Fig.1 Schematic of Earth's ecosystem biogeochemical cycles

Fig.2 Current status of control variables for all nine planetary boundaries. Adapted from [49].

Fig.3 Combined application of metaOmics and isotope labeling or signature techniques to decipher the interactions between microorganisms and the environment in biogeochemical processes DNA-based analytical techniques, such as high-throughput sequencing of marker genes represented by SSU rRNA genes and metagenomes followed with construction of metagenome-assembled genomes, allow for the analyses of microbial community composition, phylogenetic classification of species, and the functional potential of species and communities. RNA-based metatranscriptomics is utilized to analyze gene transcription levels and to identify key metabolic pathways. Subcellular localization and regulation occur at the protein level. Post-translational modifications can alter the location and function of proteins. Consequently, metaproteomics and metabolomics reflect the expression and activity of functional proteins. Combined with stable or radioactive isotope labeling or signature techniques, visualization methods based on isotope and elemental imaging are employed to observe and enumerate metabolically active cells, enabling quantitative analyses of substrate update and transform rates, pathway composition, and nutrient fluxes. ① represents that, the metabolically active cells update and assimilate the isotope-labeled substrates, which are then can be observed and identified via the MAR- or nanoSIMS methods. ② express that, different stable isotope fractionation effects exist in different biochemical reactions or pathways, leading to different isotope signatures of products, which enables identification of predominant metabolic pathway by analyzing the natural stable isotope composition; on the other hand, by tracing the flux of labeled isotopes in the substrates and metabolic products, the metabolic pathways can be quantitatively calculated. The integrated application of these techniques facilitates the study, across multiple levels and different spatiotemporal scales, of the adaptation-feedback relationship between organisms and their environment, as well as the roles they played in biogeochemical processes, such as the interaction between microbial functional groups driving the coupled cycle of sulfur and CH4 in the ocean. Such research has revealed that, the convergence of global organic metabolic functions shapes biochemical gradients in the oceans, such as concentrations of SO 4 2 -, H2S, CH4 at different depths, leading to the formation of ecological niches for different microbial functional groups, and fostering co-evolution between life and the marine environment.

Fig.4 Translational biogeochemistry: bidirectional feedbacks between social and Earth's biogeochemical systems. Adapted from [64].