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Advances in microbial ecology research are more often than not limited by the capabilities of available methodologies. Aerobic autotrophic nitrification is one of the most important and well studied microbiological processes in terrestrial and aquatic ecosystems. We have developed and validated a microbial diagnostic microarray based on the ammonia-monooxygenase subunit A (amoA) gene, enabling the in-depth analysis of the community structure of bacterial and archaeal ammonia oxidisers. The amoA microarray has been successfully applied to analyse nitrifier diversity in marine, estuarine, soil and wastewater treatment plant environments. The microarray has moderate costs for labour and consumables and enables the analysis of hundreds of environmental DNA or RNA samples per week per person. The array has been thoroughly validated with a range of individual and complex targets (amoA clones and environmental samples, respectively), combined with parallel analysis using traditional sequencing methods. The moderate cost and high throughput of the microarray makes it possible to adequately address broader questions of the ecology of microbial ammonia oxidation requiring high sample numbers and high resolution of the community composition.

The effects of sediment hypoxia, resulting from increased carbon loads or decreased dissolved oxygen (DO), on nitrogen cycling in estuarine environments is poorly understood. The important role played by bacterial and archaeal ammonia oxidizers in the eventual removal of nitrogen from estuarine environments is likely to be strongly affected by hypoxic events. In this study, an analysis of the effects of different levels of sediment hypoxia (5%, 20% and 75% DO) was performed in a microcosm experiment. Changes in the nutrient fluxes related to nitrification at 5% DO were observed after 4 h. Quantification of the key nitrification gene ammonium monooxygenase (amoA) in both DNA and RNA extracts suggests that bacterial amoA transcription was reduced at both of the lower DO concentrations, while changes in DO had no significant effect on archaeal amoA transcription. There was no change in the diversity of expressed archaeal amoA, but significant change in bacterial amoA transcriptional diversity, indicative of low- and high-DO phylotypes. This study suggests that groups of ammonia oxidizers demonstrate differential responses to changes in sediment DO, which may be a significant factor in niche partitioning of different ammonia oxidizer groups., (© 2010 CSIRO. FEMS Microbiology Ecology © 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd.)

The unsaturation ratio of C(37) alkenones (U(37)(K')) produced by haptophyte microalgae such as Emiliania huxleyi is often used as proxy for past sea surface temperature. In this study, 29 bacterial strains were isolated from cultures of the strain E. huxleyi TWP1. Among alkenone-degrading isolates, the strain Dietzia maris sp. S1 appeared to be able to selectively degrade alkenones leading to increases in the palaeoenvironmental proxy U(37)(K') by +0.05 to +0.10 units, which is equivalent to the change seen when the growth temperature is increased by 1.5-3.0 degrees C. This degradation was shown to involve initial epoxidation of the alkenone double bonds presumably by a monooxygenase, which showed a preference for oxidation of the omega29 double bond. Inconsistencies observed in previous studies of the aerobic microbial degradation of alkenones may simply reflect which species of bacteria were present. Our results confirm that intense aerobic bacterial degradative processes can introduce a bias in palaeotemperature reconstructions especially when there is evidence of substantial aerobic bacterial degradation of the deposited organic matter. The widespread occurrence of epoxyalkenones in the marine environment strongly suggests that selective aerobic bacterial degradation could be major source of uncertainty for palaeotemperature estimation.

Nitrification and denitrification are key steps in nitrogen (N) cycling. The coupling of these processes, which affects the flow of N in ecosystems, requires close interaction of nitrifying and denitrifying microorganisms, both spatially and temporally. The diversity, temporal and spatial variations in the microbial communities affecting these processes was examined, in relation to N cycling, across 12 sites in the Fitzroy river estuary, which is a turbid subtropical estuary in central Queensland. The estuary is a major source of nutrients discharged to the Great Barrier Reef near-shore zone. Measurement of nitrogen fluxes showed an active denitrifying community during all sampling months. Archaeal ammonia monooxygenase (amoA of AOA, functional marker for nitrification) was significantly more abundant than Betaproteobacterial (beta-AOB) amoA. Nitrite reductase genes, functional markers for denitrification, were dominated by nirS and not nirK types at all sites during the year. AOA communities were dominated by the soil/sediment cluster of Crenarchaeota, with sequences found in estuarine sediment, marine and terrestrial environments, whereas nirS sequences were significantly more diverse (where operational taxonomic units were defined at both the threshold of 5% and 15% sequence similarity) and were closely related to sequences originating from estuarine sediments. Terminal-restriction fragment length polymorphism (T-RFLP) analysis revealed that AOA population compositions varied spatially along the estuary, whereas nirS populations changed temporally. Statistical analysis of individual T-RF dominance suggested that salinity and C:N were associated with the community succession of AOA, whereas the nirS-type denitrifier communities were related to salinity and chlorophyll-alpha in the Fitzroy river estuary.

Biodegradation of (E)-phytol [3,7,11, 15-tetramethylhexadec-2(E)-en-1-ol] by two bacterial communities isolated from recent marine sediments under aerobic and denitrifying conditions was studied at 20 degrees C. This isoprenoid alcohol is metabolized efficiently by these two bacterial communities via 6,10, 14-trimethylpentadecan-2-one and (E)-phytenic acid. The first step in both aerobic and anaerobic bacterial degradation of (E)-phytol involves the transient production of (E)-phytenal, which in turn can be abiotically converted to 6,10,14-trimethylpentadecan-2-one. Most of the isoprenoid metabolites identified in vitro could be detected in a fresh sediment core collected at the same site as the sediments used for the incubations. Since (E)-phytenal is less sensitive to abiotic degradation at the temperature of the sediments (15 degrees C), the major part of (E)-phytol appeared to be biodegraded in situ via (E)-phytenic acid. (Z)- and (E)-phytenic acids are present in particularly large quantities in the upper section of the core, and their concentrations quickly decrease with depth in the core. This degradation (which takes place without significant production of phytanic acid) is attributed to the involvement of alternating beta-decarboxymethylation and beta-oxidation reaction sequences induced by denitrifiers. Despite the low nitrate concentration of marine sediments, denitrifying bacteria seem to play a significant role in the mineralization of (E)-phytol.

This paper describes the production of isoprenoid wax esters during the aerobic degradation of 6,10,14-trimethylpentadecan-2-one and phytol by four bacteria (Acinetobacter sp. strain PHY9, Pseudomonas nautica [IP85/617], Marinobacter sp. strain CAB [DSMZ 11874], and Marinobacter hydrocarbonoclasticus [ATCC 49840]) isolated from the marine environment. Different pathways are proposed to explain the formation of these compounds. In the case of 6,10, 14-trimethylpentadecan-2-one, these esters result from the condensation of some acidic and alcoholic metabolites produced during the biodegradation, while phytol constitutes the alcohol moiety of most of the esters produced during growth on this isoprenoid alcohol. The amount of these esters formed increased considerably in N-limited cultures, in which the ammonium concentration corresponds to conditions often found in marine sediments. This suggests that the bacterial formation of isoprenoid wax esters might be favored in such environments. Although conflicting evidence exists regarding the stability of these esters in sediments, it seems likely that, under some conditions, bacterial esterification can enhance the preservation potential of labile compounds such as phytol.

A sedimentary bacterial isolate has been shown to contain trans-monounsaturated fatty acids (6% of the total fatty acids). The ratio of trans- to cis-acids in this isolate was in the range 3.2 to 7.6. The identification of trans-monounsaturated acids in a marine bacterium implied that the trans-acids which have been reported in recent sediments could derive, in whole or part, from direct bacterial input.