| Literature DB >> 35185810 |
Katie Sipes1, Raegan Paul1, Aubrey Fine2, Peibo Li1, Renxing Liang3, Julia Boike4,5, Tullis C Onstott3, Tatiana A Vishnivetskaya6, Sean Schaeffer2, Karen G Lloyd1.
Abstract
The active layer of permafrost in Ny Ålesund, Svalbard (79°N) around the Bayelva River in the Leirhaugen glacier moraine is measured as a small net carbon sink at the brink of becoming a carbon source. In many permafrost-dominating ecosystems, microbes in the active layers have been shown to drive organic matter degradation and greenhouse gas production, creating positive feedback on climate change. However, the microbial metabolisms linking the environmental geochemical processes and the populations that perform them have not been fully characterized. In this paper, we present geochemical, enzymatic, and isotopic data paired with 10 Pseudomonas sp. cultures and metagenomic libraries of two active layer soil cores (BPF1 and BPF2) from Ny Ålesund, Svalbard, (79°N). Relative to BPF1, BPF2 had statistically higher C/N ratios (15 ± 1 for BPF1 vs. 29 ± 10 for BPF2; n = 30, p < 10-5), statistically lower organic carbon (2% ± 0.6% for BPF1 vs. 1.6% ± 0.4% for BPF2, p < 0.02), statistically lower nitrogen (0.1% ± 0.03% for BPF1 vs. 0.07% ± 0.02% for BPF2, p < 10-6). The d13C values for inorganic carbon did not correlate with those of organic carbon in BPF2, suggesting lower heterotrophic respiration. An increase in the δ13C of inorganic carbon with depth either reflects an autotrophic signal or mixing between a heterotrophic source at the surface and a lithotrophic source at depth. Potential enzyme activity of xylosidase and N-acetyl-β-D-glucosaminidase increases twofold at 15°C, relative to 25°C, indicating cold adaptation in the cultures and bulk soil. Potential enzyme activity of leucine aminopeptidase across soils and cultures was two orders of magnitude higher than other tested enzymes, implying that organisms use leucine as a nitrogen and carbon source in this nutrient-limited environment. Besides demonstrating large variability in carbon compositions of permafrost active layer soils only ∼84 m apart, results suggest that the Svalbard active layer microbes are often limited by organic carbon or nitrogen availability and have adaptations to the current environment, and metabolic flexibility to adapt to the warming climate.Entities:
Keywords: Svalbard; active layer; carbon; cultures; enzymes; metagenome; nitrogen; permafrost
Year: 2022 PMID: 35185810 PMCID: PMC8851200 DOI: 10.3389/fmicb.2021.757812
Source DB: PubMed Journal: Front Microbiol ISSN: 1664-302X Impact factor: 5.640
FIGURE 1Sample site. (A) Active layer cores were taken from two permafrost sites near the Bayelva River in the Leirhaugen glacier moraine in Ny Ålesund, Svalbard, 79°N. Inset A-1 shows the location of the image in panel (A) within the Svalbard archipelago. (B) Picture taken from the BPF1 borehole in April 2018 at the time of retrieval. (C) Borehole location of BPF1 marked by metal permafrost probe in September 2019. (D) Example of core sample retrieved from BPF2 site.
Closest relative of 16S rRNA genes from cultured Pseudomonas spp. isolated from bulk soil.
| Sample | Svalbard site origin | Percent match | Organism name | Location | First author | NCBI reference |
|
| BPF1 24–36 cm | 99% | Various soil samples from The Peruvian Andean Plateau | Carolina Chumpitaz-Segovia | (Published) June 23rd, 2020 | |
|
| BPF1 36–48 cm | 100% | Antarctic soil | H.J. Park | (Submitted) June 3rd, 2020 | |
|
| BPF1 48–58 cm | 99% | Frozen soil samples from Council, Alaska United States. | Hyoungseok Lee | (Sample collected) June 29, 2012 | |
|
| BPF1 48–58 cm | 99% | QinLing Mountain China | R. Chen | (Accepted) February 26th, 2020 | |
|
| BPF1 0–12 cm | 99% | Sediment samples from Station Juan Carlos I., Livingston Island, Antarctica | L. Ward-Bowie | (Sample collected) February 25th, 2018 | |
|
| BPF1 0–12 cm | 99% | Antarctic soil | M. Zhou | (Submitted) January 18th, 2017 | |
|
| BPF1 0–12 cm | 100% | Antarctic soil | H.J. Park | (Submitted) June 3rd, 2020 | |
|
| BPF2 0–12 cm | 100% | Antarctic soil | H.J. Park | (Submitted) June 3rd, 2020 | |
|
| BPF2 20–30 cm | 100% |
| Qinghai-Tibet Plateau | Y. Wang | (Submitted) September 24th, 2013 |
|
| BPF1 48–58 cm | 99% | Sediment samples from Station Juan Carlos I., Livingston Island, Antarctica | L. Ward-Bowie | (Sample collected) February 25th, 2018 |
FIGURE 2Elemental Analyzer data for BPF1 and BPF2 core samples before acid treatment (red for BPF1 and blue for BPF2) and after acid treatment (yellow for BPF1 and dark blue for BPF2).
FIGURE 3Values for PO43–, NH4+, and NO3– measured in μg/g of dry soil, with the exception of DOC measured in mg/g of dry soil. Inorganic nitrogen is the sum of NH4+ and NO3–. Values below zero indicate an amount below the detectable level.
FIGURE 4Full-length 16S rRNA gene sequences of the 10 Svalbard isolates (in bold) were aligned using the Silva SINA (v1.2.11), and Arb-Silva was used to identify their closest relatives. A RAxML tree was visualized in iTOL (v5.7). The GenBank accession number for each organism is listed in parentheses. The tree is rooted with Aurantimonas sp. (AB291857).
FIGURE 5Potential enzyme activities at each temperature (red for 25°C, black for 15°C, and bright blue for 5°C) for (A) BPF1 and BPF2 and (B) 10 cultured isolates. Markers show the mean of triplicate measurements with error bars for one standard deviation. Enzymes are as follows: β-D-cellubiosidase (CB), leucine aminopeptidase (LAP), N-acetyl-β-D-glucosaminidase (NAG), phosphatase (PHOS), β-xylosidase (XYL), α-glucosidase (AG), and β-glucosidase (BG).
MiSeq metagenome information.
| BPF Metagenome library | BPF1 0–30 cm | BPF1 30–58 cm | BPF2 0–30 cm |
|
| 25,871,532 | 8,366,690 | 13,769,728 |
|
| 13,898 | 3,316 | 7,525 |
|
| 612 | 299 | 186 |
|
| 0 | 0 | 0 |
|
| 82,493 | 66,148 | 35,326 |
|
| 52,430,264 | 15,449,290 | 25,710,039 |
|
| 9,664,112 | 5,805,672 | 2,525,799 |
|
| 0 | 0 | 0 |
|
| 3,705 | 6,093 | 3,278 |
|
| 2,514 | 2,687 | 2,453 |
|
| 3,591 | 545 | 2,309 |
|
| 7,991 | 1,611 | 4,605 |
|
| 62.1 | 64 | 58.7 |
|
| 54,379 | 12,310 | 27,269 |
|
| 103.7 | 79.7 | 106.1 |
|
| 10,780 (77.6%) | 2,870 (86.6%) | 6,763 (89.9%) |
|
| 3,118 (22.4%) | 446 (13.4%) | 762 (10.1%) |
|
| 0 | 0 | 0 |
|
| 11 | 3 | 6 |
|
| 0 | 0 | 0 |
|
| 2 | 0 | 0 |
|
| 11 | 3 | 6 |
Gene counts from whole metagenomes and whole genome sequences that encode for each enzyme.
| Enzyme | BPF1 0–30 cm | BPF1 30–58 cm | BPF2 0–30 cm | B3 | B4 | B5 | B7 | E5 | E6 | E7 | G16 | G17 | G19 |
|
| 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 4 |
|
| 8 | 9 | 6 | 0 | 0 | 0 | 0 | 9 | 1 | 0 | 7 | 7 | 9 |
|
| 6 | 6 | 6 | 2 | 1 | 1 | 2 | 2 | 0 | 2 | 2 | 2 | 5 |
|
| 14 | 71 | 4 | 3 | 2 | 2 | 4 | 11 | 7 | 8 | 8 | 8 | 15 |
|
| 4 | 4 | 2 | 1 | 1 | 1 | 1 | 2 | 1 | 2 | 1 | 1 | 1 |
|
| 24 | 21 | 27 | 10 | 8 | 9 | 12 | 15 | 12 | 13 | 11 | 11 | 15 |
|
| 0 | 0 | 6 | 2 | 2 | 2 | 4 | 4 | 1 | 3 | 3 | 3 | 14 |
The list of genes contributing to these counts can be found in