MSK
Search
- Page Path
- HOME > Search
Journal Article
- Antarctic tundra soil metagenome as useful natural resources of cold-active lignocelluolytic enzymes
- Han Na Oh , Doyoung Park , Hoon Je Seong , Dockyu Kim , Woo Jun Sul
- J. Microbiol. 2019;57(10):865-873. Published online September 30, 2019
- DOI: https://doi.org/10.1007/s12275-019-9217-1
- 46 View
- 0 Download
- 20 Web of Science
- 21 Crossref
-
Abstract
- Lignocellulose composed of complex carbohydrates and aromatic heteropolymers is one of the principal materials for the production of renewable biofuels. Lignocellulose-degrading genes from cold-adapted bacteria have a potential to increase the productivity of biological treatment of lignocellulose biomass by providing a broad range of treatment temperatures. Antarctic soil metagenomes allow to access novel genes encoding for the cold-active lignocellulose-degrading enzymes, for biotechnological and industrial applications. Here, we investigated the metagenome targeting cold-adapted microbes in Antarctic organic matter-rich soil (KS 2-1) to mine lignolytic and celluloytic enzymes by performing single molecule, real-time metagenomic (SMRT) sequencing. In the assembled Antarctic metagenomic contigs with relative long reads, we found that 162 (1.42%) of total 11,436 genes were annotated as carbohydrate-active enzymes (CAZy). Actinobacteria, the dominant phylum in this soil’s metagenome, possessed most of candidates of lignocellulose catabolic genes like glycoside hydrolase families (GH13, GH26, and GH5) and auxiliary activity families (AA7 and AA3). The predicted lignocellulose degradation pathways in Antarctic soil metagenome showed synergistic role of various CAZyme harboring bacterial genera including Streptomyces, Streptosporangium, and Amycolatopsis. From phylogenetic relationships with cellular and environmental enzymes, several genes having potential for participating in overall lignocellulose degradation were also found. The results indicated the presence of lignocellulose-degrading bacteria in Antarctic tundra soil and the potential benefits of the lignocelluolytic enzymes as candidates for cold-active enzymes which will be used for the future biofuel-production industry.
-
Citations
Citations to this article as recorded by
- Metagenomic insights into the lignocellulose degradation mechanism during short-term composting of peach sawdust: Core microbial community and carbohydrate-active enzyme profile analysis
Wei-Wei Zhang, Yu-Xin Guo, Qing-Jun Chen, Yi-Yang Wang, Qiu-Ying Wang, Ya-Ru Yang, Guo-Qing Zhang
Environmental Technology & Innovation.2025; 37: 103959. CrossRef - Comprehensive characterization and resistome analysis of Antarctic Pseudomonas migulae strain CAS19
Çiğdem Otur, Sezer Okay, Ömer Konuksever, Oğuzhan Duyar, Yılmaz Kaya, Aslıhan Kurt-Kızıldoğan
World Journal of Microbiology and Biotechnology.2024;[Epub] CrossRef - Response of carbohydrate-degrading enzymes and microorganisms to land use change in the southeastern Qinghai-Tibetan Plateau, China
Renhuan Zhu, Belayneh Azene, Piotr Gruba, Kaiwen Pan, Yalemzewd Nigussie, Awoke Guadie, Xiaoming Sun, Xiaogang Wu, Lin Zhang
Applied Soil Ecology.2024; 200: 105442. CrossRef - Investigating eukaryotic and prokaryotic diversity and functional potential in the cold and alkaline ikaite columns in Greenland
Mariane Schmidt Thøgersen, Athanasios Zervas, Peter Stougaard, Lea Ellegaard-Jensen
Frontiers in Microbiology.2024;[Epub] CrossRef - Bacterial Diversity, Metabolic Profiling, and Application Potential of Antarctic Soil Metagenomes
Mario Fernández, Salvador Barahona, Fernando Gutierrez, Jennifer Alcaíno, Víctor Cifuentes, Marcelo Baeza
Current Issues in Molecular Biology.2024; 46(11): 13165. CrossRef - Cold adaptation and response genes of Antarctic Cryobacterium sp. SO2 from the Fildes Peninsula, King George Island
Chui Peng Teoh, Marcelo González‑Aravena, Paris Lavin, Clemente Michael Vui Ling Wong
Polar Biology.2024; 47(2): 135. CrossRef - A bacterial cold-active dye-decolorizing peroxidase from an Antarctic Pseudomonas strain
Célica Cagide, Juan José Marizcurrena, Diego Vallés, Beatriz Alvarez, Susana Castro-Sowinski
Applied Microbiology and Biotechnology.2023; 107(5-6): 1707. CrossRef - Role of metagenomics in prospecting novel endoglucanases, accentuating functional metagenomics approach in second-generation biofuel production: a review
Ninian Prem Prashanth Pabbathi, Aditya Velidandi, Tanvi Tavarna, Shreyash Gupta, Ram Sarvesh Raj, Pradeep Kumar Gandam, Rama Raju Baadhe
Biomass Conversion and Biorefinery.2023; 13(2): 1371. CrossRef - Different Response of Plant- and Microbial-Derived Carbon Decomposition Potential between Alpine Steppes and Meadows on the Tibetan Plateau
Yanhong Yuan, Lan Chen, Jieying Wang, Yanfang Liu, Chengjie Ren, Yaoxin Guo, Jun Wang, Ninglian Wang, Fazhu Zhao, Wenying Wang
Forests.2023; 14(8): 1580. CrossRef - Investigation of cold-active and mesophilic cellulases: opportunities awaited
Sambhaji Chavan, Ashvini Shete, Yasmin Mirza, Mahesh S. Dharne
Biomass Conversion and Biorefinery.2023; 13(10): 8829. CrossRef - Cold-Adapted Proteases: An Efficient and Energy-Saving Biocatalyst
Zhengfeng Yang, Zhendi Huang, Qian Wu, Xianghua Tang, Zunxi Huang
International Journal of Molecular Sciences.2023; 24(10): 8532. CrossRef - Reclamation of abandoned saline-alkali soil increased soil microbial diversity and degradation potential
Fating Yin, Fenghua Zhang
Plant and Soil.2022; 477(1-2): 521. CrossRef - Recent advances in metagenomic analysis of different ecological niches for enhanced biodegradation of recalcitrant lignocellulosic biomass
Deepak Kukkar, Pushpender Kumar Sharma, Ki-Hyun Kim
Environmental Research.2022; 215: 114369. CrossRef - Novel bacterial taxa in a minimal lignocellulolytic consortium and their potential for lignin and plastics transformation
Carlos Andrés Díaz Rodríguez, Laura Díaz-García, Boyke Bunk, Cathrin Spröer, Katherine Herrera, Natalia A Tarazona, Luis M Rodriguez-R, Jörg Overmann, Diego Javier Jiménez
ISME Communications.2022;[Epub] CrossRef - The Use of Response Surface Methodology as a Statistical Tool for the Optimisation of Waste and Pure Canola Oil Biodegradation by Antarctic Soil Bacteria
Khadijah Nabilah Mohd Zahri, Azham Zulkharnain, Claudio Gomez-Fuentes, Suriana Sabri, Khalilah Abdul Khalil, Peter Convey, Siti Aqlima Ahmad
Life.2021; 11(5): 456. CrossRef - Comparison of Gut Microbiota between Gentoo and Adélie Penguins Breeding Sympatrically on Antarctic Ardley Island as Revealed by Fecal DNA Sequencing
Yin-Xin Zeng, Hui-Rong Li, Wei Han, Wei Luo
Diversity.2021; 13(10): 500. CrossRef - Deconstruction of Lignin: From Enzymes to Microorganisms
Jéssica P. Silva, Alonso R. P. Ticona, Pedro R. V. Hamann, Betania F. Quirino, Eliane F. Noronha
Molecules.2021; 26(8): 2299. CrossRef - Molecular Characterization of Novel Family IV and VIII Esterases from a Compost Metagenomic Library
Jong-Eun Park, Geum-Seok Jeong, Hyun-Woo Lee, Hoon Kim
Microorganisms.2021; 9(8): 1614. CrossRef - Illite/smectite clay regulating laccase encoded genes to boost lignin decomposition and humus formation in composting habitats revealed by metagenomics analysis
Qingran Meng, Susu Wang, Qiuqi Niu, Hailong Yan, Gen Li, Qiuhui Zhu, Qunliang Li
Bioresource Technology.2021; 338: 125546. CrossRef - Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer
Ohana Y. A. Costa, Mattias de Hollander, Agata Pijl, Binbin Liu, Eiko E. Kuramae
Microbiome.2020;[Epub] CrossRef - Extremophile Microbial Communities and Enzymes for Bioenergetic Application Based on Multi-Omics Tools
Gislaine Fongaro, Guilherme Augusto Maia, Paula Rogovski, Rafael Dorighello Cadamuro, Joana Camila Lopes, Renato Simões Moreira, Aline Frumi Camargo, Thamarys Scapini, Fábio Spitza Stefanski, Charline Bonatto, Doris Sobral Marques Souza, Patrícia Hermes
Current Genomics.2020; 21(4): 240. CrossRef
- Metagenomic insights into the lignocellulose degradation mechanism during short-term composting of peach sawdust: Core microbial community and carbohydrate-active enzyme profile analysis
Research Support, Non-U.S. Gov't
- Identification of Proteolytic Bacteria from the Arctic Chukchi Sea Expedition Cruise and Characterization of Cold-active Proteases
- Ha Ju Park , Yung Mi Lee , Sunghui Kim , Ah Ram Wi , Se Jong Han , Han-Woo Kim , Il-Chan Kim , Joung Han Yim , Dockyu Kim
- J. Microbiol. 2014;52(10):825-833. Published online August 27, 2014
- DOI: https://doi.org/10.1007/s12275-014-4226-6
- 50 View
- 0 Download
- 9 Crossref
-
Abstract
- Following collection of seawater samples during an Arctic Chukchi Sea expedition cruise of the Korean icebreaker Araon in 2012, a total of 15,696 bacteria were randomly isolated from Marine Broth 2216 agar plates. Of these, 2,526 (16%) showed proteolytic activity and were identified as mainly Alteromonas (31%), Staphylococcus (27%), and Pseudoalteromonas (14%). Among the proteolytic strains, seven were selected based on their significant ability to grow and produce a halo on skim milk plates at low temperatures (<5°C) owing to cold-active proteases. These strains were affiliated with the genus Pseudoalteromonas and were divided into three groups based on phylogenetic analysis of the 16S rRNA genes. Profiling cell membrane fatty acids confirmed the 16S rRNA-based differentiation and revealed the accordance between the two analyses. Seven genes for serine protease precursors were amplified from the corresponding strains, and based on sequence similarities, these genes were divided into three groups that were identical to those identified by the 16S rRNA phylogenetic analysis. Three protease genes from the representative strains of each group were composed of 2,127–2,130 bp, encoding 708–709 amino acids, and these genes yielded products with calculated molecular weights of approximately 72.3–72.8 kDa. Amino acid sequence analysis suggested that the precursors are members of the subtilase serine endo- and exo-peptidase clan and contain four domains (signal peptide, N-terminal prosequence, catalytic domain, and two pre-peptidase C-terminal domains). Upon expression in E. coli, each recombinant protease exhibited proteolytic activity on zymogram gels.
-
Citations
Citations to this article as recorded by- The Arctic summer microbiome across Fram Strait: Depth, longitude, and substrate concentrations structure microbial diversity in the euphotic zone
Matthias Wietz, Anja Engel, Simon Ramondenc, Matomo Niwano, Wilken‐Jon von Appen, Taylor Priest, Anabel von Jackowski, Katja Metfies, Christina Bienhold, Antje Boetius
Environmental Microbiology.2024;[Epub] CrossRef - Diversity in the utilization of different molecular classes of dissolved organic matter by heterotrophic marine bacteria
Shira Givati, Elena Forchielli, Dikla Aharonovich, Noga Barak, Osnat Weissberg, Natalia Belkin, Eyal Rahav, Daniel Segrè, Daniel Sher, Jennifer F. Biddle
Applied and Environmental Microbiology.2024;[Epub] CrossRef - Benthic bacteria and archaea in the North American Arctic reflect food supply regimes and impacts of coastal and riverine inputs
Alexis M. Walker, Mary Beth Leigh, Sarah L. Mincks
Deep Sea Research Part II: Topical Studies in Oceanography.2023; 207: 105224. CrossRef - Cold-Adapted Proteases: An Efficient and Energy-Saving Biocatalyst
Zhengfeng Yang, Zhendi Huang, Qian Wu, Xianghua Tang, Zunxi Huang
International Journal of Molecular Sciences.2023; 24(10): 8532. CrossRef - Description of Polaribacter batillariae sp. nov., Polaribacter cellanae sp. nov., and Polaribacter pectinis sp. nov., novel bacteria isolated from the gut of three types of South Korean shellfish
Su-Won Jeong, Jeong Eun Han, June-Young Lee, Ji-Ho Yoo, Do-Yeon Kim, In Chul Jeong, Jee-Won Choi, Yun-Seok Jeong, Jae-Yun Lee, So-Yeon Lee, Euon Jung Tak, Hojun Sung, Hyun Sik Kim, Pil Soo Kim, Dong-Wook Hyun, Jin-Woo Bae
Journal of Microbiology.2022; 60(6): 576. CrossRef - Proteases from the marine bacteria in the genus Pseudoalteromonas: diversity, characteristics, ecological roles, and application potentials
Xiu-Lan Chen, Yan Wang, Peng Wang, Yu-Zhong Zhang
Marine Life Science & Technology.2020; 2(4): 309. CrossRef - Characterization of balofloxacin-stressed proteomics and identification of balofloxacin-binding proteins pre-peptidase and integration host factor in Edwardsiella tarda
Qi Wen, Xian-jie Liu, Wei-cong Zhu, Lu Li, Min-yi Li, Xuna-xian Peng, Hui Li
Journal of Proteomics.2019; 205: 103413. CrossRef - The Place for Enzymes and Biologically Active Peptides from Marine Organisms for Application in Industrial and Pharmaceutical Biotechnology
Jean-Étienne R.L. Morlighem, Gandhi Radis-Baptista
Current Protein & Peptide Science.2019; 20(4): 334. CrossRef - Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise
Shengwei Hou, Mario López-Pérez, Ulrike Pfreundt, Natalia Belkin, Kurt Stüber, Bruno Huettel, Richard Reinhardt, Ilana Berman-Frank, Francisco Rodriguez-Valera, Wolfgang R Hess
The ISME Journal.2018; 12(4): 981. CrossRef
- The Arctic summer microbiome across Fram Strait: Depth, longitude, and substrate concentrations structure microbial diversity in the euphotic zone
First
Prev
TOP
