Genome size evolution in the Archaea

What determines variation in genome size, gene content and genetic diversity at the broadest scales across the tree of life? Much of the existing work contrasts eukaryotes with prokaryotes, the latter represented mainly by Bacteria. But any general theory of genome evolution must also account for the Archaea, a diverse and ecologically important group of prokaryotes that represent one of the primary domains of cellular life. Here, we survey the extant diversity of Bacteria and Archaea, and ask whether the general principles of genome evolution deduced from the study of Bacteria and eukaryotes also apply to the archaeal domain. Although Bacteria and Archaea share a common prokaryotic genome architecture, the extant diversity of Bacteria appears to be much higher than that of Archaea. Compared with Archaea, Bacteria also show much greater genome-level specialisation to specific ecological niches, including parasitism and endosymbiosis. The reasons for these differences in long-term diversification rates are unclear, but might be related to fundamental differences in informational processing machineries and cell biological features that may favour archaeal diversification in harsher or more energy-limited environments. Finally, phylogenomic analyses suggest that the first Archaea were anaerobic autotrophs that evolved on the early Earth

A microbial role in the construction of Mono Lake carbonate chimneys?

Lacustrine carbonate chimneys are striking, metre‐scale constructions. If these were bioinfluenced constructions, they could be priority targets in the search for early and extraterrestrial microbial life. However, there are questions over whether such chimneys are built on a geobiological framework or are solely abiotic geomorphological features produced by mixing of lake and spring waters. Here, we use correlative microscopy to show that microbes were living around Pleistocene Mono Lake carbonate chimneys during their growth. A plausible interpretation, in line with some recent works by others on other lacustrine carbonates, is that benthic cyanobacteria and their associated extracellular organic material (EOM) formed tubular biofilms around rising sublacustrine spring vent waters, binding calcium ions and trapping and binding detrital silicate sediment. Decay of these biofilms would locally have increased calcium and carbonate ion activity, inducing calcite precipitation on and around the biofilms. Early manganese carbonate mineralisation was directly associated with cell walls, potentially related to microbial activity though the precise mechanism remains to be elucidated. Much of the calcite crystal growth was likely abiotic, and no strong evidence for either authigenic silicate growth or a clay mineral precursor framework was observed. Nevertheless, it seems likely that the biofilms provided initial sites for calcite nucleation and encouraged the primary organised crystal growth. We suggest that the nano‐, micro‐ and macroscale fabrics of these Pleistocene Mono Lake chimneys were affected by the presence of centimetre‐thick tubular and vertically stacked calcifying microbial mats. Such carbonate chimneys represent a promising macroscale target in the exploration for ancient or extraterrestrial life

Data-archive to "Imaging the internal structure of Borelis schlumbergeri Reichel (1937): Advances by high-resolution hard X-ray tomography"

The internal structure of the extant larger benthic foraminifer Borelis schlumbergeri Reichel (1937) (Alveolinidae Ehrenberg, 1839) was investigated by high resolution hard x-ray computer tomography. Scanning was carried out using a single specimen using a Phoenix nanotom m from GE Sensing & Inspection Technologies GmbH. Exposure to hard x-rays was during about 4 hours and 1440 equiangular radiographs were taken along 360°. From the 2108 virtual slices through the stack visualizations of internal microstructures of the calcareous test and sarcode reconstruction were generated after segmentation and rendering in AVIZO7 software from FEI Visualization Sciences Group and using Voxler2 software from Golden Software, LLC. The 2.6 GB set including raw images, derived stacks of AVIZO labels, and video representations illustrating the interior of the Borelis specimen is put on line in form of a zipped archive for further experimentation by the community and for usage in micropaleontological training classes. The archive comprises the original stack of dicom images generated by the nanotom device, a reduced stack of derived AVIZO7 files and labels illustrating the reconstructed inner structures and rendered surfaces, a second reduced data stack of dicom images for loading and experimentation with ImageJ and Voxler2 software, an Excel-sheet containing volume measurements of individual segmented chambers and chamberlets. In addition, several videos (GIF, AVI, MPEG) are provided illustrating the growth of the sarcode body from embryonic stage to adult stage, and showing the shell architecture of the investigated Borelis specimen in animated series of vertical slices. Using the presented data requires access to AVIZO7 and / or Voxler2, which are commercial software. Alternatively, the provided stack of dicom images can also loaded and analyzed using open source Java plugins to ImageJ, which is in the public domain (https://imagej.net/). For visualization image stacks three-dimensionally and for volume rendering the ImageJ 3D Viewer plugin can be applied (http://3dviewer.neurofly.de), and segmentation of inner structures can be done using the Segmentation Editor in ImageJ from Johannes Schindelin, Francois Kusztos and Benjamin Schmid (https://imagej.net/Segmentation_Editor)

Imaging the internal structure of Borelis schlumbergeri Reichel (1937): Advances by high-resolution hard X-ray microtomography

We explored reconstructing the internal structure of an individual of the extant alveolinid larger benthic foraminifer Borelis schlumbergeri Reichel (1937) using high-resolution hard X-ray microtomography (µCT). Chamber segmentation analysis revealed a complex void architecture once filled by the living protoplasm beginning with a subsphaerical embryo (proloculus), surrounded by a streptospiral nepionic structure. It begins with Saturn-ring like, curved tubes perpendicular to each other. In late nepionic stage, they split up into an increasing number of chamberlets. Adult growth begins when streptospiral winding changes to planispiral coiling and the test starts stretching into the typical alveolinid fusiform shape. In the investigated individual the terminal chamber #48 is subdivided in 71 chamberlets. In the terminal stage, chamber volume is reduced and chamber growth becomes irregular. The cell volume increases 7,584-fold from a prolocular size of 13,592 µm 3 to reach a cell volume of 103,077,248 µm 3 , at a length of the protoplasmic body of 1,995 µm. µCT impressively illustrates the adaptive advantage of planispiral fusiform winding for squeezing a giant protoplasmic sheet into a compact and mechanically robust body without losing cellular connection from the interior to its periphery and still allowing endosymbionts to maintain photosynthetical function under high-energy shallow marine environments. The µCT data are compared with historical drawings and plasticine models of early alveolinid growth stages fabricated by micropaleontological pioneer Manfred Reichel in the 1930s, highlighting the unprecedented quality of structural analysis during those early days