Similarities between Hyphomicrobium and Nitrobacter with respect to fatty acids

Lipids as paleomarkers to constrain the marine nitrogen cycle

Global climate is, in part, regulated by the effect of microbial processes on biogeochemical cycling. The nitrogen cycle, in particular, is driven by microorganisms responsible for the fixation and loss of nitrogen, and the reduction‐oxidation transformations of bio‐available nitrogen. Within marine systems, nitrogen availability is often the limiting factor in the growth of autotrophic organisms, intrinsically linking the nitrogen and carbon cycles. In order to elucidate the state of these cycles in the past, and help envisage present and future variability, it is essential to understand the specific microbial processes responsible for transforming bio‐available nitrogen species. As most microorganisms are soft‐bodied and seldom leave behind physical fossils in the sedimentary record, recalcitrant lipid biomarkers are used to unravel microbial processes in the geological past. This review emphasises the recent advances in marine nitrogen cycle lipid biomarkers, underlines the missing links still needed to fully elucidate past shifts in this biogeochemically‐important cycle, and provides examples of biomarker applications in the geological past.

Labrys wisconsinensis sp. nov., a budding bacterium isolated from Lake Michigan water, and emended description of the genus Labrys

Two facultatively anaerobic, budding bacterial strains, designated W1215-PCA4(T) and SRNK-1, were isolated from water from Lake Michigan, USA. The two strains showed identical ERIC-PCR-generated genomic fingerprints and shared 99.9 % 16S rRNA gene sequence similarity. Strain W1215-PCA4(T) showed highest 16S rRNA gene sequence similarities to Labrys monachus VKM B-1479(T) (95.8 %), Labrys methylaminiphilus DSM 16812(T) (95.1 %), Labrys okinawensis MAFF 210191(T) (96.0 %), Labrys miyagiensis G24103(T) (95.4 %), Labrys neptuniae BCRC 17578(T) (95.7 %) and Labrys portucalensis DSM 17916(T) (95.8 %). Data suggested that the two strains were members of a single novel species of the genus Labrys. The major cellular fatty acids of the two isolates were C(18 : 1)omega7c, C(19 : 0) cyclo omega8c and C(16 : 0). Their polar lipid profiles were highly similar to that of Labrys monachus DSM 5896(T). The primary quinone was ubiquinone Q-10, with minor amounts of Q-9 and Q-11. sym-Homospermidine was the predominant polyamine, with putrescine present in moderate amounts. The two strains were identical in terms of their biochemical and physiological traits, but were distinguishable from other species of the genus Labrys. Hence, the description of a novel species in this genus appears to be justified. The name Labrys wisconsinensis sp. nov. is proposed; the type strain is W1215-PCA4(T) (=DSM 19619(T)=NRRL B-51088(T)).

Fatty acid profiles of nitrite-oxidizing bacteria reflect their phylogenetic heterogeneity

The fatty acid profiles of all described species of the nitrite-oxidizing genera Nitrobacter, Nitrococcus, Nitrospina and Nitrospira were analyzed. The four genera had distinct profiles, which can be used for the differentiation and allocation of new isolates to these genera. The genus Nitrobacter is characterized by vaccenic acid as the main compound with up to 92% of the fatty acids and the absence of hydroxy fatty acids. The genus Nitrococcus showed cis-9-hexadecenoic acid, hexadecanoic acid and vaccenic acid as main parts. Small amounts of 3-hydroxy-dodecanoic acid were detected. The genus Nitrospina possessed tetradecanoic acid and cis-9-hcxadecenoic acid as main compounds, also 3-hydroxy-hexadecanoic acid was detected for this genus. The genus Nitrospira showed a pattern with more variations among the two described species. These organisms are characterized by the cis-7 and cis-11-isomers of hexadecenoic acid. For Nitrospira moscoviensis a specific new fatty acid was found, which represented the major constituent in the fatty acid profiles of autotrophically grown cultures. It was identified as 11-methyl-hexadecanoic acid. Since this compound is not known for other bacterial taxa, it represents a potential lipid marker for the detection of Nitrospira moscoviensis relatives in enrichment cultures and environmental samples. A cluster analysis of the fatty acid profiles is in accordance with 16S rRNA sequence-based phylogeny of the nitrite-oxidizing bacteria.

Lipid composition of the phosphatidylcholine-producing bacterium Hyphomicrobium vulgare NP-160

The extractable lipids of the PC-producing, methylotrophic, budding bacterium Hyphomicrobium vulgare NP-160 grown in a mineral-salts medium containing methanol as the carbon source, were studied by chromatographic and spectrometric methods. They were found to be comprised of PC (35% of the total lipids), PDME (33%), PMME (1%), PE (9%), PG (10%), DPG (6%), and a non-phosphorus, ornithine-containing lipoamino acid, OL (6%). No low-polarity lipids, such as fatty acid esters of glycerol or of other alcohols, were detected. The sole fatty-acyl constituents of PDME and PMME were cis-octadec-11-enoic (cis-vaccenic) acid residues, whereas the other phospholipids contained, in addition, 1 to 5 mol % of MOA (lactobacillic acid) residues located predominantly at the sn-1 position of their glycerol residues. OL consisted of two molecular species, 2-N-[3'-(cis-octadec-11"-enoyloxy)octadecanoyl]-L- ornithine and 2-N-[3'-(cis-11", 12"-methyleneoctadecanoyloxy)octadecanoyl]-L-ornithine in the molar ratio 94:6. When the culture medium was devoid of phosphate, a threefold increase in OL together with a three-fold decrease in PE were observed, no significant changes in proportions of the remaining lipids occurring. The most striking feature of the lipid composition in this case was the presence of considerable amounts of fatty acid methyl esters, mainly methyl cis-vaccenate, along with minute amounts of wax esters.

Major outer membrane proteins unique to reproductive cells of Hyphomonas jannaschiana

Separation on the basis of molecular weight resolved three proteins specific to the swarmer cell of Hyphomonas jannaschiana. In the reproductive cell, 4 major proteins were identified as cytoplasmic and 10 were identified as envelope. Of these envelope proteins, one was common to both the inner and outer membranes, four were common to the inner membrane, and five were common to the outer membrane. Four of these outer membrane proteins were specific to the reproductive cell, and two of these proteins, with apparent molecular weights of 116,000 and 29,000, constituted 19% of the total cell protein and 54% of the outer membrane protein.

Lipids of Nitrobacter and effects of cultural conditions on fatty acid composition

The nitrite-oxidizing autotroph, Nitrobacter was studied with respect to fatty acid composition and lipids. One fatty acid, shown to be cis-11-actadecenoic acid (cis-vaccenic) accounted for almost 96% of the total fatty acids of the extractable lipids of Nitrobacter agilis, Nitrobacter winogradskyi and each of several isolates from Minnesota and Moroccan soils studied. The cis-vaccenic acid was high in all organisms, ranging from 85 to 95% when grown at 27degreesC in the log growth phase, the other major acid was plamitic (16 : 1). All converted ces-vaccenic acid to a 19-carbon cyclopropanecarboxylic acid upon entering the stationary growth phase. The 11-carbon cyclopropanecarboxylic acid was not degraded when stationary phase cells were reinoculated into fresh medium. In N. agilis the levels of cis-vaccenic acid ranged from 86.8% when grown at 33degreesC to 95.6% when grown at 19degreesC. Addition of acetate or casein hydrolyzate to the inorganic medium had virtually no effect on the fatty acid composition of N. agilis, while propionate effected both qualitative and quantitative changes. In all organisms phosphatidylcholine made up a large portion of the extractable lipids. The distribution was phosphatidylcholine, 54%; phosphatidylethanolamine, 23%; phosphatidylglycerol, 10%; and neutral lipids, 11% for N. agilis.

Phospholipid composition and metabolism of Micrococcus denitrificans

The phospholipid composition of Micrococcus denitrificans was unusual in that phosphatidyl choline (PC) was a major phospholipid (30.9%). Other phospholipids were phosphatidyl glycerol (PG, 52.4%), phosphatidyl ethanolamine (PE, 5.8%), an unknown phospholipid (5.3%), cardiolipin (CL, 3.2%), phosphatidyl dimethylethanolamine (PDME, 0.9%), phosphatidyl monomethylethanolamine (PMME, 0.6%), phosphatidyl serine (PS, 0.5%), and phosphatidic acid (0.4%). Kinetics of (32)P incorporation suggested that PC was formed by the successive methylations of PE. Pulse-chase experiments with pulses of (32)P or acetate-1-(14)C to exponentially growing cells showed loss of isotopes from PMME, PDME, PS, and CL with biphasic kinetics suggesting the same type of multiple pools of these lipids as proposed in other bacteria. The major phospholipids, PC, PG, and PE, were metabolically stable under these conditions. The fatty acids isolated from the complex lipids were also unusual in being a simple mixture of seven fatty acids with oleic acid representing 86% of the total. Few free fatty acids and no non-extractable fatty acids associated with the cell wall or membrane were found.