The Effect of Nitrogen Content on Archaeal Diversity in an Arctic Lake Region
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sampling Site Description and Sample Collection
2.2. Geochemical Properties of Soils and Lake Sediments
2.3. DNA Extraction, Polymerase Chain Reaction (PCR) Amplification, and Sequencing
2.3.1. DNA Extraction and PCR Amplification
2.3.2. PCR Product Quantification, Qualification, and Purification
2.3.3. Library Preparation and Sequencing
2.3.4. Processing of Sequencing Data
2.4. Statistical Analyses
3. Results
3.1. Geochemical Properties of Soil and Sediment Samples
3.2. Archaeal Diversity and Community Composition
3.3. Correlations between Environmental Variables and Archaeal Community Structure
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Site | Sample | Water Content | pH | Organic Carbon (OrC) % | NH4+–N (μg/g) | SiO42−–Si (μg/g) | NO3−–N (μg/g) | NO2−–N (μg/g) |
---|---|---|---|---|---|---|---|---|
Hill | Hill.1 | 0.14 | 7.63 | 1.18 | 0.94 | 2.25 | 0.06 | 0.04 |
Hill.2 | 0.13 | 7.97 | 1.00 | 1.89 | 2.32 | 0.30 | 0.22 | |
Hill.3 | 0.14 | 8.03 | 1.06 | 0.50 | 1.85 | 0.62 | 0.04 | |
average | 0.14 ± 0.01 | 7.88 ± 0.22 | 1.08 ± 0.09 | 1.11 ± 0.71 | 2.14 ± 0.25 | 0.32 ± 0.28 | 0.10 ± 0.10 | |
Up | Up.1 | 0.16 | 7.62 | 1.53 | 2.85 | 1.43 | 0.62 | 0.23 |
Up.2 | 0.11 | 7.68 | 1.16 | 1.85 | 1.75 | 0.52 | 0.15 | |
Up.3 | 0.10 | 7.85 | 0.12 | 0.75 | 2.19 | 0.03 | 0.04 | |
average | 0.12 ± 0.03 | 7.72 ± 12 | 0.94 ± 0.73 | 1.82 ± 1.05 | 1.79 ± 0.38 | 0.39 ± 0.32 | 0.14 ± 0.10 | |
Down | Down.1 | 0.11 | 8.13 | 0.25 | 1.15 | 4.36 | 0.20 | 0.03 |
Down.2 | 0.11 | 8.22 | 0.21 | 0.93 | 3.11 | 0.20 | 0.03 | |
Down.3 | 0.08 | 8.11 | 0.16 | 1.39 | 4.50 | 0.44 | 0.06 | |
average | 0.10 ± 0.02 | 8.15 ± 0.06 | 0.21 ± 0.05 | 1.16 ± 0.23 | 3.99 ± 0.77 | 0.28 ± 0.14 | 0.04 ± 0.02 | |
Sediment | Sedi.1 | 0.18 | 7.91 | 0.11 | 3.27 | 3.11 | 0.05 | 0.01 |
Sedi.2 | 0.23 | 7.84 | 0.51 | 4.08 | 4.29 | 0.01 | 0.01 | |
Sedi.3 | 0.19 | 7.90 | 0.31 | 3.44 | 3.06 | 0.01 | 0.01 | |
average | 0.20 ± 0.03 | 7.88 ± 0.04 | 0.31 ± 0.2 | 3.60 ± 0.42 | 3.49 ± 0.70 | 0.02 ± 0.02 | 0.01 ± 0 |
Sample Name | Raw Tag | Effective | OTUs | Shannon (H’) | Pielou (J’) | Simpson (1-D) | chao1 | ACE | Good’s Coverage |
---|---|---|---|---|---|---|---|---|---|
Hill.1 | 29217 | 23991 | 75 | 2.491 | 0.426 | 0.773 | 83 | 90.254 | 0.999 |
Hill.2 | 21558 | 17420 | 74 | 2.629 | 0.450 | 0.796 | 65.882 | 71.368 | 0.999 |
Hill.3 | 25608 | 18117 | 87 | 2.248 | 0.385 | 0.707 | 122.667 | 123.325 | 0.998 |
Up.1 | 26854 | 23756 | 56 | 2.564 | 0.439 | 0.787 | 66 | 74.721 | 0.999 |
Up.2 | 26503 | 22461 | 60 | 2.392 | 0.410 | 0.775 | 54.667 | 56.963 | 0.999 |
Up.3 | 23635 | 20012 | 69 | 2.213 | 0.379 | 0.756 | 62.545 | 66.666 | 0.999 |
Down.1 | 28575 | 25156 | 42 | 1.803 | 0.309 | 0.632 | 36.25 | 36.296 | 1 |
Down.2 | 27944 | 22992 | 50 | 2.187 | 0.374 | 0.715 | 40.909 | 43.927 | 1 |
Down.3 | 26607 | 23313 | 65 | 2.114 | 0.362 | 0.643 | 53.077 | 57.351 | 0.999 |
Sedi.1 | 27538 | 20514 | 196 | 3.09 | 0.529 | 0.789 | 191.091 | 195.725 | 0.998 |
Sedi.2 | 31650 | 23542 | 276 | 4.116 | 0.705 | 0.851 | 280.41 | 284.337 | 0.997 |
Sedi.3 | 19396 | 14710 | 206 | 3.414 | 0.585 | 0.757 | 190.634 | 194.981 | 0.999 |
RDA1 | RDA2 | r2 | Pr (>r) | ||
---|---|---|---|---|---|
Water content | −0.963478 | 0.267788 | 0.6685 | 0.008 | ** |
pH | 0.123615 | −0.992330 | 0.0209 | 0.908 | |
OrC | 0.897715 | 0.440576 | 0.3345 | 0.149 | |
NH4+–N | −0.995861 | 0.090889 | 0.6897 | 0.008 | ** |
SiO42−–Si | −0.985292 | −0.170879 | 0.1667 | 0.431 | |
NO3−–N | 0.989857 | 0.142067 | 0.3876 | 0.108 | |
NO2−–N | 0.999554 | −0.029876 | 0.2080 | 0.362 |
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Lv, J.; Liu, F.; Han, W.; Wang, Y.; Zhu, Q.; Zang, J.; Wang, S.; Zhang, B.; Wang, N. The Effect of Nitrogen Content on Archaeal Diversity in an Arctic Lake Region. Microorganisms 2019, 7, 543. https://doi.org/10.3390/microorganisms7110543
Lv J, Liu F, Han W, Wang Y, Zhu Q, Zang J, Wang S, Zhang B, Wang N. The Effect of Nitrogen Content on Archaeal Diversity in an Arctic Lake Region. Microorganisms. 2019; 7(11):543. https://doi.org/10.3390/microorganisms7110543
Chicago/Turabian StyleLv, Jinjiang, Feng Liu, Wenbing Han, Yu Wang, Qian Zhu, Jiaye Zang, Shuang Wang, Botao Zhang, and Nengfei Wang. 2019. "The Effect of Nitrogen Content on Archaeal Diversity in an Arctic Lake Region" Microorganisms 7, no. 11: 543. https://doi.org/10.3390/microorganisms7110543