Evolutionary history of conical stromatolites
Nicole Wagner (Georgetown University, US) starts off the talk with an introduction to the stromatolites found in Lake Untersee. Nicole then explains that stromatolites could be the earth’s oldest macroscopic fossils and Conical stromatolites, which are formed in the absence of sedimentation, are considered robust records of biophysical activity.
Then, Nicole details the differences in morphology of the fossilised stromatolites of Western Australia, and the actively growing stromatolites on the benthic surface in Lake Untersee, East Antarctica.
Differences between the microbial communities, their respective interactions, and ecology are hypothesised to be the driving force of the different composition and structure of stromatolites. Nicole notes that the growth mechanisms of stromatolites are not well understood before describing how establishing the differences in the microbial communities of modern conical stromatolites may help elucidate the microbial ecology of ancient stromatolites, which can be used as a modern analogue for growth mechanisms of the older fossilised stromatolites. This, in turn, may help further our understanding of more ancient species.
Methods and workflows
To study the different morphology of stromatolite mats in Lake Untersee, samples from the same location were collected. Specifically, these samples were collected during a dive in the autumn of 2019 in the aerobic basin at a depth of thirteen metres, where it was shallow enough for natural light penetration.
Studying community composition and separating out water from samples is important. Exclusion of exogenous DNA, ensuring that there is no water or eDNA in the samples, was achieved using long-read nanopore sequences. Long nanopore sequencing reads were used to generate metagenome-assembled genomes (MAGS). Rebuilding original stromatolite genomes is important as it leads to discoveries of genomes that would otherwise be unknown and are absent from databases, thereby expanding the database of all known life.
Separation of cells was achieved with gentle lysis. Lysis steps are challenging due to the presence of a sturdy biofilm. Lysis with MetalPolyzyme took 24 hours. The last step before sequencing was DNA purification using a phenol/chloroform method.
The team used the Ligation Sequencing Kit for this work, with sequencing performed for 72 hours. Initial analysis utilised the EPI2ME 16S workflow to establish the microbial communities of samples.
Conical stromatolites are rare and only found in Lake Untersee, while pinnacle mats are known to exist in multiple other locations. Conical stromatolites are cone-shaped and 0.5 metres tall, while pinnacle mats, cuspid in shape, are no taller than 10 cm.
It was hypothesised that the community structure and function of the different stromatolite mats are responsible for the respective morphologies and that this could be confirmed by metagenomic analysis.
FASTQ 16S analysis on EPI2ME allowed for species identification and visualisation with phylogenetic trees, revealing a greater degree of diversity in conical stromatolite phylum compared to pinnacle mats. To test this finding, the relative abundances of the phyla present were examined.
Data normalisation followed by analysis with EPI2ME showed diversity was greatest in conical mats, but the dominant phyla were similar in both types of stromatolites.
Studies have shown that cyanobacteria communities are dominant in stromatolites; however, samples tested in this research showed no visible difference in the abundance of cyanobacteria.
Evaluation of the proteobacteria present revealed that the most dominant phyla present in both samples had surprising similarities at the community level.
While this unexpected degree of similarity did not support the overarching hypothesis that different community structures drive the structure and function of stromatolites, further work is required before it can be ruled out. The following steps to conclude this research include functional analysis, MAGs, metatranscriptomic and metaproteomic analysis.
No in-depth metagenomic study of these mats has been done in the past. Studying stromatolite mats could shed light on forms of life that existed for over two billion years. Additionally, this research provides insights into life in extreme environments and may provide potential astrobiological analogues.