Niche differentiation of ammonia-oxidising archaea (AOA) and bacteria (AOB) in response to paper and pulp mill effluent.

Sediment organic loading has been shown to affect estuarine nitrification and denitrification, resulting in changes to sediment biogeochemistry and nutrient fluxes detrimental to estuarine health. This study examined the effects of organic loading on nutrient fluxes and microbial communities in sediments receiving effluent from a paper and pulp mill (PPM) by applying microcosm studies and molecular microbial ecology techniques. Three sites near the PPM outfall were compared to three control sites, one upstream and two downstream of the outfall. The control sites showed coupled nitrification-denitrification with minimal ammonia release from the sediment. In contrast, the impacted sites were characterised by nitrate uptake and substantial ammonia efflux from the sediments, consistent with a decoupling of nitrification and denitrification. Analysis of gene diversity demonstrated that the composition of nitrifier communities was not significantly different at the impacted sites compared to the control sites; however, analysis of gene abundance indicated that whilst there was no difference in total bacteria, total archaea or ammonia-oxidising archaea (AOA) abundance between the control and impacted sites, there was a significant reduction in ammonia-oxidising bacteria (AOB) at the impacted sites. The results of this study demonstrate an effect of organic loading on estuarine sediment biogeochemistry and highlight an apparent niche differentiation between AOA and AOB.

Factors influencing the distributions of polyunsaturated terpenoids in the diatom, Rhizosolenia setigera.

Polyunsaturated highly branched isoprenoid (HBI) hydrocarbon distributions of laboratory cultures of five strains of the planktonic diatom Rhizosolenia setigera (Brightwell) are shown herein to be highly variable. Some strains produced both haslenes with from three to five double bonds and rhizenes. The haslenes comprised not only Delta5 alkenes but also those with C7(20) unsaturation, including hasla-7(20),9E,Z, 23-trienes and hasla-7(20),9E,Z-13, 23-tetraenes. The rhizenes contained C7(25) unsaturation and the vinyl moiety common to all algal haslenes so far characterised. The effects of temperature and salinity on HBI composition, along with isotopic content, were determined in strain CS 389/A. Increase in growth temperature from 18 to 25 degrees C increased the degree of unsaturation in the haslenes and E to Z isomerisation in the triene. There was also an increase in unsaturation in the rhizenes at the highest growth temperature, with hexaenes dominant over the pentaenes but in the rhizenes, Z to E isomerisation increased. Increased salinity from 15 to 35 psu increased cell growth and rhizene production but decreased haslene production. Unsaturation in haslenes was not changed by increased salinity but unsaturation in the rhizenes decreased. These may reflect growth rate differences. The carbon isotopic compositions of the haslenes and rhizenes were similar to that of the major sterol at 18 degrees C, but the major HBI isomers were 3-4 per mil depleted relative to phytol released by saponification from chlorophyll a. This suggests biosynthesis of HBIs from a different isotopic pool of isopentenyl biphosphate to that from which phytol is biosynthesised. At 25 degrees C, further isotopic differences were observed. The variables controlling HBI distributions in R. setigera are still not fully understood and rationalisation of the environmental controls on the sedimentary distributions of the HBIs from R. setigera may only be possible once such factors are established.

Identification of natural, anthropogenic and petroleum hydrocarbons in aquatic sediments.

Complex distributions of hydrocarbons occur in most aquatic sediments. Total concentrations can range from a few parts per million in non-polluted intertidal and oceanic areas to parts per thousand in heavily contaminated estuarine, lake and near-shore environments. Iatroscan TLC-FID provides a quick assessment of the total hydrocarbon load, but capillary GC, HPLC and GC-MS are essential for obtaining detailed composition data from which information on possible sources can be derived. Alkenes from microalgae, such as n-C21:6, n-C17:1 and unusual C25 and C30 isoprenoid alkenes, are often the most abundant single components in sedimentary hydrocarbon distributions. Some hydrocarbons are also produced from diagenetic transformation of functionalised lipids present in the sediment. Long-chain alkanes typical of plant waxes can be important constituents, even in marine sediments far from the coast. These distributions display a strong predominance of odd chain lengths, whereas n-alkane distributions in oils usually show little or no predominance of either odd or even chain lengths. However, the presence of this type of distribution in a sediment may not indicate petroleum contamination since biological sources for similar distributions are now recognised. Petroleum-derived residues are common in coastal and estuarine areas, particularly those near urban or industrial centers. This contamination is readily seen in capillary gas chromatograms of the alkanes as an unresolved complex mixture (UCM). The source of the oil can often be deduced from characteristic distributions of biomarker steranes, rearranged steranes, hopanes and methyl hopanes determined by capillary gas chromatography-mass spectrometry. Methyl hopanes are major polycyclic alkanes in oils from carbonate source rocks, such as those from the Middle East, but are uncommon in Australian oils. GC-MS fingerprinting techniques show that lubricating oils are a major source of hydrocarbon pollution in many estuaries and coastal areas around Australia. It has been estimated that natural oil seeps may also contribute as much as 10% of the hydrocarbons in the global marine environment. Examples of this include major oil seepage in the Gulf of California and the widespread occurrence of bitumen strandings on South Australian beaches. Examples from marine and estuarine environments around Australia are presented to illustrate the use of modern analytical techniques to identify, quantify and determine the origins of hydrocarbons in aquatic sediments.

Late-Holocene succession of dinoflagellates in an Antarctic fjord using a multi-proxy approach: paleoenvironmental genomics, lipid biomarkers and palynomorphs.

Recent work has shown that paleoenvironmental genomics, i.e. the application of genomic tools to analyze preserved DNA in sedimentary records, is a promising approach to reconstruct the diversity of past planktonic communities. This provides information about past ecological and environmental changes. A major advantage of this approach is that individual species, including those that did not leave other characteristic markers, can be identified. In this study, we determined which dinoflagellate marker (i.e. 18S rDNA, dinosterol or dinocysts) provided the most detailed information about the late-Holocene succession of dinoflagellates in an Antarctic Fjord (Ellis Fjord, Vestfold Hills). The preserved rDNA revealed two intervals in the 2750-year-old sediment record. The dinoflagellate diversity was the highest until approximately 1850 cal yr bp and included phylotypes related to known dinosterol producers. A lower concentration of dinosterol in sediments <1850 cal yr bp coincided with a community shift towards a predominance of the autotrophic sea-ice dinoflagellate Polarella glacialis, which is not a source of dinosterol. Remarkably, cultures of P. glacialis are known to produce other diagnostic sterols, but these were not recovered here. In addition, conspicuous resting cysts of P. glacialis were not preserved in the analyzed sediments. Overall, dinocysts were rare and the paleoenvironmental genomics approach revealed the highest diversity of dinoflagellates in Ellis Fjord, and was the only approach that recorded a shift in dinoflagellate composition at approximately 1850 cal yr bp indicative of a colder climate with more extensive ice cover - this timing coincides with a period of changing climate reported for this region.

Characterization of unusual alkenones and alkyl alkenoates by electron ionization gas chromatography/mass spectrometry.

Unusual long-chain, diunsaturated alkenones and alkyl alkenoates exhibiting double bonds separated by three methylene units instead of the more usual five were characterized by electron ionization (EI) gas chromatography/mass spectrometry. In a first step, the positions of the double bonds of these compounds (isolated from Holocene Black Sea sediments) were confirmed after OsO4 treatment and silylation. Mass spectra of the resulting tetratrimethylsilyloxy derivatives allowed unambiguous determination of the positions of unsaturations. The EI mass spectra of the non-derivatized compounds were then compared with those of the alkenones and alkyl alkenoates having double bonds separated by five methylene units. Specific fragment ions resulting from gamma-H rearrangements were found to be prominent in EI mass spectra of these unusual 'Black Sea' diunsaturated alkenones and alkyl alkenoates. These fragment ions can be used to characterize these compounds in natural samples without the need for laborious derivatization treatments.

Sterols in microorganisms.

Sterols are vital components of all eukaryotic cells. This review describes the variety of sterol structures found in microalgae, yeasts, fungi, protozoans and microheterotrophs. Reports of the occurrence of sterols in prokaryotic cells are critically assessed. Methylotrophic bacteria contain unusual 4-methylsterols, but reports of 4-desmethyl sterols in cyanobacteria and other bacteria are limited and many of these seem dubious. Possible application areas for sterols derived from mass culture of microalgae and other microorganisms are highlighted.

Biodegradation of free phytol by bacterial communities isolated from marine sediments under aerobic and denitrifying conditions.

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.

trans-Monounsaturated Acids in a Marine Bacterial Isolate.

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.