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. 2021 Jun 3;10(22):e00258-21. doi: 10.1128/MRA.00258-21

Metagenome Sequencing to Explore Phylogenomics of Terrestrial Cyanobacteria

Ryan D Ward a,b, Jason E Stajich c,d, Jeffrey R Johansen e, Marcel Huntemann f, Alicia Clum f, Brian Foster f, Bryce Foster f, Simon Roux f, Krishnaveni Palaniappan f, Neha Varghese f, Supratim Mukherjee f, T B K Reddy f, Chris Daum f, Alex Copeland f, I-M A Chen f, Natalia N Ivanova f, Nikos C Kyrpides f, Nicole Shapiro f, Emiley A Eloe-Fadrosh f, Nicole Pietrasiak a,✉
Editor: J Cameron Thrashg
PMCID: PMC8354539  PMID: 34080906

ABSTRACT

Cyanobacteria are ubiquitous microorganisms with crucial ecosystem functions, yet most knowledge of their biology relates to aquatic taxa. We have constructed metagenomes for 50 taxonomically well-characterized terrestrial cyanobacterial cultures. These data will support phylogenomic studies of evolutionary relationships and gene content among these unique algae and their aquatic relatives.

ANNOUNCEMENT

Cyanobacteria, or blue-green algae, are found in nearly all aquatic and terrestrial habitats exposed to sunlight, ranging from marine systems, freshwater bodies, and thermal springs to soils and rock surfaces. They represent important ecosystem components, which perform crucial roles in biogeochemical cycling. However, knowledge of their taxonomy, phylogenomics, and physiology has been largely based on aquatic taxa. In the past 20 years, our team has discovered and described terrestrial cyanobacteria collected from extreme environments, including desert soils, ephemerally wet rock walls, and tropical damp cave walls, greatly enriching our understanding of cyanobacterial systematics (1–15). Reference strains of genus and species types are maintained in two algae culture collections at John Carroll University (JCU) and New Mexico State University (NMSU). The cultures are nonaxenic and represent unialgal polycultures containing primarily cyanobacteria and heterotrophic microbial associates. We used shotgun metagenomics of selected strains to support future investigation of the phylogenomic relationships of these unique algae.

Fifty unialgal polycultures of cyanobacterial reference strains from the JCU and NMSU culture collections were selected, representing species taxonomically evaluated within the last 2 decades (Fig. 1). Detailed protocols for biomass growth, tissue harvesting, and DNA extraction can be found at protocols.io (dx.doi.org/10.17504/protocols.io.brg4m3yw). Briefly, biomass of each taxon was grown in liquid Z8 medium (16) and harvested after several weeks to months depending on the growth rate. Harvesting included cleaning, biomass concentration, biomass flash-freezing in liquid nitrogen, and storage at −80°C. We extracted DNA using the Qiagen DNeasy PowerLyzer microbial kit. The extraction procedure included an initial bead-beating step in a Precellys homogenizer for 45 s at 5,000 rpm, repeating four times. Samples were then processed following the manufacturer’s protocol for the kit and stored at −20°C until mailing to the Joint Genome Institute (JGI).

FIG 1.

FIG 1

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Light micrographs of representative cyanobacterial species maintained in unialgal cultures and studied in this project. Images represent cell morphologies in the stationary phase of the cyanobacterial life cycle. Wet mounts of cyanobacterial biomass were observed using a Zeiss AxioImager.A2 microscope equipped with Nomarski differential interference contrast optics and a Zeiss Axiocam 305 color camera at ×400 or ×1,000 magnification. (A) Nodosilinea sp. strain WJT8-NPBG4; (B) Myxacorys chilensis ATA2-1-KO14; (C) Trichocoleus desertorum ATA4-8-CV12; (D) Cyanosarcina radialis HA8281-LM2; (E) Aphanocapsa lilacina HA4352-LM1; (F) Pleurocapsa minor HA4340-MV1; (G) Kastovskya adunca ATA6-11-RM4; (H) Hormoscilla sp. strain CMT-3BRIN-NPC48; (I) Microcoleus vaginatus WJT46-NPBG5; (J) Mojavia pulchra JT2-VF2; (K) Spirirestis rafaelensis WJT71-NPBG6; (L) Brasilonema octagenarum HA4186-MV1. Bars, 10 μm (A–E, G–I, and K) and 20 μm (F, J, and L).

Plate-based DNA library preparation for Illumina sequencing was performed using KAPA Biosystems high-throughput library preparation kit p/n KK8235 on a PerkinElmer Sciclone next-generation sequencing (NGS) robotic liquid handling system. Then, 200 ng of sample DNA was sheared to 300 bp using a Covaris LE220 focused ultrasonicator. The sheared DNA fragments were size selected by double solid-phase reversible immobilization (SPRI), and then the selected fragments were end repaired, A tailed, and ligated with Illumina-compatible sequencing adaptors from IDT containing a unique molecular index barcode for each sample library. The prepared libraries were quantified with a KAPA Biosystems quantitative PCR (qPCR) kit on a Roche LightCycler 480 real-time PCR instrument. Genomic libraries were sequenced with a NovaSeq instrument (Illumina, San Diego, CA) using NovaSeq XP V1 reagent kits and an S4 flow cell following a 2 × 150-bp indexed run recipe. Demultiplexed reads were processed with BBDuk v38.87 (17) to remove contaminants, trim adapter sequence and “G” homopolymers ≥5 in size at the ends, quality trim reads, and remove reads with ≥4 “N” bases, with an average quality score of <3, or with a length of <51 bp. After processing, 2,021,674,638 reads remained (per sample range, 24,625,170 to 59,843,005; mean ± standard deviation, 40,433,493 ± 8,547,361).

Cleaned reads were assembled with metaSPAdes v3.13.0 (18) (-meta option) into contigs with parameters for a minimum contig length of 2 kb (-m 2000 option) and default kmer options for paired 150-bp reads. Across all assemblies, 745,331 metagenomic contigs were retained after quality control using AAFTF vecscreen v0.2.3 (19) (range of assembly GC content, 40.09% to 66.57%; GC content mean ± standard deviation, 59.94% ± 4.96%; range of assembly N50, 10,169 to 456,261 bp; N50 mean ± standard deviation, 133,466 ± 100,540 bp).

Data availability.

All reads and assemblies were deposited under the NCBI accession numbers listed in Table 1. We also provided accession identifiers linking to JGI projects associated with each sample, including available IMG (20) data (Table 1).

TABLE 1.

Metadata, accession numbers, and metagenome statistics for the 50 cyanobacterial cultures investigated in this studya

Species Available at culture collections Strain ID Alternative strain ID BioProject no. SRA run no. JGI IMGb No. of reads No. of contigs N50 (bp) GC content (%) Habitat Location
Aetokthonos hydrillicola NMSU, JCU, CCALA B3-Florida CCALA 1050 PRJNA617093 SRR12347192 3300036376 56,817,878  54,864  184,060  63.45 Aquatic epiphyte South Carolina, USA
Aphanocapsa lilacina NMSU, JCU HA4352-LM1 PRJNA677053 SRR13206895 3300039303 58,991,043  38,358  112,017  63.64 Cave rock wall Hawaii, USA
Aphanocapsa sp. NMSU, JCU GSE-SYN-MK-11-07L PRJNA621664 SRR11678123 3300035009 26,644,370  1,052  87,507  48.55 Desert wet wall Utah, USA
Aphanothece saxicola NMSU, JCU GSE-SYN-MK-01-06B PRJNA621658 SRR11676827 3300035003 50,225,611  8,874  272,324  66.57 Desert wet wall Utah, USA
Aphanothece sp. NMSU, JCU CMT-3BRIN-NPC111 PRJNA617094 SRR12347633 3300036407 41,058,001  13,407  164,105  59.69 Desert soil California, USA
Brasilonema angustatum NMSU, JCU HA4187-MV1 PRJNA617095 SRR12347719 3300036389 51,374,669  22,657  78,161  54.18 Tropical soil Hawaii, USA
Brasilonema octagenarum NMSU, JCU HA4186-MV1 PRJNA621669 SRR11678155 3300035014 41,935,410  2,727  183,890  63.68 On wood in tropics Hawaii, USA
Calothrix sp. NMSU, JCU FI2-JRJ7 PRJNA617096 SRR12347730 3300036390 26,844,447  1,488  168,980  56.22 Desert soil California, USA
Chroococcus sp. NMSU, JCU CMT-3BRIN-NPC107 PRJNA653492 SRR12688413 3300037833 47,424,890  59,802  35,531  63.26 Desert soil California, USA
Cyanomargarita calcarea NMSU, JCU GSE-NOS-MK-12-04C PRJNA621661 SRR11676926 3300035006 30,710,984  5,791  264,901  58.92 Desert wet wall Utah, USA
Cyanosarcina radialis NMSU, JCU HA8281-LM2 PRJNA653493 SRR12688412 3300037834 39,248,498  48,900  35,006  63.37 Cave rock wall Hawaii, USA
Desmonostoc geniculatum NMSU, JCU HA4340-LM1 PRJNA621655 SRR11676647 3300035000 51,944,514  29,336  130,707  61.24 Cave rock wall Hawaii, USA
Desmonostoc vinosum NMSU, JCU HA7617-LM4 PRJNA650882 SRR12951526 3300038554 36,690,552  6,487  166,368  60.96 Cave rock wall Hawaii, USA
Drouetiella hepatica NMSU, JCU UHER 2000/2452 PRJNA617097 SRR12347860 3300036391 42,783,418  20,061  28,986  65.05 Rock surface Kosice, Slovakia
Gloeocapsa sp. NMSU, JCU UFS-A4-WI-NPMV-4B04 PRJNA617098 SRR12347921 3300036443 29,499,512  17,169  32,766  60.53 Desert soil Utah, USA
Goleter apudmare NMSU, JCU, CCALA HA4340-LM2 CCALA 1075 PRJNA621659 SRR11676930 3300035004 36,243,261  714  190,367  59.38 Cave rock wall Hawaii, USA
Hassallia sp. NMSU, JCU WJT32-NPBG1 PRJNA617099 SRR12347922 3300036392 33,287,445  4,616  21,632  58.06 Desert soil California, USA
Hormoscilla sp. NMSU, JCU CMT-3BRIN-NPC48 PRJNA650881 SRR12951525 3300038553 42,048,713  5,825  143,678  59.26 Desert soil California, USA
Iphinoe sp. NMSU, JCU HA4291-MV1 PRJNA617100 SRR12349226 3300036393 31,352,639  32,008  107,621  62.85 Tropical soil Hawaii, USA
Kaiparowitsia implicata NMSU, JCU GSE-PSE-MK54-09C PRJNA650883 SRR13242888 3300038555 43,375,246  4,576  456,261  63.35 Desert wet wall Utah, USA
Kastovskya adunca NMSU, JCU, CCALA ATA6-11-RM4 CCALA 1025 PRJNA621676 SRR11678224 3300034631 42,257,751  47,939  14,667  63.07 Desert soil Atacama, Chile
Komarekiella atlantica NMSU, JCU HA4396-MV6 PRJNA650825 SRR12951531 3300038556 39,748,068  24,886  121,785  64.40 Tropical vernal pool Hawaii, USA
Lyngbya sp. NMSU, JCU HA4199-MV5 PRJNA621654 SRR11676618 3300034630 37,379,750  5,629  214,210  61.23 Tropical soil Hawaii, USA
Microcoleus vaginatus NMSU, JCU WJT46-NPBG5 PRJNA677056 SRR13207170 3300039305 40,531,812 28,602  165,791  60.22 Desert soil California, USA
Mojavia pulchra NMSU, JCU, CCALA JT2-VF2 CCALA 691 PRJNA650826 SRR12951532 3300038557 54,924,618  10,021  208,763  62.75 Desert soil California, USA
Myxacorys californica NMSU, JCU, UTEX WJT36-NPBG1 UTEX B 3157 PRJNA621674 SRR11678221 3300035019 32,998,795 9,403  81,746  64.17 Desert soil California, USA
Myxacorys chilensis NMSU, JCU, UTEX ATA2-1-KO14 UTEX B 3158 PRJNA621667 SRR11678144 3300035012 46,028,284 19,551  69,559  60.50 Desert soil Coquimbo, Chile
Nodosilinea sp. NMSU, JCU WJT8-NPBG4 PRJNA621656 SRR11676645 3300035001 36,650,447  2,944  173,054  65.12 Desert soil California, USA
Nostoc desertorum NMSU, JCU, CCALA CM1-VF14 CCALA 693 PRJNA617101 SRR12349250 3300036444 55,466,988  7,058  211,685  62.42 Desert soil California, USA
Nostoc indistinguendum NMSU, JCU, CCALA CM1-VF10 CCALA 692 PRJNA621666 SRR11678133 3300035011 34,734,084  13,226  98,409  54.74 Desert soil California, USA
Oscillatoria princeps NMSU RMCB-10 PRJNA621670 SRR11678154 3300035015 35,756,581 29,084  28,454  61.51 Surface water Lower Austria, Austria
Oscillatoria tanganyikae NMSU, JCU FI6-MK23 PRJNA621665 SRR11678132 3300035010 41,220,548  7,027  306,031  59.66 Desert soil California, USA
Pegethrix bostrychoides NMSU, JCU GSE-TBD4-15B PRJNA617102 SRR12349533 3300036394 34,506,500  2,385  397,454  61.39% Desert wet wall Utah, USA
Pelatocladus maniniholoensis NMSU, JCU HA4357-MV3 PRJNA653494 SRR12687981 3300037800 30,851,680  553  52,911  40.09% Cave rock wall Hawaii, USA
Plectolyngbya sp. NMSU, JCU WJT66-NPBG17 PRJNA617103 SRR12349534 3300036395 24,625,170  9,370  10,169  53.14 Desert soil California, USA
Pleurocapsa minor NMSU, JCU GSE-CHR-MK-17-07R PRJNA677054 SRR13207074 3300039304 44,764,195  25,094  40,205  64.01 Desert wet wall Utah, USA
Pleurocapsa minor NMSU, JCU HA4230-MV1 PRJNA617104 SRR12349680 3300036396 59,843,005  708  316,355  63.57 Tropical rock wall Hawaii, USA
Scytolyngbya sp. NMSU, JCU HA4215-MV1 PRJNA617105 SRR12349737 3300036104 33,289,893  8,107  243,918  60.55 Freshwater stream Hawaii, USA
Scytonema hyalinum NMSU, JCU WJT4-NPBG1 PRJNA617106 SRR12349874 3300036520 40,826,558  35,954  57,285  64.29 Desert soil California, USA
Scytonematopsis contorta NMSU, JCU, UTEX HA4267-MV1 UTEX 2964 PRJNA653495 SRR12688486 3300037859 41,139,075  2,560  124,805  50.66 Tropical vernal pool Hawaii, USA
Spirirestis rafaelensis NMSU, JCU WJT71-NPBG6 PRJNA683097 SRR13242887 3300042538 30,810,560  12,769  49,002  61.71 Desert soil California, USA
Stenomitos rutilans NMSU, JCU HA7619-LM2 PRJNA617107 SRR12350322 3300036446 39,342,385  29,421  125,980  59.27 Cave rock wall Hawaii, USA
Symplocastrum torsivum NMSU, JCU, CCALA, UTEX CPER-KK1 CCALA 1031
UTEX B 3163		 PRJNA617108 SRR12350505 3300036521 45,589,224  7,498  188,807  61.87 Grassland soil Colorado, USA
Tildeniella nuda NMSU, JCU ZEHNDER 1965/U140 PRJNA621657 SRR11676687 3300035002 43,732,034  26,865  163,389  64.07 Temperate wet wall Zurich, Switzerland
Tildeniella torsiva NMSU, JCU UHER 1998/13D PRJNA653496 SRR12689282 3300037860 51,170,286  22,112  16,291  50.54 Temperate wet wall Kosice, Slovakia
Timaviella obliquedivisa NMSU, JCU GSE-PSE-MK23-08B PRJNA621673 SRR11678220 3300035018 43,160,626  11,520  86,031  58.41 Desert wet wall Utah, USA
Tolypothrix brevis NMSU, JCU GSE-NOS-MK-07-07A PRJNA621662 SRR11678125 3300035007 36,087,578  9,013  171,611  59.37 Desert wet wall Utah, USA
Tolypothrix carrinoi NMSU, JCU HA7290-LM1 PRJNA621663 SRR11678124 3300035008 36,281,317  43,124  40,599  59.34 Cave rock wall Hawaii, USA
Trichocoleus desertorum NMSU, JCU ATA4-8-CV12 PRJNA621668 SRR11678143 3300035013 37,070,905 5,401  91,542  60.17 Desert soil Atacama, Chile
“Trichormus” sp. NMSU, JCU ATA11-4-KO1 PRJNA621660 SRR11676933 3300035005 32,384,820  832  238,030  52.69 Desert soil Tarapaca, Chile
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a

Cyanobacterial cultures are available upon request from the research culture collections of Jeffrey R. Johansen (johansen@jcu.edu) at John Carroll University (JCU) and Nicole Pietrasiak (npietras@nmsu.edu) at New Mexico State University (NMSU). The selected strains are also available publicly at the University of Texas Culture Collection of Algae (UTEX) and the Culture Collection of Autotrophic Organisms in Třeboň, Czech Republic (CCALA). Accordingly, alternative UTEX and CCALA strain identifiers are given in the table.

b

JGI IMG/M, Joint Genome Institute Integrated Microbial Genomes and Microbiomes database.

ACKNOWLEDGMENTS

We thank the National Park Service and Bureau of Land Management for permission to work within Joshua Tree National Park (yielding the WJT strains under permit JOTR-2006-SCI-0018), Mojave National Preserve (CMT strains, permits MOJA-2008-SCI-0024 and MOJA-2009-SCI-0039), and Grand Staircase-Escalante National Monument (GSE strains, permit UT-06-032-12-P).

We thank the National Science Foundation (NSF) for supporting J.R.J.’s sample collection of soils from the Atacama Desert, isolation of ATA strains, and sequencing of those strains (NSF grant numbers DEB-0842702 and DEB-841734, respectively), as well as the collection and floristic research of biological soil crusts from various North American desert locations (NSF grant number DEB-9870201). Any opinions, findings, conclusions, or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation. The California Desert Research Fund at The Community Foundation, Robert Lee Graduate Student Research Grant, and the Phycological Society Grants in Aid of Research fund awarded to Nicole Pietrasiak provided support for the sampling campaigns and subsequent cyanobacterial research associated with WJT and CMT strains.

We are grateful to John Carroll University for decades of support for J.R.J.’s cyanobacterial culture collection. We thank the numerous students and colleagues who over the past 30 years collaborated with J.R.J. and led to the isolation of many of the strains investigated in this study. Truc Mai assisted with initial biomass growth of cyanobacterial cultures at New Mexico State University. We also are grateful to Andrew Dominguez and Anthony Granite, who assisted R.D.W. with genomic DNA extractions at NMSU.

J.E.S. is a CIFAR fellow in the program Fungal Kingdom: Threats and Opportunities.

Software development was partially supported by NSF DEB-1441715 and USDA-NIFA Hatch project CA-R-PPA-5062-H. Data analyses performed at the High-Performance Computing Cluster at the University of California Riverside in the Institute of Integrative Genome Biology were supported by NSF grant DBI-1429826 and NIH grant S10-OD016290. The work conducted by 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 under contract number DE-AC02-05CH11231.

Contributor Information

Nicole Pietrasiak, Email: npietras@nmsu.edu.

J. Cameron Thrash, University of Southern California

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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

All reads and assemblies were deposited under the NCBI accession numbers listed in Table 1. We also provided accession identifiers linking to JGI projects associated with each sample, including available IMG (20) data (Table 1).

TABLE 1.

Metadata, accession numbers, and metagenome statistics for the 50 cyanobacterial cultures investigated in this studya

Species Available at culture collections Strain ID Alternative strain ID BioProject no. SRA run no. JGI IMGb No. of reads No. of contigs N50 (bp) GC content (%) Habitat Location
Aetokthonos hydrillicola NMSU, JCU, CCALA B3-Florida CCALA 1050 PRJNA617093 SRR12347192 3300036376 56,817,878  54,864  184,060  63.45 Aquatic epiphyte South Carolina, USA
Aphanocapsa lilacina NMSU, JCU HA4352-LM1 PRJNA677053 SRR13206895 3300039303 58,991,043  38,358  112,017  63.64 Cave rock wall Hawaii, USA
Aphanocapsa sp. NMSU, JCU GSE-SYN-MK-11-07L PRJNA621664 SRR11678123 3300035009 26,644,370  1,052  87,507  48.55 Desert wet wall Utah, USA
Aphanothece saxicola NMSU, JCU GSE-SYN-MK-01-06B PRJNA621658 SRR11676827 3300035003 50,225,611  8,874  272,324  66.57 Desert wet wall Utah, USA
Aphanothece sp. NMSU, JCU CMT-3BRIN-NPC111 PRJNA617094 SRR12347633 3300036407 41,058,001  13,407  164,105  59.69 Desert soil California, USA
Brasilonema angustatum NMSU, JCU HA4187-MV1 PRJNA617095 SRR12347719 3300036389 51,374,669  22,657  78,161  54.18 Tropical soil Hawaii, USA
Brasilonema octagenarum NMSU, JCU HA4186-MV1 PRJNA621669 SRR11678155 3300035014 41,935,410  2,727  183,890  63.68 On wood in tropics Hawaii, USA
Calothrix sp. NMSU, JCU FI2-JRJ7 PRJNA617096 SRR12347730 3300036390 26,844,447  1,488  168,980  56.22 Desert soil California, USA
Chroococcus sp. NMSU, JCU CMT-3BRIN-NPC107 PRJNA653492 SRR12688413 3300037833 47,424,890  59,802  35,531  63.26 Desert soil California, USA
Cyanomargarita calcarea NMSU, JCU GSE-NOS-MK-12-04C PRJNA621661 SRR11676926 3300035006 30,710,984  5,791  264,901  58.92 Desert wet wall Utah, USA
Cyanosarcina radialis NMSU, JCU HA8281-LM2 PRJNA653493 SRR12688412 3300037834 39,248,498  48,900  35,006  63.37 Cave rock wall Hawaii, USA
Desmonostoc geniculatum NMSU, JCU HA4340-LM1 PRJNA621655 SRR11676647 3300035000 51,944,514  29,336  130,707  61.24 Cave rock wall Hawaii, USA
Desmonostoc vinosum NMSU, JCU HA7617-LM4 PRJNA650882 SRR12951526 3300038554 36,690,552  6,487  166,368  60.96 Cave rock wall Hawaii, USA
Drouetiella hepatica NMSU, JCU UHER 2000/2452 PRJNA617097 SRR12347860 3300036391 42,783,418  20,061  28,986  65.05 Rock surface Kosice, Slovakia
Gloeocapsa sp. NMSU, JCU UFS-A4-WI-NPMV-4B04 PRJNA617098 SRR12347921 3300036443 29,499,512  17,169  32,766  60.53 Desert soil Utah, USA
Goleter apudmare NMSU, JCU, CCALA HA4340-LM2 CCALA 1075 PRJNA621659 SRR11676930 3300035004 36,243,261  714  190,367  59.38 Cave rock wall Hawaii, USA
Hassallia sp. NMSU, JCU WJT32-NPBG1 PRJNA617099 SRR12347922 3300036392 33,287,445  4,616  21,632  58.06 Desert soil California, USA
Hormoscilla sp. NMSU, JCU CMT-3BRIN-NPC48 PRJNA650881 SRR12951525 3300038553 42,048,713  5,825  143,678  59.26 Desert soil California, USA
Iphinoe sp. NMSU, JCU HA4291-MV1 PRJNA617100 SRR12349226 3300036393 31,352,639  32,008  107,621  62.85 Tropical soil Hawaii, USA
Kaiparowitsia implicata NMSU, JCU GSE-PSE-MK54-09C PRJNA650883 SRR13242888 3300038555 43,375,246  4,576  456,261  63.35 Desert wet wall Utah, USA
Kastovskya adunca NMSU, JCU, CCALA ATA6-11-RM4 CCALA 1025 PRJNA621676 SRR11678224 3300034631 42,257,751  47,939  14,667  63.07 Desert soil Atacama, Chile
Komarekiella atlantica NMSU, JCU HA4396-MV6 PRJNA650825 SRR12951531 3300038556 39,748,068  24,886  121,785  64.40 Tropical vernal pool Hawaii, USA
Lyngbya sp. NMSU, JCU HA4199-MV5 PRJNA621654 SRR11676618 3300034630 37,379,750  5,629  214,210  61.23 Tropical soil Hawaii, USA
Microcoleus vaginatus NMSU, JCU WJT46-NPBG5 PRJNA677056 SRR13207170 3300039305 40,531,812 28,602  165,791  60.22 Desert soil California, USA
Mojavia pulchra NMSU, JCU, CCALA JT2-VF2 CCALA 691 PRJNA650826 SRR12951532 3300038557 54,924,618  10,021  208,763  62.75 Desert soil California, USA
Myxacorys californica NMSU, JCU, UTEX WJT36-NPBG1 UTEX B 3157 PRJNA621674 SRR11678221 3300035019 32,998,795 9,403  81,746  64.17 Desert soil California, USA
Myxacorys chilensis NMSU, JCU, UTEX ATA2-1-KO14 UTEX B 3158 PRJNA621667 SRR11678144 3300035012 46,028,284 19,551  69,559  60.50 Desert soil Coquimbo, Chile
Nodosilinea sp. NMSU, JCU WJT8-NPBG4 PRJNA621656 SRR11676645 3300035001 36,650,447  2,944  173,054  65.12 Desert soil California, USA
Nostoc desertorum NMSU, JCU, CCALA CM1-VF14 CCALA 693 PRJNA617101 SRR12349250 3300036444 55,466,988  7,058  211,685  62.42 Desert soil California, USA
Nostoc indistinguendum NMSU, JCU, CCALA CM1-VF10 CCALA 692 PRJNA621666 SRR11678133 3300035011 34,734,084  13,226  98,409  54.74 Desert soil California, USA
Oscillatoria princeps NMSU RMCB-10 PRJNA621670 SRR11678154 3300035015 35,756,581 29,084  28,454  61.51 Surface water Lower Austria, Austria
Oscillatoria tanganyikae NMSU, JCU FI6-MK23 PRJNA621665 SRR11678132 3300035010 41,220,548  7,027  306,031  59.66 Desert soil California, USA
Pegethrix bostrychoides NMSU, JCU GSE-TBD4-15B PRJNA617102 SRR12349533 3300036394 34,506,500  2,385  397,454  61.39% Desert wet wall Utah, USA
Pelatocladus maniniholoensis NMSU, JCU HA4357-MV3 PRJNA653494 SRR12687981 3300037800 30,851,680  553  52,911  40.09% Cave rock wall Hawaii, USA
Plectolyngbya sp. NMSU, JCU WJT66-NPBG17 PRJNA617103 SRR12349534 3300036395 24,625,170  9,370  10,169  53.14 Desert soil California, USA
Pleurocapsa minor NMSU, JCU GSE-CHR-MK-17-07R PRJNA677054 SRR13207074 3300039304 44,764,195  25,094  40,205  64.01 Desert wet wall Utah, USA
Pleurocapsa minor NMSU, JCU HA4230-MV1 PRJNA617104 SRR12349680 3300036396 59,843,005  708  316,355  63.57 Tropical rock wall Hawaii, USA
Scytolyngbya sp. NMSU, JCU HA4215-MV1 PRJNA617105 SRR12349737 3300036104 33,289,893  8,107  243,918  60.55 Freshwater stream Hawaii, USA
Scytonema hyalinum NMSU, JCU WJT4-NPBG1 PRJNA617106 SRR12349874 3300036520 40,826,558  35,954  57,285  64.29 Desert soil California, USA
Scytonematopsis contorta NMSU, JCU, UTEX HA4267-MV1 UTEX 2964 PRJNA653495 SRR12688486 3300037859 41,139,075  2,560  124,805  50.66 Tropical vernal pool Hawaii, USA
Spirirestis rafaelensis NMSU, JCU WJT71-NPBG6 PRJNA683097 SRR13242887 3300042538 30,810,560  12,769  49,002  61.71 Desert soil California, USA
Stenomitos rutilans NMSU, JCU HA7619-LM2 PRJNA617107 SRR12350322 3300036446 39,342,385  29,421  125,980  59.27 Cave rock wall Hawaii, USA
Symplocastrum torsivum NMSU, JCU, CCALA, UTEX CPER-KK1 CCALA 1031
UTEX B 3163		 PRJNA617108 SRR12350505 3300036521 45,589,224  7,498  188,807  61.87 Grassland soil Colorado, USA
Tildeniella nuda NMSU, JCU ZEHNDER 1965/U140 PRJNA621657 SRR11676687 3300035002 43,732,034  26,865  163,389  64.07 Temperate wet wall Zurich, Switzerland
Tildeniella torsiva NMSU, JCU UHER 1998/13D PRJNA653496 SRR12689282 3300037860 51,170,286  22,112  16,291  50.54 Temperate wet wall Kosice, Slovakia
Timaviella obliquedivisa NMSU, JCU GSE-PSE-MK23-08B PRJNA621673 SRR11678220 3300035018 43,160,626  11,520  86,031  58.41 Desert wet wall Utah, USA
Tolypothrix brevis NMSU, JCU GSE-NOS-MK-07-07A PRJNA621662 SRR11678125 3300035007 36,087,578  9,013  171,611  59.37 Desert wet wall Utah, USA
Tolypothrix carrinoi NMSU, JCU HA7290-LM1 PRJNA621663 SRR11678124 3300035008 36,281,317  43,124  40,599  59.34 Cave rock wall Hawaii, USA
Trichocoleus desertorum NMSU, JCU ATA4-8-CV12 PRJNA621668 SRR11678143 3300035013 37,070,905 5,401  91,542  60.17 Desert soil Atacama, Chile
“Trichormus” sp. NMSU, JCU ATA11-4-KO1 PRJNA621660 SRR11676933 3300035005 32,384,820  832  238,030  52.69 Desert soil Tarapaca, Chile
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a

Cyanobacterial cultures are available upon request from the research culture collections of Jeffrey R. Johansen (johansen@jcu.edu) at John Carroll University (JCU) and Nicole Pietrasiak (npietras@nmsu.edu) at New Mexico State University (NMSU). The selected strains are also available publicly at the University of Texas Culture Collection of Algae (UTEX) and the Culture Collection of Autotrophic Organisms in Třeboň, Czech Republic (CCALA). Accordingly, alternative UTEX and CCALA strain identifiers are given in the table.

b

JGI IMG/M, Joint Genome Institute Integrated Microbial Genomes and Microbiomes database.

Articles from Microbiology Resource Announcements are provided here courtesy of American Society for Microbiology (ASM)

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