The primary focus of the microbiological studies at Site 1249 was the relationship of sedimentary microbial communities to methane hydrates. At the summit of Hydrate Ridge, the methane flux overwhelms the sulfate flux; sulfate was nonexistent in the upper sediments (see "Carbon Cycling" in "Interstitial Water Geochemistry"), and methane hydrates were present in the "mudline" cores. Because methane was present up to the seafloor (see "Hydrocarbon Gases" in "Organic Geochemistry") and the holes at Site 1249 were shallow, all sediment acquired at this site came from within the GHSZ and showed IR thermal anomalies indicative of hydrate presence (see "Infrared Scanner" in "Physical Properties").
At Site 1249, the methane that was our focus was also our nemesis. Massive hydrates made for difficult coring, gas expansion caused poor recovery, and melting hydrates liquified surrounding sediment. All microbiological sampling took place in Hole 1249F, which was drilled to 90 mbsf. The upper 40 m contained significant quantities of massive hydrate and appeared very disturbed ("wet-looking" core and pieces of sediment liberally distributed along the length of the core liner), and few sections were chosen for microbiological sampling. Cores deeper in Hole 1249F had better recovery and were sampled more often. Sampled intervals are listed in Table T10.
Microbiological samples (with the exception of those from Core 204-1249F-1H) did not show large IR temperature anomalies that might indicate massive hydrate. Smaller thermal anomalies that might indicate disseminated hydrates were present in microbiological core sections, but because postcruise processing will be required before the actual locations of these smaller anomalies are known, sampling was performed without consideration of these potential hydrates. Soupy or moussy sediments were noted and tentatively identified as hydrate influenced, and samples from the same section with different sediment textures were sampled for comparative microbiology studies.
Most gas hydrates were removed from the cores before microbiological sampling began, but the microbiologists had the opportunity to sample a core at the top of Hole 1249F that still contained massive hydrate (Core 204-1249F-1H). A 20-cm hydrate sample was taken from the top of Core 204-1249F-1H, and the remainder of the core (Sections 204-1249F-1H-1and 1H-2) was processed for microbiological investigations. The liner was slit (without splitting the core) so that the top of the liner could be removed. This was done in an attempt to minimize disturbance of the very gassy and soft material. Hydrates were present throughout the core. Two nearly circular "biscuits" of ~1-cm-thick massive hydrate were placed in liquid nitrogen, and thinner "biscuits" of hydrate with interlayered sediment were also observed. These circular layers indicate that the APC punched through near-horizontal horizons of hydrate. Millimeter-thick veins of hydrate cut through the sediment at all angles, from horizontal to subvertical. The structure of both the thick hydrate layers and thin hydrate veins was flaky and platy (like mica); the surrounding sediments looked and felt like aerated pure clay. This core was sampled with extreme caution. The outer layers were repeatedly lifted off the top of the sediment with a flame-sterilized spatula until the center of the core was exposed, and samples were removed with another sterile spatula. Sediments were not stiff enough to use syringe corers.
Contamination tests were run on cores from Hole 1249F (Table T11), but most of the results are inconclusive (see below). However, some measure of comfort can be gained from looking at the sulfate concentrations from this site (see "Carbon Cycling" in "Interstitial Water Geochemistry"). IW samples are squeezed from sediments taken from the core interior, similar to microbiological samples. Zero sulfate values below the zone of sulfate depletion indicate that the drilling fluid (sulfate-rich surface seawater) has not penetrated the interior of the core. At Site 1249, even though gas hydrates are abundant and the potential for core disturbance is high, sulfate values do not show large intrusions of seawater.
Only deeper cores were sampled for PFT at Site 1249 because of logistical difficulties. Raw data (grams of PFT per sample), uncorrected for sediment weight, are presented in Table T11. Average sample size was 5 g of sediment. Although samples from the inside of the core show a hundredfold reduction in PFT as compared to outer layers, all concentrations are extremely low and probably reflect loss from sampling vials. Samples were not analyzed until much later in the cruise, and the perfluorocarbon is extremely volatile.
Results of microsphere counts for Site 1249 are shown in Table T11. Of the eight core sections sampled, three showed successful tracer deployment and five had no detectable spheres in subsamples taken for analysis. One of the three cores with successful microsphere deployment also had a significant number of spheres in the internal sample. Both the apparent failure of deployment and interior presence of spheres are likely to be related to the difficulties encountered in coring this site.