Ben Abbas

Archaeal nitrification in the ocean

Marine Crenarchaeota are the most abundant single group of prokaryotes in the ocean, but their physiology and role in marine biogeochemical cycles are unknown. Recently, a member of this clade was isolated from a sea aquarium and shown to be capable of nitrification, tentatively suggesting that Crenarchaeota may play a role in the oceanic nitrogen cycle. We enriched a crenarchaeote from North Sea water and showed that its abundance, and not that of bacteria, correlates with ammonium oxidation to nitrite. A time series study in the North Sea revealed that the abundance of the gene encoding for the archaeal ammonia monooxygenase alfa subunit (amoA) is correlated with a decline in ammonium concentrations and with the abundance of Crenarchaeota. Remarkably, the archaeal amoA abundance was 1–2 orders of magnitude higher than those of bacterial nitrifiers, which are commonly thought to mediate the oxidation of ammonium to nitrite in marine environments. Analysis of Atlantic waters of the upper 1,000 m, where most of the ammonium regeneration and oxidation takes place, showed that crenarchaeotal amoA copy numbers are also 1–3 orders of magnitude higher than those of bacterial amoA. Our data thus suggest a major role for Archaea in oceanic nitrification.

A diatomaceous origin for long-chain diols and mid-chain hydroxy methyl alkanoates widely occurring in quaternary marine sediments: Indicators for high nutrient conditions

For the first time a biological source for the long-chain alkyl 1,14-diols and 12-hydroxy methyl alkanoates, lipids widely occurring in the marine water column and sediments, has been identified. Cultures of Proboscia indica and Proboscia alata, rhizosolenoid diatoms belonging to the widespread diatom genus Proboscia, contain C28, C28:1, C30, and C30:1 alkyl 1,14-diols, and C27 and C29 12-hydroxy methyl alkanoates as major neutral lipids. These components form a substantial fraction of lipid fractions from sediment traps or sediments, especially in areas with an elevated primary production such as upwelling regions. Examination of literature data reveals that as much as 20 to 35% of the total lipid flux in the Arabian Sea is derived from Proboscia diatoms during the start of the upwelling season. Their rapid transfer to the water-sediment interface may explain why corresponding 1,14-keto-ols, inferred oxidation products of diols, are hardly formed. These interpretations are supported by compound-specific carbon isotopic analysis of long-chain keto-ols and diols in surface sediments of the Arabian Sea. The data indicate that long-chain alkyl 1,14-diols and 12-hydroxy methyl alkanoates can be applied as indicators for high-nutrient conditions in the photic zone.

Sulfidogenesis under extremely haloalkaline conditions in soda lakes of Kulunda Steppe (Altai, Russia).

Sulfidogenic activity (SA) in anoxic sediments of several soda lakes with variable salinity in south Kulunda Steppe (Altai, Russia) has been investigated. The study included in situ measurements of sulfate reduction rates and laboratory experiments with sediment slurries in which sulfate, thiosulfate or elemental sulfur were used as electron acceptors. Despite the extreme conditions (high salt concentrations and high pH), the SA values were relatively high (ranging from 0.02 to 1.20 micromol HS(-) cm(-3) h(-1)), and only hampered under salt-saturated conditions. The highest SA was observed with elemental sulfur, followed by thiosulfate, while the lowest SA was determined in the presence of sulfate. Of all the electron donors tested, the addition of formate resulted in the highest SA with all three sulfur electron acceptors. Surprisingly, hydrogen as an electron donor had very little effect. Acetate was utilized as an electron donor only under sulfur-reducing conditions. Indigenous populations of sulfidogens in soda lake sediments showed an obligately alkaliphilic pH response of SA, showing a pattern that corresponded well to the in situ pH conditions. Sulfate reduction was much more susceptible to salt inhibition than thiosulfate and sulfur reduction. Microbiological investigations indicated that sulfate-reducing bacteria belonging to the orders Desulfovibrionales and Desulfobacterales could very likely be responsible for the SA with sulfate and thiosulfate as electron acceptors at moderate salt concentrations. Sulfur reduction at moderate salinity was carried out by a specialized group of haloalkaliphilic sulfur-reducing bacteria that utilize volatile fatty acids. In saturated soda brine, extremely natronophilic representatives of the order Halanaerobiales were responsible for the sulfur-dependent respiration.

Enrichment of DNRA bacteria in a continuous culture

Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are competing microbial nitrate-reduction processes. The occurrence of DNRA has been shown to be effected qualitatively by various parameters in the environment. A more quantitative understanding can be obtained using enrichment cultures in a laboratory reactor, yet no successful DNRA enrichment culture has been described. We showed that a stable DNRA-dominated enrichment culture can be obtained in a chemostat system. The enrichment was based on the hypothesis that nitrate limitation is the dominant factor in selecting for DNRA. First, a conventional denitrifying culture was enriched from activated sludge, with acetate and nitrate as substrates. Next, the acetate concentration in the medium was increased to obtain nitrate-limiting conditions. As a result, conversions shifted from denitrification to DNRA. In this selection of a DNRA culture, two important factors were the nitrate limitation and a relatively low dilution rate (0.026 h−1). The culture was a highly enriched population of Deltaproteobacteria most closely related to Geobacter lovleyi, based on 16S rRNA gene sequencing (97% similarity). We established a stable and reproducible cultivation method for the enrichment of DNRA bacteria in a continuously operated reactor system. This enrichment method allows to further investigate the DNRA process and address the factors for competition between DNRA and denitrification, or other N-conversion pathways.

On the origin of 24-norcholestanes and their use as age-diagnostic biomarkers

24-norcholestanes have been shown to be useful biomarkers to assess the age of sediments and petroleum, but until now, the biological sources of their precursors, i.e., 24-norsterols, were unclear. We have unambiguously identified relatively high concentrations of 24- norcholesta-5,22-dien-3β-ol in the diatom Thalassiosira aff. antarctica (6%–10% of total sterols) and, in much lower concentrations, in the dinoflagellate Gymnodinium simplex (0.2% of total sterols). These identifications and other reports of 24-norsterols in dinoflagellates suggest that both diatom and dinoflagellate species are major sources for 24-norcholestanes in sediments and petroleum. The evolutionary history of these organisms suggests that observed increases of 24-norcholestane concentration in the Jurassic and the Cretaceous are related to dinoflagellate expansion, whereas an increase in the Oligocene-Miocene is likely caused by diatom expansion. Our results also explain the biogeographical distribution of 24-norcholestanes, i.e., high concentrations at high (paleo)latitudes are likely caused by diatoms, while low concentrations at lower (paleo)latitudes are likely caused by dinoflagellates.

Biological treatment of refinery spent caustics under halo-alkaline conditions

The present research demonstrates the biological treatment of refinery sulfidic spent caustics in a continuously fed system under halo-alkaline conditions (i.e. pH 9.5; Na(+)= 0.8M). Experiments were performed in identical gas-lift bioreactors operated under aerobic conditions (80-90% saturation) at 35°C. Sulfide loading rates up to 27 mmol L(-1)day(-1) were successfully applied at a HRT of 3.5 days. Sulfide was completely converted into sulfate by the haloalkaliphilic sulfide-oxidizing bacteria belonging to the genus Thioalkalivibrio. Influent benzene concentrations ranged from 100 to 600 μM. At steady state, benzene was removed by 93% due to high stripping efficiencies and biodegradation. Microbial community analysis revealed the presence of haloalkaliphilic heterotrophic bacteria belonging to the genera Marinobacter, Halomonas and Idiomarina which might have been involved in the observed benzene removal. The work shows the potential of halo-alkaliphilic bacteria in mitigating environmental problems caused by alkaline waste.

Discovery of extremely halophilic, methyl-reducing euryarchaea provides insights into the evolutionary origin of methanogenesis

Methanogenic archaea are major players in the global carbon cycle and in the biotechnology of anaerobic digestion. The phylum Euryarchaeota includes diverse groups of methanogens that are interspersed with non-methanogenic lineages. So far, methanogens inhabiting hypersaline environments have been identified only within the order Methanosarcinales. We report the discovery of a deep phylogenetic lineage of extremophilic methanogens in hypersaline lakes and present analysis of two nearly complete genomes from this group. Within the phylum Euryarchaeota, these isolates form a separate, class-level lineage ‘Methanonatronarchaeia’ that is most closely related to the class Halobacteria. Similar to the Halobacteria, ‘Methanonatronarchaeia’ are extremely halophilic and do not accumulate organic osmoprotectants. The high intracellular concentration of potassium implies that ‘Methanonatronarchaeia’ employ the ‘salt-in’ osmoprotection strategy. These methanogens are heterotrophic methyl-reducers that use C1-methylated compounds as electron acceptors and formate or hydrogen as electron donors. The genomes contain an incomplete and apparently inactivated set of genes encoding the upper branch of methyl group oxidation to CO2 as well as membrane-bound heterodisulfide reductase and cytochromes. These features differentiate ‘Methanonatronarchaeia’ from all known methyl-reducing methanogens. The discovery of extremely halophilic, methyl-reducing methanogens related to haloarchaea provides insights into the origin of methanogenesis and shows that the strategies employed by methanogens to thrive in salt-saturating conditions are not limited to the classical methylotrophic pathway.

PHYLOGENETIC POSITION OF ATTHEYA LONGICORNIS AND ATTHEYA SEPTENTRIONALIS (BACILLARIOPHYTA)1

The phylogenetic position of diatoms belonging to the genus Attheya is presently under debate. Species belonging to this genus have been placed in the subclasses Chaetocerotophycidae and Biddulphiophycidae, but published phylogenetic trees based on 18S rDNA, morphology, and sexual reproduction indicate that this group of diatoms may be a sister group of the pennates. To clarify the position of Attheya, we studied the morphology, 18S rDNA, 16S rDNA of the chloroplasts, the rbcL large subunit (LSU) sequences of the chloroplasts, and the sterol composition of three different strains of Attheya septentrionalis (Østrup) R. M. Crawford and one strain of Attheya longicornis R. M. Crawford et C. Gardner. These data were compared with data from more than 100 other diatom species, covering the whole phylogenetic tree, with special emphasis on species belonging to the genera that have been suggested to be related to the genus Attheya. All data suggest that the investigated Attheya species form a separate group of diatoms, and there is no indication that they belong to either the Chaetocerotophycidae or the Biddulphiophycidae. Despite applying these various approaches, we were unable to determine the exact phylogenetic position of the investigated Attheya species within the diatoms.

Comparison of bacterial diversity in full scale anammox bioreactors operated under different conditions.

Bacterial community structure of full‐scale anammox bioreactor is still mainly unknown. It has never been analyzed whether different anammox bioreactor configurations might result in the development of different bacterial community structures among these systems. In this work, the bacterial community structure of six full‐scale autotrophic nitrogen removal bioreactors located in The Netherlands and China operating under three different technologies and with different influent wastewater characteristics was studied by the means of pyrotag sequencing evaluation of the bacterial assemblage yielded a great diversity in all systems. The most represented phyla were the Bacteroidetes and the Proteobacteria, followed by the Planctomycetes. 14 OTUs were shared by all bioreactors, but none of them belonged to the Brocadiales order. Statistical analysis at OTU level showed that differences in the microbial communities were high, and that the main driver of the bacterial assemblage composition was different for the distinct phyla identified in the six bioreactors, depending on bioreactor technology or influent wastewater characteristics.

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.