Investigation of the microbial community and methane cycle of a pine forest soil using Phylochips and qPCR

Background/Question/Methods

Methane (CH₄) is the second most important anthropogenic greenhouse gas. Methane is produced by methanogenic archaea in anaerobic conditions and consumed by methanotrophic bacteria in well-aerated soil. Methane accumulation in the atmosphere has become erratic in the last two decades after several decades of exponential increase. A bottom-up approach, of the root causes of methane production and consumption on local and ecosystem scales, is needed to better predict future trends. This study sought to examine the impacts of environmental variation and a nitrogen manipulation experiment on the diversity of the microbial community and the abundance of microbes involved in the CH₄ cycle of a Pine forest soil.

Field study was conducted in the NJ Pinelands at 36 plots across two sites, separated by 40-50m, which differed in water table height but shared overstory vegetation. Analysis of the microbial composition of the Pinelands sites was performed using quantitative polymerase chain reaction (qPCR) and G3 Phylochip 16S DNA microarrays. QPCR was used in order to enumerate copies of two target functional genes: pmoA, which encodes for enzymes that mediate CH₄ oxidation, and mcrA, which is involved in CH₄ production, while the Phylochips, which probe for all microorganisms on the chip within an environmental 16S DNA sample, were used to explore the metagenomic diversity of the soil under different conditions and treatments.

Results/Conclusions

Measurements performed over a five-month growing season in 2009 showed greater CH₄ consumption, and lower soil moisture, in the well-drained site. The total magnitude of CH₄ consumption in all well-drained plots at this site was -5.38 kg CH₄ ha^-1 yr^-1, which is similar to a recently published global average for forest CH₄ consumption, -5.70 kg CH₄ ha^-1 yr^-1. The well and poorly drained sites were found to differ in overall diversity of microorganisms and in the abundance of gene copies of both pmoA and mcrA. The average concentration of mcrA and pmoA

in the poorly-drained site, 47.2 and 9,406.5 gene copies/ul DNA, respectively, were greater than that of the well-drained site, 0.003 and 1,156.3 copies/ul DNA, respectively (p < 0.001). Phylochips confirmed that the diversity of the microbial communities differed between the two sites (p < 0.006) based on non-metric multi-dimensional scaling (NMDS) ordination. As the overall methane uptake by this site is similar to that of temperate forests around the world, the findings at this site may be relevant to many other forests.