Complete Genome Sequence of Nitrobacter hamburgensis X14 and Comparative Genomic Analysis of Species within the Genus Nitrobacter

Abstract

The alphaproteobacterium Nitrobacter hamburgensis X14 is a gram-negative facultative chemolithoautotroph that conserves energy from the oxidation of nitrite to nitrate. Sequencing and analysis of the Nitrobacter hamburgensis X14 genome revealed four replicons comprised of one chromosome (4.4 Mbp) and three plasmids (294, 188, and 121 kbp). Over 20% of the genome is composed of pseudogenes and paralogs. Whole-genome comparisons were conducted between N. hamburgensis and the finished and draft genome sequences of Nitrobacter winogradskyi and Nitrobacter sp. strain Nb-311A, respectively. Most of the plasmid-borne genes were unique to N. hamburgensis and encode a variety of functions (central metabolism, energy conservation, conjugation, and heavy metal resistance), yet ϳ21 kb of a ϳ28-kb "autotrophic" island on the largest plasmid was conserved in the chromosomes of Nitrobacter winogradskyi Nb-255 and Nitrobacter sp. strain Nb-311A. The N. hamburgensis chromosome also harbors many unique genes, including those for heme-copper oxidases, cytochrome b 561 , and putative pathways for the catabolism of aromatic, organic, and one-carbon compounds, which help verify and extend its mixotrophic potential. A Nitrobacter "subcore" genome was also constructed by removing homologs found in strains of the closest evolutionary relatives, Bradyrhizobium japonicum and Rhodopseudomonas palustris. Among the Nitrobacter subcore inventory (116 genes), copies of genes or gene clusters for nitrite oxidoreductase (NXR), cytochromes associated with a dissimilatory nitrite reductase (NirK), PII-like regulators, and polysaccharide formation were identified. Many of the subcore genes have diverged significantly from, or have origins outside, the alphaproteobacterial lineage and may indicate some of the unique genetic requirements for nitrite oxidation in Nitrobacter.Nitrification is a two-step process by which ammonia is converted to nitrate via nitrite. Nitrification plays a key role in transformation of fertilizer nitrogen in agricultural systems and is a key component of nitrogen removal in wastewater treatment. Production of soluble inorganic nitrogen by nitrification can lead to the contamination and eutrophication of terrestrial and aquatic ecosystems, while the gaseous products of nitrifier denitrification, nitric oxide (NO) and nitrous oxide (N 2 O), destroy stratospheric ozone and greatly contribute to global warming (26, 54, 61). Nitrite-oxidizing bacteria (NOB) participate in the process of nitrification by converting nitrite (NO 2 Ϫ ), the end product of ammonia oxidation, into nitrate (NO 3 Ϫ ) according to the following reaction; NO 2Nitrite also functions as an electron donor for the reduction of NAD ϩ via reverse electron flow as well as for the generation of ATP by oxidative phosphorylation (17).Although several phylogenetically distinct genera (Nitrospira, Nitrobacter, Nitrococcus, and Nitrospina) carry out NO 2 Ϫ oxidation, most of what is known about the physiology and biochemistry of NOB has been derived from studies of t...

d-Lactate metabolism and the obligate requirement for CO2 during growth on nitrite by the facultative lithoautotroph Nitrobacter hamburgensis

“…The ability of N. hamburgensis to metabolize lactate (a previously unknown organic carbon source for this organism) was predicted from the genome; however, the selective capacity of N. hamburgensis to grow on D-but not L-lactate was surprising given that both D-and L-iLDHs have been annotated (Starkenburg et al, 2008). The reason for the lack of growth on L-lactate is unclear as the putative L-isomer-specific iLDH (EC 1.1.2.3, Nham_1112) shares 78 % protein sequence identity with an iLDH in the close alphaproteobacterial relative of N. hamburgensis, Rhodopseudomonas, which can metabolize and grow on Llactate (Horikiri et al, 2004;Markwell & Lascelles, 1978).…”

“…The recent availability of the N. hamburgensis X14 genome sequence prompted a re-examination of mixotrophy and organotrophy in this bacterium, as three genes that could encode lactate dehydrogenases (LDHs) have been identified (Starkenburg et al, 2008). In contrast to the wellstudied NAD-dependent LDHs, these genes encode homologues of flavin-dependent LDHs (iLDHs), which oxidize lactate to pyruvate and could provide energy and/ or carbon to the cell (Garvie, 1980).…”

Oxidation kinetics and inverse isotope effect of marine nitrite-oxidizing isolates

“…comm. in Starkenburg et al 2008). Nitrococcus mobilis 231 was isolated from surface waters of the South Pacific Ocean near the Galapagos Archipelago.…”

Structural and functional genomics of plasmid pSinA of Sinorhizobium sp. M14 encoding genes for the arsenite oxidation and arsenic resistance

“…In contrast to the arsenic resistance genes, almost all found and documented arsenite oxidase genes are located within chromosomes. To date, the aio-like loci have been found only within three plasmids: megaplasmid pSI07 of Ralstonia solanacearum (Remenant et al, 2010), plasmid pPB12 of Nitrobacter hamburgiensis (Starkenburg et al, 2008), and plasmid pTT27 of Thermus thermophilus HB8 (AP008227). Information concerning above-mentioned plasmids and their functionality in the context of arsenite oxidation, as well as horizontal transfer of arsenic metabolism genes, is rather residual.…”