There are very few, if any, ecosystems that are not profoundly influenced by the activity of microbial communities. Microorganisms, encompassing domains Bacteria and Archaea as well as microscopic members of the Eukarya such as protozoa, yeasts and many other fungi, are tremendously abundant and contribute significantly to the major biogeochemical processes. In the last decade, technological advances in DNA sequencing have afforded ecologists the ability to study microbial communities at

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... o unseen resolution, with the capacity to address increasingly complex ecological questions. Here we review a selection of microbial ecology research being undertaken in New Zealand and Antarctica, from animal-and plant-hosted ecosystems, freshwater and marine habitats, and agricultural and geothermal environments. We have highlighted the broad range of high-quality and diverse microbial ecology research being conducted by New Zealand researchers and observe that much of this work underpins the greater biosecurity, ecosystem services, health and conservation efforts being undertaken in this country and globally. We conclude the review by offering some ideas for future directions in microbial ecology and, in particular, argue the importance of integrating microbiology with general ecological research.