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 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.

Analysis of microbial changes in the rhizosphere of unplanted and planted Atractylodes lancea via high-throughput sequencing

2020 ◽  
Author(s):  
Yan Xu ◽  
Junfeng Niu ◽  
Lijun Chen ◽  
Xiaoqiang Wu ◽  
Zhongmin Dong ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput ◽  
Relative Abundance ◽  
High Throughput Sequencing ◽  
Community Diversity ◽  
Continuous Cropping ◽  
Pests And Diseases ◽  
Atractylodes Lancea ◽  
Bacteria And Fungi ◽  
The Relationship

Abstract Background Atractylodes lancea is a traditional Chinese medicine, which typically requires more than 3–4 years of continuous cropping to obtain the underground medicinal components. With continuous cropping years, the quality and yields of A. lancea medicinal materials decrease, while pests and diseases increase. These aspects are intimately correlated with rhizospheric microorganisms. Methods This research paper employed high-throughput sequencing for its detection in soil that was cultivated for three years and never cultivated to clarify the relationship between the microbial diversity of the rhizosphere and continuous A. lancea cropping. Results The rhizosphere microbial community was altered following the continuous cropping of A. lancea. The bacterial diversity and richness were observed to decrease, while the fungal community diversity increased, and richness decreased. The total OUTs of the soil bacteria and fungi of unplanted and planted A. lancea were 59.58% and 37.65%, respectively. At the phylum level, the relative abundance of Proteobacteria, Gemmatimonadetes, Acidobacteria and Chloroflexi decreased, whereas the relative abundance of Mortierellomycota increased. At the genus level, Bradyrhizobium, Striaticonidium, Dactylonectria, Sphingomonas, Burkholderiaceae, Rhodanobacter, Arthrobacter, Scleroderma, Mortierella and Penicillium were significantly different between the two sample groups. Conclusions Our results revealed that following the cultivation of A. lancea, the rhizospheric microbial community was altered. This study preliminarily determined the

scholarly journals Accumulation of Sulfonamide Resistance Genes in Arable Soils Due to Repeated Application of Manure Containing Sulfadiazine

2011 ◽  
Vol 77 (7) ◽  
pp. 2527-2530 ◽  
Author(s):  
Holger Heuer ◽  
Qodiah Solehati ◽  
Ute Zimmerling ◽  
Kristina Kleineidam ◽  
Michael Schloter ◽  
...  
Keyword(s):  
Quantitative Pcr ◽  
Resistance Genes ◽  
Pig Manure ◽  
Repeated Application ◽  
Arable Soils ◽  
Sulfonamide Resistance ◽  
Repeated Applications ◽  
Sulfonamide Resistance Genes

ABSTRACTTwo soils were amended three times with pig manure. The abundance of sulfonamide resistance genes was determined by quantitative PCR 2 months after each application. In both soils treated with sulfadiazine-containing manure, the numbers of copies ofsul1andsul2significantly increased compared to numbers after treatments with antibiotic-free manure or a control and accumulated with repeated applications.

scholarly journals Assessing soil bacterial community and dynamics by integrated high-throughput absolute abundance quantification

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4514 ◽  
Author(s):  
Jun Lou ◽  
Li Yang ◽  
Haizhen Wang ◽  
Laosheng Wu ◽  
Jianming Xu
Keyword(s):  
Bacterial Community ◽  
High Throughput ◽  
Relative Abundance ◽  
High Throughput Sequencing ◽  
Laboratory Strain ◽  
Soil Bacterial Community ◽  
Absolute Abundance ◽  
Internal Reference ◽  
Biodegradation Study ◽  
Soil Bacterial

Microbial ecological studies have been remarkably promoted by the high-throughput sequencing approach with explosive information of taxonomy and relative abundance. However, relative abundance does not reflect the quantity of the microbial community and the inter-sample differences among taxa. In this study, we refined and applied an integrated high-throughput absolute abundance quantification (iHAAQ) method to better characterize soil quantitative bacterial community through combining the relative abundance (by high-throughput sequencing) and total bacterial quantities (by quantitative PCR). The proposed iHAAQ method was validated by an internal reference strain EDL933 and a laboratory strain WG5. Application of the iHAAQ method to a soil phenanthrene biodegradation study showed that for some bacterial taxa, the changes of relative and absolute abundances were coincident, while for others the changes were opposite. With the addition of a microbial activity inhibitor (NaN3), the absolute abundances of soil bacterial taxa, including several dominant genera of Bacillus, Flavobacterium, and Paenibacillus, decreased significantly, but their relative abundances increased after 28 days of incubation. We conclude that the iHAAQ method can offer more comprehensive information to reflect the dynamics of soil bacterial community with both relative and absolute abundances than the relative abundance from high-throughput sequencing alone.

scholarly journals Analyzing bacterial community in pit mud of Yibin Baijiu in China using high throughput sequencing

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9122
Author(s):  
Li Chen ◽  
Yuzhu Li ◽  
Lei Jin ◽  
Li He ◽  
Xiaolin Ao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
High Throughput ◽  
Relative Abundance ◽  
High Throughput Sequencing ◽  
Middle Layer ◽  
Ammonia Nitrogen ◽  
Western China ◽  
Rrna Gene ◽  
Linear Discriminant ◽  
Pit Mud

“Yibin Baijiu” (YB) is a special Chinese strong-aroma Baijiu (CSAB) that originated in Yibin, a city in western China. YB is fermented in cellars lined with pit mud (PM), the microbiota in which may affect YB quality. In this study, high throughput sequencing of the 16S rRNA gene was used to demonstrate the bacterial community structure and diversity in PM of YB. In addition, the physicochemical characteristics of PM were also analyzed, including moisture content, pH, and available phosphorous, ammonia nitrogen, and humic acid levels. Results showed that Firmicutes was the dominant phylum in all PM samples with abundance > 70.0%, followed by Euryarchaeota (11.3%), Bacteroidetes (6.5%), Synergistetes (3.0%), Actinobacteria (1.4%), and Proteobacteria (1.2%). Furthermore, 14 different genera with average relative abundance of > 1% were detected. The Chao1 and Shannon indexes did not vary significantly between the sub-layer and middle-layer PM (P > 0.05). However, Linear discriminant analysis Effect Size (LEfSe) analysis showed that the relative abundance of Lactobacillus in the sub-layer PM was significantly higher than in middle-layer PM. pH differed significantly (P < 0.05) between the two groups. Canonical correspondence analysis revealed that bacterial community in PM correlated significantly with available phosphorous content and pH. Our study provides basic data for further elucidating the diversity of microbiota in the PM of YB and the potential mechanism of Baijiu production.

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