Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community

Abstract

Microbial interactions have a key role in global geochemical cycles. Although we possess significant knowledge about the general biochemical processes occurring in microbial communities, we are often unable to decipher key functions of individual microorganisms within the environment in part owing to the inability to cultivate or study them in isolation. Here, we circumvent this shortcoming through the use of single-cell genome sequencing and a novel low-input metatranscriptomics protocol to reveal the intricate metabolic capabilities and microbial interactions of an alkane-degrading methanogenic community. This methanogenic consortium oxidizes saturated hydrocarbons under anoxic conditions through a thus-far-uncharacterized biochemical process. The genome sequence of a dominant bacterial member of this community, belonging to the genus Smithella, was sequenced and served as the basis for subsequent analysis through metabolic reconstruction. Metatranscriptomic data generated from less than 500 pg of mRNA highlighted metabolically active genes during anaerobic alkane oxidation in comparison with growth on fatty acids. These data sets suggest that Smithella is not activating hexadecane by fumarate addition. Differential expression assisted in the identification of hypothetical proteins with no known homology that may be involved in hexadecane activation. Additionally, the combination of 16S rDNA sequence and metatranscriptomic data enabled the study of other prevalent organisms within the consortium and their interactions with Smithella, thus yielding a comprehensive characterization of individual constituents at the genome scale during methanogenic alkane oxidation.

Flavor Profile of Chinese Liquor Is Altered by Interactions of Intrinsic and Extrinsic Microbes

“…Although there are many reports about the individual transcription shift in a mixed culture containing two microbes (30,31), the individual metabolism shift in a two-microbe coculture is not enough to represent the changes of the whole community. The recent development of metatranscriptome sequencing provides an attractive method to reveal the systems-level transcriptional response of the microbial community (32). Therefore, our future work will be focused on the investigation of the transcription and metabolic shift of each microbial community member with the extrinsic microbial perturbation and the interactions between the microbes by use of a metatranscriptomic approach.…”

Comparative analysis of metagenomes from three methanogenic hydrocarbon-degrading enrichment cultures with 41 environmental samples

“…ME-1 (Embree et al, 2014;Tan et al, 2014A) (Figure 3). Five distinct putative assA genes were identified in SCADC (Figure 3), reflecting the diversity of alkane substrates degraded by this culture (Tan et al, 2013).…”

Re-analysis of omics data indicates Smithella may degrade alkanes by addition to fumarate under methanogenic conditions

“…Here we comment on three aspects of a recent report in ISME J (Embree et al, 2013), which concluded that: the draft genome of Smithella ME-1 lacks genes encoding alkylsuccinate synthase (ASS) subunits; it therefore does not express those genes when grown on n-hexadecane in mixed culture under methanogenic conditions; and it may use an alternate mechanism to initiate anaerobic n-hexadecane degradation. We have re-analyzed the draft genome of Smithella ME-1 and three metatranscriptomes, and reached conclusions opposite to those of Embree et al (2013).…”

“…We have re-analyzed the draft genome of Smithella ME-1 and three metatranscriptomes, and reached conclusions opposite to those of Embree et al (2013).…”