Diversity of microorganisms from forest soils differently polluted with heavy metals
TL;DR: In this paper, the influence of different soil chemical properties on structure and diversity of microbial communities in soils polluted with different levels of heavy metals was assessed using PLFA analysis and the structure of soil bacterial communities using pyrosequencing of 16S rRNA genes.
About: This article is published in Applied Soil Ecology.The article was published on 2013-02-01. It has received 292 citations till now. The article focuses on the topics: Soil biology & Soil organic matter.
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TL;DR: An overview of the sequencing technologies and how they are uniquely suited to various types of metagenomic studies is provided and future trends in the field are provided with respect to tools and technologies currently under development.
Abstract: Advances in next-generation sequencing (NGS) have allowed significant breakthroughs in microbial ecology studies. This has led to the rapid expansion of research in the field and the establishment of “metagenomics”, often defined as the analysis of DNA from microbial communities in environmental samples without prior need for culturing. Many metagenomics statistical/computational tools and databases have been developed in order to allow the exploitation of the huge influx of data. In this review article, we provide an overview of the sequencing technologies and how they are uniquely suited to various types of metagenomic studies. We focus on the currently available bioinformatics techniques, tools, and methodologies for performing each individual step of a typical metagenomic dataset analysis. We also provide future trends in the field with respect to tools and technologies currently under development. Moreover, we discuss data management, distribution, and integration tools that are capable of performing comparative metagenomic analyses of multiple datasets using well-established databases, as well as commonly used annotation standards.
323 citations
TL;DR: The changes of different microbiological indices and the mechanism of microbial response to heavy metal stress in soils are comprehensively summarized and future directions of the microbial ecotoxicological diagnosis of soil contamination by heavy metals are proposed and discussed.
222 citations
TL;DR: It was found that the samples differed significantly and Zn decreased both diversity and species richness at species and family levels, while plant species richness did not correlate with bacterial diversity.
Abstract: Soil contamination with heavy metals is a widespread problem, especially prominent on grounds lying in the vicinity of mines, smelters, and other industrial facilities. Many such areas are located in Southern Poland; they are polluted mainly with Pb, Zn, Cd, or Cu, and locally also with Cr. As for now, little is known about most bacterial species thriving in such soils and even less about a core bacterial community—a set of taxa common to polluted soils. Therefore, we wanted to answer the question if such a set could be found in samples differing physicochemically and phytosociologically. To answer the question, we analyzed bacterial communities in three soil samples contaminated with Pb and Zn and two contaminated with Cr and lower levels of Pb and Zn. The communities were assessed with 16S rRNA gene fragments pyrosequencing. It was found that the samples differed significantly and Zn decreased both diversity and species richness at species and family levels, while plant species richness did not correlate with bacterial diversity. In spite of the differences between the samples, they shared many operational taxonomic units (OTUs) and it was possible to delineate the core microbiome of our sample set. The core set of OTUs comprised members of such taxa as Sphingomonas, Candidatus Solibacter, or Flexibacter showing that particular genera might be shared among sites ~40 km distant.
218 citations
Cites background from "Diversity of microorganisms from fo..."
...However, when considered with other factors, theywere not themost important variables shaping the community structure [19]....
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...The dependence of bacterial diversity and species richness on the contamination was found in Cd, Pb, and Zn [18, 19] as well as Cr and As [20] and Cu [19] contaminated soils....
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TL;DR: Investigation of microbial adaptation mechanism to contaminated sediments under natural conditions showed that sediment from a tributary of the Yellow River, which was named Dongdagou River, has evolved into an integrated system resistant to long-term heavy-metal pollution.
216 citations
Cites result from "Diversity of microorganisms from fo..."
...Previous studies showed that the abundance of phylum Chloroflexi in metal-contaminated sites was increased (Chodak et al., 2013; Azarbad et al., 2015), whereas it opposites to our observation (Figs 2 and 3)....
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TL;DR: The goal of this study was to identify the effects of HMs and soil physicochemical properties on soil microorganisms and prioritize some parameters that contributed significantly to soil microbial biomass (SMB) and bacterial community structure.
215 citations
References
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Journal Article•
TL;DR: PAST (PAleontological STatistics) as discussed by the authors is a simple-to-use software package for executing a range of standard numerical analysis and operations used in quantitative paleontology.
Abstract: A comprehensive, but simple-to-use software package for executing a range of standard numerical analysis and operations used in quantitative paleontology has been developed. The program, called PAST (PAleontological STatistics), runs on standard Windows computers and is available free of charge. PAST integrates spreadsheet-type data entry with univariate and multivariate statistics, curve fitting, timeseries analysis, data plotting, and simple phylogenetic analysis. Many of the functions are specific to paleontology and ecology, and these functions are not found in standard, more extensive, statistical packages. PAST also includes fourteen case studies (data files and exercises) illustrating use of the program for paleontological problems, making it a complete educational package for courses in quantitative methods.
19,926 citations
University of Massachusetts Amherst1, University of Michigan2, University of New Mexico3, University of British Columbia4, Texas A&M University5, University of Minnesota6, University of Warwick7, Dalhousie University8, Colorado School of Mines9, University of Ljubljana10, Graz University of Technology11, Louisiana State University12
TL;DR: M mothur is used as a case study to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments.
Abstract: mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the alpha and beta diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.
17,350 citations
TL;DR: UCHIME has better sensitivity than ChimeraSlayer (previously the most sensitive database method), especially with short, noisy sequences, and in testing on artificial bacterial communities with known composition, UCHIME de novo sensitivity is shown to be comparable to Perseus.
Abstract: Motivation: Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or fungal Internal Transcribed Spacer) to assess diversity or compare populations. Undetected chimeras may be misinterpreted as novel species, causing inflated estimates of diversity and spurious inferences of differences between populations. Detection and removal of chimeras is therefore of critical importance in such experiments.
Results: We describe UCHIME, a new program that detects chimeric sequences with two or more segments. UCHIME either uses a database of chimera-free sequences or detects chimeras de novo by exploiting abundance data. UCHIME has better sensitivity than ChimeraSlayer (previously the most sensitive database method), especially with short, noisy sequences. In testing on artificial bacterial communities with known composition, UCHIME de novo sensitivity is shown to be comparable to Perseus. UCHIME is >100× faster than Perseus and >1000× faster than ChimeraSlayer.
Contact: [email protected]
Availability: Source, binaries and data: http://drive5.com/uchime.
Supplementary information:Supplementary data are available at Bioinformatics online.
11,904 citations
Book•
01 Jan 1982
TL;DR: In this paper, the authors present an analysis of organic matter in soil using NMR Spectroscopy and analytical pyrolysis, showing that organic matter is composed of nitrogen and ammonium.
Abstract: Partial table of contents: Organic Matter in Soils: Pools, Distribution, Transformations, and Function. Extraction, Fractionation, and General Chemical Composition of Soil Organic Matter. Organic Forms of Soil Nitrogen. Native Fixed Ammonium and Chemical Reactions of Organic Matter with Ammonia and Nitrite. Organic Phosphorus and Sulfur Compounds. Soil Carbohydrates. Soil Lipids. Biochemistry of the Formation of Humic Substances. Reactive Functional Groups. Structural Components of Humic and Fulvic Acids as Revealed by Degradation Methods. Characterization of Soil Organic Matter by NMR Spectroscopy and Analytical Pyrolysis. Structural Basis of Humic Substances. Spectroscopic Approaches. Colloidal Properties of Humic Substances. Electrochemical and Ion-Exchange Properties of Humic Substances. Organic Matter Reactions Involving Pesticides in Soil. Index.
5,658 citations
TL;DR: Survey, experimental, and meta-analytical results suggest that certain bacterial phyla can be differentiated into copiotrophic and oligotrophic categories that correspond to the r- and K-selected categories used to describe the ecological attributes of plants and animals.
Abstract: Although researchers have begun cataloging the incredible diversity of bacteria found in soil, we are largely unable to interpret this information in an ecological context, including which groups of bacteria are most abundant in different soils and why. With this study, we examined how the abundances of major soil bacterial phyla correspond to the biotic and abiotic characteristics of the soil environment to determine if they can be divided into ecologically meaningful categories. To do this, we collected 71 unique soil samples from a wide range of ecosystems across North America and looked for relationships between soil properties and the relative abundances of six dominant bacterial phyla (Acidobacteria, Bacteroidetes, Firmicutes, Actinobacteria, alpha-Proteobacteria, and the beta-Proteobacteria). Of the soil properties measured, net carbon (C) mineralization rate (an index of C availability) was the best predictor of phylum-level abundances. There was a negative correlation between Acidobacteria abundance and C mineralization rates (r2 = 0.26, P < 0.001), while the abundances of beta-Proteobacteria and Bacteroidetes were positively correlated with C mineralization rates (r2 = 0.35, P < 0.001 and r2 = 0.34, P < 0.001, respectively). These patterns were explored further using both experimental and meta-analytical approaches. We amended soil cores from a specific site with varying levels of sucrose over a 12-month period to maintain a gradient of elevated C availabilities. This experiment confirmed our survey results: there was a negative relationship between C amendment level and the abundance of Acidobacteria (r2 = 0.42, P < 0.01) and a positive relationship for both Bacteroidetes and beta-Proteobacteria (r2 = 0.38 and 0.70, respectively; P < 0.01 for each). Further support for a relationship between the relative abundances of these bacterial phyla and C availability was garnered from an analysis of published bacterial clone libraries from bulk and rhizosphere soils. Together our survey, experimental, and meta-analytical results suggest that certain bacterial phyla can be differentiated into copiotrophic and oligotrophic categories that correspond to the r- and K-selected categories used to describe the ecological attributes of plants and animals. By applying the copiotroph-oligotroph concept to soil microorganisms we can make specific predictions about the ecological attributes of various bacterial taxa and better understand the structure and function of soil bacterial communities.
3,423 citations