Draft Genome Sequences of Actinobacterial and Betaproteobacterial Strains Isolated from the Stratosphere

Ellington, Adam J; Bryan, Noelle C.; Christner, Brent C.; Reisch, Christopher R

doi:10.1128/mra.01009-21

Cited by 7 publications

(9 citation statements)

References 9 publications

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“…Previous work reported that bacterial isolates from rain are often pigmented 70 , aiding their survival at high UV radiation. Rain and aerosol viruses detected in this study had a significantly higher percent G/C base content compared to marine viruses, which is a suitable adaptation for avoidance of thymine-specific damage by UV radiation in bacteria 71 and occurred in recently described bacterial isolates from the stratosphere 72 . A viral cluster specific to rain was identified, and many viruses enriched in the atmosphere compared to seawater lacked representatives in public databases.…”

Section: Discussionmentioning

confidence: 61%

Heads in the clouds: marine viruses disperse bidirectionally along the natural water cycle

Rahlff

Esser

Plewka

et al. 2022

Preprint

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Marine viruses have thoroughly been studied in seawater, yet their dispersal from neuston ecosystems at the air-sea interface towards the atmosphere remains a knowledge gap. Here, we show that 6.2 % of the studied virus population were shared between air-sea interface ecosystems and rainwater. Virus enrichment in the 1-mm thin surface microlayer and sea foams happened selectively, and variant analysis proved virus transfer to aerosols and rain. Viruses detected in rain and aerosols showed a significantly higher percent G/C base content compared to marine viruses, and a genetically distinct rain virome supports that those viruses could inhabit higher air masses. CRISPR spacer matches of marine prokaryotes to foreign viruses from rainwater prove regular virus-host encounters at the air-sea interface. Our findings on aerosolization and long-range atmospheric dispersal implicate virus-mediated carbon turnover in remote areas, viral dispersal mechanisms relevant to human health, and involvement of viruses in atmospheric processes like ice-nucleation.

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Section: Discussionmentioning

confidence: 61%

Heads in the clouds: marine viruses disperse bidirectionally along the natural water cycle

Rahlff

Esser

Plewka

et al. 2022

Preprint

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“…The disparities in UVCR tolerance between the stratospheric isolates and reference strains suggested that L6-1 and L7-7A possess genetically discernable features contributing to this phenotype. To enable comparative genomic analysis, whole genome sequences were obtained for the Curtobacterium and Noviherbaspirillum strains and deposited in GenBank (33).…”

Section: Resultsmentioning

confidence: 99%

“…L7-7A, Curtobacterium sp. L6-1, and Curtobacterium flaccumfaciens strain DSM 20129 were obtained as described previously (33). Briefly, stationary phase cultures were pelleted, frozen (-70°C), and shipped to SNPsaurus (Eugene, OR) for DNA extraction, library preparation, sequencing, and genome assembly using the PacBio Sequel II sequencing platform followed by de novo genome assembly using the Flye v2.7 assembler (102).…”

Section: Methodsmentioning

confidence: 99%

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Comparative Genomics and Directed Evolution Reveal Genetic Determinants of Extreme UVC Radiation Tolerance in Bacteria Recovered from the Stratosphere

Ellington

Schult

Christner

et al. 2023

Preprint

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Aerosolized microbes surviving transport to and in the stratosphere endure extremes of low temperature, atmospheric pressure, and relative humidity, and high shortwave ultraviolet radiation flux. However, the genetic determinants for traits enabling resistance to the combination of stresses experienced by microbes in the high atmosphere have not been systematically investigated. In this study, we examined Proteobacteria and Actinobacteria isolated from the stratosphere (18 to 29 km ASL) and that demonstrated high tolerance to desiccation (15-25% RH) and UVC radiation (UVCR; λ= 254 nm). Closely related reference strains were more sensitive to UVCR than the stratospheric isolates, indicating that extreme resistance is not universally distributed in these phylogenetically related bacteria. Comparative genomic analyses revealed DNA repair and antioxidant defense genes in the isolates that are not possessed by the related reference strains, including genes encoding photolyase, DNA nucleases and helicases, and catalases. Directed evolution by repeated exposure to increasing doses of UVCR improved the LD90in a sensitive reference strain by ~3.5-fold. The mutations acquired in Curtobacterium flaccumfaciens pv. flaccumfaciens strain DSM 20129 incrementally increased its UVCR resistance, with the accumulation of 20 point mutations in protein coding genes increasing tolerance to a level approaching that of stratospheric isolate Curtobacterium sp. L6-1. The genetic basis for the increased UVCR tolerance phenotypes observed is discussed, with a specific emphasis on the role of genes involved in DNA repair and detoxification of reactive oxygen species.

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“…In spite of being unable to form spores, Curtobacterium spp. are nevertheless abundant in soil [ 1 , 2 ], marine sediments [ 3 ] and in the air up to the stratosphere [ 4 ]. Curtobacteria demonstrate enhanced tolerance to drought, salinity, UV irradiation and metal ions, and have been suggested to play an important role in plant adaptation to stress conditions [ 5 , 6 , 7 ].…”

Section: Introductionmentioning

confidence: 99%

Prophage-Derived Regions in Curtobacterium Genomes: Good Things, Small Packages

Evseev

Lukianova

Tarakanov

et al. 2023

IJMS

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Curtobacterium is a genus of Gram-positive bacteria within the order Actinomycetales. Some Curtobacterium species (C. flaccumfaciens, C. plantarum) are harmful pathogens of agricultural crops such as soybean, dry beans, peas, sugar beet and beetroot, which occur throughout the world. Bacteriophages (bacterial viruses) are considered to be potential curative agents to control the spread of harmful bacteria. Temperate bacteriophages integrate their genomes into bacterial chromosomes (prophages), sometimes substantially influencing bacterial lifestyle and pathogenicity. About 200 publicly available genomes of Curtobacterium species, including environmental metagenomic sequences, were inspected for the presence of sequences of possible prophage origin using bioinformatic methods. The comparison of the search results with several ubiquitous bacterial groups showed the relatively low level of the presence of prophage traces in Curtobacterium genomes. Genomic and phylogenetic analyses were undertaken for the evaluation of the evolutionary and taxonomic positioning of predicted prophages. The analyses indicated the relatedness of Curtobacterium prophage-derived sequences with temperate actinophages of siphoviral morphology. In most cases, the predicted prophages can represent novel phage taxa not described previously. One of the predicted temperate phages was induced from the Curtobacterium genome. Bioinformatic analysis of the modelled proteins encoded in prophage-derived regions led to the discovery of some 100 putative glycopolymer-degrading enzymes that contained enzymatic domains with predicted cell-wall- and cell-envelope-degrading activity; these included glycosidases and peptidases. These proteins can be considered for the experimental design of new antibacterials against Curtobacterium phytopathogens.

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Draft Genome Sequences of Actinobacterial and Betaproteobacterial Strains Isolated from the Stratosphere

Cited by 7 publications

References 9 publications

Heads in the clouds: marine viruses disperse bidirectionally along the natural water cycle

Heads in the clouds: marine viruses disperse bidirectionally along the natural water cycle

Comparative Genomics and Directed Evolution Reveal Genetic Determinants of Extreme UVC Radiation Tolerance in Bacteria Recovered from the Stratosphere

Prophage-Derived Regions in Curtobacterium Genomes: Good Things, Small Packages

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