Angel and Conrad 2009

Angel RA, Conrad R. 2009. In situ measurement of methane fluxes and analysis of transcribed particulate methane monooxygenase in desert soils. Environmental Microbiology 11: 2598-2610.

These authors examined the methanotroph communities of sub-tropical desert soils in Israel, using both field and lab measurements of methane fluxes and molecular investigation of sampled microbes. Negative surface flux, indicating consumption of atmospheric methane by soil, was found only at an undisturbed site in this study; the 4 other sites were varying degrees of agricultural and did not show clear patterns of consumption of methane at low concentrations. Addition of water, simulating a typical local rainfall event, eliminated methanotroph activity for about 12 hours, then this activity rebounded to well above background for up to 48 hours. This process of apparent short-term community dynamics was not investigated or discussed in much detail by these authors, though I found it one of the most interesting observations.

Methanotrophs were identified in soil samples by the usual suite of molecular biology methods. One set of primers used here is described as also targeting certain clades of amoA, a gene prominent in ammonia oxidation. These primers were successful at amplifying sequences even from soils in which methanotrophic activity had not been detected, suggesting that many or all of the sequences amplified by these primers were not actually methanotroph sequences, but rather sequences from apparently ubiquitous ammonia oxidizing bacteria.

The target gene for methanotrophs encodes a membrane-bound protein involved in transporting methane into the cytoplasm. From the way some primers also targeted amoA, I think perhaps there is a shared ancestry among the pathways for scavenging environmental ammonia and for scavenging environmental methane, though these authors do not delve into that discussion.

This paper was apparently instrumental in structuring the thoughts of my co-author (Dr. Siciliano) regarding how we should structure the manuscripts we are preparing based on the 2009 Alexandra Fjord field season. Up to this paper, we had been considering including both molecular analysis (based mainly on qPCR) and soil-properties (nutrients, root exudates, moisture, trace gases, etc.) in our nascent “Pits & Probes” manuscript. However, this paper demonstrates the considerable volume of work required to achieve a useful molecular dataset, suggesting that we would be better off saving these DNA data for a subsequent study, where they can be described and analyzed at the appropriate level of detail.