scholarly journals Cave Drip Water-Related Samples as a Natural Environment for Aromatic Hydrocarbon-Degrading Bacteria

2019 ◽  
Vol 7 (2) ◽  
pp. 33 ◽  
Author(s):  
Eric Marques ◽  
Gislaine Silva ◽  
João Dias ◽  
Eduardo Gross ◽  
Moara Costa ◽  
...  
Keyword(s):  
Aromatic Hydrocarbon ◽  
Microbial Communities ◽  
16S Rdna ◽  
Aromatic Compounds ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Amplicon Sequencing ◽  
Drip Water ◽  
Rdna Sequencing ◽  
Degrading Bacteria ◽  
Cave Drip Water

Restricted contact with the external environment has allowed the development of microbial communities adapted to the oligotrophy of caves. However, nutrients can be transported to caves by drip water and affect the microbial communities inside the cave. To evaluate the influence of aromatic compounds carried by drip water on the microbial community, two limestone caves were selected in Brazil. Drip-water-saturated and unsaturated sediment, and dripping water itself, were collected from each cave and bacterial 16S rDNA amplicon sequencing and denaturing gradient gel electrophoresis (DGGE) of naphthalene dioxygenase (ndo) genes were performed. Energy-dispersive X-ray spectroscopy (EDX) and atomic absorption spectroscopy (AAS) were performed to evaluate inorganic nutrients, and GC was performed to estimate aromatic compounds in the samples. The high frequency of Sphingomonadaceae in drip water samples indicates the presence of aromatic hydrocarbon-degrading bacteria. This finding was consistent with the detection of naphthalene and acenaphthene and the presence of ndo genes in drip-water-related samples. The aromatic compounds, aromatic hydrocarbon-degrading bacteria and 16S rDNA sequencing indicate that aromatic compounds may be one of the sources of energy and carbon to the system and the drip-water-associated bacterial community contains several potentially aromatic hydrocarbon-degrading bacteria. To the best of our knowledge, this is the first work to present compelling evidence for the presence of aromatic hydrocarbon-degrading bacteria in cave drip water.

Comparative analysis of microbiome between accurately identified 16S rDNA and quantified bacteria in simulated samples

2014 ◽  
Vol 63 (3) ◽  
pp. 433-440 ◽  
Author(s):  
Haiyin Wang ◽  
Pengcheng Du ◽  
Juan Li ◽  
Yuanyuan Zhang ◽  
Wen Zhang ◽  
...  
Keyword(s):  
Microbial Communities ◽  
16S Rdna ◽  
Gold Standard ◽  
Clinical Utility ◽  
Bacterial Species ◽  
Relative Proportion ◽  
Rrna Gene ◽  
Low Concentrations ◽  
Rdna Sequencing ◽  
V3 Region

Although 16S rRNA gene (rDNA) sequencing is the gold standard for categorizing bacteria or characterizing microbial communities its clinical utility is limited by bias in metagenomic studies, in either the experiments or the data analyses. To evaluate the efficiency of current metagenomic methods, we sequenced seven simulated samples of ten bacterial species mixed at different concentrations. The V3 region of 16S rDNA was targeted and used to determine the distribution of bacterial species. The number of target sequences in individual simulated samples was in the range 1–1000 to provide a better reflection of natural microbial communities. However, for a given bacterial species present in the same proportion but at different concentrations, the observed percentage of 16S rDNAs was similar, except at very low concentrations that cannot be detected by real-time PCR. These results confirmed that the comparative microbiome in a sample characterized by 16S rDNA sequencing is sufficient to detect not only potential infectious pathogens, but also the relative proportion of 16S rDNA in the sample.

scholarly journals Relationships between Microbial Community Structure and Hydrochemistry in a Landfill Leachate-Polluted Aquifer

2001 ◽  
Vol 67 (10) ◽  
pp. 4619-4629 ◽  
Author(s):  
Wilfred F. M. Röling ◽  
Boris M. van Breukelen ◽  
Martin Braster ◽  
Bin Lin ◽  
Henk W. van Verseveld
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
16S Rdna ◽  
Microbial Community Structure ◽  
Landfill Leachate ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Numerical Comparison ◽  
Gram Positive ◽  
Gram Positive Bacteria

ABSTRACT Knowledge about the relationship between microbial community structure and hydrogeochemistry (e.g., pollution, redox and degradation processes) in landfill leachate-polluted aquifers is required to develop tools for predicting and monitoring natural attenuation. In this study analyses of pollutant and redox chemistry were conducted in parallel with culture-independent profiling of microbial communities present in a well-defined aquifer (Banisveld, The Netherlands). Degradation of organic contaminants occurred under iron-reducing conditions in the plume of pollution, while upstream of the landfill and above the plume denitrification was the dominant redox process. Beneath the plume iron reduction occurred. Numerical comparison of 16S ribosomal DNA (rDNA)-based denaturing gradient gel electrophoresis (DGGE) profiles of Bacteria andArchaea in 29 groundwater samples revealed a clear difference between the microbial community structures inside and outside the contaminant plume. A similar relationship was not evident in sediment samples. DGGE data were supported by sequencing cloned 16S rDNA. Upstream of the landfill members of the β subclass of the class Proteobacteria(β-proteobacteria) dominated. This group was not encountered beneath the landfill, where gram-positive bacteria dominated. Further downstream the contribution of gram-positive bacteria to the clone library decreased, while the contribution of δ-proteobacteria strongly increased and β-proteobacteria reappeared. The β-proteobacteria (Acidovorax,Rhodoferax) differed considerably from those found upstream (Gallionella, Azoarcus). Direct comparisons of cloned 16S rDNA with bands in DGGE profiles revealed that the data from each analysis were comparable. A relationship was observed between the dominant redox processes and the bacteria identified. In the iron-reducing plume members of the familyGeobacteraceae made a strong contribution to the microbial communities. Because the only known aromatic hydrocarbon-degrading, iron-reducing bacteria areGeobacter spp., their occurrence in landfill leachate-contaminated aquifers deserves more detailed consideration.

scholarly journals Effect of DNA Extraction Methods on the Apparent Structure of Yak Rumen Microbial Communities as Revealed by 16S rDNA Sequencing

2015 ◽  
Vol 64 (1) ◽  
pp. 29-36 ◽  
Author(s):  
YA-BING CHEN ◽  
DAO-LIANG LAN ◽  
CHENG TANG ◽  
XIAO-NONG YANG ◽  
JIAN LI
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Microbial Communities ◽  
16S Rdna ◽  
Dna Extraction ◽  
Extraction Methods ◽  
16S Rdna Sequencing ◽  
Bead Beating ◽  
Rdna Sequencing ◽  
Dna Extraction Methods

To more efficiently identify the microbial community of the yak rumen, the standardization of DNA extraction is key to ensure fidelity while studying environmental microbial communities. In this study, we systematically compared the efficiency of several extraction methods based on DNA yield, purity, and 16S rDNA sequencing to determine the optimal DNA extraction methods whose DNA products reflect complete bacterial communities. The results indicate that method 6 (hexadecyltrimethylammomium bromide-lysozyme-physical lysis by bead beating) is recommended for the DNA isolation of the rumen microbial community due to its high yield, operational taxonomic unit, bacterial diversity, and excellent cell-breaking capability. The results also indicate that the bead-beating step is necessary to effectively break down the cell walls of all of the microbes, especially Gram-positive bacteria. Another aim of this study was to preliminarily analyze the bacterial community via 16S rDNA sequencing. The microbial community spanned approximately 21 phyla, 35 classes, 75 families, and 112 genera. A comparative analysis showed some variations in the microbial community between yaks and cattle that may be attributed to diet and environmental differences. Interestingly, numerous uncultured or unclassified bacteria were found in yak rumen, suggesting that further research is required to determine the specific functional and ecological roles of these bacteria in yak rumen. In summary, the investigation of the optimal DNA extraction methods and the preliminary evaluation of the bacterial community composition of yak rumen support further identification of the specificity of the rumen microbial community in yak and the discovery of distinct gene resources.

scholarly journals Microbial Communities on Plastic Polymers in the Mediterranean Sea

2021 ◽  
Vol 12 ◽  
Author(s):  
Annika Vaksmaa ◽  
Katrin Knittel ◽  
Alejandro Abdala Asbun ◽  
Maaike Goudriaan ◽  
Andreas Ellrott ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Mediterranean Sea ◽  
Amplicon Sequencing ◽  
Polymer Surfaces ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Microbial Biofilms ◽  
Degrading Bacteria ◽  
The Mediterranean

Plastic particles in the ocean are typically covered with microbial biofilms, but it remains unclear whether distinct microbial communities colonize different polymer types. In this study, we analyzed microbial communities forming biofilms on floating microplastics in a bay of the island of Elba in the Mediterranean Sea. Raman spectroscopy revealed that the plastic particles mainly comprised polyethylene (PE), polypropylene (PP), and polystyrene (PS) of which polyethylene and polypropylene particles were typically brittle and featured cracks. Fluorescence in situ hybridization and imaging by high-resolution microscopy revealed dense microbial biofilms on the polymer surfaces. Amplicon sequencing of the 16S rRNA gene showed that the bacterial communities on all plastic types consisted mainly of the orders Flavobacteriales, Rhodobacterales, Cytophagales, Rickettsiales, Alteromonadales, Chitinophagales, and Oceanospirillales. We found significant differences in the biofilm community composition on PE compared with PP and PS (on OTU and order level), which shows that different microbial communities colonize specific polymer types. Furthermore, the sequencing data also revealed a higher relative abundance of archaeal sequences on PS in comparison with PE or PP. We furthermore found a high occurrence, up to 17% of all sequences, of different hydrocarbon-degrading bacteria on all investigated plastic types. However, their functioning in the plastic-associated biofilm and potential role in plastic degradation needs further assessment.

Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities

2013 ◽  
Vol 16 (9) ◽  
pp. 2659-2671 ◽  
Author(s):  
Ramiro Logares ◽  
Shinichi Sunagawa ◽  
Guillem Salazar ◽  
Francisco M. Cornejo-Castillo ◽  
Isabel Ferrera ◽  
...  
Keyword(s):  
Microbial Communities ◽  
16S Rdna ◽  
Amplicon Sequencing

scholarly journals Microbial Communities Associated with Anaerobic Benzene Degradation in a Petroleum-Contaminated Aquifer

1999 ◽  
Vol 65 (7) ◽  
pp. 3056-3063 ◽  
Author(s):  
Juliette N. Rooney-Varga ◽  
Robert T. Anderson ◽  
Jocelyn L. Fraga ◽  
David Ringelberg ◽  
Derek R. Lovley
Keyword(s):  
Microbial Communities ◽  
Aromatic Compounds ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Phospholipid Fatty Acid ◽  
Microbial Community Composition ◽  
Most Probable Number ◽  
Probable Number ◽  
Contaminated Aquifer ◽  
Benzene Degradation ◽  
Anaerobic Benzene Degradation

ABSTRACT Microbial community composition associated with benzene oxidation under in situ Fe(III)-reducing conditions in a petroleum-contaminated aquifer located in Bemidji, Minn., was investigated. Community structure associated with benzene degradation was compared to sediment communities that did not anaerobically oxidize benzene which were obtained from two adjacent Fe(III)-reducing sites and from methanogenic and uncontaminated zones. Denaturing gradient gel electrophoresis of 16S rDNA sequences amplified with bacterial orGeobacteraceae-specific primers indicated significant differences in the composition of the microbial communities at the different sites. Most notable was a selective enrichment of microorganisms in the Geobacter cluster seen in the benzene-degrading sediments. This finding was in accordance with phospholipid fatty acid analysis and most-probable-number–PCR enumeration, which indicated that members of the familyGeobacteraceae were more numerous in these sediments. A benzene-oxidizing Fe(III)-reducing enrichment culture was established from benzene-degrading sediments and contained an organism closely related to the uncultivated Geobacter spp. This genus contains the only known organisms that can oxidize aromatic compounds with the reduction of Fe(III). Sequences closely related to the Fe(III) reducer Geothrix fermentans and the aerobe Variovorax paradoxus were also amplified from the benzene-degrading enrichment and were present in the benzene-degrading sediments. However, neither G. fermentans nor V. paradoxusis known to oxidize aromatic compounds with the reduction of Fe(III), and there was no apparent enrichment of these organisms in the benzene-degrading sediments. These results suggest thatGeobacter spp. play an important role in the anaerobic oxidation of benzene in the Bemidji aquifer and that molecular community analysis may be a powerful tool for predicting a site’s capacity for anaerobic benzene degradation.

scholarly journals Isolation and Identification of Pesticides Degrading Bacteria from Farmland Soil

2019 ◽  
Vol 35 (2) ◽  
pp. 90-94
Author(s):  
Md Atikur Rahman ◽  
ASM Shamsul Arefin ◽  
Otun Saha ◽  
Md Mizanur Rahaman
Keyword(s):  
16S Rdna ◽  
Restriction Analysis ◽  
Bacterial Strains ◽  
Biochemical Tests ◽  
Isolation And Identification ◽  
Rdna Sequencing ◽  
Degrading Bacteria ◽  
Farmland Soil ◽  
Wide Range ◽  
Dna Restriction

Pesticides are recognized to be the threat to the environment and associated with a wide range of serious diseases including respiratory diseases, cancer and even birth defects. In this study, six-different bacterial strains capable of degrading Carbofuran, Emamectin Benzoate and Thiamethoxam were isolated from eight different soil samples. The isolates were characterized by using different conventional and molecular methods. The strains were identified molecularly into different genotypes using amplified ribosomal DNA restriction analysis (ARDRA) and partial sequencing of 16S rDNA. The ARDRA pattern clustered them into 3 groups. Among the isolates three were identified as Achromobacter spp. and one as Diaphorobacter sp. by biochemical tests. It was further confirmed by the partial 16S rDNA sequencing. The two identified potential bacteria can be used for biodegradation of different pesticides which can have a significant environmental impact in soil farm. Bangladesh J Microbiol, Volume 35 Number 2 December 2018, pp 90-94

Microbial communities in the larval midgut of laboratory and field populations of cotton bollworm (Helicoverpa armigera)

2006 ◽  
Vol 52 (11) ◽  
pp. 1085-1092 ◽  
Author(s):  
Hui Xiang ◽  
Gui-Fang Wei ◽  
Shihai Jia ◽  
Jianhua Huang ◽  
Xue-Xia Miao ◽  
...  
Keyword(s):  
Microbial Community ◽  
Sequence Analysis ◽  
Microbial Communities ◽  
16S Rdna ◽  
Helicoverpa Armigera ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Cotton Bollworm ◽  
Laboratory Population ◽  
Larval Midgut ◽  
Helicoverpa Armígera

We compared the bacterial communities in the larval midgut of field and laboratory populations of a polyphagous pest, the cotton bollworm (Helicoverpa armigera), using denaturing gradient gel electrophoresis (DGGE) of amplified 16S rDNA sequences and 16S library sequence analysis. DGGE profiles and 16S rDNA library sequence analysis indicated similar patterns of midgut microbial community structure and diversity: specific bacterial types existed in both populations, and a more diverse microbial community was observed in caterpillars obtained from the field. The laboratory population harbored a rather simple gut microflora consisting mostly of phylotypes belonging to Enterococcus (84%). For the field population, phylotypes belonging to Enterococcus (28%) and Lactococcus (11%), as well as Flavobacterium (10%), Acinetobacter (19%), and Stenotrophomonas (10%) were dominant members. These results provided the first comprehensive description of the microbial diversity of the midgut of the important pest cotton bollworm and suggested that the environment and food supply might influence the diversity of the gut bacterial community.Key words: cotton bollworm, midgut, microbial communities, 16S rDNA.

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