Influence of 16S rRNA variable region on perceived diversity of marine microbial communities of the Northern North Atlantic

Willis, Ciara; Desai, Dhwani; LaRoche, Julie

doi:10.1093/femsle/fnz152

Cited by 54 publications

(43 citation statements)

References 44 publications

(70 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Some of these dots were collected, as representative of sample SA. Further, immediately above these dots, blackish and hard branched formations—like cave coralloids 25 —of amorphous silica appeared as compact dry masses that were collected and named SC (Fig. 1 ).…”

Section: Resultsmentioning

confidence: 99%

Transition from unclassified Ktedonobacterales to Actinobacteria during amorphous silica precipitation in a quartzite cave environment

Ghezzi

Sauro

Columbu

et al. 2021

Sci Rep

View full text Add to dashboard Cite

The orthoquartzite Imawarì Yeuta cave hosts exceptional silica speleothems and represents a unique model system to study the geomicrobiology associated to silica amorphization processes under aphotic and stable physical–chemical conditions. In this study, three consecutive evolution steps in the formation of a peculiar blackish coralloid silica speleothem were studied using a combination of morphological, mineralogical/elemental and microbiological analyses. Microbial communities were characterized using Illumina sequencing of 16S rRNA gene and clone library analysis of carbon monoxide dehydrogenase (coxL) and hydrogenase (hypD) genes involved in atmospheric trace gases utilization. The first stage of the silica amorphization process was dominated by members of a still undescribed microbial lineage belonging to the Ktedonobacterales order, probably involved in the pioneering colonization of quartzitic environments. Actinobacteria of the Pseudonocardiaceae and Acidothermaceae families dominated the intermediate amorphous silica speleothem and the final coralloid silica speleothem, respectively. The atmospheric trace gases oxidizers mostly corresponded to the main bacterial taxa present in each speleothem stage. These results provide novel understanding of the microbial community structure accompanying amorphization processes and of coxL and hypD gene expression possibly driving atmospheric trace gases metabolism in dark oligotrophic caves.

show abstract

Section: Resultsmentioning

confidence: 99%

Transition from unclassified Ktedonobacterales to Actinobacteria during amorphous silica precipitation in a quartzite cave environment

Ghezzi

Sauro

Columbu

et al. 2021

Sci Rep

View full text Add to dashboard Cite

show abstract

“…Total DNA from each of the samples was extracted by using a total soil DNA kit (Omega, USA). The 16 S rRNA genes of distinct regions V4-V5 were amplified with the following primers: 515 F (5′-GTGCCAGCMGCCGCGGTAA-3′) and 806 R (5′-GGACTACHVGGGTWTCTAAT-3′) 27 . After the purification of polymerase chain reaction (PCR) products, a library was constructed by utilizing the DNA Library Prep Kit for Illumina (NEB, USA).…”

Section: Methodsmentioning

confidence: 99%

Pathway and kinetics of malachite green biodegradation by Pseudomonas veronii

Song

Han

Wang

et al. 2020

Sci Rep

View full text Add to dashboard Cite

Malachite green is a common environmental pollutant that poses a great threat to non-target organisms, including humans. This study reports the characterization of a bacterial strain, Pseudomonas veronii JW3-6, which was isolated from a malachite green enrichment culture. This strain degraded malachite green efficiently in a wide range of temperature and pH levels. Under optimal degradation conditions (32.4 °C, pH 7.1, and inoculum amount of 2.5 × 10 7 cfu/mL), P. veronii JW3-6 could degrade 93.5% of 50 mg/L malachite green within seven days. Five intermediate products from the degradation of malachite green were identified: leucomalachite green, 4-(dimethylamino) benzophenone, 4-dimethylaminophenol, benzaldehyde, and hydroquinone. We propose a possible degradation pathway based on these findings. The present study is the first to report the degradation of malachite green by P. veronii and the identification of hydroquinone as a metabolite in the degradation pathway.

show abstract

“…The selection of various hypervariable regions used for 16S profiling produced different taxonomic resolutions, and these behave differently across the various ecological niches, while one region may be suitable for a specific environment, it might not be as accurate for a different one [23][24][25]. Technical variations among studies, such as protocols for DNA extraction, selected primers, PCR conditions, hypervariable regions, and sequencing platforms, show a significant impact on the shrimp microbiota structure [14].…”

Section: Introductionmentioning

confidence: 99%

Doing More with Less: A Comparison of 16S Hypervariable Regions in Search of Defining the Shrimp Microbiota

et al. 2020

View full text Add to dashboard Cite

The shrimp has become the most valuable traded marine product in the world, and its microbiota plays an essential role in its development and overall health status. Massive high-throughput sequencing techniques using several hypervariable regions of the 16S rRNA gene are broadly applied in shrimp microbiota studies. However, it is essential to consider that the use of different hypervariable regions can influence the obtained data and the interpretation of the results. The present study compares the shrimp microbiota structure and composition obtained by three types of amplicons: one spanning both the V3 and V4 hypervariable regions (V3V4), one for the V3 region only (V3), and one for the V4 region only (V4) using the same experimental and bioinformatics protocols. Twenty-four samples from hepatopancreas and intestine were sequenced and evaluated using the GreenGenes and silva reference databases for clustering and taxonomic classification. In general, the V3V4 regions resulted in higher richness and diversity, followed by V3 and V4. All three regions establish an apparent clustering effect that discriminates between the two analyzed organs and describe a higher richness for the intestine and a higher diversity for the hepatopancreas samples. Proteobacteria was the most abundant phyla overall, and Cyanobacteria was more common in the intestine, whereas Firmicutes and Actinobacteria were more prevalent in hepatopancreas samples. Also, the genus Vibrio was significantly abundant in the intestine, as well as Acinetobacter and Pseudomonas in the hepatopancreas suggesting these taxa as markers for their respective organs independently of the sequenced region. The use of a single hypervariable region such as V3 may be a low-cost alternative that enables an adequate description of the shrimp microbiota, allowing for the development of strategies to continually monitor the microbial communities and detect changes that could indicate susceptibility to pathogens under real aquaculture conditions while the use of the full V3V4 regions can contribute to a more in-depth characterization of the microbial composition.

show abstract

Influence of 16S rRNA variable region on perceived diversity of marine microbial communities of the Northern North Atlantic

Cited by 54 publications

References 44 publications

Transition from unclassified Ktedonobacterales to Actinobacteria during amorphous silica precipitation in a quartzite cave environment

Transition from unclassified Ktedonobacterales to Actinobacteria during amorphous silica precipitation in a quartzite cave environment

Pathway and kinetics of malachite green biodegradation by Pseudomonas veronii

Doing More with Less: A Comparison of 16S Hypervariable Regions in Search of Defining the Shrimp Microbiota

Contact Info

Product

Resources

About