Alignment and clustering of phylogenetic markers - implications for microbial diversity studies

Microbial diversity studies of lignite mines of Rajpardi, Amod, Tadkeshwar and Panandhro, Gujarat, India, were carried out by substrate utilization-based, community-structure analysis. In Biologâ EcoPlates out of 31 different substrates, 1 to 28 substrates were metabolized. On the basis of these, similarity index and diversity indices were studied. From an extreme mine site Gram-positive, Gram-negative, fungi and yeasts were isolated and identified. One of the yeasts isolated is for the first time reported from a lignite mine ecosystem Apart from this auto- and heterotrophic iron oxidizers; sulphur oxidizers and sulphate reducers were also isolated. So, lignite mine ecosystems, inspite of the extreme environment showed rich microbial diversity.

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Accounting for 16S rRNA copy number prediction uncertainty and its implications in microbial diversity analyses

10.1101/2021.08.31.458422 ◽

2021 ◽

Author(s):

Yingnan Gao ◽

Martin Wu

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Microbial Diversity ◽

Bacterial Communities ◽

Beta Diversity ◽

Copy Number ◽

Rrna Gene ◽

Prediction Uncertainty ◽

Functional Profiles ◽

Diversity Studies

Background: 16S rRNA gene has been widely used in microbial diversity studies to determine the community composition and structure. 16S rRNA gene copy number (16S GCN) varies among microbial species and this variation introduces biases to the relative cell abundance estimated using 16S rRNA read counts. To correct the biases, methods (e.g., PICRUST2) have been developed to predict 16S GCN. 16S GCN predictions come with inherent uncertainty, which is often ignored in the downstream analyses. However, a recent study suggests that the uncertainty can be so great that copy number correction is not justified in practice. Despite the significant implications in 16S rRNA based microbial diversity studies, the uncertainty associated with 16S GCN predictions has not been well characterized and its impact on microbial diversity studies needs to be investigated. Results: Here we develop RasperGade16S, a novel method and software to better model and capture the inherent uncertainty in 16S rRNA GCN prediction. RasperGade16S implements a maximum likelihood framework of pulsed evolution model and explicitly accounts for intraspecific GCN variation and heterogeneous GCN evolution rates among species. Using cross validation, we show that our method provides robust confidence estimates for the GCN predictions and outperforms PICRUST2 in both precision and recall. We have predicted GCN for 592605 OTUs in the SILVA database and tested 113842 bacterial communities that represent an exhaustive and diverse list of engineered and natural environments. We found that the prediction uncertainty is small enough for 99% of the communities that 16S GCN correction should improve their compositional and functional profiles estimated using 16S rRNA reads. On the other hand, we found that GCN variation has limited impacts on beta-diversity analyses such as PCoA, PERMANOVA and random forest test. Conclusion: We have developed a method to accurately account for uncertainty in 16S rRNA GCN predictions and the downstream analyses. For almost all 16S rRNA surveyed bacterial communities, correction of 16S GCN should improve the results when estimating their compositional and functional profiles. However, such correction is not necessary for beta-diversity analyses.

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Application of enhanced bioreduction for hexavalent chromium-polluted groundwater cleanup: Microcosm and microbial diversity studies

Environmental Research ◽

10.1016/j.envres.2020.109296 ◽

2020 ◽

Vol 184 ◽

pp. 109296 ◽

Cited By ~ 2

Author(s):

Wei-Han Lin ◽

Ssu-Ching Chen ◽

Chih-Ching Chien ◽

Daniel C.W. Tsang ◽

Kai-Hung Lo ◽

...

Keyword(s):

Microbial Diversity ◽

Hexavalent Chromium ◽

Diversity Studies

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Extraction of DNA from Acidic, Hydrothermally Modified Volcanic Soils

Environmental Chemistry ◽

10.1071/en06013 ◽

2006 ◽

Vol 3 (2) ◽

pp. 100 ◽

Cited By ~ 13

Author(s):

Ruth M. Henneberger ◽

Malcolm R. Walter ◽

Roberto P. Anitori

Keyword(s):

Microbial Diversity ◽

Soil Samples ◽

Rock Weathering ◽

Geochemical Processes ◽

Volcanic Soils ◽

Volcanic Soil ◽

Initial Attempt ◽

Rapid Communication ◽

Extraction Procedures ◽

Diversity Studies

Environmental Context.Microorganisms are intimately involved in geochemical processes. For example, they are major players in the environmental cycling of important elements (e.g. carbon, sulfur, nitrogen, iron), rock weathering, and the formation of ores and petroleum. Identification of the environmental microbiota, commonly achieved via DNA techniques, is essential for an understanding of these processes. The main focus of this Rapid Communication is to demonstrate that endogenous DNA can be extracted from acidic, volcanic soil samples. Abstract.Acidic soils for microbial diversity studies were collected from Devil’s Kitchen, a fumarolic field on Mt Hood, USA. The very dense soils, which contain clay and other minerals, are derived from andesitic and dacitic rocks altered by volcanic heat and acidic, sulfur-rich hydrothermal steam. An initial attempt to extract biomass DNA using a mechanical-based cell lysis protocol was ineffective. However, by using various other protocols, DNA was successfully extracted, leading to the identification of several acidophilic Mt Hood extremophiles. The results emphasise the importance of testing different extraction procedures when dealing with apparently intractable samples.

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Bioremediation of 1,2-dichloroethane contaminated groundwater: Microcosm and microbial diversity studies

Environmental Pollution ◽

10.1016/j.envpol.2015.03.042 ◽

2015 ◽

Vol 203 ◽

pp. 97-106 ◽

Cited By ~ 16

Author(s):

S.Y. Wang ◽

Y.C. Kuo ◽

Y.Z. Huang ◽

C.W. Huang ◽

C.M. Kao

Keyword(s):

Microbial Diversity ◽

Contaminated Groundwater ◽

Diversity Studies

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High-Throughput Methods for Culturing Microorganisms in Very-Low-Nutrient Media Yield Diverse New Marine Isolates

Applied and Environmental Microbiology ◽

10.1128/aem.68.8.3878-3885.2002 ◽

2002 ◽

Vol 68 (8) ◽

pp. 3878-3885 ◽

Cited By ~ 476

Author(s):

Stephanie A. Connon ◽

Stephen J. Giovannoni

Keyword(s):

Microbial Diversity ◽

High Throughput ◽

Detection Sensitivity ◽

Nutrient Media ◽

Culture Collections ◽

Marine Bacterioplankton ◽

Microtiter Plates ◽

Cell Arrays ◽

Unique Cell ◽

Diversity Studies

ABSTRACT Microbial diversity studies based on the cloning and sequencing of DNA from nature support the conclusion that only a fraction of the microbial diversity is currently represented in culture collections. Out of over 40 known prokaryotic phyla, only half have cultured representatives. In an effort to culture the uncultured phylotypes from oligotrophic marine ecosystems, we developed high-throughput culturing procedures that utilize the concept of extinction culturing to isolate cultures in small volumes of low-nutrient media. In these experiments, marine bacteria were isolated and cultivated at in situ substrate concentrations—typically 3 orders of magnitude less than common laboratory media. Microtiter plates and a newly developed procedure for making cell arrays were employed to raise the throughput rate and lower detection sensitivity, permitting cell enumeration from 200-μl aliquots of cultures with densities as low as 103 cells/ml. Approximately 2,500 extinction cultures from 11 separate samplings of marine bacterioplankton were screened over the course of 3 years. Up to 14% of the cells collected from coastal seawater were cultured by this method, which was 14- to 1,400-fold higher than the numbers obtained by traditional microbiological culturing techniques. Among the microorganisms cultured were four unique cell lineages that belong to previously uncultured or undescribed marine Proteobacteria clades known from environmental gene cloning studies. These cultures are related to the clades SAR11 (α subclass), OM43 (β subclass), SAR92 (γ subclass), and OM60/OM241 (γ subclass). This method proved successful for the cultivation of previously uncultured marine bacterioplankton that have consistently been found in marine clone libraries.

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