Johannes focuses his research and teaching in soil biogeochemistry and soil fertility management. His specialization is in soil organic matter and nutrient studies of managed and natural ecosystems with a focus on soil carbon sequestration, nutrient recycling from wastes, biochar systems, circular economy, and sustainable agriculture in the tropics (especially Africa). His research stretches from ultra-fine scale microscopy to examine carbon stabilization in soils to global-scale carbon and nutrient cycles.