Protocols

The Society of Archaeal Biology plays a central role in consolidating efforts to construct a comprehensive informational resource for archaeal research. Our database of protocols is meant to serve as a community-wide repository, offering researchers a platform to access and explore a diverse array of methodological guidelines to advance the understanding of archaeal biology.

We encourage all researchers to contribute by submitting their protocols, fostering collaboration and enriching the collective knowledge base. By sharing expertise and innovative techniques, you'd be directly contributing to the archaeal research community, propelling the field forward, and uncovering the mysteries of these often-overlooked microorganisms.

You can filter the database by phylogeny or by method. As the database grows, we will look to build out a sophisticated search function.

Recent protocols

Reconstruction of Archaeal Genomes from Short-Read Metagenomes

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.

Progress and Challenges in Studying the Ecophysiology of Archaea

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.

Reprogramming CRISPR-Mediated RNA Interference for Silencing of Essential Genes in Sulfolobales

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 in Hyperthermophilic Crenarchaeon Sulfolobus islandicus

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.