ABSTRACT
We recovered 57 bacterial metagenome-assembled genomes (MAGs) from benthic microbial mat pinnacles from Lake Vanda, Antarctica. These MAGs provide access to genomes from polar environments and can assist in culturing and utilizing these Antarctic bacteria.
KEYWORDS: Antarctica, microbial mat, metagenome-assembled genomes
ANNOUNCEMENT
Most microorganisms, especially extremophilic organisms cannot be cultured easily under in vitro laboratory conditions (1, 2). Molecular methodologies like metagenomic shotgun sequencing now provide a culture-independent method of examining extremophilic taxa and the adaptations that they have for life in these extreme environments. They provide a helpful alternative approach to answer questions about the organisms and their community when culturing attempts are unsuccessful. Here, we retrieved 57 metagenome-assembled genomes (MAGs) from microbial pinnacles that were subsampled from benthic mats that grew on the floor of the perennially ice-covered Lake Vanda, Antarctica.
Samples were collected as described previously (3). Briefly, scientific divers sampled microbial mat pinnacles in Lake Vanda in the McMurdo Dry Valleys, Antarctica (−77.529, 161.578) between 8th and 18th December 2013. Microbial mats were subsampled based on color into photosynthetically active green (G) or purple (P) areas and aphotic beige (IB) areas within pinnacles (4). DNA was extracted in the field from multiple green, purple, and inner beige samples and one un-subsampled “bulk mat” sample. DNA was extracted using the Zymo Soil/Fecal miniprep kit (Zymo Research, USA). Libraries were prepared using the KAPA HyperPrep kit (KAPA Biosystems, USA) and DNA was sequenced using the Illumina HiSeq-2500 1TB platform with 2 × 151 bp paired-end sequencing and quality controlled using the standard Joint Genome Institute protocol as described previously (3). Briefly, reads with four or more “N” bases with average quality less than three or minimum length ≤51 bp or 33% of the full read length and those with 93% identity to masked human, dog, cat, mouse, and common contaminants were removed using BBDuk (version 37.36) within BBTools (5). Metagenomes were assembled using MEGAHIT v1.9.6 with a minimum contig length of 1500 (6). Reads were mapped to the assembly using Bowtie2 v1.2.2 and samtools v1.7 (7, 8). A depth file was generated using the jgi_summarize_bam_contig_depths command in MetaBAT v.2.12.1 (9). Bins were generated using metaBAT using a minimum contig size of 2,500 bp. The completeness and contamination of the bins were calculated using CheckM v1.0.7 (10). Bins > 90% complete with less than 5% contamination were retained. Average nucleotide identity (ANI) between bins was calculated using the anvi-compute-genome-similarity command in Anvi’o v6.2 using fastANI (11, 12). Bins sharing >98% ANI was considered to be the same taxon and the bin with the highest completeness was selected as the representative MAG for that taxon. Representative MAGs were classified using GTDB-tk v1.7.0 (13). Previously published MAGs were removed (3, 14, 15). Genome coverage was calculated using coverM (https://github.com/wwood/CoverM) and genomes were annotated using the NCBI Prokaryotic Genome Annotation Pipeline (16). Default parameters were used unless otherwise noted.
Metagenomes contained 177–229 million reads which assembled into 179,000–223,000 contigs (Table 1). We retrieved 57 MAGs from 20 bacterial phyla. The median contig number for MAGs was 264. The average size and GC content were 4.296 Mb and 52.828%, respectively. Average completeness was 96.41% and contamination was 1.38%. Coverage ranged from 11.1× to 111.3×. There were 2,130–6,778 protein-encoding genes (Table 1).
TABLE 1.
Summary of metagenome statistics and MAG propertiesa
| Metagenome statistics | Genome statistics | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Site | Accession | Raw read pairs (millions) | Quality controlled read pairs (millions) | Contigs | N50 | Accession | Genome name | Classification | Total length (Mb) | GC (%) | Contigs | Complete-ness (%) | Contam-ination (%) | Coverage (×) | Protein-encoding genes (total) |
| Bulk Mat | SRX3539175 | 208 | 207 | 179,859 | 4156 | SAMN38186868 | BulkMat.140 | Bacteria; Bacteroidota; Bacteroidia; Chitinophagales; Saprospiraceae; JABWAJ01 |
5.56 | 49.33 | 409 | 97.78 | 1.01 | 50.0 | 4,494 |
| SAMN38186869 | BulkMat.37 | Bacteria; Pseudomonadota; Alphaproteobacteria; Caulobacterales; TH1-2; Terricaulis |
3.7 | 62.78 | 136 | 98.62 | 1.54 | 23.1 | 3,852 | ||||||
| SAMN38186870 | BulkMat.75 | Bacteria; Zixibacteria; MSB-5A5; GN15; FEB-12; JACRAV01 |
2.7 | 48.5 | 82 | 98.84 | 0 | 44.0 | 2,246 | ||||||
| SAMN38186871 | BulkMat.82 | Bacteria; Chloroflexota; Anaerolineae; Aggregatilineales; A4b; GCA-2794515 |
3.9 | 47.52 | 509 | 96.18 | 1.82 | 15.4 | 3,595 | ||||||
| MP5G1 | SRX3539176 | 95 | 94 | 213,763 | 4255 | SAMN38186872 | MP5G1.132 | Bacteria; Bacteroidota; Bacteroidia; Chitinophagales; Saprospiraceae; JABWAJ01 |
5.76 | 49.38 | 437 | 97.78 | 2.27 | 24.6 | 4,673 |
| SAMN38186873 | MP5G1.138 | Bacteria; Spirochaetota; Leptospirae; Leptospirales; Leptospiraceae; Leptospira_A |
4.11 | 35.7 | 37 | 100 | 0 | 44.6 | 3,834 | ||||||
| SAMN38186874 | MP5G1.179 | Bacteria; Chloroflexota; Chloroflexia; Chloroflexales; Roseiflexaceae |
6.13 | 54.9 | 757 | 95.91 | 1.89 | 12.1 | 5,489 | ||||||
| SAMN38186875 | MP5G1.50 | Bacteria; Bacteroidota; Bacteroidia; AKYH767; B-17BO; UBA2475 |
3.53 | 36.14 | 190 | 97.44 | 2.66 | 28.9 | 3,021 | ||||||
| MP5IB2 | SRX3539179 | 103 | 102 | 217,012 | 4652 | SAMN38186876 | MP5IB2.11 | Bacteria; Bdellovibrionota; Bdellovibrionia; JABDDW01; JABDDW01 |
3 | 39.57 | 70 | 95.48 | 2.68 | 17.6 | 2,935 |
| SAMN38186877 | MP5IB2.114 | Bacteria; Bacteroidota; Bacteroidia; NS11-12g; SHWZ01 |
3.5 | 36.82 | 205 | 96.43 | 0.63 | 20.4 | 2,970 | ||||||
| SAMN38186878 | MP5IB2.151 | Bacteria; Planctomycetia; Pirellulales; Lacipirellulaceae; Bythopirellula |
4.77 | 56.21 | 204 | 97.63 | 0 | 42.4 | 4,053 | ||||||
| SAMN38186879 | MP5IB2.172 | Bacteria; Bacteroidota; Bacteroidia; Chitinophagales; Saprospiraceae; JADKGY01 |
3.92 | 44.25 | 298 | 95.42 | 0.41 | 18.5 | 3,141 | ||||||
| SAMN38186880 | MP5IB2.194 | Bacteria; Bacteroidota; Rhodothermia; Rhodothermales; | 5.14 | 62.43 | 304 | 95.9 | 2.19 | 21.4 | 4,229 | ||||||
| SAMN38186881 | MP5IB2.201 | Bacteria; Bdellovibrionota; Bdellovibrionia; Bdellovibrionales; SG-bin7 |
3.26 | 42.33 | 111 | 99 | 1.79 | 17.7 | 3,273 | ||||||
| SAMN38186882 | MP5IB2.37 | Bacteria; Bacteroidota; Bacteroidia; NS11-12g; UKL13-3; B1 | 3.59 | 37.51 | 149 | 95.24 | 1.59 | 23.9 | 3,020 | ||||||
| SAMN38186883 | MP5IB2.67 | Bacteria; Gemmatimonadota; Gemmatimonadota; Gemmatimonadales; GWC2-71-9; SZUA-320 |
3.29 | 67.18 | 419 | 95.6 | 2.2 | 27.9 | 3,077 | ||||||
| SAMN38186884 | MP5IB2.78 | Bacteria; Planctomycetota; Planctomycetia; Planctomycetales; Planctomycetaceae; DSVQ01 |
7.43 | 63.99 | 717 | 95.51 | 1.23 | 15.0 | 6,251 | ||||||
| MP6G1 | SRX3539172 | 101 | 100 | 223,185 | 4583 | SAMN38186885 | MP6G1.103 | Bacteria; Chloroflexota; Anaerolineae; Aggregatilineales; A4b; OLB15 |
5.21 | 59.04 | 383 | 98.18 | 0.91 | 25.8 | 4,619 |
| SAMN38186886 | MP6G1.12 | Bacteria; Planctomycetota; Phycisphaerae; Phycisphaerales; SM1A02; JAEUIT01 |
4.3 | 64.28 | 281 | 95.8 | 2.84 | 20.6 | 3,691 | ||||||
| SAMN38186887 | MP6G1.168 | Bacteria; Chloroflexota; Anaerolineae; Aggregatilineales; A4b; OLB15 |
4.44 | 61.39 | 335 | 97.27 | 0 | 28.5 | 4,031 | ||||||
| SAMN38186888 | MP6G1.198 | Bacteria; Myxococcota; Polyangiia; Palsa-1104_A |
5.23 | 59.6 | 389 | 95.81 | 1.31 | 19.8 | 4,590 | ||||||
| SAMN38186889 | MP6G1.94 | Bacteria; Bacteroidota; Bacteroidia; Flavobacteriales; UA16 | 3.7 | 41.41 | 269 | 95.61 | 0 | 16.1 | 2,907 | ||||||
| MP6IB1 | SRX3539177 | 101 | 100 | 182,767 | 5165 | SAMN38186890 | MP6IB1.110 | Bacteria; Bacteroidota; Ignavibacteria; SJA-28; B-1AR |
3.61 | 37.22 | 262 | 95.36 | 1.09 | 31.4 | 3,123 |
| SAMN38186891 | MP6IB1.118 | Bacteria; Bacteroidota; Bacteroidia; Chitinophagales; Saprospiraceae; JADJLQ01 | 4.75 | 42.75 | 325 | 95.17 | 0.99 | 23.7 | 3,981 | ||||||
| SAMN38186892 | MP6IB1.130 | Bacteria; Pseudomonadales; Alphaproteobacteria; Caulobacterales; Hyphomonadaceae; UBA7672 | 3.61 | 64.33 | 253 | 97.65 | 2.03 | 40.7 | 3,409 | ||||||
| SAMN38186893 | MP6IB1.145 | Bacteria; Proteobacteria; Alphaproteobacteria; Dongiales; Rhodospirillaceae | 3.76 | 63.88 | 143 | 98.91 | 0.82 | 30.5 | 3,523 | ||||||
| SAMN38186894 | MP6IB1.15 | Bacteria; Bacteroidota; Bacteroidia; Cytophagales; Cyclobacteriaceae; ELB16-189 |
3.46 | 50.16 | 52 | 99.45 | 0.55 | 18.2 | 3,064 | ||||||
| SAMN38186895 | MP6IB1.21 | Bacteria; Pseudomonadota; Gammaproteobacteria; Lysobacterales; SZUA-36; SHZL01 | 4.04 | 54.27 | 175 | 97.83 | 2.76 | 16.6 | 3,703 | ||||||
| SAMN38186896 | MP6IB1.62 | Bacteria; Verrucomicrobiota; Verrucomicrobiia | 2.76 | 48.16 | 132 | 95.95 | 1.38 | 16.0 | 2,590 | ||||||
| SAMN38186897 | MP6IB1.66 | Bacteria; Proteobacteria; Alphaproteobacteria; Micropepsales; Micropepsaceae; SZUA-430 |
3.53 | 58.5 | 234 | 96.35 | 0 | 41.9 | 3,561 | ||||||
| SAMN38186898 | MP6IB1.68 | Bacteria; Planctomycetota; Planctomycetia; Pirellulales; JAEUIK01 |
7.29 | 61.18 | 534 | 93.79 | 4.44 | 16.2 | 5,962 | ||||||
| SAMN38186899 | MP6IB1.8 | Bacteria; Nitrospirota; Nitrospiria; Nitrospirales; Nitrospiraceae; Palsa-1315 |
2.85 | 56.68 | 133 | 96.76 | 3.41 | 111.3 | 2,896 | ||||||
| SAMN38186900 | MP6IB1.81 | Bacteria; Bacteroidota; Kapabacteria; Kapabacteriales; Kapabacteriaceae; UBA2333 |
3.04 | 50.5 | 71 | 95.9 | 1.09 | 20.3 | 2,514 | ||||||
| SAMN38186901 | MP6IB1.97 | Bacteria; Proteobacteria; Alphaproteobacteria; Caulobacterales; TH1-2; VFBF01 |
3.33 | 65.96 | 240 | 95.94 | 1.49 | 20.3 | 3,382 | ||||||
| MP7G1 | SRX3539171 | 107 | 106 | 219,283 | 4526 | SAMN38186902 | MP7G1.125 | Bacteria; Bdellovibrionota_C; UBA2361; UBA2361 |
2.96 | 37.52 | 483 | 96.14 | 3.3 | 12.4 | 2,731 |
| SAMN38186903 | MP7G1.130 | Bacteria; Planctomycetota; UBA1135; UBA1135; GCA-002686595; JAEUIA01 |
4.49 | 64 | 287 | 97.85 | 4.48 | 26.6 | 3,736 | ||||||
| SAMN38186904 | MP7G1.139 | Bacteria; Nitrospirota; Nitrospiria; Nitrospirales; Nitrospiraceae; Palsa-1315 |
4.32 | 56.62 | 282 | 95.91 | 3.01 | 41.7 | 4,447 | ||||||
| SAMN38186905 | MP7G1.168 | Bacteria; Verrucomicrobiota; Verrucomicrobiia; Methylacidiphilales; JAAUTS01; JAAUTS01 |
2.4 | 47.45 | 74 | 97.3 | 1.69 | 17.4 | 2,307 | ||||||
| SAMN38186906 | MP7G1.59 | Bacteria; Gemmatimonadota; Gemmatimonadetes; Gemmatimonadales; GWC2-71-9 |
4.17 | 67.42 | 403 | 97.8 | 4.44 | 17.8 | 3,870 | ||||||
| MP8IB2 | SRX3539178 | 94 | 92 | 205,304 | 4796 | SAMN38186907 | MP8IB2.145 | Bacteria; Proteobacteria; Alphaproteobacteria; Micropepsales; Micropepsaceae; SZUA-430 | 5.07 | 63.43 | 186 | 99.78 | 1.74 | 30.5 | 4,930 |
| SAMN38186908 | MP8IB2.79 | Bacteria; Candidatus Eisenbacteria; RBG-16-71-46; JABDJR01 |
3.96 | 62.82 | 264 | 95.6 | 3.3 | 39.5 | 3,429 | ||||||
| MP9P1 | SRX3539181 | 116 | 115 | 200,348 | 4604 | SAMN38186909 | MP9P1.103 | Bacteria; Cyanobacteria; Vampirovibrionia; Obscuribacterales; Obscuribacteraceae | 8.13 | 50.27 | 283 | 95.73 | 3.99 | 24.5 | 6,547 |
| SAMN38186910 | MP9P1.11 | Bacteria; Bacteroidota; Bacteroidia; Chitinophagales; CAIOSU01 |
4.53 | 44.3 | 137 | 96.55 | 0.33 | 40.0 | 3,885 | ||||||
| SAMN38186911 | MP9P1.153 | Bacteria; Planctomycetota; Phycisphaerae; Phycisphaerales; SM1A02; JAEUIT01 |
4.28 | 62.58 | 288 | 96.21 | 0.57 | 32.7 | 3,735 | ||||||
| SAMN38186912 | MP9P1.20 | Bacteria; Verrucomicrobiota; Verrucomicrobiia | 2.98 | 47.26 | 138 | 97.26 | 1.35 | 17.3 | 2,763 | ||||||
| SAMN38186913 | MP9P1.49 | Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Rhodomicrobiaceae | 3.11 | 57.39 | 84 | 98.59 | 0.4 | 35.7 | 3,115 | ||||||
| SAMN38186914 | MP9P1.80 | Bacteria; Bacteroidota; Bacteroidia; CAILMK01; CAILMK01 | 2.48 | 35.43 | 128 | 98.09 | 0 | 19.9 | 2,130 | ||||||
| P2IB | SRX3539180 | 98 | 97 | 198,359 | 5291 | SAMN38186915 | P2IB.100 | Bacteria; Pseudomonadota; Gammaproteobacteria; Lysobacterales; Ahniellaceae; 0-14-3-00-62-12 |
4.41 | 60.13 | 352 | 95.64 | 1.98 | 63.2 | 3,779 |
| SAMN38186916 | P2IB.134 | Bacteria; Planctomycetota; Planctomycetia; Pirellulales; PLA5 |
5.43 | 55.33 | 599 | 95.59 | 4.18 | 11.1 | 4,619 | ||||||
| SAMN38186917 | P2IB.159 | Bacteria; Bacteroidota; Bacteroidia; Flavobacteriales; UA16; UBA4660 |
3.63 | 45.16 | 89 | 99.73 | 0.29 | 62.8 | 3,161 | ||||||
| SAMN38186918 | P2IB.169 | Bacteria; Actinomycetota; Acidimicrobiia; IMCC26256; PALSA-610 |
3.6 | 68.4 | 395 | 96.41 | 3.02 | 16.1 | 3,701 | ||||||
| SAMN38186919 | P2IB.181 | Bacteria; Planctomycetota; Planctomycetia; Pirellulales; Pirellulaceae | 7.3 | 51.16 | 310 | 95.22 | 1.18 | 31.4 | 5,757 | ||||||
| SAMN38186920 | P2IB.185 | Bacteria; Bacteroidota; Bacteroidia; Chitinophagales; Chitinophagaceae; JJ008 |
4.66 | 39.15 | 404 | 96.19 | 1.01 | 22.0 | 4,274 | ||||||
| SAMN38186921 | P2IB.3 | Bacteria; Acidobacteriota; Terriglobia; Bryobacterales; Bryobacteraceae; JACMLA01 |
7.5 | 61 | 456 | 98.48 | 0.87 | 17.3 | 6,778 | ||||||
| SAMN38186922 | P2IB.85 | Bacteria; Candidatus Hydrogenedentota; Hydrogenedentia; Hydrogenedentiales; SLHB01; JABWCD01 |
5.17 | 57 | 280 | 96.6 | 1.1 | 13.9 | 4,543 | ||||||
| SP4G1 | SRX3539186 | 97 | 96 | 182,794 | 4400 | SAMN38186923 | SP4G1.39 | Bacteria; Bacteroidota; Bacteroidia; Chitinophagales; Chitinophagaceae; JJ008 | 4.42 | 41.53 | 224 | 99.51 | 0 | 17.7 | 3,896 |
| SAMN38186924 | SP4G1.84 | Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Hyphomicrobiaceae; Hyphomicrobium aestuarii | 3.69 | 61.99 | 258 | 95.35 | 2 | 17.9 | 3,472 | ||||||
Alternating grey and white bars indicate MAGs derived from the same metagenome.
These Antarctic MAGs help to remove barriers to researchers interested in the Antarctic by expanding the catalog of Antarctic bacterial genomes. They provide information that can be used to inform culturing efforts and be used in parallel with in vitro studies to understand how these organisms adapt to their extreme environment and may respond to ongoing climate change.
ACKNOWLEDGMENTS
Samples used in this project were collected during a field season supported by the New Zealand Foundation for Research, Science, and Technology (grant CO1X0306) with field logistics provided by Antarctica New Zealand (project K-081). Sequencing was provided by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility under Contract No. CSP502867. The U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy and operated under Contract No. DE-AC02-05CH11231. Data analysis was supported by NSF grants OPP-1745341, OPP-1937748, and BII-2022126.
Contributor Information
Christen Grettenberger, Email: clgrett@ucdavis.edu.
Elinne Becket, California State University San Marcos, San Marcos, California, USA.
DATA AVAILABILITY
Quality-controlled reads are available in the NCBI Sequence Read Archive under accession numbers SRR6448204–SRR6448219. Draft genomes are available under Genbank accession numbers JAWXAL01–JAWXCP01. Raw reads are available in IMG under project number Gs0127369.
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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
Quality-controlled reads are available in the NCBI Sequence Read Archive under accession numbers SRR6448204–SRR6448219. Draft genomes are available under Genbank accession numbers JAWXAL01–JAWXCP01. Raw reads are available in IMG under project number Gs0127369.