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1. Fine-Scale Adaptations to Environmental Variation and Growth Strategies Drive Phyllosphere Methylobacterium Diversity

   https://doi.org/10.1128/mbio.03175-21  

   Leducq, Jean-Baptiste ; Seyer-Lamontagne, Émilie ; Condrain-Morel, Domitille ; Bourret, Geneviève ; Sneddon, David ; Foster, James A. ; Marx, Christopher J. ; Sullivan, Jack M. ; Shapiro, B. Jesse ; Kembel, Steven W. ( February 2022 , mBio)

   Keim, Paul (Ed.)

   ABSTRACT Methylobacterium is a prevalent bacterial genus of the phyllosphere. Despite its ubiquity, little is known about the extent to which its diversity reflects neutral processes like migration and drift, versus environmental filtering of life history strategies and adaptations. In two temperate forests, we investigated how phylogenetic diversity within Methylobacterium is structured by biogeography, seasonality, and growth strategies. Using deep, culture-independent barcoded marker gene sequencing coupled with culture-based approaches, we uncovered a considerable diversity of Methylobacterium in the phyllosphere. We cultured different subsets of Methylobacterium lineages depending upon the temperature of isolation and growth (20°C or 30°C), suggesting long-term adaptation to temperature. To a lesser extent than temperature adaptation, Methylobacterium diversity was also structured across large (>100 km; between forests) and small (<1.2 km; within forests) geographical scales, among host tree species, and was dynamic over seasons. By measuring the growth of 79 isolates during different temperature treatments, we observed contrasting growth performances, with strong lineage- and season-dependent variations in growth strategies. Finally, we documented a progressive replacement of lineages with a high-yield growth strategy typical of cooperative, structured communities in favor of those characterized by rapid growth, resulting in convergence and homogenization of community structure at the end of the growing season. Together, our results show how Methylobacterium is phylogenetically structured into lineages with distinct growth strategies, which helps explain their differential abundance across regions, host tree species, and time. This work paves the way for further investigation of adaptive strategies and traits within a ubiquitous phyllosphere genus. IMPORTANCE Methylobacterium is a bacterial group tied to plants. Despite the ubiquity of methylobacteria and the importance to their hosts, little is known about the processes driving Methylobacterium community dynamics. By combining traditional culture-dependent and -independent (metabarcoding) approaches, we monitored Methylobacterium diversity in two temperate forests over a growing season. On the surface of tree leaves, we discovered remarkably diverse and dynamic Methylobacterium communities over short temporal (from June to October) and spatial (within 1.2 km) scales. Because we cultured different subsets of Methylobacterium diversity depending on the temperature of incubation, we suspected that these dynamics partly reflected climatic adaptation. By culturing strains under laboratory conditions mimicking seasonal variations, we found that diversity and environmental variations were indeed good predictors of Methylobacterium growth performances. Our findings suggest that Methylobacterium community dynamics at the surface of tree leaves results from the succession of strains with contrasting growth strategies in response to environmental variations. 

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2. Recycling and metabolic flexibility dictate life in the lower oceanic crust

   https://doi.org/10.1038/241586-020-2075-5  

   Li, Jiangtao ; Mara, Paraskevi ; Schubotz, Florence ; Sylvan, Jason B. ; Klein, Frieder ; Beaudoin, David ; Wee, Shu Ying ; Dick, Henry J.B. ; Lott, Sarah ; Cox, Rebecca ; et al ( March 2020 , Nature)

   The lithified lower oceanic crust is one of Earth’s last biological frontiers as it is difficult to access. It is challenging for microbiota that live in marine subsurface sediments or igneous basement to obtain sufficient carbon resources and energy to support growth1–3 or to meet basal power requirements4 during periods of resource scarcity. Here we show how limited and unpredictable sources of carbon and energy dictate survival strategies used by low-biomass microbial communities that live 10– 750 m below the seafloor at Atlantis Bank, Indian Ocean, where Earth’s lower crust is exposed at the seafloor. Assays of enzyme activities, lipid biomarkers, marker genes and microscopy indicate heterogeneously distributed and viable biomass with ultralow cell densities (fewer than 2,000 cells per cm3). Expression of genes involved in unexpected heterotrophic processes includes those with a role in the degradation of polyaromatic hydrocarbons, use of polyhydroxyalkanoates as carbon-storage molecules and recycling of amino acids to produce compounds that can participate in redox reactions and energy production. Our study provides insights into how microorganisms in the plutonic crust are able to survive within fractures or porous substrates by coupling sources of energy to organic and inorganic carbon resources that are probably delivered through the circulation of subseafloor fluids or seawater. 

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3. Mariana Convergent Margin and South Chamorro Seamount

   https://doi.org/10.14379/iodp.proc.366.2018  

   Fryer, P. ; Wheat, C.G. ; Williams, T. ( February 2018 , Proceedings of the International Ocean Discovery Program)

   null (Ed.)

   Geologic processes at convergent plate margins control geochemical cycling, seismicity, and deep biosphere activity in subduction zones and suprasubduction zone lithosphere. International Ocean Discovery Program Expedition 366 was designed to address the nature of these processes in the shallow to intermediate depth of the Mariana subduction channel. Although no technology is available to permit direct sampling of the subduction channel of an intraoceanic convergent margin at depths up to 19 km, the Mariana forearc region (between the trench and the active volcanic arc) provides a means to access materials from this zone. Active conduits, resulting from fractures in the forearc, are prompted by along- and across-strike extension that allows slab-derived fluids and materials to ascend to the seafloor along associated faults, resulting in the formation of serpentinite mud volcanoes. Serpentinite mud volcanoes of the Mariana forearc are the largest mud volcanoes on Earth. Their positions adjacent to or atop fault scarps on the forearc are likely related to the regional extension and vertical tectonic deformation in the forearc. Serpentinite mudflows at these volcanoes include serpentinized forearc mantle clasts, crustal and subducted Pacific plate materials, a matrix of serpentinite muds, and deep-sourced formation fluid. Mud volcanism on the Mariana forearc occurs within 100 km of the trench, representing a range of depths and temperatures to the downgoing plate and the subduction channel. These processes have likely been active for tens of millions of years at the Mariana forearc and for billions of years on Earth. At least 19 active serpentinite mud volcanoes have been located in the Mariana forearc. Two of these mud volcanoes are Conical and South Chamorro Seamounts, which are the farthest from the Mariana Trench at 86 and 78 km, respectively. Both seamounts were cored during Ocean Drilling Program Legs 125 and 195, respectively. Data from these two seamounts represent deeper, warmer examples of the continuum of slab-derived materials as the Pacific plate subducts, providing a snapshot of how slab subduction affects fluid release, the composition of ascending fluids, mantle hydration, and the metamorphic paragenesis of subducted oceanic lithosphere. Data from the study of these two mud volcanoes constrain the pressure, temperature, and composition of fluids and materials within the subduction channel at depths of up to 19 km. Understanding such processes is necessary for elucidating factors that control seismicity in convergent margins, tectonic and magma genesis processes in the volcanic arc and backarc areas, fluid and material fluxes, and the nature and variability of environmental conditions that impact subseafloor microbial communities. Expedition 366 focused on data collection from cores recovered from three serpentinite mud volcanoes that define a continuum of subduction-channel processes to compare with results from drilling at the two previously cored serpentinite mud volcanoes and with previously collected gravity, piston, and remotely operated vehicle push cores across the trench-proximal forearc. Three serpentinite mud volcanoes (Yinazao, Fantangisña, and Asùt Tesoro) were chosen at distances 55 to 72 km from the Mariana Trench. Cores were recovered from active sites of eruption on their summit regions and on the flanks where ancient flows are overlain by more recent ones. Recovered materials show the effects of dynamic processes that are active at these sites, bringing a range of materials to the seafloor, including materials from the crust of the Pacific plate, most notably subducted seamounts (even corals). Most of the recovered material consists of serpentinite mud containing lithic clasts, which are derived from the underlying forearc crust and mantle and the subducting Pacific plate. A thin cover of pelagic sediment was recovered at many Expedition 366 sites, and at Site U1498 we cored through distal serpentinite mudflows and into the underlying pelagic sediment and volcanic ash deposits. Recovered serpentinized ultramafic rocks and mudflow matrix materials are largely uniform in major element composition, spanning a limited range in SiO2, MgO, and Fe2O3 compositions. However, variation in trace element composition reflects interstitial water composition, which differs as a function of the temperature and pressure of the underlying subduction channel. Dissolved gases H2, CH4, and C2H6 are highest at the site farthest from the trench, which also has the most active fluid discharge of the Expedition 366 serpentinite mud volcanoes. These dissolved gases and their active discharge from depth likely support active microbial communities, which were the focus of in-depth subsampling and preservation for shore-based analytical and culturing procedures. The effects of fluid discharge were also registered in the porosity and gamma ray attenuation density data indicated by higher than expected values at some of the summit sites. These higher values are consistent with overpressured fluids that slow compaction of serpentinite mud deposits. In contrast, flank sites have significantly greater decreases in porosity with depth, suggesting that processes in addition to compaction are required to achieve the observed data. Thermal measurements reveal higher heat flow values on the flanks (~31 mW/m2) than on the summits (~17 mW/m2) of the seamounts. The new 2G Enterprises superconducting rock magnetometer (liquid helium free) revealed relatively high values of both magnetization and bulk magnetic susceptibility of discrete samples related to ultramafic rocks, particularly dunite. Magnetite, a product of serpentinization, and authigenic carbonates were observed in the mudflow matrix materials. In addition to coring operations, Expedition 366 focused on the deployment and remediation of borehole casings for future observatories and set the framework for in situ experimentation. Borehole work commenced at South Chamorro Seamount, where the original-style CORK was partially removed. Work then continued at each of the three summit sites following coring operations. Cased boreholes with at least three joints of screened casing were deployed, and a plug of cement was placed at the bottom of each hole. Water samples were collected from two of the three boreholes, revealing significant inputs of formation fluids. This suggests that each of the boreholes tapped a hydrologic zone, making these boreholes suitable for experimentation with the future deployment of a CORK-Lite. 

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4. Expedition 366 Preliminary Report: Mariana Convergent Margin and South Chamorro Seamount

   https://doi.org/10.14379/iodp.pr.366.2017  

   Fryer, P. ; Wheat, G. ; Williams, T. ( November 2017 , Preliminary report)

   null (Ed.)

   Geologic processes at convergent plate margins control geochemical cycling, seismicity, and deep biosphere activity in subduction zones and suprasubduction zone lithosphere. International Ocean Discovery Program (IODP) Expedition 366 was designed to address the nature of these processes in the shallow to intermediate depth of the Mariana subduction channel. Although no technology is available to permit direct sampling of the subduction channel of an intraoceanic convergent margin at depths up to 18 km, the Mariana forearc region (between the trench and the active volcanic arc) provides a means to access this zone. Active conduits, resulting from fractures in the forearc, are prompted by along- and across-strike extension that allows slab-derived fluids and materials to ascend to the seafloor along associated faults, resulting in the formation of serpentinite mud volcanoes. Serpentinite mud volcanoes of the Mariana forearc are the largest mud volcanoes on Earth. Their positions adjacent to or atop fault scarps on the forearc are likely related to the regional extension and vertical tectonic deformation in the forearc. Serpentinite mudflows at these volcanoes include serpentinized forearc mantle clasts, crustal and subducted Pacific plate materials, a matrix of serpentinite muds, and deep-sourced formation fluid. Mud volcanism on the Mariana forearc occurs within 100 km of the trench, representing a range of depths and temperatures to the downgoing plate and the subduction channel. These processes have likely been active for tens of millions of years at this site and for billions of years on Earth. At least 10 active serpentinite mud volcanoes have been located in the Mariana forearc. Two of these mud volcanoes are Conical and South Chamorro Seamounts, which are the furthest from the Mariana Trench at 86 and 78 km, respectively. Both seamounts were cored during Ocean Drilling Program (ODP) Legs 125 and 195, respectively. Data from these two seamounts represent deeper, warmer examples of the continuum of slab-derived materials as the Pacific plate subducts, providing a snapshot of how slab subduction affects fluid release, the composition of ascending fluids, mantle hydration, and the metamorphic paragenesis of subducted oceanic lithosphere. Data from the study of these two mud volcanoes constrain the pressure, temperature, and composition of fluids and materials within the subduction channel at depths of about 18 to 19 km. Understanding such processes is necessary for elucidating factors that control seismicity in convergent margins, tectonic and magma genesis processes in the forearc and volcanic arc, fluid and material fluxes, and the nature and variability of environmental conditions that impact subseafloor microbial communities. Expedition 366 centered on data collection from cores recovered from three serpentinite mud volcanoes that define a continuum of subduction-channel processes defined by the two previously cored serpentinite mud volcanoes and the trench. Three serpentinite mud volcanoes (Yinazao, Fantangisña, and Asùt Tesoro) were chosen at distances 55 to 72 km from the Mariana Trench. Cores were recovered from active sites of eruption on their summit regions and on the flanks where ancient flows are overlain by more recent ones. Recovered materials show the effects of dynamic processes that are active at these sites, bringing a range of materials to the seafloor, including materials from the lithosphere of the Pacific plate and from subducted seamounts (including corals). Most of the recovered material consists of serpentinite mud containing lithic clasts, which are derived from the underlying forearc crust and mantle and the subducting Pacific plate. Cores from each of the three seamounts drilled during Expedition 366, as well as those from Legs 125 and 195, include material from the underlying Pacific plate. A thin cover of pelagic sediment was recovered at many Expedition 366 sites, and at Site U1498 we cored through serpentinite flows to the underlying pelagic sediment and volcanic ash deposits. Recovered serpentinites are largely uniform in major element composition, with serpentinized ultramafic rocks and serpentinite muds spanning a limited range in SiO2 , MgO, and Fe2 O3 compositions. However, variation in trace element composition reflects pore fluid composition, which differs as a function of the temperature and pressure of the underlying subduction channel. Dissolved gases H2 , CH4 , and C2 H6 are highest at the site furthest from the trench, which also has the most active fluid discharge of the Expedition 366 serpentinite mud volcanoes. These dissolved gases and their active discharge from depth likely support active microbial communities, which were the focus of in-depth subsampling and preservation for shore-based analytical and culturing procedures. The effects of fluid discharge were also registered in the porosity and GRA density data indicated by higher than expected values at some of the summit sites. These higher values are consistent with overpressured fluids that minimize compaction of serpentinite mud deposits. In contrast, flank sites have significantly greater decreases in porosity with depth, suggesting that processes in addition to compaction are required to achieve the observed data. Thermal measurements reveal higher heat flow values on the flanks (~31 mW/m2) than on the summits (~17 mW/m2) of the seamounts. The new 2G Enterprises superconducting rock magnetometer (liquid helium free) revealed relatively high values of both magnetization and bulk magnetic susceptibility of discrete samples related to ultramafic rocks, particularly in dunite. Magnetite, a product of serpentinization, and authigenic carbonates were observed in the mudflow matrix materials. In addition to coring operations, Expedition 366 focused on the deployment and remediation of borehole casings for future observatories and set the framework for in situ experimentation. Borehole work commenced at South Chamorro Seamount, where the original-style CORK was partially removed. Work then continued at each of the three summit sites following coring operations. Cased boreholes with at least three joints of screened casing were deployed, and a plug of cement was placed at the bottom of each hole. Water samples were collected from two of the three boreholes, revealing significant inputs of formation fluids. This suggests that each of the boreholes tapped a hydrologic zone, making these boreholes suitable for experimentation with the future deployment of a CORK-lite. An active education and outreach program connected with many classrooms on shore and with the general public through social media. 

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5. South China Sea Rifted Margin

   https://doi.org/10.14379/iodp.proc.367368.2018  

   Sun, Z. ; Jian, Z. ; Stock, J.M. ; Larsen, H.C. ; Klaus, A. ; Alvarez Zarikian, C.A. ( September 2018 , Proceedings of the International Ocean Discovery Program)

   null (Ed.)

   The primary objectives of International Ocean Discovery Program (IODP) Expedition 367/368 to the northern South China Sea (SCS) margin were to (1) examine its history of continental breakup and (2) compare it with other nonvolcanic or magma-poor rifted margins with the broader goal of testing models for continental breakup. A secondary objective was to further our understanding of the paleoceanographic and environmental development of the SCS and southeast Asia during the Cenozoic. Four primary sites were selected for the overall program: one in the outer margin high (OMH) and three seaward of the OMH on distinct, margin-parallel basement ridges. These three ridges are informally labeled A, B, and C and are located in the continent–ocean transition (COT) zone ranging from the OMH to the interpreted steady-state oceanic crust (Ridge C) of the SCS. The main scientific objectives include the following: Determining the nature of the basement in crustal units across the COT of the SCS that are critical to constrain style of rifting, Constraining the time interval from initial crustal extension and plate rupture to the initial generation of igneous ocean crust, Constraining vertical crustal movements during breakup, and Examining the nature of igneous activity from rifting to seafloor spreading. In addition, the sediment cores from the drill sites targeting primarily tectonic and basement objectives will provide information on the Cenozoic regional environmental development of the Southeast Asia margin. Site U1499 on Ridge A and Site U1500 on Ridge B were drilled during Expedition 367. Expedition 368 was planned to drill at two primary sites (U1501 and U1503) at the OMH and Ridge C, respectively, but based on drilling results from Expedition 367, Expedition 368 chose to insert an alternate site on Ridge A (Site U1502). In addition, Expedition 368 added two more sites on the OMH (Sites U1504 and U1505). Expedition 367/368 completed operations at six of the seven sites (U1499–U1502, U1504, and U1505). Site U1503, however, was not completed beyond casing without coring to 990 m because of mechanical problems with the drilling equipment that prevented the expedition, after 25 May 2017, from operating with a drill string longer than 3400 m. New alternate Site U1504, proposed during Expedition 367, met this condition. Original Site U1505 also met the operational constraints of the 3400 m drill string (total) and was an alternate site for the already-drilled Site U1501. At Site U1499, we cored to 1081.8 m in 22.1 days with 52% recovery and then logged downhole data from 655 to 1020 m. In 31 days at Site U1500, we penetrated to 1529 m, cored a total of 1012.8 m with 37% recovery, and collected log data from 842 to 1133 m. At Site U1501, we cored to 697.1 m in 9.4 days with 78.5% recovery. We also drilled ahead for 433.5 m in Hole U1501D and then logged downhole data from 78.3 to 399.3 m. In 19.3 days at Site U1502, we penetrated 1679.0 m in Holes U1502A (758 m) and U1502B (921 m), set 723.7 m of casing and cored a total of 576.3 m with 53.5% recovery, and collected downhole log data from 785.3 to 875.3 m and seismic data through the 10¾ inch casing. At Site U1503, we penetrated 995.1 m and set 991.5 m of 10¾ inch casing, but no cores were taken because of a mechanical problem with the drawworks. At Site U1504, we took 40 rotary core barrel (RCB) cores over two holes. The cored interval between both holes was 277.3 m with 26.8% recovery. An 88.2 m interval was drilled in Hole U1504B. At Site U1505, we cored 668.0 m with 101.1% recovery. Logging data was collected from 80.1 to 341.2 m. Operations at this site covered 6.1 days. Except for Sites U1503 and U1505, all sites were drilled to acoustic basement. A total of 6.65 days were lost due to mechanical breakdown or waiting on spare supplies for repair of drilling equipment, but drilling options were severely limited from 25 May to the end of the expedition by the defective drawworks limiting deployment of drill string longer than 3400 m. At Site U1499, coring ~200 m into the interpreted acoustic basement sampled sedimentary rocks, possibly including early Miocene chalks underlain by Oligocene polymict breccias and poorly cemented gravels of unknown age comprising sandstone pebbles and cobbles. Preliminary structural and lithologic analysis suggests that the gravels might be early to late synrift sediment. At Site U1500, the main seismic reflector corresponds to the top of a basalt sequence at ~1379.1 m. We cored 149.90 m into this volcanic package and recovered 114.92 m (77%) of sparsely to moderately plagioclase-phyric basalt comprising numerous lava flows, including pillow lavas with glass, chilled margins, altered veins, hyaloclastites, and minor sediment. Preliminary geochemical analyses indicate that the basalt is tholeiitic. Sampling of the Pleistocene to lower Miocene sedimentary section at Sites U1499 and U1500 was not continuous for two reasons. First, there was extremely poor recovery in substantial intervals interpreted to be poorly lithified sands, possibly turbidites. Second, we chose to drill down without coring in some sections at Site U1500 to ensure sufficient time to achieve this site’s high-priority deep drilling objectives. The upper Miocene basin sequence, which consists of interbedded claystone, siltstone, and sandstone can be correlated between the two sites by seismic stratigraphic mapping and biostratigraphy. At Site U1501 on the OMH, coring ~45 m into the acoustic basement sampled prerift(?) deposits comprising sandstone to conglomerate of presumed Mesozoic age. These deposits are overlain by siliciclastic synrift sediments of Eocene to Oligocene age followed by primarily carbonaceous postrift sediments of early Miocene to Pleistocene age. Site U1502 on Ridge A was cased to 723.7 m. No coring was attempted shallower than 380 m to save operational time and because of low expectations for core recovery in the upper Plio–Pleistocene sequence. At this site, we recovered 180 m of hydrothermally altered brecciated basalts comprising sheet and pillow lavas below deep-marine sediments of Oligocene to late Miocene age. At Site U1503 on Ridge C, 991.5 m of casing was installed in preparation for the planned deep drilling to ~1800 m. No coring was performed due to mechanical failures, and the site was abandoned without further activity except for installation of a reentry cone. Coring at Site U1504 on the OMH, located ~45 km east of Site U1501, recovered mostly foliated, greenschist facies metamorphic rocks below late Eocene(?) carbonate rocks (partly reef debris) and early Miocene to Pleistocene sediments. At Site U1505, we cored to 480.15 m through Pleistocene to late Oligocene mainly carbonaceous ooze followed at depth by early Oligocene siliciclastic sediments. Efforts were made at every drill site to correlate the core with the seismic data and seismic stratigraphic unconformities interpreted in the Eocene to Plio–Pleistocene sedimentary sequence prior to drilling. The predrilling interpretation of ages of these unconformities was in general confirmed by drilling results, although some nontrivial corrections can be expected from detailed postexpedition work on integrating seismic stratigraphic interpretations with detailed bio- and lithostratigraphy. As a result of the limited length of drill string that could be deployed during the later part of Expedition 368, the secondary expedition objectives addressing the environmental history of the SCS and Southeast Asia received more focus than originally planned, allowing Site U1505 (alternate to Site U1501) to be included. Despite this change in focus, Expedition 367/368 provided solid evidence for a process of breakup that included vigorous synrift magmatism as opposed to the often-favored interpretation of the SCS margin as a magma-starved margin or a margin possibly overprinted at a much later stage by plume-related magmatism. In this broader perspective, Expedition 367/368 accomplished a fundamental objective of the two-expedition science program. 

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