Methane-Oxidizing Communities in Lichen-Dominated Forested Tundra Are Composed Exclusively of High-Affinity USCα Methanotrophs
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Site
2.2. Methane Flux Measurements
2.3. Determination of CH4 Oxidation Activity of Soil Samples
2.4. Chemical Analysis of the Soil Samples
2.5. DNA Extraction, PCR Amplification, and Illumina Sequencing
2.6. Bioinformatic Analysis of Amplicon Sequences
2.7. Molecular Identification of Methanotrophic Bacteria
2.8. qPCR-based Quantification of Methanotrophs
2.9. Sequence Accession Numbers
3. Results and Discussion
3.1. Measurements of CH4 Fluxes
3.2. Distribution of Methane Oxidation Activity over the Soil Profile
3.3. Identification and Quantification of Methanotrophs Using pmoA-Based Analysis
3.4. Molecular Analysis of Bacterial Diversity in Tundra Soil
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Parameter | Organic Layer | Gray Sand | |
---|---|---|---|
C org | % | 1.51 ± 0.30 | 0.11 ± 0.02 |
N total | 0.06 ± 0.01 | 0.01 ± 0.002 | |
N-NO3 | mg/kg | 7.30 ± 0.55 | 7.00 ± 0.53 |
N-NH4 | 14.00 ± 1.05 | 9.00 ± 0.68 | |
P total | 165.0 ± 33.0 | 39.0 ± 7.8 | |
SO42- | 19.40 ± 4.85 | 1.50 ± 0.38 | |
Ca | 13600 ± 2176 | 440.0 ± 70.4 | |
Mg | 450.0 ± 72.0 | 26.0 ± 4.16 | |
Fe | 1821.0 ± 291.0 | 1621.0 ± 259.4 | |
pH | 4.1 ± 0.1 | 6.1 ± 0.1 |
Phylotype | Number of Sequences | GenBank Accession Numbers | Identity to Cand. M. lahnbergensis (%) | Identity to M. gorgona (%) |
---|---|---|---|---|
pmoA-1 * | 148 | KX534008, KX534009, KX534010, KX534011, KX534012, KX534013, KX534014, KX534015, KX534016, KX534017, KX534018, KX534020, KX534021, KX534022, KX534023, KX534025, KX534026, KX534027, KX534028, KX534029, KX534031, KX534035, KX534037, KX534038, KX534039, KX534040, KX534041, KX534044, KX534046, KX534048, KX534051, KX534052, KX534055, KX534056 | 97.5 | 84.2 |
pmoA-2 * | 19 | KX534053, KX534045, KX534030, KX534047, KX534036, KX534033 | 96.4 | 83.1 |
pmoA-3 * | 18 | KX534034, KX534049, KX534019 | 99.2 | 83.5 |
pmoA-4 * | 15 | KX534032, KX534042 | 95.8 | 84.0 |
pmoA-5 * | 11 | KX534043 | 95.0 | 80.8 |
pmoA-6 | 8 | KX534007, KX534054 | 96.4 | 83.1 |
pmoA-7 | 3 | KX534050 | 97.5 | 83.8 |
OTU ID | Relative Abundance (%) | Taxonomy | Closest Silva Match (Similarity, %) | Reported Habitat | Similarity MG203879 (%) | Similarity M. gorgona (%) |
---|---|---|---|---|---|---|
16S-1 | 2.358 | Beijerinckiaceae uncultured | AY913480 (100) | bulk soil | 99 | 98.6 |
16S-2 | 1.902 | Beijerinckiaceae uncultured | AY913598 (100) | limestone cave | 100 | 97.6 |
16S-3 | 0.167 | Beijerinckiaceae | KX509291 (100) | rainwater | 98.6 | 98.1 |
16S-4 | 0.021 | Beijerinckiaceae | KT182565 (100) | bioreactor | 96.6 | 96.2 |
16S-5 | 0.019 | Beijerinckiaceae | JQ905994 (99) | acid mine | 96.6 | 97.1 |
16S-6 | 0.016 | Beijerinckiaceae | FPLS01031837 (100) | unknown | 98.6 | 98.1 |
16S-7 | 0.01 | Beijerinckiaceae | KF100807 (99) | human skin | 96.6 | 95.7 |
16S-8 | 0.004 | Beijerinckiaceae uncultured | HG528987 (100) | peatland | 98.1 | 98.6 |
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Belova, S.E.; Danilova, O.V.; Ivanova, A.A.; Merkel, A.Y.; Dedysh, S.N. Methane-Oxidizing Communities in Lichen-Dominated Forested Tundra Are Composed Exclusively of High-Affinity USCα Methanotrophs. Microorganisms 2020, 8, 2047. https://doi.org/10.3390/microorganisms8122047
Belova SE, Danilova OV, Ivanova AA, Merkel AY, Dedysh SN. Methane-Oxidizing Communities in Lichen-Dominated Forested Tundra Are Composed Exclusively of High-Affinity USCα Methanotrophs. Microorganisms. 2020; 8(12):2047. https://doi.org/10.3390/microorganisms8122047
Chicago/Turabian StyleBelova, Svetlana E., Olga V. Danilova, Anastasia A. Ivanova, Alexander Y. Merkel, and Svetlana N. Dedysh. 2020. "Methane-Oxidizing Communities in Lichen-Dominated Forested Tundra Are Composed Exclusively of High-Affinity USCα Methanotrophs" Microorganisms 8, no. 12: 2047. https://doi.org/10.3390/microorganisms8122047
APA StyleBelova, S. E., Danilova, O. V., Ivanova, A. A., Merkel, A. Y., & Dedysh, S. N. (2020). Methane-Oxidizing Communities in Lichen-Dominated Forested Tundra Are Composed Exclusively of High-Affinity USCα Methanotrophs. Microorganisms, 8(12), 2047. https://doi.org/10.3390/microorganisms8122047