Biomedical subjects
Publications and source records attributed to James P Cowen.
Low-temperature hydrothermal fluids, circulating within the vast volume of sediment-buried upper oceanic basement on the flanks of the global mid-ocean ridge system, represent a largely unexplored habitat that could potentially host a significant and unique microbial biosphere. The present state of knowledge and many remaining challenges are discussed.
Particles are often regarded as microniches of enhanced microbial production and activities in the pelagic ocean and are vehicles of vertical material transport from the euphotic zone to the deep sea. Fluorescence in situ hybridization (FISH) can be a useful tool to study the microbial community structures associated with these particles, and thus their ecological significance, yet an appropriate protocol for processing deep-sea particle-rich water samples is lacking. Some sample processing considerations are discussed in the present study, and different combinations of existing procedures for preservation, size fractionation sequential filtration, and sonication were tested in conjunction with FISH. Results from this study show that water samples should be filtered and processed within no more than 10 to 12 h after collection, or else preservation is necessary. The commonly used prefiltration formaldehyde fixation was shown to be inadequate for the rRNA targeted by FISH. However, prefiltration formaldehyde fixation followed by immediate freezing and postfiltration paraformaldehyde fixation yielded highly consistent cell abundance estimates even after 96 days or potentially longer storage. Size fractionation sequential filtration and sonication together enhanced cell abundance estimates by severalfold. Size fractionation sequential filtration effectively separated particle-associated microbial communities from their free-living counterparts, while sonication detached cells from particles or aggregates for more-accurate cell counting using epifluorescence microscopy. Optimization in sonication time is recommended for different specific types of samples. These tested and optimized procedures can be incorporated into a FISH protocol for sampling in deep-sea particle-rich waters.
A pseudohomologous series of branched aliphatic alkanes with a quaternary substituted carbon atom (BAQCs, specifically 2,2-dimethylalkanes and 3,3- and 5,5-diethylalkanes) were identified in warm (65 degrees C) deep-sea hydrothermal waters and Late Cretaceous black shales. 5,5-Diethylalkanes were also observed in modern and Holocene marine shelf sediments and in shales spanning the last 800 million years of the geological record. The carbon number distribution of BAQCs indicates a biological origin. These compounds were observed but not identified in previous studies of 2.0 billion- to 2.2 billion-year-old metasediments and were commonly misidentified in other sediment samples, indicating that BAQCs are widespread in the geological record. The source organisms of BAQCs are unknown, but their paleobiogeographic distribution suggests that they have an affinity for sulfides and might be nonphotosynthetic sulfide oxidizers.
Little is known about the potential for life in the vast, low-temperature (<100 degrees C) reservoir of fluids within mid-ocean ridge flank and ocean basin crust. Recently, an overpressured 300-meter-deep borehole was fitted with an experimental seal (CORK) delivering crustal fluids to the sea floor for discrete and large-volume sampling and characterization. Results demonstrate that the 65 degrees C fluids from 3.5-million-year-old ocean crust support microbial growth. Ribosomal RNA gene sequence data indicate the presence of diverse Bacteria and Archaea, including gene clones of varying degrees of relatedness to known nitrate reducers (with ammonia production), thermophilic sulfate reducers, and thermophilic fermentative heterotrophs, all consistent with fluid chemistry.