1
|
Altshuler I, Raymond-Bouchard I, Magnuson E, Tremblay J, Greer CW, Whyte LG. Unique high Arctic methane metabolizing community revealed through in situ 13CH 4-DNA-SIP enrichment in concert with genome binning. Sci Rep 2022; 12:1160. [PMID: 35064149 PMCID: PMC8782848 DOI: 10.1038/s41598-021-04486-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/30/2021] [Indexed: 12/15/2022] Open
Abstract
Greenhouse gas (GHG) emissions from Arctic permafrost soils create a positive feedback loop of climate warming and further GHG emissions. Active methane uptake in these soils can reduce the impact of GHG on future Arctic warming potential. Aerobic methane oxidizers are thought to be responsible for this apparent methane sink, though Arctic representatives of these organisms have resisted culturing efforts. Here, we first used in situ gas flux measurements and qPCR to identify relative methane sink hotspots at a high Arctic cytosol site, we then labeled the active microbiome in situ using DNA Stable Isotope Probing (SIP) with heavy 13CH4 (at 100 ppm and 1000 ppm). This was followed by amplicon and metagenome sequencing to identify active organisms involved in CH4 metabolism in these high Arctic cryosols. Sequencing of 13C-labeled pmoA genes demonstrated that type II methanotrophs (Methylocapsa) were overall the dominant active methane oxidizers in these mineral cryosols, while type I methanotrophs (Methylomarinovum) were only detected in the 100 ppm SIP treatment. From the SIP-13C-labeled DNA, we retrieved nine high to intermediate quality metagenome-assembled genomes (MAGs) belonging to the Proteobacteria, Gemmatimonadetes, and Chloroflexi, with three of these MAGs containing genes associated with methanotrophy. A novel Chloroflexi MAG contained a mmoX gene along with other methane oxidation pathway genes, identifying it as a potential uncultured methane oxidizer. This MAG also contained genes for copper import, synthesis of biopolymers, mercury detoxification, and ammonia uptake, indicating that this bacterium is strongly adapted to conditions in active layer permafrost and providing new insights into methane biogeochemical cycling. In addition, Betaproteobacterial MAGs were also identified as potential cross-feeders with methanotrophs in these Arctic cryosols. Overall, in situ SIP labeling combined with metagenomics and genome binning demonstrated to be a useful tool for discovering and characterizing novel organisms related to specific microbial functions or biogeochemical cycles of interest. Our findings reveal a unique and active Arctic cryosol microbial community potentially involved in CH4 cycling.
Collapse
Affiliation(s)
- Ianina Altshuler
- Department of Natural Resource Sciences, McGill University, 21,111 Lakeshore Rd., Ste. Anne de Bellevue, QC, H9X 3V9, Canada.
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences NMBU, Universitetstunet 3, 1430, Ås, Norway.
| | - Isabelle Raymond-Bouchard
- Department of Natural Resource Sciences, McGill University, 21,111 Lakeshore Rd., Ste. Anne de Bellevue, QC, H9X 3V9, Canada
| | - Elisse Magnuson
- Department of Natural Resource Sciences, McGill University, 21,111 Lakeshore Rd., Ste. Anne de Bellevue, QC, H9X 3V9, Canada
| | - Julien Tremblay
- Energy, Mining and Environment Research Centre, National Research Council of Canada, 6100 Royalmount Ave., Montreal, QC, H4P 2R2, Canada
| | - Charles W Greer
- Department of Natural Resource Sciences, McGill University, 21,111 Lakeshore Rd., Ste. Anne de Bellevue, QC, H9X 3V9, Canada
- Energy, Mining and Environment Research Centre, National Research Council of Canada, 6100 Royalmount Ave., Montreal, QC, H4P 2R2, Canada
| | - Lyle G Whyte
- Department of Natural Resource Sciences, McGill University, 21,111 Lakeshore Rd., Ste. Anne de Bellevue, QC, H9X 3V9, Canada
| |
Collapse
|
2
|
Gupta R, Anand G, Gaur R, Yadav D. Plant-microbiome interactions for sustainable agriculture: a review. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:165-179. [PMID: 33627969 PMCID: PMC7873154 DOI: 10.1007/s12298-021-00927-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 12/22/2020] [Accepted: 01/07/2021] [Indexed: 05/03/2023]
Abstract
Plant-microbiome interactions are significant determinant for plant growth, fitness and productivity. Depending upon the specific habitat, plants' microbial communities are classified as the rhizo-, phyllo-, and endospheric regions. Understanding the plant microbiome interactions could provide an opportunity to develop strategies for sustainable agricultural practices. There is a necessity to decipher the complex structural and functional diversity within plant microbiomes to reveal its immense potential in agriculture. The plant microbiota harbors enormous microbial communities that defy analytical methodologies to study dynamics underlying plant microbiome interactions. Findings based on conventional approaches have ignored many beneficial microbial strains, which creates a serious gap in understanding the microbial communications along with the genetic adaptations, which favors their association with host plant. The new era of next generation sequencing techniques and modern cost-effective high-throughput molecular approaches can decipher microbial community composition and function. In this review, we have presented the overview of the various compartments of plants, approaches to allow the access to microbiome and factors that influence microbial community composition and function. Next, we summarize how plant microbiome interactions modulate host beneficial properties particularly nutrient acquisition and defense, along with future agricultural applications. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at. 10.1007/s12298-021-00927-1.
Collapse
Affiliation(s)
- Rupali Gupta
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, The Volcani Center, Rishon LeTsiyon, Israel
| | - Gautam Anand
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, The Volcani Center, Rishon LeTsiyon, Israel
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh India
| | - Rajeeva Gaur
- Department of Microbiology, Dr. Ram Manohar Lohia Avadh University, Ayodhya, 224001 Uttar Pradesh India
| | - Dinesh Yadav
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh India
| |
Collapse
|