Environmental Biogeochemistry

Environmental biogeochemistry examines the cycles of chemical elements—carbon, nitrogen, sulphur, phosphorus and others—through air, water, soils and living organisms. It integrates geological, chemical and biological perspectives to trace how nutrients and pollutants are transformed, transported and stored in natural and human-affected systems. Central to this field are processes such as photosynthesis and chemosynthesis, which convert inorganic carbon into organic matter; microbial respiration and fermentation, which return carbon dioxide and other by-products to the environment; and the redox-driven interconversions of nitrogen and sulphur species. Biogeochemical reactions underlie soil fertility, water quality and greenhouse-gas fluxes, and they provide the basis for practical applications including remediation of contaminated sites, management of water resources and optimisation of agricultural productivity. Advances in isotope tracing, genomics and in situ sensing continue to refine our understanding of reaction rates, microbial community function and feedbacks between element cycles and climate change.

Research from Nature Portfolio

Studies on the marine methanogen Methanothermococcus thermolithotrophicus have revealed a complete assimilatory sulfate reduction pathway in an archaeon that typically produces methane. Structural and biochemical analyses show that this organism employs an unusual phosphoadenosine phosphosulfate reductase and non-canonical phosphatase—likely acquired by horizontal gene transfer—to generate sulfide for biosynthesis, thereby linking carbon and sulfur metabolisms.

Work on a newly isolated acidobacterium has demonstrated its capacity for alternate respiration of sulphate and oxygen, coupled to the breakdown of complex polysaccharides. Metatranscriptomic data indicate that under alternating oxic–anoxic conditions this microbe deploys distinct respiratory complexes, blurring the conventional separation between aerobic heterotrophs and strict anaerobic sulfate reducers.

Research from all publishers

A comprehensive survey of nearly a thousand genome-resolved metagenomes has expanded the known diversity of organisms encoding the dissimilatory sulfite reductase (DsrAB). This effort has identified previously unrecognised bacterial and archaeal lineages capable of energy-conserving sulfate or sulfite reduction, and has refined the distribution of key accessory genes (dsrL, dsrD) that predict the directionality of sulfur transformations.

Comparative phylogenomics has reconstructed the stepwise evolution of the dissimilatory sulfite/sulfate reduction pathway from an ancestral archaeal sulfite reductase through successive acquisitions of membrane-associated electron-transfer complexes. Independent evolutionary events have also given rise to reverse-operating pathways for sulfur oxidation in diverse bacterial groups.

Metagenomic analyses of deep-sea ferromanganese nodule sediments have uncovered microbial communities that couple oxidation of manganese and reduced sulfur compounds to heterotrophic and chemolithoautotrophic growth. These microbes appear to exploit metal-rich, nutrient-limited environments by linking metal resistance mechanisms with carbon fixation pathways, illustrating novel intersections of elemental cycles in the abyssal zone.

Environmental Biogeochemistry publication trend

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

Technical terms

Biogeochemical cycle: The movement and transformation of an element through biological, geological and chemical reservoirs.

Assimilatory sulfate reduction: Biosynthetic pathway converting sulfate to sulfide for incorporation into cellular biomass.

Dissimilatory sulfite reductase (DsrAB): Enzyme complex that catalyses the reduction of sulfite to sulfide during anaerobic energy conservation.

Terminal oxidase: An enzyme in respiratory chains that reduces oxygen, determining microbial tolerance to inhibitors.

Chemosynthesis: The fixation of carbon dioxide into organic matter using energy derived from the oxidation of inorganic compounds rather than light.

References

1. Assimilatory sulfate reduction in the marine methanogen Methanothermococcus thermolithotrophicus. Nature Microbiology (2023).
2. Oxygen respiration and polysaccharide degradation by a sulfate-reducing acidobacterium. Nature Communications (2023).
3. Global diversity and inferred ecophysiology of microorganisms with the potential for dissimilatory sulfate/sulfite reduction. FEMS Microbiology Reviews (2023).
4. Stepwise pathway for early evolutionary assembly of dissimilatory sulfite and sulfate reduction. The ISME Journal: Multidisciplinary Journal of Microbial Ecology (2023).
5. Microbe-driven elemental cycling enables microbial adaptation to deep-sea ferromanganese nodule sediment fields. Microbiome (2023).
6. Biogeochemistry and Its Complexity.