Structure and function of methanogens along a short-term restoration chronosequence in the Florida Everglades

Abstract

The removal of plants and soil to bedrock to eradicate exotic invasive plants within the Hole-in-the-Donut (HID) region, part of the Everglades National Park (Florida), presented a unique opportunity to study the redevelopment of soil and the associated microbial communities in the context of short-term primary succession and ecosystem restoration. The goal of this study was to identify relationships between soil redevelopment and activity and composition of methanogenic assemblages in HID soils. Methane production potentials indicated a general decline in methanogenic activity with restoration age. Microcosm incubations strongly suggested hydrogenotrophic methanogenesis as the most favorable pathway for methane formation in HID soils from all sites. Culture-independent techniques targeting methyl coenzyme M reductase genes (mcrA) were used to assess the dynamics of methanogenic assemblages. Clone libraries were dominated by sequences related to hydrogenotrophic methanogens of the orders Methanobacteriales and Methanococcales and suggested a general decline in the relative abundance of Methanobacteriales mcrA with time since restoration. Terminal restriction fragment length polymorphism analysis indicated methanogenic assemblages remain relatively stable between wet and dry seasons. Interestingly, analysis of soils across the restoration chronosequence indicated a shift in Methanobacteriales populations with restoration age, suggesting genotypic shifts due to site-specific factors.

FIG. 1.

Neighbor-joining mcrA tree for representative clones from April 2004 soils. Scale bar represents 10% sequence divergence. Numbers at nodes represent percentage of bootstrap resamplings based on 100 replicates. Values greater than 85 are shown, while black dots (•) on nodes represent values between 50 and 85.

FIG. 2.

Distribution of mcrA sequences obtained from dry season soils within designated phylogenetic clusters.

FIG. 3.

Community dynamics for mcrA in dry season HID soils determined by T-RFLP analysis. y-axis values represent percentages of total fluorescence.

FIG. 4.

Community dynamics for the mcrA gene in wet season HID soils determined by T-RFLP analysis. y-axis values represent percentages of total fluorescence.