scholarly journals Biodiversity of Microorganisms Colonizing the Surface of Polystyrene Samples Exposed to Different Aqueous Environments

2020 ◽  
Vol 12 (9) ◽  
pp. 3624 ◽  
Author(s):  
Tatyana Tourova ◽  
Diyana Sokolova ◽  
Tamara Nazina ◽  
Denis Grouzdev ◽  
Eugeni Kurshev ◽  
...  
Keyword(s):  
Amino Acids ◽  
High Throughput Sequencing ◽  
Freshwater Ecosystems ◽  
Microbial Populations ◽  
Rrna Gene ◽  
Petrochemical Plant ◽  
Industrial Water ◽  
Aqueous Environments ◽  
The 16S Rrna Gene ◽  
Xenobiotic Degradation

The contamination of marine and freshwater ecosystems with the items from thermoplastics, including polystyrene (PS), necessitates the search for efficient microbial degraders of these polymers. In the present study, the composition of prokaryotes in biofilms formed on PS samples incubated in seawater and the industrial water of a petrochemical plant were investigated. Using a high-throughput sequencing of the V3–V4 region of the 16S rRNA gene, the predominance of Alphaproteobacteria (Blastomonas), Bacteroidetes (Chryseolinea), and Gammaproteobacteria (Arenimonas and Pseudomonas) in the biofilms on PS samples exposed to industrial water was revealed. Alphaproteobacteria (Erythrobacter) predominated on seawater-incubated PS samples. The local degradation of the PS samples was confirmed by scanning microscopy. The PS-colonizing microbial communities in industrial water differed significantly from the PS communities in seawater. Both communities have a high potential ability to carry out the carbohydrates and amino acids metabolism, but the potential for xenobiotic degradation, including styrene degradation, was relatively higher in the biofilms in industrial water. Bacteria of the genera Erythrobacter, Maribacter, and Mycobacterium were potential styrene-degraders in seawater, and Pseudomonas and Arenimonas in industrial water. Our results suggest that marine and industrial waters contain microbial populations potentially capable of degrading PS, and these populations may be used for the isolation of efficient PS degraders.

scholarly journals Red Cusk-Eel (Genypterus chilensis) Gut Microbiota Description of Wild and Aquaculture Specimens

2022 ◽  
Vol 10 (1) ◽  
pp. 105
Author(s):  
Jaime Romero ◽  
Osmán Díaz ◽  
Claudio D. Miranda ◽  
Rodrigo Rojas
Keyword(s):  
Intestinal Microbiota ◽  
High Throughput Sequencing ◽  
Acid Synthesis ◽  
Intestinal Content ◽  
Meat Production ◽  
Rrna Gene ◽  
Potential Contribution ◽  
Ion Torrent ◽  
The 16S Rrna Gene ◽  
Genypterus Chilensis

Chile has promoted the diversification of aquaculture and red cusk-eel (Genypterus chilensis) is one of the prioritized species. However, many aspects of the biology of the species are unknown or have little information available. These include intestinal microbiota, an element that may play an important role in the nutrition and defense of cultured animals for meat production. This study compares the microbiota composition of the intestinal contents of wild and aquaculture fish to explore the microbial communities present and their potential contribution to the host. DNA was extracted from the intestinal content samples and the V4 region of the 16S rRNA gene was amplified and sequenced using the Ion Torrent platform. After the examination of the sequences, strong differences were found in the composition at the level of phylum, being Firmicutes and Tenericutes the most abundant in aquaculture and wild condition, respectively. At the genus level, the Vagococcus (54%) and Mycoplasma (97%) were the most prevalent in the microbial community of aquaculture and wild condition, respectively. The evaluation of predicted metabolic pathways in these metagenomes showed that in wild condition there is an important presence of lipid metabolism belonging to the unsaturated fatty acid synthesis. In the aquaculture condition, the metabolism of terpenoids and polyketides were relevant. To our knowledge, this is the first study to characterize and compare the intestinal microbiota of red cusk-eel (Genypterus chilensis) of wild and aquaculture origin using high-throughput sequencing.

scholarly journals Comparison of invertebrate diversity in lake waters and their resting eggs in sediments, as revealed by high-throughput sequencing (HTS)

2020 ◽  
pp. 19
Author(s):  
Xiaoyan Wang ◽  
Qing Wang ◽  
Yufeng Yang ◽  
Wenbo Yu
Keyword(s):  
High Throughput ◽  
Water Samples ◽  
High Throughput Sequencing ◽  
Essential Feature ◽  
Resting Eggs ◽  
Freshwater Ecosystems ◽  
Rrna Gene ◽  
Promising Alternative ◽  
Invertebrate Diversity ◽  
Significant Difference

Aquatic invertebrate diversity reflects water quality and the health of aquatic ecosystems and should be monitored as an essential feature of freshwater ecosystems. The resting eggs of aquatic invertebrates in sediments populate the overlying water. The diversity of invertebrates in waters and their resting eggs in sediments in Baiyangdian Lake, Xiongan, North China, were assessed using high-throughput sequencing (HTS) with a pair of 18S rRNA gene adaptor-linked primers. The total of 99 operational taxonomic units (OTUs) derived from 353,755 invertebrate sequences (mostly zooplankton) were revealed by this study. A total of 50 species in the water samples including 20 rotifers, 11 copepods, 1 cladoceran and 18 other species were sorted out. In the sediment 37 species, including 21 rotifers, 3 copepods, 1 cladoceran and 12 other species, were identified. There were 24 species in common between water and corresponding sediments. Invertebrate OTU richness in water samples was higher than that in sediments (p < 0.01), while there was no significant difference in the Shannon-Wiener index. These results suggest that HTS is a promising alternative for efficient biodiversity assessment and monitoring.

scholarly journals Soehngenia longivitae sp. nov., a Fermenting Bacterium Isolated from a Petroleum Reservoir in Azerbaijan, and Emended Description of the Genus Soehngenia

2020 ◽  
Vol 8 (12) ◽  
pp. 1967
Author(s):  
Tamara N. Nazina ◽  
Salimat K. Bidzhieva ◽  
Denis S. Grouzdev ◽  
Diyana S. Sokolova ◽  
Tatyana P. Tourova ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
High Throughput Sequencing ◽  
Biochemical Characterization ◽  
Sequence Similarity ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Petroleum Reservoir ◽  
Ph Range ◽  
The 16S Rrna Gene

A methanogenic enrichment growing on a medium with methanol was obtained from a petroleum reservoir (Republic of Azerbaijan) and stored for 33 years without transfers to fresh medium. High-throughput sequencing of the V4 region of the 16S rRNA gene revealed members of the genera Desulfovibrio, Soehngenia, Thermovirga, Petrimonas, Methanosarcina, and Methanomethylovorans. A novel gram-positive, rod-shaped, anaerobic fermentative bacterium, strain 1933PT, was isolated from this enrichment and characterized. The strain grew at 13–55 °C (optimum 35 °C), with 0–3.0% (w/v) NaCl (optimum 0–2.0%) and in the pH range of 6.7–8.0 (optimum pH 7.0). The 16S rRNA gene sequence similarity, the average nucleotide identity (ANI) and in silico DNA–DNA hybridization (dDDH) values between strain 1933PT and the type strain of the most closely related species Soehngenia saccharolytica DSM 12858T were 98.5%, 70.5%, and 22.6%, respectively, and were below the threshold accepted for species demarcation. Genome-based phylogenomic analysis and physiological and biochemical characterization of the strain 1933PT (VKM B-3382T = KCTC 15984T) confirmed its affiliation to a novel species of the genus Soehngenia, for which the name Soehngenia longivitae sp. nov. is proposed. Genome analysis suggests that the new strain has potential in the degradation of proteinaceous components.

scholarly journals Comparison of the Fecal Microbiota of Healthy Horses and Horses with Colitis by High Throughput Sequencing of the V3-V5 Region of the 16S rRNA Gene

PLoS ONE ◽  
2012 ◽  
Vol 7 (7) ◽  
pp. e41484 ◽  
Author(s):  
Marcio C. Costa ◽  
Luis G. Arroyo ◽  
Emma Allen-Vercoe ◽  
Henry R. Stämpfli ◽  
Peter T. Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
The 16S Rrna Gene

scholarly journals Microbial Community Structure in the Sediments and Its Relation to Environmental Factors in Eutrophicated Sancha Lake

2019 ◽  
Vol 16 (11) ◽  
pp. 1931 ◽  
Author(s):  
Yong Li ◽  
Jiejie Zhang ◽  
Jianqiang Zhang ◽  
Wenlai Xu ◽  
Zishen Mou
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Total Phosphorus ◽  
Microbial Community Structure ◽  
High Throughput Sequencing ◽  
Pearson Correlation ◽  
Microbial Populations ◽  
Rrna Gene ◽  
Overlying Water ◽  
Four Seasons

To study the microbial community structure in sediments and its relation to eutrophication environment factors, the sediments and the overlying water of Sancha Lake were collected in the four seasons. MiSeq high-throughput sequencing was conducted for the V3–V4 hypervariable regions of the 16S rRNA gene and was used to analyze the microbial community structure in sediments. Pearson correlation and redundancy analysis (RDA) were conducted to determine the relation between microbial populations and eutrophic factors. The results demonstrated four main patterns: (1) in the 36 samples that were collected, the classification annotation suggested 64 phyla, 259 classes, 476 orders, 759 families, and 9325 OTUs; (2) The diversity indices were ordered according to their values as with summer > winter > autumn > spring; (3) The microbial populations in the four seasons belonged to two distinct characteristic groups; (4) pH, dissolved oxygen (DO), total phosphorus (TP), and total nitrogen (TN) had significant effects on the community composition and structure, which further affected the dissolved total phosphorus (DTP) significantly. The present study demonstrates that the microbial communities in Sancha Lake sediments are highly diverse, their compositions and distributions are significantly different between spring and non-spring, and Actinobacteria and Cyanobacteria may be the key populations or indicator organisms for eutrophication.

scholarly journals Miniprimer PCR, a New Lens for Viewing the Microbial World

2007 ◽  
Vol 74 (3) ◽  
pp. 840-849 ◽  
Author(s):  
Thomas A. Isenbarger ◽  
Michael Finney ◽  
Carlos Ríos-Velázquez ◽  
Jo Handelsman ◽  
Gary Ruvkun
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Microbial Populations ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Microbial World ◽  
Pcr Method ◽  
Environmental Sequences ◽  
The 16S Rrna Gene

ABSTRACT Molecular methods based on the 16S rRNA gene sequence are used widely in microbial ecology to reveal the diversity of microbial populations in environmental samples. Here we show that a new PCR method using an engineered polymerase and 10-nucleotide “miniprimers” expands the scope of detectable sequences beyond those detected by standard methods using longer primers and Taq polymerase. After testing the method in silico to identify divergent ribosomal genes in previously cloned environmental sequences, we applied the method to soil and microbial mat samples, which revealed novel 16S rRNA gene sequences that would not have been detected with standard primers. Deeply divergent sequences were discovered with high frequency and included representatives that define two new division-level taxa, designated CR1 and CR2, suggesting that miniprimer PCR may reveal new dimensions of microbial diversity.

scholarly journals Growth in Coculture Stimulates Metabolism of the Phenylurea Herbicide Isoproturon by Sphingomonas sp. Strain SRS2

2002 ◽  
Vol 68 (7) ◽  
pp. 3478-3485 ◽  
Author(s):  
Sebastian R. Sørensen ◽  
Zeev Ronen ◽  
Jens Aamand
Keyword(s):  
Amino Acids ◽  
Soil Bacteria ◽  
Soil Microflora ◽  
Rrna Gene ◽  
Culture Collections ◽  
Culture Studies ◽  
Phenylurea Herbicide ◽  
Previously Treated ◽  
The 16S Rrna Gene

ABSTRACT Metabolism of the phenylurea herbicide isoproturon by Sphingomonas sp. strain SRS2 was significantly enhanced when the strain was grown in coculture with a soil bacterium (designated strain SRS1). Both members of this consortium were isolated from a highly enriched isoproturon-degrading culture derived from an agricultural soil previously treated regularly with the herbicide. Based on analysis of the 16S rRNA gene, strain SRS1 was assigned to the β-subdivision of the proteobacteria and probably represents a new genus. Strain SRS1 was unable to degrade either isoproturon or its known metabolites 3-(4-isopropylphenyl)-1-methylurea, 3-(4-isopropylphenyl)-urea, or 4-isopropyl-aniline. Pure culture studies indicate that Sphingomonas sp. SRS2 is auxotrophic and requires components supplied by association with other soil bacteria. A specific mixture of amino acids appeared to meet these requirements, and it was shown that methionine was essential for Sphingomonas sp. SRS2. This suggests that strain SRS1 supplies amino acids to Sphingomonas sp. SRS2, thereby leading to rapid metabolism of 14C-labeled isoproturon to 14CO2 and corresponding growth of strain SRS2. Proliferation of strain SRS1 suggests that isoproturon metabolism by Sphingomonas sp. SRS2 provides unknown metabolites or cell debris that supports growth of strain SRS1. The role of strain SRS1 in the consortium was not ubiquitous among soil bacteria; however, the indigenous soil microflora and some strains from culture collections also stimulate isoproturon metabolism by Sphingomonas sp. strain SRS2 to a similar extent.

16S rRNA Gene Primer Validation for Bacterial Diversity Analysis of Vegetable Products

2018 ◽  
Vol 81 (5) ◽  
pp. 848-859
Author(s):  
MIYO NAKANO
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Diversity ◽  
High Throughput Sequencing ◽  
Animal Feed ◽  
Rrna Gene ◽  
Universal Primer ◽  
Food Matrices ◽  
Taxonomic Groups ◽  
The 16S Rrna Gene

ABSTRACT High-throughput sequencing of the 16S rRNA gene enhances understanding of microbial diversity from complex environmental samples. The 16S rRNA gene is currently the most important target in bacterial evolution and ecology studies, particularly for determination of phylogenetic relationships among taxa, exploration of bacterial diversity in a given environment, and quantification of the relative abundance of taxa at various levels. However, some parts of the conserved region of the bacterial 16S rRNA gene are similar to the conserved regions of plant chloroplasts and eukaryotic mitochondria. Therefore, if DNA contains a large amount of nontarget DNA, this nontarget DNA can be coamplified and consequently produce useless sequence reads. We experimentally assessed the primer pair 335f/769r and the widely used bacterial primer pair SD (S-D-Bact-0341-b-S-17/S-D-Bact-0785-a-A-21). The primer pair 335f/769r was examined for its ability to amplify bacterial DNA in plant and animal feed samples by using the single-strand confirmation polymorphism method. In our present study, these primer pairs were validated for microbial community structure analysis with complex food matrices by using next-generation sequencing. The sequencing results revealed that the primer pair 335f/769r successfully resulted in fewer chloroplast and mitochondrial sequence reads than generated by the universal primer pair SD and therefore is comparatively suitable for metagenomic analyses of complex food matrices, particularly those that are rich in plant DNA. Additionally, some taxonomic groups were missed entirely when only the SD primer pair was used.

Molecular characterization of hot spring cyanobacteria and evaluation of their photoprotective compounds

2012 ◽  
Vol 58 (6) ◽  
pp. 719-727 ◽  
Author(s):  
Rajesh P. Rastogi ◽  
Sunita Kumari ◽  
Richa ◽  
Taejun Han ◽  
Rajeshwar P. Sinha
Keyword(s):  
Amino Acids ◽  
High Performance ◽  
Hot Springs ◽  
Hot Spring ◽  
Polar Compounds ◽  
Rrna Gene ◽  
Negative Impacts ◽  
Highly Polar Compounds ◽  
The 16S Rrna Gene

Phylogenetic analysis of 4 cyanobacterial strains isolated from hot springs in Rajgir, India, was carried out using the 16S rRNA gene (1400 bp). These strains were identified as members of Chroococcales ( Cyanothece sp. strain HKAR-1) and Nostocales ( Nostoc sp. strain HKAR-2, Scytonema sp. strain HKAR-3, and Rivularia sp. strain HKAR-4). Furthermore, we evaluated the presence of ultraviolet-screening and (or) photoprotective compounds, such as mycosporine-like amino acids (MAAs) and scytonemin, in these cyanobacteria by using high-performance liquid chromatography. Well-characterized MAAs, including the critical and highly polar compounds shinorine, porphyra-334, and mycosporine-glycine, as well as several unknown MAAs, were found in these hot-spring-inhabiting microorganisms. The presence of scytonemin was detected only in Scytonema sp. strain HKAR-3 and Rivularia sp. strain HKAR-4. The results indicate that hot spring cyanobacteria, namely Cyanothece, Nostoc, Scytonema, and Rivularia, belonging to different groups possess various photoprotective compounds to cope up with the negative impacts of damaging radiations.

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