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Secondary minerals in basalts from Holes 495 and 500 include smectite and chlorite, both of which have partially replaced the basalt groundmass. In addition to these two minerals, amphibole, laumontite, albite, and a corrensitelike mineral are present in Holes 499B and 499C. Smectite, chlorite, talc, calcite, phillipsite, mica, and mixed-layer chlorite-montmorillonite also fill veins in the basalts of Hole 495. The secondary mineral assemblages from Site 499 are characteristic of the initial stage of greenschist facies metamorphism.

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Interstitial water chemistry has proved to be a sensitive indicator for early diagenetic reactions, particularly those related to organic matter oxidation. Downhole chemical variations in the pore waters from Deep Sea Drilling Project Holes 496 and 497 on the Middle America Trench slope off Guatemala are anomalous because both salinity and chlorinity show strong decreases to half the values of seawater, and d18O values become positive (maximum of about +2.5% at the bottom of the holes). These observations are explained in terms of dilution of pore waters after retrieval as a result of decomposition of the gas hydrates before removal of pore waters by shipboard squeezing techniques. In all holes, except Hole 495 (drilled in pelagic sediments), decomposition of organic matter leads to rapid sulfate depletion and subsequent methane generation. Associated with methane generation are large increases in alkalinity and dissolved ammonia. The latter component causes ion exchange reactions with clay minerals, which results in maxima in magnesium and perhaps potassium. At greater depths, as yet unidentified reactions cause the removal of magnesium. Especially in the deeper Trench Sites 499 and 500, rapid variations in calcium, magnesium, and alkalinity occur in turbidite sequences.