Microbially Mediated Redox Cycling at the Oxic–Anoxic Boundary in Sediments: Comparison of Animal and Plants Habitats

Agent-based modelling of iron cycling bacteria provides a framework for testing alternative environmental conditions and modes of action

Iron-reducing and iron-oxidizing bacteria are of interest in a variety of environmental and industrial applications. Such bacteria often co-occur at oxic-anoxic gradients in aquatic and terrestrial habitats. In this paper, we present the first computational agent-based model of microbial iron cycling, between the anaerobic ferric iron (Fe³⁺)-reducing bacteria Shewanella spp. and the microaerophilic ferrous iron (Fe²⁺)-oxidizing bacteria Sideroxydans spp. By including the key processes of reduction/oxidation, movement, adhesion, Fe²⁺-equilibration and nanoparticle formation, we derive a core model which enables hypothesis testing and prediction for different environmental conditions including temporal cycles of oxic and anoxic conditions. We compared (i) combinations of different Fe³⁺-reducing/Fe²⁺-oxidizing modes of action of the bacteria and (ii) system behaviour for different pH values. We predicted that the beneficial effect of a high number of iron-nanoparticles on the total Fe³⁺ reduction rate of the system is not only due to the faster reduction of these iron-nanoparticles, but also to the nanoparticles' additional capacity to bind Fe²⁺ on their surfaces. Efficient iron-nanoparticle reduction is confined to pH around 6, being twice as high than at pH 7, whereas at pH 5 negligible reduction takes place. Furthermore, in accordance with experimental evidence our model showed that shorter oxic/anoxic periods exhibit a faster increase of total Fe³⁺ reduction rate than longer periods.

Orange leads to black: evaluating the efficacy of co-culturing iron-oxidizing and sulfate-reducing bacteria to discern ecological relationships

Two global cycles, iron and sulfur, are critically interconnected in estuarine environments by microbiological actors. To this point, the methods of laboratory study of this interaction have been limited. Here we propose a methodology for co-culturing from numerous coastal environments, from the same source inocula, iron-oxidizing and sulfate-reducing bacteria. The use of same source inocula is largely beneficial to understand real-world interactions that are likely occurring in situ. Through the use of this methodology, the ecological interactions between these groups can be studied in a more controlled environment. Here, we characterize the oxygen and hydrogen sulfide concentrations using microelectrode depth profiling in the co-cultures of iron-oxidizing bacteria and sulfate-reducing bacteria. These results suggest that while oxygen drives the relationship between these organisms and sulfate-reducers are reliant on iron-oxidizers in this culture to create an anoxic environment, there is likely another environmental driver that also influences the interaction as the two remain spatially distinct, as trends in FeS precipitation changed within the anoxic zone relative to the presence of Fe(III) oxyhydroxides. Understanding the relationship between iron-oxidizing and sulfate-reducing bacteria will ultimately have implications for understanding microbial cycling in estuarine environments as well as in processes such as controlling microbially influenced corrosion.

An ounce of prevention is worth a pound of cure: Managing macrophytes for nitrate mitigation in irrigated agricultural watersheds

Although ubiquitous elements of agricultural landscapes, the interest on ditches and canals as effective filters to buffer nitrate pollution has been raised only recently. The aim of the present study was to investigate the importance of in-ditch denitrification supported by emergent aquatic vegetation in the context of N budget in agricultural lands of a worldwide hotspot of nitrate contamination and eutrophication, i.e. the lowlands of the Po River basin (Northern Italy). The effectiveness of N abatement in the ditch network (>18,500 km) was evaluated by extrapolating up to the watershed reach-scale denitrification rates measured in a wide range of environmental conditions. Scenarios of variable extents of vegetation maintenance were simulated (25%, 50% and 90%), and compared to the current situation when the natural development occurs in only 5% of the ditch network length, subjected to mechanical mowing in summer. Along the typical range of nitrate availability in the Po River lowlands waterways (0.5-8 mg N L^-1), the current N removal performed by the ditch network was estimated in 3300-4900 t N yr^-1, accounting for at most 11% of the N excess from agriculture. The predicted nitrate mitigation potential would increase up to 4000-33,600 t N yr^-1 in case of vegetation maintenance in 90% of the total ditch length. Moreover, a further significant enhancement (57% on average) of this key ecosystem function would be achieved by postponing the mowing of vegetation at the end of the growing season. The simulated outcomes suggest that vegetated ditches may offer new agricultural landscape management opportunities for effectively decreasing nitrate loads in surface waters, with potential improved water quality at the watershed level and in the coastal zones. In conclusion, ditches and canals may act as metabolic regulators and providers of ecosystem services if conservative management practices of in-stream vegetation are properly implemented and coupled to hydraulic needs.

Estimate of gas transfer velocity in the presence of emergent vegetation using argon as a tracer: Implications for whole-system denitrification measurements

Denitrification associated with emergent macrophytes is a pivotal process underlying the treatment performance of wetlands and slow-flow waterways. Laboratory scale experiments targeting N losses via denitrification in sediments colonized by emergent macrophytes require the use of mesocosms that are necessarily open to the atmosphere. Thus, the proper quantification of N₂ effluxes relies on the accurate characterization of the air-water gas exchanges. In this study, we present a simple approach for direct measurements of the gas transfer velocity, in open-top mesocosms with Phragmites australis, by using argon as a tracer. Different conditions of water velocity (0, 1.5, 3, and 6 cm s^-1) and temperature (8.5, 16, and 28 °C), were tested, along with, for the first time, the presence of emergent vegetation. The outcomes demonstrated that water velocity and temperature are not the only factors regulating aeration at the mesocosm scale. Indeed, the gas transfer velocity was systematically higher, in the range of 42-53%, in vegetated compared to unvegetated sediments. The increase of small-local turbulence patterns created within water parcels moving around plant stems translated into significant modifications of the reaeration process. The adopted approach may be used to improve the accuracy of denitrification measurements by N₂ efflux-based methods in wetland and slow-flow waterway sediments colonized by emergent macrophytes. Moreover, the present outcomes may have multiple implications for whole-system metabolism estimations from which largely depend our understanding of biogeochemical dynamics in inland waters that have strong connections to worldwide issues, such as nitrate contamination and greenhouse gas emissions.

Diversity of dissimilatory sulfite reductase genes (dsrAB) in a salt marsh impacted by long-term acid mine drainage

Sulfate-reducing bacteria (SRB) play a major role in the coupled biogeochemical cycling of sulfur and chalcophilic metal(loid)s. By implication, they can exert a strong influence on the speciation and mobility of multiple metal(loid) contaminants. In this study, we combined DsrAB gene sequencing and sulfur isotopic profiling to identify the phylogeny and distribution of SRB and to assess their metabolic activity in salt marsh sediments exposed to acid mine drainage (AMD) for over 100 years. Recovered dsrAB sequences from three sites sampled along an AMD flow path indicated the dominance of a single Desulfovibrio species. Other major sequence clades were related most closely to Desulfosarcina, Desulfococcus, Desulfobulbus, and Desulfosporosinus species. The presence of metal sulfides with low delta(34)S values relative to delta(34)S values of pore water sulfate showed that sediment SRB populations were actively reducing sulfate under ambient conditions (pH of approximately 2), although possibly within less acidic microenvironments. Interestingly, delta(34)S values for pore water sulfate were lower than those for sulfate delivered during tidal inundation of marsh sediments. 16S rRNA gene sequence data from sediments and sulfur isotope data confirmed that sulfur-oxidizing bacteria drove the reoxidation of biogenic sulfide coupled to oxygen or nitrate reduction over a timescale of hours. Collectively, these findings imply a highly dynamic microbially mediated cycling of sulfate and sulfide, and thus the speciation and mobility of chalcophilic contaminant metal(loid)s, in AMD-impacted marsh sediments.