Diversity of the Ring-Cleaving Dioxygenase Gene pcaH in a Salt Marsh Bacterial Community

Abstract

Degradation of lignin-related aromatic compounds is an important ecological process in the highly productive salt marshes of the southeastern United States, yet little is known about the mediating organisms or their catabolic pathways. Here we report the diversity of a gene encoding a key ring-cleaving enzyme of the ␤-ketoadipate pathway, pcaH, amplified from bacterial communities associated with decaying Spartina alterniflora, the salt marsh grass that dominates these coastal systems, as well as from enrichment cultures with aromatic substrates (p-hydroxybenzoate, anthranilate, vanillate, and dehydroabietate). Sequence analysis of 149 pcaH clones revealed 85 unique sequences. Thirteen of the 53 amino acid residues compared were invariant in the PcaH proteins, suggesting that these residues have a required catalytic or structural function. Fifty-eight percent of the clones matched sequences amplified from a collection of 36 bacterial isolates obtained from seawater, marine sediments, or senescent Spartina. Fifty-two percent of the pcaH clones could be assigned to the roseobacter group, a marine lineage of the class ␣-Proteobacteria abundant in coastal ecosystems. Another 6% of the clones matched genes retrieved from isolates belonging to the genera Acinetobacter, Bacillus, and Stappia, and 42% of the clones could not be assigned to a cultured bacterium based on sequence identity. These results suggest that the diversity of the genes encoding a single step in aromatic compound degradation in the coastal marsh examined is high.

Physiological, Ecological, and Phylogenetic Characterization of Stappia , a Marine CO-Oxidizing Bacterial Genus

“…Stappia sp. strains SE 09 and SE11 were obtained from the Duplin River, Georgia (A. Buchan, University of Tennessee) (3). Stappia strains M4 and M8 were obtained from enrichments based on marine macroalgae as previously described (13).…”

“…Stappia stellulata and Stappia aggregata were originally isolated from coastal marine water column and sediment samples, assigned to the genus Agrobacterium, and subsequently transferred to the genus Stappia (1,29,38). Stappia alba (27), Stappia marina (9), and various Stappia-like isolates have since been obtained from numerous widely distributed sources, including warm temperate surface and permanently cold deep-sea waters, sediments, phytoplankton, macroalgae, invertebrates, and salt marshes (2,3,5,9,13,17,26,27,33; Donachie et al, unpublished data). In addition, the presence of Stappia or Stappia-like taxa in a similar range of habitats has also been inferred from cultivation-independent analyses (3,26;Donachie et al,unpublished).…”

“…Results of subsequent studies have shown that Stappia-like isolates can account for a significant percentage of cultivable ␣-Proteobacteria containing dioxygenase genes (3). Stappia or Stappia-like isolates have been reported to produce sodium channel-blocking proteins (5,34) and a rhizobactin-like siderophore (20).…”

Diverse Organization of Genes of the β-Ketoadipate Pathway in Members of the Marine Roseobacter Lineage

“…Representatives of this lineage are abundant in coastal seawater, aerobic sediments, and decaying plant material from coastal salt marshes (9,19,28,45). The presence of the protocatechuate branch of the ␤-ketoadipate pathway has been demonstrated in several isolates, and roseobacters have widespread capabilities for the transformation of lignin-related aromatic monomers, including p-hydroxybenzoate, vanillate, and ferulate (4,5). Furthermore, more than half of the pcaH genes retrieved by PCR amplification from salt marsh bacterial communities could be traced to members of the Roseobacter lineage (5).…”

“…The presence of the protocatechuate branch of the ␤-ketoadipate pathway has been demonstrated in several isolates, and roseobacters have widespread capabilities for the transformation of lignin-related aromatic monomers, including p-hydroxybenzoate, vanillate, and ferulate (4,5). Furthermore, more than half of the pcaH genes retrieved by PCR amplification from salt marsh bacterial communities could be traced to members of the Roseobacter lineage (5). To gain a better perspective on the conservation of sequence and gene arrangement in closely related organisms, we analyzed the protocatechuate branch of the ␤-ketoadipate pathway in eight Roseobacter group isolates.…”