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Halmi MFA, Simarani K. Response of soil microbial glycoside hydrolase family 6 cellulolytic population to lignocellulosic biochar reveals biochar stability toward microbial degradation. JOURNAL OF ENVIRONMENTAL QUALITY 2024; 53:546-551. [PMID: 38840421 DOI: 10.1002/jeq2.20588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 04/15/2024] [Indexed: 06/07/2024]
Abstract
Biochar produced from lignocellulosic biomass offers an opportunity to recycle waste into a valuable soil amendment. The application of biochar has been proposed to mitigate climate change by sequestering carbon in the soil. However, the field impact of biochar treatment on the cellulolytic microbial populations involved in the earlier steps of cellulose degradation is poorly understood. A field trial spanning three consecutive crop cycles of Zea mays was conducted in a degraded tropical Ultisol of Peninsular Malaysia. The soil was amended with two contrasting biochar made from oil palm kernel shells (pyrolyzed at 400°C) and rice husks (gasified at 800°C) with or without fertilizer supplementation. Soil samples were taken at each harvesting stage and analyzed for total organic carbon, labile active organic carbon, total cellulase, and β-glucosidase. Microbial glycoside hydrolase family 6 (GH6) cellulase genes and transcripts, involved in the early steps of cellulose degradation, were quantified from the extracted soil deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), respectively. Total organic carbon, labile active organic carbon, and β-glucosidase activity were significantly increased, while no effect on total cellulase activity was found. Both biochars stimulated the total population (DNA-derived) abundance of soil microorganisms harboring the GH6 cellulase genes. The biochar amendment did not affect the active population (RNA-derived) of the GH6 cellulolytic community, showing no significant changes in transcript expression. This indirectly corroborates the role of biochar as a potential carbon sequester in the soil.
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Affiliation(s)
- Muhammad Farid Azlan Halmi
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
- Department of Chemistry Malaysia, Kota Kinabalu, Malaysia
| | - Khanom Simarani
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
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He Z, Ding B, Ali Q, Liu H, Zhao Y, Wang X, Han Y, Dong H, Divvela PK, Juan Y. Screening and isolation of cold-adapted cellulose degrading bacterium: A candidate for straw degradation and De novo genome sequencing analysis. Front Microbiol 2023; 13:1098723. [PMID: 36713214 PMCID: PMC9880256 DOI: 10.3389/fmicb.2022.1098723] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/19/2022] [Indexed: 01/14/2023] Open
Abstract
Degradation of crop straw in natural environment has been a bottleneck. There has been a recent increase in the exploration of cold-adapted microorganisms as they can solve the problem of corn straw degradation under low temperatures and offer new alternatives for the sustainable development of agriculture. The study was conducted in low-temperature (10°C) and high-efficiency cellulose-degrading bacteria were screened using carboxymethyl cellulose (CMC) selection medium and subjected to genome sequencing by the third-generation Pacbio Sequl and the second-generation Illumina Novaseq platform, and their cellulase activity was detected by 3,5-dinitrosalicylic acid (DNS) method. The results showed that the low-temperature (10°C) and high-efficiency cellulose-degrading bacterium Bacillus subtilis K1 was 4,060,823 bp in genome size, containing 4,213 genes, with 3,665, 3,656, 2,755, 3,240, 1,261, 3,336 and 4,003 genes annotated in the non-redundant protein sequence database (NR), Pfam, clusters of orthologous groups of proteins (COGs), Genome Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Annotation databases, respectively. In addition, a large number of lignocellulose degradation-related genes were annotated in the genome. The cellulose activity of B. subtilis K1 was higher, exhibiting the highest activity of endo-β-glucanase (24.69 U/ml), exo-β-glucanase (1.72 U/ml) and β-glucosaccharase (1.14 U/ml). It was found that through adding cold-adapted cellulose-degrading bacteriaK1 in the corn straw composting under 6°C (ambient temperature), the average temperature of straw composting was 58.7°C, and higher 86.7% as compared to control. The HA/FA was higher 94.02% than the control and the lignocellulose degradation rate was lower 18.01-41.39% than the control. The results provide a theoretical basis for clarifying the degradation potential of cold-adapted cellulose-degrading bacteria and improving the cellulose degradation efficiency.
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Affiliation(s)
- Zhigang He
- Institute of Plant Nutrition and Environmental Resources, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Baopeng Ding
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Qurban Ali
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Huiyu Liu
- Institute of Plant Nutrition and Environmental Resources, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Ying Zhao
- Institute of Plant Nutrition and Environmental Resources, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Xiujuan Wang
- Institute of Plant Nutrition and Environmental Resources, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Yingzuo Han
- Institute of Plant Nutrition and Environmental Resources, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Huan Dong
- Institute of Plant Nutrition and Environmental Resources, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | | | - Yinghua Juan
- Institute of Plant Nutrition and Environmental Resources, Liaoning Academy of Agricultural Sciences, Shenyang, China,*Correspondence: Yinghua Juan,
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Chen Y, Zhang Y, Shi X, Xu L, Zhang L, Zhang L. The succession of GH 6 cellulase-producing microbial communities and temporal profile of GH 6 gene abundance during vermicomposting of maize stover and cow dung. BIORESOURCE TECHNOLOGY 2022; 344:126242. [PMID: 34744029 DOI: 10.1016/j.biortech.2021.126242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/23/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
Vermicomposting eco-friendly converts lignocellulosic wastes into bio-organic fertilizer. Cellulose is the most abundant carbohydrate in lignocellulose. Glycoside hydrolase family 6 (GH6) plays a key role in the early step of cellulose degradation, which is essential for stabilizing lignocellulose. This study intends to quantify the abundance of GH6 gene and to clarify the succession of GH6 cellulase-producing microbial communities during vermicomposting. 100% of maize stover (A) and maize stover and cow dung at 60:40 ratio (B) were used. The results showed that different native genera were observed in the starting materials. Cellulomonas and Cellulosimicrobium were dominant genera harboring GH6 gene. The peak relative abundance of Cellulomonas was 76% and 30% in B and A during vermicomposting phase, and the corresponding values of Cellulosimicrobium was 36% and 37%. Earthworms increased the abundance of GH6 gene, which reached 1.51E + 09 from 3.46E + 08 copies/g in B. The results partially interpreted promoting effect of earthworms.
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Affiliation(s)
- Yuxiang Chen
- College of Biological and Agricultural Engineering, Jilin University, Changchun 130022, China.
| | - Yan Zhang
- Costal Research and Extension Center, Mississippi State University, MS 39567, United States
| | - Xiong Shi
- College of Biological and Agricultural Engineering, Jilin University, Changchun 130022, China
| | - Lixin Xu
- College of Life Science, Jilin University, Changchun 130012, China
| | - Lei Zhang
- College of Biological and Agricultural Engineering, Jilin University, Changchun 130022, China
| | - Luwen Zhang
- College of Biological and Agricultural Engineering, Jilin University, Changchun 130022, China
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Hu T, Wang X, Zhen L, Gu J, Zhang K, Wang Q, Ma J, Peng H, Lei L, Zhao W. Effects of inoculating with lignocellulose-degrading consortium on cellulose-degrading genes and fungal community during co-composting of spent mushroom substrate with swine manure. BIORESOURCE TECHNOLOGY 2019; 291:121876. [PMID: 31377509 DOI: 10.1016/j.biortech.2019.121876] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/19/2019] [Accepted: 07/22/2019] [Indexed: 06/10/2023]
Abstract
Composting is used widely for recycling spent mushroom substrate (SMS). This study investigated the effects of inoculating a lignocellulose-degrading consortium at two levels comprising 0% (control: CK) and 10% (T) on the fungal community and cellulose-degrading genes during SMS co-composting with swine manure. Lignocellulose degradation rate in T was 8.77-34.45% higher compared with CK. Inoculation affected the distribution of the fungal community, increased the community diversity, and inhibited pathogens. Network analysis showed that inoculation changed the co-occurrence patterns of the fungal communities and made the co-composting system more stable. The relative abundances of glycoside hydrolase genes GH3E (fungal GH3), GH6, and GH7 were 0.45, 0.09, and 0.39 logs higher in T, respectively, than CK. Partial least-squares path modeling suggested that the variations in cellulose-degrading genes were driven mainly by changes in the fungal community during co-composting. Therefore, the lignocellulose-degrading consortium accelerated the transformation of lignocellulose to facilitate safer composting.
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Affiliation(s)
- Ting Hu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Province Institute of Microbiology, Xian, Shaanxi 710043, China
| | - Xiaojuan Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lisha Zhen
- Shaanxi Province Institute of Microbiology, Xian, Shaanxi 710043, China
| | - Jie Gu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Research Center of Recycle Agricultural Engineering and Technology of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Kaiyu Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qianzhi Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jiyue Ma
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Huiling Peng
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Liusheng Lei
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wenya Zhao
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
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Zhao P, Liu J, Jia T, Wang Y, Chai B. Environmental filtering drives bacterial community structure and function in a subalpine area of northern China. J Basic Microbiol 2018; 59:337-347. [PMID: 30561145 DOI: 10.1002/jobm.201800314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 10/12/2018] [Accepted: 10/23/2018] [Indexed: 11/11/2022]
Abstract
Microbial community assembly is affected by the trade-off between deterministic and stochastic processes, but the mechanisms underpinning their relative influences remain elusive. This knowledge gap strongly limits our ability to predict the effect of environmental filtering on microbial community structure and function. To improve the understanding of mechanisms underlying community assembly processes, we investigated bacterial community structure and function on a subalpine shady slope and a sunny slope in the Pangquangou National Nature Reserve in North China. By integrating the results of a null model and the RC metric, we inferred that a deterministic process, that is, environmental filtering, drove bacterial community biogeographical patterns. Edaphic factors caused the largest contribution to microbial community structure, followed by vegetation and spatial variables. Among edaphic factors, total carbon (TC) and total nitrogen (TN) were the most important factors as determined by redundancy analysis (RDA). Moreover, network analysis suggested that the status of bacterial community co-occurrence was significantly greater than that of exclusive relationships. Under environmental stress, there was no significant difference in the overall bacterial community structure on the different slopes, while significant differences were observed in relation to community functions. Given this, we inferred that the degrees of response of bacterial community structure and function to varying environments were not consistent. In conclusion, our results contribute to the understanding of deterministic versus stochastic balance in bacterial community assembly and the response mechanisms of community structure and function to environmental heterogeneity.
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Affiliation(s)
- Pengyu Zhao
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
| | - Jinxian Liu
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
| | - Tong Jia
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
| | - Yinggang Wang
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
| | - Baofeng Chai
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
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Characterization of truncated endo-β-1,4-glucanases from a compost metagenomic library and their saccharification potentials. Int J Biol Macromol 2018; 115:554-562. [DOI: 10.1016/j.ijbiomac.2018.04.102] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 04/18/2018] [Accepted: 04/19/2018] [Indexed: 11/23/2022]
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Tian X, Yang T, He J, Chu Q, Jia X, Huang J. Fungal community and cellulose-degrading genes in the composting process of Chinese medicinal herbal residues. BIORESOURCE TECHNOLOGY 2017; 241:374-383. [PMID: 28578278 DOI: 10.1016/j.biortech.2017.05.116] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 05/16/2017] [Accepted: 05/18/2017] [Indexed: 06/07/2023]
Abstract
The fungal community and the population of 16S rRNA, 18S rRNA and cellulose-degrading genes during the 30-day composting process of Chinese medicinal herbal residues were investigated using Illumina MiSeq and quantitative real-time PCR. An obvious succession of fungal communities occurred during the composting process. Unidentified fungi predominated in the raw materials. As composting progressed, Ascomycota became the most dominant phylum, with Aspergillus being the most dominant genus, and Aspergillus fumigatus making up 99.65% of that genus. Because of the inoculation of cellulolytic fungi in the mature stage, the cellulose degradation rate in inoculation groups was faster and the relative abundances of Aspergillus and the glycoside hydrolase family 7 genes were significantly higher than those in the control groups. These indicated that the fungal inoculants facilitated the degradation of cellulose, increased cellulolytic fungi and optimized the community structure.
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Affiliation(s)
- Xueping Tian
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China
| | - Tao Yang
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China
| | - Jingzhong He
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China
| | - Qian Chu
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China
| | - Xiaojun Jia
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China
| | - Jun Huang
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China.
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