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Nguyen TM, Pombubpa N, Huntemann M, Clum A, Foster B, Foster B, Roux S, Palaniappan K, Varghese N, Mukherjee S, Reddy TBK, Daum C, Copeland A, Chen IMA, Ivanova NN, Kyrpides NC, Harmon-Smith M, Eloe-Fadrosh EA, Pietrasiak N, Stajich JE, Hom EFY. Whole community shotgun metagenomes of two biological soil crust types from the Mojave Desert. Microbiol Resour Announc 2024; 13:e0098023. [PMID: 38329355 DOI: 10.1128/mra.00980-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/23/2024] [Indexed: 02/09/2024] Open
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.
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Affiliation(s)
- Thuy M Nguyen
- Department of Biology and Center for Biodiversity and Conservation Research, University of Mississippi, University, Mississippi, USA
| | - Nuttapon Pombubpa
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, USA
| | - Marcel Huntemann
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Alicia Clum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Brian Foster
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Bryce Foster
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Simon Roux
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Krishnaveni Palaniappan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Neha Varghese
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Supratim Mukherjee
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - T B K Reddy
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Chris Daum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Alex Copeland
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - I-Min A Chen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Natalia N Ivanova
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Nikos C Kyrpides
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Miranda Harmon-Smith
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Emiley A Eloe-Fadrosh
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Nicole Pietrasiak
- School of Life Sciences, University of Nevada-Las Vegas, Las Vegas, Nevada, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, USA
| | - Erik F Y Hom
- Department of Biology and Center for Biodiversity and Conservation Research, University of Mississippi, University, Mississippi, USA
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Nguyen TM, Pombubpa N, Huntemann M, Clum A, Foster B, Foster B, Roux S, Palaniappan K, Varghese N, Mukherjee S, Reddy TBK, Daum C, Copeland A, Chen IMA, Ivanova NN, Kyrpides NC, Harmon-Smith M, Eloe-Fadrosh EA, Pietrasiak N, Stajich JE, Hom EFY. Metatranscriptomes of two biological soil crust types from the Mojave desert in response to wetting. Microbiol Resour Announc 2024; 13:e0108023. [PMID: 38189307 PMCID: PMC10868201 DOI: 10.1128/mra.01080-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 12/13/2023] [Indexed: 01/09/2024] Open
Abstract
We present eight metatranscriptomic datasets of light algal and cyanolichen biological soil crusts from the Mojave Desert in response to wetting. These data will help us understand gene expression patterns in desert biocrust microbial communities after they have been reactivated by the addition of water.
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Affiliation(s)
- Thuy M. Nguyen
- Department of Biology and Center for Biodiversity and Conservation Research, University, University of Mississippi, Mississippi, USA
| | - Nuttapon Pombubpa
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, USA
| | - Marcel Huntemann
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Alicia Clum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Brian Foster
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Bryce Foster
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Simon Roux
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Krishnaveni Palaniappan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Neha Varghese
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Supratim Mukherjee
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - T. B. K. Reddy
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Chris Daum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Alex Copeland
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - I-Min A. Chen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Natalia N. Ivanova
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Nikos C. Kyrpides
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Miranda Harmon-Smith
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Emiley A. Eloe-Fadrosh
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Nicole Pietrasiak
- School of Life Sciences, University of Nevada-Las Vegas, Las Vegas, Nevada, USA
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, USA
| | - Erik F. Y. Hom
- Department of Biology and Center for Biodiversity and Conservation Research, University, University of Mississippi, Mississippi, USA
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Akagha MU, Pietrasiak N, Bustos DF, Vondrášková A, Lamb SC, Johansen JR. Albertania and Egbenema gen. nov. from Nigeria and the United States, expanding biodiversity in the Oculatellaceae (cyanobacteria). J Phycol 2023; 59:1217-1236. [PMID: 37696506 DOI: 10.1111/jpy.13389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 09/13/2023]
Abstract
Knowledge of the tropical terrestrial cyanobacterial flora from the African continent is still limited. Of 31 strains isolated from soil and subaerial samples collected in Lagos State, Nigeria, three were found to be in the Oculatellaceae, including two species in a new genus. Subsequently, isolates from microbial mats in White Sands National Park in New Mexico, United States, and from a rock near the ocean in Puerto Rico, United States, were found to belong to the new genus as well. Cyanobacterial isolates were characterized microscopically, sequenced for the 16S rRNA gene and associated ITS region, and phylogenetically analyzed. Egbenema gen. nov., with three new species, as well as two new species of Albertania were differentiated from all other Oculatellaceae. Both genera belong to a supported clade within the Oculatellaceae that includes Trichotorquatus and Komarkovaea. The two new species of Albertania, A. egbensis and A. latericola, were from the same sample, but were evolutionarily separate based on 16S rRNA gene phylogenies, percent identity below the 98.7% threshold, and ITS rRNA percent dissimilarity >7.0%. Egbenema aeruginosum gen. et sp. nov. was phylogenetically separated from Trichotorquatus and Albertania but was in a clade with other strains belonging to Egbenema. The two Egbenema strains from the United States are here named Egbenema epilithicum sp. nov. and Egbenema gypsiphilum sp. nov. Our results support the hypothesis that further species discoveries of novel cyanobacteria will likely be made in soils and subaerial habitats, as these habitats continue to be studied, both in tropical and temperate biomes.
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Affiliation(s)
- Mildred U Akagha
- Department of Biology, John Carroll University, University Heights, Ohio, USA
| | - Nicole Pietrasiak
- School of Life Sciences, University of Nevada-Las Vegas, Las Vegas, Nevada, USA
- Plant & Environmental Sciences Department, New Mexico State University, Las Cruces, New Mexico, USA
| | - David F Bustos
- US DOI White Sands National Park, Alamogordo, New Mexico, USA
| | - Alžběta Vondrášková
- Department of Botany, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Sandra C Lamb
- Department of Marine Sciences, University of Lagos, Akoka, Nigeria
| | - Jeffrey R Johansen
- Department of Biology, John Carroll University, University Heights, Ohio, USA
- Department of Botany, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
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Hansen FA, James DK, Anderson JP, Meredith CS, Dominguez AJ, Pombubpa N, Stajich JE, Romero-Olivares AL, Salley SW, Pietrasiak N. Landscape characteristics shape surface soil microbiomes in the Chihuahuan Desert. Front Microbiol 2023; 14:1135800. [PMID: 37350785 PMCID: PMC10282155 DOI: 10.3389/fmicb.2023.1135800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 05/02/2023] [Indexed: 06/24/2023] Open
Abstract
Introduction Soil microbial communities, including biological soil crust microbiomes, play key roles in water, carbon and nitrogen cycling, biological weathering, and other nutrient releasing processes of desert ecosystems. However, our knowledge of microbial distribution patterns and ecological drivers is still poor, especially so for the Chihuahuan Desert. Methods This project investigated the effects of trampling disturbance on surface soil microbiomes, explored community composition and structure, and related patterns to abiotic and biotic landscape characteristics within the Chihuahuan Desert biome. Composite soil samples were collected in disturbed and undisturbed areas of 15 long-term ecological research plots in the Jornada Basin, New Mexico. Microbial diversity of cross-domain microbial groups (total Bacteria, Cyanobacteria, Archaea, and Fungi) was obtained via DNA amplicon metabarcode sequencing. Sequence data were related to landscape characteristics including vegetation type, landforms, ecological site and state as well as soil properties including gravel content, soil texture, pH, and electrical conductivity. Results Filamentous Cyanobacteria dominated the photoautotrophic community while Proteobacteria and Actinobacteria dominated among the heterotrophic bacteria. Thaumarchaeota were the most abundant Archaea and drought adapted taxa in Dothideomycetes and Agaricomycetes were most abundant fungi in the soil surface microbiomes. Apart from richness within Archaea (p = 0.0124), disturbed samples did not differ from undisturbed samples with respect to alpha diversity and community composition (p ≥ 0.05), possibly due to a lack of frequent or impactful disturbance. Vegetation type and landform showed differences in richness of Bacteria, Archaea, and Cyanobacteria but not in Fungi. Richness lacked strong relationships with soil variables. Landscape features including parent material, vegetation type, landform type, and ecological sites and states, exhibited stronger influence on relative abundances and microbial community composition than on alpha diversity, especially for Cyanobacteria and Fungi. Soil texture, moisture, pH, electrical conductivity, lichen cover, and perennial plant biomass correlated strongly with microbial community gradients detected in NMDS ordinations. Discussion Our study provides first comprehensive insights into the relationships between landscape characteristics, associated soil properties, and cross-domain soil microbiomes in the Chihuahuan Desert. Our findings will inform land management and restoration efforts and aid in the understanding of processes such as desertification and state transitioning, which represent urgent ecological and economical challenges in drylands around the world.
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Affiliation(s)
- Frederick A. Hansen
- Department of Biology, New Mexico State University, Las Cruces, NM, United States
| | - Darren K. James
- Jornada Experimental Range Department, New Mexico State University, Las Cruces, NM, United States
| | - John P. Anderson
- Jornada Experimental Range Department, New Mexico State University, Las Cruces, NM, United States
| | | | - Andrew J. Dominguez
- Plant and Environmental Sciences Department, New Mexico State University, Las Cruces, NM, United States
| | - Nuttapon Pombubpa
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | | | - Shawn W. Salley
- U.S. Department of Agriculture-Natural Resources Conservation Service, Jornada Experimental Range, Las Cruces, NM, United States
| | - Nicole Pietrasiak
- Plant and Environmental Sciences Department, New Mexico State University, Las Cruces, NM, United States
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
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Hoellrich MR, James DK, Bustos D, Darrouzet-Nardi A, Santiago LS, Pietrasiak N. Biocrust carbon exchange varies with crust type and time on Chihuahuan Desert gypsum soils. Front Microbiol 2023; 14:1128631. [PMID: 37234525 PMCID: PMC10208066 DOI: 10.3389/fmicb.2023.1128631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/30/2023] [Indexed: 05/28/2023] Open
Abstract
Introduction In dryland systems, biological soil crusts (biocrusts) can occupy large areas of plant interspaces, where they fix carbon following rain. Although distinct biocrust types contain different dominant photoautotrophs, few studies to date have documented carbon exchange over time from various biocrust types. This is especially true for gypsum soils. Our objective was to assess the carbon exchange of biocrust types established at the world's largest gypsum dune field at White Sands National Park. Methods We sampled five different biocrust types from a sand sheet location in three different years and seasons (summer 2020, fall 2021, and winter 2022) for carbon exchange measurements in controlled lab conditions. Biocrusts were rehydrated to full saturation and light incubated for 30 min, 2, 6, 12, 24, and 36 h. Samples were then subject to a 12-point light regime with a LI-6400XT photosynthesis system to determine carbon exchange. Results Biocrust carbon exchange values differed by biocrust type, by incubation time since wetting, and by date of field sampling. Lichens and mosses had higher gross and net carbon fixation rates than dark and light cyanobacterial crusts. High respiration rates were found after 0.5 h and 2 h incubation times as communities recovered from desiccation, leveling off after 6 h incubation. Net carbon fixation of all types increased with longer incubation time, primarily as a result of decreasing respiration, which suggests rapid recovery of biocrust photosynthesis across types. However, net carbon fixation rates varied from year to year, likely as a product of time since the last rain event and environmental conditions preceding collection, with moss crusts being most sensitive to environmental stress at our study sites. Discussion Given the complexity of patterns discovered in our study, it is especially important to consider a multitude of factors when comparing biocrust carbon exchange rates across studies. Understanding the dynamics of biocrust carbon fixation in distinct crust types will enable greater precision of carbon cycling models and improved forecasting of impacts of global climate change on dryland carbon cycling and ecosystem functioning.
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Affiliation(s)
- Mikaela R. Hoellrich
- Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States
| | - Darren K. James
- USDA-ARS Jornada Experimental Range, New Mexico State University, Las Cruces, NM, United States
| | - David Bustos
- US DOI White Sands National Park, Alamogordo, NM, United States
| | | | - Louis S. Santiago
- Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Nicole Pietrasiak
- Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
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Palmer B, Pietrasiak N, Cobb P, Lipson D. Using simulated wildland fire to assess microbial survival at multiple depths from biocrust and bare soils. Front Microbiol 2023; 14:1123790. [PMID: 37007522 PMCID: PMC10064808 DOI: 10.3389/fmicb.2023.1123790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/23/2023] [Indexed: 03/19/2023] Open
Abstract
IntroductionSurface soil microbial communities are directly exposed to the heat from wildland fires. Due to this, the microbial community composition may be stratified within the soil profile with more heat tolerant microbes near the surface and less heat tolerant microbes, or mobile species found deeper in the soil. Biological soil crusts, biocrusts, are found on the soil surface and contain a diverse microbial community that is directly exposed to the heat from wildland fires.MethodsHere, we used a simulated fire mesocosm along with a culture-based approach and molecular characterization of microbial isolates to understand the stratification of biocrust and bare soil microbes after low severity (450°C) and high severity (600°C) fires. We cultured and sequenced microbial isolates from 2 to 6 cm depth from both fire types.ResultsThe isolates were stratified along the soil depth. Green algal isolates were less thermotolerant and found in the deeper depths (4–6 cm) and the control soils, while several cyanobacteria in Oscillatoriales, Synechococcales, and Nostocales were found at 2–3 cm depth for both fire temperatures. An Alphaproteobacteria isolate was common across several depths, both fire types, and both fire temperatures. Furthermore, we used RNA sequencing at three depths after the high severity fire and one control to determine what microbial community is active following a fire. The community was dominated by Gammaproteobacteria, however some Cyanobacteria ASVs were also present.DiscussionHere we show evidence of stratification of soil and biocrust microbes after a fire and provide evidence that these microbes are able to survive the heat from the fire by living just below the soil surface. This is a steppingstone for future work on the mechanisms of microbial survival after fire and the role of soil insulation in creating resilient communities.
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Affiliation(s)
- Brianne Palmer
- Department of Biology, San Diego State University, San Diego, CA, United States
- Department of Plant Science, University of California, Davis, Davis, CA, United States
- *Correspondence: Brianne Palmer,
| | - Nicole Pietrasiak
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Polina Cobb
- Department of Biology, San Diego State University, San Diego, CA, United States
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, San Diego, CA, United States
| | - David Lipson
- Department of Biology, San Diego State University, San Diego, CA, United States
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Baldarelli LM, Pietrasiak N, Osorio-Santos K, Johansen JR. Mojavia aguilerae and M. dolomitestris - two new Nostocaceae (Cyanobacteria) species from the Americas. J Phycol 2022; 58:502-516. [PMID: 35727130 DOI: 10.1111/jpy.13275] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 02/26/2022] [Indexed: 06/15/2023]
Abstract
While nostocacean cyanobacteria are ubiquitous and play critical roles in terrestrial ecosystems, their taxonomy and biogeography still entail mysteries. We isolated two Nostoc-like cyanobacteria from biological soil crusts of the Atacama (Chile) and Mojave (USA) Deserts. An initial 16S rRNA gene phylogeny placed both in monophyly with Mojavia pulchra. Here, we describe two new species of the previously monotypic Mojavia using a polyphasic approach including morphology, 16S rRNA phylogenies, secondary structure, and percent similarity of the 16S-23S ITS region. Like M. pulchra, both new species produce compact microcolonies, arthrospore-like akinetes, and monocytes, traits characteristic of the genus. Mojavia aguilerae sp. nov. is morphologically distinct from both other species in producing bluntly conical end cells, abundant enlarged akinetes in multiseriate filaments, and gold-colored cells during senescence. Mojavia dolomitestris sp. nov. exhibited distinctly firm, light-colored, compartmentalized mucilage. M. dolomitestris is somewhat cryptic with M. pulchra, but has more densely packed microcolonies, rarity and later onset of brownish sheath pigmentation, and an origin from soils derived from dolomite. The two new species strengthened the position of Mojavia as a robust genus sister to Nostoc. Although 16S rRNA gene data could not separate the Mojavia species from each other, the three species showed distinct dissimilarities in secondary ITS structure and differed greatly from Nostoc sensu stricto. The high dissimilarities between their 16S-23S ITS regions suggest a long evolutionary history of the three species as separate lineages. Mojavia is an evolutionary and ecologically unique nostocacean genus, and its rarity and restricted habitat point to an urgent need for recognition and protection.
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Affiliation(s)
- Lauren M Baldarelli
- Department of Biological Sciences, Kent State University, Kent, Ohio, 44242, USA
| | - Nicole Pietrasiak
- Plant and Environmental Sciences Department, New Mexico State University, 945 College Drive. Las Cruces, New Mexico, 88003, USA
| | - Karina Osorio-Santos
- Departamento de Biología Comparada, Universidad Nacional Autónoma de México (UNAM), Colonia Coyoacán, Código Postal 04451070474, P.O. Box 70-474, Ciudad de México, Mexico
| | - Jeffrey R Johansen
- Department of Biology, John Carroll University, University Heights, Ohio, 44118, USA
- Department of Botany, Faculty of Sciences, University of South Bohemia, Branišovská 31, České Budějovice, 370 05, Czech Republic
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Huang IS, Pietrasiak N, Gobler CJ, Johansen JR, Burkholder JM, D'Antonio S, Zimba PV. Diversity of bioactive compound content across 71 genera of marine, freshwater, and terrestrial cyanobacteria. Harmful Algae 2021; 109:102116. [PMID: 34815023 DOI: 10.1016/j.hal.2021.102116] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 09/16/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
Cyanobacterial blooms have increased in frequency, distribution, and intensity due to climate change and anthropogenic nutrient input. The release of bioactive compounds accumulated in these blooms can affect the health of humans and the environment. The co-occurrence of bioactive metabolites is well-documented in bloom samples from marine and freshwater ecosystems, with fewer reports from unialgal isolates. Cyanobacteria also are important terrestrial ecosystem components, especially in drylands, but reports on bioactive molecules from terrestrial cyanobacteria are sparse. This study determined bioactive metabolite profiles for 71 genera of cyanobacteria from seven orders isolated from freshwater (12 genera), marine (15 genera), and terrestrial (44 genera) habitats originally. Cultures were harvested for bioactive metabolites when entering the late-exponential phase for all 157 strains, and 33 were sampled at both early and late exponential phases. Bioactive metabolites were analyzed using an ultra high performance/pressure liquid chromatography in-line with a time-of-flight mass spectrometer. Overall, 12 bioactive classes of the 28 identified were ubiquitous in all samples. On average, each freshwater genus produced ∼12 bioactive classes, whereas each marine genus contained > 4 bioactive classes, and each terrestrial genus contained ∼6 bioactive classes. While 10 of 12 freshwater genera produced at least 10 bioactive classes, only a single genus each from marine and terrestrial habitats had the same number of bioactive classed accumulated. Aeruginosin was found in 58 of 71 total genera, carmabin in 51 of 71 genera, and anabaenopeptin in 48 of 71 genera. Chemotaxonomic use of these secondary metabolites may help resolve higher-level genetic classification(s). An additional growth curve experiment showed that bioactive metabolites were produced at both early and late exponential growth phases. The bioactive metabolite accumulation pattern between early and late exponential phases differed by bioactive classes, genera, and habitats. This survey of 55 bioactive classes in cyanobacteria isolated from freshwater, marine, and terrestrial habitats (71 genera) provides as one of the first systematic bioactive metabolite profiles for cyanobacteria, which should be useful in environmental and drinking water management. Further, it offers novel insights about the toxin potential of selected terrestrial cyanobacteria.
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Affiliation(s)
- I-Shuo Huang
- Center for Coastal Studies, Texas A&M University-Corpus Christi, 6300 Ocean Dr., Corpus Christi, TX 78412,USA; United States Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5001 Campus Drive, College Park, MD 20740,USA.
| | - Nicole Pietrasiak
- Department of Plant and Environmental Sciences, New Mexico State University, 1780 E University Ave, Las Cruces, NM 88003,USA
| | - Christopher J Gobler
- School of Marine and Atmospheric Science, Stony Brook University, 100 Nicolls Rd, Stony Brook, NY 11794,USA
| | - Jeffrey R Johansen
- Department of Biology, John Carroll University, 1 John Carroll Blvd, University Heights, OH 44118,USA; Department of Botany, Faculty of Sciences, University of South Bohemia, Branišovská 31, České Budějovice 37005, Czechia,USA
| | - JoAnn M Burkholder
- Center for Applied Aquatic Ecology, North Carolina State University, Raleigh, NC 27695,USA
| | - Sue D'Antonio
- Agilent Technologies Inc., 1834 TX-71 W, Cedar Creek, TX 78612,USA
| | - Paul V Zimba
- Center for Coastal Studies, Texas A&M University-Corpus Christi, 6300 Ocean Dr., Corpus Christi, TX 78412,USA; PVZimba, Inc., 12241 Percival St, Chester, VA 23831, USA
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Veste M, Felde VJMNL, Warren SD, Pietrasiak N. Editorial: Ecological Development and Functioning of Biological Soil Crusts After Natural and Human Disturbances. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.713584] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Pietrasiak N, Reeve S, Osorio-Santos K, Lipson DA, Johansen JR. Trichotorquatus gen. nov. - a new genus of soil cyanobacteria discovered from American drylands 1. J Phycol 2021; 57:886-902. [PMID: 33583028 DOI: 10.1111/jpy.13147] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 11/15/2020] [Accepted: 12/06/2020] [Indexed: 05/25/2023]
Abstract
Cyanobacteria are crucial ecosystem components in dryland soils. Advances in describing α-level taxonomy are needed to understand what drives their abundance and distribution. We describe Trichotorquatus gen. nov. (Oculatellaceae, Synechococcales, Cyanobacteria) based on four new species isolated from dryland soils including the coastal sage scrub near San Diego, California (USA), the Mojave and Colorado Deserts with sites at Joshua Tree National Park and Mojave National Preserve, California (USA), and the Atacama Desert (Chile). The genus is morphologically characterized by having thin trichomes (<4.5 μm wide), cells both shorter and longer than wide, rarely occurring single and double false branching, necridia appearing singly or in rows, and sheaths with a distinctive collar-like fraying and widening mid-filament, the feature for which the genus is named. The genus is morphologically nearly identical with Leptolyngbya sensu stricto but is phylogenetically quite distant from that genus. It is consequently a cryptic genus that will likely be differentiated in future studies based on 16S rRNA sequence data. The type species, T. maritimus sp. nov. is morphologically distinct from the other three species, T. coquimbo sp. nov., T. andrei sp. nov. and T. ladouxae sp. nov. However, these latter three species are morphologically very close and are considered by the authors to be cryptic species. All species are separated phylogenetically based on sequence of the 16S-23S ITS region. Three distinct ribosomal operons were recovered from the genus, lending difficulty to recognizing further diversity in this morphologically cryptic genus.
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Affiliation(s)
- Nicole Pietrasiak
- Plant and Environmental Sciences Department, New Mexico State University, 945 College Drive, Las Cruces, New Mexico, 88003, USA
| | - Sharon Reeve
- Department of Biology, San Diego State University, 5500 Campanile Drive, Mail Code 4614, San Diego, California, 92182, USA
| | - Karina Osorio-Santos
- Departamento de Biología Comparada, Universidad Nacional Autónoma de México (UNAM), Colonia Coyoacán, Código Postal 04451070474, P.O. Box 70-474, Ciudad de México, México
| | - David A Lipson
- Department of Biology, San Diego State University, 5500 Campanile Drive, Mail Code 4614, San Diego, California, 92182, USA
| | - Jeffrey R Johansen
- Department of Biology, John Carroll University, University Heights, Ohio, 44118, USA
- Department of Botany, Faculty of Sciences, University of South Bohemia, Branišovská 31, České Budějovice, 370 05, Czech Republic
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Pombubpa N, Pietrasiak N, De Ley P, Stajich JE. Insights into dryland biocrust microbiome: geography, soil depth and crust type affect biocrust microbial communities and networks in Mojave Desert, USA. FEMS Microbiol Ecol 2021; 96:5861315. [PMID: 32573682 DOI: 10.1093/femsec/fiaa125] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/22/2020] [Indexed: 12/31/2022] Open
Abstract
Biocrusts are the living skin of drylands, comprising diverse microbial communities that are essential to desert ecosystems. Despite there being extensive knowledge on biocrust ecosystem functions and lichen and moss biodiversity, little is known about factors structuring diversity among their microbial communities. We used amplicon-based metabarcode sequencing to survey microbial communities from biocrust surface and subsurface soils at four sites located within the Mojave Desert. Five biocrust types were examined: Light-algal/Cyanobacteria, Cyanolichen, Green-algal lichen, Smooth-moss and Rough-moss crust types. Microbial diversity in biocrusts was structured by several characteristics: (i) central versus southern Mojave sites displayed different community signatures, (ii) indicator taxa of plant-associated fungi (plant pathogens and wood saprotrophs) were identified at each site, (iii) surface and subsurface microbial communities were distinct and (iv) crust types had distinct indicator taxa. Network analysis ranked bacteria-bacteria interactions as the most connected of all within-domain and cross-domain interaction networks in biocrust surface samples. Actinobacteria, Proteobacteria, Cyanobacteria and Ascomycota functioned as hubs among all phyla. The bacteria Pseudonocardia sp. (Pseudonocardiales, Actinobacteria) and fungus Alternaria sp. (Pleosporales, Ascomycota) were the most connected had the highest node degree. Our findings provide crucial insights for dryland microbial community ecology, conservation and sustainable management.
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Affiliation(s)
- Nuttapon Pombubpa
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, CA 92521, USA.,Institute for Integrative Genome Biology, University of California-Riverside, Riverside, CA 92521 USA
| | - Nicole Pietrasiak
- Plant and Environmental Sciences Department, New Mexico State University, Las Cruces, NM 88003, USA
| | - Paul De Ley
- Department of Nematology, University of California-Riverside, Riverside, CA 92521, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, CA 92521, USA.,Institute for Integrative Genome Biology, University of California-Riverside, Riverside, CA 92521 USA
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Condon LA, Pietrasiak N, Rosentreter R, Pyke DA. Passive restoration of vegetation and biological soil crusts following 80 years of exclusion from grazing across the Great Basin. Restor Ecol 2019. [DOI: 10.1111/rec.13021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lea A. Condon
- Forest and Rangeland Ecosystem Science Center U.S. Geological Survey Corvallis OR 97331 U.S.A
| | - Nicole Pietrasiak
- Plant and Environmental Sciences Department New Mexico State University Las Cruces New Mexico 88003 U.S.A
| | | | - David A. Pyke
- Forest and Rangeland Ecosystem Science Center U.S. Geological Survey Corvallis OR 97331 U.S.A
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Pietrasiak N, Osorio-Santos K, Shalygin S, Martin MP, Johansen JR. When Is A Lineage A Species? A Case Study In Myxacorys gen. nov. (Synechococcales: Cyanobacteria) With The Description of Two New Species From The Americas. J Phycol 2019; 55:976-996. [PMID: 31233617 DOI: 10.1111/jpy.12897] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 06/05/2019] [Indexed: 06/09/2023]
Abstract
Soil cyanobacteria are crucial components of biological soil crusts and carry out many functions in dryland ecosystems. Despite this importance, their taxonomy and population genetics remain poorly known. We isolated 42 strains of simple filamentous cyanobacteria previously identified as Pseudophormidium hollerbachianum from 26 desert locations in the North and South America and characterized these strains using a total evidence approach, that is, using both morphological and molecular data to arrive at taxonomic decisions. Based on a phylogenetic analysis of 16S rRNA gene sequences, we propose and characterize Myxacorys gen. nov. with two new species Myxacorys chilensis, the generitype, and M. californica. We also found distinct 16S-23S ITS sequence variability within species in our dataset. Especially interesting was the presence of two distinct lineages of M. californica obtained from locations in close spatial proximity (within a few meters to kilometers from each other) suggesting niche differentiation. The detection of such unrecognized lineage-level variability in soil cyanobacteria has important implications for biocrust restoration practices and conservation efforts.
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Affiliation(s)
- Nicole Pietrasiak
- Plant and Environmental Sciences Department, New Mexico State University, 945 College Drive., Las Cruces, New Mexico, 88003, USA
| | - Karina Osorio-Santos
- Department of Comparative Biology, Faculty of Science, Universidad Nacional Autonóma de México, Coyoacán, Distrito Federal, 04510, México
| | - Sergei Shalygin
- Plant and Environmental Sciences Department, New Mexico State University, 945 College Drive., Las Cruces, New Mexico, 88003, USA
| | - Michael P Martin
- Department of Biology, John Carroll University, University Heights, Ohio, 44118, USA
| | - Jeffrey R Johansen
- Department of Biology, John Carroll University, University Heights, Ohio, 44118, USA
- Department of Botany, Faculty of Sciences, University of South Bohemia, Branišovská 31, České Budějovice, 370 05, Czech Republic
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Shalygin S, Shalygina R, Johansen JR, Pietrasiak N, Berrendero Gómez E, Bohunická M, Mareš J, Sheil CA. Cyanomargarita gen. nov. (Nostocales, Cyanobacteria): convergent evolution resulting in a cryptic genus. J Phycol 2017; 53:762-777. [PMID: 28403525 DOI: 10.1111/jpy.12542] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 03/04/2017] [Indexed: 05/25/2023]
Abstract
Two populations of Rivularia-like cyanobacteria were isolated from ecologically distinct and biogeographically distant sites. One population was from an unpolluted stream in the Kola Peninsula of Russia, whereas the other was from a wet wall in the Grand Staircase-Escalante National Monument, a desert park-land in Utah. Though both were virtually indistinguishable from Rivularia in field and cultured material, they were both phylogenetically distant from Rivularia and the Rivulariaceae based on both 16S rRNA and rbcLX phylogenies. We here name the new cryptic genus Cyanomargarita gen. nov., with type species C. melechinii sp. nov., and additional species C. calcarea sp. nov. We also name a new family for these taxa, the Cyanomargaritaceae.
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Affiliation(s)
- Sergei Shalygin
- Department of Biology, John Carroll University, University Heights, Ohio, 44118, USA
- Polar-Alpine Botanical Garden-Institute, Kola Science Center, Russian Academy of Science, Kirovsk-6, 184230, Russia
| | - Regina Shalygina
- Institute of Industrial Ecology Problems of the North, Kola Science Center, Russian Academy of Science, Akademgorodok 14a, Apatity, 184209, Russia
| | - Jeffrey R Johansen
- Department of Biology, John Carroll University, University Heights, Ohio, 44118, USA
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 31, České Budějovice, 370 05, Czech Republic
| | - Nicole Pietrasiak
- Department of Plant and Environmental Sciences, New Mexico State University, 945 College Drive, Las Cruces, New Mexico, 88003, USA
| | - Esther Berrendero Gómez
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 31, České Budějovice, 370 05, Czech Republic
| | - Markéta Bohunická
- Institute of Botany of the Academy of Sciences of the Czech Republic, Dukelská 135, Třeboň, 379 82, Czech Republic
- Research and Breeding Institute of Pomology, Holovousy 129, Hořice, 508 01, Czech Republic
| | - Jan Mareš
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 31, České Budějovice, 370 05, Czech Republic
- Institute of Botany of the Academy of Sciences of the Czech Republic, Dukelská 135, Třeboň, 379 82, Czech Republic
- Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Hydrobiology, Na Sádkách 702/7, České Budějovice, 37005, Czech Republic
| | - Christopher A Sheil
- Department of Biology, John Carroll University, University Heights, Ohio, 44118, USA
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Bowker MA, Belnap J, Büdel B, Sannier C, Pietrasiak N, Eldridge DJ, Rivera-Aguilar V. Controls on Distribution Patterns of Biological Soil Crusts at Micro- to Global Scales. Biological Soil Crusts: An Organizing Principle in Drylands 2016. [DOI: 10.1007/978-3-319-30214-0_10] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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Garcia V, Aranibar J, Pietrasiak N. Multiscale effects on biological soil crusts cover and spatial distribution in the Monte Desert. Acta Oecologica 2015. [DOI: 10.1016/j.actao.2015.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Burke DJ, Pietrasiak N, Situ SF, Abenojar EC, Porche M, Kraj P, Lakliang Y, Samia ACS. Iron Oxide and Titanium Dioxide Nanoparticle Effects on Plant Performance and Root Associated Microbes. Int J Mol Sci 2015; 16:23630-50. [PMID: 26445042 PMCID: PMC4632718 DOI: 10.3390/ijms161023630] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 09/23/2015] [Accepted: 09/25/2015] [Indexed: 01/19/2023] Open
Abstract
In this study, we investigated the effect of positively and negatively charged Fe₃O₄ and TiO₂ nanoparticles (NPs) on the growth of soybean plants (Glycine max.) and their root associated soil microbes. Soybean plants were grown in a greenhouse for six weeks after application of different amounts of NPs, and plant growth and nutrient content were examined. Roots were analyzed for colonization by arbuscular mycorrhizal (AM) fungi and nodule-forming nitrogen fixing bacteria using DNA-based techniques. We found that plant growth was significantly lower with the application of TiO₂ as compared to Fe₃O₄ NPs. The leaf carbon was also marginally significant lower in plants treated with TiO₂ NPs; however, leaf phosphorus was reduced in plants treated with Fe₃O₄. We found no effects of NP type, concentration, or charge on the community structure of either rhizobia or AM fungi colonizing plant roots. However, the charge of the Fe₃O₄ NPs affected both colonization of the root system by rhizobia as well as leaf phosphorus content. Our results indicate that the type of NP can affect plant growth and nutrient content in an agriculturally important crop species, and that the charge of these particles influences the colonization of the root system by nitrogen-fixing bacteria.
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Affiliation(s)
| | | | - Shu F Situ
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Eric C Abenojar
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Mya Porche
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Pawel Kraj
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA.
- Department of Chemistry, Mercer University, Macon, GA 31207, USA.
| | - Yutthana Lakliang
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA.
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Patzelt DJ, Hodač L, Friedl T, Pietrasiak N, Johansen JR. Biodiversity of soil cyanobacteria in the hyper-arid Atacama Desert, Chile. J Phycol 2014; 50:698-710. [PMID: 26988453 DOI: 10.1111/jpy.12196] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 04/11/2014] [Indexed: 06/05/2023]
Abstract
The cyanobacterial diversity of soils of the Atacama Desert (Chile) was investigated using 16S rRNA gene cloning/sequencing directly from soil samples and 16S rRNA gene sequencing from unialgal cultures. Within the hyper-arid Atacama Desert, one of the driest parts of the world, 10 sites with differing altitude and distance to the shore were sampled along a total air-line distance (from south to north) of ~1,100 km. Filamentous cyanobacteria belonging to Nostocophycideae and Synechococcophycideae were present. Oscillatoriophycideae exhibited the highest species richness among the subclasses of cyanobacteria, and included mostly filamentous species along with some coccoids (e.g., Chroococcidiopsis). Thirty species-level phylotypes could be recognized using a cut-off of 99% 16S rRNA sequence similarity within the 22 genera defined at 97% 16S rRNA sequence similarity. Eight of the 30 taxa could be detected by both clonal and culture sequences. Five taxa were observed only in cultures, whereas the cloning approach revealed 17 additional taxa, which might be in the collection but unsequenced, hard-to-cultivate, or entirely unculturable species using standard cultivation media. The Atacama Desert soils have a high diversity of phylotypes, among which are likely both new genera and new species awaiting characterization and description.
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Affiliation(s)
- Dominik J Patzelt
- Universität Göttingen, Experimentelle Phykologie und Sammlung von Algenkulturen (SAG), Nikolausberger Weg 18, Göttingen, 37073, Germany
| | - Ladislav Hodač
- Universität Göttingen, Experimentelle Phykologie und Sammlung von Algenkulturen (SAG), Nikolausberger Weg 18, Göttingen, 37073, Germany
| | - Thomas Friedl
- Universität Göttingen, Experimentelle Phykologie und Sammlung von Algenkulturen (SAG), Nikolausberger Weg 18, Göttingen, 37073, Germany
| | - Nicole Pietrasiak
- Department of Biology, John Carroll University, University Heights, Ohio, 44118, USA
| | - Jeffrey R Johansen
- Department of Biology, John Carroll University, University Heights, Ohio, 44118, USA
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 31, České Budějovice, 370 05, Czech Republic
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Flechtner VR, Pietrasiak N, Lewis LA. Newly Revealed Diversity of Green Microalgae from Wilderness Areas of Joshua Tree National Park (JTNP). ACTA ACUST UNITED AC 2013. [DOI: 10.3398/042.006.0103] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Pietrasiak N, Johansen JR, LaDoux T, Graham RC. Comparison of Disturbance Impacts to and Spatial Distribution of Biological Soil Crusts in the Little San Bernardino Mountains of Joshua Tree National Park, California. WEST N AM NATURALIST 2011. [DOI: 10.3398/064.071.0412] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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