New publication on methylotrophic methanogens in freshwater wetlands

This study uses field work, laboratory microcosms, and multiple types of omics data to gain new insights into how methylotrophic methanogens contribute to carbon cycling in the Old Woman Creek freshwater wetlands.

Narrowe, A.B., Borton, M.A., Hoyt, D.W., Smith, G.J., Daly, R.A., Angle, J.C., Eder, E.K., Wong, A.R., Wolfe, R.A., Pappas, A., Bohrer, G., Miller, C.S. & Wrighton, K.C., 2019. Uncovering the Diversity and Activity of Methylotrophic Methanogens in Freshwater Wetland Soils W. Orsi, ed. mSystems, 4(6), pp.e00320-19. [link to mSystems]

ABSTRACT

Wetland soils are one of the largest natural contributors to the emission of methane, a potent greenhouse gas. Currently, microbial contributions to methane emissions from these systems emphasize the roles of acetoclastic and hydrogenotrophic methanogens, while less frequently considering methyl-group substrates (e.g., methanol and methylamines). Here, we integrated laboratory and field experiments to explore the potential for methylotrophic methanogenesis in Old Woman Creek (OWC), a temperate freshwater wetland located in Ohio, USA. We first demonstrated the capacity for methylotrophic methanogenesis in these soils using laboratory soil microcosms amended with trimethylamine. However, subsequent field porewater nuclear magnetic resonance (NMR) analyses to identify methanogenic substrates failed to detect evidence for methylamine compounds in soil porewaters, instead noting the presence of the methylotrophic substrate methanol. Accordingly, our wetland soil-derived metatranscriptomic data indicated that methanol utilization by the Methanomassiliicoccaceae was the likely source of methylotrophic methanogenesis. Methanomassiliicoccaceae relative contributions to mcrA transcripts nearly doubled with depth, accounting for up to 8% of the mcrA transcripts in 25-cm-deep soils. Longitudinal 16S rRNA amplicon and mcrA gene surveys demonstrated that Methanomassiliicoccaceae were stably present over 2 years across lateral and depth gradients in this wetland. Meta-analysis of 16S rRNA sequences similar (>99%) to OWC Methanomassiliicoccaceae in public databases revealed a global distribution, with a high representation in terrestrial soils and sediments. Together, our results demonstrate that methylotrophic methanogenesis likely contributes to methane flux from climatically relevant wetland soils.

New publication utilizing metagenomic data for understanding the evolution of translation

Complex evolutionary history of translation Elongation Factor 2 and diphthamide biosynthesis in Archaea and parabasalids

This is the product of a great collaboration with some excellent labs and people.

Diphthamide is a modified histidine residue which is uniquely present in archaeal and eukaryotic elongation factor 2 (EF-2), an essential GTPase responsible for catalyzing the coordinated translocation of tRNA and mRNA through the ribosome. In part due to the role of diphthamide in maintaining translational fidelity, it was previously assumed that diphthamide biosynthesis genes (dph) are conserved across all eukaryotes and archaea. Here, comparative analysis of new and existing genomes reveals that some archaea (i.e., members of the Asgard superphylum, Geoarchaea, and Korarchaeota) and eukaryotes (i.e., parabasalids) lack dph. In addition, while EF-2 was thought to exist as a single copy in archaea, many of these dph-lacking archaeal genomes encode a second EF-2 paralog missing key-residues required for diphthamide modification and for normal translocase function, perhaps suggesting functional divergence linked to loss of diphthamide biosynthesis. Interestingly, some Heimdallarchaeota previously suggested to be most closely related to the eukaryotic ancestor maintain dph genes and a single gene encoding canonical EF-2. Our findings reveal that the ability to produce diphthamide, once thought to be a universal feature in archaea and eukaryotes, has been lost multiple times during evolution, and suggest that anticipated compensatory mechanisms evolved independently.

GBE paper figure 3

Graduation

The lab feels like it’s emptying out, with 1 PhD, 1 MS, and 2 BS graduates this May. Congratulations to:
Dr. Adrienne Narrowe, PhD (with both the College of Liberal Arts and Sciences and the Department of Integrative Biology outstanding Defense awards)
David Banks-Richardson, MS Biology
Maria Nikulkova, BS Biology
Connor Jacobs, BS Biology

A great accomplishment for each of them, and I can’t wait to see what each accomplishes next.

New freshwater wetlands / methane publication

Our Old Woman Creek Wetlands team has a new publication out revealing that much of the methane in this wetland appears to come from a novel methanogen residing in surface, oxygenated soils.  Congratulations and thanks to the Wrighton and Bohrer labs, who led this work.

Angle, J.C., Morin, T.H., Solden, L.M., Narrowe, A.B., Smith, G.J., Borton, M.A., Rey-Sanchez, C., Daly, R.A., Mirfenderesgi, G., Hoyt, D.W., Riley, W.J., Miller, C.S., Bohrer, G. & Wrighton, K.C., 2017. Methanogenesis in oxygenated soils is a substantial fraction of wetland methane emissions. Nature Communications, 8(1), p.1567.

https://www.nature.com/articles/s41467-017-01753-4

Figure 2 explains why this archaea is called Candidatus Methanothrix paradoxum.  This paper is the whole enchilada: genomics, transcriptomics, extensive in situ methane measurements, emissions modeling, 16S and biogeography.

 

Mallika Iyer, MS

Congratulations to Mallika, who successfully defended her MS Thesis, “Prediction of Prokaryotic Optimum Growth Temperature Based on Genomic And Proteomic Features.”  Mallika did a great job, showing her mastery of her research and the literature.

Mallika is off to the Burnham Institute to pursue her PhD with Adam Godzik.