Permafrost contains one of the least known soil microbiomes, where microbial populations reside in an ice-locked environment. Here, 56 prokaryotic metagenome-assembled genome (MAG) sequences from 13 phyla are reported. These MAGs will provide information on metabolic pathways that could mediate biogeochemical cycles in Svalbard permafrost.
ABSTRACT
Permafrost contains one of the least known soil microbiomes, where microbial populations reside in an ice-locked environment. Here, 56 prokaryotic metagenome-assembled genome (MAG) sequences from 13 phyla are reported. These MAGs will provide information on metabolic pathways that could mediate biogeochemical cycles in Svalbard permafrost.
ANNOUNCEMENT
Permafrost covers over 25% of the exposed land surface of the Northern Hemisphere and hosts a diversity of microbes proposed to be unique to cold habitats (1). These frozen soils contain a large reservoir of soil organic matter (SOM) that can have a significant impact on global climate upon thawing (2). The permafrost thaw may stimulate microbial activity and thus enable SOM decomposition. Previous studies have shown differences in microbial diversity between active layer (seasonally thawed and refrozen topsoil) and permafrost microbial communities (1–5). Although permafrost microbiomes are known to be highly diverse (1), they are largely underrepresented in global surveys. In this study, we investigated the microbial communities through a depth profile from Svalbard, and we report the binned metagenomic coassembly of five metagenome samples (6) and 56 metagenome-assembled genome (MAG) sequences.
Soil samples were obtained from an ice-wedge polygon site in the Adventdalen Valley in Svalbard, Norway (78.186N, 15.9248E). The site soil geochemistry was described previously (6). Five depth segments, namely, one active layer mineral horizon and four permafrost layers, were collected at the following depths: 0 to 14, 101 to 118, 118 to 126, 126 to 144, and 161 to 181 cm below the soil surface. Total community genomic DNA was extracted using a PowerSoil DNA isolation kit, and sequencing libraries were prepared using a TruSeq DNA library kit. An Illumina HiSeq 2500 instrument was used to acquire paired-end 150-bp metagenomic sequences, generating 20 Gb of raw reads per sample (7). The microbial community diversity and composition were reported elsewhere (6).
After adapter and low-quality reads were trimmed using MOCAT2 v2.0.0 (7), all cleaned reads were merged and then coassembled with MEGAHIT v1.1.3 (8), resulting in 566,254 contigs of ≥1 kb. We binned the contigs with MaxBin2 v2.2.5 (9) and MetaBAT2 v2.12.1 (10) and then dereplicated and aggregated them into MAGs using DAS Tool v1.1.0 (11), which resulted in 64 MAGs. We used CheckM v1.0.11 (12) to determine the completeness and contamination of these MAGs. We further examined the taxonomic distribution of contigs within each MAG based on Kaiju v1.6.2 (13) annotations and removed contaminating contigs. This process resulted in a total of 56 MAGs with contamination less than 10%. Default parameters were used with all software. We recovered 8 high-, 44 medium-, and 4 low-quality draft MAGs in accordance with minimum information about metagenome-assembled genome (MIMAG) standards (14). The MAGs were distributed across the following phyla: Actinobacteria, 11; Proteobacteria, 11; Bacteroidetes, 8; Acidobacteria, 7; Chloroflexi, 6; Verrucomicrobia, 4; Saccharibacteria, 2; Gemmatimonadetes, 2; candidate phylum Dormibacteraeota (AD3), 1; candidate phylum Levybacteria, 1; Firmicutes, 1; Nitrospirae, 1; and Thaumarchaeota, 1 (Table 1). Here, we report MAGs with 31.07 to 98.20% estimated completeness, and therefore the MAG sizes range from 731,988 to 5,534,727 bp. The MAGs will be used to investigate metabolic pathways that could impact SOM decomposition in permafrost soils. Results from the comparative genomic analyses of these MAGs will be published elsewhere.
TABLE 1.
Detailed completeness and contamination results, genome size, GC content, MIMAG status, taxonomy, and ENA accession information of MAGs
| MAG alias | Completeness (%) | Contamination (%) | Genome size (bp) | GC content (%) | MIMAG classification | Taxonomya | ENA accession no. |
|---|---|---|---|---|---|---|---|
| Maxbin2.039_sub | 98.2 | 9.2 | 3,147,504 | 55.5 | Medium | Acidobacteria sp. | ERZ870056 |
| Metabat.113 | 96.8 | 0.9 | 2,959,789 | 67.9 | High | Actinobacteria sp. | ERZ870109 |
| Metabat.158 | 96.6 | 2.4 | 4,406,707 | 63.9 | High | Alphaproteobacteria sp. | ERZ870094 |
| Metabat.151 | 96.4 | 5.1 | 4,482,786 | 36.9 | Medium | Bacteroidetes sp. | ERZ870080 |
| Metabat.89 | 96.3 | 2.2 | 2,753,811 | 53.6 | High | Verrucomicrobia sp. | ERZ870097 |
| Metabat.179 | 95.3 | 0.9 | 2,724,314 | 69.2 | High | Chloroflexi sp. | ERZ870110 |
| Metabat.143 | 94.4 | 2.0 | 2,442,640 | 66.0 | High | Chloroflexi sp. | ERZ870099 |
| Metabat.177_sub | 94.3 | 6.7 | 4,572,140 | 59.2 | Medium | Proteobacteria | ERZ870074 |
| Metabat.40 | 93.6 | 3.4 | 3,692,750 | 65.4 | High | Betaproteobacteria | ERZ870086 |
| Metabat.123_sub | 93.2 | 9.6 | 4,243,256 | 68.2 | Medium | Actinobacteria sp. | ERZ870064 |
| Metabat.14 | 92.6 | 3.9 | 2,553,466 | 66.1 | High | Chloroflexi sp. | ERZ870083 |
| Metabat.133 | 91.6 | 1.9 | 2,305,255 | 67.3 | High | Candidate Dormibacteraeota sp. | ERZ870101 |
| Metabat.147 | 91.3 | 7.9 | 4,040,741 | 55.9 | Medium | Verrucomicrobia sp. | ERZ870070 |
| Metabat.67 | 89.9 | 5.5 | 1,906,190 | 68.3 | Medium | Actinobacteria sp. | ERZ870077 |
| Maxbin2.041 | 89.7 | 2.2 | 3,901,541 | 59.3 | Medium | Acidobacteria sp. | ERZ870096 |
| Metabat.164_sub | 89.4 | 4.7 | 2,849,413 | 64.2 | Medium | Chloroflexi sp. | ERZ870081 |
| Maxbin2.071_sub | 86.5 | 8.3 | 3,144,416 | 70.1 | Medium | Actinobacteria sp. | ERZ870067 |
| Metabat.51 | 85.9 | 8.2 | 2,827,458 | 60.8 | Medium | Gemmatimonadetes sp. | ERZ870069 |
| Maxbin2.021_sub | 85.7 | 6.8 | 2,132,093 | 70.0 | Medium | Chloroflexi sp. | ERZ870073 |
| Metabat.154 | 84.8 | 2.5 | 2,330,430 | 69.6 | Medium | Actinobacteria sp. | ERZ870091 |
| Metabat.156 | 84.7 | 1.5 | 2,372,385 | 35.6 | Medium | Bacteroidetes sp. | ERZ870107 |
| Maxbin2.102_sub | 84.6 | 1.8 | 2,720,713 | 64.2 | Medium | Acidobacteriaceae sp. | ERZ870102 |
| Metabat.138 | 84.4 | 2.0 | 2,813,002 | 55.1 | Medium | Verrucomicrobia sp. | ERZ870098 |
| Metabat.172_sub | 83.2 | 2.4 | 2,237,822 | 65.1 | Medium | Rhizobiales sp. | ERZ870093 |
| Maxbin2.128 | 82.1 | 9.8 | 2,270,224 | 51.7 | Medium | Alphaproteobacteria sp. | ERZ870062 |
| Maxbin2.086_sub | 81.9 | 9.7 | 3,605,629 | 57.9 | Medium | Acidobacteria sp. | ERZ870063 |
| Metabat.159_sub | 81.7 | 8.7 | 2,099,345 | 55.9 | Medium | Verrucomicrobia sp. | ERZ870066 |
| Metabat.121 | 80.2 | 3.5 | 2,452,147 | 35.8 | Medium | Bacteroidetes sp. | ERZ870085 |
| Metabat.122 | 77.3 | 8.3 | 2,004,053 | 67.9 | Medium | Actinobacteria sp. | ERZ870068 |
| Metabat.163_sub | 73.8 | 2.0 | 2,166,091 | 71.1 | Medium | Solirubrobacterales sp. | ERZ870100 |
| Metabat.72 | 72.9 | 3.2 | 3,967,186 | 40.8 | Medium | Bacteroidetes sp. | ERZ870087 |
| Metabat.167 | 72.5 | 2.3 | 2,102,822 | 70.7 | Medium | Actinobacteria sp. | ERZ870095 |
| Metabat.115 | 72.1 | 5.1 | 1,795,856 | 70.2 | Medium | Actinobacteria sp. | ERZ870079 |
| Metabat.174 | 71.6 | 2.5 | 2,317,750 | 35.4 | Medium | Bacteroidetes sp. | ERZ870092 |
| Metabat.53 | 71.3 | 8.2 | 5,534,727 | 37.1 | Medium | Bacteroidetes sp. | ERZ879091 |
| Metabat.100 | 69.8 | 0.9 | 2,344,086 | 68.8 | Medium | Solirubrobacterales sp. | ERZ870111 |
| Metabat.26 | 67.9 | 0.8 | 2,094,082 | 68.3 | Medium | Actinobacteria sp. | ERZ870112 |
| Metabat.119 | 67.2 | 0.0 | 731,988 | 47.4 | Medium | Saccharibacteria sp. | ERZ870115 |
| Metabat.140 | 67.1 | 6.0 | 1,381,010 | 69.0 | Medium | Chloroflexi sp. | ERZ870075 |
| Metabat.16 | 66.2 | 1.5 | 844,132 | 41.3 | Medium | Thaumarchaeota sp. | ERZ870108 |
| Maxbin2.015 | 65.5 | 4.0 | 2,138,105 | 49.3 | Medium | Proteobacteria sp. | ERZ870082 |
| Maxbin2.090 | 64.2 | 5.9 | 2,561,445 | 65.2 | Medium | Gemmatimonadetes sp. | ERZ870076 |
| Metabat.48 | 63.6 | 1.7 | 741,844 | 38.9 | Medium | Candidate Levybacteria sp. | ERZ870104 |
| Metabat.28 | 63.5 | 2.6 | 2,845,538 | 67.0 | Medium | Burkholderiales sp. | ERZ870090 |
| Metabat.166 | 63.3 | 0.2 | 739,124 | 45.6 | Medium | Saccharibacteria sp. | ERZ870114 |
| Maxbin2.012 | 63.2 | 6.9 | 2,750,113 | 55.1 | Medium | Proteobacteria sp. | ERZ870072 |
| Metabat.12 | 63.0 | 1.6 | 2,221,067 | 39.3 | Medium | Bacteroidetes sp. | ERZ870106 |
| Metabat.155_sub | 58.6 | 2.9 | 1,479,786 | 56.8 | Medium | Nitrosomonadales sp. | ERZ870089 |
| Metabat.94 | 58.2 | 3.1 | 3,546,342 | 59.7 | Medium | Acidobacteria sp. | ERZ870088 |
| Maxbin2.095_sub | 53.4 | 8.8 | 2,850,869 | 56.6 | Medium | Nitrospirae sp. | ERZ870065 |
| Metabat.1 | 51.9 | 0.6 | 1,114,730 | 51.0 | Medium | Nitrosospira sp. | ERZ870113 |
| Metabat.170 | 51.4 | 3.6 | 3,578,256 | 59.6 | Medium | Acidobacteria sp. | ERZ870084 |
| Metabat.175 | 48.3 | 1.6 | 1,833,825 | 41.8 | Low | Bacteroidetes sp. | ERZ870105 |
| Maxbin2.011 | 42.4 | 5.2 | 2,493,859 | 62.5 | Low | Rhizobiales sp. | ERZ870078 |
| Maxbin2.064_sub | 40.9 | 7.4 | 1,652,927 | 43.4 | Low | Firmicutes sp. | ERZ870071 |
| Maxbin2.096_sub | 31.1 | 1.8 | 1,233,990 | 54.5 | Low | Acidobacteria sp. | ERZ870103 |
Uncultured isolates were used.
Data availability.
The shotgun sequence data were deposited in the European Nucleotide Archive (ENA) database under the study number PRJEB30872 with the accession numbers ERR3078909 to ERR3078913. The MAGs are publicly available in the ENA under the analysis accession numbers ERZ870056, ERZ870062 to ERZ870115, and ERZ879091.
ACKNOWLEDGMENTS
This work was supported by a grant from the National Research School in Bioinformatics, Biostatistics, and Systems Biology (NORBIS) to Yaxin Xue. Funding for this work was provided to Neslihan Taş by the Office of Biological and Environmental Research in the DOE Office of Science—Early Career Research Program. This study is part of the project “Microorganisms in the Arctic: major drivers of biogeochemical cycles and climate change” (RCN 227062), funded by the Norwegian Research Council (principal investigator [PI], Lise Øvreås). Lise Øvreås was awarded the Fulbright Arctic Chair 2012 to 2013 (Fulbright Foundation).
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
The shotgun sequence data were deposited in the European Nucleotide Archive (ENA) database under the study number PRJEB30872 with the accession numbers ERR3078909 to ERR3078913. The MAGs are publicly available in the ENA under the analysis accession numbers ERZ870056, ERZ870062 to ERZ870115, and ERZ879091.