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

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3247 ◽  
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 ofStreptomycesfrom 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. A total of 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 genusStreptomyceswas 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 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 Experimental and molecular approximation to microbial niche: trophic interactions between oribatid mites and microfungi in an oligotrophic freshwater system

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5200 ◽  
Author(s):  
Patricia Velez ◽  
Margarita Ojeda ◽  
Laura Espinosa-Asuar ◽  
Tila M. Pérez ◽  
Luis E. Eguiarte ◽  
...  
Keyword(s):  
Nutrient Dynamics ◽  
Chihuahuan Desert ◽  
Extreme Environments ◽  
Genetic Lineage ◽  
Direct Pcr ◽  
Culture Independent ◽  
Freshwater System ◽  
Cuatro Ciénegas Basin ◽  
Fungal Interactions

Mite-fungal interactions play a key role in structuring core ecosystem processes such as nutrient dynamics. Despite their ecological relevance, these cross-kingdom interactions remain poorly understood particularly in extreme environments. Herein, we investigated feeding preferences of a novel genetic lineage of aquatic oribatids obtained from an oligotrophic freshwater system in the Cuatro Ciénegas Basin (CCB) within the Chihuahuan Desert, Mexico. During in vitro diet preference bioassays, transient aquatic microfungi (Aspergillus niger, Talaromyces sp., and Pleosporales sp.) recovered from the same mesocosm samples were offered individually and simultaneously to mites. Gut content was analyzed using classic plating and culture-independent direct PCR (focusing on the fungal barcoding region) methods. Our results indicated that oribatids fed on all tested fungal isolates, yet the profusely developing A. niger was preferentially consumed with all fungal components being digested. This feeding habit is particularly interesting since A. niger has been reported as an unsuitable dietary element for population growth, being consistently avoided by mites in previous laboratory experiments. It is possible that our mites from the CCB have adapted to exploit available resources within this oligotrophic site. This work confirms the trophic relationship between microfungi and mites, two rarely investigated major components of the microbial community, shedding light on the niche dynamics under low-nutrient conditions.

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.

Net precipitation assessment in a grassland and soil moisture response at plot scale in a temperate climate

2021 ◽  
Author(s):  
Gökben Demir ◽  
Johanna Clara Metzger ◽  
Janett Filipzik ◽  
Christine Fischer ◽  
Beate Michalzik ◽  
...  
Keyword(s):  
Soil Moisture ◽  
Spatial Variation ◽  
Canopy Structure ◽  
Sampling Period ◽  
Temperate Climate ◽  
Small Scale ◽  
Spatial Effects ◽  
Mixed Effect ◽  
Canopy Development ◽  
Canopy Effect

<div> <p>Evidence on spatial variation of net precipitation in grasslands is scarce. Challenges arise due to a small-scale canopy structure of grasslands.</p> <p>In this study, we designed and tested a new in-situ measurement device (interception grid) to assess net precipitation in grasslands. The collector allows the natural development of the canopy. We tested the device both in the lab for splash loss and in the field to test its capacity to assess net precipitation. In the field, we installed 25 collectors on a grassland within the Hainich Critical Zone Exploratory (Thuringia, Germany), 23 of which were paired with soil moisture sensors. We conducted weekly measurements gross and net precipitation (above and below the canopy), along with grass height in 2019 (March-August) and 2020 (January -February). We categorized the data into two groups (‘covered,’ ‘uncovered’), accounting for canopy development.</p> <p>In the lab, we found that the drop size strongly affects splash loss. Drops of ca. 2 mm, created more than 16% splash loss, decreasing to less than 3% for drops <1.5 mm. Drop sizes <1.75 mm during the sampling period (2019) suggest low to intermediate splash loss in the field, further decreased in the covered period as the canopy contact slows down the drops. Grid measurements corrected with estimated splash loss during the uncovered period agreed well with gross precipitation. Using linear mixed effect models, we found that wind speed and grass height significantly affected the grid measurements of covered periods. Therefore, grids were able to capture net precipitation variation due to grass development. These steps encouraged us to examine the canopy effect in the soil moisture response to rainfall.</p> <p>Soil moisture response over the entire period was not related to the spatial variation of net precipitation. However, for the drier period (June-August 2019), when the spatial variation in soil moisture is higher, and the overall response to rain events stronger, net precipitation slightly affected soil moisture response. LMEM analysis to estimate factors on soil moisture response showed that grass height, net precipitation are significant predictors. Yet, there is no remarkable difference between using net precipitation and gross precipitation as potential drivers for soil moisture response, indicating that the spatial effects are comparatively small. Overall, our findings suggest that the grids are cable to catch canopy effects on the precipitation, while the effect of wind on under-catch still needs to be investigated further.</p> </div>

scholarly journals First Report of a Phytoplasma-Associated Leaf Yellowing Syndrome of Palma Jipi Plants in Southern México

Plant Disease ◽  
2000 ◽  
Vol 84 (7) ◽  
pp. 807-807 ◽  
Author(s):  
I. Cordova ◽  
C. Oropeza ◽  
H. Almeyda ◽  
N. A. Harrison
Keyword(s):  
16S Rdna ◽  
Latin American ◽  
Rural Economy ◽  
Polyacrylamide Gel Electrophoresis ◽  
Small Scale ◽  
Southern Mexico ◽  
Nuevo Leon ◽  
Fort Lauderdale ◽  
Nuevo León ◽  
Lethal Yellowing

The palm-like monocot Palma Jipi (Carludovica palmata, Cyclanthaceae), from which Panama hats are traditionally made, is important to the rural economy of southern Mexico and other Latin American countries. A lethal decline of C. palmata plants was first recognized by farmers at Kalkini in the state of Campeche, Mexico, during 1994. Characterized by a progressive yellowing of successively younger leaves, affected plants died within a few weeks after the onset of this primary symptom. Annual losses estimated at 10% of the naturalized C. palmata population have since occurred in the vicinity of Kalkini, an area in which coconut lethal yellowing (LY) disease is also prevalent. The close proximity and superficially similar symptomatology of these two diseases suggested that both might share a common etiology. DNA samples were obtained from five diseased and five healthy C. palmata plants by small scale extraction of immature leaf bases and assessed for phytoplasma DNA by use of the polymerase chain reaction (PCR) at laboratories in Mérida, INIFAP/Universidad Autónoma de Nuevo León (Nuevo León) and the University of Florida (Fort Lauderdale). Samples from symptomatic plants consistently tested positive by PCR employing universal rRNA primers (P1/P7), which amplify a 1.8-kb phytoplasma rDNA product (4), and negative when LY-specific primers LYF1/LYR1 (1) or MMF/MMR (3) were used. No PCR products were evident when DNAs of symptomless plants were evaluated with these primer combinations. Fragment patterns resolved by 8% polyacrylamide gel electrophoresis of rDNA digested separately with either AluI, BamHI, BstUI, DdeI, DraI, EcoRI, HaeIII, HhaI, HinfI, MspI, RsaI, Sau3AI, TaqI, or Tru9I endonucleases revealed no differences between phytoplasma isolates associated with five C. palmata plants. Collectively, restriction fragment length polymorphism (RFLP) patterns generated with key enzymes AluI, BamHI, DraI, and HaeIII clearly differentiated the C. palmata yellows (CPY) phytoplasma from LY and other known phytoplasmas previously characterized by this means (2). A sequence homology of 99.21% between 16S rDNA of CPY (1,537 bp; GenBank accession, AF237615) and LY (1,524 bp; accession, U18747) indicated that these strains were very similar. This relationship was confirmed by phylogenetic analysis of 16S rDNA sequence, which placed both strains into the same phytoplasma subclade. References: (1) N. A. Harrison et al. Plant Pathol. 43:998, 1994. (2) I.-M. Lee et al. Int. J. Syst. Bacteriol. 48:1153, 1998. (3) J. P. Martínez-Soriano et al. Rev. Mex. Fitopat. 12:75, 1994. (4) C. D. Smart et al. Appl. Environ. Microbiol. 62: 2988, 1996.

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 Can cyanobacteria infect underground water sources? Evidence from a small scale monitoring of natural mineral water drinking source

2017 ◽  
Vol 8 (1) ◽  
Author(s):  
Spyros Gkelis ◽  
Aristidis Vlamis
Keyword(s):  
16S Rdna ◽  
Mineral Water ◽  
Monitoring Program ◽  
Water Source ◽  
Biosynthetic Gene Cluster ◽  
Underground Water ◽  
Cyanobacterial Blooms ◽  
Small Scale ◽  
Natural Mineral ◽  
Natural Mineral Water

The expansion of harmful cyanobacterial blooms is of worldwide concern as they have increased globally in frequency and intensity in recent decades. A cyanobacterial colony was found in a bottle of natural mineral water of a small water company in July 2012, which led to a further examination for a period of five months (July-November 2012) of both the bottled filtered water and the originating groundwater source (N. Greece) for the occurrence of Cyanobacteria. Cyanobacteria occurrence was monitored by microscopy and cyanospecific 16S rDNA amplification; potentially toxic species occurrence was screened by mcyA gene (known to take part in the MC-biosynthetic gene cluster) amplification. The highest abundance of cyanobacterial cells without the simultaneous presence of the mcyA gene, was measured in July, in contrast to October when the presence of cyanobacteria was only identified by tracing cyanospecific 16S rDNA and the mcyA gene region in the underground water source. The results of this small scale monitoring program indicate the potential existence of an emerging danger for human health in a relatively manageable product such as the bottled natural mineral water. 

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