ABSTRACT
Cyanobacteria are essential to microbial communities inhabiting translucent rocks in hyper-arid deserts. Metagenomic studies revealed unique adaptations of these cyanobacteria, but validation of the corresponding metabolic pathways remained challenging without access to isolates. Here, we present high-quality metagenome-assembled genomes for cyanobacteria, and their heterotrophic companions, isolated from endolithic substrates.
ANNOUNCEMENT
In the most arid deserts, where environmental conditions are extreme, microbial communities find refuge inside rocks as a survival strategy (1). The rock habitat protects microorganisms from high UV radiation and drastic temperature fluctuations and promotes water retention within the rock matrix (2). Molecular studies of endolithic communities (within rock) revealed ecosystems spanning all domains of life and multiple trophic levels (3–5). The communities are based on the primary production of cyanobacteria, and sometimes algae, and are constituted of an assemblage of heterotrophic bacteria and/or archaea and viruses (6–10). Endolithic communities are highly specific to their lithic substrate, with fine-scale diversification of the microbial reservoir driven by substrate properties (3, 10).
Cyanobacteria inhabiting endolithic substrates in arid deserts are mostly members of the orders Chroococcales (Chroococcidiopsis and Gloeocapsa), Nostocales, and Oscillatoriales (1). Metagenomic studies of endolithic communities revealed unique adaptations of these cyanobacteria, and a large number of pathways for secondary metabolites, nonribosomal peptides, and polyketides are encoded in their genomes (7, 10). However, validation of these pathways remained challenging without access to isolates. Here, we present the metagenome-assembled genomes (MAGs) of cyanobacteria isolated from endolithic substrates collected in the Atacama and Negev Deserts (Table 1). Because these isolates are not purified cultures, their companions—heterotrophic bacteria—were also sequenced.
TABLE 1.
Metagenome and MAG statistics of endolithic cyanobacterial isolates from the Atacama Desert, Chile, and the Negev Desert, Israel
| Sample name | Substrate | IMG taxon ID | Metagenome size (Mbp) | Bin ID | Taxon/genus | MAG completion (%) | MAG contamination (%) | MAG size (Mbp) | MAG gene count | MAG scaffold count |
|---|---|---|---|---|---|---|---|---|---|---|
| C-VL-3P3 | Calcite | 3300039404 | 11 | 3300039404_1 | Chroococcidiopsis | 99.48 | 1.63 | 6.6 | 6,630 | 157 |
| 3300039404_2 | Deinococcus | 97.67 | 0.99 | 4.1 | 4,214 | 68 | ||||
| G-Km37-3P1 | Gypsum | 3300039405 | 18.2 | 3300039405_1 | Methylobacterium | 100 | 0 | 6.9 | 6,942 | 64 |
| 3300039405_2 | Deinococcus | 97.67 | 0.99 | 4.1 | 4,212 | 67 | ||||
| G-Km37-3P3 | Gypsum | 3300039416 | 42.9 | 3300039416_1 | Chroococcidiopsis | 99.48 | 1.63 | 6.6 | 6,618 | 153 |
| 3300039416_2 | Deinococcus | 97.67 | 0.99 | 4.1 | 4,213 | 66 | ||||
| G-MTQ-3P1 | Gypsum | 3300038622 | 16.2 | 3300038622_1 | Chroococcidiopsis | 99.48 | 1.63 | 6.6 | 6,601 | 163 |
| 3300038622_2 | Methylobacterium | 52.45 | 1.25 | 4.2 | 4,745 | 668 | ||||
| G-MTQ-3P2 | Gypsum | 3300037877 | 9.9 | 3300037877_1 | Chroococcidiopsis | 99.48 | 1.63 | 6.6 | 6,608 | 161 |
| H-SG-1P1 | Gypsum | 3300039034 | 38.8 | 3300039034_1 | Chroococcidiopsis | 99.48 | 1.63 | 6.6 | 6,605 | 160 |
| H-SG-2P1 | Gypsum | 3300039035 | 43.1 | 3300039035_2 | Chroococcidiopsis | 99.48 | 1.63 | 6.6 | 6,619 | 155 |
| 3300039035_3 | Deinococcus | 97.67 | 0.99 | 4.1 | 4,230 | 70 | ||||
| I-MTQ-2P3 | Ignimbrite | 3300039417 | 20 | 3300039417_1 | Chroococcidiopsis | 97.11 | 4.52 | 7.6 | 7,825 | 531 |
| 3300039417_2 | Deinococcus | 98.52 | 0.99 | 4.2 | 4,428 | 95 | ||||
| 3300039417_3 | Thermomicrobiales | 63.91 | 1.89 | 2.4 | 2,800 | 503 | ||||
| I-MTQ-3P1 | Ignimbrite | 3300039418 | 28.2 | 3300039418_3 | Deinococcus | 97.67 | 0.99 | 4.1 | 4,241 | 70 |
| I-MTQ-3P3 | Ignimbrite | 3300039424 | 30.6 | 3300039424_2 | Aquamicrobium | 99.59 | 0.75 | 4.4 | 4,417 | 7 |
| 3300039424_3 | Deinococcus | 97.25 | 0.99 | 4.1 | 4,315 | 99 | ||||
| 3300039424_4 | Microcella | 99.38 | 0.25 | 2.5 | 2,464 | 5 | ||||
| I-MTQ-4P3 | Ignimbrite | 3300039425 | 10.3 | 3300039425_1 | Deinococcus | 97.67 | 0.99 | 4.1 | 4,237 | 70 |
| S-NGV-2P1 | Sandstone | 3300039401 | 43 | 3300039401_1 | Chroococcidiopsis | 99.48 | 1.63 | 6.6 | 6,617 | 153 |
| 3300039401_2 | Deinococcus | 97.67 | 0.99 | 4.1 | 4,214 | 67 | ||||
| S-NGV-2P2 | Sandstone | 3300039032 | 6.8 | 3300039032_1 | Chroococcidiopsis | 99.48 | 1.63 | 6.5 | 6,596 | 163 |
| S-NGV-3P2 | Sandstone | 3300039033 | 6.8 | 3300039033_1 | Chroococcidiopsis | 99.48 | 1.63 | 6.6 | 6,618 | 158 |
Cyanobacterial isolates were obtained by incubating ground colonized rock samples collected in the Atacama and Negev Deserts (3, 4) in Bold’s basal medium (11) and in BG11 liquid medium (12) for 5 weeks at 25°C under 24 μM photons/m2/s of white light (WL) using Philips daylight deluxe linear fluorescent T12 40-W light bulbs and a combination of neutral-density filters (299 1.2ND and 298 0.15ND; Lee Filters, Burbank, CA). Single colonies from 1% agar BG11 plates were then transferred to liquid BG11 medium and grown under WL; it is important to note that these were not anoxic cyanobacterial cultures but, rather, a mixture of cyanobacteria and heterotrophic bacteria. Total DNA was extracted from cell pellets using the PowerSoil DNA extraction kit (MoBio Laboratories, Inc., Solana Beach, CA). Nextera libraries, with Ranger size technology, were made with total DNA and sequenced to a 2-Gb depth using 2 × 150-nucleotide (nt) reads on an Illumina NovaSeq instrument at the Department of Energy (DOE) Joint Genome Institute (JGI). Sequence quality control was performed with the BBTools package (https://jgi.doe.gov/data-and-tools/bbtools/), and sequence reads were assembled with metaSPAdes version 3.13.0 using the “metagenome” flag and running the assembly module without error correction and with kmer sizes 33, 55, 77, 99, and 127 (13). MetaBAT v2.12.1 (14) was used for binning. MAGs were evaluated with CheckM v1.0.12 (15) and annotated with GTDB-Tk version v0.2.2 and the GTDB database release 86 (16). Default parameters were used for all software unless otherwise noted. Only high-quality (HQ) and medium-quality (MQ) bins were reported based on Minimum Information about a Metagenome-Assembled Genome (MIMAG) standards (17).
High-quality MAGs of cyanobacteria, together with MAGs of heterotrophic bacteria, were recovered from most samples (Table 1). All cyanobacteria belonged to the Chroococcidiopsis genus; Deinococcus was the most common heterotrophic bacterium, but we also found members of the Proteobacteria, Actinobacteria, and Chloroflexi, illustrating the diversity of these communities.
Data availability.
The raw sequencing data are available from the National Centre for Biotechnology Information under BioProject numbers PRJNA654119, PRJNA654120, PRJNA654121, PRJNA654122, PRJNA654123, PRJNA654124, PRJNA677471, PRJNA677472, PRJNA677473, PRJNA677474, PRJNA677475, PRJNA677476, PRJNA677477, and PRJNA677478. The metagenome coassembly and functional annotation are available from the JGI Genome Portal under the IMG taxon IDs reported in Table 1. To obtain cultures of cyanobacterial isolates, please contact the corresponding author.
ACKNOWLEDGMENTS
These sequence data were produced by the U.S. Department of Energy Joint Genome Institute (http://www.jgi.doe.gov/) in collaboration with the user community. We thank the following individuals for their support for library preparation, sequencing, and analysis: Marcel Huntemann, Alicia Clum, Brian Foster, Bryce Foster, Simon Roux, Krishnaveni Palaniappan, Neha Varghese, Supratim Mukherjee, T. B. K. Reddy, Chris Daum, Alex Copeland, I.-Min A. Chen, Natalia N. Ivanova, Nikos C. Kyrpides, Miranda Harmon-Smith, and Emiley A. Eloe-Fadrosh.
This work was supported by NSF grant DEB1556574 and NASA grant NNX15AP18G.
Contributor Information
Jocelyne DiRuggiero, Email: jdiruggiero@jhu.edu.
Frank J. Stewart, Montana State University
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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 raw sequencing data are available from the National Centre for Biotechnology Information under BioProject numbers PRJNA654119, PRJNA654120, PRJNA654121, PRJNA654122, PRJNA654123, PRJNA654124, PRJNA677471, PRJNA677472, PRJNA677473, PRJNA677474, PRJNA677475, PRJNA677476, PRJNA677477, and PRJNA677478. The metagenome coassembly and functional annotation are available from the JGI Genome Portal under the IMG taxon IDs reported in Table 1. To obtain cultures of cyanobacterial isolates, please contact the corresponding author.