scholarly journals 16S rRNA Gene Amplicon Sequencing Data of the Iron Quadrangle Ferruginous Caves (Brazil) Shows the Importance of Conserving This Singular and Threatened Geosystem

Diversity ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 494
Author(s):  
Camila G. C. Lemes ◽  
Morghana M. Villa ◽  
Érica B. Felestrino ◽  
Luiza O. Perucci ◽  
Renata A. B. Assis ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Diversity ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Metabolic Potential ◽  
Microbial Life ◽  
Iron Quadrangle ◽  
Abundance And Diversity

The Iron Quadrangle (IQ) is one of the main iron ore producing regions of the world. The exploitation of its reserves jeopardizes the high biological endemism associated with this region. This work aimed to understand the diversity and bacterial potential associated with IQ caves. Floor and ceiling samples of seven ferruginous caves and one quartzite cave were collected, and their microbial relative abundance and diversity were established by 16S rRNA gene amplicon sequencing data. The results showed that ferruginous caves present higher microbial abundance and greater microbial diversity compared to the quartzite cave. Many species belonging to genera found in these caves, such as Pseudonocardia and Streptacidiphilus, are known to produce biomolecules of biotechnological interest as macrolides and polyketides. Moreover, comparative analysis of microbial diversity and metabolic potential in a biofilm in pendant microfeature revealed that the microbiota associated with this structure is more similar to the floor rather than ceiling samples, with the presence of genera that may participate in the genesis of these cavities, for instance, Ferrovum, Geobacter, and Sideroxydans. These results provide the first glimpse of the microbial life in these environments and emphasize the need of conservation programs for these areas, which are under intense anthropogenic exploration.

Superior resolution characterisation of microbial diversity in anaerobic digesters using full-length 16S rRNA gene amplicon sequencing

2020 ◽  
Vol 178 ◽  
pp. 115815 ◽  
Author(s):  
Theo Y.C. Lam ◽  
Ran Mei ◽  
Zhuoying Wu ◽  
Patrick K.H. Lee ◽  
Wen-Tso Liu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Diversity ◽  
Amplicon Sequencing ◽  
Full Length ◽  
Rrna Gene ◽  
Anaerobic Digesters

scholarly journals Species-level resolution of 16S rRNA gene amplicons sequenced through the MinIONTM portable nanopore sequencer

2015 ◽  
Author(s):  
Alfonso Benítez-Páez ◽  
Kevin J. Portune ◽  
Yolanda Sanz
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Diversity ◽  
Amplicon Sequencing ◽  
Species Level ◽  
Taxonomic Resolution ◽  
Universal Primers ◽  
Rrna Gene ◽  
Rdna Sequences ◽  
Dna Sequencer

AbstractBackgroundThe miniaturised and portable DNA sequencer MinIONTM has been released to the scientific community within the framework of an early access programme to evaluate its application for a wide variety of genetic approaches. This technology has demonstrated great potential, especially in genome-wide analyses. In this study, we tested the ability of the MinIONTM system to perform amplicon sequencing in order to design new approaches to study microbial diversity using nearly full-length 16S rDNA sequences.ResultsUsing R7.3 chemistry, we generated more than 3.8 million events (nt) during a single sequencing run. These data were sufficient to reconstruct more than 90% of the 16S rRNA gene sequences for 20 different species present in a mock reference community. After read mapping and 16S rRNA gene assembly, consensus sequences and 2d reads were recovered to assign taxonomic classification down to the species level. Additionally, we were able to measure the relative abundance of all the species present in a mock community and detected a biased species distribution originating from the PCR reaction using ‘universal’ primers.ConclusionsAlthough nanopore-based sequencing produces reads with lower per-base accuracy compared with other platforms, the MinIONTM DNA sequencer is valuable for both high taxonomic resolution and microbial diversity analysis. Improvements in nanopore chemistry, such as minimising base-calling errors and the nucleotide bias reported here for 16S amplicon sequencing, will further deliver more reliable information that is useful for the specific detection of microbial species and strains in complex ecosystems.

scholarly journals 16S rRNA Gene Amplicon Sequencing Data of Tailing and Nontailing Rhizosphere Soils of Mimosa pudica from a Heavy Metal-Contaminated Ex-Tin Mining Area

2020 ◽  
Vol 9 (42) ◽  
Author(s):  
Saidu Abdullahi ◽  
Hazzeman Haris ◽  
Kamarul Z. Zarkasi ◽  
Hamzah G. Amir
Keyword(s):  
Heavy Metal ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Data ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Mimosa Pudica ◽  
Sequencing Data ◽  
Content Type ◽  
Rhizosphere Soils

ABSTRACT The 16S rRNA gene amplicon sequence data from tailing and nontailing rhizosphere soils of Mimosa pudica from a heavy metal-contaminated area are reported here. Diverse bacterial taxa were represented in the results, and the most dominant phyla were Proteobacteria (41.2%), Acidobacteria (17.1%), and Actinobacteria (14.4%).

scholarly journals The evolution of realized niches within freshwater Synechococcus

2019 ◽  
Author(s):  
Nicolas Tromas ◽  
Zofia E. Taranu ◽  
Mathieu Castelli ◽  
Juliana S. M. Pimentel ◽  
Daniel A. Pereira ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Environmental Parameters ◽  
Amplicon Sequencing ◽  
Fundamental Question ◽  
Rrna Gene ◽  
Biological Interactions ◽  
Sequencing Data ◽  
Evolutionary Time ◽  
Genus Level

SummaryUnderstanding how ecological traits have changed over evolutionary time is a fundamental question in biology. Specifically, the extent to which more closely-related organisms share similar ecological preferences due to phylogenetic conservation – or if they are forced apart by competition – is still debated. Here we explored the co-occurrence patterns of freshwater cyanobacteria at the sub-genus level to investigate whether more closely-related taxa share more similar niches, and to what extent these niches were defined by abiotic or biotic variables. We used deep 16S rRNA gene amplicon sequencing and measured several abiotic environmental parameters (nutrients, temperature, etc.) in water samples collected over time and space in Furnas Reservoir, Brazil. We found that relatively more closely-related Synechococcus (in the continuous range of 93-100% nucleotide identity in 16S) had an increased tendency to co-occur with one another (i.e. had similar realized niches). This tendency could not be easily explained by shared preferences for measured abiotic niche dimensions. Thus, commonly measured abiotic parameters might not be sufficient to characterize, nor to predict community assembly or dynamics. Rather, co-occurrence between Synechococcus and the surrounding community (whether or not they represent true biological interactions) may be a more sensitive measure of realized niches. Overall, our results suggest that realized niches are phylogenetically conserved, at least at the sub-genus level and at the resolution of the 16S marker. Determining how these results generalize to other genera and at finer genetic resolution merits further investigation.Originality-Significance StatementWe address a fundamental question in ecology and evolution: how do niche preferences change over evolutionary time? Using time-series analysis of 16S rRNA gene amplicon sequencing data, we develop an approach to highlight the importance of biotic factors in defining realized niches, and show how niche preferences change proportionally with the 16S gene molecular clock within the genus Synechococcus. Ours is also one of few studies on the ecology of freshwater Synechococcus, adding significantly to our knowledge about this abundant and widespread lineage of Cyanobacteria.

scholarly journals The archives are half-empty: a field-wide assessment of the availability of microbial community sequencing data

2020 ◽  
Author(s):  
Stephanie D. Jurburg ◽  
Maximilian Konzack ◽  
Nico Eisenhauer ◽  
Anna Heintz-Buschart
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Amplicon Sequencing ◽  
Data Reuse ◽  
Rrna Gene ◽  
Data Loss ◽  
Sequencing Data ◽  
Data Archiving ◽  
The 16S Rrna Gene ◽  
Over Time

AbstractThe sequencing revolution has resulted in the explosive growth of public genetic repositories. These repositories now hold invaluable collections of 16S rRNA gene amplicon sequences, but the extent to which the currently archived data is findable, accessible, and reusable has not been evaluated. We conducted a field-wide assessment of the availability and state of publicly archived 16S rRNA gene amplicon sequencing data. Using custom-built pattern-based text extraction algorithms, we searched 26,927 publications in 17 microbiology or microbial ecology journals, and identified 2,015 studies which performed 16S rRNA gene amplicon sequencing. We found, for example, that 7.2% of these had not been made public at the time of analysis, a trend which increased over time. Of the 635 studies targeting the V3-V4 region of the 16S rRNA gene, 40.3% contained data which was not available or not reusable, and for 25.5% of the studies, faults in data formatting or data labelling were likely to create obstacles in data reuse. Taken together, only 34% of these datasets had potentially reusable data. Our study reveals significant gaps in the availability of currently deposited community sequencing data, identifies major contributors to data loss, and offers suggestions for improving data archiving practices in the future.

scholarly journals Microbial Diversity Analysis of Sediment from Yeosu New Harbor of South Korea Using 16S rRNA Gene Amplicon Sequencing

2021 ◽  
Vol 10 (2) ◽  
Author(s):  
Junho Lee ◽  
Ilwon Jeong ◽  
Jong-Oh Kim ◽  
Kyunghoi Kim
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Diversity ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Diversity Analysis ◽  
Tsushima Current ◽  
South Korean ◽  
Benthic Environment ◽  
Seomjin River

ABSTRACT The Yeosu New Harbor in the South Korean benthic environment shows a mesotrophic environment affected by the Tsushima Current and the Seomjin River. Here, we report microbial diversity in sediments of Yeosu New Harbor based on 16S rRNA gene amplicon sequencing. The dominant bacterial phylum was Proteobacteria (relative abundance, 72.5 to 78.1%).

scholarly journals 16S rRNA Gene Amplicon Sequencing Data from Flooded Rice Paddy Mesocosms Treated with Different Silicon-Rich Soil Amendments

2021 ◽  
Vol 10 (27) ◽  
Author(s):  
Gretchen E. Dykes ◽  
Clara S. Chan ◽  
Angelia L. Seyfferth
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Soil Amendments ◽  
16S Rrna Gene Sequencing ◽  
Amplicon Sequencing ◽  
Rice Paddy ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Flooded Rice ◽  
Rrna Gene Sequencing

How silicon-rich soil amendments impact the microbial community is unresolved. We report 16S rRNA gene sequencing data from flooded rice paddy mesocosms treated with different silicon amendments sampled over the growing season. We generated 11,678 operational taxonomic units (OTUs) and found that microbial communities were significantly different across treatments, time points, and biospheres.

scholarly journals Microbial Diversity of the Hell Creek Watershed at the Tri-Faith Community in Nebraska, Based on 16S rRNA Gene Amplicon Sequencing

2020 ◽  
Vol 9 (22) ◽  
Author(s):  
John A. Kyndt
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Diversity ◽  
Amplicon Sequencing ◽  
Flood Plain ◽  
Rrna Gene ◽  
Land Area ◽  
Native Land ◽  
Creek Watershed ◽  
Microbial Analysis

ABSTRACT Hell Creek’s watershed is a historically important native land area located in Omaha, Nebraska, that includes Hell Creek and an adjacent flood plain. This initial microbial analysis showed that even though samples were isolated from the same watershed area, there were significant differences between the creek itself and the nearby pond.

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