Report on ICDP Deep Dust workshops: probing continental climate of the late Paleozoic icehouse–greenhouse transition and beyond

Chamberlin and Salisbury's assessment of the Permian a century ago captured the essence of the period: it is an interval of extremes yet one sufficiently recent to have affected a biosphere with near-modern complexity. The events of the Permian - the orogenic episodes, massive biospheric turnovers, both icehouse and greenhouse antitheses, and Mars-analog lithofacies - boggle the imagination and present us with great opportunities to explore Earth system behavior. The ICDP-funded workshops dubbed "Deep Dust," held in Oklahoma (USA) in March 2019 (67 participants from nine countries) and Paris (France) in January 2020 (33 participants from eight countries), focused on clarifying the scientific drivers and key sites for coring continuous sections of Permian continental (loess, lacustrine, and associated) strata that preserve high-resolution records. Combined, the two workshops hosted a total of 91 participants representing 14 countries, with broad expertise. Discussions at Deep Dust 1.0 (USA) focused on the primary research questions of paleoclimate, paleoenvironments, and paleoecology of icehouse collapse and the run-up to the Great Dying and both the modern and Permian deep microbial biosphere. Auxiliary science topics included tectonics, induced seismicity, geothermal energy, and planetary science. Deep Dust 1.0 also addressed site selection as well as scientific approaches, logistical challenges, and broader impacts and included a mid-workshop field trip to view the Permian of Oklahoma. Deep Dust 2.0 focused specifically on honing the European target. The Anadarko Basin (Oklahoma) and Paris Basin (France) represent the most promising initial targets to capture complete or near-complete stratigraphic coverage through continental successions that serve as reference points for western and eastern equatorial Pangaea. © 2020 Copernicus GmbH. All rights reserved

Metagenomes from High-Temperature Chemotrophic Systems Reveal Geochemical Controls on Microbial Community Structure and Function

The Yellowstone caldera contains the most numerous and diverse geothermal systems on Earth, yielding an extensive array of unique high-temperature environments that host a variety of deeply-rooted and understudied Archaea, Bacteria and Eukarya. The combination of extreme temperature and chemical conditions encountered in geothermal environments often results in considerably less microbial diversity than other terrestrial habitats and offers a tremendous opportunity for studying the structure and function of indigenous microbial communities and for establishing linkages between putative metabolisms and element cycling. Metagenome sequence (14–15,000 Sanger reads per site) was obtained for five high-temperature (>65°C) chemotrophic microbial communities sampled from geothermal springs (or pools) in Yellowstone National Park (YNP) that exhibit a wide range in geochemistry including pH, dissolved sulfide, dissolved oxygen and ferrous iron. Metagenome data revealed significant differences in the predominant phyla associated with each of these geochemical environments. Novel members of the Sulfolobales are dominant in low pH environments, while other Crenarchaeota including distantly-related Thermoproteales and Desulfurococcales populations dominate in suboxic sulfidic sediments. Several novel archaeal groups are well represented in an acidic (pH 3) Fe-oxyhydroxide mat, where a higher O2 influx is accompanied with an increase in archaeal diversity. The presence or absence of genes and pathways important in S oxidation-reduction, H2-oxidation, and aerobic respiration (terminal oxidation) provide insight regarding the metabolic strategies of indigenous organisms present in geothermal systems. Multiple-pathway and protein-specific functional analysis of metagenome sequence data corroborated results from phylogenetic analyses and clearly demonstrate major differences in metabolic potential across sites. The distribution of functional genes involved in electron transport is consistent with the hypothesis that geochemical parameters (e.g., pH, sulfide, Fe, O2) control microbial community structure and function in YNP geothermal springs

Report on ICDP Deep Dust workshops: probing continental climate of the late Paleozoic icehouse–greenhouse transition and beyond

Chamberlin and Salisbury's assessment of the Permian a century ago captured the essence of the period: it is an interval of extremes yet one sufficiently recent to have affected a biosphere with near-modern complexity. The events of the Permian - the orogenic episodes, massive biospheric turnovers, both icehouse and greenhouse antitheses, and Mars-analog lithofacies - boggle the imagination and present us with great opportunities to explore Earth system behavior. The ICDP-funded workshops dubbed "Deep Dust," held in Oklahoma (USA) in March 2019 (67 participants from nine countries) and Paris (France) in January 2020 (33 participants from eight countries), focused on clarifying the scientific drivers and key sites for coring continuous sections of Permian continental (loess, lacustrine, and associated) strata that preserve high-resolution records. Combined, the two workshops hosted a total of 91 participants representing 14 countries, with broad expertise. Discussions at Deep Dust 1.0 (USA) focused on the primary research questions of paleoclimate, paleoenvironments, and paleoecology of icehouse collapse and the run-up to the Great Dying and both the modern and Permian deep microbial biosphere. Auxiliary science topics included tectonics, induced seismicity, geothermal energy, and planetary science. Deep Dust 1.0 also addressed site selection as well as scientific approaches, logistical challenges, and broader impacts and included a mid-workshop field trip to view the Permian of Oklahoma. Deep Dust 2.0 focused specifically on honing the European target. The Anadarko Basin (Oklahoma) and Paris Basin (France) represent the most promising initial targets to capture complete or near-complete stratigraphic coverage through continental successions that serve as reference points for western and eastern equatorial Pangaea.This research has been supported by the ICDP (DeepDust2019 grant).Ye

Metagenome sequence analysis of filamentous microbial communities obtained from geochemically distinct geothermal channels reveals specialization of three aquificales lineages.

The Aquificales are thermophilic microorganisms that inhabit hydrothermal systems worldwide and are considered one of the earliest lineages of the domain Bacteria. We analyzed metagenome sequence obtained from six thermal ‘filamentous streamer’ communities (~40 Mbp per site), which targeted three different groups of Aquificales found in Yellowstone National Park (YNP). Unassembled metagenome sequence and PCR-amplified 16S rRNA gene libraries revealed that acidic, sulfidic sites were dominated by Hydrogenobaculum (Aquificaceae) populations, whereas the circumneutral pH (6.5 - 7.8) sites containing dissolved sulfide were dominated by Sulfurihydrogenibium spp. (Hydrogenothermaceae). Thermocrinis (Aquificaceae) populations were found primarily in the circumneutral sites with undetectable sulfide, and to a lesser extent in one sulfidic system at pH 8. Phylogenetic analysis of assembled sequence containing 16S rRNA genes as well as conserved protein-encoding genes revealed that the composition and function of these communities varied across geochemical conditions. Each Aquificales lineage contained genes for CO2 fixation by the reverse TCA cycle, but only the Sulfurihydrogenibium populations perform citrate cleavage using ATP citrate lyase (Acl). The Aquificaceae populations use an alternative pathway catalyzed by two separate enzymes, citryl CoA synthetase (Ccs) and citryl CoA lyase (Ccl). All three Aquificales lineages contained evidence of aerobic respiration, albeit due to completely different types of heme Cu oxidases (subunit I) involved in oxygen reduction. The distribution of Aquificales populations and differences among functional genes involved in energy generation and electron transport is consistent with the hypothesis that geochemical parameters (e.g., pH, sulfide, H2, O2) have resulted in niche specialization among members of the Aquificales

Diversity in Butane Monooxygenases among Butane-Grown Bacteria

Butane monooxygenases of butane-grown Pseudomonas butanovora, Mycobacterium vaccae JOB5, and an environmental isolate, CF8, were compared at the physiological level. The presence of butane monooxygenases in these bacteria was indicated by the following results. (i) O(2) was required for butane degradation. (ii) 1-Butanol was produced during butane degradation. (iii) Acetylene inhibited both butane oxidation and 1-butanol production. The responses to the known monooxygenase inactivator, ethylene, and inhibitor, allyl thiourea (ATU), discriminated butane degradation among the three bacteria. Ethylene irreversibly inactivated butane oxidation by P. butanovora but not by M. vaccae or CF8. In contrast, butane oxidation by only CF8 was strongly inhibited by ATU. In all three strains of butane-grown bacteria, specific polypeptides were labeled in the presence of [(14)C]acetylene. The [(14)C]acetylene labeling patterns were different among the three bacteria. Exposure of lactate-grown CF8 and P. butanovora and glucose-grown M. vaccae to butane induced butane oxidation activity as well as the specific acetylene-binding polypeptides. Ammonia was oxidized by all three bacteria. P. butanovora oxidized ammonia to hydroxylamine, while CF8 and M. vaccae produced nitrite. All three bacteria oxidized ethylene to ethylene oxide. Methane oxidation was not detected by any of the bacteria. The results indicate the presence of three distinct butane monooxygenases in butane-grown P. butanovora, M. vaccae, and CF8

Microbial Population Dynamics Associated with Crude-Oil Biodegradation in Diverse Soils

Soil bacterial population dynamics were examined in several crude-oil-contaminated soils to identify those organisms associated with alkane degradation and to assess patterns in microbial response across disparate soils. Seven soil types obtained from six geographically distinct areas of the United States (Arizona, Oregon, Indiana, Virginia, Oklahoma, and Montana) were used in controlled contamination experiments containing 2% (wt/wt) crude oil spiked with [1-(14)C]hexadecane. Microbial populations present during hydrocarbon degradation were analyzed using both 16S rRNA gene sequence analysis and by traditional methods for cultivating hydrocarbon-oxidizing bacteria. After a 50-day incubation, all seven soils showed comparable hydrocarbon depletion, where >80% of added crude oil was depleted and approximately 40 to 70% of added [(14)C]hexadecane was converted to (14)CO(2). However, the initial rates of hydrocarbon depletion differed up to 10-fold, and preferential utilization of shorter-chain-length n-alkanes relative to longer-chain-length n-alkanes was observed in some soils. Distinct microbial populations developed, concomitant with crude-oil depletion. Phylogenetically diverse bacterial populations were selected across different soils, many of which were identical to hydrocarbon-degrading isolates obtained from the same systems (e.g., Nocardioides albus, Collimonas sp., and Rhodococcus coprophilus). In several cases, soil type was shown to be an important determinant, defining specific microorganisms responding to hydrocarbon contamination. However, similar Rhodococcus erythropolis-like populations were observed in four of the seven soils and were the most common hydrocarbon-degrading organisms identified via cultivation