Alkane hydroxylase genes in psychrophile genomes and the potential for cold active catalysis.

BackgroundPsychrophiles are presumed to play a large role in the catabolism of alkanes and other components of crude oil in natural low temperature environments. In this study we analyzed the functional diversity of genes for alkane hydroxylases, the enzymes responsible for converting alkanes to more labile alcohols, as found in the genomes of nineteen psychrophiles for which alkane degradation has not been reported. To identify possible mechanisms of low temperature optimization we compared putative alkane hydroxylases from these psychrophiles with homologues from nineteen taxonomically related mesophilic strains.ResultsSeven of the analyzed psychrophile genomes contained a total of 27 candidate alkane hydroxylase genes, only two of which are currently annotated as alkane hydroxylase. These candidates were mostly related to the AlkB and cytochrome p450 alkane hydroxylases, but several homologues of the LadA and AlmA enzymes, significant for their ability to degrade long-chain alkanes, were also detected. These putative alkane hydroxylases showed significant differences in primary structure from their mesophile homologues, with preferences for specific amino acids and increased flexibility on loops, bends, and α-helices.ConclusionA focused analysis on psychrophile genomes led to discovery of numerous candidate alkane hydroxylase genes not currently annotated as alkane hydroxylase. Gene products show signs of optimization to low temperature, including regions of increased flexibility and amino acid preferences typical of psychrophilic proteins. These findings are consistent with observations of microbial degradation of crude oil in cold environments and identify proteins that can be targeted in rate studies and in the design of molecular tools for low temperature bioremediation

The role of bacteria in the turnover of organic carbon in deep-sea sediments

The cycling of organic carbon in the deep sea was inferred from measurements of sediment trap and box core samples taken on the Biscay and Demerara abyssal plains of the North Atlantic. Of the input of organic carbon to the bottom, less than 10% was buried, i.e., not consumed biologically. Based on laboratory measurements of bacterial activity in the sediment samples, incubated under in situ temperature and pressure, it was possible to attribute at least 13 to 30% of the total inferred biological consumption of organic carbon to microbial utilization. The complementarity of results from these biochemical and microbiological measurements implies that the decompression of cold abyssal samples during retrieval efforts does not prevent meaningful experiments on the microbial inhabitants, once returned to in situ pressure

Unprocessed holographic data of cryopeg fluids viewed at sub-micron resolution from Alaskan Arctic Coast Permafrost Tunnel and landfast sea ice from May 2017

Dataset: Cryopeg Holographic ImagesUnprocessed (raw) holographic data of cryopeg and sea ice brines viewed using a digital holographic microscope at sub-micron resolution. Samples collected from Alaskan Arctic Coast Permafrost Tunnel and landfast sea ice near Utqiagvik in May 2017. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/817454Gordon and Betty Moore Foundation: Marine Microbiology Initiative (MMI) GBMF548

Microbial Morphology and Motility as Biosignatures for Outer Planet Missions

Meaningful motion is an unambiguous biosignature, but because life in the Solar System is most likely to be microbial, the question is whether such motion may be detected effectively on the micrometer scale. Recent results on microbial motility in various Earth environments have provided insight into the physics and biology that determine whether and how microorganisms as small as bacteria and archaea swim, under which conditions, and at which speeds. These discoveries have not yet been reviewed in an astrobiological context. This paper discusses these findings in the context of Earth analog environments and environments expected to be encountered in the outer Solar System, particularly the jovian and saturnian moons. We also review the imaging technologies capable of recording motility of submicrometer-sized organisms and discuss how an instrument would interface with several types of sample-collection strategies

Modeled energetics of bacterial communities in ancient subzero brines

Cryopeg brines are isolated volumes of hypersaline water in subzero permafrost. The cryopeg system at Utqiaġvik, Alaska, is estimated to date back to 40 ka BP or earlier, a remnant of a late Pleistocene Ocean. Surprisingly, the cryopeg brines contain high concentrations of organic carbon, including extracellular polysaccharides, and high densities of bacteria. How can these physiologically extreme, old, and geologically isolated systems support such an ecosystem? This study addresses this question by examining the energetics of the Utqiaġvik cryopeg brine ecosystem. Using literature-derived assumptions and new measurements on archived borehole materials, we first estimated the quantity of organic carbon when the system formed. We then considered two bacterial growth trajectories to calculate the lower and upper bounds of the cell-specific metabolic rate of these communities. These bounds represent the first community estimates of metabolic rate in a subzero hypersaline environment. To assess the plausibility of the different growth trajectories, we developed a model of the organic carbon cycle and applied it to three borehole scenarios. We also used dissolved inorganic carbon and nitrogen measurements to independently estimate the metabolic rate. The model reconstructs the growth trajectory of the microbial community and predicts the present-day cell density and organic carbon content. Model input included measured rates of the in-situ enzymatic conversion of particulate to dissolved organic carbon under subzero brine conditions. A sensitivity analysis of model parameters was performed, revealing an interplay between growth rate, cell-specific metabolic rate, and extracellular enzyme activity. This approach allowed us to identify plausible growth trajectories consistent with the observed bacterial densities in the cryopeg brines. We found that the cell-specific metabolic rate in this system is relatively high compared to marine sediments. We attribute this finding to the need to invest energy in the production of extracellular enzymes, for generating bioavailable carbon from particulate organic carbon, and the production of extracellular polysaccharides for cryoprotection and osmoprotection. These results may be relevant to other isolated systems in the polar regions of Earth and to possible ice-bound brines on worlds such as Europa, Enceladus, and Mars

The Northeast Water polynya as an atmospheric CO2 sink: a seasonal rectification hypothesis

During the multidisciplinary ‘NEW92’ cruise of the United States Coast Guard Cutter (USCGC) Polar Sea to the recurrent Northeast Water (NEW) Polynya (77–81°N, 6–17°W; July–August 1992), total dissolved inorganic carbon and total alkalinity in the water column were measured with high precision to determine the quantitative impact of biological processes on the regional air-sea flux of carbon. Biological processes depleted the total inorganic carbon of summer surface waters by up to 2 mol C m−2 or about 3%. On a regional basis this depletion correlated with depth-integrated values of chlorophyll a, particulate organic carbon, and the inorganic nitrogen deficit. Replacement of this carbon through exchange with the atmosphere was stalled owing to the low wind speeds during the month of the cruise, although model calculations indicate that the depletion could be replenished by a few weeks of strong winds before ice forms in the autumn. These measurements and observations allowed formulation of a new hypothesis whereby seasonally ice-covered regions like the NEW Polynya promote a unique biologically and physically mediated “rectification” of the typical (ice free, low latitude) seasonal cycle of air-sea CO2 flux. The resulting carbon sink is consistent with other productivity estimates and represents an export of biologically cycled carbon either to local sediments or offshore. If this scenario is representative of seasonally ice-covered Arctic shelves, then the rectification process could provide a small, negative feedback to excess atmospheric CO2

Ice and ocean velocity in the Arctic marginal ice zone: Ice roughness and momentum transfer

The interplay between sea ice concentration, sea ice roughness, ocean stratification, and momentum transfer to the ice and ocean is subject to seasonal and decadal variations that are crucial to understanding the present and future air-ice-ocean system in the Arctic. In this study, continuous observations in the Canada Basin from March through December 2014 were used to investigate spatial differences and temporal changes in under-ice roughness and momentum transfer as the ice cover evolved seasonally. Observations of wind, ice, and ocean properties from four clusters of drifting instrument systems were complemented by direct drill-hole measurements and instrumented overhead flights by NASA operation IceBridge in March, as well as satellite remote sensing imagery about the instrument clusters. Spatially, directly estimated ice-ocean drag coefficients varied by a factor of three with rougher ice associated with smaller multi-year ice floe sizes embedded within the first-year-ice/multi-year-ice conglomerate. Temporal differences in the ice-ocean drag coefficient of 20–30% were observed prior to the mixed layer shoaling in summer and were associated with ice concentrations falling below 100%. The ice-ocean drag coefficient parameterization was found to be invalid in September with low ice concentrations and small ice floe sizes. Maximum momentum transfer to the ice occurred for moderate ice concentrations, and transfer to the ocean for the lowest ice concentrations and shallowest stratification. Wind work and ocean work on the ice were the dominant terms in the kinetic energy budget of the ice throughout the melt season, consistent with free drift conditions. Overall, ice topography, ice concentration, and the shallow summer mixed layer all influenced mixed layer currents and the transfer of momentum within the air-ice-ocean system. The observed changes in momentum transfer show that care must be taken to determine appropriate parameterizations of momentum transfer, and imply that the future Arctic system could become increasingly seasonal