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Molecular ecology

The microbial deep biosphere at the Chicxulub impact crater

The end-Cretaceous Chicxulub asteroid impact (Yucatan, Mexico) led to the world-wide extinction of non-avian dinosaurs and ~75% of all species on the Earth’s surface, but little is known about how meteorite impacts influenced the ability of the deep microbial biosphere to recover. WA-OIGC participated in the 2016 IODP-ICDP Expedition 364 to study the microbial abundance, diversity, and their predicted activities within the 813 m-long core that was obtained from the peak ring of the Chicxulub impact crater. We are currently investigating to what extent microbial cell abundance, diversity and their role in the cycling of ancient organic matter and minerals is influenced by geological deformations caused by the impact:

(a) To what extent thermophilic microbial life is still supported by the presence of nutritionally diverse substrates and/or elevated fluid flow at impact-induced geological interfaces in the otherwise biologically impoverished granitic rocks, 65 Ma after impact.

(b) To what extent the impact suevite, which was deposited within the first few hours of the Cenozoic, still represents a lithological horizon that did not exist prior to impact and acts as a long-term improvement in deep subsurface colonization potential.

(c) using a combination of molecular ecology and lipid biomarker approaches we are investigating to what extent ancient organic matter and minerals in these horizons as well as in the overlying consolidated Cenozoic marine sediments provide carbon and energy sources to support microbial life that is still present today.

Images of core from the Chicxulub impact crater
Core recovered from the Chicxulub impact crater by IODP-ICDP Expedition 364 (2016). Core images from IODP / ICDP. Stratigraphy adapted from Morgan, J.V., et al., 2016. The formation of peak rings in large impact craters. Science 354, 878-882.

Microbial functional gene expression and community responses to oil exposure in Shark Bay’s microbial mats

Microbial mats occurring in hypersaline environments represent analogues to extinct geobiological formations dating back to 3.5 Ga. We have analysed metabolic properties at the transcriptional level through the sequencing of reverse-transcribed metatranscriptomes to investigate to what extent physiological processes differ between different microbial mat types (smooth vs. pustular) and during diel and seasonal cycles. Processes of interest were protective mechanisms against elevated salinity conditions and to prevent build-up of ammonium produced by nitrate-reducing bacteria, as well as which energy-yielding processes were expressed. In addition we have used microcosm time-series incubations and a combination of microbiology, molecular ecology, and lipid biomarker geochemistry tools to elucidate the short- and long-term effects of petroleum exposure on the diversity and predictive functions of both types of microbial mat microbiomes.

Microbial mats sampled from Shark Bay in April 2017
Microbial mats sampled from Shark Bay in April 2017
Formation of biofilm by microbial mats in microcosm experiments in response to introduced crude oil contamination
Formation of biofilm by microbial mats in microcosm experiments in response to introduced crude oil contamination

Marine microbial community responses to glacial-interglacial climate perturbations

Subseafloor microbial communities are generally thought to be vertically structured based on the availability of in situ growth factors such as electron acceptors and donors. In the emerging field of paleomicrobiology we have shown that a subset of subseafloor microbial communities were seeded from the overlying water column and form a long-term genomic record of the paleodepositional environment. Using paleometagenomic and lipid biomarker environmental proxy data from a well-dated sedimentary record of the Black Sea we have reconstructed microbial communities and processes involved in the sulfur cycle that occurred in the overlying water column during key climate stages spanning the deglacial and Holocene. We furthermore showed that subseafloor archaeal communities in northern Red Sea sediments correlated with sea level- and salinity changes associated with the penultimate glacial maximum (Marine Isotope Stage 6) to the Holocene.

A 1 Ma record of climate-induced vegetation changes using sed aDNA and pollen in a biodiversity hotspot: Lake Towuti, Indonesia

Several studies have shown that ancient plant-derived DNA can be extracted and sequenced from lake sediments and complement the analysis of fossil pollen in reconstructing past vegetation responses to climate variability and anthropogenic perturbations. The majority of such studies have been performed on Holocene lakes located in cooler higher latitude regions whereas similar studies from warm climate tropical lakes are greatly lacking. We have successfully reconstructed vegetation changes from a ~1 Ma sediment record in tropical biodiversity hotspot Lake Towuti (Sulawesi, Indonesia) through parallel pollen and chloroplast sed aDNA analysis. Both pollen and sed aDNA showed significant shifts in vegetation associated with the transition from a swamp to a permanent lake ~1 Ma ago and again 150 kyr later associated with increased volcanic activity and soil fertilisation from phosphorus-rich tephra deposits. While pollen recorded mostly remove tree vegetation, chloroplast sed aDNA mainly recorded catchment vegetation from the main rivers entering the lake based on strong correlations with riverine discharged ultramafic vs. felsic sediments.

Medical geochemistry

Medical Geochemistry is a new area of research in the Earth Science discipline which uses methods and approaches from organic geochemistry and paleogenetic research and applies them to determine the interactions between the environment, geology and human health. In collaboration with Fiona Stanley Hospital, WA-OIGC investigated the role of bacteria in the formation of human gallstones.

Example publications

More, K.D., Wuchter, C., Irigoien, X., Tierney, J.E., Giosan, L., Grice, K., Coolen, M.J.L., 2021. Subseafloor Archaea reflect 139 kyrs of paleodepositional changes in the northern Red Sea. Geobiology 19, 162-172.

Campbell, M.A., Grice, K., Visscher, P.T., Morris, T., Wong, H.L., White, R.A., Burns, B.P., Coolen, M.J.L., 2020. Functional Gene Expression in Shark Bay Hypersaline Microbial Mats: Adaptive Responses. Frontiers in Microbiology 11, 2741.

Schaefer, B., Grice, K., Coolen, M.J.L., Summons, R.E., Cui, X., Bauersachs, T., Schwark, L., Böttcher, M.E., Bralower, T.J., Lyons, S.L., Freeman, K.H., Cockell, C.S., Gulick, S.P.S., Morgan, J.V., Whalen, M.T., Lowery, C.M., Vajda, V., 2020. Microbial life in the nascent Chicxulub crater. Geology 48, 328-332.

Armbrecht, L.H., Coolen, M.J.L., Lejzerowicz, F., George, S.C., Negandhi, K., Suzuki, Y., Young, J., Foster, N.R., Armand, L.K., Cooper, A., Ostrowski, M., Focardi, A., Stat, M., Moreau, J.W., Weyrich, L.S., 2019. Ancient DNA from marine sediments: Precautions and considerations for seafloor coring, sample handling and data generation. Earth-Science Reviews 196, 102887.

More, K.D., Giosan, L., Grice, K., Coolen, M.J.L., 2019. Holocene paleodepositional changes reflected in the sedimentary microbiome of the Black Sea. Geobiology 17, 436-448.

Kose, S.H., Grice, K., Orsi, W.D., Ballal, M., Coolen, M.J.L., 2018. Metagenomics of pigmented and cholesterol gallstones: the putative role of bacteria. Scientific Reports 8, 11218.