Chapter 4 - Molecular Methods for Studying Microorganisms From Atypical Environments
Publication date: 2018Source: Methods in Microbiology, Volume 45Author(s): Hirak Ranjan Dash, Surajit DasAbstractAdvanced molecular biology tools have unravelled the omnipresence of microbes in environments either in the form of cultivable or uncultivable fractions. However, research on microbial diversity in low biomass environments is still in its nascent stage. Microbial diversity of atypical environments has gained interest due to their adaptive features in extreme habitats, evolutionary and phylogenetic uniqueness, rich functional perspective and the presence of novel enzymes with biotechnological applications. Though...
Source: Methods in Microbiology - October 26, 2018 Category: Microbiology Source Type: research
Chapter 5 - Measuring Microbial Metabolism in Atypical Environments
Publication date: 2018Source: Methods in Microbiology, Volume 45Author(s): Wendy Stone, Gideon WolfaardtAbstractMicrobial metabolism in extreme environments has two defining characteristics: it is slow, and it tends towards the lower measurement thresholds of all current techniques and methodological trends. This provides the crucible of challenge to drive novel techniques, forcing researchers to employ new ideas, as well as reinvent old ideas that have fallen out of favour or become overshadowed by current buzzwords in the field. Some of the techniques that have been creatively harnessed to successfully shed light on the ...
Source: Methods in Microbiology - October 26, 2018 Category: Microbiology Source Type: research
Chapter 6 - Territories of Rock-Inhabiting Fungi: Survival on and Alteration of Solid Air-Exposed Surfaces
Publication date: 2018Source: Methods in Microbiology, Volume 45Author(s): Nicole Knabe, Anna A. GorbushinaAbstractSubaerial biofilms that are omnipresent at the interface between all solid substrates and the atmosphere are composed of a unique and widespread group of ascomycetes called rock-inhabiting fungi or microcolonial fungi (MCF), typically in communities with other microorganisms. While subaerial biofilms in toto have important roles in mineral weathering and biodeterioration of materials, methodological approaches to subaerial biofilm communities are diverse and frequently focussed on MCF. Here, we review the hist...
Source: Methods in Microbiology - October 26, 2018 Category: Microbiology Source Type: research
Chapter 7 - Taxonomy of Oral Bacteria
Publication date: 2018Source: Methods in Microbiology, Volume 45Author(s): Samantha J. Byrne, Catherine A. Butler, Eric C. Reynolds, Stuart G. DashperAbstractThe oral cavity is a collection of diverse microenvironments, each inhabited by a community of microorganisms, the majority of which are bacteria and their phages. Given the appropriate conditions, some of these bacteria can cause destruction of the teeth or their supporting hard and soft tissues. For over 300 years microbiologists have been characterising these microbial communities, in both oral health and disease. In this chapter, we take the reader on a journey th...
Source: Methods in Microbiology - October 26, 2018 Category: Microbiology Source Type: research
Chapter 8 - Aqueous Methods for Extraction/Recovery of Macromolecules From Microorganisms of Atypical Environments: A Focus on Three Phase Partitioning
Publication date: 2018Source: Methods in Microbiology, Volume 45Author(s): Mohammed GagaouaAbstractDownstream processing is a major cost in the production of macromolecules, including proteins and enzymes. Thus, development of efficient and economical downstream processing strategies has become an important area in microbiology, biochemistry and biotechnology. The trend is to develop protocols, which have fewer steps, do not require any preprocessing and have unit processes, which integrate well. This chapter deals with these aspects and explores one of the interesting aqueous separation methods, Three Phase Partitioning (...
Source: Methods in Microbiology - October 26, 2018 Category: Microbiology Source Type: research
Chapter 9 - Microbial Community Composition and Predicted Functional Attributes of Antarctic Lithobionts Using Targeted Next-Generation Sequencing and Bioinformatics Tools
Publication date: 2018Source: Methods in Microbiology, Volume 45Author(s): Hyunmin Koo, Joseph A. Hakim, Casey D. Morrow, Dale T. Andersen, Asim K. BejAbstractThis chapter focuses on the rationale and implementation of a suite of software in the data management, processing, and statistical analysis used towards establishing reliable microbial community compositions, predictive functions, and other useful downstream bioinformatics analyses, using NGS data generated by the Illumina Miseq targeted metagenomics approach. This chapter also emphasizes the importance of using multiple taxonomic databases and software to obtain a ...
Source: Methods in Microbiology - October 26, 2018 Category: Microbiology Source Type: research
Chapter 10 - Methods for Collection and Characterization of Samples From Icy Environments
Publication date: 2018Source: Methods in Microbiology, Volume 45Author(s): Manuel Bedrossian, Jody W. Deming, Jay NadeauAbstractEnvironments where the prevailing temperature is below 0°C include both solid (frozen) substrates, such as glacier ice and permafrost, and liquid environments such as cold springs and cryopegs. Some of these environments have low solute concentrations, whereas others have very high levels of salts and other solutes, with corresponding freezing point depression. Some have high microbial density, while others represent the limits of cell survival. All of these present specific challenges for identi...
Source: Methods in Microbiology - October 26, 2018 Category: Microbiology Source Type: research
Chapter 11 - Cryo-Electron Microscopy of Extremely Halophilic Microbes
Publication date: 2018Source: Methods in Microbiology, Volume 45Author(s): Harold Engelhardt, Daniel BollschweilerAbstractHalophilic and extremely halophilic microorganisms in particular have been a challenge for conventional electron microscopy (EM) as well as for state-of-the-art cryo-EM and cryo-electron tomography (cryo-ET). Conventional preparation techniques such as negative staining of isolated macromolecular complexes and plastic embedding of whole cells for ultrathin sectioning suffer from the problem of eliminating most of the salt without destroying the biological samples. Cryo-EM on the other hand, which is int...
Source: Methods in Microbiology - October 26, 2018 Category: Microbiology Source Type: research
Chapter 12 - Methods to Study Magnetotactic Bacteria and Magnetosomes
Publication date: 2018Source: Methods in Microbiology, Volume 45Author(s): Lei Yan, Weijia XingAbstractMagnetotactic bacteria (MTB) are microorganisms capable of directed migration along geomagnetic field lines due to the presence of magnetosomes (MS) in the cells. Because of the special structures of MS consisting of lipid membranes and crystalline magnetic minerals, MTB have implications for environmental magnetism, development of magnetic materials, and iron biomineralization. Additionally, MS have potential uses for applications in modern biomedicine. Therefore, they have attracted attention from researchers in differe...
Source: Methods in Microbiology - October 26, 2018 Category: Microbiology Source Type: research
Chapter 13 - Molecular Methods to Study Vibrio parahaemolyticus and Vibrio vulnificus From Atypical Environments
Publication date: 2018Source: Methods in Microbiology, Volume 45Author(s): Indrani Karunasagar, Biswajit Maiti, Ballamoole Krishna KumarAbstractVibrio parahaemolyticus and Vibrio vulnificus are autochthonous flora of the aquatic environment. In their natural habitat, they are present in water and in association with aquatic fauna and flora. The human gut is not a natural habitat and therefore when these vibrios are isolated from the stool samples or from human tissue such as wound, blood, etc., they are in an atypical environment. Recent data have shown that the incidence of V. parahaemolyticus and V. vulnificus-associated...
Source: Methods in Microbiology - October 26, 2018 Category: Microbiology Source Type: research
The Study of Microbial Survival in Extraterrestrial Environments Using Low Earth Orbit and Ground-Based Experiments
Publication date: Available online 19 October 2018Source: Methods in MicrobiologyAuthor(s): Karen Olsson-Francis, Nisha K. Ramkissoon, Alex B. Price, David J. Slade, Micheal C. Macey, Victoria K. PearsonAbstractMicroorganisms can be used as model systems for studying the biological responses to extraterrestrial conditions. Understanding how cells degrade under such conditions is important for identifying potential biosignatures for future life detection missions. The facilities used to study such responses are extremely challenging and expensive. Therefore, these studies depend on a combination of ground-based simulation a...
Source: Methods in Microbiology - October 20, 2018 Category: Microbiology Source Type: research
Molecular Methods to Study Vibrio parahaemolyticus and Vibrio vulnificus From Atypical Environments
Publication date: Available online 16 October 2018Source: Methods in MicrobiologyAuthor(s): Indrani Karunasagar, Biswajit Maiti, Ballamoole Krishna KumarAbstractVibrio parahaemolyticus and Vibrio vulnificus are autochthonous flora of the aquatic environment. In their natural habitat, they are present in water and in association with aquatic fauna and flora. The human gut is not a natural habitat and therefore when these vibrios are isolated from the stool samples or from human tissue such as wound, blood, etc., they are in an atypical environment. Recent data have shown that the incidence of V. parahaemolyticus and V. vuln...
Source: Methods in Microbiology - October 17, 2018 Category: Microbiology Source Type: research
Molecular Methods for Studying Microorganisms From Atypical Environments
Publication date: Available online 16 October 2018Source: Methods in MicrobiologyAuthor(s): Hirak Ranjan Dash, Surajit DasAbstractAdvanced molecular biology tools have unravelled the omnipresence of microbes in environments either in the form of cultivable or uncultivable fractions. However, research on microbial diversity in low biomass environments is still in its nascent stage. Microbial diversity of atypical environments has gained interest due to their adaptive features in extreme habitats, evolutionary and phylogenetic uniqueness, rich functional perspective and the presence of novel enzymes with biotechnological app...
Source: Methods in Microbiology - October 17, 2018 Category: Microbiology Source Type: research
Microbial Community Composition and Predicted Functional Attributes of Antarctic Lithobionts Using Targeted Next-Generation Sequencing and Bioinformatics Tools
Publication date: Available online 8 October 2018Source: Methods in MicrobiologyAuthor(s): Hyunmin Koo, Joseph A. Hakim, Casey D. Morrow, Dale T. Andersen, Asim K. BejAbstractThis chapter focuses on the rationale and implementation of a suite of software in the data management, processing, and statistical analysis used towards establishing reliable microbial community compositions, predictive functions, and other useful downstream bioinformatics analyses, using NGS data generated by the Illumina Miseq targeted metagenomics approach. This chapter also emphasizes the importance of using multiple taxonomic databases and softw...
Source: Methods in Microbiology - October 9, 2018 Category: Microbiology Source Type: research
Persistence of Fungi in Atypical, Closed Environments: Cultivation to Omics
Publication date: Available online 25 September 2018Source: Methods in MicrobiologyAuthor(s): Adriana Blachowicz, Kasthuri Venkateswaran, Clay C.C. WangAbstractFilamentous fungi are dual organisms that can be both useful for mankind and threatening to human habitats and health. These omnipresent extremotolerant microorganisms are associated with a range of hostile environments and the human body. Immense adaptability to a variety of conditions enables fungi residing on people to thrive anywhere they go, including man-made closed habitats. One such habitat is the International Space Station (ISS), which is a research platfo...
Source: Methods in Microbiology - October 4, 2018 Category: Microbiology Source Type: research
