Wiebke Ziebis

Advective Transport Affecting Metal and Nutrient Distributions and Interfacial Fluxes in Permeable Sediments

Abstract Our laboratory flume experiments demonstrate that advective porewater flows produce biogeochemical reaction zones in permeable sediments, leading to specific and reproducible complex patterns of Fe, Mn, and nutrients. Oxygenated water, forced into the sediment when boundary flows were deflected by protruding sediment structures, generated distinct zones of nitrification and ferric iron precipitation. This inflow was balanced by ammonium-rich porewater ascending from deeper sediment layers, thereby creating an anoxic channel where dissolved Fe2+ and Mn2+ could reach the surface. Between the zones of ferric iron precipitation and Fe2+ upwelling, a layer with increased manganese oxide and solid phase Fe(II) concentrations formed, indicating redox reaction between these components. The establishment of topography on the previously smooth sediment surface reversed the net interfacial flux of solutes. While the smooth control core was found to be a sink for metals and nutrients, the sediment with mounds acted as a source for these substances. Our experiments show that in sandy sediment with an oxidised surface layer, reduced metal species can be released to the water column by flow-topography interactions. We conclude that advective transport processes constitute an important process controlling biogeochemical zonations and fluxes in permeable sea beds.

Micron-scale mapping of sulfur cycling across the oxycline of a cyanobacterial mat: a paired nanoSIMS and CARD-FISH approach.

The metabolic activities of microbial mats have likely regulated biogeochemical cycling over most of Earths history. However, the relationship between metabolic activity and the establishment of isotopic geochemical gradients in these mats remains poorly constrained. Here we present a parallel microgeochemical and microbiological study of micron-scale sulfur cycling within hypersaline microbial mats from Guerrero Negro, Baja California Sur, Mexico. Dissolved sulfide within the mats was captured on silver discs and analyzed for its abundance and δ34S isotopic composition using high-resolution secondary ion mass spectrometry (nanoSIMS). These results were compared to sulfide and oxygen microelectrode profiles. Two-dimensional microgeochemical mapping revealed well-defined laminations in sulfide concentration (on scales from 1 to 200 μm), trending toward increased sulfide concentrations at depth. Sulfide δ34S decreased from ∼+10‰ to −20‰ in the uppermost 3 mm and oscillated repeatedly between −10‰ and −30‰ down to a depth of 8 mm. These variations are attributed to spatially variable bacterial sulfate reduction within the mat. A parallel examination of the spatial distribution of known sulfate-reducing bacteria within the family Desulfobacteraceae was conducted using catalyzed reporter deposition fluorescence in situ hybridization. Significant concentrations of Desulfobacteraceae were observed in both oxic and anoxic zones of the mat and occurred in several distinct layers, in large aggregates and heterogeneously dispersed as single cells throughout. The spatial distribution of these microorganisms is consistent with the variation in sulfide concentration and isotopic composition we observed. The parallel application of the methodologies developed here can shed light on micron-scale sulfur cycling within microbially dominated sedimentary environments.

Biodiversity of benthic microbial communities in bioturbated coastal sediments is controlled by geochemical microniches

We used a combination of field and laboratory approaches to address how the bioturbation activity of two crustaceans, the ghost shrimp Neotrypaea californiensis and the fiddler crab Uca crenulata, affects the microbial diversity in the seabed of a coastal lagoon (Catalina Harbor, Santa Catalina Island, CA, USA). Detailed geochemical analyses, including oxygen microsensor measurements, were performed to characterize environmental parameters. We used a whole-assemblage fingerprinting approach (ARISA: amplified ribosomal intergenic spacer analysis) to compare bacterial diversity along geochemical gradients and in relation to subsurface microniches. The two crustaceans have different burrowing behaviors. The ghost shrimp maintains complex, deep-reaching burrows and permanently lives subterranean, supplying its burrow with oxygen-rich water. In contrast, the fiddler crab constructs simpler, J-shaped burrows, which it does not inhabit permanently and does not actively ventilate. Our goal was to address how varying environmental parameters affect benthic microbial communities. An important question in benthic microbial ecology has been whether burrows support similar or unique communities compared with the sediment surface. Our results showed that sediment surface microbial communities are distinct from subsurface assemblages and that different burrow types support diverse bacterial taxa. Statistical comparisons by canonical correspondence analysis indicated that the availability of oxidants (oxygen, nitrate, ferric iron) play a key role in determining the presence and abundance of different taxa. When geochemical parameters were alike, microbial communities associated with burrows showed significant similarity to sediment surface communities. Our study provides implications on the community structure of microbial communities in marine sediments and the factors controlling their distribution.

Pediatric Cystic Fibrosis Sputum Can Be Chemically Dynamic, Anoxic, and Extremely Reduced Due to Hydrogen Sulfide Formation

ABSTRACT Severe and persistent bacterial lung infections characterize cystic fibrosis (CF). While several studies have documented the microbial diversity within CF lung mucus, we know much less about the inorganic chemistry that constrains microbial metabolic processes and their distribution. We hypothesized that sputum is chemically heterogeneous both within and between patients. To test this, we measured microprofiles of oxygen and sulfide concentrations as well as pH and oxidation-reduction potentials in 48 sputum samples from 22 pediatric patients with CF. Inorganic ions were measured in 20 samples from 12 patients. In all cases, oxygen was depleted within the first few millimeters below the sputum-air interface. Apart from this steep oxycline, anoxia dominated the sputum environment. Different sputum samples exhibited a broad range of redox conditions, with either oxidizing (16 mV to 355 mV) or reducing (−300 to −107 mV) potentials. The majority of reduced samples contained hydrogen sulfide and had a low pH (2.9 to 6.5). Sulfide concentrations increased at a rate of 0.30 µM H2S/min. Nitrous oxide was detected in only one sample that also contained sulfide. Microenvironmental variability was observed both within a single patient over time and between patients. Modeling oxygen dynamics within CF mucus plugs indicates that anoxic zones vary as a function of bacterial load and mucus thickness and can occupy a significant portion of the mucus volume. Thus, aerobic respiration accounts only partially for pathogen survival in CF sputum, motivating research to identify mechanisms of survival under conditions that span fluctuating redox states, including sulfidic environments. IMPORTANCE Microbial infections are the major cause of morbidity and mortality in people living with CF, and yet microbial growth and survival in CF airways are not well understood. Insufficient information about the chemistry of the in vivo environment contributes to this knowledge gap. Our documentation of variable redox states corresponding to the presence or absence of sulfide begins to fill this void and motivates understanding of how different opportunistic pathogens adapt in these dynamic environments. Given the changing chemical state of CF sputum over time, it is important to consider a spectrum of aerobic and anaerobic lifestyles when studying CF pathogens in the laboratory. This work not only provides relevant constraints that can shape the design of laboratory experiments, it also suggests that sulfide might be a useful proxy for assessing the redox state of sputum in the clinic. Microbial infections are the major cause of morbidity and mortality in people living with CF, and yet microbial growth and survival in CF airways are not well understood. Insufficient information about the chemistry of the in vivo environment contributes to this knowledge gap. Our documentation of variable redox states corresponding to the presence or absence of sulfide begins to fill this void and motivates understanding of how different opportunistic pathogens adapt in these dynamic environments. Given the changing chemical state of CF sputum over time, it is important to consider a spectrum of aerobic and anaerobic lifestyles when studying CF pathogens in the laboratory. This work not only provides relevant constraints that can shape the design of laboratory experiments, it also suggests that sulfide might be a useful proxy for assessing the redox state of sputum in the clinic.

Relative abundance of Archaea and Bacteria along a thermal gradient of a shallow-water hydrothermal vent quantified by rRNA slot-blot hybridization.

Slot-blot hybridization of rRNA with domain-specific oligonucleotide probes targeting the 16S rRNA of Archaea and Bacteria was utilized to assess the relative abundance of these domains along a thermal gradient at a shallow submarine hydrothermal vent near Milos Island (Greece). The highest prokaryotic rRNA concentrations (defined as the sum of bacterial and archaeal rRNA) were found in the uppermost sediment surface (0-20 mm), decreasing strongly with depth. This indicates that the microbial activity was mainly occurring in the surface layer of this hydrothermal vent. Furthermore, rRNA concentrations were higher in regions closer to the vent, suggesting that the hydrothermal activity stimulated microbial activity. Archaea seemed to be a minor component of the microbial community at this vent site, even in the zones with higher temperatures. Bacteria made up at least 78% (mean 95%) of the prokaryotic rRNA. However, along the steepest temperature gradient, the proportion of archaeal rRNA increased. Nevertheless, even in the hottest sediment layer where a quantification was possible (in situ temperature 82 degrees C) archaeal rRNA made up only 11.9% of the prokaryotic rRNA. This suggests that Archaea were generally of minor importance at this vent site and were probably restricted to a narrow niche. The factors that allow Bacteria to dominate in a high temperature environment that was once believed to be the realm of Archaea remain elusive.

Bioturbation and the role of microniches for sulfate reduction in coastal marine sediments

The effects of bioturbation in marine sediments are mainly associated with an increase in oxic and oxidized zones through an influx of oxygen-rich water deeper into the sediment and the rapid transport of particles between oxic and anoxic conditions. However, macrofaunal activity also can increase the occurrence of reduced microniches and anaerobic processes, such as sulfate reduction. Our goal was to determine the two-dimensional distribution of microniches associated with burrows of a ghost shrimp (Neotrypaea californiensis) and to determine microbial activities. In laboratory experiments, detailed measurements of sulfate reduction rates (SRR) were measured by injecting, in a 1 cm grid, radiolabelled sulfate directly into a narrow aquarium (40 cm × 30 cm × 3 cm) containing the complex burrow of an actively burrowing shrimp. Light-coloured oxidized burrow walls, along with black reduced microniches, were clearly visible through the aquarium walls. Direct injection of radiotracers allowed for whole-aquarium incubation to obtain two-dimensional documentation of sulfate reduction. Results indicated SRR were up to three orders of magnitude higher (140-790 nmol SO(4) (2-) cm(-3) day(-1) ) in reduced microniches associated with burrows when compared with the surrounding sediment. Additionally, some of the subsurface sulfate-reducing microniches associated with the burrow system appeared to be zones of dinitrogen fixation. Bioturbation may also lead to decreased sulfate reduction in other microniches and the sum of the activity in all microniches might not result in a total increase of sulfate reduction compared with non-bioturbated control sediments.

Carbonate-hosted methanotrophy represents an unrecognized methane sink in the deep sea

The atmospheric flux of methane from the oceans is largely mitigated through microbially mediated sulphate-coupled methane oxidation, resulting in the precipitation of authigenic carbonates. Deep-sea carbonates are common around active and palaeo-methane seepage, and have primarily been viewed as passive recorders of methane oxidation; their role as active and unique microbial habitats capable of continued methane consumption has not been examined. Here we show that seep-associated carbonates harbour active microbial communities, serving as dynamic methane sinks. Microbial aggregate abundance within the carbonate interior exceeds that of seep sediments, and molecular diversity surveys reveal methanotrophic communities within protolithic nodules and well-lithified carbonate pavements. Aggregations of microbial cells within the carbonate matrix actively oxidize methane as indicated by stable isotope FISH-nanoSIMS experiments and (14)CH4 radiotracer rate measurements. Carbonate-hosted methanotrophy extends the known ecological niche of these important methane consumers and represents a previously unrecognized methane sink that warrants consideration in global methane budgets.

Respiration Strategies Utilized by the Gill Endosymbiont from the Host Lucinid Codakia Orbicularis (Bivalvia: Lucinidae)

ABSTRACT The large tropical lucinid clam Codakia orbicularis has a symbiotic relationship with intracellular, sulfide-oxidizing chemoautotrophic bacteria. The respiration strategies utilized by the symbiont were explored using integrative techniques on mechanically purified symbionts and intact clam-symbiont associations along with habitat analysis. Previous work on a related symbiont species found in the host lucinid Lucinoma aequizonata showed that the symbionts obligately used nitrate as an electron acceptor, even under oxygenated conditions. In contrast, the symbionts of C. orbicularis use oxygen as the primary electron acceptor while evidence for nitrate respiration was lacking. Direct measurements obtained by using microelectrodes in purified symbiont suspensions showed that the symbionts consumed oxygen; this intracellular respiration was confirmed by using the redox dye CTC (5-cyano-2,3-ditolyl tetrazolium chloride). In the few intact chemosymbioses tested in previous studies, hydrogen sulfide production was shown to occur when the animal-symbiont association was exposed to anoxia and elemental sulfur stored in the thioautotrophic symbionts was proposed to serve as an electron sink in the absence of oxygen and nitrate. However, this is the first study to show by direct measurements using sulfide microelectrodes in enriched symbiont suspensions that the symbionts are the actual source of sulfide under anoxic conditions.

Denitrification and nitrogen fixation dynamics in the area surrounding an individual ghost shrimp (Neotrypaea californiensis) burrow system.

ABSTRACT Bioturbated sediments are thought of as areas of increased denitrification or fixed-nitrogen (N) loss; however, recent studies have suggested that not all N may be lost from these environments, with some N returning to the system via microbial dinitrogen (N2) fixation. We investigated denitrification and N2 fixation in an intertidal lagoon (Catalina Harbor, CA), an environment characterized by bioturbation by thalassinidean shrimp (Neotrypaea californiensis). Field studies were combined with detailed measurements of denitrification and N2 fixation surrounding a single ghost shrimp burrow system in a narrow aquarium (15 cm by 20 cm by 5 cm). Simultaneous measurements of both activities were performed on samples taken within a 1.5-cm grid for a two-dimensional illustration of their intensity and distribution. These findings were then compared with rate measurements performed on bulk environmental sediment samples collected from the lagoon. Results for the aquarium indicated that both denitrification and N2 fixation have a patchy distribution surrounding the burrow, with no clear correlation to each other, sediment depth, or distance from the burrow. Field denitrification rates were, on average, lower in a bioturbated region than in a seemingly nonbioturbated region; however, replicates showed very high variability. A comparison of denitrification field results with previously reported N2 fixation rates from the same lagoon showed that in the nonbioturbated region, depth-integrated (10 cm) denitrification rates were higher than integrated N2 fixation rates (∼9 to 50 times). In contrast, in the bioturbated sediments, depending on the year and bioturbation intensity, some (∼6.2%) to all of the N lost via denitrification might be accounted for via N2 fixation.

Evidence for fungal and chemodenitrification based N2O flux from nitrogen impacted coastal sediments

Although increasing atmospheric nitrous oxide (N2O) has been linked to nitrogen loading, predicting emissions remains difficult, in part due to challenges in disentangling diverse N2O production pathways. As coastal ecosystems are especially impacted by elevated nitrogen, we investigated controls on N2O production mechanisms in intertidal sediments using novel isotopic approaches and microsensors in flow-through incubations. Here we show that during incubations with elevated nitrate, increased N2O fluxes are not mediated by direct bacterial activity, but instead are largely catalysed by fungal denitrification and/or abiotic reactions (e.g., chemodenitrification). Results of these incubations shed new light on nitrogen cycling complexity and possible factors underlying variability of N2O fluxes, driven in part by fungal respiration and/or iron redox cycling. As both processes exhibit N2O yields typically far greater than direct bacterial production, these results emphasize their possibly substantial, yet widely overlooked, role in N2O fluxes, especially in redox-dynamic sediments of coastal ecosystems.