Microbial Ecology

Summary

Microbial ecology examines how microorganisms interact with each other and with their environments to shape fundamental processes on Earth. From the depths of hydrothermal vents to the roots of crops and the human gut, microbial communities drive nutrient cycles, influence host health and underpin ecosystem stability. In aquatic systems, bacteria and archaea harness chemical gradients—oxidising sulphur, hydrogen or methane—to fix carbon and regulate elemental fluxes, while protists and viruses control microbial turnover through grazing and infection. In soils, vast assemblages of bacteria, fungi and archaea decompose organic matter, solubilise minerals and form symbiotic partnerships with plants in the rhizosphere, thereby sustaining terrestrial productivity. Within animal and human hosts, resident microbiomes contribute to digestion, immune development and resistance to pathogens. Advances in molecular methods have revealed that many microbes engage in complex cross-kingdom signalling—via small molecules such as siderophores, secondary metabolites and quorum-sensing signals—to coordinate gene expression, compete for resources or form beneficial alliances. In an era of global change, understanding microbial ecology is vital for managing soil fertility, water quality, human health and biodiversity.

Research from Nature Portfolio

A hydrogen-oxidising bacterium of the genus Sulfurimonas has been shown to dominate cold, oxygen-rich hydrothermal plumes worldwide. Genomic analysis reveals streamlined genomes optimised for aerobic chemolithotrophy, notably the loss of nitrate reductases and acquisition of high-affinity cytochromes, underlining hydrogenotrophy as a major driver of plume carbon fixation and sulphur cycling. Microbiota-derived metabolites enhance iron uptake by regulatory T cells in the intestine. A short-chain fatty acid produced by commensal bacteria stimulates expression of the transferrin receptor on Tregs, boosting intracellular iron and promoting hypoxia-inducible factor-2α activity. Restoration of this pathway in colitis models corrects iron deficiency, strengthens immune tolerance and preserves mucosal barrier integrity. A global survey of vineyard soils has mapped microbial biogeography across continents, revealing that spatial distance is the principal driver of bacterial and fungal community composition, while climate correlates with fungal alpha diversity. Core prokaryotic taxa such as Proteobacteria and Acidobacteria persist worldwide, yet regional “microbial terroirs” exhibit distinct profiles that correlate with vineyard location and wine characteristics.

Research from all publishers

Global soil metagenomics has uncovered that Deltaproteobacteria—especially Anaeromyxobacteraceae and Geobacteraceae—constitute a core, globally distributed cohort of nitrogen-fixers, predominating in anoxic microsites such as paddy and wetland soils. Their ubiquity underscores the importance of anaerobic hotspots in terrestrial N₂ fixation. After three decades of fertilisation, long-term application of green manure in intercropping systems has been shown to enhance biological nitrogen fixation by co-enriching diazotrophs and arbuscular mycorrhizal fungi. The resulting co-occurrence networks, anchored by genera such as Azospirillum and Skermanella, stabilise soil N inputs and rebuild soil fertility. Reviews of nitrogen-fixing symbioses and free-living diazotrophs in cereal cropping systems highlight the dual role of rhizobial legumes and associative bacteria in meeting crop N demand. Strategies for ecological intensification include optimised rotations, targeted microbial inoculants and emerging biotechnologies to extend fixation capacity to non-legume crops.

Microbial Ecology publication trend

The graph below shows the total number of articles in microbial ecology across all publications each year (not limited to Nature Index journals).

Technical terms

Microbiome: The community of microorganisms and their collective genomes in a defined habitat.

Rhizosphere: The narrow zone of soil directly influenced by plant roots, rich in microbial activity and nutrient exchange.

Chemolithoautotrophy: Metabolic process in which energy is derived from inorganic compounds and used to fix carbon dioxide.

Siderophore: A high-affinity iron-chelating compound secreted by microbes to acquire ferric iron from the environment.

Biofilm: A structured microbial community embedded in an extracellular matrix, adherent to surfaces and highly tolerant to stress.

Metagenomics: The sequencing and analysis of DNA from entire microbial communities to reveal taxonomic and functional diversity.

Biological nitrogen fixation (BNF): Microbial conversion of atmospheric dinitrogen into bioavailable ammonia via the enzyme nitrogenase.

References

  1. A hydrogenotrophic Sulfurimonas is globally abundant in deep-sea oxygen-saturated hydrothermal plumes. Nature Microbiology (2023).
  2. Microbiota-assisted iron uptake promotes immune tolerance in the intestine. Nature Communications (2023).
  3. A global microbiome survey of vineyard soils highlights the microbial dimension of viticultural terroirs. Communications Biology (2022).
  4. Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome. Microbiome (2024).
  5. Synergistic effects of diazotrophs and arbuscular mycorrhizal fungi on soil biological nitrogen fixation after three decades of fertilization. iMeta (2023).
  6. Biological nitrogen fixation and prospects for ecological intensification in cereal-based cropping systems. Field Crops Research (2022).

About these summaries

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