Eight genome sequences of bacterial environmental isolates from Marr Pond, Antarctica

TL;DR

This paper presents genome sequences of eight bacteria from an Antarctic pond, revealing insights into their genetic makeup and potential roles in the environment.

Contribution

The study provides new genomic data for eight bacterial isolates from Marr Pond, expanding knowledge of Antarctic microbial diversity.

Findings

Eight bacterial isolates from Marr Pond were sequenced, representing three major phyla.

The genomes offer a resource for understanding microbial adaptation in extreme environments.

These isolates contribute to the biogeochemical processes in inland Antarctic meltwater ponds.

Abstract

Inland meltwater ponds are common throughout the dry valley region of Antarctica, with seasonal meltwater inputs driving their biogeochemistry. Here, we report the genomic sequences of eight environmental bacterial isolates covering three major phyla from Marr Pond, Taylor Valley, Antarctica.

Tables

TABLE 1. Summary of genome characteristicsa

Organism(% match to genus, accession #)accession number	# reads	Coverage(×)	Completeness (%)	Contamination (%)	# contigs	L50/N50 (bp)	Size(bp)	GC (%)	# genes	# C RISPR
Arthrobacter sp. MP_2.3(99.4; NR_178602.1)JBJXHZ000000000SRR30853865	44,764,632	380.4	99.7	0.0	88	11/86,476	4,038,123	65.98	3,918	1
Cryobacterium sp. MP_3.1(99.3; NR_108605.1)JAXCHV000000000SRR25764249	10,570,838	407.5	99.5	1.52	82	11/113,724	3,899,650	67.91	3,760	1
Chryseobacterium sp. MP_3.2(99.5; KY476414.1)JAXCHW000000000SRR25764257	10,587,412	517.7	100	0.0	20	4/214,192	2,896,799	35.72	2,872	1
Massilia sp. MP_M2(99.6; NR_042502.1)JBCHJF000000000SRR25764246	10,124,380	291.7	100	0.2	27	4/481,589	5,390,661	63.50	4,868	–
Cryobacterium sp. MP_M3(98.9; NR_043892.1)JADOVI000000000SRR13164991	9,144,084	355.8	99.5	1.01	56	6/231,442	3,940,246	68.44	3,724	1
Arthrobacter sp. MP_M4(99.3; NR_178602.1)JAXCHX000000000SRR25764245	7,644,976	285.4	99.7	0.0	73	10/111,605	4,093,838	65.87	3,903	–
Cryobacterium sp. MP_M5(90.0; NR_043892.1)JAXCHY000000000SRR25764250	14,177,762	395.8	99.5	1.01	63	7/175,936	3,941,243	68.45	3,732	1
Arthrobacter sp. MP_M7(99.5; NR_178602.1)JAXCHZ000000000SRR25764255	11,663,040	373.9	99.7	0.0	76	11/116,442	4,096,488	65.87	3,895	–

Full text

ANNOUNCEMENT

Although inland meltwater ponds are common in the McMurdo Dry Valleys, their biology has received little study to date. The Nussbaum Riegel in the center of Taylor Valley, Antarctica, constricts the valley bottom into a narrow defile. The Riegel enhances the climatic delineation between the wider, lower section and the more narrow, upper section of the valley (1, 2). Above the Nussbaum Riegel (~750 m above sea level) lies a series of upland ponds.

The Marr Ponds (officially known as Kaki Ponds) consist of five ponds. The ponds are fed by meltwater from the Marr Glacier. Ponds 1–4 are hydrologically connected. The Marr Ponds have a thick ice cover with high albedo and varying moat size (3, 4). The geochemistry of these ponds is dilute, reflecting glacial meltwater inputs (4). Major ion concentration, however, can vary between ponds based on increased meltwater flushing or evaporative losses (4). Meltwater-driven changes in the size of these ponds also affect the size of the marginal wetlands and, thus, the substrate that can be exposed to chemical weathering (5). The area occupied by the Marr Ponds is among the oldest surfaces in the Taylor Valley (6). Meltwater ponds are transient and can undergo seasonal freeze-thaw cycles and thermal or chemical stratification/gradients (5). Genome features of bacteria may reflect adaptations to these strong selective pressures of the local environment.

Meltwater was collected from the Marr Ponds (77°42′S, 162°44′E) in December 2010. Bacteria were isolated aerobically on R2A agar plates at 4°C in the dark. The cetyltrimethylammonium bromide procedure was used for extracting DNA from bacterial isolates grown to the late exponential phase in R2A broth at 4°C while shaking at 150 rpm (7). Standard draft genomes were generated at JGI using the Illumina sequencing technologies (8). An input of 200 ng of genomic DNA per genome was sheared around 400 bp using the LE220-plus Focused-ultrasonicator (Covaris) and size-selected with a double SPRI method using Mag-Bind Total Pure NGS beads (Omega Bio-tek). Samples were treated with the KAPA HyperPrep kit’s (Roche) one-tube chemistry of end-repair, A-tailing, and ligation with NEXTFLEX UDI Barcodes (PerkinElmer). Illumina standard shotgun libraries were sequenced on the Illumina NovaSeq S4 platform (2 × 151 bp). Raw Illumina sequences were quality filtered using BBTools (9) per SOP 1061 and assembled with SPAdes (≥version 3.14.1; –phred-offset 33 –cov-cutoff auto -t 16 m 64 –careful -k 25,55,95) (10). Contigs with a length <1 kb (BBTools ≥version 38.86, reformat.sh: minlength = 1000 ow = t) were discarded. CRISPR elements were identified using the program CRT version 1.8.2 (11). All genomes were annotated in the Integrated Microbial Genomes (IMG) database (≥IMG Annotation Pipeline version 5.0.19) (12). Genome completeness was estimated using checkM version 1.2.2 (13). The genome-sequence-acquired 16S ribosomal RNA gene was queried in command line against the SILVA database 138.1 with blastn, from BLAST+ 2.13.0 for taxonomic classification (14). Sequence details are given in Table 1.