Periodic Reporting for period 1 - DatingSuCy (Timing the evolution of the dissimilatory sulfur cycle: a bridge between genes and geochemistry)
Reporting period: 2023-01-01 to 2024-12-31
This MSC Action is titled “Timing the evolution of the dissimilatory sulfur cycle: a bridge between genes and geochemistry”. This project aims to elucidate the evolution of dissimilatory sulfur metabolisms and their interplay with sulfur geochemistry. The dissimilatory sulfur metabolisms, evolved primarily in microbes, are catalysed by a linked suite of "enzymatic machineries" composed largely of multimeric protein complexes. Over geological timescales, these “machineries” have co-opted to create a dissimilatory metabolic network at planetary scale, which has had tremendous consequences on the Earth’s major biogeochemical cycles, surface redox states, and climate stability. Despite the significant role in shaping the history of Earth and life, the timing of the onset of diverse dissimilatory sulfur metabolisms and their interplay with sulfur geochemistry remain unconstrained, due to the rarity of microbial fossils and ambiguity of ancient stable isotope signatures.
This project proposed to tackle the knowledge gap by leveraging expanded genome catalogs of bacteria and archaea from metagenomes, advances in molecular clock and quantitative evolutionary models, and extensive compilations of sedimentary sulfur isotope records. The objectives of this project include (1) the derivation of phylogenies for a comprehensive set of genes encoding dissimilatory metabolisms of inorganic and organic sulfur compounds; (2) recapitulation of the evolutionary history of sulfur-cycling genes over the course of sulfur geochemistry development as recorded in rocks.
This project proposed to tackle the knowledge gap by leveraging expanded genome catalogs of bacteria and archaea from metagenomes, advances in molecular clock and quantitative evolutionary models, and extensive compilations of sedimentary sulfur isotope records. The objectives of this project include (1) the derivation of phylogenies for a comprehensive set of genes encoding dissimilatory metabolisms of inorganic and organic sulfur compounds; (2) recapitulation of the evolutionary history of sulfur-cycling genes over the course of sulfur geochemistry development as recorded in rocks.
Systematic phylogenetic analyses were conducted on 110 genes/proteins involved in dissimilatory sulfur cycling processes, including sulfate reduction, sulfur oxidation, sulfur disproportionation, and organosulfur respiration. Monophyletic clades of functional orthologs were identified based on bootstrap support, biochemical verification, gene neighborhood patterns, and conserved catalytic residues. Hidden Markov Models (HMMs) were developed for these clades, optimizing both sensitivity and specificity for homology searches. These HMMs were then applied to screen the Genome Taxonomy Database (GTDB), leading to the discovery of previously unknown sulfur-cycling genes in uncultured microbial lineages. This work established phylogenetic frameworks for 110 sulfur-cycling protein families, identified 174 monophyletic clades, and expanded the known phylogenetic diversity of sulfur-cycling microorganisms by approximately 40%. A web-based database was created to compile the phylogenetic frameworks, clade-specific HMMs, and associated descriptions.
We further reconstructed the evolution of the sulfur oxidation (Sox) pathway and explored ancient biological sulfur oxidation mechanisms. Using the newly developed HMMs, genes involved in Sox, rDsr, and sHdr pathways were screened across GTDB genomes. Phylogenomic analyses of Sox system components and associated pathways were conducted, and their evolutionary development was inferred by reconciling gene trees with a dated bacterial tree of life. A machine learning approach was applied to differentiate ecological and phylogenetic drivers in the evolution of the Sox pathway. These analyses traced the origin of a truncated Sox system before the Great Oxidation Event (GOE, ~2.35 billion years ago), which later expanded to include complete thiosulfate oxidation pathways following the GOE. This expansion occurred through the acquisition of additional Sox components (SoxCD) or reverse dissimilatory sulfite reductases (rDsr).
Dating results also revealed an unresolved puzzle regarding sulfide oxidation in the Archean era, where known oxidants (e.g. oxygen and nitrate) were seemingly absent. A hypothesis was proposed that iron(III) oxides, abundant in anoxic Archean environments, may have served as electron acceptors for microbial sulfide oxidation. We validated this hypothesis by physiological experiments with a microorganism that encodes the genetic capacity to to couple sulfide oxidation with ferrihydrite reduction. Transcriptomic data suggested that this process involved a reversal of the dissimilatory sulfate reduction pathway. The electrons yielded by this reaction may have been transferred to ferrihydrite via extracellular electron transfer mechanisms, potentially mediated by multi-heme cytochromes. These findings revealed a previously unknowm microbial metabolism and support a geological scenario in which iron(III) oxides could have facilitated sulfur oxidation in anoxic Archean environments, providing new insights into ancient sulfur cycling processes on early Earth.
We further reconstructed the evolution of the sulfur oxidation (Sox) pathway and explored ancient biological sulfur oxidation mechanisms. Using the newly developed HMMs, genes involved in Sox, rDsr, and sHdr pathways were screened across GTDB genomes. Phylogenomic analyses of Sox system components and associated pathways were conducted, and their evolutionary development was inferred by reconciling gene trees with a dated bacterial tree of life. A machine learning approach was applied to differentiate ecological and phylogenetic drivers in the evolution of the Sox pathway. These analyses traced the origin of a truncated Sox system before the Great Oxidation Event (GOE, ~2.35 billion years ago), which later expanded to include complete thiosulfate oxidation pathways following the GOE. This expansion occurred through the acquisition of additional Sox components (SoxCD) or reverse dissimilatory sulfite reductases (rDsr).
Dating results also revealed an unresolved puzzle regarding sulfide oxidation in the Archean era, where known oxidants (e.g. oxygen and nitrate) were seemingly absent. A hypothesis was proposed that iron(III) oxides, abundant in anoxic Archean environments, may have served as electron acceptors for microbial sulfide oxidation. We validated this hypothesis by physiological experiments with a microorganism that encodes the genetic capacity to to couple sulfide oxidation with ferrihydrite reduction. Transcriptomic data suggested that this process involved a reversal of the dissimilatory sulfate reduction pathway. The electrons yielded by this reaction may have been transferred to ferrihydrite via extracellular electron transfer mechanisms, potentially mediated by multi-heme cytochromes. These findings revealed a previously unknowm microbial metabolism and support a geological scenario in which iron(III) oxides could have facilitated sulfur oxidation in anoxic Archean environments, providing new insights into ancient sulfur cycling processes on early Earth.
The outcome of the project provides necessary foundations for large-scale ecological studies of microbial sulfur cycle. The development of the comprehensive sulfur cycling gene database and phylogenies brings together microbial evolution and ecology under a unified framework. The phylogeny-based sequence classification system enables effective exploration of environmental diversity of diverse dissimilatory sulfur metabolism processes, guide the discovery of novel sulfur microbes encoding uncharted metabolic potential, and allow to identify new features of the biogeochemical sulfur cycle in complex microbial ecosystems. The database resource and tools will be made publicly available upon its publication.
The delineation of a key sulfur oxidation system across geological time reveals a compelling evolutionary trajectory toward the modern, complex dissimilatory sulfur oxidation metabolism, shaped by the Earth’s progressive oxygenation. These findings illuminate the intricate interplay between sulfur redox chemistry, microbial evolutionary adaptation, and planetary history, offering a more holistic understanding of how life have co-evolved with biogeochemical cycles. By integrating molecular phylogenies with geochemical and geological evidence, this research exemplifies a framework for reconstructing the evolution of Earth's biogeochemical systems, highlighting the dynamic feedbacks between microbial innovation and environmental change over deep time.
The novel microbial metabolism discovered extended the known physiology of bacteria, and implied iron oxides as potential oxidants for biological sulfide oxidation in anoxic environment before the GOE. This reconciles the timing of dissimilatory sulfide oxidation along the Earth’s geochemical evolution and offers a more nuanced picture of sulfur cycle in the ancient Earth.
The new information about tempo and mode of sulfur cycle evolution from this project may represent a foundation to better inform future ecosystem models that can predict the outcome of anthropogenic activities and global change on planetary element cycles. This fits EU’s environment policy and the Sustainable Development Goal 13-15 by the WHO, targeting sustainable marine and terrestrial ecosystems.
The delineation of a key sulfur oxidation system across geological time reveals a compelling evolutionary trajectory toward the modern, complex dissimilatory sulfur oxidation metabolism, shaped by the Earth’s progressive oxygenation. These findings illuminate the intricate interplay between sulfur redox chemistry, microbial evolutionary adaptation, and planetary history, offering a more holistic understanding of how life have co-evolved with biogeochemical cycles. By integrating molecular phylogenies with geochemical and geological evidence, this research exemplifies a framework for reconstructing the evolution of Earth's biogeochemical systems, highlighting the dynamic feedbacks between microbial innovation and environmental change over deep time.
The novel microbial metabolism discovered extended the known physiology of bacteria, and implied iron oxides as potential oxidants for biological sulfide oxidation in anoxic environment before the GOE. This reconciles the timing of dissimilatory sulfide oxidation along the Earth’s geochemical evolution and offers a more nuanced picture of sulfur cycle in the ancient Earth.
The new information about tempo and mode of sulfur cycle evolution from this project may represent a foundation to better inform future ecosystem models that can predict the outcome of anthropogenic activities and global change on planetary element cycles. This fits EU’s environment policy and the Sustainable Development Goal 13-15 by the WHO, targeting sustainable marine and terrestrial ecosystems.