Denitrification Associated with Periphyton Communities

Assessment of marine benthic diatom communities: insights from a combined morphological-metabarcoding approach in Mediterranean shallow coastal waters

We investigated the advantages and disadvantages of light microscope (LM)-based identifications and DNA metabarcoding, based on a 312-bp rbcL marker, for examining benthic diatom communities from Mediterranean shallow coastal environments. For this, we used biofilm samples collected from different substrata in the Ebro delta bays. We show that 1) Ebro delta bays harbour high-diversity diatom communities [LM identified 249 taxa] and 2) DNA metabarcoding effectively reflects this diversity at genus- but not species level, because of the incompleteness of the DNA reference library. Nevertheless, DNA metabarcoding offers new opportunities for detecting small, delicate and rare diatom species missed by LM and diatoms that lack silica frustules. The primers used, though designed for diatoms, successfully amplified rarely reported members of other stramenopile groups. Combining LM and DNA approaches offers stronger support for ecological studies of benthic microalgal communities in shallow coastal environments than using either approach on its own.

Got acetylene: a personal research retrospective

In research, sometimes sheer happenstance and serendipity make for an unexpected discovery. Once revealed and if interesting enough, such a finding and its follow-up investigations can lead to advances by others that leave its originators 'scooped' and mulling about what next to do with their unpublished data, specifically what journals could it still be published in and be perceived as original. This is what occurred with us nearly 40 years ago with regard to our follow-up observations of acetylene fermentation and led us to concoct a 'cock-and-bull' story. We hypothesized about a plausible role for acetylene metabolism in the primordial biogeochemistry of Earth and the possibility of acetylene serving as a key life-sustaining substrate for alien microbes dwelling in the orbs of the outer solar system. With the passage of time, advances were made in whole-genome sequencing coupled with major in silico progress in bioinformatics. In parallel came the results of explorations of the outer solar system (i.e. the Cassini mission to Saturn and its moons). It now appears that these somewhat harebrained ideas of ours, arisen at first out of a sense of desperation, actually ring true in fact, and particularly well in song: 'Tell a tale of cock and bull, Of convincing detail full Tale tremendous, Heav'n defend us! What a tale of cock and bull!' From 'The Yeoman of the Guard' by Gilbert & Sullivan.

Quantifying in-stream retention of nitrate at catchment scales using a practical mass balance approach

As field data on in-stream nitrate retention is scarce at catchment scales, this study aimed at quantifying net retention of nitrate within the entire river network of a fourth-order stream. For this purpose, a practical mass balance approach combined with a Lagrangian sampling scheme was applied and seasonally repeated to estimate daily in-stream net retention of nitrate for a 17.4 km long, agriculturally influenced, segment of the Steinlach River in southwestern Germany. This river segment represents approximately 70% of the length of the main stem and about 32% of the streambed area of the entire river network. Sampling days in spring and summer were biogeochemically more active than in autumn and winter. Results obtained for the main stem of Steinlach River were subsequently extrapolated to the stream network in the catchment. It was demonstrated that, for baseflow conditions in spring and summer, in-stream nitrate retention could sum up to a relevant term of the catchment's nitrogen balance if the entire stream network was considered.

Floodplain restoration enhances denitrification and reach-scale nitrogen removal in an agricultural stream

Streams of the agricultural Midwest, USA, export large quantities of nitrogen, which impairs downstream water quality, most notably in the Gulf of Mexico. The two-stage ditch is a novel restoration practice, in which floodplains are constructed alongside channelized ditches. During high flows, water flows across the floodplains, increasing benthic surface area and stream water residence time, as well as the potential for nitrogen removal via denitrification. To determine two-stage ditch nitrogen removal efficacy, we measured denitrification rates in the channel and on the floodplains of a two-stage ditch in north-central Indiana for one year before and two years after restoration. We found that instream rates were similar before and after the restoration, and they were influenced by surface water NO3- concentration and sediment organic matter content. Denitrification rates were lower on the constructed floodplains and were predicted by soil exchangeable NO3- concentration. Using storm flow simulations, we found that two-stage ditch restoration contributed significantly to NO3- removal during storm events, but because of the high NO3- loads at our study site, < 10% of the NO3- load was removed under all storm flow scenarios. The highest percentage of NO3- removal occurred at the lowest loads; therefore, the two-stage ditch's effectiveness at reducing downstream N loading will be maximized when the practice is coupled with efforts to reduce N inputs from adjacent fields.

Hydrogen metabolism by decomposing cyanobacterial aggregates in big soda lake, nevada

Hydrogen production by incubated cyanobacterial epiphytes occurred only in the dark, was stimulated by C(2)H(2), and was inhibited by O(2). Addition of NO(3) inhibited dark, anaerobic H(2) production, whereas the addition of NH(4) inhibited N(2) fixation (C(2)H(2) reduction) but not dark H(2) production. Aerobically incubated cyanobacterial aggregates consumed H(2), but light-incubated rates (3.6 mumol of H(2) g h) were statistically equivalent to dark uptake rates (4.8 mumol of H(2) g h), which were statistically equivalent to dark, anaerobic production rates (2.5 to 10 mumol of H(2) g h). Production rates of H(2) were fourfold higher for aggregates in a more advanced stage of decomposition. Enrichment cultures of H(2)-producing fermentative bacteria were recovered from freshly harvested, H(2)-producing cyanobacterial aggregates. Hydrogen production in these cyanobacterial communities appears to be caused by the resident bacterial flora and not by the cyanobacteria. In situ areal estimates of dark H(2) production by submerged epiphytes (6.8 mumol of H(2) m h) were much lower than rates of light-driven N(2) fixation by the epiphytic cyanobacteria (310 mumol of C(2)H(4) m h).

Nitrogen fixation dynamics of two diazotrophic communities in mono lake, california

Two types of diazotrophic microbial communities were found in the littoral zone of alkaline hypersaline Mono Lake, California. One consisted of anaerobic bacteria inhabiting the flocculent surface layers of sediments. Nitrogen fixation (acetylene reduction) by flocculent surface layers occurred under anaerobic conditions, was not stimulated by light or by additions of organic substrates, and was inhibited by O(2), nitrate, and ammonia. The second community consisted of a ball-shaped association of a filamentous chlorophyte (Ctenocladus circinnatus) with diazotrophic, nonheterocystous cyanobacteria, as well as anaerobic bacteria (Ctenocladus balls). Nitrogen fixation by Ctenocladus balls was usually, but not always, stimulated by light. Rates of anaerobic dark fixation equaled those in the light under air. Fixation in the light was stimulated by 3-(3,4-dichlorophenyl)-1, 1-dimethylurea and by propanil [N-(3,4-dichlorophenyl)propanamide]. 3-(3,4-Dichlorophenyl)-1,1-dimethyl urea-elicited nitrogenase activity was inhibited by ammonia (96%) and nitrate (65%). Fixation was greatest when Ctenocladus balls were incubated anaerobically in the light with sulfide. Dark anaerobic fixation was not stimulated by organic substrates in short-term (4-h) incubations, but was in long-term (67-h) ones. Areal estimates of benthic N(2) fixation were measured seasonally, using chambers. Highest rates ( approximately 29.3 mumol of C(2)H(4) m h) occurred under normal diel regimens of light and dark. These estimates indicate that benthic N(2) fixation has the potential to be a significant nitrogen source in Mono Lake.

Redox transformations of arsenic oxyanions in periphyton communities

Periphyton (Cladophora sp.) samples from a suburban stream lacking detectable dissolved As were able to reduce added As(V) to As(III) when incubated under anoxic conditions and, conversely, oxidized added As(III) to As(V) with aerobic incubation. Both types of activity were abolished in autoclaved controls, thereby demonstrating its biological nature. The reduction of As(V) was inhibited by chloramphenicol, indicating that it required the synthesis of new protein. Nitrate also inhibited As(V) reduction, primarily because it served as a preferred electron acceptor to which the periphyton community was already adapted. However, part of the inhibition was also caused by microbial reoxidation of As(III) linked to nitrate. Addition of [14C]glucose to anoxic samples resulted in the production of 14CO2, suggesting that the observed As(V) reduction was a respiratory process coupled to the oxidation of organic matter. The population density of As(V)-reducing bacteria within the periphyton increased with time and with the amount of As(V) added, reaching values as high as approximately 10(6) cells ml(-1) at the end of the incubation. This indicated that dissimilatory As(V) reduction in these populations was linked to growth. However, As(V)-respiring bacteria were found to be present, albeit at lower numbers (approximately 10(2) ml(-1)), in freshly sampled periphyton. These results demonstrate the presence of a bacterial population within the periphyton communities that is capable of two key arsenic redox transformations that were previously studied in As-contaminated environments, which suggests that these processes are widely distributed in nature. This assumption was reinforced by experiments with estuarine samples of Cladophora sericea in which we detected a similar capacity for anaerobic As(V) reduction and aerobic As(III) oxidation.

Denitrification in San Francisco Bay Intertidal Sediments

The acetylene block technique was employed to study denitrification in intertidal estuarine sediments. Addition of nitrate to sediment slurries stimulated denitrification. During the dry season, sediment-slurry denitrification rates displayed Michaelis-Menten kinetics, and ambient NO 3 − + NO 2 − concentrations (≤26 μM) were below the apparent K m (50 μM) for nitrate. During the rainy season, when ambient NO 3 − + NO 2 − concentrations were higher (37 to 89 μM), an accurate estimate of the K m could not be obtained. Endogenous denitrification activity was confined to the upper 3 cm of the sediment column. However, the addition of nitrate to deeper sediments demonstrated immediate N 2 O production, and potential activity existed at all depths sampled (the deepest was 15 cm). Loss of N 2 O in the presence of C 2 H 2 was sometimes observed during these short-term sediment incubations. Experiments with sediment slurries and washed cell suspensions of a marine pseudomonad confirmed that this N 2 O loss was caused by incomplete blockage of N 2 O reductase by C 2 H 2 at low nitrate concentrations. Areal estimates of denitrification (in the absence of added nitrate) ranged from 0.8 to 1.2 μmol of N 2 m −2 h −1 (for undisturbed sediments) to 17 to 280 μmol of N 2 m −2 h −1 (for shaken sediment slurries).