Filter protocols by phylogeny
Asymmetrical flow field-flow fractionation (AF4) is a separation method based on hydrodynamic size of the sample components. It can separate a broad size range of components (~103 to 109 Da; particle diameter from ~1 nm to ~1 μm), but is especially well suited for high molecular weight samples such as virus-sized particles and extracellular vesicles. Separation takes place in an open channel where the flows control sample elution. Separation does not involve stationary phase, allowing gentle separation and good recoveries.
Membrane vesicles (MVs), also described as extracellular vesicles (EVs), exosomes, or outer membrane vesicles (OMVs), are nano-sized (10–300 nm) spherical, membrane-bound structures deriving from the cell envelope. MVs have been studied extensively in both eukaryotic and prokaryotic systems, revealing a plethora of unique functions including cell-to-cell communication and protection of the cell. They are able to encapsulate specific cargos from nucleic acids to proteins, thereby concentrating cargo and providing protection from the extracellular environment.
The labeling and specific detection of nascent DNA by the incorporation of thymidine analogs provide crucial information about DNA replication dynamics without requiring the intracellular expression of fluorescent proteins. After cell fixation and permeabilization, specific detection of thymidine analogs by antibodies can be performed using super-resolution imaging techniques.
Cell adhesion to surfaces and ulterior biofilm formation are critical processes in microbial development since living in biofilms is the preferred way of life within microorganisms. These processes are known to influence not only microorganisms development in the environment, but also their participation in biotechnological processes and have been the focus of intense research that as a matter of fact, was mainly directed to the bacterial domain.
Biofilms are aggregates of cells surrounded by an extracellular matrix providing protection from external stresses. While biofilms are commonly studied in bacteria, archaea also form such cell aggregates both in liquid cultures and on solid surfaces. Biofilm architectures vary when in liquid cultures versus on surfaces as well as when incubated under static conditions versus under shear forces of flowing liquid. Moreover, biofilms develop dynamically over time.
Biofilms are cellular aggregates encased in extracellular polymeric substances and are commonly formed by single-celled eukaryotes, bacteria, and archaea. In addition to attaching to solid surfaces, these cellular aggregates can also be observed floating on or immersed within liquid cultures. While biofilms on surfaces have been studied in some archaea, little is known about liquid biofilms. Surprisingly, immersed liquid biofilms of the model archaeon Haloferax volcanii do not require the same set of machinery needed to form surface-attached biofilms.
Over the past decades there has been a growing interest in the domain of archaea. In this chapter we highlight the recent advances that have been made in studying the cell biology of archaea. We particularly focus on methods for genetic manipulation and imaging of different archaeal species and discuss the technical limitations at the often-extreme growth conditions. Several ongoing developments will help us overcoming these limitations, thereby facilitating future studies in the existing field of archaeal cell biology.
As the majority of biological diversity remains unexplored and uncultured, investigating it requires culture-independent approaches. Archaea in particular suffer from a multitude of issues that make their culturing problematic, from them being frequently members of the rare biosphere, to low growth rates, to them thriving under very specific and often extreme environmental and community conditions that are difficult to replicate.
It has been less than two decades since the study of archaeal ecophysiology has become unshackled from the limitations of cultivation and amplicon sequencing through the advent of metagenomics. As a primer to the guide on producing archaeal genomes from metagenomes, we briefly summarize here how different meta’omics, imaging, and wet lab methods have contributed to progress in understanding the ecophysiology of Archaea.
The manipulation of gene expression levels in vivo is often key to elucidating gene function and regulatory network interactions, especially when it comes to the investigation of essential genes that cannot be deleted from the model organism’s genome. Several techniques have been developed for prokaryotes that allow to interfere with transcription initiation of specific genes by blocking or modifying promoter regions. However, a tool functionally similar to RNAi used in eukaryotes to efficiently degrade mRNA posttranscriptionally did not exist until recently.
Transposon insertion mutagenesis is a forward genetic approach that has been widely utilized for genetic characterization of bacteria and single-celled eukaryotes, and its applications are being rapidly expanded into a few archaeal model organisms for gene function analysis. Previously, we developed a Tn5-based in vivo transposon insertion mutagenesis system in the hyperthermophilic crenarchaeon S. islandicucs M.16.4 and defined the essential gene set under laboratory growth conditions.
Homologous recombination–based gene targeting is a powerful and classic reverse genetics approach to precisely elucidate in vivo gene functions in the organisms across all three domains of life. Gene function studies in Archaea, particularly for those flourishing in inhospitable natural environments that are anaerobic, usually hot, and acidic, have been a great challenge; however, this situation was recently overturned with the increasing availability of genetic manipulation systems in several cultivable archaeal species.
A well-functioning genetic system, which is important for studying gene functions in vivo, requires a transformation method, a vector system and a selection system. Sulfolobus acidocaldarius is a crenarchaeal model organism that grows optimally at 75 °C and a pH of 3. These extreme growth conditions cause some difficulties in developing a genetic system. With continuous efforts, versatile genetic tools have been developed for different species from the order of Sulfolobales.
Methanogenic archaea of the order Methanobacteriales are widespread in anaerobic environments and play pivotal roles in microbial communities. The family of Methanobacteriaceae encompasses mesophilic and thermophilic hydrogenotrophic species. Mesophilic species are found in various natural and anthropogenic environments (e.g., are associated with the microbiome in animals and humans).
Genetic manipulation through markerless exchange enables the modification of several genomic regions without leaving a selection marker in the genome. Here, a method using hpt coding for hypoxanthine phosphoribosyltransferase as a counter selectable marker is described. For Methanosarcina species a chromosomal deletion of the hpt gene is firstly generated, which confers resistance to the purine analogue 8-aza-2,6-diaminopurine (8-ADP).
Archaea inhabit a wide variety of habitats and are well-placed to provide insights into the origins of eukaryotes. In this primer, we examine the available model archaeal genetic systems. We consider the limitations and barriers involved in genetically modifying different archaeal species, the techniques and breakthroughs that have contributed to their tractability, and potential areas for future development.
Many research areas, e.g., basic research but also applied fields of biotechnology, biomedicine, and
diagnostics often suffer from the unavailability of metabolic compounds. This is mostly due to missing
easy and efficient synthesis procedures. We herein describe the biocatalytic/enzymatic production of
2-keto-3-deoxy-D-gluconate, an intermediate of central metabolic pathways in all three domains of life
and also of bacterial polysaccharides, lipopolysaccharides, and cell wall components. The method is based
This protocol describes how to synchronise a S. acidocaldarius cell culture. The first step is to administer acetic acid to arrest the cells in a G2-like state. Once washed, the culture proceeds synchronously through division and DNA replication for about two cell cycles.
Patro, M., van Wolferen, M., Ye, X., Albers, SV., Quax, T.E.F. (2022). Methods to Analyze Motility in Eury- and Crenarchaea. In: Ferreira-Cerca, S. (eds) Archaea. Methods in Molecular Biology, vol 2522. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2445-6_25
Compiled and edited by Dr Mike Dyall-Smith
Sulfolobus acidocaldarius is one of few genetically tractable archaeal species. This protocol outlines how to transform S. acidocaldarius with electroporation.
