Preprints
Filtering by Subject: Microbiology
Opening Doors to Physical Sample Data Discovery, Integration, and Credit
Published: 2024-05-31
Subjects: Biochemistry, Biophysics, and Structural Biology, Earth Sciences, Ecology and Evolutionary Biology, Environmental Sciences, Life Sciences, Microbiology, Physical Sciences and Mathematics, Systems Biology
Physical samples and their associated (meta)data underpin scientific discoveries across disciplines, and can enable new science when appropriately archived. However, there are significant gaps in community practices and infrastructure that currently prevent accurate provenance tracking, reproducibility, and attribution. For the vast majority of samples, descriptive metadata is often sparse, [...]
Forecasting Urban Water Escherichia coli Contamination Using Machine Learning Models
Published: 2024-03-26
Subjects: Microbiology
The state of Indiana ranks first in the nation for water recreation impairments due to contaminated waterways. According to U.S. Environmental Protection Agency, 73% of rivers and streams and 23% of lakes and reservoirs have recreational use impairments like swimming, fishing and boating. Increased density of urban population and agricultural activities are some of the key contributors to run-off [...]
Subsurface microbial community structure shifts along the geological features of the Central American Volcanic Arc
Published: 2024-02-05
Subjects: Biodiversity, Biogeochemistry, Earth Sciences, Environmental Microbiology and Microbial Ecology Life Sciences, Geochemistry, Geology, Microbiology, Volcanology
Subduction of the Cocos and Nazca oceanic plates beneath the Caribbean plate drives the upward movement of deep fluids enriched in carbon, nitrogen, sulfur, and iron along the Central American Volcanic Arc (CAVA). These compounds fuel diverse subsurface microbial communities that in turn alter the distribution, redox state, and isotopic composition of these compounds. Microbial community [...]
Reactive iron as an important reservoir of marine organic carbon over geological timescales
Published: 2023-09-20
Subjects: Biogeochemistry, Earth Sciences, Environmental Microbiology and Microbial Ecology Life Sciences, Microbiology
Reactive iron (FeR) has been suggested to serve as a semi-persistent sink of organic carbon (OC) in surface marine sediments, where approximately 10-20% of total OC (TOC) is associated with FeR (FeR-OC). However, the persistence of FeR-OC on geological timescales remains poorly constrained. Here, we retrieved FeR-OC records in two long sediment cores of the northern South China Sea spanning [...]
Sustainable irrigation reduces arsenic bioavailability in fluvio-alluvial soils promoting microbial responses, high rice productivity and economic profit
Published: 2023-07-26
Subjects: Agricultural Science, Agriculture, Agronomy and Crop Sciences Life Sciences, Biodiversity, Environmental Studies, Microbiology
Minimizing arsenic (74.92As33) loading into rice plants, we suggest adopting alternating wetting and drying (AWD) irrigation as a sustainable water management strategy allowing greater silicon (28.08Si14) availability. This two-year field-based project is the first report on AWD's impact on As-Si distribution in fluvio-alluvial soils of the entire Ganga valley (24 study sites divided into six [...]
Oxidoreductases and metal cofactors in the functioning of Earth
Published: 2023-05-15
Subjects: Biochemistry, Biophysics, and Structural Biology, Biogeochemistry, Biology, Microbiology
Life sustains itself using energy generated by thermodynamic disequilibria, commonly existing as redox disequilibria. Metals are significant players in controlling redox reactions, as they are essential components of the engine that life uses to tap into the thermodynamic disequilibria necessary for metabolism. The number of proteins that evolved to catalyze redox reactions is extraordinary, as [...]
Geosphere and Biosphere coevolution: the role of trace metals availability in the evolution of biogeochemistry
Published: 2022-11-21
Subjects: Biochemistry, Biophysics, and Structural Biology, Biogeochemistry, Earth Sciences, Ecology and Evolutionary Biology, Microbiology, Planetary Sciences
Earth’s geosphere and biosphere have coevolved over time, influencing each other’s stability and keeping our planet habitable for most of its 4.543 billion years of history. Biogeochemical cycles play a key role in controlling this interaction, connecting long-term geological cycles and the much faster evolution of the Earth’s outer biologically dominated envelopes. A small set of [...]
Trait-based modeling revealed higher microbial diversity leads to greater ecological resilience in response to an ecosystem disturbance
Published: 2022-10-15
Subjects: Biogeochemistry, Earth Sciences, Environmental Microbiology and Microbial Ecology Life Sciences, Microbiology, Oceanography, Oil, Gas, and Energy, Physical Sciences and Mathematics, Sustainability, Terrestrial and Aquatic Ecology
To quantitatively understand the ecological resilience of an ecosystem with specialized habitats, we focused on deep-sea microbial communities and simulated the response of diverse microbes in specialized habitats to a pulse ecosystem disturbance - the Deepwater Horizon Oil Spill in the Gulf of Mexico. Two microbial communities with equivalent metabolic libraries were acclimated to the presence [...]
Sampling across large-scale geological gradients to study geosphere-biosphere interactions
Published: 2022-07-25
Subjects: Biogeochemistry, Earth Sciences, Environmental Sciences, Geochemistry, Life Sciences, Microbiology
Despite being one of the largest microbial ecosystems on Earth, with >1029 microbial cells, many basic open questions remain about how life exists and thrives in the deep subsurface biosphere, inside Earth’s crust. Much of this ambiguity is due to the fact that it is exceedingly difficult and (often prohibitively expensive) to directly sample the deep subsurface, requiring elaborate drilling [...]
Description of the continuous nature of organic matter in models of soil carbon dynamics
Published: 2020-05-29
Subjects: Applied Mathematics, Earth Sciences, Environmental Microbiology and Microbial Ecology Life Sciences, Geochemistry, Life Sciences, Microbiology, Physical Sciences and Mathematics, Soil Science
The understanding of soil organic matter (SOM) dynamics has considerably advanced in recent years. It was previously assumed that most SOM consisted of recalcitrant compounds, whereas the emerging view considers SOM as a range of polymers continuously processed into smaller molecules by decomposer enzymes. Mainstreaming these new insights in current models is challenging because of their [...]
Weak influence of paleoenvironmental conditions on the subsurface biosphere of lake Ohrid in the last 515 ka
Published: 2020-04-13
Subjects: Earth Sciences, Environmental Microbiology and Microbial Ecology Life Sciences, Environmental Sciences, Life Sciences, Microbiology, Other Earth Sciences, Paleobiology, Physical Sciences and Mathematics
Understanding the response of geo- and biosystems to past climatic disturbance is primordial to assess the short to long terms effects of current global change. Lacustrine sediments are commonly used to investigate the impact of climatic change on biogeochemical cycling. In these sediments, subsurface microbial communities play a primordial role in nutrient, organic matter and elemental cycling, [...]
Iron mineral dissolution releases iron and associated organic carbon during permafrost thaw
Published: 2020-02-08
Subjects: Environmental Microbiology and Microbial Ecology Life Sciences, Environmental Sciences, Life Sciences, Microbiology, Physical Sciences and Mathematics
It has been shown that reactive soil minerals, specifically iron(III) (oxyhydr)oxides, can trap organic carbon in soils overlying intact permafrost, and may limit carbon mobilization and degradation as it is observed in other environments. However, the use of iron(III)-bearing minerals as terminal electron acceptors in permafrost environments and thus their stability and capacity to prevent [...]
Plate tectonics drive deep biosphere microbial community structure
Published: 2019-10-13
Subjects: Earth Sciences, Environmental Microbiology and Microbial Ecology Life Sciences, Life Sciences, Microbiology, Other Earth Sciences, Physical Sciences and Mathematics
The deep subsurface is one of Earth’s largest biomes. Here, microorganisms modify volatiles moving between the deep and surface Earth. However, it is unknown whether large-scale tectonic processes affect the distribution of microorganisms across this subterranean landscape. We sampled subsurface microbial ecosystems in deeply-sourced springs across the Costa Rican convergent margin. Noble gases, [...]
Possible Tectonic Impact of Biosphere
Published: 2019-09-19
Subjects: Environmental Microbiology and Microbial Ecology Life Sciences, Life Sciences, Microbiology
This paper explores the possibility of existence of ultra-deep biosphere (deeper than 10 km under the surface) and the biogenic earthquake hypothesis -- the idea that subsurface microorganisms might be directly related to earthquake activity. The importance of electroautotrophic type of metabolism is underlined, and the role of telluric currents in this process is explored in some detail, as well [...]
Probing the chemical transformation of seawater-soluble crude oil components during microbial oxidation
Published: 2019-06-18
Subjects: Biogeochemistry, Chemistry, Earth Sciences, Environmental Chemistry, Environmental Sciences, Life Sciences, Microbiology, Oceanography, Oceanography and Atmospheric Sciences and Meteorology, Oil, Gas, and Energy, Physical Sciences and Mathematics
Studies assessing the environmental impacts of oil spills focus primarily on the non-water-soluble components, leaving the fate of the water-soluble fraction (WSF) largely unexplored. We employed untargeted chemical analysis along with biological information to probe the transformation of crude oil WSF in seawater, in the absence of light, in a laboratory experiment. Over a 14-day incubation, [...]