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I don't think industry bloggers are your issue. If these are legitimate bloggers writing about topics in your industry then they should be great links. I don't think you want to get these removed.

Hello SEO community.  I have started an online marketing company that focuses on a specific niche and have been researching how micro sites can be beneficial for SEO.  For example the "Nifty" presentation mentioned how micro sites are going to be key for local seo.

However I have also heard that link networks are increasingly bad and are penalized by the Panda updated.

While we are writing good, original content for our clients, I like the microsites because:

1. URL - we can choose urls for the main keywords
2. Content Focus - we can focus on specific content
3. Ranking - these sites seem to rank pretty well
4. Citations - we are able to give citations for our clients from these sites

But am I worried, am I creating a link network?  Even thought I am putting out useful, good content, is this more hurting me than helping me?  Should I give up on this strategy or continue?  Help!

I just want to be sure, but if I install a Wordpress blog in a subfolder of a HTML site, Google will see that as one site, not two different sites, correct?  Even if there is two index files?

I don't think industry bloggers are your issue. If these are legitimate bloggers writing about topics in your industry then they should be great links. I don't think you want to get these removed.