Attributes of Drying Define the Structure and Functioning of Microbial Communities in Temperate Riverbed Sediment

Light over mechanics: microbial community structure and activity in simulated migrating bedforms are controlled by oscillating light rather than by mechanical forces

Sandy sediments of lowland streams are transported as migrating ripples. Benthic microorganisms colonizing sandy grains are exposed to frequent moving-resting cycles and are believed to be shaped by two dominant environmental factors: mechanical stress during the moving phase causing biofilm abrasion, and alternating light-dark cycles during the resting phase. Our study consisted of two laboratory experiments and aimed to decipher which environmental factor causes the previously observed hampered sediment-associated microbial activity and altered community structure during ripple migration. The first experiment tested the effect of three different migration velocities under comparable light conditions. The second experiment compared migrating and stationary sediments under either constant light exposure or light oscillation. We hypothesized that microbial activity and community structure would be more strongly affected by (1) higher compared to lower migration velocities, and by (2) light oscillation compared to mechanical stress. Combining the results from both experiments, we observed lower microbial activity and an altered community structure in sediments exposed to light oscillation, whereas migration velocity had less impact on community activity and structure. Our findings indicate that light oscillation is the predominating environmental factor acting during ripple migration, resulting in an increased vulnerability of light-dependent photoautotrophs and a possible shift toward heterotrophy.

Enhancing Native Plant Establishment in Mine Tailings under Drought Stress Conditions through the Application of Organo-Mineral Amendments and Microbial Inoculants

The implementation of phytoremediation strategies under arid and semiarid climates requires the use of appropriate plant species capable of withstanding multiple abiotic stresses. In this study, we assessed the combined effects of organo-mineral amendments and microbial inoculants on the chemical and biological properties of mine tailings, as well as on the growth of native plant species under drought stress conditions. Plants were cultivated in pots containing 1 kg of a mixture of mine tailings and topsoil (i.e., pre-mined superficial soil) in a 60:40 ratio, 6% marble sludge, and 10% sheep manure. Moreover, a consortium of four drought-resistant plant growth-promoting rhizobacteria (PGPR) was inoculated. Three irrigation levels were applied: well-watered, moderate water deficit, and severe water deficit, corresponding to 80%, 45%, and 30% of field capacity, respectively. The addition of topsoil and organo-mineral amendments to mine tailings significantly improved their chemical and biological properties, which were further enhanced by bacterial inoculation and plants' establishment. Water stress negatively impacted enzymatic activities in amended tailings, resulting in a significant decrease in acid and alkaline phosphatases, urease, and dehydrogenase activities. Similar results were obtained for bacteria, fungi, and actinomycete abundance. PGPR inoculation positively influenced the availability of phosphorus, total nitrogen, and organic carbon, while it increased alkaline phosphatase, urease (by about 10%), and dehydrogenase activity (by 50%). The rhizosphere of Peganum harmala showed the highest enzymatic activity and number of culturable microorganisms, especially in inoculated treatments. Severe water deficit negatively affected plant growth, leading to a 40% reduction in the shoot biomass of both Atriplex halimus and Pennisetum setaceum compared to well-watered plants. P. harmala showed greater tolerance to water stress, evidenced by lower decreases observed in root and shoot length and dry weight compared to well-watered plants. The use of bioinoculants mitigated the negative effects of drought on P. harmala shoot biomass, resulting in an increase of up to 75% in the aerial biomass in plants exposed to severe water deficit. In conclusion, the results suggest that the combination of organo-mineral amendments, PGPR inoculation, and P. harmala represents a promising approach to enhance the phytoremediation of metal-polluted soils under semiarid conditions.

Soil fungal diversity and assembly along a xeric stress gradient in the central Namib Desert

The Namib Desert of south-western Africa is one of the oldest deserts in the world and possesses unique geographical, biological and climatic features. While research through the last decade has generated a comprehensive survey of the prokaryotic communities in Namib Desert soils, little is yet known about the diversity and function of edaphic fungal communities, and even less of their responses to aridity. In this study, we have characterized soil fungal community diversity across the longitudinal xeric gradient across the Namib desert (for convenience, divided into the western fog zone, the central low-rainfall zone and the eastern high-rainfall zone), using internal transcribed sequence (ITS) metabarcoding. Ascomycota, Basidiomycota and Chytridiomycota consistently dominated the Namib Desert edaphic fungal communities and a core mycobiome composed of only 15 taxa, dominated by members of the class Dothideomycetes (Ascomycota), was identified. However, fungal community structures were significantly different in the fog, low-rainfall and high-rainfall zones. Furthermore, Namib Desert gravel plain fungal community assembly was driven by both deterministic and stochastic processes; the latter dominating in the all three xeric zones. We also present data that suggest that the inland limit of fog penetration represents an ecological barrier to fungal dispersal across the Namib Desert.

Drying shapes the ecological niche of aquatic fungi with implications on ecosystem functioning

Fungi are among the most abundant and diverse organisms on Earth and play pivotal roles in global carbon processing, nutrient cycling and food webs. Despite their abundant and functional importance, little is known about the patterns and mechanisms governing their community composition in intermittent rivers and ephemeral streams, which are the most common fluvial ecosystems globally. Thus far, it is known that aquatic fungi have evolved various life-history strategies and functional adaptations to cope with drying. Nevertheless, some of these adaptations have a metabolic cost and trade-offs between growth, reproduction and dispersion that may affect ecosystem functioning. Thus, understanding their ecological strategies along a gradient of drying is crucial to assess how species will respond to global change and to identify meaningful taxa to maintain ecosystem functions. By combining in situ hydrological information with a niche-based approach, we analysed the role of drying in explaining the spatial segregation of fungal species, and we determined their specialization and affinity over a gradient of drying. In addition, we estimated whether species niches are good predictors of two key ecosystem processes: organic matter decomposition and fungal biomass accrual. Overall, we found that annual drying duration and frequency were the most influential variables upon species niche differentiation across the 15 studied streams. Our cluster analysis identified four drying niche-based groups with contrasting distributions and responses over the drying gradient: drying-sensitive, partly tolerant to drying, generalist, and drying-resistant specialist. In addition, we found that species belonging to the drying specialist group showed a weak contribution to both ecosystem processes, suggesting trade-offs between drying resistance strategies and the energy invested in growth. Taken together, our results suggest that increased water scarcity may jeopardise the capacity of aquatic fungi to guarantee ecosystem functioning and to maintain biogeochemical cycles despite their ability to cope with drying.

When water returns: Drying history shapes respiration and nutrients release of intermittent river sediment

Climate change and anthropogenic water demand have increased the frequency and duration of drying periods across rivers and streams worldwide. However, the biogeochemical processes during the water return in desiccated riverbeds are still unclear. Drying is a complex and diverse process and biogeochemical implications upon flow resumption may depend on attributes of the drying and river sediment characteristics (i.e., organic matter content [OM]). In order to understand the effect of drying duration and intensity on the biogeochemical dynamics following flow resumption, we exposed OM- and non-enriched river sediment from an intermittent river section to three different drying intensities (low: shade and rain; moderate: no shade and rain; high: no shade and no rain), each for three drying durations (10, 30 and 90 days). We determined the sediment-associated microbial respiration and dissolved organic carbon (DOC), ammonium‑nitrogen (NH₄-N), nitrate‑nitrogen (NO₃-N) and soluble reactive phosphorus (SRP) net release/retention rates of the nine drying treatments in flow-through microcosms over four days past flow resumption. Under the most intense and prolonged drying, non-enriched sediments showed a lag response in respiration on the first day after flow resumption, while all other treatments had either a linear increase or an early pulse in respiration. After 48 h, respiration remained constant, with minor changes in respiration dynamics regardless of the OM content of the sediment and drying attributes. The drying duration and intensity had greater effects on SRP release/retention soon after the flow resumption, while NH₄-N and NO₃-N release/retention rates were more strongly affected four days later. Our results suggest that drying attributes influence the biogeochemical dynamics more strongly during the first 24 h upon flow resumption. However, neither respiration nor nutrient dynamics recovered within four days to levels of the sediments before drying for any drying treatments. Hence, the atrributes of the drying have considerable implications in rivers biogeochemistry upon flow resumption.

Metal nanoparticles increased the lag period and shaped the microbial community in slurry-electrode microbial electrosynthesis

Concerns about energy crisis and CO₂ emission have motivated the development of microbial electrosynthesis (MES); recent studies have showed the potential of novel slurry-electrode MES. In this study, the effect of nonprecious metal nanoparticles (NPs) on the performance of slurry-electrode MES was systematically evaluated in terms of chemical production, physicochemical properties, electrochemical characterization, and microbial community. Ni and Cu NPs increased the lag period from 6 to 15 days for acetate production, while Mo NPs showed no apparent effect. However, these metal NPs slightly affected the final total acetate production (ca. 10 g L^-1), Faradic efficiency (ca. 50%), net water flux across the anion exchange membrane (ca. 6 mL d^-1), or electrochemical characterization of catholyte. BRH-c20a was enriched as the dominated microbe (>48%), and its relative abundance was largely affected by the addition of metal NPs. This study demonstrates that metal NPs affect the performance of biocathodes, mainly by shaping the microbial community.