Metagenomic sequence analysis for marine bacterial alkaline phosphatases

Haiwei Luo

（罗海伟，南卡罗莱那大学生物科学系）

Department of Biological Sciences

University of South Carolina

时间：12月17日，下午7：00-9：00

地点：曾呈奎楼 B-206

Talk Abstract：

In this talk, I will discuss some new aspects of ecology and evolution of alkaline phosphatase(APase). Based upon computational techniques and literature survey, we identified five prokaryotic APase gene families (PhoA1, PhoA2, PhoD, PhoX, PhoV) which catalyze the hydrolysis of phosphoester compounds in the ocean. We apply the PSI-BLAST technique with  sensitive position-specific scoring matrix as well as profile Hidden Markov Model, and find that some APase sequences from marine metagenome can be repeated recovered by different APase family sequences, indicating that those APase families may be ancient duplications, and that they may have been subject to divergent evolution rather than convergent evolution. This finding is also consistent with other experimental evidence for their specialized but overlapping niches in phosphoester compound hydrolysis.

We develop a bioinformatics pipeline for orthologue identification in metagenome. By applyingthis pipeline to APase gene families, we demonstrate that the normalized APase gene abundance is significantly higher in the surface waters of the Sargasso Sea than that of the North Pacific Subtropical Gyre (NPSG.). In conjugating with previous studies which have reported that the phosphate level in the surface water of the Sargasso Sea can be approximately two orders of magnitude lower than that in the NPSG, our results tentatively indicate that the microbial community in the Sargasso Sea may experience phosphate limitation to a much larger extent than that in the NPSG. Tentative taxonomic assignments of APase genes suggest that Alteromonadales and Burkholderiales appear to be responsible for the production of the majority of PhoA (1 & 2),PhoX, and PhoD sequences, while Bacteroidetes / Chlorobi group may potentially be an important phylotype in PhoV production in oligotrophic oceans.

We also examined the APase gene distribution in the genomes of representative marine bacterial genera. We find correlation with different lifestyles, i.e. that marine heterotrophic bacteria contain significantly more APase genes than marine autotrophic bacteria; genera associated with nutrient replete environments have less copies per genome than those for low nutrient regimes. Lastly,APase families are not randomly distributed among the dominant marine cyanobacteria genera.