Diversity and distribution of proteorhodopsin-containing microorganisms in marine environments

doi:10.1007/s11783-010-0278-y

Front Envir Sci Eng

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Issue () : 98-106 https://doi.org/10.1007/s11783-010-0278-y

RESEARCH ARTICLE

Diversity and distribution of proteorhodopsin-containing microorganisms in marine environments

Bo WEI(

)

School of Life Sciences, Xiamen University, Xiamen 361005, China

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Abstract

Proteorhodopsin (PR) is a recently discovered protein involved in the utilization of light energy. Several studies have shown that PR-containing microorganisms are widespread and compose a large proportion of the biomass in marine ecosystems. A better understanding of the ecological role of PR will help clarify the effect of the global flow of energy and the carbon cycle on marine communities. In this study, a bioinformatical database of PR codon sequences, the Global Distribution Database of Proteorhodopsin (GDDP), as a tool for analyzing the diversity and distribution of PR-containing microorganisms in marine environments throughout the world was designed. The community structure of PR microorganisms were also compared using PCR assays and UniFrac analyses of 12 samples collected from three water layers (0, 75, and 200 m) at four representative sites in the Pacific, Atlantic, and Indian Oceans. The results indicate that PR-containing microorganisms can be grouped into two distribution types: widespread and location-specific. Representative cases of the former include SAR11-PR and HOT2C01-PR. Interestingly, PR communities cluster by geographic locale but not by water depth.

Keywords proteorhodopsin (PR) microorganism community diversity marine environments

Corresponding Author(s): WEI Bo,Email:weibo88@gmail.com

Issue Date: 01 February 2012

Cite this article:

Bo WEI. Diversity and distribution of proteorhodopsin-containing microorganisms in marine environments[J]. Front Envir Sci Eng, 0, (): 98-106.

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https://academic.hep.com.cn/fese/EN/10.1007/s11783-010-0278-y
https://academic.hep.com.cn/fese/EN/Y0/V/I/98

Fig.1 Map of global ocean indicating the four sampling profile sites; a mosaic base map of chlorophyll—remote sensed images (Aqua-MODIS; http://oceancolor.gsfc.nasa.gov/) from 2005 to 2006

Tab.1 Richness and diversity as well as coverage estimates in all extract PR sequences based on comparison of number of OTUs calculated by the ACE nonparametric richness estimator and OTUs for varying percent protein sequence differences

Fig.2 Unrooted phylogenetic tree of 2100 PR sequences from global ocean samples that were extracted from GDDP with a bootstrap replicating 100 times. The taxonomy was noted around the tree

Fig.3 Phylogenetic analysis of PR sequences retrieved from four profiles sits. The tree was constructed by Bayesian method. All the nodes of the tree were supported by more than 50% MCMC posterior probability. Additional symbols show the total number of clones and where were they retrieved as represented by a sequence. Scale bars 5% estimated sequence divergence for PR

Fig.4 PCoA of PR sequences among 12 clone libraries as calculated using unweighted UniFrac analysis

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