Carolin Löscher

Giant hydrogen sulfide plume in the oxygen minimum zone off Peru supports chemolithoautotrophy

In Eastern Boundary Upwelling Systems nutrient-rich waters are transported to the ocean surface, fuelling high photoautotrophic primary production. Subsequent heterotrophic decomposition of the produced biomass increases the oxygen-depletion at intermediate water depths, which can result in the formation of oxygen minimum zones (OMZ). OMZs can sporadically accumulate hydrogen sulfide (H2S), which is toxic to most multicellular organisms and has been implicated in massive fish kills. During a cruise to the OMZ off Peru in January 2009 we found a sulfidic plume in continental shelf waters, covering an area >5500 km2, which contained ∼2.2×104 tons of H2S. This was the first time that H2S was measured in the Peruvian OMZ and with ∼440 km3 the largest plume ever reported for oceanic waters. We assessed the phylogenetic and functional diversity of the inhabiting microbial community by high-throughput sequencing of DNA and RNA, while its metabolic activity was determined with rate measurements of carbon fixation and nitrogen transformation processes. The waters were dominated by several distinct γ-, δ- and ε-proteobacterial taxa associated with either sulfur oxidation or sulfate reduction. Our results suggest that these chemolithoautotrophic bacteria utilized several oxidants (oxygen, nitrate, nitrite, nitric oxide and nitrous oxide) to detoxify the sulfidic waters well below the oxic surface. The chemolithoautotrophic activity at our sampling site led to high rates of dark carbon fixation. Assuming that these chemolithoautotrophic rates were maintained throughout the sulfidic waters, they could be representing as much as ∼30% of the photoautotrophic carbon fixation. Postulated changes such as eutrophication and global warming, which lead to an expansion and intensification of OMZs, might also increase the frequency of sulfidic waters. We suggest that the chemolithoautotrophically fixed carbon may be involved in a negative feedback loop that could fuel further sulfate reduction and potentially stabilize the sulfidic OMZ waters.

Aerobic Microbial Respiration In Oceanic Oxygen Minimum Zones

Oxygen minimum zones are major sites of fixed nitrogen loss in the ocean. Recent studies have highlighted the importance of anaerobic ammonium oxidation, anammox, in pelagic nitrogen removal. Sources of ammonium for the anammox reaction, however, remain controversial, as heterotrophic denitrification and alternative anaerobic pathways of organic matter remineralization cannot account for the ammonium requirements of reported anammox rates. Here, we explore the significance of microaerobic respiration as a source of ammonium during organic matter degradation in the oxygen-deficient waters off Namibia and Peru. Experiments with additions of double-labelled oxygen revealed high aerobic activity in the upper OMZs, likely controlled by surface organic matter export. Consistently observed oxygen consumption in samples retrieved throughout the lower OMZs hints at efficient exploitation of vertically and laterally advected, oxygenated waters in this zone by aerobic microorganisms. In accordance, metagenomic and metatranscriptomic analyses identified genes encoding for aerobic terminal oxidases and demonstrated their expression by diverse microbial communities, even in virtually anoxic waters. Our results suggest that microaerobic respiration is a major mode of organic matter remineralization and source of ammonium (~45-100%) in the upper oxygen minimum zones, and reconcile hitherto observed mismatches between ammonium producing and consuming processes therein.

Air-Sea Interactions of Natural Long-Lived Greenhouse Gases (CO2, N2O, CH4)in a Changing Climate

Understanding and quantifying ocean–atmosphere exchanges of the long-lived greenhouse gases carbon dioxide (CO2), nitrous oxide (N2O) and methane (CH4) are important for understanding the global biogeochemical cycles of carbon and nitrogen in the context of ongoing global climate change. In this chapter we summarise our current state of knowledge regarding the oceanic distributions, formation and consumption pathways, and oceanic uptake and emissions of CO2, N2O and CH4, with a particular emphasis on the upper ocean. We specifically consider the role of the ocean in regulating the tropospheric content of these important radiative gases in a world in which their tropospheric content is rapidly increasing and estimate the impact of global change on their present and future oceanic uptake and/or emission. Finally, we evaluate the various uncertainties associated with the most commonly used methods for estimating uptake and emission and identify future research needs.

Construction and Screening of Marine Metagenomic Libraries

Marine microbial communities are highly diverse and have evolved during extended evolutionary processes of physiological adaptations under the influence of a variety of ecological conditions and selection pressures. They harbor an enormous diversity of microbes with still unknown and probably new physiological characteristics. Besides, the surfaces of marine multicellular organisms are typically covered by a consortium of epibiotic bacteria and act as barriers, where diverse interactions between microorganisms and hosts take place. Thus, microbial diversity in the water column of the oceans and the microbial consortia on marine tissues of multicellular organisms are rich sources for isolating novel bioactive compounds and genes. Here we describe the sampling, construction of large-insert metagenomic libraries from marine habitats and exemplarily one function based screen of metagenomic clones.

Influence of Ocean Acidification and Deep Water Upwelling on Oligotrophic Plankton Communities in the Subtropical North Atlantic: Insights from an In situ Mesocosm Study

Oceanic uptake of anthropogenic carbon dioxide (CO2) causes pronounced shifts in marine carbonate chemistry and a decrease in seawater pH. Increasing evidence indicates that these changes—summarized by the term ocean acidification (OA)—can significantly affect marine food webs and biogeochemical cycles. However, current scientific knowledge is largely based on laboratory experiments with single species and artificial boundary conditions, whereas studies of natural plankton communities are still relatively rare. Moreover, the few existing community-level studies were mostly conducted in rather eutrophic environments, while less attention has been paid to oligotrophic systems such as the subtropical ocean gyres. Here we report from a recent in situ mesocosm experiment off the coast of Gran Canaria in the eastern subtropical North Atlantic, where we investigated the influence of OA on the ecology and biogeochemistry of plankton communities in oligotrophic waters under close-to-natural conditions. This paper is the first in this Research Topic of Frontiers in Marine Biogeochemistry and provides (1) a detailed overview of the experimental design and important events during our mesocosm campaign, and (2) first insights into the ecological responses of plankton communities to simulated OA over the course of the 62-day experiment. One particular scientific objective of our mesocosm experiment was to investigate how OA impacts might differ between oligotrophic conditions and phases of high biological productivity, which regularly occur in response to upwelling of nutrient-rich deep water in the study region. Therefore, we specifically developed a deep water collection system that allowed us to obtain ~85 m3 of seawater from ~650 m depth. Thereby, we replaced ~20% of each mesocosms volume with deep water and successfully simulated a deep water upwelling event that induced a pronounced plankton bloom. Our study revealed significant effects of OA on the entire food web, leading to a restructuring of plankton communities that emerged during the oligotrophic phase, and was further amplified during the bloom that developed in response to deep water addition. Such CO2-related shifts in plankton community composition could have consequences for ecosystem productivity, biomass transfer to higher trophic levels, and biogeochemical element cycling of oligotrophic ocean regions.

Characterization of phosphate solubilizing rhizobacteria isolated from lentil growing areas of Ethiopia

Lentil (Lens culnaris Medik.) is an invaluable source of dietary protein for the majority of Ethiopian population. The low availability of phosphorus is one of the major soil related stresses that limit the production of this crop. This study was aimed at isolation and characterization of phosphate solubilizing bacteria from lentil growing areas of Ethiopia and evaluating their effects on growth of this crop under greenhouse conditions. In total, 41 phosphate solubilizing bacterial strains were isolated from lentil rhizosphere and characterized using biochemical tests and 16S rDNA sequence analysis. The results showed the presence of genera Acinetobacter, Agrobacterium, Bacillus, Burkholderia, Chryseomonas, Enterobacter, Pseudomonas, Ralstonia and Sphingomonas. Phosphate solubilzing efficiencies of these isolates were evaluated in liquid medium using different insoluble P-sources and the result indicated that they released considerable amount of phosphates from tricalcium phosphate, rock phosphate and bone meal. Besides, some of these isolates exhibited multiple plant growth promoting characteristics such as indole acetic acid production and growth inhibition of Fusarium oxysporum under in vitro conditions. The effects of inoculation of Enterobacter kobei (PSBL5), Bacillus subtilis (PSBL21), Enterobacter species (PSBL26), Bacillus species (PSBL31) and Pseudomonas fluorescence (PSBL37) on lentil growth, nodulation, N and P content of shoot were evaluated under a greenhouse conditions and the results showed that these features were significantly increased over uninoculated control plants. Based on the results of this study, we conclude that lentil rhizosphere soil from producing areas of Ethiopia harbor diverse phosphate solubilizing bacterial strains with excellent phosphate solubilization and plant growth promotion ability. Thus, most of the promising strains should be tested in the field conditions under different agroecology of the country. Key words: Rhizosphere soil, PGPR, rock phosphate, bone meal.

Low oxygen eddies in the eastern tropical North Atlantic: Implications for N2O cycling

Nitrous oxide (N2O) is a climate relevant trace gas, and its production in the ocean generally increases under suboxic conditions. The Atlantic Ocean is well ventilated, and unlike the major oxygen minimum zones (OMZ) of the Pacific and Indian Oceans, dissolved oxygen and N2O concentrations in the Atlantic OMZ are relatively high and low, respectively. This study, however, demonstrates that recently discovered low oxygen eddies in the eastern tropical North Atlantic (ETNA) can produce N2O concentrations much higher (up to 115 nmol L−1) than those previously reported for the Atlantic Ocean, and which are within the range of the highest concentrations found in the open-ocean OMZs of the Pacific and Indian Oceans. N2O isotope and isotopomer signatures, as well as molecular genetic results, also point towards a major shift in the N2O cycling pathway in the core of the low oxygen eddy discussed here, and we report the first evidence for potential N2O cycling via the denitrification pathway in the open Atlantic Ocean. Finally, we consider the implications of low oxygen eddies for bulk, upper water column N2O at the regional scale, and point out the possible need for a reevaluation of how we view N2O cycling in the ETNA.

Mechanisms of P* Reduction in the Eastern Tropical South Pacific

Water masses influenced by oxygen minimum zones (OMZ) feature low inorganic nitrogen (N) to phosphorus (P) ratios. The surplus of P over N is thought to favor non-Redfield primary production by bloom-forming phytoplankton species. Additionally, excess phosphate (P*) is thought to provide a niche for nitrogen fixing organisms. In order to assess the effect of low inorganic nutrient ratios on the stoichiometry and composition of primary producers, biogeochemical measurements were carried out in 2012 during a research cruise in the eastern tropical South Pacific (ETSP). Based on pigment analyses, a succession of different phytoplankton functional groups was observed along onshore – offshore transects with diatoms dominating the productive upwelling region, and prymnesiophytes, cryptophytes and Synechococcus prevailing in the oligotrophic open ocean. Although inorganic nutrient supply ratios were below Redfield proportions throughout the sampling area, the stoichiometry of particulate organic nitrogen to phosphorus (PON:POP) generally exceeded ratios of 16:1. Despite PON:POP ≥ 16, high P* values in the surface layer (0-50 m) above the shelf rapidly decreased as water masses were advected offshore. There are three mechanisms which can explain these observations: (1) non-Redfield primary production, where the excess phosphorus in the biomass is directly released as dissolved organic phosphorus (DOP), (2) non-Redfield primary production, which is masked by a particulate organic matter pool mainly consisting of P-depleted detrital biomass, and/or (3) Redfield primary production combined with dinitrogen (N2) fixation. Our observations suggest that the three processes occur simultaneously in the study area; quantifying the relative importance of each of these mechanisms needs further investigation. Therefore, it remains uncertain whether the ETSP is a net sink for bioavailable N or whether the N-deficit in this area is replenished locally.

Oxygen minimum zone cryptic sulfur cycling sustained by offshore transport of key sulfur oxidizing bacteria

Members of the gammaproteobacterial clade SUP05 couple water column sulfide oxidation to nitrate reduction in sulfidic oxygen minimum zones (OMZs). Their abundance in offshore OMZ waters devoid of detectable sulfide has led to the suggestion that local sulfate reduction fuels SUP05-mediated sulfide oxidation in a so-called “cryptic sulfur cycle”. We examined the distribution and metabolic capacity of SUP05 in Peru Upwelling waters, using a combination of oceanographic, molecular, biogeochemical and single-cell techniques. A single SUP05 species, UThioglobus perditus, was found to be abundant and active in both sulfidic shelf and sulfide-free offshore OMZ waters. Our combined data indicated that mesoscale eddy-driven transport led to the dispersal of UT. perditus and elemental sulfur from the sulfidic shelf waters into the offshore OMZ region. This offshore transport of shelf waters provides an alternative explanation for the abundance and activity of sulfide-oxidizing denitrifying bacteria in sulfide-poor offshore OMZ waters.The presence and activity of sulfide-oxidizing denitrifying bacteria in sulfide-poor offshore oxygen minimum zone waters remains unclear. Here, the authors combine oceanography, molecular, biogeochemical and single-cell techniques to examine their distribution, metabolic capacity, and origins.

Benthic Dinitrogen Fixation Traversing the Oxygen Minimum Zone Off Mauritania (NW Africa)

Despite its potential to provide new nitrogen (N) to the environment, knowledge on benthic dinitrogen (N2) fixation remains relatively sparse and its contribution to the marine N budget, is regarded as minor. Benthic N2 fixation is often observed in organic-rich sediments coupled to heterotrophic metabolisms, such as sulfate reduction. In the present study, benthic N2 fixation together with sulfate reduction and other heterotrophic metabolisms were investigated at six station between 47 and 1108 m water depth along the 18°N transect traversing the highly productive upwelling region known as Mauritanian oxygen minimum zone (OMZ). Bottom water oxygen concentrations ranged between 30 and 138 µM. Benthic N2 fixation determined by the acetylene reduction assay was detected at all stations with highest rates (0.15 mmol m-2 d-1) on the shelf (47 and 90 m water depth) and lowest rates (0.08 mmol m-2 d-1) below 412 m water depth. The biogeochemical data suggest that part of the N2 fixation could be linked to sulfate- and iron-reducing bacteria. Molecular analysis of the key functional marker gene for N2 fixation, nifH, confirmed the presence of sulfate- and iron-reducing diazotrophs. High N2 fixation further coincided with bioirrigation activity caused by burrowing macrofauna, both of which showed high rates at the shelf sites and low rates in deeper waters. However, statistical analyses proved that none of these processes and environmental variables were significantly correlated with benthic diazotrophy, which lead to the conclusion that either the key parameter controlling benthic N2 fixation in Mauritanian sediments remains unidentified or that a more complex interaction of control mechanisms exists. N2 fixation rates in Mauritanian sediments were 2.7 times lower than those from the anoxic Peruvian OMZ.