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

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.

We thank the BLM Needles CA office for their assistance with permitting at the Sheephole Valley Wilderness and Dr. Hung Phan (Iowa State) for help with cleaning and submitting data to NCBI.

This work was performed and supported in part by the following: the Facilities Integrating Collaborations for User Science (FICUS) program (proposal: https://doi.org/10.46936/fics.proj.2018.50356/60000035) and used resources at the DOE Joint Genome Institute (JGI) (https://ror.org/04xm1d337) and the National Energy Research Scientific Computing Center (NERSC) (https://ror.org/05v3mvq14), which are DOE Office of Science User Facilities operated under contract no. DE-AC02-05CH11231; Bureau of Land Management (BLM) Cooperative Agreement L15AC00153 to N. Pietrasiak and BLM permit number 6850-CAD0000.06 to N. Pietrasiak and J.E.S.; the U.S. Department of Agriculture, National Institute of Food and Agriculture Hatch project CA-R-PPA-211–5062-H to N. Pombubpa and J.E.S.; a Royal Thai Government Scholarship to N. Pombubpa; and NSF GoLife grant DEB-1541538 and CAREER grant DEB-1846376 to E.F.Y.H. J.E.S. is a CIFAR fellow in the Fungal Kingdom: Threats and Opportunities program. This is UM’s Center for Biodiversity and Conservation Research Publication No. 40.