Collaborators: David A. C. Beck (eScience & Chemical Engineering), Mila Chistoserdova (Chemical Engineering), Mary Lidstrom (Chemical Engineering, Microbiology)
Nonmetric multidimensional scaling (NMDS) of read counts. NMDS was computed with vegan (Oksanen et al., 2013) using the Bray-Curtis dissimilarity index with a final stress of 0.156. The unamended sediment samples appear grouped at the figure left-top. Trajectories for the first replicate of each HO and LO condition are shown using cyan and magenta lines, respectively, connecting the sampling points. Samples from other replicates are also shown using the same color scheme. OTUs appear as text.
We observe the dynamics of bacterial communities in response to methane stimulus in laboratory microcosm incubations prepared with Lake Washington sediment samples. We first measured taxonomic compositions of eleven independent long-term enrichment cultures and determined that, while dominated by Methylococcaceae types, these cultures also contained accompanying types belonging to a limited number of bacterial taxa, both methylotrophs and non-methylotrophs. We then followed the short-term community dynamics, in two oxygen tension regimens (‘high’, 150 mM and ‘low’, 15 mM), observing rapid loss of species diversity. In all microcosms, a single type of Methylobacter represented the major methane-oxidizing partner in the community. The accompanying members of the communities revealed different trajectories in response to different oxygen tensions. While Methylotenera species were the early responders to methane stimulus under both conditions, under the ‘high’ oxygen condition they were replaced by successions of other bacteria, both methylotrophs and non-methylotrophs. Under the ‘low’ oxygen condition, the Methylotenera partners were more persistent, with the early-responder ecotype being succeeded by a different ecotype. The communities in both conditions were convergent in terms of their assemblage, suggesting selection for specific taxa. Our results support prior observations from metagenomics on distribution of carbon from methane among diverse bacterial populations and further suggest that communities are jointly responsible for methane cycling, rather than a single type of microbe.
Publications:
- Methane-fed microbial microcosms show differential community dynamics and pinpoint taxa involved in communal response
- Genomics of methylotrophy in Gram-positive methylamine-utilizing bacteria
- Multiphyletic origins of methylotrophy in Alphaproteobacteria, exemplified by comparative genomics of Lake Washington isolates
- Oxygen availability is a major factor in determining the composition of microbial communities involved in methane oxidation
- New Insights into the Factors Defining the Composition of Methane-oxidizing Communities and the Role of Oxygen
Software:
- 16S community profiling pipeline for analysis of ribosomal amplicon sequencing & analysis
- 16S profiling analysis of variable oxygen tension methane enrichments sequenced by illumina
Data: