Temporal and Spatial Coexistence of Archaeal and Bacterial amoA Genes and Gene Transcripts in Lake Lucerne

Despite their crucial role in the nitrogen cycle, freshwater ecosystems are relatively rarely studied for active ammonia oxidizers (AO). This study of Lake Lucerne determined the abundance of both amoA genes and gene transcripts of ammonia-oxidizing archaea (AOA) and bacteria (AOB) over a period of 16 months, shedding more light on the role of both AO in a deep, alpine lake environment. At the surface, at 42 m water depth, and in the water layer immediately above the sediment, AOA generally outnumbered AOB. However, in the surface water during summer stratification, when both AO were low in abundance, AOB were more numerous than AOA. Temporal distribution patterns of AOA and AOB were comparable. Higher abundances of amoA gene transcripts were observed at the onset and end of summer stratification. In summer, archaeal amoA genes and transcripts correlated negatively with temperature and conductivity. Concentrations of ammonium and oxygen did not vary enough to explain the amoA gene and transcript dynamics. The observed herbivorous zooplankton may have caused a hidden flux of mineralized ammonium and a change in abundance of genes and transcripts. At the surface, AO might have been repressed during summer stratification due to nutrient limitation caused by active phytoplankton.

What Limits Bacterial Production in the Suboxic Region of Permanently Ice-Covered Lake Bonney, Antarctica?

Bacterial production assays (thymidine incorporation rates) were used to evaluate the activity of heterotrophic bacteria at the chemocline region in both the East (ELB) and West (WLB) Lobes of permanently ice-covered Lake Bonney, in the Taylor Valley of Antarctica. The magnitude of activity varied dramatically within the depth interval of 1 to 2 m from moderate to very low levels below the chemocline, especially in the East Lobe, where chemical distributions indicate the absence of a normally functioning nitrogen cycle. Several parameters (e.g. addition of nutrients or chelators, dilution) were manipulated in incubation experiments in order to identify factors that would enhance activity in the suboxic deep waters of the East Lobe. Activity, in terms of thymidine incorporation, was consistently detected in the deep-water communities, implying that, although the water may be 'toxic', the cells remain viable. None of the treatments resulted in consistent enhancement of thymidine incorporation rates in samples from below the chemocline. Bacterial populations above the chemocline appear to be phosphorus-limited. The nature of the limitation, toxicity or inhibition that limits bacterial activity in the suboxic waters has not been identified.

Changes of dissolved organic matter compositions in artifical and natural seawater during Pseudovibrio growth experiment

To study the consumption of dissolved organic matter (DOM) by bacteria living in untra-oligotrophic artificial or natural seawater, we analyzed the composition of DOM before (timepoint t0, directly after inoculation) and after (timepoint t2, 3 weeks of incubation) growth of the bacteria using Fourier transform ion cyclotron mass spectrometry (ESI FT-ICR-MS). The oligotrophic natural seawater used originates from the South Pacific Gyre. Our data show that the bacteria were able to utilize a variety of different organic compounds. These compounds belong to different chemical compound groups and likely fuel the bacterial energy, carbon and nitrogen requirements under the ultra-oligotrophic conditions.

Benthic foraminiferal denitrification rates and nitrate storage

The discovery that foraminifera are able to use nitrate instead of oxygen as energy source for their metabolism has challenged our understanding of nitrogen cycling in the ocean. It was evident before that only prokaryotes and fungi are able to denitrify. Rate estimates of foraminiferal denitrification were very sparse on a regional scale. Here, we present estimates of benthic foraminiferal denitrification rates from six stations at intermediate water depths in and below the Peruvian oxygen minimum zone (OMZ). Foraminiferal denitrification rates were calculated from abundance and assemblage composition of the total living fauna in both, surface and subsurface sediments, as well as from individual species specific denitrification rates. A comparison with total benthic denitrification rates as inferred by biogeochemical models revealed that benthic foraminifera account for the total denitrification on the shelf between 80 and 250 m water depth. They are still important denitrifiers in the centre of the OMZ around 320 m (29-56% of the benthic denitrification) but play only a minor role at the lower OMZ boundary and below the OMZ between 465 and 700 m (3-7% of total benthic denitrification). Furthermore, foraminiferal denitrification was compared to the total benthic nitrate loss measured during benthic chamber experiments. Foraminiferal denitrification contributes 1 to 50% to the total nitrate loss across a depth transect from 80 to 700 m, respectively. Flux rate estimates ranged from 0.01 to 1.3 mmol m?2 d?1. Furthermore we show that the amount of nitrate stored in living benthic foraminifera (3 to 705 µmol L?1) can be higher by three orders of magnitude as compared to the ambient pore waters in near surface sediments sustaining an important nitrate reservoir in Peruvian OMZ sediments. The substantial contribution of foraminiferal nitrate respiration to total benthic nitrate loss at the Peruvian margin, which is one of the main nitrate sink regions in the world oceans, underpins the importance of previously underestimated role of benthic foraminifera in global biochemical cycles.

Hydrochemistry measured on water bottle samples during the R/V Meteor cruise M96 (May, 2013) across the Tropical North Atlantic

The table includes hydrography (salinity, temperature, density, oxygen concentrations) and nutrient (nitrate, nitrite, ammonium, phosphate) measurements from surface waters (upper 200 m) across a 14 °N transect of the Tropical North Atlantic.

Stable isotope analysis of Porites coral core from the Andaman Islands

North Atlantic climate variations are reflected in sedimentary records from the northern Indian Ocean in which two basins, the Arabian Sea and the Bay of Bengal, are strongly affected by the monsoon. Contrary to the Bay of Bengal the Arabian Sea plays an important role in the global marine nitrogen cycle. In its mid-water oxygen minimum zone (OMZ) bioavailable fixed nitrogen is reduced to nitrogen gas (NO3- - > N2), whereas oxygen concentrations are slightly above the threshold of nitrate reduction in the OMZ of the Bay of Bengal. A coral colony (Porites lutea) growing south of Port Blair on the Andaman Islands in the Bay of Bengal was studied for its response to changes in the monsoon system and its link to temperature changes in the North Atlantic Ocean, between 1975 and 2006. Its linear extension rates, d13C and d18O values measured within the coral skeleton reveal a strong seasonality, which seems to be caused by the monsoon-driven reversal of the surface ocean circulation. The sampling site appears to be influenced by low salinity Bay of Bengal Water during the NE monsoon (boreal winter) and by the high salinity Arabian Sea Water during the SW monsoon in summer. The high salinity Arabian Sea Water circulates along with the Summer Monsoon Current (S-MC) from the Arabia Sea into the Bay of Bengal. Decreasing d18O and reconstructed salinity values correlate to the increasing SSTs in the North Atlantic Ocean indicating a reduced influence of the S-MC at the sampling site in the course of northern hemispheric warming. During such periods oxygen-depletion became stronger in the OMZ of the Arabian Sea as indicated by the sedimentary records. A reduced propagation of oxygen-depleted high salinity Arabian Sea Water into the Bay of Bengal could be a mechanism maintaining oxygen concentration above the threshold of nitrate reduction in the OMZ of the Bay of Bengal in times of global warming.