Functional analysis of the archaea, bacteria, and viruses from a halite endolithic microbial community

Halite endoliths in the Atacama Desert represent one of the most extreme microbial ecosystems on Earth. Here we sequenced and characterized a shotgun metagenome from halite nodules collected in Salar Grande, Chile. The community is dominated by archaea and functional analysis attributed most of the autotrophic CO2 fixation to a unique cyanobacterium. The assembled 1.1 Mbp genome of a novel nanohaloarchaeon, Candidatus Nanopetramus SG9, revealed a photoheterotrophic life style and a low median isoelectric point (pI) for all predicted proteins, suggesting a "salt-in" strategy for osmotic balance. Predicted proteins of the algae identified in the community also had pI distributions similar to "salt-in" strategists. The Nanopetramus genome contained a unique CRISPR/Cas system with a spacer that matched a partial viral genome from the metagenome. A combination of reference-independent methods identified over 30 complete or near complete viral or proviral genomes with diverse genome structure, genome size, gene content, and hosts. Putative hosts included Halobacteriaceae, Nanohaloarchaea, and Cyanobacteria. Despite the dependence of the halite community on deliquescence for liquid water availability, this study exposed an ecosystem spanning three phylogenetic domains, containing a large diversity of viruses, and a predominant salt-in strategy to balance the high osmotic pressure of the environment.

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CaptureSeq: Hybridization-Based Enrichment of cpn60 Gene Fragments Reveals the Community Structures of Synthetic and Natural Microbial Ecosystems

Microorganisms ◽

10.3390/microorganisms9040816 ◽

2021 ◽

Vol 9 (4) ◽

pp. 816

Author(s):

Matthew G. Links ◽

Tim J. Dumonceaux ◽

E. Luke McCarthy ◽

Sean M. Hemmingsen ◽

Edward Topp ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Dna Sequences ◽

Pcr Amplification ◽

Shotgun Sequencing ◽

Natural Ecosystems ◽

Gene Markers ◽

Microbial Profile ◽

Microbial Ecosystems ◽

Pcr Targeting

Background. The molecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with “universal” PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. However, both amplicon-based and shotgun sequencing approaches have shortcomings that limit the ability to study microbiome dynamics. Methods. We present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. Molecular profiles of a commercially available synthetic microbial community standard were compared using CaptureSeq, whole metagenome sequencing, and 16S universal target amplification. Profiles were also generated for natural ecosystems including antibiotic-amended soils, manure storage tanks, and an agricultural reservoir. Results. The CaptureSeq method generated a microbial profile that encompassed all of the bacteria and eukaryotes in the panel with greater reproducibility and more accurate representation of high G/C content microorganisms compared to 16S amplification. In the natural ecosystems, CaptureSeq provided a much greater depth of coverage and sensitivity of detection compared to shotgun sequencing without prior selection. The resulting community profiles provided quantitatively reliable information about all three domains of life (Bacteria, Archaea, and Eukarya) in the different ecosystems. The applications of CaptureSeq will facilitate accurate studies of host-microbiome interactions for environmental, crop, animal and human health. Conclusions: cpn60-based hybridization enriched for taxonomically informative DNA sequences from complex mixtures. In synthetic and natural microbial ecosystems, CaptureSeq provided sequences from prokaryotes and eukaryotes simultaneously, with quantitatively reliable read abundances. CaptureSeq provides an alternative to PCR amplification of taxonomic markers with deep community coverage while minimizing amplification biases.

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Viral Genome Structure

The Plant Viruses ◽

10.1007/978-1-4684-4937-2_3 ◽

1985 ◽

pp. 57-81 ◽

Cited By ~ 8

Author(s):

Robert H. Symons

Keyword(s):

Viral Genome ◽

Genome Structure

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Optimization of electron donors to improve CO2 fixation efficiency by a non-photosynthetic microbial community under aerobic condition using statistical experimental design

Bioresource Technology ◽

10.1016/j.biortech.2010.03.138 ◽

2010 ◽

Vol 101 (18) ◽

pp. 7062-7067 ◽

Cited By ~ 10

Author(s):

Jia-jun Hu ◽

Lei Wang ◽

Shi-ping Zhang ◽

Xiao-hua Fu ◽

Yi-quan Le

Keyword(s):

Microbial Community ◽

Experimental Design ◽

Co2 Fixation ◽

Aerobic Condition ◽

Electron Donors ◽

Statistical Experimental Design

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Pharmacotherapy for SARS-CoV-2 and Seizures for drug repurposing presumed on Mechanistic Targets

Current Molecular Pharmacology ◽

10.2174/1874467214666211013122528 ◽

2021 ◽

Vol 14 ◽

Author(s):

Divya Goel ◽

Ankit Srivastava ◽

Ángel Aledo-Serrano ◽

Anuja Krishnan ◽

Divya Vohora

Keyword(s):

Valproic Acid ◽

Viral Genome ◽

Drug Targeting ◽

Literature Search ◽

Genome Structure ◽

Drug Repurposing ◽

Drug Candidate ◽

Atypical Pneumonia ◽

Comparative Toxicogenomics Database ◽

Indirect Association

Background: The currently circulating novel SARS-CoV-2 coronavirus disease (COVID-19) has brought the whole world to a standstill. Recent studies have deciphered the viral genome structure, epidemiology and are in the process of unveiling multiple mechanisms of pathogenesis. Apart from atypical pneumonia and lung disease manifestations, this disease has also been found to be associated with neurological symptoms, which include dizziness, headache, stroke, or seizures, among others. However, a possible direct or indirect association between SARS-CoV-2 and seizures is still not clear. In any manner, it may be of interest to analyze the drugs being used for viral infection in the background of epilepsy or vice versa. Objective: To identify the most credible drug candidate for COVID-19 in persons with epilepsy or COVID-19 patients experiencing seizures. Methods: A literature search for original and review articles was performed, and further, the Comparative Toxicogenomics Database was used to unearth the most credible drug candidate. Results: Our search based on common mechanistic targets affecting SARS-CoV-2 and seizures revealed ivermectin, dexamethasone, anakinra, and tocilizumab for protection against both COVID-19 and seizures. Amongst the antiseizure medications, we found valproic acid as the most probable pharmacotherapy for COVID-19 patients experiencing seizures. Conclusion: These findings would hopefully provide the basis for initiating further studies on the pathogenesis and drug targeting strategies for this emerging infection accompanied with seizures or in people with epilepsy.

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The Calvin cycle enzyme phosphoglycerate kinase of Xanthobacter flavus required for autotrophic CO2 fixation is not encoded by the cbb operon.

Journal of Bacteriology ◽

10.1128/jb.176.19.6120-6126.1994 ◽

1994 ◽

Vol 176 (19) ◽

pp. 6120-6126 ◽

Cited By ~ 16

Author(s):

W G Meijer

Keyword(s):

Co2 Fixation ◽

Calvin Cycle ◽

Phosphoglycerate Kinase ◽

Autotrophic Co2 Fixation ◽

Cycle Enzyme ◽

Xanthobacter Flavus

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Water availability shapes edaphic and lithic cyanobacterial communities in the Atacama Desert

Journal of Phycology ◽

10.1111/jpy.12908 ◽

2019 ◽

Vol 55 (6) ◽

pp. 1306-1318 ◽

Cited By ~ 5

Author(s):

Patrick Jung ◽

Michael Schermer ◽

Laura Briegel‐Williams ◽

Karen Baumann ◽

Peter Leinweber ◽

...

Keyword(s):

Water Availability ◽

Atacama Desert

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Physicochemical Parameters Affecting the Distribution and Diversity of the Water Column Microbial Community in the High-Altitude Andean Lake System of La Brava and La Punta

Microorganisms ◽

10.3390/microorganisms8081181 ◽

2020 ◽

Vol 8 (8) ◽

pp. 1181

Author(s):

Reynaldo Núñez Salazar ◽

Carlos Aguirre ◽

Jorge Soto ◽

Pamela Salinas ◽

Carlos Salinas ◽

...

Keyword(s):

Microbial Community ◽

High Altitude ◽

Water Column ◽

Physicochemical Parameters ◽

Microbial Community Composition ◽

Atacama Desert ◽

Rrna Gene ◽

16S Rrna Gene Analysis ◽

Lake System ◽

Influence Of Water

Due to the low incidence of precipitation attributed to climate change, many high-altitude Andean lakes (HAALs) and lagoons distributed along the central Andes in South America may soon disappear. This includes La Brava–La Punta, a brackish lake system located south of the Salar de Atacama within a hyper-arid and halophytic biome in the Atacama Desert. Variations in the physicochemical parameters of the water column can induce changes in microbial community composition, which we aimed to determine. Sixteen sampling points across La Brava–La Punta were studied to assess the influence of water physicochemical properties on the aquatic microbial community, determined via 16S rRNA gene analysis. Parameters such as pH and the concentrations of silica, magnesium, calcium, salinity, and dissolved oxygen showed a more homogenous pattern in La Punta samples, whereas those from La Brava had greater variability; pH and total silica were significantly different between La Brava and La Punta. The predominant phyla were Proteobacteria, Bacteroidetes, Actinobacteria, and Verrucomicrobia. The genera Psychroflexus (36.85%), Thiomicrospira (12.48%), and Pseudomonas (7.81%) were more abundant in La Brava, while Pseudospirillum (20.73%) and Roseovarius (17.20%) were more abundant in La Punta. Among the parameters, pH was the only statistically significant factor influencing the diversity within La Brava lake. These results complement the known microbial diversity and composition in the HAALs of the Atacama Desert.

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