Whole community shotgun metagenomes of two biological soil crust types from the Mojave Desert

ABSTRACT

We present six whole community shotgun metagenomic sequencing data sets of two types of biological soil crusts sampled at the ecotone of the Mojave Desert and Colorado Desert in California. These data will help us understand the diversity and function of biocrust microbial communities, which are essential for desert ecosystems.

ANNOUNCEMENT

Biological soil crusts (BSCs) cover approximately 30% of the global dryland surface area (1) and carry out important ecological services (2). As ecosystem pioneers, BSCs colonize bare soil surfaces in low-water, extreme-temperature environments. However, the underlying mechanisms for how microbes give rise to the structure and function of biocrusts and how they interact to provide ecosystem services are still not well understood.

Dry light cyanobacterial/algal crust (LAC) and cyano lichen crust (CLC) samples (~5 cm² in size) were collected at Sheephole Valley Wilderness within the ecotone of the Mojave Desert and Colorado Desert of San Bernardino County, CA, on 9 September 2018 with each of three replicate samples taken 250 m apart from each other at GPS location 34.1736 N, 115.3888 W, and placed in sealed glass mason jars (cushioned by paper towels) for transport back to the laboratory. One hundred milligrams of each sample were randomly subsampled and used for DNA extraction using a MoBio PowerSoil DNA Isolation Kit (12888-50; QIAGEN, Germantown, MD) following the manufacturer’s instructions and sent to the DOE Joint Genome Institute (JGI) for library construction and sequencing. One hundred nanograms of extracted DNA were sheared to a target length of 656 bp using a Covaris LE220 Focused-ultrasonicator (Covaris LLC, Woburn, MA) and size selected using SPRI magnetic beads (Beckman Coulter Life Sciences, Indianapolis, IN). DNA fragments were treated with end-repair, A-tailing, and ligated to Illumina compatible adapters (Integrated DNA Technologies, Inc., Coralville, IA) using a KAPA-Illumina library kit (Roche Diagnostics Corporation, Indianapolis, IN). Libraries were quantified using a KAPA Biosystems next-generation sequencing library qPCR kit and a Roche LightCycler 480 real-time PCR instrument (Roche Diagnostics Corporation, Indianapolis, IN).

Sequencing was performed on an Illumina NovaSeq sequencer (Illumina, Inc., San Diego, CA) using XP V1 reagent kits, S4 flowcells, and a 2 × 151 indexed recipe. Reads were processed with the standard JGI Metagenome workflow (3). Briefly, BBDuk version 38.79 from the BBTools package (https://jgi.doe.gov/data-and-tools/bbtools/) was used to process raw reads, which were then corrected using BBCMS version 38.34 (k-mer count ≥2, high-count fraction ≥0.6) (4) and assembled using metaSPAdes version 3.13.0 (metagenome flag, no error correction, k-mer sizes of 33, 55, 77, 99, and 127) (5) and MEGAHIT version 1.2.9 with default settings (6). Processed reads were mapped to the final assembly, and coverage information was generated using BBMap version 38.34 (4).

Approximately 98% of raw reads passed trimming/quality control filters, and over 70% of processed reads were assembled into contigs. On average, more reads were assembled into contigs using MEGAHIT (75.8%) than metaSPAdes (72.7%) with an estimated metagenome coverage of ~13×. MetaSPAdes assemblies were more compact in terms of total assembly length, with generally longer maximum contig lengths than those of MEGAHIT, although MEGAHIT generated fewer contigs than metaSPAdes. The JGI Integrated Microbial Genomes analysis pipeline (https://genome.jgi.doe.gov/portal/ProMicSoilCrusts/ProMicSoilCrusts.info.html) revealed few eukaryotic microbes, likely due to poor DNA extraction yields from these microbes with the conventional commercial soil DNA isolation kit used. Nevertheless, these data can provide useful initial insights into the prokaryotic diversity of LAC and CLC biocrust types.

DATA AVAILABILITY

Raw sequencing data and metagenome assemblies are available at the NCBI using the hyperlinked BioSample and BioProject ID numbers that are listed in Table 1. Data are also available from JGI’s genome portal (https://genome.jgi.doe.gov/portal/ProMicSoilCrusts/ProMicSoilCrusts.info.html) and GOLD database (https://gold.jgi.doe.gov/study?id=Gs0142145).

TABLE 1.

Accession numbers and characteristics of metagenome data from two biocrust types from the Sheephole Valley Wilderness (Mojave Desert, CA)^a

Metagenome	NCBI BioSample ID	NCBI BioProject ID	No. of filtered reads	Assembly BioSample ID	No. of contigs	No. of assembled (150 bp) reads	Metagenome assembly length (bp)	Metagenome coverage	N50 (bp)	Max contig length (kb)
LAC replicate 1	SAMN14510913	PRJNA620793	215,587,996	PRJNA1021617 PRJNA1021621	2,550,257 2,332,566	166,293,935 170,423,036	1,742,734,840 1,868,428,908	14.3× 13.7×	458,966 441,759	651.104 546.176
LAC replicate 2	SAMN14510861	PRJNA620794	219,555,444	PRJNA1021629 PRJNA1021637	2,663,237 2,365,106	162,376,141 166,589,100	1,700,000,691 1,813,819,568	14.3× 13.8×	513,765 479,343	1000.405 1000.030
LAC replicate 3	SAMN14510934	PRJNA620795	208,714,792	PRJNA1021639 PRJNA1021640	2,353,418 2,177,883	158,432,369 162,939,834	1,571,681,495 1,713,465,883	15.1× 14.3×	415,201 416,349	1301.000 541.813
CLC replicate 1	SAMN14510746	PRJNA620790	191,564,444	PRJNA1021643 PRJNA1021649	2,437,969 2,319,548	134,704,800 139,237,529	1,670,634,364 1,835,861,038	12.1× 11.4×	422,767 453,111	609.588 169.489
CLC replicate 2	SAMN14510985	PRJNA620791	200,791,158	PRJNA1021657 PRJNA1021659	2,812,278 2,605,836	142,285,895 146,893,754	1,913,908,387 2,049,607,909	11.2× 10.8×	508,862 526,639	756.686 384.386
CLC replicate 3	SAMN14510745	PRJNA620792	209,432,468	PRJNA1021660 PRJNA1021664	3,121,332 2,934,558	142,063,838 147,954,872	1,959,209,449 2,157,330,921	10.9× 10.3×	649,941 653,857	949.882 345.113

^a All the contigs are ≥0.1 kb. Assembly statistics for metaSPAdes and MEGAHIT assemblies are listed on the top and bottom (in italics) of each row, respectively.