The tenses you're trying to decide between are called past and present perfect continuous. The second one sounds intimidating, but it just describes something that started in the past and is still happening. It is characterized by "has/have" and "been." "Have you been waiting all this time?" might be a question asked by someone who just bumped into their friend waiting on a date. He or she started waiting some time in the past, and is still waiting now. That's an example of the tense in action.
Now, onto your sentence:
Although the importance of the bacteria in water sea has often never been realized/ was not realized, it has been found/it is found that they are useful.
To decide what tenses you should use, you're going to have to think about the chronological sequence of events in your sentence. To me, it seems that in the past, some bacteria species was seen as useless. However, at some more recent point in the past and in the present, they was and are still found to be useful. Logically speaking, the bacteria would have to be considered useless before its purpose could be realized. Therefore, this is how I personally would write the sentence:
Although the importance of the bacteria in water sea was not often realized, it has been found that they are useful.
The sequence of events this sentence demonstrates is: sometime before now, a bacteria species was considered useless, but at some point later, their purpose was realized. Now, they continue to be utilized for that purpose, so they continue to be useful. Hopefully that's what you were trying to say.
Disclaimer: I might be slightly wrong on the point that it's present perfect continuous and not present perfect; I'm not that great at tense classification. However, I'm still confident that the sentence I provided uses the correct tense (feel free to prove me wrong).