scholarly journals Growing the recalcitrant

2007 ◽  
Vol 28 (3) ◽  
pp. 127
Author(s):  
Peter H Janssen
Keyword(s):  
16S Rrna ◽  
Microbial Diversity ◽  
16S Rrna Genes ◽  
Rrna Genes

Unculturable microorganisms are those that have been identifiedby microscopy, by their activity or by detection of phylogenetic markers such as their 16S rRNA genes, and have not been able to be cultured, despite reasonable efforts having been made. Recent successes in the cultivation of so-called unculturable microorganisms have revealed that the key ingredient in therecipe for growing them in the laboratory is patience. Beyond that, there is probably no single secret to success and microbial diversity must be matched by experimental ingenuity.

scholarly journals High Diversity in Iron Cycling Microbial Communities in Acidic, Iron-Rich Water of the Pyhäsalmi Mine, Finland

Geofluids ◽  
2019 ◽  
Vol 2019 ◽  
pp. 1-17 ◽  
Author(s):  
Malin Bomberg ◽  
Jarno Mäkinen ◽  
Marja Salo ◽  
Päivi Kinnunen
Keyword(s):  
16S Rrna ◽  
Microbial Diversity ◽  
Microbial Communities ◽  
Mine Water ◽  
Ferrous Iron ◽  
Great Part ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Iron Oxidizers

Microbial communities of iron-rich water in the Pyhäsalmi mine, Finland, were investigated with high-throughput amplicon sequencing and qPCR targeting bacteria, archaea, and fungi. In addition, the abundance ofLeptospirillumandAcidithiobacilluswas assessed with genus-specific qPCR assays, and enrichment cultures targeting aerobic ferrous iron oxidizers and ferric iron reducers were established. The acidic (pH 1.4–2.3) mine water collected from 240 m, 500 m, and 600 m depth from within the mine had a high microbial diversity consisting of 63-114 bacterial, 10-13 archaeal, and 104-117 fungal genera. The most abundant microorganisms in the mine water were typical acid mine drainage (AMD) taxa, such as acidophilic, iron-oxidizingLeptospirillum,Acidiphilum,Acidithiobacillus,Ferrovum, andThermoplasma. The fungi belonged mostly to the phylum Ascomycetes, although a great part of the fungal sequences remained unclassified. The number of archaeal 16S rRNA genes in the mine water was between 0.3 and 1.2 × 107copies mL−1in the samples from 500 m and 600 m, but only 3.9 × 103at 240 m and archaea were in general not enriched in cultures. The number of fungal 5.8S rRNA genes was high only in the mine water from 500 m and 600 m, where 0.2–3.4 × 104spore equivalents mL−1were detected. A high number ofLeptospirillum16S rRNA genes, 0.6–1.6 × 1010copies mL−1, were detected at 500 m and 600 m depth and in cultures containing ferrous iron, showing the importance of iron oxidizers in this environment. The abundance of bacteria in general was between 103and 10616S rRNA gene copies mL−1. Our results showed a high microbial diversity in the acid- and iron-impacted waters of the Pyhäsalmi mine, whereLeptospirillumbacteria were especially prominent. These iron oxidizers are also the main nitrogen-fixing microorganisms in this ecosystem.

scholarly journals Seasonal Variation of Microbial Diversity of Coastal Sediment in Tongyeong, South Korea, Using 16S rRNA Gene Amplicon Sequencing

2021 ◽  
Vol 10 (27) ◽  
Author(s):  
Nur Indradewi Oktavitri ◽  
Jong-Oh Kim ◽  
Kyunghoi Kim
Keyword(s):  
Seasonal Variation ◽  
Microbial Community ◽  
16S Rrna ◽  
South Korea ◽  
Microbial Diversity ◽  
Amplicon Sequencing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Generation Sequencing

Benthic microbial diversity in Tongyeong, South Korea, was analyzed using next-generation sequencing of the 16S rRNA genes, to reveal the effects of seasonal variations on the microbial community in sediment. Proteobacteria was the dominant phylum, with a relative abundance of 61.5 to 68.1%.

scholarly journals Animal-to-Animal Variation in Fecal Microbial Diversity among Beef Cattle

2010 ◽  
Vol 76 (14) ◽  
pp. 4858-4862 ◽  
Author(s):  
Lisa M. Durso ◽  
Gregory P. Harhay ◽  
Timothy P. L. Smith ◽  
James L. Bono ◽  
Todd Z. DeSantis ◽  
...  
Keyword(s):  
Food Safety ◽  
16S Rrna ◽  
Beef Cattle ◽  
Microbial Diversity ◽  
Intestinal Microbiota ◽  
Animal Health ◽  
Methane Emissions ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Health Food

ABSTRACT The intestinal microbiota of beef cattle are important for animal health, food safety, and methane emissions. This full-length sequencing survey of 11,171 16S rRNA genes reveals animal-to-animal variation in communities that cannot be attributed to breed, gender, diet, age, or weather. Beef communities differ from those of dairy. Core bovine taxa are identified.

Microbial Diversity in a Brazilian Acid Moderate Drainage and Experimental Nickel Bioleaching System

2009 ◽  
Vol 71-73 ◽  
pp. 117-120 ◽  
Author(s):  
L. Alves ◽  
C. Bernardelli ◽  
V.A. Leão ◽  
Monica Teixeira ◽  
Edgardo R. Donati
Keyword(s):  
16S Rrna ◽  
Microbial Diversity ◽  
Mine Drainage ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Complete Characterization ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Universal Primers ◽  
Fish Analysis ◽  
Acidithiobacillus Thiooxidans

The aim of this work was to determine the microbial diversity of the acid mine drainage (AMD) material collected at an abandoned pyrite mine in Ouro Preto, Brazil. AMD samples were compared to a nickel sulfide column bioleaching pregnant solution which was used as reference. Fluorescent in situ hybridization analyses (FISH) and Denaturing Gradient Gel Electrophoresis (DGGE) were used. FISH analysis was carried out using specific 16S rRNA probes. The extracted DNA was amplified using universal primers for bacterial 16S rRNA genes and analyzed by DGGE. Acidithiobacillus. ferrooxidans was not detected in AMD samples. However, the presence of Acidithiobacillus thiooxidans was confirmed. In other hand, in the bioleaching tanks samples studied, both bacteria species were detected. The non-identified DNA bands were cloned and sequenced for complete characterization.

scholarly journals The Problem with ‘Microbiome’

Diversity ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 138
Author(s):  
Stuart Donachie ◽  
Claire Fraser ◽  
Ethan Hill ◽  
Marguerite Butler
Keyword(s):  
16S Rrna ◽  
Microbial Diversity ◽  
Sensu Stricto ◽  
Ribosomal Gene ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Community Members ◽  
Etiologic Agents ◽  
Microbiome Research ◽  
Marine Microbial Diversity

The term “microbiome” is currently applied predominantly to assemblages of organisms with 16S rRNA genes. In this context, “microbiome” is a misnomer that has been conferred a wide-ranging primacy over terms for community members lacking such genes, e.g., mycobiome, eukaryome, and virome, yet these are also important subsets of microbial communities. Widespread convenient and affordable 16S rRNA sequencing pipelines have accelerated continued use of such a “microbiome”, but at what intellectual and practical costs? Here we show that the use of “microbiome” in ribosomal gene-based studies has been egregiously misapplied, and discuss potential impacts. We argue that the current focus of “microbiome” research, predominantly on only ‘bacteria’, presents a dangerous narrowing of scope which encourages dismissal and even ignorance of other organisms’ contributions to microbial diversity, sensu stricto, and as etiologic agents; we put this in context by discussing cases in both marine microbial diversity and the role of pathogens in global amphibian decline. Fortunately, the solution is simple. We must use descriptive nouns that strictly reflect the outcomes attainable by the methods used. “Microbiome”, as a descriptive noun, should only be used when diversity in the three recognized domains is explored.

Molecular Assessment of Microbial Diversity and Community Structure at Uranium Mines of Jaduguda, India

2007 ◽  
Vol 20-21 ◽  
pp. 413-416 ◽  
Author(s):  
Pinaki Sar ◽  
Paltu K. Dhal ◽  
Ekramul Islam ◽  
Sufia K. Kazy
Keyword(s):  
16S Rrna ◽  
Microbial Diversity ◽  
Molecular Level ◽  
Restriction Analysis ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Uranium Mine ◽  
Rrna Gene ◽  
Wide Range ◽  
Mine Sites

Microbial diversity associated with uranium mine areas of Jaduguda, India has been investigated using a culture independent molecular approach. Soil samples collected from existing and proposed mine sites were analyzed for physicochemical parameters. Community DNA was extracted from five samples. Small subunit rRNA gene (16S rRNA) was PCR amplified using bacterial primers. The diversity of the total bacterial community was described at molecular level by amplified ribosomal DNA restriction analysis (ARDRA). Dominant bacterial groups (represents by OTUs) selected by ARDRA were identified by sequencing the 16S rRNA genes. From the bacterial rDNA clone library around 230 clones were used for further analysis. The unique OTUs and number of clones representing such OTUs were determined. Dominant OTUs were sequenced and identified. These phylotypes spanned a wide range within the bacterial domain occupying Proteobacteria, Acidobacteria, Bacteroidetes, Firmicutes, Cyanobacteria as major phyla. About 46 % of clones sequenced from various sites were identified as Proteobacteria. The present findings on microbial diversity at the molecular level are the first of its kind for uranium mine sites of India. Around 20 % of the clone sequences showed little affiliation with known taxa and probably represent new organisms adapted to this habitat.

scholarly journals Influence of an Oyster Reef on Development of the Microbial Heterotrophic Community of an Estuarine Biofilm

2004 ◽  
Vol 70 (11) ◽  
pp. 6834-6845 ◽  
Author(s):  
Andreas Nocker ◽  
Joe E. Lepo ◽  
Richard A. Snyder
Keyword(s):  
Species Richness ◽  
16S Rrna ◽  
Microbial Diversity ◽  
Oyster Reef ◽  
Molecular Techniques ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Muddy Sand ◽  
Pcr Products ◽  
Sand Bottom

ABSTRACT We characterized microbial biofilm communities developed over two very closely located but distinct benthic habitats in the Pensacola Bay estuary using two complementary cultivation-independent molecular techniques. Biofilms were grown for 7 days on glass slides held in racks 10 to 15 cm over an oyster reef and an adjacent muddy sand bottom. Total biomass and optical densities of dried biofilms showed dramatic differences for oyster reef versus non-oyster reef biofilms. This study assessed whether the observed spatial variation was reflected in the heterotrophic prokaryotic species composition. Genomic biofilm DNA from both locations was isolated and served as a template to amplify 16S rRNA genes with universal eubacterial primers. Fluorescently labeled PCR products were analyzed by terminal restriction fragment length polymorphism, creating a genetic fingerprint of the composition of the microbial communities. Unlabeled PCR products were cloned in order to construct a clone library of 16S rRNA genes. Amplified ribosomal DNA restriction analysis was used to screen and define ribotypes. Partial sequences from unique ribotypes were compared with existing database entries to identify species and to construct phylogenetic trees representative of community structures. A pronounced difference in species richness and evenness was observed at the two sites. The biofilm community structure from the oyster reef setting had greater evenness and species richness than the one from the muddy sand bottom. The vast majority of the bacteria in the oyster reef biofilm were related to members of the γ- and δ-subdivisions of Proteobacteria, the Cytophaga-Flavobacterium -Bacteroides cluster, and the phyla Planctomyces and Holophaga-Acidobacterium. The same groups were also present in the biofilm harvested at the muddy sand bottom, with the difference that nearly half of the community consisted of representatives of the Planctomyces phylum. Total species richness was estimated to be 417 for the oyster reef and 60 for the muddy sand bottom, with 10.5% of the total unique species identified being shared between habitats. The results suggest dramatic differences in habitat-specific microbial diversity that have implications for overall microbial diversity within estuaries.

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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