Phylogenetically diverse ureC genes and their expression suggest the urea utilization by bacterial symbionts in marine sponge Xestospongia testudinaria - PubMed (original) (raw)

Phylogenetically diverse ureC genes and their expression suggest the urea utilization by bacterial symbionts in marine sponge Xestospongia testudinaria

Jing Su et al. PLoS One. 2013.

Abstract

Urea is one of the dominant organic nitrogenous compounds in the oligotrophic oceans. Compared to the knowledge of nitrogen transformation of nitrogen fixation, ammonia oxidization, nitrate and nitrite reduction mediated by sponge-associated microbes, our knowledge of urea utilization in sponges and the phylogenetic diversity of sponge-associated microbes with urea utilization potential is very limited. In this study, Marinobacter litoralis isolated from the marine sponge Xestospongia testudinaria and the slurry of X. testudinaria were found to have urease activity. Subsequently, phylogenetically diverse bacterial ureC genes were detected in the total genomic DNA and RNA of sponge X. testudinaria, i.e., 19 operative taxonomic units (OTUs) in genomic DNA library and 8 OTUs in cDNA library at 90% stringency. Particularly, 6 OTUs were common to both the genomic DNA library and the cDNA library, which suggested that some ureC genes were expressed in this sponge. BLAST and phylogenetic analysis showed that most of the ureC sequences were similar with the urease alpha subunit of members from Proteobacteria, which were the predominant component in sponge X. testudinaria, and the remaining ureC sequences were related to those from Magnetococcus, Cyanobacteria, and Actinobacteria. This study is the first assessment of the role of sponge bacterial symbionts in the regenerated utilization of urea by the detection of transcriptional activity of ureC gene, as well as the phylogenetic diversity of ureC gene of sponge bacterial symbionts. The results suggested the urea utilization by bacterial symbionts in marine sponge X. testudinaria, extending our understanding of nitrogen cycling mediated by sponge-associated microbiota.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1. Urease activity of marine sponge X. testudinaria.

A: negative control; B: activity of sponge slurry; C: Marinobacter litoralis (bacterium isolated from the sponge).

Figure 2. Rarefaction curves of _ure_C and 16S rRNA gene sequences.

(Clusterization stringency at 90% and 97% for _ure_C and 16S rRNA gene, respectively.).

Figure 3. Unrooted phylogenetic tree based on urease alpha subunit (130aa) of sponge X. testudinaria using Neighbour-joining method.

The scale bar represents 0.05 substitutions per amino acids position. Bootstrap values (1,000 replicates) higher than 50% are shown. ○mark and _ure_C-D mean the OTU in genomic DNA library, and •mark and _ure_C-R mean the OTU in cDNA library. The number inside the parenthesis means the number of sequences within each OTU.

Figure 4. Unrooted phylogenetic tree based on bacterial 16S rRNA gene sequences (ca.1,400bp) of sponge X. testudinaria using Neighbour-joining method.

The scale bar represents 0.05 substitutions per nucleotide position. Bootstrap values (1,000 replicates) higher than 50% are shown. The number in brackets shows the number of sequences in each OTU. •mark means sequences from sponge X. testudinaria.

Figure 5. Pie charts illustrating the bacterial community based on 16S rRNA gene libraries of sponge X. testudinaria.

Sequences in libraries were classified using the Classifier Tool provided by the Ribosomal Database Project. Hierarchical taxa assignment was based on RDP naive Bayesian rRNA Classifier. Percentage represented specific value between the number of clones in each taxon and the number of all clones in 16S rRNA gene library.

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Phylogenetically diverse ureC genes and their expression suggest the urea utilization by bacterial symbionts in marine sponge Xestospongia testudinaria - PubMed (original) (raw)