The use of molecular techniques to characterize the microbial communities in contaminated soil and water

doi:10.1016/j.envint.2007.09.001

Environment International

Volume 34, Issue 2, February 2008, Pages 265-276

https://doi.org/10.1016/j.envint.2007.09.001 Get rights and content

Abstract

Traditionally, the identification and characterization of microbial communities in contaminated soil and water has previously been limited to those microorganisms that are culturable. The application of molecular techniques to study microbial populations at contaminated sites without the need for culturing has led to the discovery of unique and previously unrecognized microorganisms as well as complex microbial diversity in contaminated soil and water which shows an exciting opportunity for bioremediation strategies. Nucleic acid extraction from contaminated sites and their subsequent amplification by polymerase chain reaction (PCR) has proved extremely useful in assessing the changes in microbial community structure by several microbial community profiling techniques. This review examines the current application of molecular techniques for the characterization of microbial communities in contaminated soil and water. Techniques that identify and quantify microbial population and catabolic genes involved in biodegradation are examined. In addition, methods that directly link microbial phylogeny to its ecological function at contaminated sites as well as high throughput methods for complex microbial community studies are discussed.

Introduction

Traditionally, characterization of microbial community composition in contaminated soil and water has been limited to the ability to culture microorganisms from environmental samples. Unfortunately, only a fraction of the microorganisms involved in the biodegradation of contaminants in soil and water can currently be cultured in the laboratory. It has been estimated that the microbial community in one gram of soil may contain over one thousand different bacterial species (Rossello-Mora and Amann, 2001), but less than 1% of these may be culturable. It has been observed that fast growing organisms or strains best adapted to particular culture conditions grow preferentially than those which are not, and therefore do not accurately represent the actual microbial community composition of contaminated environments (Rappe and Giovannoni, 2003, Gilbride et al., 2006). Hence culture-dependent characterization of microorganisms at contaminated sites may limit the scope of microbial biodiversity and the ecological importance of unculturable organisms at contaminated sites may go undetected (Brockman, 1995, Van Hamme et al., 2003, Widada et al., 2002b).

Modern molecular techniques provide an exciting opportunity to overcome the requirement for culturing and have therefore greatly increased our understanding of microbial diversity and functionality in the environment. These methods rely on the characterization of cellular constituents such as nucleic acids, proteins, fatty acids and other taxa-specific compounds (Rossello-Mora and Amann, 2001). Such molecules can be extracted directly from environmental samples without the need for culturing and analysis of the molecular composition can be used to elucidate the composition of the microbial community (Amann et al., 1995, Greene and Voordouw, 2003). Another advantage of culture-independent molecular characterization includes the capacity to preserve in situ metabolic function and the microbial community composition by immediately preserving samples (Moller et al., 1998, Wilson et al., 1999a) or direct extraction of molecules of interest from environmental samples (Tsai and Olson, 1991).

This review is aimed at presenting and evaluating current molecular applications in the assessment of microbial community composition from contaminated soil and water environments in a bid to identify the dominant microbial communities or catabolic genes.

Section snippets

Phospholipids fatty acids (PLFA)

Phospholipids are important components of living cells membranes and constitute a significant proportion of organism biomass under natural conditions (Kozdroj and van Elsas, 2001). Microorganisms have the ability to change the lipid composition of their membranes in response to environmental conditions such as chemical stress (Frostegard et al., 1993) and temperatures fluctuations (Bartlett, 1999). PLFA rapidly degrade upon cell death thus making it good indicator of living organisms (Drenovsky

Polymerase chain reaction (PCR)

The polymerase chain reaction has the ability to produce millions of copies of a portion of a desired gene, entire gene or gene clusters with high fidelity within 3 to 4 h. It is the most widely used method for the amplification of 16S rRNA, or its gene, prior to fingerprinting studies. PCR-based methods have also used in the detection and quantification of microorganisms found in soil and water (Wilson et al., 1999b).

The technique can also be applied for the analysis of catabolic genes

Fluorescent in situ hybridization (FISH)

FISH is a method used to quantify the presence and relative abundance of microbial populations in a community sample. Microbial cells are treated with fixative, hybridized with specific probes (usually 15–25 bp oligonucleotide-fluorescently labelled probes) on a glass slide then visualised with either epiflourescence or confocal laser microscopy (Sanz and Kochling, 2007).

Hybridization with rRNA-targeted probes enhances the characterization of uncultured microorganisms and also facilitates the

Stable isotope probing (SIP)

Stable isotope probing (SIP) enables the characterization or identification of microbial populations actively involved in specific metabolic processes in the environment with the aim of linking the microbial phylogeny with function (Radajewski et al., 2000). SIP involves the incorporation of stable isotope-labelled substrates into cellular biomarkers that can be used to identify organisms assimilating the substrate (Boschker and Middelburg, 2002). Labelled biomarkers such as PLFA (Bull et al.,

Microarray technologies

DNA microarray technology is a very powerful taxonomic and functional tool that is widely used to study biological processes, including mixed microbial communities. This technique is similar to FISH, but provides a means for simultaneous analysis of many genes (Cho and Tiedje, 2002). DNA microarray is a miniaturized array of complementary DNA probes (∼ 500–5000 nucleotides in length) or oligonucleotides (15–70 bp) attached directly to a solid support, which permits simultaneous hybridization of

Conclusion

Culture independent molecular tools applied for the analyses of mixed microbial communities from contaminated soil and water have undoubtedly advanced our knowledge and understanding about microbial diversity and biochemistry of contaminants catabolism. Molecular techniques have contributed significantly to the detection and identification of microorganisms and catabolic genes especially in non-culturable organisms as well as the quantification or enumeration of the relative abundance of

References (169)

BaiY. et al.
Phylogenetic diversity of culturable bacteria from alpine permafrost in the Tianshan Mountains, northwestern China
Res Microbiol
(2006)
BoschkerH.T.S. et al.
Stable isotopes and biomarkers in microbial ecology
FEMS Microbiol Ecol
(2002)
ChangY.J. et al.
Phylogenetic analysis of aerobic freshwater and marine enrichment cultures efficient in hydrocarbon degradation: effect of profiling method
J Microbiol Methods
(2000)
DrenovskyR.E. et al.
Comparison of phospholipids fatty acid (PLFA) and total soil fatty acid methyl esters (TSFAME) for characterizing soil microbial communities
Soil Biol Biochem
(2004)
DeversM. et al.
Real-time reverse transcription PCR analysis of expression of atrazine catabolism genes in two bacterial strains isolated from soil
J Microbiol Methods
(2004)
DubeyS.K. et al.
Exploration of soil bacterial communities for their potential as bioresource
Bioresour Technol
(2006)
FediS. et al.
T-RFLP analysis of bacterial communities in cyclodextrin-amended bioreactors developed for biodegradation of polychlorinated biphenyls
Res Microbiol
(2005)
FischerS.G. et al.
Length-independent separation of DNA restriction fragments in two-dimensional gel electrophoresis
Cell
(1979)
ForneyL.J. et al.
Molecular microbial ecology: land of the one-eyed king
Curr Opin Microbiol
(2004)
FullerM.E. et al.
Microbiological changes during bioremediation of explosives-contaminated soils in laboratory and pilot-scale bioslurry reactors
Bioresour Technol
(2004)

GeetsJ. et al.

DsrB gene-based DGGE for community and diversity surveys of sulfate-reducing bacteria

J Microbiol Methods

(2006)

GilbrideK.A. et al.

Molecular techniques in wastewater: understanding microbial communities, detecting pathogens, and real-time process control

J Microbiol Methods

(2006)

GreeneE.A. et al.

Analysis of environmental microbial communities by reverse sample genome probing

J Microbiol Methods

(2003)

JardillierL. et al.

Relative importance of nutrients and mortality factors on prokaryotic community composition in two lakes of different trophic status: microcosm experiments

FEMS Microbiol Ecol

(2005)

KamaludeenS.P. et al.

Microbial activity and phospholipid fatty acid pattern in long-term tannery waste-contaminated soil

Ecotoxicol Environ Saf

(2003)

KirkJ.L. et al.

Methods of studying soil microbial diversity

J Microbiol Methods

(2004)

KohringL.L. et al.

Comparison of phylogenetic relationships based on phospholipid fatty acid profiles and ribosomal RNA sequence similarities among dissimilatory sulfate-reducing bacteria

FEMS Microbiol Lett

(1994)

KozdrojJ. et al.

Structural diversity of microorganisms in chemically perturbed soil assessed by molecular and cytochemical approaches

J Microbiol Methods

(2001)

KrizovaJ. et al.

Evaluation of amplified ribosomal DNA restriction analysis (ARDRA) and species-specific PCR for identification of Bifidobacterium species

Syst Appl Microbiol

(2006)

MarshT.L.

Terminal restriction fragment length polymorphism (T-RFLP): an emerging method for characterizing diversity among homologous populations of amplification products

Curr Opin Microbiol

(1999)

Milcic-TerzicJ. et al.

Detection of catabolic genes in indigenous microbial consortia isolated from a diesel-contaminated soil

Bioresour Technol

(2001)

MiskoA.L. et al.

Taxonomic and functional diversity of pseudomonads isolated from the roots of field-grown canola

FEMS Microbiol Ecol

(2002)

MuyzerG

DGGE/TGGE a method for identifying genes from natural ecosystems

Curr Opin Microbiol

(1999)

AdamczykJ. et al.

The isotope array, a new tool that employs substrate-mediated labeling of rRNA for determination of microbial community structure and function

Appl Environ Microbiol

(2003)

AebersoldR. et al.

Mass spectrometry-based proteomics

Nature

(2003)

AmannR.I. et al.

Phylogenetic identification and in situ detection of individual microbial cells without cultivation

Microbiol Rev

(1995)

BaldwinB.R. et al.

Detection and enumeration of aromatic oxygenase genes by multiplex and real-time PCR

Appl Environ Microbiol

(2003)

BartlettD.H.

Microbial adaptations to the psychrosphere/piezosphere

J Mol Microbiol Biotechnol

(1999)

BellerH.R. et al.

A real-time polymerase chain reaction method for monitoring anaerobic, hydrocarbon-degrading bacteria based on a catabolic gene

Environ Sci Technol

(2002)

BesM. et al.

Population diversity of Staphylococcus intermedius isolates from various host species: typing by 16S–23S intergenic ribosomal DNA spacer polymorphism analysis

J Clin Microbiol

(2002)

BourqueS.N. et al.

Comparative analysis of the 16S to 23S Ribosomal intergenic spacer sequences of Bacillus thuringiensis strains and subspecies and of closely related species

Appl Environ Microbiol

(1995)

BrockmanF.J.

Nucleic-acid-based methods for monitoring the performance of in situ bioremediation

Mol Ecol

(1995)

BullI.D. et al.

Detection and classification of atmospheric methane oxidizing bacteria in soil

Nature

(2000)

CastiglioniB. et al.

Development of a universal microarray based on the ligation detection reaction and 16S rrna gene polymorphism to target diversity of cyanobacteria

Appl Environ Microbiol

(2004)

ChandlerD.P. et al.

Suspension array analysis of 16S rRNA from Fe− and SO(4)2− reducing bacteria in uranium-contaminated sediments undergoing bioremediation

Appl Environ Microbiol

(2006)

ChangY.J. et al.

Diversity and characterization of sulfate-reducing bacteria in groundwater at a uranium mill tailings site

Appl Environ Microbiol

(2001)

ChoJ.C. et al.

Quantitative detection of microbial genes by using DNA microarrays

Appl Environ Microbiol

(2002)

ChunJ. et al.

Analysis of 16S–23S rRNA intergenic spacer of Vibrio cholerae and Vibrio mimicus for detection of these species

Methods Mol Biol

(2002)

CollinsG. et al.

Accessing the black box of microbial diversity and ecophysiology: recent advances through polyphasic experiments

J Environ Sci Health A Tox Hazard Subst Environ Eng

(2006)

CummingsD.E. et al.

Diversity of Geobacteraceae species inhabiting metal-polluted freshwater lake sediments ascertained by 16S rDNA analyses

Microb Ecol

(2003)

DaffonchioD. et al.

Nature of polymorphisms in 16S–23S rRNA gene intergenic transcribed spacer fingerprinting of Bacillus and related genera

Appl Environ Microbiol

(2003)

DenaroR. et al.

Assessing terminal restriction fragment length polymorphism suitability for the description of bacterial community structure and dynamics in hydrocarbon-polluted marine environments

Environ Microbiol

(2005)

DenefV.J. et al.

Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities

Environ Microbiol

(2003)

DeRisiJ.L. et al.

Exploring the metabolic and genetic control of gene expression on a genomic scale

Science

(1997)

DumontM.G. et al.

Identification of a complete methane monooxygenase operon from soil by combining stable isotope probing and metagenomic analysis

Environ Microbiol

(2006)

DunbarJ. et al.

Assessment of microbial diversity in four southwestern United States soils by 16S rRNA gene terminal restriction fragment analysis

Appl Environ Microbiol

(2000)

EbieY. et al.

Community analysis of nitrifying bacteria in an advanced and compact Gappei-Johkasou by FISH and PCR-DGGE

Water Sci Technol

(2002)

EdgcombV.P. et al.

Estimation of bacterial cell numbers in humic acid-rich salt marsh sediments with probes directed to 16S ribosomal DNA

Appl Environ Microbiol

(1999)

El FantroussiS. et al.

Direct profiling of environmental microbial populations by thermal dissociation analysis of native rRNAs hybridized to oligonucleotide microarrays

Appl Environ Microbiol

(2003)

El-Latif HeshamA. et al.

Application of PCR-DGGE to analyse the yeast population dynamics in slurry reactors during degradation of polycyclic aromatic hydrocarbons in weathered oil

Yeast

(2006)

Cited by (138)

Revealing the seed microbiome: Navigating sequencing tools, microbial assembly, and functions to amplify plant fitness
2024, Microbiological Research
Microbial communities within seeds play a vital role in transmitting themselves to the next generation of plants. These microorganisms significantly impact seed vigor and early seedling growth, for successful crop establishment. Previous studies reported on seed-associated microbial communities and their influence on processes like dormancy release, germination, and disease protection. Modern sequencing and conventional methods reveal microbial community structures and environmental impacts, these information helps in microbial selection and manipulation. These studies form the foundation for using seed microbiomes to enhance crop resilience and productivity. While existing research has primarily focused on characterizing microbiota in dried mature seeds, a significant gap exists in understanding how these microbial communities assemble during seed development. The review also discusses applying seed-associated microorganisms to improve crops in the context of climate change. However, limited knowledge is available about the microbial assembly pattern on seeds, and their impact on plant growth. The review provides insight into microbial composition, functions, and significance for plant health, particularly regarding growth promotion and pest control.
Recent trends in genomic approaches for microbial bioprospecting
2022, Bioprospecting of Microbial Diversity: Challenges and Applications in Biochemical Industry, Agriculture and Environment Protection
The next-generation sequencing and advanced bioinformatics allow the rapid access and analyses of various microbial genomes that possess hidden treasures in the form of gene clusters. This produces various biologically active novel compounds, evident in the heterologous expression of biosynthetic genes for undetected and potentially valuable natural products. Most of these genes, remain unexpressed in laboratory conditions and must be triggered to get heterologous expression and activated to ensure the production of secondary metabolites in adequate quantities for biological testing and structural elucidation. Bacterial host with genetic tractability remains as the best alternative for heterologous expression. But in various instances, both transcriptional and translational signals in the gene clusters must be replaced. In this case, synthetic biology plays a major role in the re-factoring and re-designing of gene clusters to take control over their functioning which leads to drug discovery by recognizing the microbial genetic potential to synthesize bioactive compounds.
Biofilm interceded microbial prospecting of bioremediation
2022, Bioprospecting of Microbial Diversity: Challenges and Applications in Biochemical Industry, Agriculture and Environment Protection
Biofilm communities have an incredible knack to endure mechanical and noxious chemical perturbations that eradicate their planktonic cell counterparts. The characteristics of biofilm include an extracellular matrix, revolutionize within cellular biochemistry, social exchanges that aid the replacement of metabolites, signal molecules and genetic material connecting cells are shield the microbial cells. Even though biofilms are considered a threat in clinical diagnostics and industrial processes but they have enormous beneficial properties in environmental aspects especially in bioremediation. Biofilm-mediated bioremediation organizations such as biofilters, aerobic and anaerobic granular sludge reactors, and rotating disk contractors are extensively worn systems. Biofilm establishment and protection rely on a composite interface of diverse machinery comprised of bacterial association and accessory mediated by swimming, swarming, and twitching motility, quorum sensing mechanisms, biosurfactant secretion, and the presence of chemotactic responses which includes reactions to inorganic group and xenobiotics that are normally present in ruined aquatic or soil environment through the diverse industrial processes which leads to a predicament situation in the environment. The microbial bioremediation of contaminants is lucrative, trustworthy as well as several strategies are pervasive in industrial use. These processes construct the use of the metabolic activities of biofilm-dwelling microbes which are conscientious for the mainstream of pollutant deprivation in natural environments. Microbes exhibit a positive chemotactic response can swim towards an adsorbed chemical, following biofilm formation; can increase pollutant by surfactant synthesis, further impacting the rate and extent of pollutant degradation or transformation. In the present scenario, bioremediation technologies using the bioaugmentation approach have received significant attention within the scientific commune and remediation industry due to transformed microbes are added to a tainted spot near hasten detoxification and deprivation. Such microbes may exist as a solitary bacterial strain or else a syntropic bacterial association, which are inaccessible from the natural atmosphere or genetically engineered in the laboratory. Bioremediation is documented as a significant tool to refurbish contaminated place, reforest areas, and tarnished ecosystems. This chapter provides an elaborative view on the establishment of biofilm consortia towards remediation of noxious components in the environment.
The use of molecular tools to characterize functional microbial communities in contaminated areas
2022, Microbial Biodegradation and Bioremediation: Techniques and Case Studies for Environmental Pollution
In the modern era of microbial ecology studies, use of high-throughput methods for culture-independent assessment of microbial communities from contaminated sites can pave the way of development of sustainable bioremediation approaches. Numerous culture-independent techniques involving molecular tools can provide a mechanistic understanding of the structure and functions of microbial communities, including their observable changes in contaminated sites. In particular, next-generation sequencing (NGS) approaches have revolutionized assessment of microbial communities across contaminated sites and have provided deeper understanding of their metabolism linked to breakdown of contaminants. Therefore these techniques help toward direct analysis of natural microbial communities and can help toward restoration of contaminated sites. This chapter discusses the application of some of the well-established molecular tools, including NGS toward characterization of microbial communities in contaminated sites.
A review on the enzymes and metabolites identified by mass spectrometry from bacteria and microalgae involved in the degradation of high molecular weight PAHs
2021, Science of the Total Environment
Citation Excerpt :
Metagenomics has emerged as a powerful tool that allows genomic analysis of microbial DNA that is directly extracted from microbial communities of environmental samples (Singh et al., 2017). Metagenomics techniques can be used for monitoring and identifying enzymes, mechanisms, and functions of microorganisms involved in the degradation process of pollutants (Malik et al., 2008; Wéry et al., 2010; Santos-Zavaleta et al., 2011). Metagenomics libraries are processed by cloning DNA fragments extracted from environmental samples in a suitable vector-like plasmid, cosmid, or bacterial artificial chromosome, followed by transformation into a suitable host strain.
High molecular weight PAHs (HMW PAHs) are dangerous pollutants widely distributed in the environment. The use of microorganisms represents an important tool for HMW PAHs bioremediation, so, the understanding of their biochemical pathways facilitates the development of biodegradation strategies. For this reason, the potential role of species of microalgae, bacteria, and microalga-bacteria consortia in the degradation of HMW PAHs is discussed. The identification of their metabolites, mostly by GC–MS and LC-MS, allows a better approach to the enzymes involved in the key steps of the metabolic pathways of HMW PAHs biodegradation. So, this review intends to address the proteomic research on enzyme activities and their involvement in regulating essential biochemical functions that help bacteria and microalgae in the biodegradation processes of HMW PAHs. It is noteworthy that, given that to the best of our knowledge, this is the first review focused on the mass spectrometry identification of the HMW PAHs metabolites; whereby and due to the great concern of the presence of HMW PAHs in the environment, this material could help the urgency of developing new bioremediation methods. The elucidation of the metabolic pathways of persistent pollutant degrading microorganisms should lead to a better knowledge of the enzymes involved, which could contribute to a very ecological route to the control of environmental contamination in the future.
Biochar-amended coastal wetland soil enhances growth of Suaeda salsa and alters rhizosphere soil nutrients and microbial communities
2021, Science of the Total Environment
Citation Excerpt :
The quantity (nmol·g−1 dry soil) of each PLFA was calculated based on the 19:0 internal standard (5 μg·mL−1). The concentration of PLFAs in each sample was used to estimate the biomass of specific microbial groups in soil samples (Malik et al., 2008; Wang et al., 2020a). Before analyses, the data were checked for normality and homogeneity of variance and no data transformation was done.
Biochar has the potential to improve soil properties and increase plant productivity. However, due to the different types of soil, plants, and environmental factors, the impact of biochar is likely to vary. We explored the impacts of biochar prepared from an invasive plant Spartina alterniflora on plant performance and soil characteristics in a simulated coastal wetland ecosystem. We investigated the impact of three application ratios (control, 1%, and 5%; weight ratio) of biochar on the germination and growth of a native plant Suaeda salsa, the nutrient content and microbial community characteristics of the rhizosphere soil under three flooding treatments (no flooding, episodic flooding, and continuous flooding). Biochar application had no impact on seed germination of S. salsa, but promoted its seedling growth (biomass, height, root length) and nitrogen content. Biochar application also enhanced soil nutrient content and affected soil microbial community characteristics. Seed germination and seedling growth of S. salsa were sensitive to flooding and were the best under episodic flooding. Notably, flooding inhibited the impact of biochar on S. salsa and rhizosphere soil. In conclusion, biochar can positively affect the growth of S. salsa and improve the quality of rhizosphere soil, especially under no flooding. Our findings highlight the possibility of applying biochar for the restoration of S. salsa in coastal wetlands.

View all citing articles on Scopus

View full text

Review articleThe use of molecular techniques to characterize the microbial communities in contaminated soil and water

Abstract

Introduction

Section snippets

Phospholipids fatty acids (PLFA)

Polymerase chain reaction (PCR)

Fluorescent in situ hybridization (FISH)

Stable isotope probing (SIP)

Microarray technologies

Conclusion

Res Microbiol

FEMS Microbiol Ecol

J Microbiol Methods

Soil Biol Biochem

J Microbiol Methods

Bioresour Technol

Res Microbiol

Cell

Curr Opin Microbiol

Bioresour Technol

J Microbiol Methods

J Microbiol Methods

J Microbiol Methods

FEMS Microbiol Ecol

Ecotoxicol Environ Saf

J Microbiol Methods

FEMS Microbiol Lett

J Microbiol Methods

Syst Appl Microbiol

Curr Opin Microbiol

Bioresour Technol

FEMS Microbiol Ecol

Curr Opin Microbiol

The isotope array, a new tool that employs substrate-mediated labeling of rRNA for determination of microbial community structure and function

Appl Environ Microbiol

Mass spectrometry-based proteomics

Nature

Phylogenetic identification and in situ detection of individual microbial cells without cultivation

Microbiol Rev

Detection and enumeration of aromatic oxygenase genes by multiplex and real-time PCR

Appl Environ Microbiol

Microbial adaptations to the psychrosphere/piezosphere

J Mol Microbiol Biotechnol

A real-time polymerase chain reaction method for monitoring anaerobic, hydrocarbon-degrading bacteria based on a catabolic gene

Environ Sci Technol

Population diversity of Staphylococcus intermedius isolates from various host species: typing by 16S–23S intergenic ribosomal DNA spacer polymorphism analysis

J Clin Microbiol

Comparative analysis of the 16S to 23S Ribosomal intergenic spacer sequences of Bacillus thuringiensis strains and subspecies and of closely related species

Appl Environ Microbiol

Nucleic-acid-based methods for monitoring the performance of in situ bioremediation

Mol Ecol

Detection and classification of atmospheric methane oxidizing bacteria in soil

Nature

Development of a universal microarray based on the ligation detection reaction and 16S rrna gene polymorphism to target diversity of cyanobacteria

Appl Environ Microbiol

Suspension array analysis of 16S rRNA from Fe− and SO(4)2− reducing bacteria in uranium-contaminated sediments undergoing bioremediation

Appl Environ Microbiol

Diversity and characterization of sulfate-reducing bacteria in groundwater at a uranium mill tailings site

Appl Environ Microbiol

Quantitative detection of microbial genes by using DNA microarrays

Appl Environ Microbiol

Analysis of 16S–23S rRNA intergenic spacer of Vibrio cholerae and Vibrio mimicus for detection of these species

Methods Mol Biol

Accessing the black box of microbial diversity and ecophysiology: recent advances through polyphasic experiments

J Environ Sci Health A Tox Hazard Subst Environ Eng

Diversity of Geobacteraceae species inhabiting metal-polluted freshwater lake sediments ascertained by 16S rDNA analyses

Microb Ecol

Nature of polymorphisms in 16S–23S rRNA gene intergenic transcribed spacer fingerprinting of Bacillus and related genera

Appl Environ Microbiol

Assessing terminal restriction fragment length polymorphism suitability for the description of bacterial community structure and dynamics in hydrocarbon-polluted marine environments

Environ Microbiol

Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities

Environ Microbiol

Exploring the metabolic and genetic control of gene expression on a genomic scale

Science

Identification of a complete methane monooxygenase operon from soil by combining stable isotope probing and metagenomic analysis

Environ Microbiol

Assessment of microbial diversity in four southwestern United States soils by 16S rRNA gene terminal restriction fragment analysis

Appl Environ Microbiol

Community analysis of nitrifying bacteria in an advanced and compact Gappei-Johkasou by FISH and PCR-DGGE

Review article
The use of molecular techniques to characterize the microbial communities in contaminated soil and water