scholarly journals Diversity across Seasons of CulturablePseudomonasfrom a Desiccation Lagoon in Cuatro Cienegas, Mexico

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Alejandra Rodríguez-Verdugo ◽  
Valeria Souza ◽  
Luis E. Eguiarte ◽  
Ana E. Escalante
Keyword(s):  
16S Rdna ◽  
Seasonal Changes ◽  
Chihuahuan Desert ◽  
Water System ◽  
Rdna Sequences ◽  
Rdna Sequencing ◽  
Biodiversity Inventories ◽  
Different Temperatures ◽  
Cuatro Ciénegas ◽  
Cuatro Ciénegas Basin

Cuatro Cienegas basin (CCB) is a biodiversity reservoir within the Chihuahuan desert that includes several water systems subject to marked seasonality. While several studies have focused on biodiversity inventories, this is the first study that describes seasonal changes in diversity within the basin. We sampledPseudomonaspopulations from a seasonally variable water system at four different sampling dates (August 2003, January 2004, January 2005, and August 2005). A total of 70Pseudomonasisolates across seasons were obtained, genotyped by fingerprinting (BOX-PCR), and taxonomically characterized by 16S rDNA sequencing. We found 35 unique genotypes, and two numerically dominant lineages (16S rDNA sequences) that made up 64% of the sample:P. cuatrocienegasensisandP. otitidis. We did not recover genotypes across seasons, but lineages reoccurred across seasons;P. cuatrocienegasensiswas isolated exclusively in winter, whileP. otitidiswas only recovered in summer. We statistically show that taxonomic identity of isolates is not independent of the sampling season, and that winter and summer populations are different. In addition to the genetic description of populations, we show exploratory measures of growth rates at different temperatures, suggesting physiological differences between populations. Altogether, the results indicate seasonal changes in diversity of free-living aquaticPseudomonaspopulations from CCB.

scholarly journals The Geographic Structure of Viruses in the Cuatro Ciénegas Basin, a Unique Oasis in Northern Mexico, Reveals a Highly Diverse Population on a Small Geographic Scale

2018 ◽  
Vol 84 (11) ◽  
Author(s):  
B. Taboada ◽  
P. Isa ◽  
A. L. Gutiérrez-Escolano ◽  
R. M. del Ángel ◽  
J. E. Ludert ◽  
...  
Keyword(s):  
Fish Species ◽  
Phylogenetic Trees ◽  
Biological Diversity ◽  
Chihuahuan Desert ◽  
Geographic Scale ◽  
Geographic Structure ◽  
Virus Diversity ◽  
Intestinal Contents ◽  
Cuatro Ciénegas ◽  
Cuatro Ciénegas Basin

ABSTRACT The Cuatro Ciénegas Basin (CCB) is located in the Chihuahuan desert in the Mexican state of Coahuila; it has been characterized as a site with high biological diversity despite its extreme oligotrophic conditions. It has the greatest number of endemic species in North America, containing abundant living microbialites (including stromatolites and microbial mats) and diverse microbial communities. With the hypothesis that this high biodiversity and the geographic structure should be reflected in the virome, the viral communities in 11 different locations of three drainage systems, Churince, La Becerra, and Pozas Rojas, and in the intestinal contents of 3 different fish species, were analyzed for both eukaryotic and prokaryotic RNA and DNA viruses using next-generation sequencing methods. Double-stranded DNA (dsDNA) virus families were the most abundant (72.5% of reads), followed by single-stranded DNA (ssDNA) viruses (2.9%) and ssRNA and dsRNA virus families (0.5%). Thirteen families had dsDNA genomes, five had ssDNA, three had dsRNA, and 16 had ssRNA. A highly diverse viral community was found, with an ample range of hosts and a strong geographical structure, with very even distributions and signals of endemicity in the phylogenetic trees from several different virus families. The majority of viruses found were bacteriophages but eukaryotic viruses were also frequent, and the large diversity of viruses related to algae were a surprise, since algae are not evident in the previously analyzed aquatic systems of this ecosystem. Animal viruses were also frequently found, showing the large diversity of aquatic animals in this oasis, where plants, protozoa, and archaea are rare. IMPORTANCE In this study, we tested whether the high biodiversity and geographic structure of CCB is reflected in its virome. CCB is an extraordinarily biodiverse oasis in the Chihuahuan desert, where a previous virome study suggested that viruses had followed the marine ancestry of the marine bacteria and, as a result of their long isolation, became endemic to the site. In this study, which includes a larger sequencing coverage and water samples from other sites within the valley, we confirmed the high virus biodiversity and uniqueness as well as the strong biogeographical diversification of the CCB. In addition, we also analyzed fish intestinal contents, finding that each fish species eats different prey and, as a result, presents different viral compositions even if they coexist in the same pond. These facts highlight the high and novel virus diversity of CCB and its “lost world” status.

scholarly journals 16S Ribosomal DNA Sequence Analysis of a Large Collection of Environmental and Clinical Unidentifiable Bacterial Isolates

2000 ◽  
Vol 38 (10) ◽  
pp. 3623-3630 ◽  
Author(s):  
Michel Drancourt ◽  
Claude Bollet ◽  
Antoine Carlioz ◽  
Rolland Martelin ◽  
Jean-Pierre Gayral ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rdna ◽  
Similarity Score ◽  
16S Rdna Sequencing ◽  
16S Rdna Sequence ◽  
16S Rdna Sequence Analysis ◽  
Rdna Sequences ◽  
Rdna Sequencing ◽  
16S Rdna Sequences ◽  
Identification Of Bacteria

Some bacteria are difficult to identify with phenotypic identification schemes commonly used outside reference laboratories. 16S ribosomal DNA (rDNA)-based identification of bacteria potentially offers a useful alternative when phenotypic characterization methods fail. However, as yet, the usefulness of 16S rDNA sequence analysis in the identification of conventionally unidentifiable isolates has not been evaluated with a large collection of isolates. In this study, we evaluated the utility of 16S rDNA sequencing as a means to identify a collection of 177 such isolates obtained from environmental, veterinary, and clinical sources. For 159 isolates (89.8%) there was at least one sequence in GenBank that yielded a similarity score of ≥97%, and for 139 isolates (78.5%) there was at least one sequence in GenBank that yielded a similarity score of ≥99%. These similarity score values were used to defined identification at the genus and species levels, respectively. For isolates identified to the species level, conventional identification failed to produce accurate results because of inappropriate biochemical profile determination in 76 isolates (58.7%), Gram staining in 16 isolates (11.6%), oxidase and catalase activity determination in 5 isolates (3.6%) and growth requirement determination in 2 isolates (1.5%). Eighteen isolates (10.2%) remained unidentifiable by 16S rDNA sequence analysis but were probably prototype isolates of new species. These isolates originated mainly from environmental sources (P = 0.07). The 16S rDNA approach failed to identify Enterobacter andPantoea isolates to the species level (P = 0.04; odds ratio = 0.32 [95% confidence interval, 0.10 to 1.14]). Elsewhere, the usefulness of 16S rDNA sequencing was compromised by the presence of 16S rDNA sequences with >1% undetermined positions in the databases. Unlike phenotypic identification, which can be modified by the variability of expression of characters, 16S rDNA sequencing provides unambiguous data even for rare isolates, which are reproducible in and between laboratories. The increase in accurate new 16S rDNA sequences and the development of alternative genes for molecular identification of certain taxa should further improve the usefulness of molecular identification of bacteria.

scholarly journals High diversity and suggested endemicity of culturable Actinobacteria in an extremely oligotrophic desert oasis

2017 ◽  
Author(s):  
Hector Fernando Arocha-Garza ◽  
Ricardo Canales-Del Castillo ◽  
Luis E. Eguiarte ◽  
Valeria Souza ◽  
Susana De la Torre-Zavala
Keyword(s):  
16S Rdna ◽  
Chihuahuan Desert ◽  
Extreme Environments ◽  
Sampling Period ◽  
Dispersal Limitation ◽  
Small Scale ◽  
Rarefaction Analysis ◽  
Biogeographic Patterns ◽  
Evolutionary Context ◽  
Cuatro Ciénegas Basin

The phylum Actinobacteria constitutes one of the largest and anciently divergent phyla within the Bacteria domain. Actinobacterial diversity has been thoroughly researched in various environments due to its unique biotechnological potential. Such studies have focused mostly on soil communities, but more recently marine and extreme environments have also been explored, finding rare taxa and demonstrating dispersal limitation and biogeographic patterns for Streptomyces. To test the distribution of Actinobacteria populations on a small scale, we chose the extremely oligotrophic and biodiverse Cuatro Cienegas Basin (CCB), an endangered oasis in the Chihuahuan desert to assess the diversity and uniqueness of Actinobacteria in the Churince System with a culture-dependent approach over a period of three years, using nine selective media. The 16S rDNA of putative Actinobacteria were sequenced using both bacteria universal and phylum-specific primer pairs. Phylogenetic reconstructions were performed to analyze OTUs clustering and taxonomic identification of the isolates in an evolutionary context, using validated type species of Streptomyces from previously phylogenies as a reference. Rarefaction analysis for total Actinobacteria and for Streptomyces isolates were performed to estimate species´ richness in the intermediate lagoon (IL) in the oligotrophic Churince system. A total of 350 morphologically and nutritionally diverse isolates were successfully cultured and characterized as members of the Phylum Actinobacteria. 105 from the total isolates were successfully subcultured, processed for DNA extraction and 16S-rDNA sequenced. All strains belong to the order Actinomycetales, encompassing 11 genera of Actinobacteria; the genus Streptomyces was found to be the most abundant taxa in all the media tested throughout the 3-year sampling period. Phylogenetic analysis of our isolates and another 667 reference strains of the family Streptomycetaceae shows that our isolation effort produced 38 unique OTUs in six new monophyletic clades. This high biodiversity and uniqueness of Actinobacteria in an extreme oligotrophic environment, which has previously been reported for its diversity and endemicity, is a suggestive sign of microbial biogeography of Actinobacteria and it also represents an invaluable source of biological material for future ecological and bioprospecting studies.

scholarly journals CDC Group IV c-2: a New RalstoniaSpecies Close to Ralstonia eutropha

1999 ◽  
Vol 37 (6) ◽  
pp. 1777-1781 ◽  
Author(s):  
Didier Moissenet ◽  
Christophe P. Goujon ◽  
Antoine Garbarg-Chenon ◽  
Hoang Vu-Thien
Keyword(s):  
16S Rdna ◽  
Biochemical Characterization ◽  
Ralstonia Eutropha ◽  
Rapd Analysis ◽  
Group Iv ◽  
Clinical Isolates ◽  
Rdna Sequences ◽  
Rdna Sequencing ◽  
16S Rdna Sequences ◽  
Type Strains

CDC group IV c-2, an environmental gram-negative bacillus recently proposed for inclusion in the genus Ralstonia, has been isolated in several human infections. Biochemical characterization and 16S ribosomal DNA (rDNA) sequencing with phylogenetic analysis were used to characterize eight clinical isolates and four type strains. Other typing tools, such as pulsed-field gel electrophoresis (PFGE) and randomly amplified polymorphic DNA (RAPD) analysis, were also used. PFGE typing of clinical isolates was unsuccessful because the DNA was degraded, and RAPD analysis was poorly discriminatory. In contrast, the type strains were clearly distinguished with both PFGE and RAPD analysis. All of the 16S rDNA sequences were identical. Comparison of the 16S rDNA sequences to the GenBank sequences showed that they were consistent with CDC group IV c-2 belonging to the genusRalstonia. The closest matches were obtained withRalstonia eutropha. However, four differences in 32 biochemical tests separated R. eutropha from CDC group IV c-2, which suggests that CDC group IV c-2 is a new species of the genusRalstonia.

scholarly journals Modern microbial mats from the Chihuahuan Desert provide insights into ecological stability throughout Earth's history

2021 ◽  
Author(s):  
David Madrigal-Trejo ◽  
Jazmín Sánchez-Pérez ◽  
Laura Espinosa-Asuar ◽  
Valeria Souza
Keyword(s):  
Fossil Record ◽  
Microbial Mats ◽  
Chihuahuan Desert ◽  
Extreme Environments ◽  
Taxonomic Composition ◽  
Ecological Stability ◽  
The Face ◽  
Microbial System ◽  
Cuatro Ciénegas ◽  
Cuatro Ciénegas Basin

Microbial mats are complex ecological assemblages that are found in the Precambrian fossil record and in extant extreme environments. Hence, these structures are regarded as highly stable ecosystems. In this work, we assess the ecological stability in a modern, fluctuating, hypersaline pond from the Cuatro Ciénegas Basin. From the 2016 to 2019 metagenomic sampling of this site, we found that this microbial site is sensitive to disturbances, which leads to high taxonomic replacement. Additionally, the mats have shown to be functionally stable throughout time, and could be differentiated between dry and rainy seasonal states. We speculate that this microbial system could represent a modern analog of ancient, hypersaline coastal microbial mats, where functions were preserved over time, whereas taxonomic composition was subject to diversification in the face of local and planetary perturbations.

scholarly journals Molecular Analysis of Methanogen Richness in Landfill and Marshland Targeting 16S rDNA Sequences

Archaea ◽  
2015 ◽  
Vol 2015 ◽  
pp. 1-9 ◽  
Author(s):  
Shailendra Yadav ◽  
Sharbadeb Kundu ◽  
Sankar K. Ghosh ◽  
S. S. Maitra
Keyword(s):  
16S Rdna ◽  
Methane Emission ◽  
Alternative Energy ◽  
Methanogenic Archaea ◽  
Molecular Techniques ◽  
Rdna Sequences ◽  
Rdna Sequencing ◽  
16S Rdna Sequences ◽  
Landfill Sites ◽  
Seventh Order

Methanogens, a key contributor in global carbon cycling, methane emission, and alternative energy production, generate methane gas via anaerobic digestion of organic matter. The methane emission potential depends upon methanogenic diversity and activity. Since they are anaerobes and difficult to isolate and culture, their diversity present in the landfill sites of Delhi and marshlands of Southern Assam, India, was analyzed using molecular techniques like 16S rDNA sequencing, DGGE, and qPCR. The sequencing results indicated the presence of methanogens belonging to the seventh order and also the order Methanomicrobiales in the Ghazipur and Bhalsawa landfill sites of Delhi. Sequences, related to the phyla Crenarchaeota (thermophilic) and Thaumarchaeota (mesophilic), were detected from marshland sites of Southern Assam, India. Jaccard analysis of DGGE gel using Gel2K showed three main clusters depending on the number and similarity of band patterns. The copy number analysis of hydrogenotrophic methanogens using qPCR indicates higher abundance in landfill sites of Delhi as compared to the marshlands of Southern Assam. The knowledge about “methanogenic archaea composition” and “abundance” in the contrasting ecosystems like “landfill” and “marshland” may reorient our understanding of the Archaea inhabitants. This study could shed light on the relationship between methane-dynamics and the global warming process.

scholarly journals Diversity of Archaea Domain in Cuatro Cienegas Basin: Archaean Domes

2019 ◽  
Author(s):  
Nahui Olin Medina-Chávez ◽  
Mariette Viladomat-Jasso ◽  
Gabriela Olmedo-Álvarez ◽  
Luis E Eguiarte ◽  
Valeria Souza ◽  
...  
Keyword(s):  
Microbial Mats ◽  
Chihuahuan Desert ◽  
Unusual Site ◽  
Community Assemblage ◽  
Rare Biosphere ◽  
Low Phosphorus ◽  
Cuatro Ciénegas ◽  
Metagenome Sequencing ◽  
Study Sites ◽  
Cuatro Ciénegas Basin

AbstractHerein we describe the Archaea diversity in a shallow pond in the Cuatro Ciénegas Basin (CCB), Northeast Mexico, with fluctuating hypersaline conditions containing elastic microbial mats that can form small domes where their anoxic inside reminds us of the characteristics of the Archaean Eon, rich in methane and sulfur gases; thus, we named this site the Archaean Domes (AD). These domes only form after heavy rains that are rare in the Chihuahuan desert. CCB is a unique oasis with hundreds of ponds, containing endemic species of animals, plants and highly diverse and unique microbial communities, despite its very biased stoichiometry, due mostly to extreme low phosphorus content (soils, water columns and sediments). This extreme oligotrophy has favored survival of ancestral microorganisms. Whole metagenome sequencing approach was performed for this unusual site in three different seasons to assess the extent of the Archaea biodiversity, with a focus on extremophiles, since members of the Archaea had been underrepresented in different study sites within the oasis. We found a highly diverse Archaea community compassing ∼5% of the metagenomes. The archaeal portion in all three metagenomes maintained its abundance and most of the strains showed to form a resilient core during three seasonal samplings (2016-2017), despite environmental fluctuations. However, relative abundances of all 230 archaeal OTUs (defined using a 97% cutoff) were low enough (<0.1%) to be considered part of the rare biosphere. AD finding and their description within CCB confirms that this particular pond is the most diverse for Archaea that we are aware of and opens new paths for understanding the forces that once drove and keep shaping microbial community assemblage.

scholarly journals High diversity and suggested endemicity of culturable Actinobacteria in an extremely oligotrophic desert oasis

2017 ◽  
Author(s):  
Hector Fernando Arocha-Garza ◽  
Ricardo Canales-Del Castillo ◽  
Luis E. Eguiarte ◽  
Valeria Souza ◽  
Susana De la Torre-Zavala
Keyword(s):  
16S Rdna ◽  
Chihuahuan Desert ◽  
Extreme Environments ◽  
Sampling Period ◽  
Dispersal Limitation ◽  
Small Scale ◽  
Rarefaction Analysis ◽  
Biogeographic Patterns ◽  
Evolutionary Context ◽  
Cuatro Ciénegas Basin

The phylum Actinobacteria constitutes one of the largest and anciently divergent phyla within the Bacteria domain. Actinobacterial diversity has been thoroughly researched in various environments due to its unique biotechnological potential. Such studies have focused mostly on soil communities, but more recently marine and extreme environments have also been explored, finding rare taxa and demonstrating dispersal limitation and biogeographic patterns for Streptomyces. To test the distribution of Actinobacteria populations on a small scale, we chose the extremely oligotrophic and biodiverse Cuatro Cienegas Basin (CCB), an endangered oasis in the Chihuahuan desert to assess the diversity and uniqueness of Actinobacteria in the Churince System with a culture-dependent approach over a period of three years, using nine selective media. The 16S rDNA of putative Actinobacteria were sequenced using both bacteria universal and phylum-specific primer pairs. Phylogenetic reconstructions were performed to analyze OTUs clustering and taxonomic identification of the isolates in an evolutionary context, using validated type species of Streptomyces from previously phylogenies as a reference. Rarefaction analysis for total Actinobacteria and for Streptomyces isolates were performed to estimate species´ richness in the intermediate lagoon (IL) in the oligotrophic Churince system. A total of 350 morphologically and nutritionally diverse isolates were successfully cultured and characterized as members of the Phylum Actinobacteria. 105 from the total isolates were successfully subcultured, processed for DNA extraction and 16S-rDNA sequenced. All strains belong to the order Actinomycetales, encompassing 11 genera of Actinobacteria; the genus Streptomyces was found to be the most abundant taxa in all the media tested throughout the 3-year sampling period. Phylogenetic analysis of our isolates and another 667 reference strains of the family Streptomycetaceae shows that our isolation effort produced 38 unique OTUs in six new monophyletic clades. This high biodiversity and uniqueness of Actinobacteria in an extreme oligotrophic environment, which has previously been reported for its diversity and endemicity, is a suggestive sign of microbial biogeography of Actinobacteria and it also represents an invaluable source of biological material for future ecological and bioprospecting studies.

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