scholarly journals Characterization and Performance of Lactate-Feeding Consortia for Reductive Dechlorination of Trichloroethene

2021 ◽  
Vol 9 (4) ◽  
pp. 751
Author(s):  
Jiangwei Li ◽  
Anyi Hu ◽  
Shijie Bai ◽  
Xiaoyong Yang ◽  
Qian Sun ◽  
...  
Keyword(s):  
Community Assembly ◽  
Reductive Dechlorination ◽  
Amplicon Sequencing ◽  
Underlying Mechanism ◽  
Contaminated Sites ◽  
Bioinformatics Analyses ◽  
16S Rdna Amplicon Sequencing ◽  
And Performance ◽  
Stochastic Forces ◽  
Anaerobic Media

Understanding the underlying mechanism that drives the microbial community mediated by substrates is crucial to enhance the biostimulation in trichloroethene (TCE)-contaminated sites. Here, we investigated the performance of stable TCE-dechlorinating consortia by monitoring the variations in TCE-related metabolites and explored their underlying assembly mechanisms using 16S rDNA amplicon sequencing and bioinformatics analyses. The monitoring results indicated that three stable TCE-dechlorinating consortia were successfully enriched by lactate-containing anaerobic media. The statistical analysis results demonstrated that the microbial communities of the enrichment cultures changed along with time and were distinguished by their sample sources. The deterministic and stochastic processes were simultaneously responsible for shaping the TCE-dechlorinating community assembly. The indicator patterns shifted with the exhaustion of the carbon source and the pollutants, and the tceA-carrying Dehalococcoides, as an indicator for the final stage samples, responded positively to TCE removal during the incubation period. Pseudomonas, Desulforhabdus, Desulfovibrio and Methanofollis were identified as keystone populations in the TCE-dechlorinating process by co-occurrence network analysis. The results of this study indicate that lactate can be an effective substrate for stimulated bioremediation of TCE-contaminated sites, and the reduction of the stochastic forces or enhancement of the deterministic interventions may promote more effective biostimulation.

scholarly journals Gut Microbial Composition Differs Extensively among Indian Native Chicken Breeds Originated in Different Geographical Locations and a Commercial Broiler Line, but Breed-Specific, as Well as Across-Breed Core Microbiomes, Are Found

2021 ◽  
Vol 9 (2) ◽  
pp. 391
Author(s):  
Shyam Sundar Paul ◽  
Rudra Nath Chatterjee ◽  
Mantena Venkata Lakshmi Narasimha Raju ◽  
Bhukya Prakash ◽  
Savaram Venkata Rama Rao ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Operational Taxonomic Unit ◽  
Amplicon Sequencing ◽  
Microbial Composition ◽  
Linear Discriminant ◽  
Specific Complex ◽  
Commercial Broiler ◽  
16S Rdna Amplicon Sequencing ◽  
Chicken Breeds ◽  
And Performance

Gut microbiota plays an important role in the health and performance of the host. Characterizations of gut microbiota, core microbiomes, and microbial networks in different chicken breeds are expected to provide clues for pathogen exclusion, improving performance or feed efficiency. Here, we characterized the gut microbiota of “finishing” chickens (at the end of production life) of indigenous Indian Nicobari, Ghagus, and Aseel breeds, originating from the Nicobari island, coastal India, and the Indian mainland, respectively, as well as a global commercial broiler line, VenCobb 400, using 16S rDNA amplicon sequencing. We found that diversity, as well as richness of microbiota, was higher in indigenous breeds than in the broiler line. Beta diversity analysis indicated the highest overlap between Ghagus and Nicobari breeds and a very low overlap between the broiler line and all indigenous breeds. Linear discriminant analysis effect size (LEfSe) revealed 82 breed- or line-specific phylotype operational taxonomic unit (OTU) level biomarkers. We confirm the presence of breed specific and across-breed core microbiomes. Additionally, we show the existence of breed specific complex microbial networks in all groups. This study provides the first (and comprehensive) insight into the gut microbiota of three indigenous breeds and one commercial broiler line of chickens reared without antimicrobials, and underscores the need to study microbial diversity in other indigenous breeds.

Beyond the usual suspects: methanogenic communities in eastern North American peatlands are also influenced by nickel and copper concentrations

2021 ◽  
Author(s):  
Sydney E Bear ◽  
James D Seward ◽  
Louis Jamie Lamit ◽  
Nathan Basiliko ◽  
Tim Moore ◽  
...  
Keyword(s):  
Strong Predictor ◽  
Methanogenic Archaea ◽  
Community Analysis ◽  
Amplicon Sequencing ◽  
Contaminated Sites ◽  
Methanogenic Community ◽  
Primary Driver ◽  
High Concentrations ◽  
Methyl Coenzyme M Reductase ◽  
Eastern Half

Abstract Peatlands both accumulate carbon and release methane, but their broad range in environmental conditions means that the diversity of microorganisms responsible for carbon cycling is still uncertain. Here we describe a community analysis of methanogenic archaea responsible for methane production in 17 peatlands from 36 to 53 N latitude across the eastern half of North America, including three metal-contaminated sites. Methanogenic community structure was analyzed through Illumina amplicon sequencing of the mcrA gene. Whether metal-contaminated sites were included or not, metal concentrations in peat were a primary driver of methanogenic community composition, particularly nickel, a trace element required in the F430 cofactor in methyl-coenzyme M reductase that is also toxic at high concentrations. Copper was also a strong predictor, likely due to inhibition at toxic levels and/or to cooccurrence with nickel, since copper enzymes are not known to be present in anaerobic archaea. The methanogenic groups Methanocellales and Methanosarcinales were prevalent in peatlands with low nickel concentrations, while Methanomicrobiales and Methanomassiliicoccales were abundant in peatlands with higher nickel concentrations. Results suggest that peat-associated trace metals are predictors of methanogenic communities in peatlands.

Molecular characterisation of Tyr530Ser and IVS16–1G>T mutations causing severe factor V deficiency

2010 ◽  
Vol 104 (09) ◽  
pp. 536-543 ◽  
Author(s):  
Weidong Zheng ◽  
Yanhui Liu ◽  
Ying Luo ◽  
Zhihong Chen ◽  
Yan Wang ◽  
...  
Keyword(s):  
Deletion Mutant ◽  
Coagulation Factor ◽  
Underlying Mechanism ◽  
Procoagulant Activity ◽  
Site Directed Mutagenesis ◽  
Factor V ◽  
Wild Type ◽  
Site Mutation ◽  
Bioinformatics Analyses ◽  
Mutant Transcript

SummaryOur previous study reported a missense mutation (Tyr530Ser) and a splicing site mutation (IVS16–1G>T) in blood coagulation factor V (FV) gene in a two-year-old Chinese boy. However, the linkage between the mutations and severe FV deficiency and the underlying mechanism has not been elucidated. The present study was designed to investigate the effect of the two mutations and the possible pathogenetic mechanism. FV procoagulant activity showed tremendous decrease in the patient with two mutations. The bioinformatics analyses predicted that IVS16–1G>T mutation may cause the entire exon 17 of FV to be skipped in transcription and thereby result in a deletion mutant. To confirm the predicted results, the fragment of exon 16 to exon 18 containing IVS16–1G>T mutation was obtained by PCR and site-directed mutagenesis. IVS16–1G>T mutant and wild-type constructs were transfected into COS-7 cells. Sequence analysis showed that mutant transcript lacked the entire 180-bp length of exon 17. Moreover, compared to wild-type, the expression of the two mutant proteins was decreased and the procoagulant activity was also reduced when the deletion mutant cDNA and Tyr530Ser site mutant cDNA were transfected into COS-7 cells, respectively. Our results indicate that Tyr530Ser and IVS16–1G>T could be separately responsible for severe FV deficiency, while the phenotype in the proband could be caused by the combination effect of the two defects.

Isolation and Performance for Two Strains of Benzo[a]pyrene Degradation

2011 ◽  
Vol 233-235 ◽  
pp. 1920-1923
Author(s):  
Shuai Ran Li ◽  
Jun Feng Dou ◽  
Li Rong Cheng ◽  
Ai Zhong Ding ◽  
Lin Jiang ◽  
...  
Keyword(s):  
Carbon Source ◽  
Removal Efficiency ◽  
Sole Carbon Source ◽  
Contaminated Sites ◽  
Pyrene Degradation ◽  
And Performance ◽  
Achromobacter Sp

This is the report describing the biodegradation of benzo[a]pyrene （BaP） by strains isolated from the soil of the PAH contaminated sites. Achromobacter sp and Alcaligenes sp were found with the capability of degrading Bap as sole carbon source, their biodegradation performance of BaP was evaluated when the initial BaP concentrations was approximately 0.25mg/L, 0.40mg/L and 0.90mg/L. The results demonstrated Alcaligenes sp could degrade Bap completely within two weeks when the initial Bap concentration was 0.40mg/L. Alcaligenes sp showed higher removal efficiency than Achromobacter sp.

scholarly journals Hill-based Dissimilarity Indices and Null Models for Analysis of Microbial Community Assembly

2020 ◽  
Author(s):  
Oskar Modin ◽  
Raquel Liebana ◽  
Soroush Saheb-Alam ◽  
Britt-Marie Wilén ◽  
Carolina Suarez ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Assembly ◽  
Null Model ◽  
Amplicon Sequencing ◽  
Null Models ◽  
Marker Genes ◽  
Experimental Systems ◽  
Microbial Community Assembly ◽  
The Impact

Abstract Background: High-throughput amplicon sequencing of marker genes, such as the 16S rRNA gene in Bacteria and Archaea, provides a wealth of information about the composition of microbial communities. To quantify differences between samples and draw conclusions about factors affecting community assembly, dissimilarity indices are typically used. However, results are subject to several biases and data interpretation can be challenging. The Jaccard and Bray-Curtis indices, which are often used to quantify taxonomic dissimilarity, are not necessarily the most logical choices. Instead, we argue that Hill-based indices, which make it possible to systematically investigate the impact of relative abundance on dissimilarity, should be used for robust analysis of data. In combination with a null model, mechanisms of microbial community assembly can be analyzed. Here, we also introduce a new software, qdiv, which enables rapid calculations of Hill-based dissimilarity indices in combination with null models.Results: Using amplicon sequencing data from two experimental systems, aerobic granular sludge (AGS) reactors and microbial fuel cells (MFC), we show that the choice of dissimilarity index can have considerable impact on results and conclusions. High dissimilarity between replicates because of random sampling effects make incidence-based indices less suited for identifying differences between groups of samples. Determining a consensus table based on count tables generated with different bioinformatic pipelines reduced the number of low-abundant, potentially spurious amplicon sequence variants (ASVs) in the data sets, which led to lower dissimilarity between replicates. Analysis with a combination of Hill-based indices and a null model allowed us to show that different ecological mechanisms acted on different fractions of the microbial communities in the experimental systems.Conclusions: Hill-based indices provide a rational framework for analysis of dissimilarity between microbial community samples. In combination with a null model, the effects of deterministic and stochastic community assembly factors on taxa of different relative abundances can be systematically investigated. Calculations of Hill-based dissimilarity indices in combination with a null model can be done in qdiv, which is freely available as a Python package (https://github.com/omvatten/qdiv). In qdiv, a consensus table can also be determined from several count tables generated with different bioinformatic pipelines.

scholarly journals Dietary Amylose/Amylopectin Ratio Modulates Cecal Microbiota and Metabolites in Weaned Goats

2021 ◽  
Vol 8 ◽  
Author(s):  
Kefyalew Gebeyew ◽  
Kai Chen ◽  
Teketay Wassie ◽  
Md. Abul Kalam Azad ◽  
Jianhua He ◽  
...  
Keyword(s):  
Acid Ethyl Ester ◽  
Amplicon Sequencing ◽  
Underlying Mechanism ◽  
Stearidonic Acid ◽  
16S Amplicon Sequencing ◽  
Body Weights ◽  
Cecal Microbiota ◽  
Dodecanedioic Acid ◽  
Factor Α ◽  
High Amylose

Increasing the ratio of amylose in the diet can increase the quantity of starch that flows to the large intestine for microbial fermentation. This leads to the alteration of microbiota and metabolite of the hindgut, where the underlying mechanism is not clearly understood. The present study used a combination of 16S amplicon sequencing technology and metabolomics technique to reveal the effects of increasing ratios of amylose/amylopectin on cecal mucosa- and digesta-associated microbiota and their metabolites in young goats. Twenty-seven Xiangdong black female goats with average body weights (9.00 ± 1.12 kg) were used in this study. The goats were randomly allocated to one of the three diets containing starch with 0% amylose corn (T1), 50% high amylose corn (T2), and 100% high amylose corn (T3) for 35 days. Results showed that cecal valerate concentration was higher (P < 0.05) in the T2 group than those in the T1 and T3 groups. The levels of tumor necrosis factor-α (TNF-α) and interleukin (IL)-6 were decreased (P < 0.05) in cecal tissue while IL-10 was increased (P < 0.05) in the T2 group when compared with T1 or T3 groups. At the phylum level, the proportion of mucosa-associated Spirochaetes was increased (P < 0.05), while Proteobacteria was deceased by feeding high amylose ratios (P < 0.05). The abundance of Verrucomicrobia was decreased (P < 0.05) in the T3 group compared with the T1 and T2 groups. The abundance of digesta-associated Firmicutes was increased (P < 0.05) while Verrucomicrobia and Tenericutes were deceased (P < 0.05) with the increment of amylose/amylopectin ratios. The LEfSe analysis showed that a diet with 50% high amylose enriched the abundance of beneficial bacteria such as Faecalibacterium and Lactobacillus in the digesta and Akkermansia in the mucosa compared with the T1 diet. The metabolomics results revealed that feeding a diet containing 50% high amylose decreased the concentration of fatty acyls-related metabolites, including dodecanedioic acid, heptadecanoic acid, and stearidonic acid ethyl ester compared with the T1 diet. The results suggested that a diet consisting of 50% high amylose could maintain a better cecal microbiota composition and host immune function.

scholarly journals Microbial Communities Associated with Sustained Anaerobic Reductive Dechlorination of α-, β-, γ-, and δ-Hexachlorocyclohexane Isomers to Monochlorobenzene and Benzene

2019 ◽  
Author(s):  
Wenjing Qiao ◽  
Luz A. Puentes Jácome ◽  
Xianjin Tang ◽  
Line Lomheim ◽  
Minqing Ivy Yang ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Amplicon Sequencing ◽  
Contaminated Sites ◽  
Molar Ratio ◽  
Rrna Gene ◽  
Absolute Abundance ◽  
Hch Isomers ◽  
Persistent Pesticide ◽  
Hexachlorocyclohexane Isomers ◽  
Archaeal Communities

AbstractIntensive historical and worldwide use of the persistent pesticide technical-grade hexachlorocyclohexane (HCH), composed of the active ingredient γ-HCH (called lindane) along with several other HCH isomers, has led to widespread contamination. We derived four anaerobic enrichment cultures from HCH-contaminated soil capable of sustainably dechlorinating each of α-, β-, γ-, and δ-HCH isomers stoichiometrically and completely to benzene and monochlorobenzene (MCB). For each isomer, the dechlorination rates increased progressively from <3 µM/day to ∼12 µM/day over two years. The molar ratio of benzene to MCB produced was a function of the substrate isomer, and ranged from β (0.77±0.15), α (0.55±0.09), γ (0.13±0.02) to δ (0.06±0.02) in accordance with pathway predictions based on prevalence of antiperiplanar geometry. Cultivation with a different HCH isomer resulted in distinct bacterial communities, but similar archaeal communities. Data from 16S rRNA gene amplicon sequencing and quantitative PCR revealed significant increases in the absolute abundance of Pelobacter and Dehalobacter, especially in the α-HCH and δ-HCH cultures. This study provides the first direct comparison of shifts in anaerobic microbial communities induced by the dechlorination of distinct HCH isomers. It also uncovers candidate microorganisms responsible for the dechlorination of α-, β-, γ-, and δ-HCH, a key step towards better understanding and monitoring of natural attenuation processes and improving bioremediation technologies for HCH-contaminated sites.

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