scholarly journals Las Quínoas oncoids: a new deposit of microbialites in the Salar de Antofalla (Catamarca, Argentina)

2021 ◽  
Vol 48 (2) ◽  
pp. 281
Author(s):  
Patricio Guillermo Villafañe ◽  
Agustina Inés Lencina ◽  
Mariana Soria ◽  
Luis Alberto Saona ◽  
Fernando Javier Gómez ◽  
...  
Keyword(s):  
Microbial Mats ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Clastic Material ◽  
Microbial Biodiversity ◽  
Thin Sections ◽  
Salt Flat ◽  
Modern System ◽  
Carbonate Matrix ◽  
Groundwater Springs

The Salar de Antofalla (salt flat) is located in the Puna region of Catamarca, in northern Argentina. In this paper we report and provide the first descriptive data of Las Quínoas, a modern system of oncoids located in the western margin of the salt flat. Oncoids were studied by insitu logging, polished and thin sections analysis. In addition, the 16s rRNA genes of microbial mats associated with these oncoids were amplified and sequenced to characterize the microbial biodiversity. Oncoids present discoidal to subrounded morphologies and sizes up to 15 cm in diameter. They are scattered along channels, which originate from the groundwater springs of a wetland and enter the salt flat. Its macrostructure is concentric and composed by three zones: 1. A nucleus zone built by clastic material in a carbonate matrix. 2. A well-laminated zone around the nucleus that shows two types of mesostructures: concentrically stacked spheroids (SS-C) and randomly stacked hemispheroids (SS-R), both showing an alternation of dense and dark micritic laminae with light micritic to microsparitic laminae. 3. A poorly-laminated zone, in the outermost sector of oncoids, with two types of mesostructures too: a laminated mesostructure composed also of an alternation of dense and dark micritic laminae with light micritic to microsparitic laminae, and a non-laminated mesostructure composed of agglomerated and cemented clastic material within a calcareous matrix (wackestones-packstones). Regarding the microbial diversity, the analyzed oncoids in this work are mainly inhabited by Proteobacteria (ca. 37.5%), Bacteroidetes (ca. 25.0%), and in less proportion Planctomycetes, Actinobacteria and Cyanobacteria.

scholarly journals Influence of Molecular Resolution on Sequence-Based Discovery of Ecological Diversity amongSynechococcusPopulations in an Alkaline Siliceous Hot Spring Microbial Mat

2010 ◽  
Vol 77 (4) ◽  
pp. 1359-1367 ◽  
Author(s):  
Melanie C. Melendrez ◽  
Rachel K. Lange ◽  
Frederick M. Cohan ◽  
David M. Ward
Keyword(s):  
16S Rrna ◽  
Internal Transcribed Spacer ◽  
Microbial Mats ◽  
Hot Spring ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Ecological Diversity ◽  
Protein Encoding ◽  
Internal Transcribed Spacer Sequences

ABSTRACTPrevious research has shown that sequences of 16S rRNA genes and 16S-23S rRNA internal transcribed spacer regions may not have enough genetic resolution to define all ecologically distinctSynechococcuspopulations (ecotypes) inhabiting alkaline, siliceous hot spring microbial mats. To achieve higher molecular resolution, we studied sequence variation in three protein-encoding loci sampled by PCR from 60°C and 65°C sites in the Mushroom Spring mat (Yellowstone National Park, WY). Sequences were analyzed using the ecotype simulation (ES) and AdaptML algorithms to identify putative ecotypes. Between 4 and 14 times more putative ecotypes were predicted from variation in protein-encoding locus sequences than from variation in 16S rRNA and 16S-23S rRNA internal transcribed spacer sequences. The number of putative ecotypes predicted depended on the number of sequences sampled and the molecular resolution of the locus. Chao estimates of diversity indicated that few rare ecotypes were missed. Many ecotypes hypothesized by sequence analyses were different in their habitat specificities, suggesting different adaptations to temperature or other parameters that vary along the flow channel.

scholarly journals Quantifying Microbial Diversity: Morphotypes, 16S rRNA Genes, and Carotenoids of Oxygenic Phototrophs in Microbial Mats

1999 ◽  
Vol 65 (2) ◽  
pp. 422-430 ◽  
Author(s):  
Ulrich Nübel ◽  
Ferran Garcia-Pichel ◽  
Michael Kühl ◽  
Gerard Muyzer
Keyword(s):  
16S Rrna ◽  
Microbial Mats ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Morphological Diversity ◽  
Numerical Approach ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Specific Pcr ◽  
Phototrophic Microorganisms

ABSTRACT We quantified the diversity of oxygenic phototrophic microorganisms present in eight hypersaline microbial mats on the basis of three cultivation-independent approaches. Morphological diversity was studied by microscopy. The diversity of carotenoids was examined by extraction from mat samples and high-pressure liquid chromatography analysis. The diversity of 16S rRNA genes from oxygenic phototrophic microorganisms was investigated by extraction of total DNA from mat samples, amplification of 16S rRNA gene segments from cyanobacteria and plastids of eukaryotic algae by phylum-specific PCR, and sequence-dependent separation of amplification products by denaturing-gradient gel electrophoresis. A numerical approach was introduced to correct for crowding the results of chromatographic and electrophoretic analyses. Diversity estimates typically varied up to twofold among mats. The congruence of richness estimates and Shannon-Weaver indices based on numbers and proportional abundances of unique morphotypes, 16S rRNA genes, and carotenoids unveiled the underlying diversity of oxygenic phototrophic microorganisms in the eight mat communities studied.

scholarly journals Phylogenetic Evidence for the Existence of Novel Thermophilic Bacteria in Hot Spring Sulfur-Turf Microbial Mats in Japan

1998 ◽  
Vol 64 (5) ◽  
pp. 1680-1687 ◽  
Author(s):  
Hiroyuki Yamamoto ◽  
Akira Hiraishi ◽  
Kenji Kato ◽  
Hiroshi X. Chiura ◽  
Yonosuke Maki ◽  
...  
Keyword(s):  
16S Rrna ◽  
Microbial Mats ◽  
Hot Springs ◽  
Hot Spring ◽  
Thermophilic Bacteria ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rdna Sequences ◽  
Major Cluster ◽  
The Common

ABSTRACT So-called sulfur-turf microbial mats, which are macroscopic white filaments or bundles consisting of large sausage-shaped bacteria and elemental sulfur particles, occur in sulfide-containing hot springs in Japan. However, no thermophiles from sulfur-turf mats have yet been isolated as cultivable strains. This study was undertaken to determine the phylogenetic positions of the sausage-shaped bacteria in sulfur-turf mats by direct cloning and sequencing of 16S rRNA genes amplified from the bulk DNAs of the mats. Common clones with 16S rDNA sequences with similarity levels of 94.8 to 99% were isolated from sulfur-turf mat samples from two geographically remote hot springs. Phylogenetic analysis showed that the phylotypes of the common clones formed a major cluster with members of theAquifex-Hydrogenobacter complex, which represents the most deeply branching lineage of the domain bacteria. Furthermore, the bacteria of the sulfur-turf mat phylotypes formed a clade distinguishable from that of other members of theAquifex-Hydrogenobacter complex at the order or subclass level. In situ hybridization with clone-specific probes for 16S rRNA revealed that the common phylotype of sulfur-turf mat bacteria is that of the predominant sausage-shaped bacteria.

scholarly journals Differences in Temperature and Water Chemistry Shape Distinct Diversity Patterns in Thermophilic Microbial Communities

2017 ◽  
Vol 83 (21) ◽  
Author(s):  
Cecilia M. Chiriac ◽  
Edina Szekeres ◽  
Knut Rudi ◽  
Andreea Baricz ◽  
Adriana Hegedus ◽  
...  
Keyword(s):  
Water Chemistry ◽  
Microbial Communities ◽  
Community Composition ◽  
Microbial Mats ◽  
Hot Spring ◽  
Environmental Data ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Thermal Gradients ◽  
Content Type

ABSTRACT This report describes the biodiversity and ecology of microbial mats developed in thermal gradients (20 to 65°C) in the surroundings of three drillings (Chiraleu [CH], Ciocaia [CI], and Mihai Bravu [MB]) tapping a hyperthermal aquifer in Romania. Using a metabarcoding approach, 16S rRNA genes were sequenced from both DNA and RNA transcripts (cDNA) and compared. The relationships between the microbial diversity and the physicochemical factors were explored. Additionally, the cDNA data were used for in silico functionality predictions, bringing new insights into the functional potential and dynamics of these communities. The results showed that each hot spring determined the formation of distinct microbial communities. In the CH mats (40 to 53°C), the abundance of Cyanobacteria decreased with temperature, opposite to those of Chloroflexi and Proteobacteria. Ectothiorhodospira, Oscillatoria, and methanogenic archaea dominated the CI communities (20 to 65°C), while the MB microbial mats (53 to 65°C) were mainly composed of Chloroflexi, Hydrogenophilus, Thermi, and Aquificae. Alpha-diversity was negatively correlated with the increase in water temperature, while beta-diversity was shaped in each hot spring by the unique combination of physicochemical parameters, regardless of the type of nucleic acid analyzed (DNA versus cDNA). The rank correlation analysis revealed a unique model that associated environmental data with community composition, consisting in the combined effect of Na+, K+, HCO3 −, and PO4 3− concentrations, together with temperature and electrical conductivity. These factors seem to determine the grouping of samples according to location, rather than with the similarities in thermal regimes, showing that other parameters beside temperature are significant drivers of biodiversity. IMPORTANCE Hot spring microbial mats represent a remarkable manifestation of life on Earth and have been intensively studied for decades. Moreover, as hot spring areas are isolated and have a limited exchange of organisms, nutrients, and energy with the surrounding environments, hot spring microbial communities can be used in model studies to elucidate the colonizing potential within extreme settings. Thus, they are of great importance in evolutionary biology, microbial ecology, and exobiology. In spite of all the efforts that have been made, the current understanding of the influence of temperature and water chemistry on the microbial community composition, diversity, and abundance in microbial mats is limited. In this study, the composition and diversity of microbial communities developed in thermal gradients in the vicinity of three hot springs from Romania were investigated, each having particular physicochemical characteristics. Our results expose new factors that could determine the formation of these ecosystems, expanding the current knowledge in this regard.

scholarly journals Bacterial Diversity and Sulfur Cycling in a Mesophilic Sulfide-Rich Spring

2003 ◽  
Vol 69 (9) ◽  
pp. 5609-5621 ◽  
Author(s):  
Mostafa S. Elshahed ◽  
John M. Senko ◽  
Fares Z. Najar ◽  
Stephen M. Kenton ◽  
Bruce A. Roe ◽  
...  
Keyword(s):  
Microbial Community ◽  
Clone Library ◽  
Microbial Mats ◽  
Large Fraction ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Anoxygenic Phototrophic Bacteria ◽  
Sulfur Cycling ◽  
Cloning And Sequencing ◽  
Sulfate Reducing

ABSTRACT An artesian sulfide- and sulfur-rich spring in southwestern Oklahoma is shown to sustain an extremely rich and diverse microbial community. Laboratory incubations and autoradiography studies indicated that active sulfur cycling is occurring in the abundant microbial mats at Zodletone spring. Anoxygenic phototrophic bacteria oxidize sulfide to sulfate, which is reduced by sulfate-reducing bacterial populations. The microbial community at Zodletone spring was analyzed by cloning and sequencing 16S rRNA genes. A large fraction (83%) of the microbial mat clones belong to sulfur- and sulfate-reducing lineages within δ-Proteobacteria, purple sulfur γ-Proteobacteria, ε-Proteobacteria, Chloroflexi, and filamentous Cyanobacteria of the order Oscillatoria as well as a novel group within γ-Proteobacteria. The 16S clone library constructed from hydrocarbon-exposed sediments at the source of the spring had a higher diversity than the mat clone library (Shannon-Weiner index of 3.84 compared to 2.95 for the mat), with a higher percentage of clones belonging to nonphototrophic lineages (e.g., Cytophaga, Spirochaetes, Planctomycetes, Firmicutes, and Verrucomicrobiae). Many of these clones were closely related to clones retrieved from hydrocarbon-contaminated environments and anaerobic hydrocarbon-degrading enrichments. In addition, 18 of the source clones did not cluster with any of the previously described microbial divisions. These 18 clones, together with previously published or database-deposited related sequences retrieved from a wide variety of environments, could be clustered into at least four novel candidate divisions. The sulfate-reducing community at Zodletone spring was characterized by cloning and sequencing a 1.9-kb fragment of the dissimilatory sulfite reductase (DSR) gene. DSR clones belonged to the Desulfococcus-Desulfosarcina-Desulfonema group, Desulfobacter group, and Desulfovibrio group as well as to a deeply branched group in the DSR tree with no representatives from cultures. Overall, this work expands the division-level diversity of the bacterial domain and highlights the complexity of microbial communities involved in sulfur cycling in mesophilic microbial mats.

scholarly journals Microscopic Examination of Distribution and Phenotypic Properties of Phylogenetically Diverse Chloroflexaceae-Related Bacteria in Hot Spring Microbial Mats

2002 ◽  
Vol 68 (9) ◽  
pp. 4593-4603 ◽  
Author(s):  
Ulrich Nübel ◽  
Mary M. Bateson ◽  
Verona Vandieken ◽  
Andrea Wieland ◽  
Michael Kühl ◽  
...  
Keyword(s):  
Microbial Mats ◽  
Hot Spring ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Small Scale ◽  
Phenotypic Properties ◽  
In Situ Conditions ◽  
Type C ◽  
Microelectrode Measurements

ABSTRACT We investigated the diversity, distribution, and phenotypes of uncultivated Chloroflexaceae-related bacteria in photosynthetic microbial mats of an alkaline hot spring (Mushroom Spring, Yellowstone National Park). By applying a directed PCR approach, molecular cloning, and sequence analysis of 16S rRNA genes, an unexpectedly large phylogenetic diversity among these bacteria was detected. Oligonucleotide probes were designed to target 16S rRNAs from organisms affiliated with the genus Chloroflexus or with the type C cluster, a group of previously discovered Chloroflexaceae relatives of this mat community. The application of peroxidase-labeled probes in conjunction with tyramide signal amplification enabled the identification of these organisms within the microbial mats by fluorescence in situ hybridization (FISH) and the investigation of their morphology, abundance, and small-scale distribution. FISH was combined with oxygen microelectrode measurements, microscope spectrometry, and microautoradiography to examine their microenvironment, pigmentation, and carbon source usage. Abundant type C-related, filamentous bacteria were found to flourish within the cyanobacterium-dominated, highly oxygenated top layers and to predominate numerically in deeper orange-colored zones of the investigated microbial mats, correlating with the distribution of bacteriochlorophyll a. Chloroflexus sp. filaments were rare at 60°C but were more abundant at 70°C, where they were confined to the upper millimeter of the mat. Both type C organisms and Chloroflexus spp. were observed to assimilate radiolabeled acetate under in situ conditions.

scholarly journals Survey of Archaeal Diversity Reveals an Abundance of Halophilic Archaea in a Low-Salt, Sulfide- and Sulfur-Rich Spring

2004 ◽  
Vol 70 (4) ◽  
pp. 2230-2239 ◽  
Author(s):  
Mostafa S. Elshahed ◽  
Fares Z. Najar ◽  
Bruce A. Roe ◽  
Aharon Oren ◽  
Thomas A. Dewers ◽  
...  
Keyword(s):  
16S Rrna ◽  
Microbial Mats ◽  
Stream Water ◽  
High Salt ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Source Analysis ◽  
Natural Ecosystems ◽  
Wide Range ◽  
Low Salt

ABSTRACT The archaeal community in a sulfide- and sulfur-rich spring with a stream water salinity of 0.7 to 1.0% in southwestern Oklahoma was studied by cloning and sequencing of 16S rRNA genes. Two clone libraries were constructed from sediments obtained at the hydrocarbon-exposed source of the spring and the microbial mats underlying the water flowing from the spring source. Analysis of 113 clones from the source library and 65 clones from the mat library revealed that the majority of clones belonged to the kingdom Euryarchaeota, while Crenarchaeota represented less than 10% of clones. Euryarchaeotal clones belonged to the orders Methanomicrobiales, Methanosarcinales, and Halobacteriales, as well as several previously described lineages with no pure-culture representatives. Those within the Halobacteriales represented 36% of the mat library and 4% of the source library. All cultivated members of this order are obligately aerobic halophiles. The majority of halobacterial clones encountered were not affiliated with any of the currently described genera of the family Halobacteriaceae. Measurement of the salinity at various locations at the spring, as well as along vertical gradients, revealed that soils adjacent to spring mats have a much higher salinity (NaCl concentrations as high as 32%) and a lower moisture content than the spring water, presumably due to evaporation. By use of a high-salt-plus-antibiotic medium, several halobacterial isolates were obtained from the microbial mats. Analysis of 16S rRNA genes indicated that all the isolates were members of the genus Haloferax. All isolates obtained grew at a wide range of salt concentrations, ranging from 6% to saturation, and all were able to reduce elemental sulfur to sulfide. We reason that the unexpected abundance of halophilic Archaea in such a low-salt, highly reduced environment could be explained by their relatively low salt requirement, which could be satisfied in specific locations of the shallow spring via evaporation, and their ability to grow under the prevalent anaerobic conditions in the spring, utilizing zero-valent sulfur compounds as electron acceptors. This study demonstrates that members of the Halobacteriales are not restricted to their typical high-salt habitats, and we propose a role for the Halobacteriales in sulfur reduction in natural ecosystems.

scholarly journals Diversity and Distribution in Hypersaline Microbial Mats of Bacteria Related to Chloroflexusspp

2001 ◽  
Vol 67 (9) ◽  
pp. 4365-4371 ◽  
Author(s):  
Ulrich Nübel ◽  
Mary M. Bateson ◽  
Michael T. Madigan ◽  
Michael Kühl ◽  
David M. Ward
Keyword(s):  
16S Rrna ◽  
Microbial Mats ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Phylogenetic Analyses ◽  
Pcr Primers ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Gradient Gel Electrophoresis ◽  
Hypersaline Microbial Mats

ABSTRACT Filamentous bacteria containing bacteriochlorophylls cand a were enriched from hypersaline microbial mats. Based on phylogenetic analyses of 16S rRNA gene sequences, these organisms form a previously undescribed lineage distantly related toChloroflexus spp. We developed and tested a set of PCR primers for the specific amplification of 16S rRNA genes from filamentous phototrophic bacteria within the kingdom of “green nonsulfur bacteria.” PCR products recovered from microbial mats in a saltern in Guerrero Negro, Mexico, were subjected to cloning or denaturing gradient gel electrophoresis and then sequenced. We found evidence of a high diversity of bacteria related toChloroflexus which exhibit different distributions along a gradient of salinity from 5.5 to 16%.

Differentiation Of Clarias Batrachus, C. Gariepinus And Heteropneustes Fossilis By Pcr-Sequencing Of Mitochondrial 16s Rrna Gene

2015 ◽  
Vol 41 (1) ◽  
pp. 51-58
Author(s):  
Mohammad Shamimul Alam ◽  
Hawa Jahan ◽  
Rowshan Ara Begum ◽  
Reza M Shahjahan
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Fish Larva ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Valuable Insight ◽  
Multiple Sequence ◽  
Pcr Rflp ◽  
Alternative Means

Heteropneustesfossilis, Clariasbatrachus and C. gariepinus are three major catfishes ofecological and economic importance. Identification of these fish species becomes aproblem when the usual external morphological features of the fish are lost or removed,such as in canned fish. Also, newly hatched fish larva is often difficult to identify. PCRsequencingprovides accurate alternative means of identification of individuals at specieslevel. So, 16S rRNA genes of three locally collected catfishes were sequenced after PCRamplification and compared with the same gene sequences available from othergeographical regions. Multiple sequence alignment of the 16S rRNA gene fragments ofthe catfish species has revealed polymorphic sites which can be used to differentiate thesethree species from one another and will provide valuable insight in choosing appropriaterestriction enzymes for PCR-RFLP based identification in future. Asiat. Soc. Bangladesh, Sci. 41(1): 51-58, June 2015

scholarly journals Effects of Supplement of Marichromatium gracile YL28 on Water Quality and Microbial Structures in Shrimp Mariculture Ecosystems

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 40
Author(s):  
Liang Cui ◽  
Bitong Zhu ◽  
Xiaobo Zhang ◽  
Zhuhua Chan ◽  
Chungui Zhao ◽  
...  
Keyword(s):  
Water Quality ◽  
16S Rrna ◽  
Relative Abundance ◽  
Animal Health ◽  
Denitrifying Bacteria ◽  
Nitrite Reduction ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sequencing Analysis ◽  
Shrimp Culture

The elevated NH3-N and NO2-N pollution problems in mariculture have raised concerns because they pose threats to animal health and coastal and offshore environments. Supplement of Marichromatium gracile YL28 (YL28) into polluted shrimp rearing water and sediment significantly decreased ammonia and nitrite concentrations, showing that YL28 functioned as a novel safe marine probiotic in the shrimp culture industry. The diversity of aquatic bacteria in the shrimp mariculture ecosystems was studied by sequencing the V4 region of 16S rRNA genes, with respect to additions of YL28 at the low and high concentrations. It was revealed by 16S rRNA sequencing analysis that Proteobacteria, Planctomycete and Bacteroidetes dominated the community (>80% of operational taxonomic units (OTUs)). Up to 41.6% of the predominant bacterial members were placed in the classes Gammaproteobacteria (14%), Deltaproteobacteria (14%), Planctomycetacia (8%) and Alphaproteobacteria (5.6%) while 40% of OTUs belonged to unclassified ones or others, indicating that the considerable bacterial populations were novel in our shrimp mariculture. Bacterial communities were similar between YL28 supplements and control groups (without addition of YL28) revealed by the β-diversity using PCoA, demonstrating that the additions of YL28 did not disturb the microbiota in shrimp mariculture ecosystems. Instead, the addition of YL28 increased the relative abundance of ammonia-oxidizing and denitrifying bacteria. The quantitative PCR analysis further showed that key genes including nifH and amoA involved in nitrification and nitrate or nitrite reduction significantly increased with YL28 supplementation (p < 0.05). The supplement of YL28 decreased the relative abundance of potential pathogen Vibrio. Together, our studies showed that supplement of YL28 improved the water quality by increasing the relative abundance of ammonia-oxidizing and denitrifying bacteria while the microbial community structure persisted in shrimp mariculture ecosystems.

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