Structural characterisation of unsaturated bacterial hopanoids by atmospheric pressure chemical ionisation liquid chromatography/ion trap mass spectrometry.

The production of bacteriohopanepolyols (BHPs) is widespread in many different groups of prokaryotes; however, unsaturated components are less common except amongst the acetic acid bacteria. Here we describe the characterisation of mono- (Delta(6) or Delta(11)) and diunsaturated (Delta(6,11)) bacteriohopanetetrols isolated from the acetic acid bacterium Gluconacetobacter xylinus (formerly Acetobacter aceti ssp. xylinum) by atmospheric pressure chemical ionisation ion trap mass spectrometry (APCI-MS(n)). APCI-MS(2) spectra are compared with equivalent electron ionisation (EI) spectra and differences in fragmentation pathways are discussed. Having established characteristic spectral features for a range of unsaturated BHPs we now have the ability to rapidly detect the presence of unsaturated BHPs in both natural environmental samples (soils, sediments, water columns) as well as in microbial cultures.

Rapid structural elucidation of composite bacterial hopanoids by atmospheric pressure chemical ionisation liquid chromatography/ion trap mass spectrometry.

Bacteriohopanepolyols (BHPs) are membrane lipids produced by a wide range of eubacteria. Their use, however, as molecular markers of bacterial populations and processes has until recently been hampered by the lack of a suitable rapid method for fingerprinting their composition in complex environmental matrices. New analytical procedures employing ion trap mass spectrometry now allow us to investigate the occurrence of BHPs in diverse biological and environmental samples including bacterial cultures, soils, and recent and ancient sediments. Here, we describe the structural characterisation using atmospheric pressure chemical ionisation liquid chromatography/ion trap mass spectrometry (APCI-LC/MS(n)) of a number of previously identified but less commonly occurring BHPs such as adenosylhopane and ribonylhopane. Many of the structures described here have previously only been reported in one or just a small number of cultured organisms having been isolated from large amounts of cellular mass (4-26 g) and identified by nuclear magnetic resonance (NMR) techniques after purification of individual compounds. Now, having established characteristic APCI fragmentation patterns, it is possible to rapidly screen many more bacterial cultures using only small amounts of material (<50 mg) as well as environmental samples for these atypical structures and a rapidly growing suite of novel structures.

Characteristic fragmentation of bacteriohopanepolyols during atmospheric pressure chemical ionisation liquid chromatography/ion trap mass spectrometry.

Bacteriohopanepolyols (BHPs) fragment via characteristic pathways during atmospheric pressure chemical ionisation liquid chromatography/ion trap mass spectrometry (APCI-LC/MS(n)). Comparison of the MS(2) spectra of bacteriohopane-32,33,34,35-tetrol (BHT) and 2 beta-methylbacteriohopane-32,33,34,35-tetrol has confirmed the previously proposed ring-C cleavage occurring between C-9 and 11 and C-8 and 14. This fragmentation, diagnostic of all hopanoids, also occurs in BHPs containing an amino group (-NH(2)) at C-35 although the higher relative stability of the ion limits this fragmentation to a minor process after protonation of the basic nitrogen function. Studies of a number of cell cultures including a prochlorophyte (Prochlorothrix hollandica) and a cyanobacterium (Chlorogloeopsis LA) demonstrate the power of this technique to detect composite BHPs with a complex biological functionality at C-35. We also report the first observation of intact pentafunctionalised bacteriohopanepolyols using this method.

Atmospheric pressure chemical ionisation reversed-phase liquid chromatography/ion trap mass spectrometry of intact bacteriohopanepolyols.

Atmospheric pressure chemical ionisation liquid chromatography/multi-stage ion trap mass spectrometry (APCI-LC/MS(n)) has been applied to the study of intact bacteriohopanepolyols. Spectral characterisation of bacteriohopanepolyols of known structure present in bacterial extracts (Zymomonas mobilis and a fermenter containing methanotrophs including Methylococcus capsulatus) has revealed greater structural detail than previous liquid chromatography/mass spectrometry (LC/MS) methods and identified characteristic fragmentations indicative of numerous biohopanoid structures. Analysis of a Recent sedimentary extract from Lake Druzhby (Antarctica) has demonstrated the power of this technique to detect biohopanoids in complex samples including at least partial characterisation of previously unknown composite structures.

Identification of novel bacterial lineages as active members of microbial populations in a freshwater sediment using a rapid RNA extraction procedure and RT-PCR.

A rapid method for the extraction of RNA from the indigenous bacterial communities in environmental samples was developed. The method was tested using anoxic sediment samples from a productive freshwater lake (Priest Pot, Cumbria, UK). The simple protocol yielded rRNA and mRNA of a purity suitable for amplification by reverse transcriptase PCR (RT-PCR). The integrity of the RT-PCR was demonstrated by amplifying 16S rRNA and mRNA for the mercury resistance regulatory gene merR. The diversity of 16S rRNA sequences recovered from RNA and DNA extracted from anoxic Priest Pot sediments was analysed. The 5' end of extracted 16S rRNA was amplified by RT-PCR and the 16S rRNA PCR products were cloned and sequenced to identify active constituents of the sediment bacterial community. Corresponding analyses were performed upon DNA templates from the same sediment samples. Partial 16S rRNA sequences were obtained from a total of 147 clones (71 rRNA-derived and 76 rDNA-derived). The clone libraries included sequences related to Pirellula staleyi, an aerobic planktonic member of the Planctomycetales, and the recently described candidate bacterial division OP5. Sequences from these groups were recovered in libraries generated from a DNA template but were also present in RNA-derived libraries. Previous studies of anoxic environments have identified sequences most closely related to Pirellula spp. This study, which utilized RT-PCR of 16S rRNA, has provided the first evidence that Pirellula-like bacteria are active in situ in an anoxic environment. Furthermore, members of the recently described candidate division, OP5, were also identified as active constituents of the bacterial community of anoxic Priest Pot sediments. This not only supports the widespread occurrence of OP5 members in diverse environments but suggests that they are active under anoxic conditions.