Establishment and dynamics of methane-oxidizing microbial communities in marine sediments

Marine sediments are vast sources and reservoirs of methane, a potent greenhouse gas. Most of this methane is anaerobically oxidized by archaea before it can reach the overlying ocean, though the efficiency of this process often depends on methane fluxes and mechanisms of fluid transport. Anaerobic methanotrophic archaea, or ANME, often aggregate with sulfate-reducing bacteria in consortia using sulfate as an electron acceptor, and thus are active at sulfate-methane interfaces of marine sediments. ANME are known to double on the order of months, but have not been isolated in pure culture. Their temporal responses to variation in sulfate supply or methane flux as sediment conditions change are not well understood, but would help constrain estimates of methane emission to the hydrosphere. The focus of this dissertation was to gain an integrated understanding of how ANME, sulfate reducing bacteria, microbial community composition, and rates of methane oxidation change in response to fluctuations in biogeochemical conditions. Using two field studies and one laboratory incubation, we hypothesized that methane influx or addition would increase ANME and sulfate-reducing bacteria populations and abundances as well as methane oxidation rates, but only after lag periods of several months. Samples were collected from Storfjordrenna, offshore Svalbard in the high Arctic, where increases in methane flux inferred from reactive-transport modeling brought methane into shallower sediment horizons. Sediments from this area were also incubated at in situ temperature and pressure for different lengths of time and under different methane concentrations. At the active Venere mud volcano in the Mediterranean, microbial communities from a freshly extruded summit mud breccia flow were analyzed in combination with geochemical data to infer the development of methanotrophy and examine whether deep-sourced fluids hosted unique microbial communities. At Venere mud volcano, methane and sulfate structured microbial communities to a greater extent than deep-sourced fluids, and methanotrophs present in mud flows consisted of aerobic Gammaproteobacteria. These low-biomass fresh mud flows, probably a few years old, are likely too young for active ANME populations to develop. In contrast, at Storfjordrenna, ANME were most abundant near sulfate-methane transitions where methane was moving up the sediment column, suggesting these populations can respond after a year or less of methane intrusion. This methane intrusion fueled a boom in ANME and sulfate-reducing bacteria and decreased community diversity, which reverted after methane influx stopped. Some parallels were also observed in incubations: rates of anaerobic methane oxidation and ANME percent abundances increased with added methane concentrations, but only in a sediment from an active area of seepage and after a few months. These results provide a path forward for understanding the dynamics and capacity of this globally significant microbial subseafloor methane filter, and further the understanding of how microbial community structures and activities are linked

Distinct methane-dependent biogeochemical states in Arctic seafloor gas hydrate mounds

Archaea mediating anaerobic methane oxidation are key in preventing methane produced in marine sediments from reaching the hydrosphere; however, a complete understanding of how microbial communities in natural settings respond to changes in the flux of methane remains largely uncharacterized. We investigate microbial communities in gas hydrate-bearing seafloor mounds at Storfjordrenna, offshore Svalbard in the high Arctic, where we identify distinct methane concentration profiles that include steady-state, recently-increasing subsurface diffusive flux, and active gas seepage. Populations of anaerobic methanotrophs and sulfate-reducing bacteria were highest at the seep site, while decreased community diversity was associated with a recent increase in methane influx. Despite high methane fluxes and methanotroph doubling times estimated at 5–9 months, microbial community responses were largely synchronous with the advancement of methane into shallower sediment horizons. Together, these provide a framework for interpreting subseafloor microbial responses to methane escape in a warming Arctic Ocean

A Network Time Interface M-Module for Distributing GPS-Time over LANs

This paper provides a comprehensive overview of our Network Time Interface (NTI) M-Module, which facilitates high-accuracy time distribution in LAN-based distributed real-time systems. Built around our custom UTCSU VLSI chip, it hosts all the hardware support required for interval-based external clock synchronization: A high-resolution state- and rate-adjustable clock, local accuracy intervals, interfaces to GPS receivers, and various timestamping features. Maximum network controller and CPU independence ensures that the available NTI prototype can be employed in virtually any COTS-based system with MA-Module interface. Our experimental evaluation shows that time distribution with s-accuracy is possible even in Ethernet-based system architectures, provided that the available configuration parameters are suitably chosen to cope with the various hidden sources of timing uncertainty

Soil Microsite Outweighs Cultivar Genotype Contribution to Brassica Rhizobacterial Community Structure

Microorganisms residing on root surfaces play a central role in plant development and performance and may promote growth in agricultural settings. Studies have started to uncover the environmental parameters and host interactions governing their assembly. However, soil microbial communities are extremely diverse and heterogeneous, showing strong variations over short spatial scales. Here, we quantify the relative effect of meter-scale variation in soil bacterial community composition among adjacent field microsites, to better understand how microbial communities vary by host plant genotype as well as soil microsite heterogeneity. We used bacterial 16S rDNA amplicon sequencing to compare rhizosphere communities from four Brassica rapa cultivars grown in three contiguous field plots (blocks) and evaluated the relative contribution of resident soil communities and host genotypes in determining rhizosphere community structure. We characterize concomitant meter-scale variation in bacterial community structure among soils and rhizospheres and show that this block-scale variability surpasses the influence of host genotype in shaping rhizosphere communities. We identified biomarker amplicon sequence variants (ASVs) associated with bulk soil and rhizosphere habitats, each block, and three of four cultivars. Numbers and percent abundances of block-specific biomarkers in rhizosphere communities far surpassed those from bulk soils. These results highlight the importance of fine-scale variation in the pool of colonizing microorganisms during rhizosphere assembly and demonstrate that microsite variation may constitute a confounding effect while testing biotic and abiotic factors governing rhizosphere community structure

Spatiotemporal Heterogeneity and Intragenus Variability in Rhizobacterial Associations with Brassica rapa Growth

Microbial communities in the rhizosphere are distinct from those in soils and are influenced by stochastic and deterministic processes during plant development. These communities contain bacteria capable of promoting growth in host plants through various strategies. While some interactions are characterized in mechanistic detail using model systems, others can be inferred from culture-independent methods, such as 16S amplicon sequencing, using machine learning methods that account for this compositional data type. To characterize assembly processes and identify community members associated with plant growth amid the spatiotemporal variability of the rhizosphere, we grew Brassica rapa in a greenhouse time series with amended and reduced microbial treatments. Inoculation with a native soil community increased plant leaf area throughout the time series by up to 28%. Despite identifying spatially and temporally variable amplicon sequence variants (ASVs) in both treatments, inoculated communities were more highly connected and assembled more deterministically overall. Using a generalized linear modeling approach controlling for spatial variability, we identified 43 unique ASVs that were positively or negatively associated with leaf area, biomass, or growth rates across treatments and time stages. ASVs of the genus Flavobacterium dominated rhizosphere communities and showed some of the strongest positive and negative correlations with plant growth. Members of this genus, and growth-associated ASVs more broadly, exhibited variable connectivity in networks independent of growth association (positive or negative). These findings suggest host-rhizobacterial interactions vary temporally at narrow taxonomic scales and present a framework for identifying rhizobacteria that may work independently or in concert to improve agricultural yields