Browsing by Author "Yu, Hang"

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Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea
(Public Library of Science, 2022-01) Chadwick, Grayson L.; Skennerton, Connor T.; Laso-Pérez, Rafael; Leu, Andy O.; Speth, Daan R.; Yu, Hang; Morgan-Lang, Connor; Hatzenpichler, Roland; Goudeau, Danielle; Malmstrom, Rex; Brazelton, William J.; Woyke, Tanja; Hallam, Steven J.; Tyson, Gene W.; Wegener, Gunter; Boetius, Antje; Orphan, Victoria J.
The anaerobic oxidation of methane coupled to sulfate reduction is a microbially mediated process requiring a syntrophic partnership between anaerobic methanotrophic (ANME) archaea and sulfate-reducing bacteria (SRB). Based on genome taxonomy, ANME lineages are polyphyletic within the phylum Halobacterota, none of which have been isolated in pure culture. Here, we reconstruct 28 ANME genomes from environmental metagenomes and flow sorted syntrophic consortia. Together with a reanalysis of previously published datasets, these genomes enable a comparative analysis of all marine ANME clades. We review the genomic features that separate ANME from their methanogenic relatives and identify what differentiates ANME clades. Large multiheme cytochromes and bioenergetic complexes predicted to be involved in novel electron bifurcation reactions are well distributed and conserved in the ANME archaea, while significant variations in the anabolic C1 pathways exists between clades. Our analysis raises the possibility that methylotrophic methanogenesis may have evolved from a methanotrophic ancestor.
Dynamical tides during the inspiral of rapidly spinning neutron stars: Solutions beyond mode resonance
(American Physical Society, 2024-07) Yu, Hang; Arras, Phil; Weinberg, Nevin N.
We investigate the dynamical tide in a gravitational wave (GW)-driven coalescing binary involving at least one neutron star (NS). The deformed NS is assumed to spin rapidly, with its spin axis antialigned with the orbit. Such an NS may exist if the binary forms dynamically in a dense environment, and it can lead to a particularly strong tide because the NS f-mode can be resonantly excited during the inspiral. We present a new analytical solution for the f-mode resonance by decomposing the tide into a resummed equilibrium component varying at the tidal forcing frequency and a dynamical component varying at the f-mode eigenfrequency that is excited only around mode resonance. This solution simplifies numerical implementations by avoiding the subtraction of two diverging terms as was done in previous analyses. It also extends the solution’s validity to frequencies beyond mode resonance. When the dynamical tide back reacts on the orbit, we demonstrate that the commonly adopted effective Love number is insufficient because it does not capture the tidal torque on the orbit that dominates the back reaction during mode resonance. An additional dressing factor originating from the imaginary part of the Love number is therefore introduced to model the torque. The dissipative interaction between the NS and the orbital mass multipoles is computed including the dynamical tide and shown to be subdominant compared to the conservative energy transfer from the orbit to the NS modes. Our study shows that orbital phase shifts caused by the 𝑙=3 and 𝑙=2 f-modes can reach 0.5 and 10 radians at their respective resonances if the NS has a spin rate of 850 Hz and direction antialigned with the orbit. Because of the large impact of the 𝑙=2 dynamical tide, a linearized analytical description becomes insufficient, calling for future developments to incorporate higher-order corrections. After mode excitation, the orbit cannot remain quasicircular, and the eccentricity excited by the 𝑙=2 dynamical tide can approach nearly 𝑒≃0.1, leading to nonmonotonic frequency evolution which breaks the stationary phase approximation commonly adopted by frequency domain phenomenological waveform constructions. Lastly, we demonstrate that the GW radiation from the resonantly excited f-mode alone can be detected with a signal-to-noise ratio exceeding unity at a distance of 50 Mpc with the next-generation GW detectors.
Physiological potential and evolutionary trajectories of syntrophic sulfate-reducing bacterial partners of anaerobic methanotrophic archaea
(Public Library of Science, 2023-09) Murali, Ranjani; Yu, Hang; Speth, Daan R.; Wu, Fabai; Metcalfe, Kyle S.; Crémière, Antoine; Laso-Pèrez, Rafael; Malmstrom, Rex R.; Goudeau, Danielle; Woyke, Tanja; Hatzenpichler, Roland; Chadwick, Grayson L.; Connon, Stephanie A.; Orphan, Victoria J.
Sulfate-coupled anaerobic oxidation of methane (AOM) is performed by multicellular consortia of anaerobic methanotrophic archaea (ANME) in obligate syntrophic partnership with sulfate-reducing bacteria (SRB). Diverse ANME and SRB clades co-associate but the physiological basis for their adaptation and diversification is not well understood. In this work, we used comparative metagenomics and phylogenetics to investigate the metabolic adaptation among the 4 main syntrophic SRB clades (HotSeep-1, Seep-SRB2, Seep-SRB1a, and Seep-SRB1g) and identified features associated with their syntrophic lifestyle that distinguish them from their non-syntrophic evolutionary neighbors in the phylum Desulfobacterota. We show that the protein complexes involved in direct interspecies electron transfer (DIET) from ANME to the SRB outer membrane are conserved between the syntrophic lineages. In contrast, the proteins involved in electron transfer within the SRB inner membrane differ between clades, indicative of convergent evolution in the adaptation to a syntrophic lifestyle. Our analysis suggests that in most cases, this adaptation likely occurred after the acquisition of the DIET complexes in an ancestral clade and involve horizontal gene transfers within pathways for electron transfer (CbcBA) and biofilm formation (Pel). We also provide evidence for unique adaptations within syntrophic SRB clades, which vary depending on the archaeal partner. Among the most widespread syntrophic SRB, Seep-SRB1a, subclades that specifically partner ANME-2a are missing the cobalamin synthesis pathway, suggestive of nutritional dependency on its partner, while closely related Seep-SRB1a partners of ANME-2c lack nutritional auxotrophies. Our work provides insight into the features associated with DIET-based syntrophy and the adaptation of SRB towards it.