Variation in prokaryotic community composition as a function of resource availability in tidal creek sediments

Abstract

In anaerobic coastal sediments, hydrolytic and/or fermentative bacteria degrade polymeric material and produce labile intermediates, which are used by terminal metabolizers to complete the conversion of organic material to CO(2). We used molecular approaches to evaluate the response of two bacterial terminal metabolizer groups from a coastal tidal creek sediments, sulfate reducers and methanogens, to controlled changes in carbon resource supply. Tidal creek sediment bioreactors were established in April and August 2004. For each date, intact sediment sections were continuously supplied with flowthrough seawater that was either unamended or amended with the high-molecular-weight polysaccharide dextran. Biogeochemical data indicate that the activity of fermenting bacteria and the terminal metabolizers was limited by organic carbon supply during both experiments, with a significant increase in net volatile fatty acid (VFA) production and rates of sulfate reduction and methanogenesis following dextran addition. Community composition (measured by using terminal restriction fragment length polymorphism analysis, and functional gene [dsrA, mcrA] clone libraries) changed from April to August. However, community composition was not different between amended and unamended cores within each month, despite the change in resource level. Moreover, there was no relationship between community richness and evenness with resource level. This lack of variation in community composition with C addition could be attributed to the dynamic environment these sediment communities experience in situ. Fluctuations in VFA concentrations are most likely very high, so that the dominant bacterial species must be able to outcompete other species at both high and low resource levels.

FIG. 1.

Conceptual diagram predicting the pattern in microbial community richness and evenness in response to varying resource levels in a carbon amended (carbon amended, open symbols; unamended, closed symbols) experiment conducted in coastal marine sediments on two dates (April, circles; August, triangles).

FIG. 2.

Rates of microbial activity and bacterial fatty acid content in flowthrough sediment bioreactor experiments in April and August of 2004. Black bars represent values from unamended cores, white bars the carbon amended treatment. The x-axis and y-axis units are the same for all graphs except where indicated. Values were summed for the entire 9-day period of the carbon amendment except for PFLAs which denote sediment content at the termination of the experiment. Error bars are ±1 standard deviation (n = 2).

FIG. 3.

Multidimensional scaling of the Bray-Curtis similarity matrix generated using the relative abundance of T-RFLP peaks generated from 16S rRNA genes (A), OTUs assigned using dsrA genes (B), and OTUs assigned using mcrA genes (C). Carbon-amended (open symbols) and unamended (closed symbols) data are graphed for both April (circles) and August (triangles). Temporal (April versus August) differences were determined by using ANOSIM and were statistically significant for all datasets. For T-RFLP data, R = 0.573 and P = 0.029 (A); for dsrA sequences, R = 0.654 and P = 0.029 (B); and for mcrA sequences, R = 0.573 and P = 0.029 (C).

FIG. 4.

Community richness (left panels) and evenness (right panels) in sediment microbial communities calculated using dsrA sequences (A and B) and mcrA sequences (C and D) collected on day 9. x-axis values are the amount of carbon consumed during fermentation throughout the entire experiment, which should be equivalent to the amount of organic acids produced and therefore available to the terminal metabolizers. Carbon-amended (open symbols) and unamended (closed symbols) data are graphed for both April (circles) and August (triangles). Quadratic or linear regressions are shown when statistically significant (P < 0.10).

FIG. 5.

Neighbor-joining tree showing taxonomic positions of dsrA gene sequences from coastal marine sediments. Numbers in parentheses indicate the number of clones obtained for each sequence. Bootstrap values (percentage of 200 trials) for branch points are indicated when >50. Bar, 0.05 substitutions per sequence position. The presence of a particular OTU in carbon-amended (open symbols) and unamended (closed symbols) treatments are indicated for both April (circles) and August (triangles) directly adjacent to the OTU name.

FIG. 6.

Neighbor-joining tree showing taxonomic positions of mcrA gene sequences cloned from coastal marine sediments. Numbers in parentheses indicate the number of clones obtained for each sequence. Bootstrap values (percentage of 200 trials) for branch points are indicated when >50. Bar, 0.05 substitutions per sequence position. The presence of a particular OTU in carbon-amended (open symbols) and unamended (closed symbols) treatments are indicated for both April (circles) and August (triangles) directly adjacent to the OTU name.