@phdthesis {4862, title = {Microbial life in challenging environments}, volume = {Ph.D.}, year = {2023}, school = {University of Colorado Boulder}, type = {doctoral}, address = {Boulder, CO}, abstract = {

Microorganisms are nearly ubiquitous on Earth, but the identity and function of microbial communities are inherently dependent on the properties of the specific environment in question. Here, I have studied soils around the world to answer questions about how the functional attributes of microorganisms allow them to respond to challenging environmental conditions. First, I explore how microbial communities in soils change across environmental gradients in Antarctica. I show that microbes in Antarctic surface soils are most restricted by low temperatures, low water availability, and high concentrations of salt. Microbial communities near the polar plateau, the most challenging environment, are dominated by Actinobacteria and Chloroflexi, and are enriched in genes associated with the oxidation of hydrogen gas as an energy source. Second, I show that the earliest microbial colonizers of a newly-formed volcanic island in the Kingdom of Tonga are chemolithotrophs that appear to have come from nearby geothermal systems. While many of these microbes utilize sulfur as an energy source, the most abundant organisms have genes that indicate they can oxidize trace gases including carbon monoxide and hydrogen. Finally, I show that organisms associated with carbon limited subsurface soils tend to have smaller genomes, grow more slowly, and have more gene pathways associated with metabolism and the storage of carbon. Taken together, these studies shed light on microbial survival in challenging soil environments and show the varied ways in which microbial communities interact with and are affected by their surroundings.

}, keywords = {LTER-MCM, Antarctica, environmental conditions, microbial ecology, microorganisms, soils, tonga}, url = {https://www.proquest.com/docview/2814734209}, author = {Dragone, Nicholas B.}, editor = {Noah Fierer} } @article {4718, title = {Elevational constraints on the composition and genomic attributes of microbial communities in Antarctic soils}, journal = {mSystems}, volume = {7}, year = {2022}, month = {01/2022}, pages = {e01330-21}, abstract = {

The inland soils found on the Antarctic continent represent one of the more challenging environments for microbial life on Earth. Nevertheless, Antarctic soils harbor unique bacterial and archaeal (prokaryotic) communities able to cope with extremely cold and dry conditions. These communities are not homogeneous, and the taxonomic composition and functional capabilities (genomic attributes) of these communities across environmental gradients remain largely undetermined. We analyzed the prokaryotic communities in soil samples collected from across the Shackleton Glacier region of Antarctica by coupling quantitative PCR, marker gene amplicon sequencing, and shotgun metagenomic sequencing. We found that elevation was the dominant factor explaining differences in the structures of the soil prokaryotic communities, with the drier and saltier soils found at higher elevations harboring less diverse communities and unique assemblages of cooccurring taxa. The higher-elevation soil communities also had lower maximum potential growth rates (as inferred from metagenome-based estimates of codon usage bias) and an overrepresentation of genes associated with trace gas metabolism. Together, these results highlight the utility of assessing community shifts across pronounced environmental gradients to improve our understanding of the microbial diversity found in Antarctic soils and the strategies used by soil microbes to persist at the limits of habitability.

}, keywords = {LTER-MCM, Antarctica, microbial ecology, soil microbiology, soils}, doi = {10.1128/msystems.01330-21}, url = {https://journals.asm.org/doi/full/10.1128/msystems.01330-21}, author = {Dragone, Nicholas B. and Henley, Jessica B. and Holland-Moritz, Hannah and Melisa A. Diaz and Hogg, Ian D. and W. Berry Lyons and Diana H. Wall and Byron Adams and Noah Fierer}, editor = {Mackelprang, Rachel} } @article {4689, title = {Response of Antarctic soil fauna to climate-driven changes since the Last Glacial Maximum}, journal = {Global Change Biology}, volume = {28}, year = {2022}, month = {01/2022}, abstract = {

Understanding how terrestrial biotic communities have responded to glacial recession since the Last Glacial Maximum (LGM) can inform present and future responses of biota to climate change. In Antarctica, the Transantarctic Mountains (TAM) have experienced massive environmental changes associated with glacial retreat since the LGM, yet we have few clues as to how its soil invertebrate-dominated animal communities have responded. Here, we surveyed soil invertebrate fauna from above and below proposed LGM elevations along transects located at 12 features across the Shackleton Glacier region. Our transects captured gradients of surface ages possibly up to 4.5 million years and the soils have been free from human disturbance for their entire history. Our data support the hypothesis that soils exposed during the LGM are now less suitable habitats for invertebrates than those that have been exposed by deglaciation following the LGM. Our results show that faunal abundance, community composition, and diversity were all strongly affected by climate-driven changes since the LGM. Soils more recently exposed by glacial recession (as indicated by distances from present ice surfaces) had higher faunal abundances and species richness than older exposed soils. Higher abundances of the dominant nematode Scottnema were found in older exposed soils, while Eudorylaimus, Plectus, tardigrades, and rotifers preferentially occurred in more recently exposed soils. Approximately 30\% of the soils from which invertebrates could be extracted had only Scottnema, and these single-taxon communities occurred more frequently in soils exposed for longer periods of time. Our structural equation modeling of abiotic drivers highlighted soil salinity as a key mediator of Scottnema responses to soil exposure age. These changes in soil habitat suitability and biotic communities since the LGM indicate that Antarctic terrestrial biodiversity throughout the TAM will be highly altered by climate warming.

}, keywords = {LTER-MCM, biodiversity, climate change, glacial retreat, nematodes, Shackleton Glacier, soil invertebrates}, issn = {1354-1013}, doi = {10.1111/gcb.15940}, url = {https://onlinelibrary.wiley.com/doi/10.1111/gcb.15940}, author = {Franco, Andr{\'e} L. C. and Byron Adams and Melisa A. Diaz and Lemoine, Nathan P. and Dragone, Nicholas B. and Noah Fierer and W. Berry Lyons and Hogg, Ian D. and Diana H. Wall} } @article {4636, title = {Exploring the boundaries of microbial habitability in soil}, journal = {Journal of Geophysical Research: Biogeosciences}, volume = {126}, year = {2021}, month = {06/2021}, abstract = {

Microbes are widely assumed to be capable of colonizing even the most challenging terrestrial surface environments on Earth given enough time. We would not expect to find surface soils uninhabited by microbes as soils typically harbor diverse microbial communities and viable microbes have been detected in soils exposed to even the most inhospitable conditions. However, if uninhabited soils do exist, we might expect to find them in Antarctica. We analyzed 204 ice-free soils collected from across a remote valley in the Transantarctic Mountains (84\–85\°S, 174\–177\°W) and were able to identify a potential limit of microbial habitability. While most of the soils we tested contained diverse microbial communities, with fungi being particularly ubiquitous, microbes could not be detected in many of the driest, higher elevation soils\—results that were confirmed using cultivation-dependent, cultivation-independent, and metabolic assays. While we cannot confirm that this subset of soils is completely sterile and devoid of microbial life, our results suggest that microbial life is severely restricted in the coldest, driest, and saltiest Antarctic soils. Constant exposure to these conditions for thousands of years has limited microbial communities so that their presence and activity is below detectable limits using a variety of standard methods. Such soils are unlikely to be unique to the studied region with this work supporting previous hypotheses that microbial habitability is constrained by near-continuous exposure to cold, dry, and salty conditions, establishing the environmental conditions that limit microbial life in terrestrial surface soils.

}, keywords = {LTER-MCM, Antarctica, astrobiology, bacteria, extremophiles, fungi, soils}, issn = {2169-8953}, doi = {10.1029/2020JG006052}, url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2020JG006052}, author = {Dragone, Nicholas B. and Melisa A. Diaz and Hogg, Ian D. and W. Berry Lyons and W. Andrew Jackson and Diana H. Wall and Adams, Byron J. and Noah Fierer} }