Écosystèmes

Microbiome metabolism underlies numerous vital ecosystem functions. Individual microbiome members often perform partial catabolism of substrates or do not express all of the metabolic functions required for growth. Microbiome members can complement each other by exchanging metabolic intermediates and cellular building blocks to achieve a collective metabolism. We currently lack a mechanistic framework to explain why microbiome members adopt partial metabolism and how metabolic functions are distributed among them. Here we argue that natural selection for proteome efficiency—that is, performing essential metabolic fluxes at a minimal protein investment—explains partial metabolism of microbiome members, which underpins the collective metabolism of microbiomes. Using the carbon cycle as an example, we discuss motifs of collective metabolism, the conditions under which these motifs increase the proteome efficiency of individuals and the metabolic interactions they result in. In summary, we propose a mechanistic framework for how collective metabolic functions emerge from selection on individuals.

Ecosystem ecology needs a framework that explicitly considers the roles of organic compounds. The ecology of molecules integrates compound identity, diversity, and interactions to understand ecosystem processes, such as nutrient and carbon cycling. This approach leverages advances in analytical chemistry and molecular biology to unravel the complex chemical interplay within ecosystems.

The primary production of fjords across the Arctic and Subarctic is undergoing significant transformations due to the climatically driven retreat of glaciers and ice sheets. However, the implications of these changes for upper trophic levels remain largely unknown. In this study, we employ both bulk and compound-specific stable isotope analyses to investigate how shifts at the base of fjord food webs impact the carbon and energy sources of consumers. Focusing on two rapidly changing fjords in Southern Greenland, we used the migratory Arctic char as an indicator species, sampling populations along environmental gradients within the fjords, building upon the assumption that char populations feed primarily close to their natal stream, thereby integrating a dietary gradient. Our analysis of bulk stable isotopes in Arctic char tissue confirmed this premise, revealing a consistent change in resource use from the outer to the inner fjord, which nonetheless served as preferred feeding grounds. Essential amino acid analysis further indicated shifts in carbon and nitrogen sources, consistent with changes in nutrient use near glacier inputs characterized by low turbidity and high iron levels. Notably, these changes in the source of primary production were associated with shifts in trophic positions and the transfer of polyunsaturated fatty acids, with Arctic char in glacier-influenced inner fjords feeding at lower trophic level (size-corrected) and accumulating higher levels of high-quality docosahexaenoic acid (DHA). These findings highlight the usefulness of new analytical tools in revealing that glacial retreat can substantially alter food web dynamics, enhancing both carbon flow and the nutritional quality of fish in fjord ecosystems. The two Southern Greenland fjords studied could represent the future of other fjords, where retreating glaciers become land-terminating and glacial inputs decrease. Our study underscores the critical role of glacier dynamics in affecting high-level consumers, such as salmonids, with implications for fjords globally.