as a Real Coffee Industrial Effluent Pre-Treatment. WATER 2022. [DOI: 10.3390/w14132025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The coffee processing industry produces toxic and low biodegradable effluent, which can pollute water bodies. A pre-treatment study on coffee effluent using a dual-media biofilm reactor (DM-BR) containing sand and Hexafilter (HEX) was conducted alongside a control biofilm reactor (C-BR) containing sand media. The novelty of this study lies in the use of dual media in biofilm reactor (DM-BR) for real coffee effluent treatment, where these processes were used individually in previous studies. The performance of DM-BR and C-BR in treating coffee effluent were investigated at different hydraulic retention times (HRTs), 24, 48 and 72 h, and the degrading bacteria were identified. Both biofilm reactors were inoculated with a recycled paper mill-activated sludge and acclimatised for 97 days. The DM-BR displayed the highest removal of chemical oxygen demand (COD) and NH4+-N at 47% and 38%, respectively, within 48 h of HRT, whereas colour and tannin–lignin reached maximum average removal of 21% and 29%, respectively, at 24 h of HRT. The combination of sand and HEX media in a system showed COD and NH4+-N removal improvement at 48 h of HRT and encouraged a variety of bacterial species growth. Bacterial characterisation analysis revealed Proteobacteria to be dominant.
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16
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Li JL, Duan L, Wu Y, Ahmad M, Yin LZ, Luo XQ, Wang X, Fang BZ, Li SH, Huang LN, Wu JX, Mou XZ, Wang P, Li WJ. Unraveling microbe-mediated degradation of lignin and lignin-derived aromatic fragments in the Pearl River Estuary sediments. CHEMOSPHERE 2022; 296:133995. [PMID: 35176304 DOI: 10.1016/j.chemosphere.2022.133995] [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: 09/22/2021] [Revised: 01/13/2022] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
Estuaries are one of the most crucial areas for the transformation and burial of terrestrial organic carbon (TerrOC), playing an important role in the global carbon cycle. While the transformation and degradation of TerrOC are mainly driven by microorganisms, the specific taxa and degradation processes involved remain largely unknown in estuaries. We collected surface sediments from 14 stations along the longitudinal section of the Pearl River Estuary (PRE), P. R. China. By combining analytical chemistry, metagenomics, and bioinformatics methods, we analyzed composition, source and degradation pathways of lignin/lignin-derived aromatic fragments and their potential decomposers in these samples. A diversity of bacterial and archaeal taxa, mostly those from Proteobacteria (Deltaproteobacteria, Gammaproteobacteria etc.), including some lineages (e.g., Nitrospria, Polyangia, Tectomicrobia_uc) not previously implicated in lignin degradation, were identified as potential polymeric lignin or its aromatic fragments degraders. The abundance of lignin degradation pathways genes exhibited distinct spatial distribution patterns with the area adjacent to the outlet of Modaomen as a potential degradation hot zone and the Syringyl lignin fragments, 3,4-PDOG, and 4,5-PDOG pathways as the primary potential lignin aromatic fragments degradation processes. Notably, the abundance of ferulic acid metabolic pathway genes exhibited significant correlations with degree of lignin oxidation and demethylation/demethoxylization and vegetation source. Additionally, the abundance of 2,3-PDOG degradation pathways genes also showed a positive significant correlation with degree of lignin oxidation. Our study provides a meaningful insight into the microbial ecology of TerrOC degradation in the estuary.
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Affiliation(s)
- Jia-Ling Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, China
| | - Li Duan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, China
| | - Ying Wu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
| | - Manzoor Ahmad
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, China
| | - Ling-Zi Yin
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, China
| | - Xiao-Qing Luo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, China
| | - Xin Wang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
| | - Bao-Zhu Fang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Shan-Hui Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, China
| | - Li-Nan Huang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, China
| | - Jia-Xue Wu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, China
| | - Xiao-Zhen Mou
- Department of Biological Sciences, Kent State University, Kent, 44242, Ohio, USA
| | - Pandeng Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, Guangdong, China.
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17
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Ferrer A, Heath KD, Mosquera SL, Suaréz Y, Dalling JW. Assembly of wood-inhabiting archaeal, bacterial and fungal communities along a salinity gradient: common taxa are broadly distributed but locally abundant in preferred habitats. FEMS Microbiol Ecol 2022; 98:6566339. [PMID: 35404430 DOI: 10.1093/femsec/fiac040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 03/29/2022] [Accepted: 04/07/2022] [Indexed: 11/12/2022] Open
Abstract
Wood decomposition in water is a key ecosystem process driven by diverse microbial taxa that likely differ in their affinities for freshwater, estuarine, and marine habitats. How these decomposer communities assemble in situ or potentially colonize from other habitats remains poorly understood. At three watersheds on Coiba Island, Panama, we placed replicate sections of branch wood of a single tree species on land, and in freshwater, estuarine and marine habitats that constitute a downstream salinity gradient. We sequenced archaea, bacteria and fungi from wood samples collected after 3, 9, and 15 months to examine microbial community composition, and to examine habitat specificity and abundance patterns. We found these microbial communities were broadly structured by similar factors, with a strong effect of salinity, but little effect of watershed identity on compositional variation. Moreover, common aquatic taxa were also present in wood incubated on land. Our results suggest that taxa either dispersed to both terrestrial and aquatic habitats, or that microbes with broad habitat ranges were initially present in the wood as endophytes. Nonetheless, these habitat generalists varied greatly in abundance across habitats suggesting an important role for habitat filtering in maintaining distinct aquatic communities in freshwater, estuarine and marine habitats.
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Affiliation(s)
- Astrid Ferrer
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Katy D Heath
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Sergio L Mosquera
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Republic of Panama
| | - Yaraví Suaréz
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Republic of Panama
| | - James W Dalling
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.,Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Republic of Panama
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Margesin R, Ludwikowski TM, Kutzner A, Wagner AO. Low-Temperature Biodegradation of Lignin-Derived Aromatic Model Monomers by the Cold-Adapted Yeast Rhodosporidiobolus colostri Isolated from Alpine Forest Soil. Microorganisms 2022; 10:microorganisms10030515. [PMID: 35336090 PMCID: PMC8955795 DOI: 10.3390/microorganisms10030515] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/21/2022] [Accepted: 02/23/2022] [Indexed: 01/12/2023] Open
Abstract
The contribution of cold-adapted yeasts to the emerging field of lignin biovalorization has not yet been studied. The red-pigmented basidiomycetous yeast strain Rhodosporidiobolus colostri DBVPG 10655 was examined for its potential to degrade five selected lignin-derived aromatic monomers (syringic acid, p-coumaric acid, 4-hydroxybenzoic acid, ferulic acid, and vanillic acid). The strain utilized p-coumaric acid, 4-hydroxybenzoic acid, and ferulic acid not only as the sole carbon source; full biodegradation occurred also in mixtures of multiple monomers. Vanillic acid was not utilized as the sole carbon source, but was degraded in the presence of p-coumaric acid, 4-hydroxybenzoic acid, and ferulic acid. Syringic acid was utilized neither as the sole carbon source nor in mixtures of compounds. Biodegradation of lignin-derived aromatic monomers was detected over a broad temperature range (1–25 °C), which is of ecological significance and of biotechnological relevance.
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19
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Isolation and characterization of microorganisms capable of cleaving the ether bond of 2-phenoxyacetophenone. Sci Rep 2022; 12:2874. [PMID: 35190591 PMCID: PMC8861056 DOI: 10.1038/s41598-022-06816-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 02/07/2022] [Indexed: 11/08/2022] Open
Abstract
Lignin is a heterogeneous aromatic polymer and major component of plant cell walls. The β-O-4 alkyl aryl ether is the most abundant linkage within lignin. Given that lignin is effectively degraded on earth, as yet unknown ether bond-cleaving microorganisms could still exist in nature. In this study, we searched for microorganisms that transform 2-phenoxyacetophenone (2-PAP), a model compound for the β-O-4 linkage in lignin, by monitoring ether bond cleavage. We first isolated microorganisms that grew on medium including humic acid (soil-derived organic compound) as a carbon source. The isolated microorganisms were subsequently subjected to colorimetric assay for 2-PAP ether bond-cleaving activity; cells of the isolated strains were incubated with 2-PAP, and strains producing phenol via ether bond cleavage were selected using phenol-sensitive Gibbs reagent. This screening procedure enabled the isolation of various 2-PAP-transforming microorganisms, including 7 bacteria (genera: Acinetobacter, Cupriavidus, Nocardioides, or Streptomyces) and 1 fungus (genus: Penicillium). To our knowledge, these are the first microorganisms demonstrated to cleave the ether bond of 2-PAP. One Gram-negative bacterium, Acinetobacter sp. TUS-SO1, was characterized in detail. HPLC and GC-MS analyses revealed that strain TUS-SO1 oxidatively and selectively cleaves the ether bond of 2-PAP to produce phenol and benzoate. These results indicate that the transformation mechanism differs from that involved in reductive β-etherase, which has been well studied. Furthermore, strain TUS-SO1 efficiently transformed 2-PAP; glucose-grown TUS-SO1 cells converted 1 mM 2-PAP within only 12 h. These microorganisms might play important roles in the degradation of lignin-related compounds in nature.
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20
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Effect of hydrothermal treatment on organic matter degradation, phytotoxicity, and microbial communities in model food waste composting. J Biosci Bioeng 2022; 133:382-389. [PMID: 35115228 DOI: 10.1016/j.jbiosc.2022.01.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 01/11/2022] [Accepted: 01/11/2022] [Indexed: 01/17/2023]
Abstract
Hydrothermal treatment (HTT) as a pretreatment method for compost raw material has multiple benefits such as enhanced solubility of organic material, improved bioaugmentation, and reduced biohazard by killing harmful microorganisms. In this study, we pretreated food waste via HTT at 180 °C for 30 min to investigate its effect on food waste composting. HTT generated 8.98 mg/g-dry solid (g-ds) of 5-hydroxymethylfurfural and 4.32 mg/g-ds furfural. These furan compounds were completely decomposed in the early stage of composting, subsequently the organic matter in the food waste started to be degraded. The HTT-pretreated experiment demonstrated less organic matter degradation during composting as well as lower compost phytotoxicity compared to the non-HTT-pretreated experiment, where the conversion of carbon was 25.2% and the germination index value was 55%. HTT probably denatured part of the organic matter and making it more difficult to decompose, thereby preventing the rapid release of high concentrations of phytotoxic compounds such as organic acids and ammonium ions during composting. High-throughput microbial community analysis revealed that only Firmicutes appeared in the HTT-pretreated experiment, however, other bacterial groups also appeared in the non-HTT-pretreated experiment. This was possibly influenced by furan compounds and the changes of easily degradable organic matter to hardly degradable. Bacillus and Lysinibacillus were dominant in both composting experiments during vigorous organic matter degradation, suggesting that these bacterial groups were the main contributors to food waste composting. This study suggests that HTT is advantageous for the pretreatment of easily degradable food waste, as compost with less phytotoxicity was produced.
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Miyake K, Baba Y. De novo transcriptome assembly of the midgut glands of herbivorous land crabs, Chiromantes haematocheir, and identification of laccase genes involved in lignin degradation. J Comp Physiol B 2022; 192:247-261. [PMID: 35088170 DOI: 10.1007/s00360-021-01424-3] [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: 05/26/2021] [Revised: 11/26/2021] [Accepted: 12/12/2021] [Indexed: 11/30/2022]
Abstract
Herbivorous land crabs such as Chiromantes haematocheir and C. dehaani show biomass-degrading activities. In this study, we performed RNA-seq analysis to detect biomass-degrading enzymes. A de novo transcriptome assembly in the midgut glands of molting and non-molting C. haematocheir crabs was constructed using RNA sequencing. Illumina sequencing generated 44,937,002 and 44,394,310 reads from the two midgut glands. In total, 178,710 contigs with an average length of 750 bp and an N50 value of 1,235 bp were assembled, of which 37,890 contigs were annotated using BLASTx search against the NCBI database. We identified 22 contigs (11 genes) belonging to the laccase family and 44 contigs (22 genes) belonging to the peroxidase family. Sixteen contigs (three genes) belonging to the GH9 cellulase family were also detected. We selected the gene accounting for the majority of expressed laccase and analyzed its properties. The 24131-laccase transcript (2465 bp) had one complete open reading frame, nt 149-1987, encoding a protein of 613 amino acids with a deduced molecular mass of 67.708 kDa. The enzyme was shown to belong to the multicopper oxidase family. The 24131-laccase protein was confirmed to have oxidation activity against 2,6-dimethoxyphenol by ectopic expression in Escherichia coli. Laccase activity was significantly enhanced by feeding land crabs with plant diets. These data suggest that the enzyme plays an important role in the digestion of lignin in the guts of land crabs.
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Affiliation(s)
- Katsuhide Miyake
- Department of Environmental Technology, Faculty of Science and Technology, Meijo University, 1-501 Shiogamaguchi, Tenpaku, Nagoya, Aichi, 468-8502, Japan.
| | - Yasunori Baba
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa, 921-8836, Japan
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Effect of AM Fungi Inoculation on Litter Bacterial Community Characteristics under Heavy Metal Stress. Microorganisms 2022; 10:microorganisms10020206. [PMID: 35208661 PMCID: PMC8879951 DOI: 10.3390/microorganisms10020206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/13/2022] [Accepted: 01/16/2022] [Indexed: 11/19/2022] Open
Abstract
Because microorganisms are the primary driving force behind litter decomposition, they play an important role in maintaining ecosystem material and chemical cycling. Arbuscular mycorrhizal (AM) fungi can improve host plant tolerance to various environmental stressors, making their application in mining area remediation important. In this study, litter from the dominant plant species (Imperata cylindrica) in a copper tailings mining area was selected as the experimental material. We conducted a greenhouse-based heavy metal stress experiment to investigate how AM fungi affect litter microbial community characteristics and key ecological factors. Results showed that AM fungi species, heavy metal treatments, and their combined interaction had significant impacts on litter pH. Additionally, enzyme activities in litter were significantly affected by interactions between AM fungi species and heavy metal contaminates. Ralstonia was significantly positively correlated to lead (Pb) content, indicating that Ralstonia had a certain tolerance to Pb pollution. Sucrase and urease activity were increased when plants were inoculated with Rhizophagus irregularis under Pb stress. Furthermore, Microbacterium, Brevundimonas, and Pseudonocardia all may play important roles in litter decomposition, while a certain tolerance was observed in Kushneria and Roseivivax to heavy metal pollution when plants were inoculated with Glomus mosseae. Results showed that AM fungi affected litter bacterial community structure and function by influencing plant litter properties. By exploring interactions between AM fungi and bacterial communities in plant litter under heavy metal stress, we will better understand associative processes that promote the cycling of soil organic matter and nutrients contaminated by non-ferrous metal tailings.
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A novel Bacillus ligniniphilus catechol 2,3-dioxygenase shows unique substrate preference and metal requirement. Sci Rep 2021; 11:23982. [PMID: 34907211 PMCID: PMC8671467 DOI: 10.1038/s41598-021-03144-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 11/26/2021] [Indexed: 12/03/2022] Open
Abstract
Identification of novel enzymes from lignin degrading microorganisms will help to develop biotechnologies for biomass valorization and aromatic hydrocarbons degradation. Bacillus ligniniphilus L1 grows with alkaline lignin as the single carbon source and is a great candidate for ligninolytic enzyme identification. The first dioxygenase from strain L1 was heterologously expressed, purified, and characterized with an optimal temperature and pH of 32.5 °C and 7.4, respectively. It showed the highest activity with 3-ethylcatechol and significant activities with other substrates in the decreasing order of 3-ethylcatechol > 3-methylcatechol > 3-isopropyl catechol > 2, 3-dihydroxybiphenyl > 4-methylcatechol > catechol. It did not show activities against other tested substrates with similar structures. Most reported catechol 2,3-dioxygenases (C23Os) are Fe2+-dependent whereas Bacillus ligniniphilus catechol 2,3-dioxygenase (BLC23O) is more Mn2+- dependent. At 1 mM, Mn2+ led to 230-fold activity increase and Fe2+ led to 22-fold increase. Sequence comparison and phylogenetic analyses suggested that BL23O is different from other Mn-dependent enzymes and uniquely grouped with an uncharacterized vicinal oxygen chelate (VOC) family protein from Paenibacillus apiaries. Gel filtration analysis showed that BLC23O is a monomer under native condition. This is the first report of a C23O from Bacillus ligniniphilus L1 with unique substrate preference, metal-dependency, and monomeric structure.
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Weiland F, Kohlstedt M, Wittmann C. Guiding stars to the field of dreams: Metabolically engineered pathways and microbial platforms for a sustainable lignin-based industry. Metab Eng 2021; 71:13-41. [PMID: 34864214 DOI: 10.1016/j.ymben.2021.11.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/25/2021] [Accepted: 11/29/2021] [Indexed: 12/19/2022]
Abstract
Lignin is an important structural component of terrestrial plants and is readily generated during biomass fractionation in lignocellulose processing facilities. Due to lacking alternatives the majority of technical lignins is industrially simply burned into heat and energy. However, regarding its vast abundance and a chemically interesting richness in aromatics, lignin is presently regarded as the most under-utilized and promising feedstock for value-added applications. Notably, microbes have evolved powerful enzymes and pathways that break down lignin and metabolize its various aromatic components. This natural pathway atlas meanwhile serves as a guiding star for metabolic engineers to breed designed cell factories and efficiently upgrade this global waste stream. The metabolism of aromatic compounds, in combination with success stories from systems metabolic engineering, as reviewed here, promises a sustainable product portfolio from lignin, comprising bulk and specialty chemicals, biomaterials, and fuels.
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Affiliation(s)
- Fabia Weiland
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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Huang B, Jia H, Han X, Gou J, Huang C, Wang J, Wei J, Wang J, Zhang C. Effects of biocontrol Bacillus and fermentation bacteria additions on the microbial community, functions and antibiotic resistance genes of prickly ash seed oil meal-biochar compost. BIORESOURCE TECHNOLOGY 2021; 340:125668. [PMID: 34339999 DOI: 10.1016/j.biortech.2021.125668] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 06/13/2023]
Abstract
This study evaluated the effects of biocontrol Bacillus and fermenting bacteria addition on the microbial community, metabolic functions and antibiotic resistance genes (ARGs) of new prickly ash seed oil meal (PSOM)-biochar composting. The results showed that the addition of Bacillus subtilis and fermentation bacteria significantly increased the NH4+-N, bacterial abundance and fungal diversity of compost while decreasing the relative abundances (RAs) of carbon metabolism genes in mature compost. NH4+-N was significantly correlated with microbial abundance and diversity, and its increase was closely related to microbial amino acid metabolism. The addition of biocontrol and fermenting bacteria changed the RAs of ARGs, which was caused by changes in the potential hosts Proteobacteria, Bacteroidota and Firmicutes in the compost. Consequently, adding Bacillus and fermenting bacteria into PSOM to make composting was suggested as an effective method to promote nutrient transformation, regulate microbial activity and decrease RAs of tetracycline and vancomycin ARGs.
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Affiliation(s)
- Bin Huang
- Pest Integrated Management Key Laboratory of China Tobacco, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Haijiang Jia
- Raw Material Technology Center of Guangxi Tobacco, Nanning 530000, China
| | - Xiaobin Han
- Biological Organic Fertilizer Engineering Technology Center of China Tobacco, Zunyi 563000, China
| | - Jianyu Gou
- Biological Organic Fertilizer Engineering Technology Center of China Tobacco, Zunyi 563000, China
| | - Chongjun Huang
- Raw Material Technology Center of Guangxi Tobacco, Nanning 530000, China
| | - Jing Wang
- Pest Integrated Management Key Laboratory of China Tobacco, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Jianyu Wei
- Raw Material Technology Center of Guangxi Tobacco, Nanning 530000, China
| | - Jie Wang
- Pest Integrated Management Key Laboratory of China Tobacco, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Chengsheng Zhang
- Pest Integrated Management Key Laboratory of China Tobacco, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
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Earthworm activity optimized the rhizosphere bacterial community structure and further alleviated the yield loss in continuous cropping lily (Lilium lancifolium Thunb.). Sci Rep 2021; 11:20840. [PMID: 34675325 PMCID: PMC8531344 DOI: 10.1038/s41598-021-99597-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 09/27/2021] [Indexed: 11/09/2022] Open
Abstract
The soil microbial community plays a vital role in the biogeochemical cycles of bioelements and maintaining healthy soil conditions in agricultural ecosystems. However, how the soil microbial community responds to mitigation measures for continuous cropping obstacles remains largely unknown. Here we examined the impact of quicklime (QL), chemical fungicide (CF), inoculation with earthworm (IE), and a biocontrol agent (BA) on the soil microbial community structure, and the effects toward alleviating crop yield decline in lily. High-throughput sequencing of the 16S rRNA gene from the lily rhizosphere after 3 years of continuous cropping was performed using the Illumina MiSeq platform. The results showed that Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Chloroflexi and Gemmatimonadetes were the dominant bacterial phyla, with a total relative abundance of 86.15-91.59%. On the other hand, Betaproteobacteriales, Rhizobiales, Myxococcales, Gemmatimonadales, Xanthomonadales, and Micropepsales were the dominant orders with a relative abundance of 28.23-37.89%. The hydrogen ion concentration (pH) and available phosphorus (AP) were the key factors affecting the structure and diversity of the bacterial community. The yield of continuous cropping lily with using similar treatments decreased yearly for the leaf blight, but that of IE was significantly (p < 0.05) higher than with the other treatments in the same year, which were 17.9%, 18.54%, and 15.69% higher than that of blank control (CK) over 3 years. In addition, IE significantly (p < 0.05) increased organic matter (OM), available nitrogen (AN), AP, and available potassium (AK) content in the lily rhizosphere soil, optimized the structure and diversity of the rhizosphere bacterial community, and increased the abundance of several beneficial bacterial taxa, including Rhizobiales, Myxococcales, Streptomycetales and Pseudomonadales. Therefore, enriching the number of earthworms in fields could effectively optimize the bacterial community structure of the lily rhizosphere soil, promote the circulation and release in soil nutrients and consequently alleviate the loss of continuous cropping lily yield.
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Barraza A, Montes-Sánchez JJ, Caamal-Chan MG, Loera-Muro A. Characterization of microbial communities from rumen and large intestine of lactating creole goats grazing in arid plant communities. MICROBIOLOGY-SGM 2021; 167. [PMID: 34661515 DOI: 10.1099/mic.0.001092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Arid plant communities provide variable diets that can affect digestive microbial communities of free-foraging ruminants. Thus, we used next-generation sequencing of 16S and 18S rDNA to characterize microbial communities in the rumen (regurgitated digesta) and large intestine (faeces) and diet composition of lactating creole goats from five flocks grazing in native plant communities in the Sonoran Desert in the rainy season. The bacterial communities in the rumen and large intestine of the five flocks had similar alpha diversity (Chao1, Shannon, and Simpson indices). However, bacterial community compositions were different: a bacterial community dominated by Proteobacteria in the rumen transitioned to a community dominated by Firmicutes in the large intestine. Bacterial communities of rumen were similar across flocks; similarly occurred with large-intestine communities. Archaea had a minimum presence in the goat digestive tract. We detected phylum Basidiomycota, Ascomycota, and Apicomplexa as the main fungi and protozoa. Analyses suggested different diet compositions; forbs and grasses composed the bulk of plants in the rumen and forbs and shrubs in faeces. Therefore, lactating goats consuming different diets in the Sonoran Desert in the rainy season share a similar core bacterial community in the rumen and another in the large intestine and present low archaeal communities.
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Affiliation(s)
- Aarón Barraza
- CONACYT-Centro de Investigaciones Biológicas del Noroeste, SC. La Paz, BCS, 23096, Mexico
| | - Juan J Montes-Sánchez
- CONACYT-Centro de Investigaciones Biológicas del Noroeste, SC. Guerrero Negro, BCS, 23940, Mexico
| | - M Goretty Caamal-Chan
- CONACYT-Centro de Investigaciones Biológicas del Noroeste, SC. La Paz, BCS, 23096, Mexico
| | - Abraham Loera-Muro
- CONACYT-Centro de Investigaciones Biológicas del Noroeste, SC. La Paz, BCS, 23096, Mexico
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Risueño Y, Petri C, Conesa HM. A critical assessment on the short-term response of microbial relative composition in a mine tailings soil amended with biochar and manure compost. JOURNAL OF HAZARDOUS MATERIALS 2021; 417:126080. [PMID: 33992925 DOI: 10.1016/j.jhazmat.2021.126080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/19/2021] [Accepted: 05/05/2021] [Indexed: 06/12/2023]
Abstract
Phytomanagement of tailings requires the use of soil conditioners to favour plant establishment, but their benefits on soil microbial composition need to be assessed. The goal of this work was to evaluate the effect of two organic amendments, manure compost and biochar, on soil bacterial and fungal composition at metallic mine tailings. The addition of compost caused stronger effects in most of soil parameters and microbial composition than biochar, especially at the initial stage of the experiment. However, the higher dependence on labile organic carbon for some bacterial groups at the treatments containing compost determined their decay along time (Flavobacteriales, Sphingobacteriales) and the appearance of other taxa more dependent on recalcitrant organic matter (Xanthomonadales, Myxococcales). Biochar favoured bacterial decomposers (Actinomycetales) specialised in high lignin and other recalcitrant carbon compounds. Unlike bacteria, only a few fungal orders increased their relative abundances in the treatments containing compost (Sordariales and Microascales) while the rest showed a decrease or remained unaltered. The mix biochar-compost may result the best option to support a more diverse microbial population in terms of soil functionality that is able to decompose both labile and recalcitrant carbon compounds. This may favour the resilience of the system against environmental stressors.
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Affiliation(s)
- Yolanda Risueño
- Universidad Politécnica de Cartagena, Escuela Técnica Superior de Ingeniería Agronómica, Departamento de Ingeniería Agronómica, Paseo Alfonso XIII, 48, 30203 Cartagena, Spain.
| | - César Petri
- IHSM-UMA-CSIC La Mayora, Departamento de Fruticultura Subtropical y Mediterránea, Avenida Dr. Wienberg, s/n, 29750 Algarrobo-Costa, Málaga, Spain.
| | - Héctor M Conesa
- Universidad Politécnica de Cartagena, Escuela Técnica Superior de Ingeniería Agronómica, Departamento de Ingeniería Agronómica, Paseo Alfonso XIII, 48, 30203 Cartagena, Spain.
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Metagenomic Exploration of Bacterial Community Structure of Earthworms’ Gut. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.3.05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Living organisms are naturally bestowed with unique and imitable qualities for maintaining ecological balance and earthworms are no exceptions. These so-called keystone species of terrestrial ecosystems are equipped with wonderful machinery, allowing them to nurture soil beautifully. Earthworm gut represents a potential microbial reservoir, having a complex interdependence with the host. The study aimed to profile bacterial community structure of three earthworm species belonging to two different life forms; Perionyx excavatus and Eudrilus eugeniae (epigeic), Polypheretima elongata (endogeic) respectively. Diversity analysis using 16S amplicon sequencing revealed that the dominant phyla were Proteobacteria (34.17-77.88) followed by Actinobacteria (13.43-35.54%), Firmicutes (1.69-15.45%) and Bacteroidetes (0.51-8.12%). The alpha diversity indices explicit similar gut microbiota of Perionyx excavatus and Eudrilus eugeniae and while higher alpha diversity was recorded in comparison to Polypheretima elongata gut. The taxonomic to the phenotypic annotation of 16S rRNA metagenomes revealed that dominance of Gram-negative bacterial community in all earthworm species while, Polypheretima elongata comprises higher percentage (78%) of Gram-negative bacterial community to Perionyx excavatus (32.3%) and Eudrilus eugeniae (38.3%). The oxygen requirement phenotypic analysis showed that all earthworm species were abundant with aerobic followed by anaerobic bacterial groups. Furthermore, functional metabolism phenotypic analysis revealed that a high abundance of ammonia oxidizers (29.3-80.2%), the gut microbiomes showed the relative abundance of sulphate reducer (22.6-78.7%), nitrite reducer (19.8-73.2%), dehalogenators (12.6-25.1%), illustrating in the role of these microbial communities in various degradation and bioremediation processes. The present study signifies the intrinsic gut microbiota of earthworm species for intensified biodegradation.
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Mushroom Ligninolytic Enzymes―Features and Application of Potential Enzymes for Conversion of Lignin into Bio-Based Chemicals and Materials. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11136161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mushroom ligninolytic enzymes are attractive biocatalysts that can degrade lignin through oxido-reduction. Laccase, lignin peroxidase, manganese peroxidase, and versatile peroxidase are the main enzymes that depolymerize highly complex lignin structures containing aromatic or aliphatic moieties and oxidize the subunits of monolignol associated with oxidizing agents. Among these enzymes, mushroom laccases are secreted glycoproteins, belonging to a polyphenol oxidase family, which have a powerful oxidizing capability that catalyzes the modification of lignin using synthetic or natural mediators by radical mechanisms via lignin bond cleavage. The high redox potential laccase within mediators can catalyze the oxidation of a wide range of substrates and the polymerization of lignin derivatives for value-added chemicals and materials. The chemoenzymatic process using mushroom laccases has been applied effectively for lignin utilization and the degradation of recalcitrant chemicals as an eco-friendly technology. Laccase-mediated grafting has also been employed to modify lignin and other polymers to obtain novel functional groups able to conjugate small and macro-biomolecules. In this review, the biochemical features of mushroom ligninolytic enzymes and their potential applications in catalytic reactions involving lignin and its derivatives to obtain value-added chemicals and novel materials in lignin valorization are discussed.
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Zhang W, Ren X, Lei Q, Wang L. Screening and Comparison of Lignin Degradation Microbial Consortia from Wooden Antiques. Molecules 2021; 26:molecules26102862. [PMID: 34066118 PMCID: PMC8151908 DOI: 10.3390/molecules26102862] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 11/16/2022] Open
Abstract
Lignin, which is a component of wood, is difficult to degrade in nature. However, serious decay caused by microbial consortia can happen to wooden antiques during the preservation process. This study successfully screened four microbial consortia with lignin degradation capabilities (J-1, J-6, J-8 and J-15) from decayed wooden antiques. Their compositions were identified by genomic sequencing, while the degradation products were analyzed by GC-MS. The lignin degradation efficiency of J-6 reached 54% after 48 h with an initial lignin concentration of 0.5 g/L at pH 4 and rotation speed of 200 rpm. The fungal consortium of J-6 contained Saccharomycetales (98.92%) and Ascomycota (0.56%), which accounted for 31% of the total biomass. The main bacteria in J-6 were Shinella sp. (47.38%), Cupriavidus sp. (29.84%), and Bosea sp. (7.96%). The strongest degradation performance of J-6 corresponded to its composition, where Saccharomycetales likely adapted to the system and improved lignin degradation enzymes activities, and the abundant bacterial consortium accelerated lignin decomposition. Our work demonstrated the potential utilization of microbial consortia via the synergy of microbial consortia, which may overcome the shortcomings of traditional lignin biodegradation when using a single strain, and the potential use of J-6 for lignin degradation/removal applications.
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Affiliation(s)
- Wen Zhang
- School of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310015, China
- Correspondence: (W.Z.); (L.W.); Tel./Fax: +86-0571-88297098 (W.Z.); +86-0571-85278909 (L.W.)
| | - Xueyan Ren
- School of Engineering, Westlake University, Hangzhou 310024, China;
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Qiong Lei
- Jingzhou Conservation Center of Hubei Province, Wood Lacquer Protection Research Department, Jingzhou 434020, China;
| | - Lei Wang
- School of Engineering, Westlake University, Hangzhou 310024, China;
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou 310024, China
- Correspondence: (W.Z.); (L.W.); Tel./Fax: +86-0571-88297098 (W.Z.); +86-0571-85278909 (L.W.)
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A Novel Gene Cluster Is Involved in the Degradation of Lignin-Derived Monoaromatics in Thermus oshimai JL-2. Appl Environ Microbiol 2021; 87:AEM.01589-20. [PMID: 33741620 DOI: 10.1128/aem.01589-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 03/09/2021] [Indexed: 11/20/2022] Open
Abstract
A novel gene cluster involved in the degradation of lignin-derived monoaromatics such as p-hydroxybenzoate, vanillate, and ferulate has been identified in the thermophilic nitrate reducer Thermus oshimai JL-2. Based on conserved domain analyses and metabolic pathway mapping, the cluster was classified into upper- and peripheral-pathway operons. The upper-pathway genes, responsible for the degradation of p-hydroxybenzoate and vanillate, are located on a 0.27-Mb plasmid, whereas the peripheral-pathway genes, responsible for the transformation of ferulate, are spread throughout the plasmid and the chromosome. In addition, a lower-pathway operon was also identified in the plasmid that corresponds to the meta-cleavage pathway of catechol. Spectrophotometric and gene induction data suggest that the upper and lower operons are induced by p-hydroxybenzoate, which the strain can degrade completely within 4 days of incubation, whereas the peripheral genes are expressed constitutively. The upper degradation pathway follows a less common route, proceeding via the decarboxylation of protocatechuate to form catechol, and involves a novel thermostable γ-carboxymuconolactone decarboxylase homolog, identified as protocatechuate decarboxylase based on gene deletion experiments. This gene cluster is conserved in only a few members of the Thermales and shows traces of vertical expansion of catabolic pathways in these organisms toward lignoaromatics.IMPORTANCE High-temperature steam treatment of lignocellulosic biomass during the extraction of cellulose and hemicellulose fractions leads to the release of a wide array of lignin-derived aromatics into the natural ecosystem, some of which can have detrimental effects on the environment. Not only will identifying organisms capable of using such aromatics aid in environmental cleanup, but thermostable enzymes, if characterized, can also be used for efficient lignin valorization. However, no thermophilic lignin degraders have been reported thus far. The present study reports T. oshimai JL-2 as a thermophilic bacterium with the potential to use lignin-derived aromatics. The identification of a novel thermostable protocatechuate decarboxylase gene in the strain further adds to its significance, as such an enzyme can be efficiently used in the biosynthesis of cis,cis-muconate, an important intermediate in the commercial production of plastics.
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Margesin R, Volgger G, Wagner AO, Zhang D, Poyntner C. Biodegradation of lignin monomers and bioconversion of ferulic acid to vanillic acid by Paraburkholderia aromaticivorans AR20-38 isolated from Alpine forest soil. Appl Microbiol Biotechnol 2021; 105:2967-2977. [PMID: 33687503 PMCID: PMC8007519 DOI: 10.1007/s00253-021-11215-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/10/2021] [Accepted: 02/28/2021] [Indexed: 11/24/2022]
Abstract
Abstract Lignin bio-valorization is an emerging field of applied biotechnology and has not yet been studied at low temperatures. Paraburkholderia aromaticivorans AR20-38 was examined for its potential to degrade six selected lignin monomers (syringic acid, p-coumaric acid, 4-hydroxybenzoic acid, ferulic acid, vanillic acid, benzoic acid) from different upper funneling aromatic pathways. The strain degraded four of these compounds at 10°C, 20°C, and 30°C; syringic acid and vanillic acid were not utilized as sole carbon source. The degradation of 5 mM and 10 mM ferulic acid was accompanied by the stable accumulation of high amounts of the value-added product vanillic acid (85–89% molar yield; 760 and 1540 mg l−1, respectively) over the whole temperature range tested. The presence of essential genes required for reactions in the upper funneling pathways was confirmed in the genome. This is the first report on biodegradation of lignin monomers and the stable vanillic acid production at low and moderate temperatures by P. aromaticivorans. Key points • Paraburkholderia aromaticivorans AR20-38 successfully degrades four lignin monomers. • Successful degradation study at low (10°C) and moderate temperatures (20–30°C). • Biotechnological value: high yield of vanillic acid produced from ferulic acid.
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Affiliation(s)
- Rosa Margesin
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria.
| | - Georg Volgger
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Andreas O Wagner
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Dechao Zhang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Caroline Poyntner
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
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Identifying metabolic pathway intermediates that modulate the gallate dioxygenase (DesB) from Sphingobium sp. strain SYK-6. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.01.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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dos Santos Melo-Nascimento AO, Mota Moitinho Sant´Anna B, Gonçalves CC, Santos G, Noronha E, Parachin N, de Abreu Roque MR, Bruce T. Complete genome reveals genetic repertoire and potential metabolic strategies involved in lignin degradation by environmental ligninolytic Klebsiella variicola P1CD1. PLoS One 2020; 15:e0243739. [PMID: 33351813 PMCID: PMC7755216 DOI: 10.1371/journal.pone.0243739] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/30/2020] [Indexed: 11/23/2022] Open
Abstract
Lignin is a recalcitrant macromolecule formed by three alcohols (monolignols) predominantly connected by β-aryl ether linkages and is one of the most abundant organic macromolecules in the biosphere. However, the role played by environmental bacteria in lignin degradation is still not entirely understood. In this study, we identified an environmental Klebsiella strain isolated from sediment collected from an altitudinal region in a unique Brazilian biome called Caatinga. This organism can also grow in the presence of kraft lignin as a sole source of carbon and aromatic compounds. We performed whole-genome sequencing and conducted an extensive genome-based metabolic reconstruction to reveal the potential mechanisms used by the bacterium Klebsiella variicola P1CD1 for lignin utilization as a carbon source. We identified 262 genes associated with lignin-modifying enzymes (LMEs) and lignin-degrading auxiliary enzymes (LDAs) required for lignin and aromatic compound degradation. The presence of one DyP (Dye-decolorizing Peroxidase) gene suggests the ability of P1CD1 strain to access phenolic and nonphenolic structures of lignin molecules, resulting in the production of catechol and protocatechuate (via vanillin or syringate) along the peripheral pathways of lignin degradation. K. variicola P1CD1 uses aldehyde-alcohol dehydrogenase to perform direct conversion of vanillin to protocatechol. The upper funneling pathways are linked to the central pathways of the protocatechuate/catechol catabolic branches via β-ketoadipate pathways, connecting the more abundant catabolized aromatic compounds with essential cellular functions, such as energy cellular and biomass production (i.e., via acetyl-CoA formation). The combination of phenotypic and genomic approaches revealed the potential dissimilatory and assimilatory ability of K. variicola P1CD1 to perform base-catalyzed lignin degradation, acting on high- and low-molecular-weight lignin fragments. These findings will be relevant for developing metabolic models to predict the ligninolytic mechanism used by environmental bacteria and shedding light on the flux of carbon in the soil.
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Affiliation(s)
| | | | - Carolyne Caetano Gonçalves
- Departamento de Biologia Celular, Instituto de Biologia, Laboratório de Engenharia de Biocatalizadores, Universidade de Brasília, Brasília, Brazil
| | - Giovanna Santos
- Departamento de Biologia Celular, Instituto de Biologia, Laboratório de Engenharia de Biocatalizadores, Universidade de Brasília, Brasília, Brazil
| | - Eliane Noronha
- Departamento de Biologia Celular, Instituto de Biologia, Laboratório de Engenharia de Biocatalizadores, Universidade de Brasília, Brasília, Brazil
| | - Nádia Parachin
- Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília, Brazil
| | - Milton Ricardo de Abreu Roque
- Departamento de Microbiologia, Instituto de Biologia, Grupo de Biotecnologia Ambiental, Universidade Federal da Bahia, Salvador, Brazil
- Instituto de Ciências da Saúde, Laboratório de Bioprospecção, Universidade Federal da Bahia, Salvador, Brazil
| | - Thiago Bruce
- Departamento de Microbiologia, Instituto de Biologia, Grupo de Biotecnologia Ambiental, Universidade Federal da Bahia, Salvador, Brazil
- Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília, Brazil
- * E-mail:
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Deckmyn G, Flores O, Mayer M, Domene X, Schnepf A, Kuka K, Van Looy K, Rasse DP, Briones MJ, Barot S, Berg M, Vanguelova E, Ostonen I, Vereecken H, Suz LM, Frey B, Frossard A, Tiunov A, Frouz J, Grebenc T, Öpik M, Javaux M, Uvarov A, Vindušková O, Henning Krogh P, Franklin O, Jiménez J, Curiel Yuste J. KEYLINK: towards a more integrative soil representation for inclusion in ecosystem scale models. I. review and model concept. PeerJ 2020; 8:e9750. [PMID: 32974092 PMCID: PMC7486829 DOI: 10.7717/peerj.9750] [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: 02/11/2020] [Accepted: 07/27/2020] [Indexed: 11/20/2022] Open
Abstract
The relatively poor simulation of the below-ground processes is a severe drawback for many ecosystem models, especially when predicting responses to climate change and management. For a meaningful estimation of ecosystem production and the cycling of water, energy, nutrients and carbon, the integration of soil processes and the exchanges at the surface is crucial. It is increasingly recognized that soil biota play an important role in soil organic carbon and nutrient cycling, shaping soil structure and hydrological properties through their activity, and in water and nutrient uptake by plants through mycorrhizal processes. In this article, we review the main soil biological actors (microbiota, fauna and roots) and their effects on soil functioning. We review to what extent they have been included in soil models and propose which of them could be included in ecosystem models. We show that the model representation of the soil food web, the impact of soil ecosystem engineers on soil structure and the related effects on hydrology and soil organic matter (SOM) stabilization are key issues in improving ecosystem-scale soil representation in models. Finally, we describe a new core model concept (KEYLINK) that integrates insights from SOM models, structural models and food web models to simulate the living soil at an ecosystem scale.
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Affiliation(s)
- Gaby Deckmyn
- Department of Biology, Plants and Ecosystems (PLECO), Universiteit Antwerpen, Antwerpen, Belgium
| | - Omar Flores
- Department of Biology, Plants and Ecosystems (PLECO), Universiteit Antwerpen, Antwerpen, Belgium
- Biogeography and Global Change, National Museum of Natural Sciences-Spanish National Research Council (MNCN-CSIC), Madrid, Spain
| | - Mathias Mayer
- Institute of Forest Ecology, Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- Biogeochemistry Group, Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Xavier Domene
- CREAF, Cerdanyola del Vallès, Spain
- Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Andrea Schnepf
- Agrosphere Institute, IBG, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Katrin Kuka
- Institute for Crop and Soil Science, Julius Kühn-Institut (JKI), Braunschwei, Germany
| | - Kris Van Looy
- OVAM, Flemish Institute for Materials and Soils, Mechelen, Belgium
| | - Daniel P. Rasse
- Department of Biogeochemistry and Soil Quality, Norwegian Institute of Bioeconomy Research (NIBIO), Aas, Norway
| | - Maria J.I. Briones
- Departamento de Ecología y Biología Animal, Universidad de Vigo, Vigo, Spain
| | - Sébastien Barot
- Institute of Ecology and Environmental Sciences, IRD, UPEC, CNRS, INRA, Sorbonne Université, Paris, France
| | - Matty Berg
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | | | - Ivika Ostonen
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Harry Vereecken
- Agrosphere Institute, IBG, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Laura M. Suz
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, London, UK
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Aline Frossard
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Alexei Tiunov
- A.N. Severtsov Institute of Ecology and Evolution RAS, Moscow, Russia
| | - Jan Frouz
- Institute for Environmental Studies, Charles University, Prague, Czech Republic
| | - Tine Grebenc
- Slovenian Forestry Institute, Ljubljana, Slovenia
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Mathieu Javaux
- Agrosphere Institute, IBG, Forschungszentrum Jülich GmbH, Jülich, Germany
- Earth and Life Institute, UCLouvain, Louvain-la-Neuve, Belgium
| | - Alexei Uvarov
- A.N. Severtsov Institute of Ecology and Evolution RAS, Moscow, Russia
| | - Olga Vindušková
- Department of Biology, Plants and Ecosystems (PLECO), Universiteit Antwerpen, Antwerpen, Belgium
| | | | - Oskar Franklin
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden
- International Institute for Applied Systems Analysis IIASA, Laxenburg, Austria
| | - Juan Jiménez
- Department of Biodiversity Conservation and Ecosystem Restoration, ARAID/IPE-CSIC, Jaca, Spain
| | - Jorge Curiel Yuste
- BC3-Basque Centre for Climate Change, Scientific Campus of the University of the Basque Country, Bilbao, Bizkaia, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
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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.
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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
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Song N, Jiang HL. Coordinated photodegradation and biodegradation of organic matter from macrophyte litter in shallow lake water: Dual role of solar irradiation. WATER RESEARCH 2020; 172:115516. [PMID: 31986394 DOI: 10.1016/j.watres.2020.115516] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/31/2019] [Accepted: 01/15/2020] [Indexed: 05/20/2023]
Abstract
Eutrophication and climate warming cause macrophytes to spread rapidly in shallow lakes. The accumulation of excess decayed litter in lake water can improve the particulate organic matter content and lead to ecological deterioration. While decomposition of macrophyte litters in aquatic ecosystems is generally assumed to be biologically driven, photodegradation has been largely overlooked. In this study, the potential contribution of photodegradation to the decomposition of organic matter from macrophyte litter in a shallow lake was investigated under two types of light radiation: laboratory incubation light and natural solar radiation. Results showed that the combined photo- and biodegradation treatment removed more litter mass compared to solely photodegradation or biodegradation for over 108 days. More reactive oxygen species (ROS) were produced during litter degradation in lake water under the combined photo- and biodegradation treatments in comparison to other treatments. Removal efficiency of litter was doubled in the presence of ROS compared when ROS were captured. Additionally, NMR analysis revealed that lignin guaiacyl units were preferentially lost and the litter became more refractory under the combined photo oxidation and microbial degradation after 108 days. High-throughput sequencing analysis further indicated that solar irradiation stimulates the growth of bacteria (Treponema and Magnetospirillum) and fungi (Aspergillus) that have the ability to degrade aromatic compounds. Altogether, both ROS and specific microorganisms played important role in promoting litter degradation in lake water under light irradiation. Therefore, the role of solar radiation in particulate organic matter decomposition needs to be considered for a more accurate prediction of carbon dynamics in aquatic ecosystems.
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Affiliation(s)
- Na Song
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, PR China
| | - He-Long Jiang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, PR China.
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40
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Vanillin Production in Pseudomonas: Whole-Genome Sequencing of Pseudomonas sp. Strain 9.1 and Reannotation of Pseudomonas putida CalA as a Vanillin Reductase. Appl Environ Microbiol 2020; 86:AEM.02442-19. [PMID: 31924622 PMCID: PMC7054097 DOI: 10.1128/aem.02442-19] [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: 10/22/2019] [Accepted: 12/21/2019] [Indexed: 02/06/2023] Open
Abstract
Microbial degradation of lignin and its related aromatic compounds has great potential for the sustainable production of chemicals and bioremediation of contaminated soils. We previously isolated Pseudomonas sp. strain 9.1 from historical waste deposits (forming so-called fiber banks) released from pulp and paper mills along the Baltic Sea coast. The strain accumulated vanillyl alcohol during growth on vanillin, and while reported in other microbes, this phenotype is less common in wild-type pseudomonads. As the reduction of vanillin to vanillyl alcohol is an undesired trait in Pseudomonas strains engineered to accumulate vanillin, connecting the strain 9.1 phenotype with a genotype would increase the fundamental understanding and genetic engineering potential of microbial vanillin metabolism. The genome of Pseudomonas sp. 9.1 was sequenced and assembled. Annotation identified oxidoreductases with homology to Saccharomyces cerevisiae alcohol dehydrogenase ScADH6p, known to reduce vanillin to vanillyl alcohol, in both the 9.1 genome and the model strain Pseudomonas putida KT2440. Recombinant expression of the Pseudomonas sp. 9.1 FEZ21_09870 and P. putida KT2440 PP_2426 (calA) genes in Escherichia coli revealed that these open reading frames encode aldehyde reductases that convert vanillin to vanillyl alcohol, and that P. putida KT2440 PP_3839 encodes a coniferyl alcohol dehydrogenase that oxidizes coniferyl alcohol to coniferyl aldehyde (i.e., the function previously assigned to calA). The deletion of PP_2426 in P. putida GN442 engineered to accumulate vanillin resulted in a decrease in by-product (vanillyl alcohol) yield from 17% to ∼1%. Based on these results, we propose the reannotation of PP_2426 and FEZ21_09870 as areA and PP_3839 as calA-II IMPORTANCE Valorization of lignocellulose (nonedible plant matter) is of key interest for the sustainable production of chemicals from renewable resources. Lignin, one of the main constituents of lignocellulose, is a heterogeneous aromatic biopolymer that can be chemically depolymerized into a heterogeneous mixture of aromatic building blocks; those can be further converted by certain microbes into value-added aromatic chemicals, e.g., the flavoring agent vanillin. We previously isolated a Pseudomonas sp. strain with the (for the genus) unusual trait of vanillyl alcohol production during growth on vanillin. Whole-genome sequencing of the isolate led to the identification of a vanillin reductase candidate gene whose deletion in a recombinant vanillin-accumulating P. putida strain almost completely alleviated the undesired vanillyl alcohol by-product yield. These results represent an important step toward biotechnological production of vanillin from lignin using bacterial cell factories.
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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.
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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.
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Cragg SM, Friess DA, Gillis LG, Trevathan-Tackett SM, Terrett OM, Watts JEM, Distel DL, Dupree P. Vascular Plants Are Globally Significant Contributors to Marine Carbon Fluxes and Sinks. ANNUAL REVIEW OF MARINE SCIENCE 2020; 12:469-497. [PMID: 31505131 DOI: 10.1146/annurev-marine-010318-095333] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
More than two-thirds of global biomass consists of vascular plants. A portion of the detritus they generate is carried into the oceans from land and highly productive blue carbon ecosystems-salt marshes, mangrove forests, and seagrass meadows. This large detrital input receives scant attention in current models of the global carbon cycle, though for blue carbon ecosystems, increasingly well-constrained estimates of biomass, productivity, and carbon fluxes, reviewed in this article, are now available. We show that the fate of this detritus differs markedly from that of strictly marine origin, because the former contains lignocellulose-an energy-rich polymer complex of cellulose, hemicelluloses, and lignin that is resistant to enzymatic breakdown. This complex can be depolymerized for nutritional purposes by specialized marine prokaryotes, fungi, protists, and invertebrates using enzymes such as glycoside hydrolases and lytic polysaccharide monooxygenases to release sugar monomers. The lignin component, however, is less readily depolymerized, and detritus therefore becomes lignin enriched, particularly in anoxic sediments, and forms a major carbon sink in blue carbon ecosystems. Eventual lignin breakdown releases a wide variety of small molecules that may contribute significantly to the oceanic pool of recalcitrant dissolved organic carbon. Marine carbon fluxes and sinks dependent on lignocellulosic detritus are important ecosystem services that are vulnerable to human interventions. These services must be considered when protecting blue carbon ecosystems and planning initiatives aimed at mitigating anthropogenic carbon emissions.
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Affiliation(s)
- Simon M Cragg
- Institute of Marine Sciences, University of Portsmouth, Portsmouth PO4 9LY, United Kingdom;
| | - Daniel A Friess
- Department of Geography, National University of Singapore, Singapore 117570;
| | - Lucy G Gillis
- Leibniz-Zentrum für Marine Tropenforschung (ZMT), 28359 Bremen, Germany;
| | - Stacey M Trevathan-Tackett
- Centre for Integrative Ecology, School of Life and Environmental Science, Deakin University, Burwood, Victoria 3125, Australia;
| | - Oliver M Terrett
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom; ,
| | - Joy E M Watts
- School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom;
| | - Daniel L Distel
- Ocean Genome Legacy Center of New England Biolabs, Marine Science Center, Northeastern University, Nahant, Massachusetts 01908, USA;
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom; ,
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López-Mondéjar R, Algora C, Baldrian P. Lignocellulolytic systems of soil bacteria: A vast and diverse toolbox for biotechnological conversion processes. Biotechnol Adv 2019; 37:107374. [DOI: 10.1016/j.biotechadv.2019.03.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/06/2019] [Accepted: 03/21/2019] [Indexed: 12/12/2022]
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Li C, Chen C, Wu X, Tsang CW, Mou J, Yan J, Liu Y, Lin CSK. Recent advancement in lignin biorefinery: With special focus on enzymatic degradation and valorization. BIORESOURCE TECHNOLOGY 2019; 291:121898. [PMID: 31395402 DOI: 10.1016/j.biortech.2019.121898] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 05/07/2023]
Abstract
With the intensive development of lignocellulosic biorefineries to produce fuels and chemicals from biomass-derived carbohydrates, lignin was generated at a large quantity every year. Therefore, lignin has received increasing attention as an abundant aromatics resource in terms of research and development efforts for value-added chemicals production. In this review, studies about lignin degradation especially the crucial enzymes involved and the reaction mechanism were substantially discussed, which provided the molecular basis of lignin biodegradation. Then, the latest improvements in lignin valorization by biological methods were summarized and case studies about value-added compounds from lignin were introduced. Afterwards, challenges, opportunities and prospects regarding biorefinery of lignin were presented.
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Affiliation(s)
- Chong Li
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, People's Republic of China
| | - Chao Chen
- BioZone, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - Xiaofen Wu
- Hunan Institute of Nuclear Agricultural Science and Space Breeding, Hunan Academy of Agricultural Sciences, Changsha, Hunan 410125, People's Republic of China
| | - Chi-Wing Tsang
- Faculty of Science and Technology, Technological and Higher Education Institute of Hong Kong, Hong Kong, China
| | - Jinhua Mou
- School of Energy and Environment, City University of Hong Kong, Hong Kong
| | - Jianbin Yan
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, People's Republic of China
| | - Yun Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Hong Kong.
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Prasad RK, Chatterjee S, Mazumder PB, Gupta SK, Sharma S, Vairale MG, Datta S, Dwivedi SK, Gupta DK. Bioethanol production from waste lignocelluloses: A review on microbial degradation potential. CHEMOSPHERE 2019; 231:588-606. [PMID: 31154237 DOI: 10.1016/j.chemosphere.2019.05.142] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 04/02/2019] [Accepted: 05/17/2019] [Indexed: 05/15/2023]
Abstract
Tremendous explosion of population has led to about 200% increment of total energy consumptions in last twenty-five years. Apart from conventional fossil fuel as limited energy source, alternative non-conventional sources are being explored worldwide to cater the energy requirement. Lignocellulosic biomass conversion for biofuel production is an important alternative energy source due to its abundance in nature and creating less harmful impacts on the environment in comparison to the coal or petroleum-based sources. However, lignocellulose biopolymer, the building block of plants, is a recalcitrant substance and difficult to break into desirable products. Commonly used chemical and physical methods for pretreating the substrate are having several limitations. Whereas, utilizing microbial potential to hydrolyse the biomass is an interesting area of research. Because of the complexity of substrate, several enzymes are required that can act synergistically to hydrolyse the biopolymer producing components like bioethanol or other energy substances. Exploring a range of microorganisms, like bacteria, fungi, yeast etc. that utilizes lignocelluloses for their energy through enzymatic breaking down the biomass, is one of the options. Scientists are working upon designing organisms through genetic engineering tools to integrate desired enzymes into a single organism (like bacterial cell). Studies on designer cellulosomes and bacteria consortia development relating consolidated bioprocessing are exciting to overcome the issue of appropriate lignocellulose digestions. This review encompasses up to date information on recent developments for effective microbial degradation processes of lignocelluloses for improved utilization to produce biofuel (bioethanol in particular) from the most plentiful substances of our planet.
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Affiliation(s)
- Rajesh Kumar Prasad
- Defence Research Laboratory, DRDO, Tezpur, 784001, Assam, India; Assam University, Silchar, 788011, Assam, India
| | | | | | | | - Sonika Sharma
- Defence Research Laboratory, DRDO, Tezpur, 784001, Assam, India
| | | | | | | | - Dharmendra Kumar Gupta
- Gottfried Wilhelm Leibniz Universität Hannover, Institut für Radioökologie und Strahlenschutz (IRS), HerrenhäuserStr. 2, 30419, Hannover, Germany
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Herzog C, Hartmann M, Frey B, Stierli B, Rumpel C, Buchmann N, Brunner I. Microbial succession on decomposing root litter in a drought-prone Scots pine forest. ISME JOURNAL 2019; 13:2346-2362. [PMID: 31123321 PMCID: PMC6776048 DOI: 10.1038/s41396-019-0436-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 04/16/2019] [Accepted: 05/03/2019] [Indexed: 12/21/2022]
Abstract
Decomposition is a major flux of the carbon cycle in forest soils and understanding the involved processes is a key for budgeting carbon turnover. Decomposition is constrained by the presence of biological agents such as microorganisms and the underlying environmental conditions such as water availability. A metabarcoding approach of ribosomal markers was chosen to study the succession of bacterial and fungal decomposers on root litter. Litterbags containing pine roots were buried in a pine forest for two years and sequentially sampled. Decomposition and the associated communities were surveyed under ambient dry and long-term irrigation conditions. Early decomposition stages were characterized by the presence of fast-cycling microorganisms such as Bacteroidetes and Helotiales, which were then replaced by more specialized bacteria and litter-associated or parasitic groups such as Acidobacteria, white rots, and Pleosporales. This succession was likely driven by a decrease of easily degradable carbohydrates and a relative increase in persistent compounds such as lignin. We hypothesize that functional redundancy among the resident microbial taxa caused similar root decomposition rates in control and irrigated forest soils. These findings have important implications for drought-prone Alpine forests as frequent drought events reduce litter fall, but not litter decomposition, potentially resulting in lower carbon stocks.
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Affiliation(s)
- Claude Herzog
- Swiss Federal Research Institute WSL, CH-8903, Birmensdorf, Switzerland.,ETH Zürich, CH-8092, Zürich, Switzerland
| | - Martin Hartmann
- Swiss Federal Research Institute WSL, CH-8903, Birmensdorf, Switzerland.,ETH Zürich, CH-8092, Zürich, Switzerland
| | - Beat Frey
- Swiss Federal Research Institute WSL, CH-8903, Birmensdorf, Switzerland
| | - Beat Stierli
- Swiss Federal Research Institute WSL, CH-8903, Birmensdorf, Switzerland
| | - Cornelia Rumpel
- Centre Nationale de Recherche Scientifique (CNRS), Institute of Ecology and Environment (IEES), Thiverval-Grignon, 78850, France
| | | | - Ivano Brunner
- Swiss Federal Research Institute WSL, CH-8903, Birmensdorf, Switzerland.
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47
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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.
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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
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48
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Piché-Choquette S, Constant P. Molecular Hydrogen, a Neglected Key Driver of Soil Biogeochemical Processes. Appl Environ Microbiol 2019; 85:e02418-18. [PMID: 30658976 PMCID: PMC6414374 DOI: 10.1128/aem.02418-18] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The atmosphere of the early Earth is hypothesized to have been rich in reducing gases such as hydrogen (H2). H2 has been proposed as the first electron donor leading to ATP synthesis due to its ubiquity throughout the biosphere as well as its ability to easily diffuse through microbial cells and its low activation energy requirement. Even today, hydrogenase enzymes enabling the production and oxidation of H2 are found in thousands of genomes spanning the three domains of life across aquatic, terrestrial, and even host-associated ecosystems. Even though H2 has already been proposed as a universal growth and maintenance energy source, its potential contribution as a driver of biogeochemical cycles has received little attention. Here, we bridge this knowledge gap by providing an overview of the classification, distribution, and physiological role of hydrogenases. Distribution of these enzymes in various microbial functional groups and recent experimental evidence are finally integrated to support the hypothesis that H2-oxidizing microbes are keystone species driving C cycling along O2 concentration gradients found in H2-rich soil ecosystems. In conclusion, we suggest focusing on the metabolic flexibility of H2-oxidizing microbes by combining community-level and individual-level approaches aiming to decipher the impact of H2 on C cycling and the C-cycling potential of H2-oxidizing microbes, via both culture-dependent and culture-independent methods, to give us more insight into the role of H2 as a driver of biogeochemical processes.
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49
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Zhang L, Ding L, He X, Ma H, Fu H, Wang J, Ren H. Effect of continuous and intermittent electric current on lignin wastewater treatment and microbial community structure in electro-microbial system. Sci Rep 2019; 9:805. [PMID: 30692563 PMCID: PMC6349836 DOI: 10.1038/s41598-018-34379-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 10/11/2018] [Indexed: 12/17/2022] Open
Abstract
In this study, complex structured soluble lignin wastewater was treated by electro-microbial system (EMS) using different direct current (DC) application modes (CR (continuous ON), IR12h (12 h-ON/12 h-OFF) and IR2h (2 h-ON/2 h-OFF)), and physiological characteristics and microbial communities were investigated. Results showed that CR, IR12h and IR2h had higher lignin removals, which were almost two times that of the control reactor (R0′, no current), and IR2h performed best and stably. Furthermore, IR2h exhibited the lowest ohmic resistance (Rs) of electrode biofilms, which could be explained by its higher abundance of electroactive bacteria. In the activated sludge of EMS, the concentration of dehydrogenase activity (DHA) and electronic transport system (ETS) in IR2h were the highest (1.48 and 1.28 times of R0′), which contributed to its high content of adenosine triphosphate (ATP). The viability of activated sludge was not affected by different DC application modes. Phospholipid fatty acids (PLFA) analysis indicated that IR2h had the maximum content of C15:1 anteiso A, C16:0 and C18:0; CR increased the content of C15:0 anteiso and decreased the content of saturated fatty acids. Genus-level results revealed that lignin-degrading bacteria, Pseudoxanthomonas and Mycobacterium, could be enriched in IR2h and CR, respectively.
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Affiliation(s)
- Lulu Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, Jiangsu, PR China
| | - Lili Ding
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, Jiangsu, PR China
| | - Xuemeng He
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, Jiangsu, PR China
| | - Haijun Ma
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, Jiangsu, PR China
| | - Huimin Fu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, Jiangsu, PR China
| | - Jinfeng Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, Jiangsu, PR China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, Jiangsu, PR China.
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50
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Liu D, Yan X, Si M, Deng X, Min X, Shi Y, Chai L. Bioconversion of lignin into bioplastics by Pandoraea sp. B-6: molecular mechanism. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:2761-2770. [PMID: 30484053 DOI: 10.1007/s11356-018-3785-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 11/15/2018] [Indexed: 06/09/2023]
Abstract
Lignin is a byproduct in the pulp and paper industry and is considered as a promising alternative for the provision of energy and chemicals. Currently, the efficient valorization of lignin is a challenge owing to its polymeric structure complexity. Here, we present a platform for bio-converting Kraft lignin (KL), to polyhydroxyalkanoate (PHA) by Pandoraea sp. B-6 (hereafter B-6). Depolymerization of KL by B-6 was first confirmed, and > 40% KL was degraded by B-6 in the initial 4 days. Characterization of PHA showed that up to 24.7% of PHA accumulated in B-6 grown in 6-g/L KL mineral medium. The composition, structure, and thermal properties of the produced PHA were analyzed, revealing that 3-hydroxybutyrate was the only monomer and that PHA was comparable with the commercially available bioplastics. Moreover, the genomic analysis illustrated three core enzymatic systems for lignin depolymerization including laccases, peroxidases, and Fenton-reaction enzymes; five catabolic pathways for LDAC degradation and a gene cluster consisting of bktB, phaR, phaB, phaA, and phaC genes involved in PHA biosynthesis. Accordingly, a basic model for the process from lignin depolymerization to PHA production was constructed. Our findings provide a comprehensive perspective for lignin valorization and bio-material production from waste.
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Affiliation(s)
- Dan Liu
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, Changsha, 410083, China
| | - Xu Yan
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, Changsha, 410083, China
- Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, Changsha, 410083, China
| | - Mengying Si
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, Changsha, 410083, China
| | - Xinhui Deng
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, Changsha, 410083, China
| | - Xiaobo Min
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, Changsha, 410083, China
- Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, Changsha, 410083, China
| | - Yan Shi
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, Changsha, 410083, China.
- Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, Changsha, 410083, China.
| | - Liyuan Chai
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, Changsha, 410083, China.
- Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, Changsha, 410083, China.
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