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1. Microbial colonization and persistence in deep fractured shales is guided by metabolic exchanges and viral predation

   https://doi.org/10.1186/s40168-021-01194-8  

   Amundson, Kaela K. ; Borton, Mikayla A. ; Daly, Rebecca A. ; Hoyt, David W. ; Wong, Allison ; Eder, Elizabeth ; Moore, Joseph ; Wunch, Kenneth ; Wrighton, Kelly C. ; Wilkins, Michael J. ( December 2022 , Microbiome)

   Abstract Background Microbial colonization of subsurface shales following hydraulic fracturing offers the opportunity to study coupled biotic and abiotic factors that impact microbial persistence in engineered deep subsurface ecosystems. Shale formations underly much of the continental USA and display geographically distinct gradients in temperature and salinity. Complementing studies performed in eastern USA shales that contain brine-like fluids, here we coupled metagenomic and metabolomic approaches to develop the first genome-level insights into ecosystem colonization and microbial community interactions in a lower-salinity, but high-temperature western USA shale formation. Results We collected materials used during the hydraulic fracturing process (i.e., chemicals, drill muds) paired with temporal sampling of water produced from three different hydraulically fractured wells in the STACK ( S ooner T rend A nadarko Basin, C anadian and K ingfisher) shale play in OK, USA. Relative to other shale formations, our metagenomic and metabolomic analyses revealed an expanded taxonomic and metabolic diversity of microorganisms that colonize and persist in fractured shales. Importantly, temporal sampling across all three hydraulic fracturing wells traced the degradation of complex polymers from the hydraulic fracturing process to the production and consumption of organic acids that support sulfate- and thiosulfate-reducing bacteria. Furthermore, we identified 5587 viral genomes and linked many of these to the dominant, colonizing microorganisms, demonstrating the key role that viral predation plays in community dynamics within this closed, engineered system. Lastly, top-side audit sampling of different source materials enabled genome-resolved source tracking, revealing the likely sources of many key colonizing and persisting taxa in these ecosystems. Conclusions These findings highlight the importance of resource utilization and resistance to viral predation as key traits that enable specific microbial taxa to persist across fractured shale ecosystems. We also demonstrate the importance of materials used in the hydraulic fracturing process as both a source of persisting shale microorganisms and organic substrates that likely aid in sustaining the microbial community. Moreover, we showed that different physicochemical conditions (i.e., salinity, temperature) can influence the composition and functional potential of persisting microbial communities in shale ecosystems. Together, these results expand our knowledge of microbial life in deep subsurface shales and have important ramifications for management and treatment of microbial biomass in hydraulically fractured wells. 

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2. South Atlantic Transect

   Coggon, R.M. ; Teagle, D.A.H. ; Sylvan, J.B. ; Reece, J. ; Estes, E.R. ; Williams, T.J. ; Christeson, G.L. ( January 2024 , Proceedings of the International Ocean Discovery Program Expedition reports)

   The South Atlantic Transect (SAT) is a multidisciplinary scientific ocean drilling experiment designed to investigate the evolution of the ocean crust and overlying sediments across the western flank of the Mid-Atlantic Ridge. This project comprises four International Ocean Discovery Program expeditions: fully staffed Expeditions 390 and 393 (April–August 2022) built on engineering preparations during Expeditions 390C and 395E (October–December 2020 and April–June 2021, respectively) that took place without science parties during the height of the Coronavirus Disease 2019 (COVID-19) pandemic. Through operations along a crustal flow line at ~31°S, the SAT recovered complete sedimentary sections and the upper ~40–340 m of the underlying ocean crust formed at a slow- to intermediate-spreading rate at the Mid-Atlantic Ridge over the past ~61 My. The sediments along this transect were originally spot cored more than 50 y ago during Deep Sea Drilling Project Leg 3 (December 1968–January 1969) to help verify the theories of seafloor spreading and plate tectonics. The SAT expeditions targeted six primary sites on 7, 15, 31, 49, and 61 Ma ocean crust that fill critical gaps in our sampling of intact in situ ocean crust with regard to crustal age, spreading rate, and sediment thickness. Drilling these sites was required to investigate the history, duration, and intensity of the low-temperature hydrothermal interactions between the aging ocean crust and the evolving South Atlantic Ocean. This knowledge will improve the quantification of past hydrothermal contributions to global biogeochemical cycles and help develop a predictive understanding of the impacts of variable hydrothermal processes and exchanges. Samples from the transect of the previously unexplored sediment- and basalt-hosted deep biosphere beneath the South Atlantic Gyre are essential to refine global biomass estimates and examine microbial ecosystems' responses to variable conditions in a low-energy gyre and aging ocean crust. The transect, located near World Ocean Circulation Experiment Line A10, provides records of carbonate chemistry and deepwater mass properties across the western South Atlantic through key Cenozoic intervals of elevated atmospheric CO2 and rapid climate change. Reconstruction of the history of the deep western boundary current and deepwater formation in the Atlantic basins will yield crucial data to test hypotheses regarding the role of evolving thermohaline circulation patterns in climate change and the effects of tectonic gateways and climate on ocean acidification. During engineering Expeditions 390C and 395E (5 October–5 December 2020 and 6 April–6 June 2021, respectively), a single hole was cored through the sediment cover and into the uppermost rocks of the ocean crust with the advanced piston corer and extended core barrel systems at five of the six primary proposed SAT sites. Reentry systems with casing were then installed either into basement or within 10 m of basement at each of those five sites. Expedition 390 (7 April–7 June 2022) conducted operations at three of the SAT sites, recovering 700 m of core (77% recovery) over 30.3 days of on-site operations. Sediment coring, basement coring, and wireline logging were conducted at two sites on ~61 Ma crust (Sites U1556 and U1557), and sediment coring was completed at the 7 Ma Site U1559. During Expedition 390, more than 1.2 km of sediments was characterized, including 793 m of core collected during Expeditions 390C and 395E at Sites U1556, U1557, and U1559 as well as Expedition 395E Site U1561, which was cored on thinly (<50 m) sedimented ~61 Ma crust. The uppermost ~342 and ~120 m of ~61 Ma ocean crust was cored at Sites U1556 and U1557, respectively. Geophysical wireline logging was achieved at both sites, but the basement hole at Site U1556 was not preserved as a legacy hole because of subsidence of the reentry cone below the seafloor. At Site U1557, the drill bit was deposited on the seafloor prior to downhole logging, leaving Hole U1557D available for future deepening and establishing a legacy borehole for basement hydrothermal and microbiological experiments. Expedition 393 (7 June–7 August 2022) operated at four sites, drilling in 12 holes to complete this initial phase of the SAT. Complete sedimentary sections were collected at Sites U1558, U1583, and U1560 on 49, 31, and 15 Ma crust, respectively, and together with 257.7 m of sediments cored during earlier operations, more than 600 m of sediments was characterized. The uppermost ocean crust was drilled at Sites U1558, U1560, and U1583 with good penetration (~130 to ~204 meters subbasement); however, at the youngest ~7 Ma Site U1559, only ~43 m of basement penetration was achieved in this initial attempt. Geophysical wireline logs were achieved at Sites U1583 and U1560 only. Expeditions 390 and 393 established legacy sites available for future deepening and downhole basement hydrothermal and microbiological experiments at Sites U1557, U1560, and U1559 on 61, 15, and 7 Ma crust, respectively. Highlights of the SAT expeditions include (1) recovering abundant altered glass, hydrothermal veins, complex breccias, and a wide range of alteration halos in the volcanic sequences of the uppermost ocean crust formed at 7–61 Ma, indicating low-temperature hydrothermal processes and exchanges between seawater and basalts across the western flank of the southern Mid-Atlantic Ridge for millions to tens of millions of years; (2) documenting extended redox gradients from both the seafloor and the sediment/basement interface that indicate significant subsurface fluid flow and may support a diversity of microorganisms and metabolisms; and (3) recovering an almost complete stratigraphic record of the Cenozoic (including the Paleocene/Eocene Thermal Maximum and other key climate events) composed of nannofossil oozes with varying amounts of clay indicating the shoaling and deepening of the calcite compensation depth. 

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3. Expedition 390/393 summary

   Coggon, R.M. ; Teagle, D.A.H. ; Sylvan, J.B. ; Reece, J. ; Estes, E.R. ; Williams, T.J. ; Christeson, G.L. ; Aizawa, M. ; Albers, E. ; Amadori, C. ; et al ( January 2024 , Proceedings of the International Ocean Discovery Program Expedition reports)

   The South Atlantic Transect (SAT) is a multidisciplinary scientific ocean drilling experiment designed to investigate the evolution of the ocean crust and overlying sediments across the western flank of the Mid-Atlantic Ridge. This project comprises four International Ocean Discovery Program expeditions: fully staffed Expeditions 390 and 393 (April–August 2022) built on engineering preparations during Expeditions 390C and 395E (October–December 2020 and April–June 2021, respectively) that took place without science parties during the height of the Coronavirus Disease 2019 (COVID-19) pandemic. Through operations along a crustal flow line at ~31°S, the SAT recovered complete sedimentary sections and the upper ~40–340 m of the underlying ocean crust formed at a slow- to intermediate-spreading rate at the Mid-Atlantic Ridge over the past ~61 My. The sediments along this transect were originally spot cored more than 50 y ago during Deep Sea Drilling Project Leg 3 (December 1968–January 1969) to help verify the theories of seafloor spreading and plate tectonics. The SAT expeditions targeted six primary sites on 7, 15, 31, 49, and 61 Ma ocean crust that fill critical gaps in our sampling of intact in situ ocean crust with regard to crustal age, spreading rate, and sediment thickness. Drilling these sites was required to investigate the history, duration, and intensity of the low-temperature hydrothermal interactions between the aging ocean crust and the evolving South Atlantic Ocean. This knowledge will improve the quantification of past hydrothermal contributions to global biogeochemical cycles and help develop a predictive understanding of the impacts of variable hydrothermal processes and exchanges. Samples from the transect of the previously unexplored sediment- and basalt-hosted deep biosphere beneath the South Atlantic Gyre are essential to refine global biomass estimates and examine microbial ecosystems' responses to variable conditions in a low-energy gyre and aging ocean crust. The transect, located near World Ocean Circulation Experiment Line A10, provides records of carbonate chemistry and deepwater mass properties across the western South Atlantic through key Cenozoic intervals of elevated atmospheric CO2 and rapid climate change. Reconstruction of the history of the deep western boundary current and deepwater formation in the Atlantic basins will yield crucial data to test hypotheses regarding the role of evolving thermohaline circulation patterns in climate change and the effects of tectonic gateways and climate on ocean acidification. During engineering Expeditions 390C and 395E (5 October–5 December 2020 and 6 April–6 June 2021, respectively), a single hole was cored through the sediment cover and into the uppermost rocks of the ocean crust with the advanced piston corer and extended core barrel systems at five of the six primary proposed SAT sites. Reentry systems with casing were then installed either into basement or within 10 m of basement at each of those five sites. Expedition 390 (7 April–7 June 2022) conducted operations at three of the SAT sites, recovering 700 m of core (77% recovery) over 30.3 days of on-site operations. Sediment coring, basement coring, and wireline logging were conducted at two sites on ~61 Ma crust (Sites U1556 and U1557), and sediment coring was completed at the 7 Ma Site U1559. During Expedition 390, more than 1.2 km of sediments was characterized, including 793 m of core collected during Expeditions 390C and 395E at Sites U1556, U1557, and U1559 as well as Expedition 395E Site U1561, which was cored on thinly (<50 m) sedimented ~61 Ma crust. The uppermost ~342 and ~120 m of ~61 Ma ocean crust was cored at Sites U1556 and U1557, respectively. Geophysical wireline logging was achieved at both sites, but the basement hole at Site U1556 was not preserved as a legacy hole because of subsidence of the reentry cone below the seafloor. At Site U1557, the drill bit was deposited on the seafloor prior to downhole logging, leaving Hole U1557D available for future deepening and establishing a legacy borehole for basement hydrothermal and microbiological experiments. Expedition 393 (7 June–7 August 2022) operated at four sites, drilling in 12 holes to complete this initial phase of the SAT. Complete sedimentary sections were collected at Sites U1558, U1583, and U1560 on 49, 31, and 15 Ma crust, respectively, and together with 257.7 m of sediments cored during earlier operations, more than 600 m of sediments was characterized. The uppermost ocean crust was drilled at Sites U1558, U1560, and U1583 with good penetration (~130 to ~204 meters subbasement); however, at the youngest ~7 Ma Site U1559, only ~43 m of basement penetration was achieved in this initial attempt. Geophysical wireline logs were achieved at Sites U1583 and U1560 only. Expeditions 390 and 393 established legacy sites available for future deepening and downhole basement hydrothermal and microbiological experiments at Sites U1557, U1560, and U1559 on 61, 15, and 7 Ma crust, respectively. Highlights of the SAT expeditions include (1) recovering abundant altered glass, hydrothermal veins, complex breccias, and a wide range of alteration halos in the volcanic sequences of the uppermost ocean crust formed at 7–61 Ma, indicating low-temperature hydrothermal processes and exchanges between seawater and basalts across the western flank of the southern Mid-Atlantic Ridge for millions to tens of millions of years; (2) documenting extended redox gradients from both the seafloor and the sediment/basement interface that indicate significant subsurface fluid flow and may support a diversity of microorganisms and metabolisms; and (3) recovering an almost complete stratigraphic record of the Cenozoic (including the Paleocene/Eocene Thermal Maximum and other key climate events) composed of nannofossil oozes with varying amounts of clay indicating the shoaling and deepening of the calcite compensation depth. 

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4. Expedition 385 Preliminary Report: Guaymas Basin Tectonics and Biosphere

   https://doi.org/10.14379/iodp.pr.385.2020  

   Teske, A. ; Lizarralde, D. ; Höfig, T.W. ( December 2020 , Preliminary report)

   null (Ed.)

   International Ocean Discovery Program (IODP) Expedition 385 drilled organic-rich sediments with sill intrusions on the flanking regions and in the northern axial graben in Guaymas Basin, a young marginal rift basin in the Gulf of California. Guaymas Basin is characterized by a widely distributed, intense heat flow and widespread off-axis magmatism expressed by a dense network of sill intrusions across the flanking regions, which is in contrast to classical mid-ocean ridge spreading centers. The numerous off-axis sills provide multiple transient heat sources that mobilize buried sedimentary carbon, in part as methane and other hydrocarbons, and drive hydrothermal circulation. The resulting thermal and geochemical gradients shape abundance, composition, and activity of the deep subsurface biosphere of the basin. Drill sites extend over the flanking regions of Guaymas Basin, covering a distance of ~81 km from the from the northwest to the southeast. Adjacent Sites U1545 and U1546 recovered the oldest and thickest sediment successions (to ~540 meters below seafloor [mbsf]; equivalent to the core depth below seafloor, Method A [CSF-A] scale), one with a thin sill (a few meters in thickness) near the drilled bottom (Site U1545), and one with a massive, deeply buried sill (~356–430 mbsf) that chemically and physically affects the surrounding sediments (Site U1546). Sites U1547 and U1548, located in the central part of the northern Guaymas Basin segment, were drilled to investigate a 600 m wide circular mound (bathymetric high) and its periphery. The dome-like structure is outlined by a ring of active vent sites called Ringvent. It is underlain by a remarkably thick sill at shallow depth (Site U1547). Hydrothermal gradients steepen at the Ringvent periphery (Holes U1548A–U1548C), which in turn shifts the zones of authigenic carbonate precipitation and of highest microbial cell abundance toward shallower depths. The Ringvent sill was drilled several times and yielded remarkably diverse igneous rock textures, sediment–sill interfaces, and hydrothermal alteration, reflected by various secondary minerals in veins and vesicles. Thus, the Ringvent sill became the target of an integrated sampling and interdisciplinary research effort that included geological, geochemical, and microbiological specialties. The thermal, lithologic, geochemical, and microbiological contrasts between the two deep northwestern sites (U1545 and U1546) and the Ringvent sites (U1547 and U1548) form the scientific centerpiece of the expedition. These observations are supplemented by results from sites that represent attenuated cold seepage conditions in the central basin (Site U1549), complex and disturbed sediments overlying sills in the northern axial trough (Site U1550), terrigenous sedimentation events on the southeastern flanking regions (Site U1551), and hydrate occurrence in shallow sediments proximal to the Sonora margin (Site U1552). The scientific outcomes of Expedition 385 will (1) revise long-held assumptions about the role of sill emplacement in subsurface carbon mobilization versus carbon retention, (2) comprehensively examine the subsurface biosphere of Guaymas Basin and its responses and adaptations to hydrothermal conditions, (3) redefine hydrothermal controls of authigenic mineral formation in sediments, and (4) yield new insights into many geochemical and geophysical aspects of both architecture and sill–sediment interaction in a nascent spreading center. The generally high quality and high degree of completeness of the shipboard datasets present opportunities for interdisciplinary and multidisciplinary collaborations during shore-based studies. In comparison to Deep Sea Drilling Project Leg 64 to Guaymas Basin in 1979, sophisticated drilling strategies (for example, the advanced piston corer [APC] and half-length APC systems) and numerous analytical innovations have greatly improved sample recovery and scientific yield, particularly in the areas of organic geochemistry and microbiology. For example, microbial genomics did not exist 40 y ago. However, these technical refinements do not change the fact that Expedition 385 will in many respects build on the foundations laid by Leg 64 for understanding Guaymas Basin, regardless of whether adjustments are required in the near future. 

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5. Guaymas Basin Tectonics and Biosphere

   https://doi.org/10.14379/iodp.proc.385.2021  

   Teske, A. ; Lizarralde, D. ; Höfig, T.W. ( September 2021 , Proceedings of the International Ocean Discovery Program)

   null (Ed.)

   International Ocean Discovery Program Expedition 385 drilled organic-rich sediments and intruded sills in the off-axis region and axial graben of the northern spreading segment of Guaymas Basin, a young marginal seafloor spreading system in the Gulf of California. Guaymas Basin is characterized by high heat flow and magmatism in the form of sill intrusions into sediments, which extends tens of kilometers off axis, in contrast with the localized volcanism found at most mid-ocean ridge spreading centers. Sill intrusions provide transient heat sources that mobilize buried sedimentary carbon, in part as methane and other hydrocarbons, and drive hydrothermal circulation. The resulting thermal and geochemical gradients shape abundance, composition, and activity of the deep subsurface biosphere of the basin. Drill sites extend over a broad region of Guaymas Basin. Adjacent Sites U1545 and U1546, located ~52 km northwest of the northern Guaymas Basin axial graben, recovered sediment successions to ~540 meters below seafloor (mbsf) (equivalent to the core depth below seafloor, Method A [CSF-A] scale), including a thin sill (a few meters thick) drilled near the bottom of Site U1545 and a massive sill (~355–430 mbsf) at Site U1546 that chemically and physically affects the surrounding sediments. Sites U1547 and U1548, located ~27 km northwest of the axial graben, were drilled to investigate an active sill-driven hydrothermal system evident at the seafloor as an 800 m wide, circular bathymetric high called Ringvent because of its outline of a ring of active vent sites. Ringvent is underlain by a thick sill at shallow depth (Site U1547). Geothermal gradients steepen toward the Ringvent periphery (Holes U1548A–U1548C), and the zones of authigenic carbonate precipitation and of highest microbial cell abundance correspondingly shallow toward the periphery. The underlying sill was drilled several times and yielded diverse igneous rock textures, sediment/sill interfaces, and alteration minerals in veins and vesicles. The Ringvent sill became the target of an integrated, interdisciplinary sampling and research effort that included geological, geochemical, and microbiological components. The thermal, lithologic, geochemical, and microbiological contrasts between the northwestern sites (U1545 and U1546) and the Ringvent sites (U1547 and U1548) form the core scientific observations informing the direct influence of sill-sediment interaction. These observations are supplemented by results from sites that exhibit persistent influence of thermally equilibrated sill intrusions, including supporting long-lived methane cold seeps, as observed at off-axis Sites U1549 and U1552, and the persistent geochemical record of hydrocarbon formation near the sill/sediment contact, as observed at the northern axial trough Site U1550, which confirms observations from Deep Sea Drilling Project (DSDP) Leg 64. Drilling at Site U1551 ~29 km southeast of the axial graben was not successful due to unstable shallow sands, but it confirmed the dominant influence of gravity-flow sedimentation processes southeast of the axial graben. The scientific outcomes of Expedition 385 will (1) revise long-held assumptions about the role of sill emplacement in subsurface carbon mobilization versus carbon retention, (2) comprehensively examine the subsurface biosphere of Guaymas Basin and its responses and adaptations to hydrothermal conditions, (3) redefine hydrothermal controls on authigenic mineral formation in sediments, and (4) yield new insights into the long term influence of sill-sediment interaction on sediments deposited at the earliest stages of seafloor spreading, that is, when spreading centers are proximal to a continental margin. The generally high quality and high degree of completeness of the shipboard data sets present opportunities for inter- and multidisciplinary collaborations during shore-based studies. In comparison to DSDP Leg 64 to Guaymas Basin in 1979, continuous availability of sophisticated drilling strategies (e.g., the advanced piston corer [APC] and half-length APC systems) and numerous analytical innovations greatly improved sample recovery and scientific yield, particularly in the areas of organic geochemistry and microbiology. For example, microbial metagenomics did not exist 40 y ago. However, these technical refinements do not change the fact that Expedition 385 in many respects builds on the foundations of understanding laid by Leg 64 drilling in Guaymas Basin. 

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