Survey of the bacteriophage phoH gene in wetland sediments in northeast China

Xiang Li,Qin Yao,Junjie Liu,Yan Sun,Guanghua Wang

doi:10.1038/s41598-018-37508-4

Xiang Li, Qin Yao + Show 3 more

Open Access

https://doi.org/10.1038/s41598-018-37508-4

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Abstract

PhoH is a host-derived auxiliary metabolic gene that can be used as a new biomarker for surveying phage diversity in marine and paddy waters. However, the applicability of this gene in other environments has not been addressed. In this paper, we surveyed the phoH gene in four wetland sediments in northeast China. DNA was extracted directly from sediments and used for PCR amplification with the degenerate primers vPhoHf and vPhoHr. In total, 44 and 58 phoH sequences were identified as belonging to bacteria and phages, respectively, suggesting that this primer set is not highly specific to the phage phoH gene. A BLASTp search showed that the 58 phage phoH sequences had the highest identity to the known viral sequences, ranging from 48% to 100%. Phylogenetic analysis showed that all phage sequences from wetlands distributed into the previously designated Groups 2, 3, 4 and 6. In addition, two new subgroups, Groups 2c and 4c, which contained sequences exclusively from wetlands, were detected in this study. Nonmetric multidimensional scaling analysis showed that the phage phoH assemblage from a coastal wetland was similar to that in marine environments, while the phage phoH assemblage from a lake wetland was similar to that in paddy waters. These findings indicated that different types of wetlands had distinct phage phoH compositions.

Highlights

Phage auxiliary metabolic genes (AMGs) were originally from the genomes of cellular microorganisms but have been detected in several phage genomic sequences[1]
More than 400 phage phoH sequences were recently obtained from several paddy floodwaters in northeast China, and 4 specific groups and 7 subgroups of phage phoH were detected in paddy waters[14]
Our research group further isolated 424 sequences of phage phoH from four paddy floodwaters in northeast China, indicating that this primer set was applicable for studying phage diversity in both marine and paddy waters[14]

Summary

Introduction

Phage auxiliary metabolic genes (AMGs) were originally from the genomes of cellular microorganisms but have been detected in several phage genomic sequences[1]. The phoH gene was detected in various morphological types of phages (including siphophages, myophages and podophages) and in a wide host range (including autotrophic and heterotrophic bacteria) and even in the viruses of autotrophic eukaryotes[8] By using this gene, viral phoH sequences in the Sargasso Sea and worldwide oceans were clustered into six novel groups (Groups 1~6). More than 400 phage phoH sequences were recently obtained from several paddy floodwaters in northeast China, and 4 specific groups and 7 subgroups of phage phoH were detected in paddy waters[14] These findings suggest that this biomarker gene can be used to investigate the diversity of phages in both marine and terrestrial environments. The objectives were (i) to test whether the phage phoH gene can be obtained from natural wetlands; (ii) to compare the phage phoH sequence diversity and novelty with known sequences; and (iii) to compare the difference or similarity of phage phoH assemblages in natural wetlands with that in marine and paddy fields

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