Microbial metabolism in deep terrestrial subsurface communities - amino acids as biosignatures

TL;DR

This study explores how deep underground microbes use amino acids, finding that some processes remain stable despite changes in nutrients.

Contribution

The study identifies amino acid degradation as a core metabolic process in deep biosphere communities, unaffected by nutrient variations.

Findings

Amino acids and organic acids were degraded under different nutrient conditions.

Phenylalanine and valine degradation remained unaffected by changes in nutrient availability.

Metabolic pathways involving phenylalanine, cysteine, and methionine were most prominent.

Abstract

•Salinity and nutrient availability affect the utilization and secretion of amino acids by deep biosphere microbial consortia.•Anoxic deep biosphere enrichment cultures were compared to Desulfovibrio desulfuricans.•Amino acids and organic acids were degraded under different nutrient conditions.•Phe and Val degradation remained unaffected by changes in nutrient availability.•Metabolic pathways involving Phe, Cys and Met were most prominent.

Salinity and nutrient availability affect the utilization and secretion of amino acids by deep biosphere microbial consortia.

Anoxic deep biosphere enrichment cultures were compared to Desulfovibrio desulfuricans.

Amino acids and organic acids were degraded under different nutrient conditions.

Phe and Val degradation remained unaffected by changes in nutrient availability.

Metabolic pathways involving Phe, Cys and Met were most prominent.

The deep terrestrial subsurface (DTS) biosphere consists of a variety of distinct microbial taxa, mostly bacterial. The mechanisms by which microbes dynamically manage the uptake and concurrent utilization of nutrients within the DTS environments remain largely unexplored. Here, we examined the utilization patterns of amino acids and other polar metabolites in cultured DTS bacterial communities to investigate the adaptive responses and metabolic pathways employed under varying nutrient conditions to gain insight into how environmental shifts impact the metabolism of these communities. Previously, we found that changes in growth conditions affected the composition and size of the bacterial communities enriched from these oligotrophic, anoxic environments and induced changes in the production of primary and secondary metabolites. In the present study, metabolic fingerprinting was used to investigate the primary and secondary metabolite utilization and main metabolic pathways present in the enriched DTS bacterial consortium originating from the deep bedrock of the Fennoscandian Shield. We found that especially amino acids were predominantly degraded under different nutrient conditions. Notably, the degradation of phenylalanine and valine constituted a 'core' metabolic process that remained unaffected by variations in available nutrients within this community. Further, the most significant metabolic pathways employed were those connected to phenylalanine, cysteine and methionine.

Image, graphical abstract

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