Chapter 31: Microbes in Soils & Terrestrial Ecosystems

Soil structure and health rely fundamentally on soil organic matter (SOM), which is produced and recycled by microbes, who break down complex plant polymers like cellulose and the highly recalcitrant lignin—a process often requiring specialized white rot fungi and actinobacteria operating under specific environmental conditions, particularly the Carbon-to-Nitrogen (C/N) ratio. The chapter details the sheer density and diversity of life in soil, encompassing vast bacterial communities (including phyla like Acidobacteria and Proteobacteria), ammonia-oxidizing archaea (Thaumarchaeota), and extensive fungal networks that form rhizomorphs. Microbe-plant relationships are categorized as mutualistic, commensalistic, or pathogenic, taking place in distinct niches: the stress-resistant phyllosphere (aerial parts) and the nutrient-rich root zones known as the rhizoplane and rhizosphere. Key mutualisms include mycorrhizae (fungal-root associations) which facilitate nutrient uptake for 80% of land plants, distinguishing between the external ectomycorrhizae (ECM) that form a Hartig net, and the widespread internal arbuscular mycorrhizae (AM). Furthermore, the chapter thoroughly explains the complex rhizobium-legume symbiosis, where bacteria use molecular signals (Nod factors triggered by plant flavonoids) to induce root hair curling and form specialized root nodules containing nitrogen-fixing bacteroids protected by leghemoglobin. In contrast, detrimental relationships are exemplified by the plant pathogen Agrobacterium tumefaciens, which causes crown gall tumors by transferring T DNA from its Ti plasmid into the host genome, forcing the plant to synthesize unique food sources called opines. Finally, the text explores the extensive subsurface biosphere, where microbial life kilometers below the surface sustains itself through anaerobic chemolithoautotrophy fueled by geologically derived substrates, demonstrating that a significant portion of Earth's biomass is independent of surface photosynthesis.