Elevated nitrate enriches microbial functional genes for potential bioremediation of complexly contaminated sediments

Abstract

Nitrate is an important nutrient and electron acceptor for microorganisms, having a key role in nitrogen (N) cycling and electron transfer in anoxic sediments. High-nitrate inputs into sediments could have a significant effect on N cycling and its associated microbial processes. However, few studies have been focused on the effect of nitrate addition on the functional diversity, composition, structure and dynamics of sediment microbial communities in contaminated aquatic ecosystems with persistent organic pollutants (POPs). Here we analyzed sediment microbial communities from a field-scale in situ bioremediation site, a creek in Pearl River Delta containing a variety of contaminants including polybrominated diphenyl ethers (PBDEs) and polycyclic aromatic hydrocarbons (PAHs), before and after nitrate injection using a comprehensive functional gene array (GeoChip 4.0). Our results showed that the sediment microbial community functional composition and structure were markedly altered, and that functional genes involved in N-, carbon (C)-, sulfur (S)-and phosphorus (P)- cycling processes were highly enriched after nitrate injection, especially those microorganisms with diverse metabolic capabilities, leading to potential in situ bioremediation of the contaminated sediment, such as PBDE and PAH reduction/degradation. This study provides new insights into our understanding of sediment microbial community responses to nitrate addition, suggesting that indigenous microorganisms could be successfully stimulated for in situ bioremediation of POPs in contaminated sediments with nitrate addition.

Figure 1

Cluster analysis of functional genes detected using GeoChip 4.0. The figure was generated using CLUSTER and visualized in TREEVIEW (http://rana.lbl.gov/EisenSoftware.htm). Black indicates signal intensities below the threshold value, and red indicates a positive hybridization signal. The color intensity indicates differences in signal intensity. The samples from different sampling points were clearly separated. Five different gene patterns were observed and indicated by numbers in the tree (a), and they were represented as group 1 to 5 on axis x and the relative abundances of the gene signal intensity contained in different groups were presented on axis y in the graphs (b).

Figure 2

The commonly significantly increased functional genes from the microorganisms with metabolic versatility. ^aThe number of gene family detected for C-, N-, P- and S-cycling processes. The calculation of percentage change was based on the average signal intensity of each microorganism. Significances between the samples from the initial stage and different time points following nitrate amendment were performed by the Student t-test. ***P<0.01; **P<0.05; *P<0.1.

Figure 3

Effects of nitrate addition on abundances of functional genes involved in N cycling. The upward bars present the positive percentage changes, whereas the downward bars present the negative percentage changes. Significances between the samples from the initial stage and different time points following nitrate amendment were performed by the Student t-test. ***P<0.01; **P<0.05; *P<0.1.

Figure 4

Effects of nitrate addition on abundances of functional genes involved in S cycling. Significances between the samples from the initial stage and different time points following nitrate amendment were performed by the Student t-test. ***P<0.01; **P<0.05; *P<0.1.

Figure 5

A concept model for effects of nitrate on microbial functional communities in complexly contaminated sediments.