scholarly journals Environmental Sequencing Provides Reasonable Estimates of the Relative Abundance of Specific Picoeukaryotes

2016 ◽  
Vol 82 (15) ◽  
pp. 4757-4766 ◽  
Author(s):  
Caterina R. Giner ◽  
Irene Forn ◽  
Sarah Romac ◽  
Ramiro Logares ◽  
Colomban de Vargas ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
High Throughput ◽  
Relative Abundance ◽  
Ribosomal Dna ◽  
18S Rdna ◽  
High Throughput Sequencing ◽  
454 Sequencing ◽  
Epifluorescence Microscopy ◽  
Environmental Sequencing

ABSTRACTHigh-throughput sequencing (HTS) is revolutionizing environmental surveys of microbial diversity in the three domains of life by providing detailed information on which taxa are present in microbial assemblages. However, it is still unclear how the relative abundance of specific taxa gathered by HTS correlates with cell abundances. Here, we quantified the relative cell abundance of 6 picoeukaryotic taxa in 13 planktonic samples from 6 European coastal sites using epifluorescence microscopy on tyramide signal amplification-fluorescencein situhybridization preparations. These relative abundance values were then compared with HTS data obtained in three separate molecular surveys: 454 sequencing of the V4 region of the 18S ribosomal DNA (rDNA) using DNA and RNA extracts (DNA-V4 and cDNA-V4) and Illumina sequencing of the V9 region (cDNA-V9). The microscopic and molecular signals were generally correlated, indicating that a relative increase in specific 18S rDNA was the result of a large proportion of cells in the given taxa. Despite these positive correlations, the slopes often deviated from 1, precluding a direct translation of sequences to cells. Our data highlighted clear differences depending on the nucleic acid template or the 18S rDNA region targeted. Thus, the molecular signal obtained using cDNA templates was always closer to relative cell abundances, while the V4 and V9 regions gave better results depending on the taxa. Our data support the quantitative use of HTS data but warn about considering it as a direct proxy of cell abundances.IMPORTANCEDirect studies on marine picoeukaryotes by epifluorescence microscopy are problematic due to the lack of morphological features and due to the limited number and poor resolution of specific phylogenetic probes used in fluorescencein situhybridization (FISH) routines. As a consequence, there is an increasing use of molecular methods, including high-throughput sequencing (HTS), to study marine microbial diversity. HTS can provide a detailed picture of the taxa present in a community and can reveal diversity not evident using other methods, but it is still unclear what the meaning of the sequence abundance in a given taxon is. Our aim is to investigate the correspondence between the relative HTS signal and relative cell abundances in selected picoeukaryotic taxa. Environmental sequencing provides reasonable estimates of the relative abundance of specific taxa. Better results are obtained when using RNA extracts as the templates, while the region of 18S ribosomal DNA had different influences depending on the taxa assayed.

scholarly journals Analysis of Microbial Diversity and Variation Law During Xiaoqu Baijiu Fermentation using High-throughput Sequencing Technology

2021 ◽  
Author(s):  
Qing Wang ◽  
Xiaoqing Xiang ◽  
PengFei Wu ◽  
Guoqiang Han
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
High Throughput ◽  
Relative Abundance ◽  
High Throughput Sequencing ◽  
Sequencing Technology ◽  
Theoretical Support ◽  
Brewing Process ◽  
Dominant Bacteria ◽  
Brewing Time

Abstract In this study, high-throughput sequencing (HTS) was used to compare and analyze the microbial diversity and variation law during the brewing process of xiaoqu Baijiu. The results showed that 34 phyla, 378 genera of bacteria and 4 phyla, 32 genera of fungi were detected. At the phylum level, Firmicutes, Proteobacteria, Bacteroidetes, Ascomycota and Bacteroidetes were the dominant groups. During the brewing process of xiaoqu Baijiu, the dominant bacteria were Weissella and unidentified Rickettsiales 2 days before brewing and Lactobacillus 3 days after brewing until the end of brewing. The dominant fungi were Rhizopus, Saccharomyces and Issatchenkia. The relative abundance of Rhizopus decreased with the extension of brewing time, while the relative abundance of Saccharomyces increased and became the dominant bacteria after the second day of brewing. This study revealed the diversity and variation of microbial community in the brewing process of xiaoqu Baijiu, and provide theoretical support and lay the foundation for future study on the contribution of microbial metabolism during brewing of xiaoqu Baijiu, thereby promote the development of xiaoqu baijiu industry.

scholarly journals Dynamics of Diversity and Abundance of Sulfonamide Resistant Bacteria in a Silt Loam Soil Fertilized by Compost

Antibiotics ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 699
Author(s):  
Hui Han ◽  
Mohan Bai ◽  
Yanting Chen ◽  
Yali Gong ◽  
Ming Wu ◽  
...  
Keyword(s):  
High Throughput ◽  
Relative Abundance ◽  
High Throughput Sequencing ◽  
Resistant Bacteria ◽  
Arable Soils ◽  
Soil Bacterial Communities ◽  
Sulfonamide Resistance ◽  
Loam Soil ◽  
Abundance And Diversity ◽  
Sulfonamide Resistance Genes

Although composting is effective in deactivating antibiotic substances in manure, the influence of compost fertilization on the occurrence and dissemination of antibiotic resistance in arable soils remains to be controversial. Herein, the abundance and diversity of two sulfonamide resistance genes (sul1 and sul2) in soil fertilized by compost spiked with two concentrations of sulfadiazine (1 and 10 mg kg−1) were studied intensively by qPCR and high throughput sequencing based on a two-month microcosm experiment. The concentration of sulfadiazine decreased rapidly after spiking from 25% at Day 1 to less than 2.7% at Day 60. Relative abundance of both sul1 and sul2 were significantly higher in soil amended with compost than the non-amended control at Day 1 and slightly decreased with incubation time except for sul2 in the S10 treatment. Soil bacterial communities were transiently shifted by compost fertilization regardless of the presence of sulfadiazine. Relative abundance of genera in three hubs positively interlinked with sul1 and sul2 were significantly higher in compost treated soil than the control at Day 1, 7 and 21, but not at Day 60. High throughput sequencing analyses revealed that most detected (>67% in relative abundance) sul1 and sul2 genotypes sharing >99% similarity with those found in gammaproteobacterial pathogens frequently were commonly present in compost and soil. These results indicated that compost fertilization might increase the abundance rather than diversity of sulfadiazine-resistant populations in soil, which may be facilitated by the presence of sulfadiazine.

scholarly journals Paired high‐throughput, in situ imaging and high‐throughput sequencing illuminate acantharian abundance and vertical distribution

2020 ◽  
Vol 65 (12) ◽  
pp. 2953-2965
Author(s):  
Margaret Mars Brisbin ◽  
Otis Davey Brunner ◽  
Mary Matilda Grossmann ◽  
Satoshi Mitarai
Keyword(s):  
Vertical Distribution ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
In Situ Imaging

scholarly journals High-throughput sequencing of the microbial diversity of roasted-sesame-like flavored Daqu with different characteristics

3 Biotech ◽  
2020 ◽  
Vol 10 (11) ◽  
Author(s):  
Xianyu Wu ◽  
Ruixue Jing ◽  
Wenhao Chen ◽  
Xiaojie Geng ◽  
Miao Li ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Different Characteristics

scholarly journals Satellite DNA in Paphiopedilum subgenus Parvisepalum as revealed by high-throughput sequencing and fluorescent in situ hybridization

BMC Genomics ◽  
2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Yung-I Lee ◽  
Jing Wei Yap ◽  
Shairul Izan ◽  
Ilia J. Leitch ◽  
Michael F. Fay ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
High Throughput ◽  
Satellite Dna ◽  
Fluorescent In Situ Hybridization ◽  
High Throughput Sequencing

scholarly journals Microbial diversity of extreme habitats in human homes

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2376 ◽  
Author(s):  
Amy M. Savage ◽  
Justin Hills ◽  
Katherine Driscoll ◽  
Daniel J. Fergus ◽  
Amy M. Grunden ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Extreme Environments ◽  
Extreme Temperature ◽  
Hot Water ◽  
Extreme Conditions ◽  
Extreme Temperatures ◽  
Environmental Extremes ◽  
Extreme Habitats

High-throughput sequencing techniques have opened up the world of microbial diversity to scientists, and a flurry of studies in the most remote and extreme habitats on earth have begun to elucidate the key roles of microbes in ecosystems with extreme conditions. These same environmental extremes can also be found closer to humans, even in our homes. Here, we used high-throughput sequencing techniques to assess bacterial and archaeal diversity in the extreme environments inside human homes (e.g., dishwashers, hot water heaters, washing machine bleach reservoirs, etc.). We focused on habitats in the home with extreme temperature, pH, and chemical environmental conditions. We found a lower diversity of microbes in these extreme home environments compared to less extreme habitats in the home. However, we were nonetheless able to detect sequences from a relatively diverse array of bacteria and archaea. Habitats with extreme temperatures alone appeared to be able to support a greater diversity of microbes than habitats with extreme pH or extreme chemical environments alone. Microbial diversity was lowest when habitats had both extreme temperature and one of these other extremes. In habitats with both extreme temperatures and extreme pH, taxa with known associations with extreme conditions dominated. Our findings highlight the importance of examining interactive effects of multiple environmental extremes on microbial communities. Inasmuch as taxa from extreme environments can be both beneficial and harmful to humans, our findings also suggest future work to understand both the threats and opportunities posed by the life in these habitats.

scholarly journals Paired high-throughput, in-situ imaging and high-throughput sequencing illuminate acantharian abundance and vertical distribution

2020 ◽  
Author(s):  
Margaret Mars Brisbin ◽  
Otis Davey Brunner ◽  
Mary Matilda Grossmann ◽  
Satoshi Mitarai
Keyword(s):  
Vertical Distribution ◽  
High Throughput ◽  
Deep Sea ◽  
Carbon Flux ◽  
High Throughput Sequencing ◽  
Size Range ◽  
Life Cycles ◽  
Sequencing Data ◽  
In Situ Imaging

AbstractAcantharians are important contributors to surface primary production and to carbon flux to the deep sea, but are often underestimated because their delicate structures are destroyed by plankton nets or dissolved by preservatives. As a result, relatively little is known about acantharian biology, especially regarding their life cycles. Here, we take a paired approach, bringing together high-throughput, in-situ imaging and high-throughput sequencing, to investigate acantharian abundance, vertical distribution, and life-history in the western North Pacific. Observed concentrations of acantharian cells correlated well with sequence abundances from acantharians with known, recognizable morphologies, but not to sequences from those without known morphology (basal environmental clades). These results suggest basal clades may lack characteristic star-shaped skeletons or are much smaller than known acantharians. The decreased size-range of acantharians imaged at depth supports current hypotheses regarding asymbiotic acantharian life cycles: cysts or vegetative cells release reproductive swarmer cells at depth and juvenile cells grow as they ascend towards the surface. Moreover, sequencing data present the possibility that photosymbiotic acantharians also reproduce at depth, like their asymbiotic, encysting relatives, which is counter to previous hypotheses. Finally, in-situ imaging captured a new acantharian behavior that may be a previously undescribed predation strategy.

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