This document summarizes an approach to automatically extract microorganisms and their habitats from free text using text mining workflows. The approach uses a named entity recognizer combining dictionaries and machine learning to identify organisms and habitats. It then employs relation mining to extract sentences expressing relationships between organisms and habitats. Evaluation shows the organism recognition achieves 84% precision but habitat recognition is lower at 68% precision, limiting the relation mining performance. Ongoing work aims to improve the habitat model and make the overall approach more robust to noise from PDF to text conversion.