Editorial: Editorial for thematic issue on Archaea

Simulation of Scenarios of a Deep Population Crisis in a Rapidly Growing Population

Abstract-This article focuses on the modeling of crisis and threshold development of the population process during the formation of a new population in a competitive environment. As a population spreads, a deep population crisis may arise as a result an abrupt triggering of biotic countermeasures before resources for a further increase in population size are exhausted. A bottleneck occurred in the history of many populations, including humans at the time of the Neolithic crash in Europe. Invaders with high reproductive potential often exert deleterious effects on biosystems. The emergence of efficient competition can not only cause classical cyclical fluctuations, but also lead to a complete extinction of the population after a series of high peaks in its abundance. Two alternative scenarios provide classical examples of induced population crises. One was observed in Gause's experiments where an introduction of a predatory ciliate drove another ciliate species to extinction. The other scenario was observed in a series of experiments where bacteriophages were introduced into colonies of actively dividing bacteria that had a dynamically adapting antiviral mechanism. In this work, modifications to the model were proposed to describe the actual scenarios of crisis effects in population dynamics. Equations with deviating arguments in the time variable allowed a threshold effect of conditions on reproduction of the invasive species and an aggregated nature of the lagging regulation with two time factors. The computational scenarios described both completion of the process after a repeated outbreak and successful elimination of the population crisis via rapid adaptation. Deep crisis phenomena are characteristic of local population dynamics when organisms interact with viruses that are new to them.

A Single-Molecule View of Archaeal Transcription

The discovery of the archaeal domain of life is tightly connected to an in-depth analysis of the prokaryotic RNA world. In addition to Carl Woese's approach to use the sequence of the 16S rRNA gene as phylogenetic marker, the finding of Karl Stetter and Wolfram Zillig that archaeal RNA polymerases (RNAPs) were nothing like the bacterial RNAP but are more complex enzymes that resemble the eukaryotic RNAPII was one of the key findings supporting the idea that archaea constitute the third major branch on the tree of life. This breakthrough in transcriptional research 40years ago paved the way for in-depth studies of the transcription machinery in archaea. However, although the archaeal RNAP and the basal transcription factors that fine-tune the activity of the RNAP during the transcription cycle are long known, we still lack information concerning the architecture and dynamics of archaeal transcription complexes. In this context, single-molecule measurements were instrumental as they provided crucial insights into the process of transcription initiation, the architecture of the initiation complex and the dynamics of mobile elements of the RNAP. In this review, we discuss single-molecule approaches suitable to examine molecular mechanisms of transcription and highlight findings that shaped our understanding of the archaeal transcription apparatus. We furthermore explore the possibilities and challenges of next-generation single-molecule techniques, for example, super-resolution microscopy and single-molecule tracking, and ask whether these approaches will ultimately allow us to investigate archaeal transcription in vivo.