D1FHS, the Type Strain of the Ammonia-Oxidizing Bacterium Nitrosococcus wardiae spec. nov.: Enrichment, Isolation, Phylogenetic, and Growth Physiological Characterization.

Lin Wang,Chee Kent Lim,Martin G. Klotz,Hongyue Dang,Thomas E. Hanson

doi:10.3389/fmicb.2016.00512

Abstract

An ammonia-oxidizing bacterium, strain D1FHS, was enriched into pure culture from a sediment sample retrieved in Jiaozhou Bay, a hyper-eutrophic semi-closed water body hosting the metropolitan area of Qingdao, China. Based on initial 16S rRNA gene sequence analysis, strain D1FHS was classified in the genus Nitrosococcus, family Chromatiaceae, order Chromatiales, class Gammaproteobacteria; the 16S rRNA gene sequence with highest level of identity to that of D1FHS was obtained from Nitrosococcus halophilus Nc4T. The average nucleotide identity between the genomes of strain D1FHS and N. halophilus strain Nc4 is 89.5%. Known species in the genus Nitrosococcus are obligate aerobic chemolithotrophic ammonia-oxidizing bacteria adapted to and restricted to marine environments. The optimum growth (maximum nitrite production) conditions for D1FHS in a minimal salts medium are: 50 mM ammonium and 700 mM NaCl at pH of 7.5 to 8.0 and at 37°C in dark. Because pertinent conditions for other studied Nitrosococcus spp. are 100–200 mM ammonium and <700 mM NaCl at pH of 7.5 to 8.0 and at 28–32°C, D1FHS is physiologically distinct from other Nitrosococcus spp. in terms of substrate, salt, and thermal tolerance.

Highlights

Jiaozhou Bay (36◦7 24.44 N 120◦14 44.3 E; Figure 1) is a semi-enclosed water body with a surface area of about 390 km2 and an average water depth of 7 m, located on the Southwestern coast of Shandong Peninsula, China
PCR performed with metagenomic DNA extracted from D1 enrichment culture targeting at universal 16S rRNA, gamma 16S rRNA and gamma-haoA genes, yielded correctly sized fragments, indicating that the D1 enrichment culture contained gamma-ammonia-oxidizing bacteria (AOB)
Universal 16S rRNA gene sequences were analyzed based on BLASTN searches of the NCBI database; 29 of the 40 sequences were best hits to 16S rRNA gene sequences from Nitrosococcus species: 87–98% identity to N. halophilus Nc4; 93–98% identity to N. oceani C-107, and 93– 98% identity to N. watsonii C-113

Summary

Introduction

Jiaozhou Bay (36◦7 24.44 N 120◦14 44.3 E; Figure 1) is a semi-enclosed water body with a surface area of about 390 km2 and an average water depth of 7 m, located on the Southwestern coast of Shandong Peninsula, China. Gamma-AOB in the genus Nitrosococcus are adapted to and restricted to marine environments (Table 1; Ward and O’Mullan, 2002) and strains representing three species are being maintained in pure culture (Campbell et al, 2011).

Results

Conclusion