Comparative genomics of the Nap2-2B clade reveals substrate partitioning and niche diversification among uncultured hydrocarbon-degrading Desulfotomaculales
- 1Institutional Research Office, Manila Central University
- 2Department of Biology, College of Arts and Sciences, Manila Central University
Abstract
Uncultured Nap2-2B bacteria (order Desulfotomaculales; formerly family Peptococcaceae) are frequently detected in methanogenic hydrocarbon-degrading environments, yet their metabolic diversity remains poorly understood. Here, we analysed 17 GTDB r232 metagenome-assembled genomes (MAGs) from four genera within this clade. A bac120 phylogeny places Nap2-2B as a monophyletic family-level lineage within Desulfotomaculales. Glycyl radical enzyme phylogeny and operon context reveal strict substrate partitioning: SCADC1-2-3 encodes alkylsuccinate synthase for aliphatic hydrocarbon activation, 46–80 and UBA4053 encode benzylsuccinate synthase for aromatic activation, and JAIMBK01 lacks hydrocarbon activation genes but retains complete dissimilatory sulfate reduction pathway genes. Pangenome-level pathway reconstruction identifies complementary cofactor biosynthetic potential, notably in cobalamin and pantothenate biosynthesis, consistent with possible cofactor complementation. Genome-scale metabolic modeling suggests that the alkane-degrading SCADC1-2-3 lineage can support syntrophic hexane degradation, whereas the aromatic lineage cannot grow on the alkane FBA test because it lacks AssA and PFOR. A parallel aromatic-substrate FBA for 46–80 MAGs did not yield growth under minimal curation, reflecting the greater complexity of the downstream benzoyl-CoA pathway. Together, these data support a syntrophic guild structured by substrate partitioning, putative cofactor complementation, and distinct electron-disposal strategies that may shape methanogenic hydrocarbon attenuation in anoxic tailings environments.
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BibTeX
@article{tan2026comparative,
title = {{Comparative genomics of the Nap2-2B clade reveals substrate partitioning and niche diversification among uncultured hydrocarbon-degrading Desulfotomaculales}},
author = {Boonfei Tan and Christian Zafra and Charmaine Ng},
journal = {Scientific Reports},
year = {2026},
month = jul,
doi = {10.1038/s41598-026-63016-x},
url = {https://doi.org/10.1038/s41598-026-63016-x},
note = {CC BY},
}
RIS
TY - JOUR
TI - Comparative genomics of the Nap2-2B clade reveals substrate partitioning and niche diversification among uncultured hydrocarbon-degrading Desulfotomaculales
AU - Boonfei Tan
AU - Christian Zafra
AU - Charmaine Ng
PY - 2026
DA - 2026/07/01
JO - Scientific Reports
DO - 10.1038/s41598-026-63016-x
UR - https://doi.org/10.1038/s41598-026-63016-x
AB - Uncultured Nap2-2B bacteria (order Desulfotomaculales; formerly family Peptococcaceae) are frequently detected in methanogenic hydrocarbon-degrading environments, yet their metabolic diversity remains poorly understood. Here, we analysed 17 GTDB r232 metagenome-assembled genomes (MAGs) from four genera within this clade. A bac120 phylogeny places Nap2-2B as a monophyletic family-level lineage within Desulfotomaculales. Glycyl radical enzyme phylogeny and operon context reveal strict substrate partitioning: SCADC1-2-3 encodes alkylsuccinate synthase for aliphatic hydrocarbon activation, 46–80 and UBA4053 encode benzylsuccinate synthase for aromatic activation, and JAIMBK01 lacks hydrocarbon activation genes but retains complete dissimilatory sulfate reduction pathway genes. Pangenome-level pathway reconstruction identifies complementary cofactor biosynthetic potential, notably in cobalamin and pantothenate biosynthesis, consistent with possible cofactor complementation. Genome-scale metabolic modeling suggests that the alkane-degrading SCADC1-2-3 lineage can support syntrophic hexane degradation, whereas the aromatic lineage cannot grow on the alkane FBA test because it lacks AssA and PFOR. A parallel aromatic-substrate FBA for 46–80 MAGs did not yield growth under minimal curation, reflecting the greater complexity of the downstream benzoyl-CoA pathway. Together, these data support a syntrophic guild structured by substrate partitioning, putative cofactor complementation, and distinct electron-disposal strategies that may shape methanogenic hydrocarbon attenuation in anoxic tailings environments.
SN - 2045-2322
ER -