scholarly journals Diversity Assessment of Toxic Cyanobacterial Blooms during Oxidation

Toxins ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 728
Author(s):  
Saber Moradinejad ◽  
Hana Trigui ◽  
Juan Francisco Guerra Maldonado ◽  
Jesse Shapiro ◽  
Yves Terrat ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Treatment Plant ◽  
Principal Component ◽  
Abundant Species ◽  
Chemical Oxidation ◽  
Cyanobacterial Blooms ◽  
Cyanobacterial Community ◽  
Cell Counts ◽  
Diversity Assessment

Fresh-water sources of drinking water are experiencing toxic cyanobacterial blooms more frequently. Chemical oxidation is a common approach to treat cyanobacteria and their toxins. This study systematically investigates the bacterial/cyanobacterial community following chemical oxidation (Cl2, KMnO4, O3, H2O2) using high throughput sequencing. Raw water results from high throughput sequencing show that Proteobacteria, Actinobacteria, Cyanobacteria and Bacteroidetes were the most abundant phyla. Dolichospermum, Synechococcus, Microcystis and Nostoc were the most dominant genera. In terms of species, Dolichospermum sp.90 and Microcystis aeruginosa were the most abundant species at the beginning and end of the sampling, respectively. A comparison between the results of high throughput sequencing and taxonomic cell counts highlighted the robustness of high throughput sequencing to thoroughly reveal a wide diversity of bacterial and cyanobacterial communities. Principal component analysis of the oxidation samples results showed a progressive shift in the composition of bacterial/cyanobacterial communities following soft-chlorination with increasing common exposure units (CTs) (0–3.8 mg·min/L). Close cyanobacterial community composition (Dolichospermum dominant genus) was observed following low chlorine and mid-KMnO4 (287.7 mg·min/L) exposure. Our results showed that some toxin producing species may persist after oxidation whether they were dominant species or not. Relative persistence of Dolichospermum sp.90 was observed following soft-chlorination (0.2–0.6 mg/L) and permanganate (5 mg/L) oxidation with increasing oxidant exposure. Pre-oxidation using H2O2 (10 mg/L and one day contact time) caused a clear decrease in the relative abundance of all the taxa and some species including the toxin producing taxa. These observations suggest selectivity of H2O2 to provide an efficient barrier against toxin producing cyanobacteria entering a water treatment plant.

scholarly journals Microbial diversity in raw milk and Sayram Ketteki from southern of Xinjiang, China

2021 ◽  
Author(s):  
Dongla Gao ◽  
Weihua Wang ◽  
Zhanjiang Han ◽  
Qian Xi ◽  
Ruicheng Guo ◽  
...  
Keyword(s):  
High Throughput ◽  
Fungal Community ◽  
High Throughput Sequencing ◽  
Principal Component ◽  
Raw Milk ◽  
Fermented Milk ◽  
Community Diversity ◽  
Sampling Location ◽  
Fungal Community Structure ◽  
Microbial Resources

Raw milk and fermented milk are rich in microbial resources, which are essential for the formation of texture, flavor and taste. In order to gain a deeper knowledge of the bacterial and fungal community diversity in local raw milk and home-made yogurts from Sayram town, Baicheng county, Akesu area, southern of Xinjiang, China,30 raw milk and 30 home-made yogurt samples were collected and experiment of high-throughput sequencing was implemented.The results of experiments revealed the species of fungi in raw milk was the most, and the species of bacteria in fermented milk was the least.Based on principal component analysis (PCA), it was found that the bacterial and fungal community structure differed in samples from two types of dairy products.And the presence of 15 bacterial and 12 fungal phyla, comprising 218 bacterial and 495 fungal genera respectively, among all samples. Firmicutes and Ascomycota,Lactobacillus and Candida were the predominant phyla and genera of bacteria and fungi, respectively. The results indicated that the microbial community of raw milk differs from home-made yogurts due to sampling location and manufacturing process. The study suggested that high-throughput sequencing could provide a better understanding of microbiological diversity as well as lay a theoretical foundation for selecting beneficial microbial resources from this natural yogurt.

scholarly journals Revealing Cryptic Changes of Cyanobacterial Community Structure in Two Eutrophic Lakes Using eDNA Sequencing

2020 ◽  
Vol 17 (17) ◽  
pp. 6356
Author(s):  
Yongguang Jiang ◽  
Peng Xiao ◽  
Gongliang Yu ◽  
Gaofei Song ◽  
Renhui Li
Keyword(s):  
Community Structure ◽  
High Throughput Sequencing ◽  
Environmental Dna ◽  
Cyanobacterial Blooms ◽  
Erhai Lake ◽  
Water Safety ◽  
Cyanobacterial Community ◽  
Eutrophic Lakes ◽  
Abundant Otus ◽  
Cyanobacterial Diversity

Harmful cyanobacterial blooms pose a risk to human health worldwide. To enhance understanding on the bloom-forming mechanism, the spatiotemporal changes in cyanobacterial diversity and composition in two eutrophic lakes (Erhai Lake and Lushui Reservoir) of China were investigated from 2010 to 2011 by high-throughput sequencing of environmental DNA. For each sample, 118 to 260 cpcBA-IGS operational taxonomic units (OTUs) were obtained. Fifty-two abundant OTUs were identified, which made up 95.2% of the total sequences and were clustered into nine cyanobacterial groups. Although the cyanobacterial communities of both lakes were mainly dominated by Microcystis, Erhai Lake had a higher cyanobacterial diversity. The abundance of mixed Nostocales species was lower than that of Microcystis, whereas Phormidium and Synechococcus were opportunistically dominant. The correlation between the occurrence frequency and relative abundance of OTUs was poorly fitted by the Sloan neutral model. Deterministic processes such as phosphorus availability were shown to have significant effects on the cyanobacterial community structure in Erhai Lake. In summary, the Microcystis-dominated cyanobacterial community was mainly affected by the deterministic process. Opportunistically dominant species have the potential to replace Microcystis and form blooms in eutrophic lakes, indicating the necessity to monitor these species for drinking water safety.

scholarly journals Deciphering the Diversities of Astroviruses and Noroviruses in Wastewater Treatment Plant Effluents by a High-Throughput Sequencing Method

2015 ◽  
Vol 81 (20) ◽  
pp. 7215-7222 ◽  
Author(s):  
B. Prevost ◽  
F. S. Lucas ◽  
K. Ambert-Balay ◽  
P. Pothier ◽  
L. Moulin ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Clinical Data ◽  
High Throughput ◽  
Human Population ◽  
High Throughput Sequencing ◽  
Treatment Plant ◽  
Enteric Viruses ◽  
Viral Diversity ◽  
Wwtp Effluent ◽  
Human Astroviruses

ABSTRACTAlthough clinical epidemiology lists human enteric viruses to be among the primary causes of acute gastroenteritis in the human population, their circulation in the environment remains poorly investigated. These viruses are excreted by the human population into sewers and may be released into rivers through the effluents of wastewater treatment plants (WWTPs). In order to evaluate the viral diversity and loads in WWTP effluents of the Paris, France, urban area, which includes about 9 million inhabitants (approximately 15% of the French population), the seasonal occurrence of astroviruses and noroviruses in 100 WWTP effluent samples was investigated over 1 year. The coupling of these measurements with a high-throughput sequencing approach allowed the specific estimation of the diversity of human astroviruses (human astrovirus genotype 1 [HAstV-1], HAstV-2, HAstV-5, and HAstV-6), 7 genotypes of noroviruses (NoVs) of genogroup I (NoV GI.1 to NoV GI.6 and NoV GI.8), and 16 genotypes of NoVs of genogroup II (NoV GII.1 to NoV GII.7, NoV GII.9, NoV GII.12 to NoV GII.17, NoV GII.20, and NoV GII.21) in effluent samples. Comparison of the viral diversity in WWTP effluents to the viral diversity found by analysis of clinical data obtained throughout France underlined the consistency between the identified genotypes. However, some genotypes were locally present in effluents and were not found in the analysis of the clinical data. These findings could highlight an underestimation of the diversity of enteric viruses circulating in the human population. Consequently, analysis of WWTP effluents could allow the exploration of viral diversity not only in environmental waters but also in a human population linked to a sewerage network in order to better comprehend viral epidemiology and to forecast seasonal outbreaks.

scholarly journals Composition and Origin of the Fermentation Microbiota of Mahewu, a Zimbabwean Fermented Cereal Beverage

2019 ◽  
Vol 85 (11) ◽  
Author(s):  
Felicitas Pswarayi ◽  
Michael G. Gänzle
Keyword(s):  
16S Rrna ◽  
Quantitative Pcr ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Starter Cultures ◽  
Rrna Gene ◽  
Culture Methods ◽  
Content Type ◽  
Cell Counts

ABSTRACTMahewu is a fermented cereal beverage produced in Zimbabwe. This study determined the composition and origin of mahewu microbiota. The microbiota of mahewu samples consisted of 3 to 7 dominant strains of lactobacilli and two strains of yeasts.Enterobacteriaceaewere not detected.Candida glabratawas present in high cell counts from samples collected in summer but not from samples collected in winter. Millet malt is the only raw ingredient used in the production of mahewu and is a likely source of fermentation microbiota; therefore, malt microbiota was also analyzed by culture-dependent and high-throughput 16S rRNA gene sequencing methodologies. Millet malt contained 8 to 19 strains ofEnterobacteriaceae, lactobacilli, bacilli, and very few yeasts. Strain-specific quantitative PCR assays were established on the basis of the genome sequences ofLactobacillus fermentumFUA3588 and FUA3589 andLactobacillus plantarumFUA3590 to obtain a direct assessment of the identity of strains from malt and mahewu.L. fermentumFUA3588 and FUA3589 were detected in millet malt, demonstrating that millet malt is a main source of mahewu microbiota. Strains which were detected in summer were not detected in samples produced at the same site in winter. Model mahewu fermentations conducted with a 5-strain inoculum consisting of lactobacilli,Klebsiella pneumoniae,andCronobacter sakazakiidemonstrated that lactobacilli outcompeteEnterobacteriaceae, which sharply decreased in the first 24 h. In conclusion, mahewu microbiota is mainly derived from millet malt microbiota, but minor components of malt microbiota rapidly outcompeteEnterobacteriaceaeandBacillusspecies during fermentation.IMPORTANCEThis study provides insight into the composition and origin of the microbiota of mahewu and the composition of millet malt microbiota. Fermentation microbiota are often hypothesized to be derived from the environment, but the evidence remains inconclusive. Our findings confirm that millet malt is the major source of mahewu microbiota. By complementing culture methods with high-throughput sequencing of 16S rRNA amplicons and strain-specific quantitative PCR, this study provides evidence about the source of mahewu microbiota, which can inform the development of starter cultures for mahewu production. The study also documents the fate ofEnterobacteriaceaeduring the fermentation of mahewu. There are concerns regarding the safety of traditionally prepared mahewu, and this requires in-depth knowledge of the fermentation process. Therefore, this study elucidated millet malt microbiota and identified cultures that are able to control the high numbers ofEnterobacteriaceaethat are initially present in mahewu fermentations.

scholarly journals ANGSD-wrapper: utilities for analyzing next generation sequencing data

2016 ◽  
Author(s):  
Arun Durvasula ◽  
Paul J Hoffman ◽  
Tyler V Kent ◽  
Chaochih Liu ◽  
Thomas J Y Kono ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Molecular Ecology ◽  
Principal Component ◽  
Next Generation Sequencing Data ◽  
Sequencing Data ◽  
Genome Data ◽  
High Throughput Sequencing Data ◽  
Genome Wide ◽  
User Friendly

High throughput sequencing has changed many aspects of population genetics, molecular ecology, and related fields, affecting both experimental design and data analysis. The software package ANGSD allows users to perform a number of population genetic analyses on high-throughput sequencing data. ANGSD uses probabilistic approaches to calculate genome-wide descriptive statistics. The package makes use of genotype likelihood estimates rather than SNP calls and is specifically designed to produce more accurate results for samples with low sequencing depth. ANGSD makes use of full genome data while handling a wide array of sampling and experimental designs. Here we present ANGSD-wrapper, a set of wrapper scripts that provide a user-friendly interface for running ANGSD and visualizing results. ANGSD-wrapper supports multiple types of analyses including esti- mates of nucleotide sequence diversity and performing neutrality tests, principal component analysis, estimation of admixture proportions for individuals samples, and calculation of statistics that quantify recent introgression. ANGSD-wrapper also provides interactive graphing of ANGSD results to enhance data exploration. We demonstrate the usefulness of ANGSD-wrapper by analyzing resequencing data from populations of wild and domesticated Zea. ANGSD-wrapper is freely available from https://github.com/mojaveazure/angsd-wrapper.

scholarly journals ANGSD-wrapper: utilities for analyzing next generation sequencing data

2016 ◽  
Author(s):  
Arun Durvasula ◽  
Paul J Hoffman ◽  
Tyler V Kent ◽  
Chaochih Liu ◽  
Thomas J Y Kono ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Molecular Ecology ◽  
Principal Component ◽  
Next Generation Sequencing Data ◽  
Sequencing Data ◽  
Genome Data ◽  
High Throughput Sequencing Data ◽  
Genome Wide ◽  
User Friendly

High throughput sequencing has changed many aspects of population genetics, molecular ecology, and related fields, affecting both experimental design and data analysis. The software package ANGSD allows users to perform a number of population genetic analyses on high-throughput sequencing data. ANGSD uses probabilistic approaches to calculate genome-wide descriptive statistics. The package makes use of genotype likelihood estimates rather than SNP calls and is specifically designed to produce more accurate results for samples with low sequencing depth. ANGSD makes use of full genome data while handling a wide array of sampling and experimental designs. Here we present ANGSD-wrapper, a set of wrapper scripts that provide a user-friendly interface for running ANGSD and visualizing results. ANGSD-wrapper supports multiple types of analyses including esti- mates of nucleotide sequence diversity and performing neutrality tests, principal component analysis, estimation of admixture proportions for individuals samples, and calculation of statistics that quantify recent introgression. ANGSD-wrapper also provides interactive graphing of ANGSD results to enhance data exploration. We demonstrate the usefulness of ANGSD-wrapper by analyzing resequencing data from populations of wild and domesticated Zea. ANGSD-wrapper is freely available from https://github.com/mojaveazure/angsd-wrapper.

scholarly journals Can Cyanobacterial Diversity in the Source Predict the Diversity in Sludge and the Risk of Toxin Release in a Drinking Water Treatment Plant?

Toxins ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 25
Author(s):  
Farhad Jalili ◽  
Hana Trigui ◽  
Juan Francisco Guerra Maldonado ◽  
Sarah Dorner ◽  
Arash Zamyadi ◽  
...  
Keyword(s):  
Drinking Water ◽  
Water Treatment ◽  
Treatment Plant ◽  
Drinking Water Treatment ◽  
Water Treatment Plant ◽  
Raw Water ◽  
Cyanobacterial Community ◽  
Shotgun Metagenomics ◽  
Drinking Water Treatment Plant ◽  
Cell Counts

Conventional processes (coagulation, flocculation, sedimentation, and filtration) are widely used in drinking water treatment plants and are considered a good treatment strategy to eliminate cyanobacterial cells and cell-bound cyanotoxins. The diversity of cyanobacteria was investigated using taxonomic cell counts and shotgun metagenomics over two seasons in a drinking water treatment plant before, during, and after the bloom. Changes in the community structure over time at the phylum, genus, and species levels were monitored in samples retrieved from raw water (RW), sludge in the holding tank (ST), and sludge supernatant (SST). Aphanothece clathrata brevis, Microcystis aeruginosa, Dolichospermum spiroides, and Chroococcus minimus were predominant species detected in RW by taxonomic cell counts. Shotgun metagenomics revealed that Proteobacteria was the predominant phylum in RW before and after the cyanobacterial bloom. Taxonomic cell counts and shotgun metagenomic showed that the Dolichospermum bloom occurred inside the plant. Cyanobacteria and Bacteroidetes were the major bacterial phyla during the bloom. Shotgun metagenomics also showed that Synechococcus, Microcystis, and Dolichospermum were the predominant detected cyanobacterial genera in the samples. Conventional treatment removed more than 92% of cyanobacterial cells but led to cell accumulation in the sludge up to 31 times more than in the RW influx. Coagulation/sedimentation selectively removed more than 96% of Microcystis and Dolichospermum. Cyanobacterial community in the sludge varied from raw water to sludge during sludge storage (1–13 days). This variation was due to the selective removal of coagulation/sedimentation as well as the accumulation of captured cells over the period of storage time. However, the prediction of the cyanobacterial community composition in the SST remained a challenge. Among nutrient parameters, orthophosphate availability was related to community profile in RW samples, whereas communities in ST were influenced by total nitrogen, Kjeldahl nitrogen (N- Kjeldahl), total and particulate phosphorous, and total organic carbon (TOC). No trend was observed on the impact of nutrients on SST communities. This study profiled new health-related, environmental, and technical challenges for the production of drinking water due to the complex fate of cyanobacteria in cyanobacteria-laden sludge and supernatant.

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