Site history and edaphic features override the influence of plant species on microbial communities in restored tidal freshwater wetlands

Abstract

Restored wetland soils differ significantly in physical and chemical properties from their natural counterparts even when plant community compositions are similar, but effects of restoration on microbial community composition and function are not well understood. Here, we investigate plant-microbe relationships in restored and natural tidal freshwater wetlands from two subestuaries of the Chesapeake Bay. Soil samples were collected from the root zone of Typha latifolia, Phragmites australis, Peltandra virginica, and Lythrum salicaria. Soil microbial composition was assessed using 454 pyrosequencing, and genes representing bacteria, archaea, denitrification, methanogenesis, and methane oxidation were quantified. Our analysis revealed variation in some functional gene copy numbers between plant species within sites, but intersite comparisons did not reveal consistent plant-microbe trends. We observed more microbial variations between plant species in natural wetlands, where plants have been established for a long period of time. In the largest natural wetland site, sequences putatively matching methanogens accounted for ∼17% of all sequences, and the same wetland had the highest numbers of genes coding for methane coenzyme A reductase (mcrA). Sequences putatively matching aerobic methanotrophic bacteria and anaerobic methane-oxidizing archaea (ANME) were detected in all sites, suggesting that both aerobic and anaerobic methane oxidation are possible in these systems. Our data suggest that site history and edaphic features override the influence of plant species on microbial communities in restored wetlands.

FIG 1

Principal component analysis (PCoA) ordination of the microbial community composition rarified to 1,922 sequences per sample. Mean relative abundance ± standard errors (SE) is plotted by site alone (n = 12) (a) and site by plant species (n = 3) (b).

FIG 2

Percent relative abundance of Bacteria (a) and Archaea (b) for five freshwater tidal wetlands (n = 12). The top 12 phyla in panel a represent the majority of the total bacterial sequences across all five sites (48 to 72%). The “Other” category represents the sum of 59 additional phyla, with 5% of the bar accounting for unclassified bacteria. The two major phyla in panel b represent 99% of the total identified archaeal sequences. Unclassified archaeal sequences are not shown.

FIG 3

Gene copy numbers gram⁻¹ of wet soil for genes targeting bacterial 16S rRNA (a), archaeal 16S rRNA (b), methyl coenzyme A reductase (mcrA) (c), and particulate methane monooxygenase (pmoA) (d). Values were calculated based on a linearized plasmid standard, and efficiencies were adjusted with a soil standard to account for inhibition. Each bar represents the mean (n = 3) ± SE. Note that panels have different y-axis ranges, and stars denote missing Lythrum at Wootons.

FIG 4

Percent relative abundance of sequences putatively identified as belonging to methanogen (a) and methanotroph (b) taxa; bars represent the site means (n = 12) ± SE. Methanoplasmatales represents the recently reclassified Thermoplasmata (47).

FIG 5

Gene copy numbers gram⁻¹ of wet soil for genes targeting nitric oxide reductase (nirK) (a), nitric oxide reductase (nirS) (b), and nitrous oxide reductase (nosZ) (c). Values were calculated based on a linearized plasmid standard, and efficiencies were adjusted with a soil standard to account for inhibition. Each bar represents the mean (n = 3) ± SE. Stars denote missing Lythrum at Wootons.