Distribution and diversity of archaeal ammonia monooxygenase genes associated with corals

Abstract

Corals are known to harbor diverse microbial communities of Bacteria and Archaea, yet the ecological role of these microorganisms remains largely unknown. Here we report putative ammonia monooxygenase subunit A (amoA) genes of archaeal origin associated with corals. Multiple DNA samples drawn from nine coral species and four different reef locations were PCR screened for archaeal and bacterial amoA genes, and archaeal amoA gene sequences were obtained from five different species of coral collected in Bocas del Toro, Panama. The 210 coral-associated archaeal amoA sequences recovered in this study were broadly distributed phylogenetically, with most only distantly related to previously reported sequences from coastal/estuarine sediments and oceanic water columns. In contrast, the bacterial amoA gene could not be amplified from any of these samples. These results offer further evidence for the widespread presence of the archaeal amoA gene in marine ecosystems, including coral reefs.

FIG. 1.

Phylogenetic relationships among coral-associated archaeal amoA sequences and previously reported environmental sequences. This tree is a neighbor-joining tree based on Jukes-Cantor-corrected DNA distances and is midpoint rooted. Sequences are color coded according to coral sample, and each sequence name denotes the coral species, the sample number, and the individual sequence number. For example, DS4-7 represents Diploria strigosa, sample number 4, sequence number 7. Previously reported environmental sequences are shown in black, and (meta)genomic sequences are in bold. Clusters are color coded by the most well-represented library within the cluster. A distance scale bar is at the lower left, and bootstrap values (>60%) are indicated at branch points, with distance bootstrap values above the line and parsimony values below. The tree includes 370 environmental sequences from soils, sediments, and the ocean (10) (accession no. DQ14825 to DQ14848 and DQ148573 to DQ148905), 3 sequences from Monterey Bay and Antarctic surface waters (13) (accession no. DQ333419, DQ333421, and DQ433422), 99 sequences from wastewater treatment plants and estuarine sediments (31) (accession no. DQ278494 to DQ278592), 74 soil sequences (25) (accession no. DQ534815 to DQ534888), 218 sequences from estuarine sediments (1) (accession no. DQ500959 to DQ501176), metagenomic sequences from the Sargasso Sea and German soil (accession no. AACY01435967 and AJ627422), the amoA gene from N. maritimus (accession no. DQ085098), and two amoA genes from C. symbiosum (accession no. DQ397569 and DQ397580).