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To interpret microbially influenced paleoenvironments in the sedimentary record, it is crucial to understand what processes control the development of microbial mats in modern environments. This article reports results from a multiyear study of Little Ambergris Cay, Turks and Caicos Islands, an uninhabited island floored by broad tracts of well-developed microbial mats on the wind-dominated and wave-dominated Caicos Platform. Uncrewed aerial vehicle-based imaging, differential global positioning system topographic surveys, radiocarbon data, and in situ sedimentological and microbial ecological observations were integrated to identify and quantify the environmental factors that influence the distribution and morphologies of Little Ambergris Cay microbial mats, including their response to large storm events. Based on these data, this study proposes that Little Ambergris Cay initially developed from the accretion and rapid lithification of carbonate sediment delivered by converging wave fronts in the lee of adjacent Big Ambergris Cay. Broad tracts of microbial mats developed during late Holocene time as the interior became restricted due to beach ridge development. Minor elevation differences regulate subaerial exposure time and lead to three categories of microbial mats, differentiated by surface texture and morphology: smooth mats, polygonal mats and blister mats. The surface texture and morphology of the mats is controlled by subaerial exposure time. In addition to elevation, the spatial distribution of mats is largely controlled by hydrodynamics and sediment transport during large storm events. This detailed assessment of the controls on mat formation and preservation at Little Ambergris Cay provides a framework within which to identify and understand the interactions between microbial communities and sediment transport processes in ancient high-energy carbonate depositional systems.

Sulfate-coupled anaerobic oxidation of methane (AOM) is performed by multicellular consortia of anaerobic methanotrophic archaea (ANME) in obligate syntrophic partnership with sulfate-reducing bacteria (SRB). Diverse ANME and SRB clades co-associate but the physiological basis for their adaptation and diversification is not well understood. In this work, we used comparative metagenomics and phylogenetics to investigate the metabolic adaptation among the 4 main syntrophic SRB clades (HotSeep-1, Seep-SRB2, Seep-SRB1a, and Seep-SRB1g) and identified features associated with their syntrophic lifestyle that distinguish them from their non-syntrophic evolutionary neighbors in the phylum Desulfobacterota. We show that the protein complexes involved in direct interspecies electron transfer (DIET) from ANME to the SRB outer membrane are conserved between the syntrophic lineages. In contrast, the proteins involved in electron transfer within the SRB inner membrane differ between clades, indicative of convergent evolution in the adaptation to a syntrophic lifestyle. Our analysis suggests that in most cases, this adaptation likely occurred after the acquisition of the DIET complexes in an ancestral clade and involve horizontal gene transfers within pathways for electron transfer (CbcBA) and biofilm formation (Pel). We also provide evidence for unique adaptations within syntrophic SRB clades, which vary depending on the archaeal partner. Among the most widespread syntrophic SRB, Seep-SRB1a, subclades that specifically partner ANME-2a are missing the cobalamin synthesis pathway, suggestive of nutritional dependency on its partner, while closely related Seep-SRB1a partners of ANME-2c lack nutritional auxotrophies. Our work provides insight into the features associated with DIET-based syntrophy and the adaptation of SRB towards it.

This thesis investigates ecological interactions in the seafloor between microbial taxa (Chapters 1 and 2) and between these microorganisms and their mineral hosts (Chapters 2 through 4). In seafloor sediments, electron acceptors are often limited, forcing microorganisms inhabiting these sediments to acquire symbiotic partners and/or perform extracellular electron transfer to insoluble electron acceptors. Seafloor methane seeps present an endmember case wherein extremely reducing fluids charged with methane advect through sediment. In these benthic ecosystems, anaerobic methanotrophic archaea (ANME) form symbiotic partnerships with sulfate-reducing bacteria (SRB), but it remained unclear if certain ANME exhibit a preference for certain SRB partners. In Chapter 1, I present results documenting such a pattern of partnership specificity in ANME-SRB consortia. In Chapter 2, I further examine these patterns in rare ANME taxa through development and application of a density-separation protocol refined from published work. This protocol exploits the co-association of microbial taxa on mineral surfaces to aid in the detection of novel symbioses, and further is useful to detect microbial interactions with certain minerals. In Chapter 3, I focus on the interaction between ANME-SRB consortia and authigenic silicates that have been observed on consortium exteriors, finding evidence to support that the precipitation of these silicates is actively mediated by ANME-SRB. In Chapter 4, I perform geochemical modeling benchmarked by synchrotron X-ray analysis to examine the imprint of extracellular electron transport by metal-reducing microorganisms on Precambrian manganese-rich sedimentary rocks.

Sulfate-coupled anaerobic oxidation of methane (AOM) is performed by multicellular consortia of anaerobic methanotrophic archaea (ANME) in obligate syntrophic partnership with sulfate-reducing bacteria (SRB). Diverse ANME and SRB clades co-associate but the physiological basis for their adaptation and diversification is not well understood. In this work, we explore the metabolic adaptation of four syntrophic SRB clades (HotSeep-1, Seep-SRB2, Seep-SRB1a and Seep-SRB1g) from a phylogenomics perspective, tracing the evolution of conserved proteins in the syntrophic SRB clades, and comparing the genomes of syntrophic SRB to their nearest evolutionary neighbors in the phylum Desulfobacterota. We note several examples of gain, loss or biochemical adaptation of proteins within pathways involved in extracellular electron transfer, electron transport chain, nutrient sharing, biofilm formation and cell adhesion. We demonstrate that the metabolic adaptations in each of these syntrophic clades are unique, suggesting that they have independently evolved, converging to a syntrophic partnership with ANME. Within the clades we also investigated the specialization of different syntrophic SRB species to partnerships with different ANME clades, using metagenomic sequences obtained from ANME and SRB partners in individual consortia after fluorescent-sorting of cell aggregates from anaerobic sediments. In one instance of metabolic adaptation to different partnerships, we show that Seep-SRB1a partners of ANME-2c appear to lack nutritional auxotrophies, while the related Seep-SRB1a partners of a different methanotrophic archaeal lineage, ANME-2a, are missing the cobalamin synthesis pathway, suggesting that the Seep-SRB1a partners of ANME-2a may have a nutritional dependence on its partner. Together, our paired genomic analysis of AOM consortia highlights the specific adaptation and diversification of syntrophic SRB clades linked to their associated ANME lineages.

Microorganisms in marine subsurface sediments substantially contribute to global biomass.Sediments warmer than 40°C account for roughly half the marine sediment volume, but theprocesses mediated by microbial populations in these hard-to-access environments are poorlyunderstood. We investigated microbial life in up to 1.2-kilometer-deep and up to 120°C hotsediments in the Nankai Trough subduction zone. Above 45°C, concentrations of vegetativecells drop two orders of magnitude and endospores become more than 6000 times more abundantthan vegetative cells. Methane is biologically produced and oxidized until sediments reach 80°to 85°C. In 100° to 120°C sediments, isotopic evidence and increased cell concentrationsdemonstrate the activity of acetate-degrading hyperthermophiles. Above 45°C, populated zonesalternate with zones up to 192 meters thick where microbes were undetectable

X-ray computed tomography (XCT) can be used to identify lithologies and deformation structures within geological core, with the potential for the identification processes to be applied automatically. However, because of drilling disturbance and other artifacts, the use of large XCT-datasets in automated processes requires methods of quality control that can be applied systematically. We propose a new systematic method for quality control of XCT data that applies numerical measures to CT slices, and from this obtains data reflective of core quality. Because the measures are numerical they can be applied quickly and consistently between different sections and cores. This quality control processing protocol produces downhole radiodensity profiles from mean CT-values that can be used for geological interpretation. The application of this quality control protocols was applied to XCT data from International Ocean Discovery Program (IODP) Expedition 370 Site C0023 located at the toe of the Nankai accretionary complex. The evaluation of core quality based on this protocol was found to be a good fit to standard-evaluations based on the visual description of core, and could be used to select samples free from drilling disturbance or contamination. The quality-controlled downhole mean CT-value profile has features that can be used to identify lithologies within a formation, the presence and type of deformation structures and to distinguish formations.

Microbial mats are multi-layered structures built by morphol. and metabolically diverse consortiums of microorganisms. In many mats, the predominant fabric and biovolume of the structures are primarily generated by Cyanobacteria, which carry out photosynthesis at or near the mat surface. Both the mat-building and mat-dwelling communities shape the morphol. and geochem. gradients with depth in the mat. After dioxygen, redox transformations of sulfur fuel mat biogeochem. and provide a useful window into understanding community structure and biogeochem. cycling in the mat. In particular, it has been shown that the top of the zone of sulfide accumulation migrates through the day in response diel light cycles: it lies at a greater depth in the day when dioxygen is produced by photosynthetic Cyanobacteria, and moves towards the surface at night when photosynthesis is no longer active and oxygen accumulation is limited by rates of diffusion through the mat surface. We analyzed sulfur isotope patterns in pore water sulfide in order to understand how different types of microbial communities and environmental conditions influence microbial-driven geochem. reactions in two Cyanobacteria-rich systems:. (1) saline microbial mats lining a shallow lagoon at Little Ambergris Cay, Turks and Caicos Islands, and. (2) benthic microbial mats underlying brackish, low-O_2 waters in Middle Island Sinkhole in Lake Huron, near Alpena, Michigan. We find that diel variations in pore water sulfide sulfur isotope gradients penetrate to depths of up to 8cm below the zone of active photosynthetic activity. This implies that, although photosynthetic activity may play a role in influencing vertical migrations of the top of the zone of sulfide accumulation, other phys., chem. and biol. processes influence sulfur cycling at greater depths. By comparing these two sites, we provide insight into how both environmental conditions and microbial communities shape biogeochem. patterns in microbial mats.

The study investigates the in-situ strength of sediments across a plate boundary décollement using drilling parameters recorded when a 1180-m-deep borehole was established during International Ocean Discovery Program (IODP) Expedition 370, Temperature-Limit of the Deep Biosphere off Muroto (T-Limit). Information of the in-situ strength of the shallow portion in/around a plate boundary fault zone is critical for understanding the development of accretionary prisms and of the décollement itself. Studies using seismic reflection surveys and scientific ocean drillings have recently revealed the existence of high pore pressure zones around frontal accretionary prisms, which may reduce the effective strength of the sediments. A direct measurement of in-situ strength by experiments, however, has not been executed due to the difficulty in estimating in-situ stress conditions. In this study, we derived a depth profile for the in-situ strength of a frontal accretionary prism across a décollement from drilling parameters using the recently established equivalent strength (EST) method. At site C0023, the toe of the accretionary prism area off Cape Muroto, Japan, the EST gradually increases with depth but undergoes a sudden change at ~ 800 mbsf, corresponding to the top of the subducting sediment. At this depth, directly below the décollement zone, the EST decreases from ~ 10 to 2 MPa, with a change in the baseline. This mechanically weak zone in the subducting sediments extends over 250 m (~ 800–1050 mbsf), corresponding to the zone where the fluid influx was discovered, and high-fluid pressure was suggested by previous seismic imaging observations. Although the origin of the fluids or absolute values of the strength remain unclear, our investigations support previous studies suggesting that elevated pore pressure beneath the décollement weakens the subducting sediments. Keywords: Plate boundary décollement, Nankai Trough, Excess fluid pressure, Equivalent strength, Drilling pa, Japan Society for the Promotion of Science (16H04064), Japan Society for the Promotion of Science (15H05717)

International Ocean Discovery Program (IODP) Expedition 370 aimed to explore the limits of life in the deep subseafloor biosphere at a location where temperature increases with depth at an intermediate rate and exceeds the known temperature maximum of microbial life (~120°C) at the sediment/basement interface ~1.2 km below the seafloor. Drilling Site C0023 is located in the vicinity of Ocean Drilling Program (ODP) Sites 808 and 1174 at the protothrust zone in the Nankai Trough off Cape Muroto at a water depth of 4776 m. ODP Leg 190 in 2000, revealed the presence of microbial cells at Site 1174 to a depth of ~600 meters below seafloor (mbsf), which corresponds to an estimated temperature of ~70°C, and reliably identified a single zone of higher cell concentrations just above the décollement at around 800 mbsf, where temperature presumably reached 90°C; no cell count data was reported for other sediment layers in the 70°–120°C range, because the limit of manual cell count for low-biomass samples was not high enough. With the establishment of Site C0023, we aimed to detect and investigate the presence or absence of life and biological processes at the biotic–abiotic transition with unprecedented analytical sensitivity and precision. Expedition 370 was the first expedition dedicated to subseafloor microbiology that achieved time-critical processing and analyses of deep biosphere samples by simultaneous shipboard and shore-based investigations. Our primary objectives during Expedition 370 were to study the relationship between the deep subseafloor biosphere and temperature. We aimed to comprehensively study the factors that control biomass, activity, and diversity of microbial communities in a subseafloor environment where temperatures increase from ~2°C at the seafloor to ~120°C at the sediment/basement interface and thus likely encompasses the biotic–abiotic transition zone. We also aimed to determine geochemical, geophysical, and hydrogeological characteristics in sed