Population Dynamics and Community Composition of Ammonia Oxidizers in Salt Marshes after the Deepwater Horizon Oil Spill

Abstract

The recent oil spill in the Gulf of Mexico had significant effects on microbial communities in the Gulf, but impacts on nitrifying communities in adjacent salt marshes have not been investigated. We studied persistent effects of oil on ammonia-oxidizing archaeal (AOA) and bacterial (AOB) communities and their relationship to nitrification rates and soil properties in Louisiana marshes impacted by the Deepwater Horizon oil spill. Soils were collected at oiled and unoiled sites from Louisiana coastal marshes in July 2012, 2 years after the spill, and analyzed for community differences based on ammonia monooxygenase genes (amoA). Terminal Restriction Fragment Polymorphism and DNA sequence analyses revealed significantly different AOA and AOB communities between the three regions, but few differences were found between oiled and unoiled sites. Community composition of nitrifiers was best explained by differences in soil moisture and nitrogen content. Despite the lack of significant oil effects on overall community composition, we identified differences in correlations of individual populations with potential nitrification rates between oiled and unoiled sites that help explain previously published correlation patterns. Our results suggest that exposure to oil, even 2 years post-spill, led to subtle changes in population dynamics. How, or if, these changes may impact ecosystem function in the marshes, however, remains uncertain.

Keywords: Deepwater Horizon; amoA; nitrification; oil spill; salt marsh.

FIGURE 1

Terminal Restriction Fragment Polymorphism (TRFLP) patterns of archaeal amoA genes from individual sediment samples collected from oiled and unoiled marshes in Terrebonne (TB), western Barataria (WB), and eastern Barataria (EB) bays. Each sample is labeled by the region, site number, and plot number. No data are available from EB1–2 due to low amplification signal. Samples used for clone library construction and sequencing of amoA genes are indicated with an asterisk.

FIGURE 2

Phylogenetic relationships among archaeal ammonia monooxygenase genes (amoA) inferred by the neighbor-joining algorithm. Numbers in parentheses indicate the number of clones in each OTU and symbols represent where sequences were recovered. OTUs in red are those that are unique to Louisiana marshes. Bootstrap values greater than 70% are shown on internal nodes.

FIGURE 3

Non-metric multidimensional scaling ordination based on TRFLP patterns of archaeal (A) and betaproteobacterial (B) amoA genes. Vectors indicate environmental variables (dashed lines) or TRFs (solid lines) significantly (p ≤ 0.01) correlated with one or both axes. The length and orientation of the lines indicate the relative strength and direction of the correlation, respectively. Percent of variation explained by each axis is indicated parenthetically.

FIGURE 4

Terminal Restriction Fragment Polymorphism patterns of betoproteobacterial amoA genes from individual sediment samples collected from oiled and unoiled marshes in Terrebonne (TB), western Barataria (WB), and eastern Barataria (EB) bays. Each sample is labeled by the region, site number, and plot number. No data are available from TB1–1, EB1–2, and EB1–4 due to low amplification signal. Samples used for clone library construction and sequencing of amoA genes are indicated with an asterisk.

FIGURE 5

Phylogenetic relationships among betaproteobacterial ammonia monooxygenase (amoA) deduced amino acid sequences inferred by the neighbor-joining algorithm. Numbers in parentheses indicate the number of clones in each OTU and symbols represent where sequences were recovered. OTUs in red are those that are unique to Louisiana marshes. Bootstrap values greater than 70% are shown on internal nodes.