You can apply rich text formatting by manually adding the following HTML-like tags to fields in your Zotero library:
Zotero will automatically replace these tags by the specified formatting in bibliographic output. E.g. “<i>Pseudomonas aureofaciens</i> nov. spec. and its pigments” will become “Pseudomonas aureofaciens nov. spec. and its pigments”.
Note that if rich text formatting has to be applied indiscriminately to entire fields (e.g. a style guide may dictate that titles should be in italics), you can modify the relevant Citation Style Language (CSL) style (see the CSL documentation and the CSL field formatting options).