Two-Dimensional Mapping of Arsenic Concentration and Speciation with Diffusive Equilibrium in Thin-Film Gels.

We present a new approach combining diffusive equilibrium in thin-film gels and spectrophotometric methods to determine the spatial distribution of arsenite, arsenate, and phosphate at submillimeter resolution. The method relies on the simultaneous deployment of three gel probes. Each retrieved gel is exposed to malachite green reagent gels differing in acidity and oxidant addition, leading to green coloration dependent on analyte speciation and concentration. Hyperspectral images of the gels enable mapping the three analytes in the 2.5-20 µM range. This method was applied in a contaminated brook in the Harz mountains, Germany, together with established mapping of dissolved iron. The use of two-dimensional (2D) gel probes was compared to traditional porewater extraction. The gels revealed banded porewater patterns on a mm-scale, which were undetectable using traditional methods. Small-scale correlation analyses of arsenic and iron microstructures in the gels suggested active iron-driven local redox cycling of arsenic. Overall, the results indicate continuous net release of arsenic from contaminant particles and deepen our understanding of arsenate transformation under anaerobic conditions. This study is the first fine-scale 2D characterization of arsenic speciation in porewater and represents a crucial step toward understanding the transfer and redox cycling of arsenic in contaminated sediment/soil ecosystems.

Non-Destructive Impedance Monitoring of Bacterial Metabolic Activity towards Continuous Lead Biorecovery.

The adverse health effects of the presence of lead in wastewater streams are well documented, with conventional methods of lead recovery and removal suffering from disadvantages such as high energy costs, the production of toxic sludge, and low lead selectivity. Klebsiella pneumoniae and Paraclostridium bifermentans have been identified as potential lead-precipitating species for use in a lead recovery bioreactor. Electrical impedance spectroscopy (EIS) on a low-cost device is used to determine the potential for the probe-free and label-free monitoring of cell growth in a bioreactor containing these bacteria. A complex polynomial is fit for several reactive equivalent circuit components. A direct correlation is found between the extracted supercapacitance and the plated colony-forming unit count during the exponential growth phase, and a qualitative correlation is found between all elements of the measured reactance outside the exponential growth phase. Strong evidence is found that Pb(II) ions act as an anaerobic respiration co-substrate for both cells observed, with changes in plated count qualitatively mirrored in the Pb(II) concentration. Guidance is given on the implementation of EIS devices for continuous impedance monitoring.

Nitrate respiration and diel migration patterns of diatoms are linked in sediments underneath a microbial mat.

Diatoms are among the few eukaryotes known to store nitrate (NO3 - ) and to use it as an electron acceptor for respiration in the absence of light and O2 . Using microscopy and 15 N stable isotope incubations, we studied the relationship between dissimilatory nitrate/nitrite reduction to ammonium (DNRA) and diel vertical migration of diatoms in phototrophic microbial mats and the underlying sediment of a sinkhole in Lake Huron (USA). We found that the diatoms rapidly accumulated NO3 - at the mat-water interface in the afternoon and 40% of the population migrated deep into the sediment, where they were exposed to dark and anoxic conditions for ~75% of the day. The vertical distribution of DNRA rates and diatom abundance maxima coincided, suggesting that DNRA was the main energy generating metabolism of the diatom population. We conclude that the illuminated redox-dynamic ecosystem selects for migratory diatoms that can store nitrate for respiration in the absence of light. A major implication of this study is that the dominance of DNRA over denitrification is not explained by kinetics or thermodynamics. Rather, the dynamic conditions select for migratory diatoms that perform DNRA and can outcompete sessile denitrifiers.

Limitation of Microbial Processes at Saturation-Level Salinities in a Microbial Mat Covering a Coastal Salt Flat.

Hypersaline microbial mats are dense microbial ecosystems capable of performing complete element cycling and are considered analogs of early Earth and hypothetical extraterrestrial ecosystems. We studied the functionality and limits of key biogeochemical processes, such as photosynthesis, aerobic respiration, and sulfur cycling, in salt crust-covered microbial mats from a tidal flat at the coast of Oman. We measured light, oxygen, and sulfide microprofiles as well as sulfate reduction rates at salt saturation and in flood conditions and determined fine-scale stratification of pigments, biomass, and microbial taxa in the resident microbial community. The salt crust did not protect the mats against irradiation or evaporation. Although some oxygen production was measurable at salinities of ≤30% (wt/vol) in situ, at saturation-level salinity (40%), oxygenic photosynthesis was completely inhibited and only resumed 2 days after reducing the porewater salinity to 12%. Aerobic respiration and active sulfur cycling occurred at low rates under salt saturation and increased strongly upon salinity reduction. Apart from high relative abundances of Chloroflexi, photoheterotrophic Alphaproteobacteria, Bacteroidetes, and Archaea, the mat contained a distinct layer harboring filamentous Cyanobacteria, which is unusual for such high salinities. Our results show that the diverse microbial community inhabiting this salt flat mat ultimately depends on periodic salt dilution to be self-sustaining and is rather adapted to merely survive salt saturation than to thrive under the salt crust. IMPORTANCE Due to their abilities to survive intense radiation and low water availability, hypersaline microbial mats are often suggested to be analogs of potential extraterrestrial life. However, even the limitations imposed on microbial processes by saturation-level salinity found on Earth have rarely been studied in situ. While abundance and diversity of microbial life in salt-saturated environments are well documented, most of our knowledge on process limitations stems from culture-based studies, few in situ studies, and theoretical calculations. In particular, oxygenic photosynthesis has barely been explored beyond 5 M NaCl (28% wt/vol). By applying a variety of biogeochemical and molecular methods, we show that despite abundance of photoautotrophic microorganisms, oxygenic photosynthesis is inhibited in salt-crust-covered microbial mats at saturation salinities, while rates of other energy generation processes are decreased several-fold. Hence, the complete element cycling required for self-sustaining microbial communities only occurs at lower salt concentrations.

Validation of Low-Cost Impedance Analyzer via Nitrate Detection.

Impedance spectroscopy is a widely used electrochemical technique with a wide variety of applications. Many of these applications benefit from the additional accessibility provided by low-cost impedance devices. With this in mind, a low-cost impedance device was designed for a high performance-to-cost ratio. The performance of this analyzer was validated against a high-performance DropSens µStat-i 400s potentiostat by performing an application-based experiment. Nitrate detection provides a relevant experiment because of the importance of maintaining precise nitrate concentrations to mitigate the impact of nitrate fluctuations on the environment. Dissolved nitrate samples of different concentrations, in the range 3-1000 mg/L, were confirmed colorimetrically and measured with both instruments. A calibration curve of the real impedance matched a sigmoidal transfer, with a linear region for concentrations below 10 mg/L. The device under investigation exhibited an average magnitude error of 1.28% and an average phase error of 0.96∘ relative to the high-performance standard, which validates the performance of the low-cost device. A cost analysis is presented that highlights some of the complexities of cost comparisons.

Use of an oxygen planar optode to assess the effect of high velocity microsprays on oxygen penetration in a human dental biofilms in-vitro.

BACKGROUND: Dental plaque biofilms are the causative agents of caries, gingivitis and periodontitis. Both mechanical and chemical strategies are used in routine oral hygiene strategies to reduce plaque build-up. If allowed to mature biofilms can create anoxic microenvironments leading to communities which harbor pathogenic Gram-negative anaerobes. When subjected to high velocity fluid jets and sprays biofilms can be fluidized which disrupts the biofilm structure and allows the more efficient delivery of antimicrobial agents. METHODS: To investigate how such jets may disrupt anoxic niches in the biofilm, we used planar optodes to measure the dissolved oxygen (DO) concentration at the base of in-vitro biofilms grown from human saliva and dental plaque. These biofilms were subject to "shooting" treatments with a commercial high velocity microspray (HVM) device. RESULTS: HVM treatment resulted in removal of much of the biofilm and a concurrent rapid shift from anoxic to oxic conditions at the base of the surrounding biofilm. We also assessed the impact of HVM treatment on the microbial community by tracking 7 target species by qPCR. There was a general reduction in copy numbers of the universal 16S RNA by approximately 95%, and changes of individual species in the target region ranged from approximately 1 to 4 log reductions. CONCLUSION: We concluded that high velocity microsprays removed a sufficient amount of biofilm to disrupt the anoxic region at the biofilm-surface interface.

Correction to: Use of an oxygen planar optode to assess the effect of high velocity microsprays on oxygen penetration in a human dental biofilms in-vitro.

An amendment to this paper has been published and can be accessed via the original article.

N2 fixation in free-floating filaments of Trichodesmium is higher than in transiently suboxic colony microenvironments.

To understand the role of micrometer-scale oxygen (O2 ) gradients in facilitating dinitrogen (N2 ) fixation, we characterized O2 dynamics in the microenvironment around free-floating trichomes and colonies of Trichodesmium erythraeum IMS101. Diurnal and spatial variability in O2 concentrations in the bulk medium, within colonies, along trichomes and within single cells were determined using O2 optodes, microsensors and model calculations. Carbon (C) and N2 fixation as well as O2 evolution and uptake under different O2 concentrations were analyzed by stable isotope incubations and membrane inlet mass spectrometry. We observed a pronounced diel rhythm in O2 fluxes, with net O2 evolution restricted to short periods in the morning and evening, and net O2 uptake driven by dark respiration and light-dependent O2 uptake during the major part of the light period. Remarkably, colonies showed lower N2 fixation and C fixation rates than free-floating trichomes despite the long period of O2 undersaturation in the colony microenvironment. Model calculations demonstrate that low permeability of the cell wall in combination with metabolic heterogeneity between single cells allows for anoxic intracellular conditions in colonies but also free-floating trichomes of Trichodesmium. Therefore, whereas colony formation must have benefits for Trichodesmium, it does not favor N2 fixation.

Filamentous Giant Beggiatoaceae from the Guaymas Basin Are Capable of both Denitrification and Dissimilatory Nitrate Reduction to Ammonium.

Filamentous large sulfur-oxidizing bacteria (FLSB) of the family Beggiatoaceae are globally distributed aquatic bacteria that can control geochemical fluxes from the sediment to the water column through their metabolic activity. FLSB mats from hydrothermal sediments of Guaymas Basin, Mexico, typically have a "fried-egg" appearance, with orange filaments dominating near the center and wider white filaments at the periphery, likely reflecting areas of higher and lower sulfide fluxes, respectively. These FLSB store large quantities of intracellular nitrate that they use to oxidize sulfide. By applying a combination of 15N-labeling techniques and genome sequence analysis, we demonstrate that the white FLSB filaments were capable of reducing their intracellular nitrate stores to both nitrogen gas and ammonium by denitrification and dissimilatory nitrate reduction to ammonium (DNRA), respectively. On the other hand, our combined results show that the orange filaments were primarily capable of DNRA. Microsensor profiles through a laboratory-incubated white FLSB mat revealed a 2- to 3-mm vertical separation between the oxic and sulfidic zones. Denitrification was most intense just below the oxic zone, as shown by the production of nitrous oxide following exposure to acetylene, which blocks nitrous oxide reduction to nitrogen gas. Below this zone, a local pH maximum coincided with sulfide oxidation, consistent with nitrate reduction by DNRA. The balance between internally and externally available electron acceptors (nitrate) and electron donors (reduced sulfur) likely controlled the end product of nitrate reduction both between orange and white FLSB mats and between different spatial and geochemical niches within the white FLSB mat.IMPORTANCE Whether large sulfur bacteria of the family Beggiatoaceae reduce NO3- to N2 via denitrification or to NH4+ via DNRA has been debated in the literature for more than 25 years. We resolve this debate by showing that certain members of the Beggiatoaceae use both metabolic pathways. This is important for the ecological role of these bacteria, as N2 production removes bioavailable nitrogen from the ecosystem, whereas NH4+ production retains it. For this reason, the topic of environmental controls on the competition for NO3- between N2-producing and NH4+-producing bacteria is of great scientific interest. Recent experiments on the competition between these two types of microorganisms have demonstrated that the balance between electron donor and electron acceptor availability strongly influences the end product of NO3- reduction. Our results suggest that this is also the case at the even more fundamental level of enzyme system regulation within a single organism.

Oxygenic and anoxygenic photosynthesis in a microbial mat from an anoxic and sulfidic spring.

Oxygenic and anoxygenic photosynthesis were studied with microsensors in microbial mats found at 9-10 m depth in anoxic and sulfidic water in Little Salt Spring (Florida, USA). The lake sediments were covered with a 1-2 mm thick red mat dominated by filamentous Cyanobacteria, below which Green Sulfur Bacteria (GSB, Chlorobiaceae) were highly abundant. Within 4 mm inside the mats, the incident radiation was attenuated to undetectable levels. In situ microsensor data showed both oxygenic photosynthesis in the red surface layer and light-induced sulfide dynamics up to 1 cm depth. Anoxygenic photosynthesis occurred during all daylight hours, with complete sulfide depletion around midday. Oxygenic photosynthesis was limited to 4 h per day, due to sulfide inhibition in the early morning and late afternoon. Laboratory measurements on retrieved samples showed that oxygenic photosynthesis was fully but reversibly inhibited by sulfide. In patches Fe(III) alleviated the inhibition of oxygenic photosynthesis by sulfide. GSB were resistant to oxygen and showed a low affinity to sulfide. Their light response showed saturation at very low intensities.

Evidence for water-mediated mechanisms in coral-algal interactions.

Although many coral reefs have shifted from coral-to-algal dominance, the consequence of such a transition for coral-algal interactions and their underlying mechanisms remain poorly understood. At the microscale, it is unclear how diffusive boundary layers (DBLs) and surface oxygen concentrations at the coral-algal interface vary with algal competitors and competitiveness. Using field observations and microsensor measurements in a flow chamber, we show that coral (massive Porites) interfaces with thick turf algae, macroalgae, and cyanobacteria, which are successful competitors against coral in the field, are characterized by a thick DBL and hypoxia at night. In contrast, coral interfaces with crustose coralline algae, conspecifics, and thin turf algae, which are poorer competitors, have a thin DBL and low hypoxia at night. Furthermore, DBL thickness and hypoxia at the interface with turf decreased with increasing flow speed, but not when thick turf was upstream. Our results support the importance of water-mediated transport mechanisms in coral-algal interactions. Shifts towards algal dominance, particularly dense assemblages, may lead to thicker DBLs, higher hypoxia, and higher concentrations of harmful metabolites and pathogens along coral borders, which in turn may facilitate algal overgrowth of live corals. These effects may be mediated by flow speed and orientation.

Direct Nitrous Oxide Emission from the Aquacultured Pacific White Shrimp (Litopenaeus vannamei).

UNLABELLED: The Pacific white shrimp (Litopenaeus vannamei) is widely used in aquaculture, where it is reared at high stocking densities, temperatures, and nutrient concentrations. Here we report that adult L. vannamei shrimp emit the greenhouse gas nitrous oxide (N2O) at an average rate of 4.3 nmol N2O/individual × h, which is 1 to 2 orders of magnitude higher than previously measured N2O emission rates for free-living aquatic invertebrates. Dissection, incubation, and inhibitor experiments with specimens from a shrimp farm in Germany indicated that N2O is mainly produced in the animal's gut by microbial denitrification. Microsensor measurements demonstrated that the gut interior is anoxic and nearly neutral and thus is favorable for denitrification by ingested bacteria. Dinitrogen (N2) and N2O accounted for 64% and 36%, respectively, of the nitrogen gas flux from the gut, suggesting that the gut passage is too fast for complete denitrification to be fully established. Indeed, shifting the rearing water bacterial community, a diet component of shrimp, from oxic to anoxic conditions induced N2O accumulation that outlasted the gut passage time. Shrimp-associated N2O production was estimated to account for 6.5% of total N2O production in the shrimp farm studied here and to contribute to the very high N2O supersaturation measured in the rearing tanks (2,099%). Microbial N2O production directly associated with aquacultured animals should be implemented into life cycle assessments of seafood production. IMPORTANCE: The most widely used shrimp species in global aquaculture, Litopenaeus vannamei, is shown to emit the potent greenhouse gas nitrous oxide (N2O) at a particularly high rate. Detailed experiments reveal that N2O is produced in the oxygen-depleted gut of the animal by bacteria that are part of the shrimp diet. Upon ingestion, these bacteria experience a shift from oxic to anoxic conditions and therefore switch their metabolism to the anaerobic denitrification process, which produces N2O as an intermediate and dinitrogen (N2) gas as an end product. The N2O/N2 production ratio is unusually high in the shrimp gut, because denitrification cannot be fully established during the short gut passage time of food-associated bacteria. Nitrous oxide emission directly mediated by L. vannamei contributes significantly to the overall N2O emission from aquaculture facilities.

Microscale profiling of photosynthesis-related variables in a highly productive biofilm photobioreactor.

In the present study depth profiles of light, oxygen, pH and photosynthetic performance in an artificial biofilm of the green alga Halochlorella rubescens in a porous substrate photobioreactor (PSBR) were recorded with microsensors. Biofilms were exposed to different light intensities (50-1,000 µmol photons m(-2) s(-1) ) and CO2 levels (0.04-5% v/v in air). The distribution of photosynthetically active radiation showed almost identical trends for different surface irradiances, namely: a relatively fast drop to a depth of about 250 µm, (to 5% of the incident), followed by a slower decrease. Light penetrated into the biofilm deeper than the Lambert-Beer Law predicted, which may be attributed to forward scattering of light, thus improving the overall light availability. Oxygen concentration profiles showed maxima at a depth between 50 and 150 µm, depending on the incident light intensity. A very fast gas exchange was observed at the biofilm surface. The highest oxygen concentration of 3.2 mM was measured with 1,000 µmol photons m(-2) s(-1) and 5% supplementary CO2. Photosynthetic productivity increased with light intensity and/or CO2 concentration and was always highest at the biofilm surface; the stimulating effect of elevated CO2 concentration in the gas phase on photosynthesis was enhanced by higher light intensities. The dissolved inorganic carbon concentration profiles suggest that the availability of the dissolved free CO2 has the strongest impact on photosynthetic productivity. The results suggest that dark respiration could explain previously observed decrease in growth rate over cultivation time in this type of PSBR. Our results represent a basis for understanding the complex dynamics of environmental variables and metabolic processes in artificial phototrophic biofilms exposed to a gas phase and can be used to improve the design and operational parameters of PSBRs.

Nitrite-driven anaerobic methane oxidation by oxygenic bacteria.

Only three biological pathways are known to produce oxygen: photosynthesis, chlorate respiration and the detoxification of reactive oxygen species. Here we present evidence for a fourth pathway, possibly of considerable geochemical and evolutionary importance. The pathway was discovered after metagenomic sequencing of an enrichment culture that couples anaerobic oxidation of methane with the reduction of nitrite to dinitrogen. The complete genome of the dominant bacterium, named 'Candidatus Methylomirabilis oxyfera', was assembled. This apparently anaerobic, denitrifying bacterium encoded, transcribed and expressed the well-established aerobic pathway for methane oxidation, whereas it lacked known genes for dinitrogen production. Subsequent isotopic labelling indicated that 'M. oxyfera' bypassed the denitrification intermediate nitrous oxide by the conversion of two nitric oxide molecules to dinitrogen and oxygen, which was used to oxidize methane. These results extend our understanding of hydrocarbon degradation under anoxic conditions and explain the biochemical mechanism of a poorly understood freshwater methane sink. Because nitrogen oxides were already present on early Earth, our finding opens up the possibility that oxygen was available to microbial metabolism before the evolution of oxygenic photosynthesis.

Hydrogen sulfide can inhibit and enhance oxygenic photosynthesis in a cyanobacterium from sulfidic springs.

We used microsensors to investigate the combinatory effect of hydrogen sulfide (H2 S) and light on oxygenic photosynthesis in biofilms formed by a cyanobacterium from sulfidic springs. We found that photosynthesis was both positively and negatively affected by H2 S: (i) H2 S accelerated the recovery of photosynthesis after prolonged exposure to darkness and anoxia. We suggest that this is possibly due to regulatory effects of H2 S on photosystem I components and/or on the Calvin cycle. (ii) H2 S concentrations of up to 210 µM temporarily enhanced the photosynthetic rates at low irradiance. Modelling showed that this enhancement is plausibly based on changes in the light-harvesting efficiency. (iii) Above a certain light-dependent concentration threshold H2 S also acted as an inhibitor. Intriguingly, this inhibition was not instant but occurred only after a specific time interval that decreased with increasing light intensity. That photosynthesis is most sensitive to inhibition at high light intensities suggests that H2 S inactivates an intermediate of the oxygen evolving complex that accumulates with increasing light intensity. We discuss the implications of these three effects of H2 S in the context of cyanobacterial photosynthesis under conditions with diurnally fluctuating light and H2 S concentrations, such as those occurring in microbial mats and biofilms.

Changes in microbial communities in coastal sediments along natural CO2 gradients at a volcanic vent in Papua New Guinea.

Natural CO2 venting systems can mimic conditions that resemble intermediate to high pCO2 levels as predicted for our future oceans. They represent ideal sites to investigate potential long-term effects of ocean acidification on marine life. To test whether microbes are affected by prolonged exposure to pCO2 levels, we examined the composition and diversity of microbial communities in oxic sandy sediments along a natural CO2 gradient. Increasing pCO2 was accompanied by higher bacterial richness and by a strong increase in rare members in both bacterial and archaeal communities. Microbial communities from sites with CO2 concentrations close to today's conditions had different structures than those of sites with elevated CO2 levels. We also observed increasing sequence abundance of several organic matter degrading types of Flavobacteriaceae and Rhodobacteraceae, which paralleled concurrent shifts in benthic cover and enhanced primary productivity. With increasing pCO2 , sequences related to bacterial nitrifying organisms such as Nitrosococcus and Nitrospirales decreased, and sequences affiliated to the archaeal ammonia-oxidizing Thaumarchaeota Nitrosopumilus maritimus increased. Our study suggests that microbial community structure and diversity, and likely key ecosystem functions, may be altered in coastal sediments by long-term CO2 exposure to levels predicted for the end of the century.

Anoxygenic photosynthesis controls oxygenic photosynthesis in a cyanobacterium from a sulfidic spring.

Before the Earth's complete oxygenation (0.58 to 0.55 billion years [Ga] ago), the photic zone of the Proterozoic oceans was probably redox stratified, with a slightly aerobic, nutrient-limited upper layer above a light-limited layer that tended toward euxinia. In such oceans, cyanobacteria capable of both oxygenic and sulfide-driven anoxygenic photosynthesis played a fundamental role in the global carbon, oxygen, and sulfur cycle. We have isolated a cyanobacterium, Pseudanabaena strain FS39, in which this versatility is still conserved, and we show that the transition between the two photosynthetic modes follows a surprisingly simple kinetic regulation controlled by this organism's affinity for H2S. Specifically, oxygenic photosynthesis is performed in addition to anoxygenic photosynthesis only when H2S becomes limiting and its concentration decreases below a threshold that increases predictably with the available ambient light. The carbon-based growth rates during oxygenic and anoxygenic photosynthesis were similar. However, Pseudanabaena FS39 additionally assimilated NO3 (-) during anoxygenic photosynthesis. Thus, the transition between anoxygenic and oxygenic photosynthesis was accompanied by a shift of the C/N ratio of the total bulk biomass. These mechanisms offer new insights into the way in which, despite nutrient limitation in the oxic photic zone in the mid-Proterozoic oceans, versatile cyanobacteria might have promoted oxygenic photosynthesis and total primary productivity, a key step that enabled the complete oxygenation of our planet and the subsequent diversification of life.

Microsensor studies on Padina from a natural CO2 seep: implications of morphology on acclimation to low pH.

Low seawater pH can be harmful to many calcifying marine organisms, but the calcifying macroalgae Padina spp. flourish at natural submarine carbon dioxide seeps where seawater pH is low. We show that the microenvironment created by the rolled thallus margin of Padina australis facilitates supersaturation of CaCO3 and calcifi-cation via photosynthesis-induced elevated pH. Using microsensors to investigate oxygen and pH dynamics in the microenvironment of P. australis at a shallow CO2 seep, we found that, under saturating light, the pH inside the microenvironment (pHME ) was higher than the external seawater (pHSW ) at all pHSW levels investigated, and the difference (i.e., pHME - pHSW ) increased with decreasing pHSW (0.9 units at pHSW 7.0). Gross photosynthesis (Pg ) inside the microenvironment increased with decreasing pHSW , but algae from the control site reached a threshold at pH 6.5. Seep algae showed no pH threshold with respect to Pg within the pHSW range investigated. The external carbonic anhydrase (CA) inhibitor, acetazolamide, strongly inhibited Pg of P. australis at pHSW 8.2, but the effect was diminished under low pHSW (6.4-7.5), suggesting a greater dependence on membrane-bound CA for the dehydration of HCO3 (-) ions during dissolved inorganic carbon uptake at the higher pHSW . In comparison, a calcifying green alga, Halimeda cuneata f. digitata, was not inhibited by AZ, suggesting efficient bicarbonate transport. The ability of P. australis to elevate pHME at the site of calcification and its strong dependence on CA may explain why it can thrive at low pHSW .

Mechanisms of damage to corals exposed to sedimentation.

We investigated the mechanisms leading to rapid death of corals when exposed to runoff and resuspended sediments, postulating that the killing was microbially mediated. Microsensor measurements were conducted in mesocosm experiments and in naturally accumulated sediment on corals. In organic-rich, but not in organic-poor sediment, pH and oxygen started to decrease as soon as the sediment accumulated on the coral. Organic-rich sediments caused tissue degradation within 1 d, whereas organic-poor sediments had no effect after 6 d. In the harmful organic-rich sediment, hydrogen sulfide concentrations were low initially but increased progressively because of the degradation of coral mucus and dead tissue. Dark incubations of corals showed that separate exposures to darkness, anoxia, and low pH did not cause mortality within 4 d. However, the combination of anoxia and low pH led to colony death within 24 h. When hydrogen sulfide was added after 12 h of anoxia and low pH, colonies died after an additional 3 h. We suggest that sedimentation kills corals through microbial processes triggered by the organic matter in the sediments, namely respiration and presumably fermentation and desulfurylation of products from tissue degradation. First, increased microbial respiration results in reduced O(2) and pH, initiating tissue degradation. Subsequently, the hydrogen sulfide formed by bacterial decomposition of coral tissue and mucus diffuses to the neighboring tissues, accelerating the spread of colony mortality. Our data suggest that the organic enrichment of coastal sediments is a key process in the degradation of coral reefs exposed to terrestrial runoff.

Close association of active nitrifiers with Beggiatoa mats covering deep-sea hydrothermal sediments.

Hydrothermal sediments in the Guaymas Basin are covered by microbial mats that are dominated by nitrate-respiring and sulphide-oxidizing Beggiatoa. The presence of these mats strongly correlates with sulphide- and ammonium-rich fluids venting from the subsurface. Because ammonium and oxygen form opposed gradients at the sediment surface, we hypothesized that nitrification is an active process in these Beggiatoa mats. Using biogeochemical and molecular methods, we measured nitrification and determined the diversity and abundance of nitrifiers. Nitrification rates ranged from 74 to 605 µmol N l(-1) mat day(-1), which exceeded those previously measured in hydrothermal plumes and other deep-sea habitats. Diversity and abundance analyses of archaeal and bacterial ammonia monooxygenase subunit A genes, archaeal 16S ribosomal RNA pyrotags and fluorescence in situ hybridization confirmed that ammonia- and nitrite-oxidizing microorganisms were associated with Beggiatoa mats. Intriguingly, we observed cells of bacterial and potential thaumarchaeotal ammonia oxidizers attached to narrow, Beggiatoa-like filaments. Such a close spatial coupling of nitrification and nitrate respiration in mats of large sulphur bacteria is novel and may facilitate mat-internal cycling of nitrogen, thereby reducing loss of bioavailable nitrogen in deep-sea sediments.