Yes. The environments are too dissimilar. Where you get cross pollination are areas where they mix. For example, animals that lived in the shallows becoming amphibious and eventually evolving to be permanent land dwellers.
Besides, going from photosynthesis to chemical synthesis (not to mention the temperature and pressure differences) requires a significant change in the basic biology of the baseline bacteria. Occam's razor would dictate that chemical-synthesizing bacteria evolved there, and communities of life sprung up from those bacteria, not adapted to that region of the ocean from life that is built around photosynthesis.
To clarify: Are you saying that the chemosynthetic autotrophs that inhabit areas around deep sea vents evolved separately and independantly and are 'normal' creatures that have adapted to the environment?
If so I would say I disagree. While the bacterial chemosynthetic autotrophs that thrive on the sulfer and carbon dioxide from the vents are unique when contrasted with phototrophs, I think looking at the food chan in these communities is quite telling. The bacteria form a mat which crustaceans feed and larger organisms like deap see vent crabs, snails, and so forth feed on. While they form their own unique ecosystem and have adaptive traits to handle the extreme heat/cold, pressure, and chemicals (both in the water and food) these creatures clearly are not unique evolutionary products from a different evolutionary chain. They are simply crabs, clams, shrimp, snails, and such that have adapted to to this environment. The mathametical odds of a completely separate evolutionary trunk producing the snails, crabs, etc is impossible. These creatures are very well adapted to the extremely harsh and divergent environment of vent life, so much so they even exhibit reproductive methods that accomodate the 'death' of a vent (e.g. some vent crab larvae can ascend up to 1,000m above the vent and 100km which allows the species to find and populate other vents).
Now this is just my opinion, but seeing how much larger (read: complex, more developed, less flexible) organisms are well suited and adapted to the special needs of vent life -- and they clearly were part of the phototroph foodchain and adapted to the chemotroph ecosystem of the vents -- I don't believe bacteria would have a difficult time adapting to this environment. Bacteria are the most savvy creatures on this planet. Bacteria are everywhere and in large numbers. Yes, chemosynthesis is a huge departure from photosynthesis in metabolic pathways, yet we don't bat an eye at bacteria like botulism that is anaerobic. Life has many adaptations in regards to how they obtain Oxygen. The contrast between a plant, fungus, and carnivor are all pretty telling imo: where there is 'food' to be preyed upon, there is an organism to fill the void. Vents offer food and the most versatile of Earth life, bacteria, are the most likely organism to adapt. The fact much larger, less flexible, organisms could adjust to form a foodchain gives me no doubt that bacteria were up to the task. The scope of pathways needed to evolve from basic building blocks like lipids, ATP, ammino acids, and so forth to a self regulating and sustaining single celled organism are crazy. So if this is possible, and for it to spontaneous develop a wide host of adaptations and divergences to cope with all sorts of harsh environments (like air!) I think these little buggers are up to the task.
Of course I think they were created that way, so what do I know
See, all that college bio and chem wasted on nothing! (Ps- sorry if I was reading your statement incorrectly).
