Microbial community composition and denitrifying enzyme activities in salt marsh sediments

Abstract

Denitrifying microbial communities and denitrification in salt marsh sediments may be affected by many factors, including environmental conditions, nutrient availability, and levels of pollutants. The objective of this study was to examine how microbial community composition and denitrification enzyme activities (DEA) at a California salt marsh with high nutrient loading vary with such factors. Sediments were sampled from three elevations, each with different inundation and vegetation patterns, across 12 stations representing various salinity and nutrient conditions. Analyses included determination of cell abundance, total and denitrifier community compositions (by terminal restriction fragment length polymorphism), DEA, nutrients, and eluted metals. Total bacterial (16S rRNA) and denitrifier (nirS) community compositions and DEA were analyzed for their relationships to environmental variables and metal concentrations via multivariate direct gradient and regression analyses, respectively. Community composition and DEA were highly variable within the dynamic salt marsh system, but each was strongly affected by elevation (i.e., degree of inundation) and carbon content as well as by selected metals. Carbon content was highly related to elevation, and the relationships between DEA and carbon content were found to be elevation specific when evaluated across the entire marsh. There were also lateral gradients in the marsh, as evidenced by an even stronger association between community composition and elevation for a marsh subsystem. Lastly, though correlated with similar environmental factors and selected metals, denitrifier community composition and function appeared uncoupled in the marsh.

FIG. 1.

Study location including 12 sampling stations. The stations are divided into four groups: stations along the main channel of West Creek (A, B, C, D, E, and I), stations on branches of West Creek (G and J), stations along the central road (H, F, and K), and a station further east of the marsh (L).

FIG. 2.

Dissolved nutrient concentrations in bulk water samples overlying low-elevation sampling sites at each station: nitrate (A), ammonium (B), and phosphate (C). Concentrations were based on single-sample measurements. Inset graphs exclude station A to emphasize differences across the remaining stations. Vertical dashed lines separate the groups of stations described in the legend to Fig. 1.

FIG. 3.

TOC (A) and DOC (B) for three elevations (high, middle, and low) at each station. Vertical dashed lines separate the groups of stations described in the legend to Fig. 1. Asterisks in panel A denote stations where TOC differed significantly across elevations. DOC differed significantly across elevations in all 12 stations. The bars represent the mean values, and the error bars represent the standard deviations (n = 3).

FIG. 4.

Ordination diagram from pCCA of 16S TRFLP data, where elevations and DOC were used as covariables. Metals are represented by arrows, the lengths of which indicate the strength of correlation between the metal and the community data. Samples are labeled using their station names and denoted by triangles and circles. Open triangles pointing upward indicate high-elevation samples, filled triangles pointing downward indicate low-elevation samples, and filled circles indicate middle-elevation samples.

FIG. 5.

Ordination diagram from pCCA of nirS TRFLP data, where elevations and DOC were the covariables. Metals are represented by arrows, the lengths of which indicate the strength of correlation between the metal and the community data. Samples are labeled using their station names and denoted by triangles and circles. Open triangles pointing upward indicate high-elevation samples, filled triangles pointing downward indicate low-elevation samples, and filled circles indicate middle-elevation samples.

FIG. 6.

Total cell counts. Vertical dashed lines separate the groups of stations described in the legend to Fig. 1. Asterisks denote stations where total cell counts differed significantly across elevations. The bars represent the mean values, and the error bars represent the standard deviations (n = 3).

FIG. 7.

DEA measurements for three elevations (high, middle, and low) at each station. The inset graph excludes stations A and B to facilitate display. Vertical dashed lines separate the groups of stations described in the legend to Fig. 1. The data points represent the mean values, and the error bars represent the standard deviations (n = 3).

FIG. 8.

Relationship between DEA and DOC. Overall regression analysis across all three elevations yielded R² values of 0.092 and P values of 0.072. The data points represent the mean values, and the error bars represent the standard deviations (n = 3).