I am building a community site in Drupal 7.
I am using the SEO checklist, which suggest to use the microdata module.
Other places I read are suggesting to use Schema.org module.
what is difference between them? Can I use both modules?
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They are different things:
If you want to use the Schema.org vocabulary, you can use the syntax Microdata, or RDFa (Lite), or JSON-LD (or any other RDF serialization, but the three mentioned syntaxes are supported by the big search engines that sponsor Schema.org).
The schemaorg module integrates the Schema.org vocabulary into Drupal 7 by using RDFa 1.0, which is the syntax used by Drupal 7 for other vocabularies, too.
The microdata integrates the Schema.org vocabulary by using Microdata (without this module, Drupal 7 does not output any Microdata).
If you can’t decide between these two modules: Go with schemaorg, because Drupal 7 already uses RDFa, RDFa is more powerful than Microdata, and parts of this module were ported into the Drupal 8 core.
From what I've experienced Google picks up all of these formats. Sites I build use the default RDF module. I would not recommend running both modules as I could only it imagine adding a lot of bloat to your system.
I would visit Google's Structured Data Testing Tool: http://www.google.com/webmasters/tools/richsnippets
Give all three modules a try, experiment with different pages and make a decision based off of those results. In the end there is no perfect SEO equation beyond what you think is proper.