Biology subjects

Song, Y. C.

Publications and source records attributed to Song, Y. C..

3 recordsLinked to original sources

bioRxiv2026

Genome-scale metabolic models reveal phylogenetic conservation of amino acid fermentation-linked metabolic traits in soil bacteria

Soil microorganisms drive biogeochemical cycling of carbon, nitrogen, and other elements, but the partitioning of metabolic fluxes among taxa remains poorly understood, limiting our ability to link community composition to ecosystem function. Genome-scale metabolic models (GEMs) offer a mechanistic framework to connect taxa and their metabolic pathways to these fluxes. However, heterogeneity of soil communities has hampered recovery of high-quality metagenome-assembled genomes (MAGs), constraining application of flux balance analysis (FBA) to soil metagenomes and skewing available GEMs towards cultured model organisms. This gap limits our understanding of soil microbial physiology and responses to disturbance. Here, we present a collection of GEMs for 550 MAGs (497 bacterial, 53 archaeal) recovered from 94 soil samples across the continental United States. As an example application, we used FBA to estimate uptake and secretion of 44 commonly exchanged metabolites and tested whether these fluxes are phylogenetically conserved. While the overall bacterial phylogenetic signal was weak (median r = 0.029), eight metabolites showed significant conservation: amino acids (L-methionine, L-leucine, L-isoleucine), fermentation intermediates (pyruvate, acetaldehyde, ethanol), and amino acid degradation by-products NH and CO2. Most bacterial MAGs were predicted to import branched-chain amino acids, and a subset also secreted pyruvate and ethanol, identifying candidate cross-feeding interactions. Thus, fermentation-linked traits may be phylogenetically conserved and predictable from community composition, whereas most other metabolites showed no detectable signal. Ultimately, this resource enables genome-resolved prediction of soil microbial metabolisms, from cross-feeding and carbon-use efficiency to community responses to disturbance, providing a mechanistic bridge between microbial taxonomy and ecosystem-scale biogeochemistry.

bioinformatics↗

bioRxiv2025

Continental-scale integration of soil metagenomes and metabolomes reveals ubiquitous microbial capacity for recalcitrant carbon decomposition.

Soil organic matter (SOM) decomposition by microorganisms represents one of the largest uncertainties in predicting terrestrial carbon-atmosphere feedbacks. Yet we lack systematic understanding of the microbial taxa that drive decomposition of chemically distinct carbon pools and of the metabolic pathways they employ across environmental gradients. Here, we address this critical gap using the first continental-scale soil dataset pairing shotgun metagenomes with high-resolution molecular characterization of SOM chemistry. We use data from 47 standardized soil cores - selected using microbial respiration rates from 106 soils across the United States - to assemble 0.76 terabases (Tbs) of prokaryotic metagenome-assembled genomes (828 MAGs) and identify 66,727 distinct SOM molecules. Integrating these datasets revealed widespread microbial potential for depolymerizing chemically-recalcitrant carbon compounds previously considered stable. Notably, we uncover complementary metabolic specialization between genera affiliated with two abundant bacterial orders, Rhizobiales and Chthoniobacterales, and an archaeal order, Nitrososphaerales. This metabolic partitioning is consistent across soil depths and activity levels, suggesting coordinated decomposition of chemically-complex carbon through distinct but complementary biochemical strategies. The metabolic potential for depolymerization of chemically-recalcitrant compounds is supported by the abundance of these molecules across the soils, as indicated by Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR-MS), and by flux balance analysis of metabolic models. Our continental-scale integration of microbial genotypes with their chemical substrates reveals that a substantial fraction of SOM that is considered to be relatively stable harbors decomposition potential that current Earth system models fail to capture. These findings provide mechanistic insight for incorporating microbial metabolic pathways into carbon cycle predictions and highlight an underappreciated vulnerability of soil carbon to environmental variability.

microbiology↗

bioRxiv2018

The cis-regulatory logic underlying abdominal Hox-mediated repression versus activation of regulatory elements in Drosophila

Hox genes encode a family of transcription factors that, despite having similar in vitro DNA binding preferences, regulate distinct genetic programs along the metazoan anterior-posterior axis. To better define mechanisms of Hox specificity, we compared and contrasted the ability of abdominal Hox factors to regulate two cis-regulatory elements within the Drosophila embryo. Both the Ultrabithorax (Ubx) and Abdominal-A (Abd-A) Hox factors form cooperative complexes with the Extradenticle (Exd) and Homothorax (Hth) transcription factors to repress the distal-less leg selector gene via the DCRE, whereas only Abd-A interacts with Exd and Hth on the RhoA element to activate a rhomboid serine protease gene that stimulates Epidermal Growth Factor secretion. By swapping binding sites between these elements, we found that the RhoA Exd/Hth/Hox site configuration that mediates Abd-A specific activation can also convey transcriptional repression by both Ubx and Abd-A when placed into the DCRE, but only in one orientation. We further show that the orientation and spacing of Hox sites relative to additional transcription factor binding sites within the RhoA and DCRE elements is critical to mediate appropriate cell- and segment-specific output. These results indicate that the interaction between Hox, Exd, and Hth neither determines activation vs repression specificity nor defines Ubx vs Abd-A specificity. Instead the precise integration of Hox sites with additional TF inputs is required for accurate transcriptional output. Taken together, these studies provide new insight into the mechanisms of Hox target and regulatory specificity as well as the constraints placed on regulatory elements to convey appropriate outputs.\n\nAuthor SummaryThe Hox genes encode a family of transcription factors that give cells within each region along the developing body plan a unique identity in animals from worms to mammals. Surprisingly, however, most of the Hox factors bind the same or highly similar DNA sequences. These findings raise a paradox: How can proteins that have highly similar DNA binding properties perform different functions in the animal by regulating different sets of target genes? In this study, we address this question by studying how two Hox factors regulate the expression of target genes that specify leg development and the making of liver-like cells in the developing fly. By comparing and contrasting how Hox target genes are activated and/or repressed, we found that the same Hox binding sites can mediate either activation or repression in a manner that depends upon context. In addition, we found that a Hox binding site that is normally regulated by only one Hox factor, can also be used by more than one Hox factor swapped into another target gene. These findings indicate that the specificity of a Hox factor to regulate target genes does not rely solely upon DNA binding specificity but also requires regulatory specificity.

developmental biology↗