Nitrosococcus watsonii sp. nov., a new species of marine obligate ammonia-oxidizing bacteria that is not omnipresent in the world's oceans: calls to validate the names 'Nitrosococcus halophilus' and 'Nitrosomonas mobilis'.

Local associations between anammox bacteria and obligate aerobic bacteria in the genus Nitrosococcus appear to be significant for ammonia oxidation in oxygen minimum zones. The literature on the genus Nitrosococcus in the Chromatiaceae family of purple sulfur bacteria (Gammaproteobacteria, Chromatiales) contains reports on four described species, Nitrosococcus nitrosus, Nitrosococcus oceani, 'Nitrosococcus halophilus' and 'Nitrosomonas mobilis', of which only N. nitrosus and N. oceani are validly published names and only N. oceani is omnipresent in the world's oceans. The species 'N. halophilus' with Nc4(T) as the type strain was proposed in 1990, but the species is not validly published. Phylogenetic analyses of signature genes, growth-physiological studies and an average nucleotide identity analysis between N. oceani ATCC19707(T) (C-107, Nc9), 'N. halophilus' strain Nc4(T) and Nitrosococcus sp. strain C-113 revealed that a proposal for a new species is warranted. Therefore, the provisional taxonomic assignment Nitrosococcus watsonii is proposed for Nitrosococcus sp. strain C-113(T) . Sequence analysis of Nitrosococcus haoAB signature genes detected in cultures enriched from Jiaozhou Bay sediments (China) identified only N. oceani-type sequences, suggesting that different patterns of distribution in the environment correlate with speciation in the genus Nitrosococcus.

Ammonia-dependent differential regulation of the gene cluster that encodes ammonia monooxygenase in Nitrosococcus oceani ATCC 19707.

Molecular analysis of the ammonia monooxygenase-encoding gene cluster in Nitrosococcus oceani revealed that the amo genes are differentially expressed from three promoters dependent on the external ammonia concentration. Whereas a distal amoRCABD operon promoter, pC1, is active only in the presence of ammonia, identified proximal amoC (pC2) and amoA (pA) sigma-70-type promoters are constitutive. Promoter region pC2 also contains a consensus sequence for binding of RpoN, usually involved in nitrogen starvation response. Additional regulation of transcript stability by anti-termination and mRNA degradation are proposed and discussed.

Characterization of two new genes, amoR and amoD, in the amo operon of the marine ammonia oxidizer Nitrosococcus oceani ATCC 19707.

Molecular analysis of the amo gene cluster in Nitrosococcus oceani revealed that it consists of five genes, instead of the three known genes, amoCAB. The two additional genes, orf1 and orf5, were introduced as amoR and amoD, respectively. Putative functions of the AmoR and AmoD proteins are discussed.

Complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium Nitrosococcus oceani ATCC 19707.

The gammaproteobacterium Nitrosococcus oceani (ATCC 19707) is a gram-negative obligate chemolithoautotroph capable of extracting energy and reducing power from the oxidation of ammonia to nitrite. Sequencing and annotation of the genome revealed a single circular chromosome (3,481,691 bp; G+C content of 50.4%) and a plasmid (40,420 bp) that contain 3,052 and 41 candidate protein-encoding genes, respectively. The genes encoding proteins necessary for the function of known modes of lithotrophy and autotrophy were identified. Contrary to betaproteobacterial nitrifier genomes, the N. oceani genome contained two complete rrn operons. In contrast, only one copy of the genes needed to synthesize functional ammonia monooxygenase and hydroxylamine oxidoreductase, as well as the proteins that relay the extracted electrons to a terminal electron acceptor, were identified. The N. oceani genome contained genes for 13 complete two-component systems. The genome also contained all the genes needed to reconstruct complete central pathways, the tricarboxylic acid cycle, and the Embden-Meyerhof-Parnass and pentose phosphate pathways. The N. oceani genome contains the genes required to store and utilize energy from glycogen inclusion bodies and sucrose. Polyphosphate and pyrophosphate appear to be integrated in this bacterium's energy metabolism, stress tolerance, and ability to assimilate carbon via gluconeogenesis. One set of genes for type I ribulose-1,5-bisphosphate carboxylase/oxygenase was identified, while genes necessary for methanotrophy and for carboxysome formation were not identified. The N. oceani genome contains two copies each of the genes or operons necessary to assemble functional complexes I and IV as well as ATP synthase (one H(+)-dependent F(0)F(1) type, one Na(+)-dependent V type).

Urease-encoding genes in ammonia-oxidizing bacteria.

Many but not all ammonia-oxidizing bacteria (AOB) produce urease (urea amidohydrolase, EC 3.5.1.5) and are capable of using urea for chemolithotrophic growth. We sequenced the urease operons from two AOB, the beta-proteobacterium Nitrosospira sp. strain NpAV and the gamma-proteobacterium Nitrosococcus oceani. In both organisms, all seven urease genes were contiguous: the three structural urease genes ureABC were preceded and succeeded by the accessory genes ureD and ureEFG, respectively. Green fluorescent protein reporter gene fusions revealed that the ure genes were under control of a single operon promoter upstream of the ureD gene in Nitrosococcus oceani. Southern analyses revealed two copies of ureC in the Nitrosospira sp. strain NpAV genome, while a single copy of the ure operon was detected in the genome of Nitrosococcus oceani. The ureC gene encodes the alpha subunit protein containing the active site and conserved nickel binding ligands; these conserved regions were suitable primer targets for obtaining further ureC sequences from additional AOB. In order to develop molecular tools for detecting the ureolytic ecotype of AOB, ureC genes were sequenced from several beta-proteobacterial AOB. Pairwise identity values ranged from 80 to 90% for the UreC peptides of AOB within a subdivision. UreC sequences deduced from AOB urease genes and available UreC sequences in the public databases were used to construct alignments and make phylogenetic inferences. The UreC proteins from beta-proteobacterial AOB formed a distinct monophyletic group. Unexpectedly, the peptides from AOB did not group most closely with the UreC proteins from other beta-proteobacteria. Instead, it appears that urease in beta-proteobacterial autotrophic ammonia oxidizers is the product of divergent evolution in the common ancestor of gamma- and beta-proteobacteria that was initiated before their divergence during speciation. Sequence motifs conserved for the proteobacteria and variable regions possibly discriminatory for ureC from beta-proteobacterial AOB were identified for future use in environmental analysis of ureolytic AOB. These gene sequences are the first publicly available for ure genes from autotrophic AOB.