Nitrification and occurrence of salt-tolerant nitrifying bacteria in the Negev desert soils

Microbial Biogeochemical Cycling of Nitrogen in Arid Ecosystems

Arid ecosystems cover ∼40% of the Earth's terrestrial surface and store a high proportion of the global nitrogen (N) pool. They are low-productivity, low-biomass, and polyextreme ecosystems, i.e., with (hyper)arid and (hyper)oligotrophic conditions and high surface UV irradiation and evapotranspiration. These polyextreme conditions severely limit the presence of macrofauna and -flora and, particularly, the growth and productivity of plant species. Therefore, it is generally recognized that much of the primary production (including N-input processes) and nutrient biogeochemical cycling (particularly N cycling) in these ecosystems are microbially mediated. Consequently, we present a comprehensive survey of the current state of knowledge of biotic and abiotic N-cycling processes of edaphic (i.e., open soil, biological soil crust, or plant-associated rhizosphere and rhizosheath) and hypo/endolithic refuge niches from drylands in general, including hot, cold, and polar desert ecosystems. We particularly focused on the microbially mediated biological nitrogen fixation, N mineralization, assimilatory and dissimilatory nitrate reduction, and nitrification N-input processes and the denitrification and anaerobic ammonium oxidation (anammox) N-loss processes. We note that the application of modern meta-omics and related methods has generated comprehensive data sets on the abundance, diversity, and ecology of the different N-cycling microbial guilds. However, it is worth mentioning that microbial N-cycling data from important deserts (e.g., Sahara) and quantitative rate data on N transformation processes from various desert niches are lacking or sparse. Filling this knowledge gap is particularly important, as climate change models often lack data on microbial activity and environmental microbial N-cycling communities can be key actors of climate change by producing or consuming nitrous oxide (N₂O), a potent greenhouse gas.

Salt tolerance-based niche differentiation of soil ammonia oxidizers

Ammonia oxidizers are key players in the global nitrogen cycle, yet little is known about their ecological performances and adaptation strategies for growth in saline terrestrial ecosystems. This study combined ¹³C-DNA stable-isotope probing (SIP) microcosms with amplicon and shotgun sequencing to reveal the composition and genomic adaptations of active ammonia oxidizers in a saline-sodic (solonetz) soil with high salinity and pH (20.9 cmol_c exchangeable Na⁺ kg^-1 soil and pH 9.64). Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) exhibited strong nitrification activities, although AOB performed most of the ammonia oxidation observed in the solonetz soil and in the farmland soil converted from solonetz soil. Members of the Nitrosococcus, which are more often associated with aquatic habitats, were identified as the dominant ammonia oxidizers in the solonetz soil with the first direct labeling evidence, while members of the Nitrosospira were the dominant ammonia oxidizers in the farmland soil, which had much lower salinity and pH. Metagenomic analysis of "Candidatus Nitrosococcus sp. Sol14", a new species within the Nitrosococcus lineage, revealed multiple genomic adaptations predicted to facilitate osmotic and pH homeostasis in this extreme habitat, including direct Na⁺ extrusion/H⁺ import and the ability to increase intracellular osmotic pressure by accumulating compatible solutes. Comparative genomic analysis revealed that variation in salt-tolerance mechanisms was the primary driver for the niche differentiation of ammonia oxidizers in saline-sodic soils. These results demonstrate how ammonia oxidizers can adapt to saline-sodic soil with excessive Na⁺ content and provide new insights on the nitrogen cycle in extreme terrestrial ecosystems.

The Ecology of Subaerial Biofilms in Dry and Inhospitable Terrestrial Environments

The ecological relationship between minerals and microorganisms arguably represents one of the most important associations in dry terrestrial environments, since it strongly influences major biochemical cycles and regulates the productivity and stability of the Earth’s food webs. Despite being inhospitable ecosystems, mineral substrata exposed to air harbor form complex and self-sustaining communities called subaerial biofilms (SABs). Using life on air-exposed minerals as a model and taking inspiration from the mechanisms of some microorganisms that have adapted to inhospitable conditions, we illustrate the ecology of SABs inhabiting natural and built environments. Finally, we advocate the need for the convergence between the experimental and theoretical approaches that might be used to characterize and simulate the development of SABs on mineral substrates and SABs’ broader impacts on the dry terrestrial environment.

Impact of Heavy Metal Pollution on Ammonia Oxidizers in Soils in the Vicinity of a Tailings Dam, Baotou, China

Soil heavy metal pollution has received increasing attention due to their toxicity to soil microorganisms. We have analyzed the effects of heavy metal pollution on ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in soils in the vicinity of a tailings dam of Baotou region, China. Results showed that AOB were dominated with Nitrosomonas-like clusters, while AOA was dominated by group1.1b (Nitrososphaera cluster). Single Cd and Cr contents, as well as compound heavy metal pollution levels, had a significant negative impact on soil potential nitrification rate and both diversities of AOA and AOB. No clear relationship was found between any single heavy metal and abundance of AOA or AOB. But compound pollution could significantly decrease AOA abundance. The results indicated that heavy metal pollution had an obviously deleterious effect on the abundance, diversity, activity and composition of ammonia oxidizers in natural soils.

Bacterial diversity and distribution in the southeast edge of the Tengger Desert and their correlation with soil enzyme activities

The nature of microbial communities and their relation to enzyme activities in desert soils is a neglected area of investigation. To address this, the bacterial diversity and distribution and soil physico-chemical factors were investigated in the soil crust, the soil beneath the crust and rhizosphere soil at the southeast edge of the Tengger Desert, using the denaturing gradient gel electrophoresis of 16S rRNA genes amplified by the polymerase chain reaction. Phylogenetic analysis of the sequenced DGGE bands revealed a great diversity of bacteria. The Proteobacteria, consisting of the alpha, beta, and gamma subdivisions, were clearly the dominant group at all depths and in rhizosphere soil. Analysis of the enzyme activities indicated that the rhizosphere soil of Caragana korshinskii exhibited the highest protease and polyphenol oxidase activities, and in the soil crust there were increased activities of catalase, urease, dehydrogenase and sucrase. The bacterial community abundance closely correlated with soil enzyme activities in different soils. The presence of Cyanobacteria correlated with significant increases in protease, catalase and sucrase in the soil crust, and increased urease in the rhizosphere soil of Artemisia ordosica. The occurrence of Acidobacteria was associated with significant increases in urease, dehydrogenase, and sucrase in the rhizosphere soil of C. korshinski. The presence of gamma-Proteobacteria correlated with a significant increase in polyphenol oxidase in the rhizosphere soil of A. ordosica. The study indicated a close relationship between the soil bacterial community and soil enzymes, suggesting the necessity of further investigations into bacterial function in this desert ecosystem.

Nitrogen transformations and diversity of ammonia-oxidizing bacteria in a desert ephemeral stream receiving untreated wastewater

Levels of inorganic nitrogen species (ammonia, nitrite, and nitrate), ammonia oxidation potential (AOP), and diversity of ammonia-oxidizing bacteria (AOB) were studied in the sediments of a 50-km-long segment of an ephemeral stream in the Negev desert, receiving untreated wastewater. Water analysis in downstream sampling points showed reductions of 91.7% in biological oxygen demand, 87.7% in chemical oxygen demand, 73.9% in total nitrogen, and 72.8% in total ammonia nitrogen. Significant AOP levels in the sediment were detected mainly in the fall and spring seasons. Denaturing gradient gel electrophoresis of AOB 16S rRNA gene fragments showed that in most sampling points, the streambed was dominated by Nitrosospira cluster 3 strains similar to those dominating the stream bank's soils and sediments in nearby springs. Nitrosomonas strains introduced by discharged wastewater and others dominated some sections of the stream characterized by high organic carbon levels. The results suggest that climatic conditions in the Negev desert select for AOB belonging to Nitrosospira cluster 3, and these conditions dominate the aquatic environment effect along most of the stream sections. In addition, the nitrification-denitrification processes were not sufficient to reduce nitrogen levels in the sediment and prevent the eutrophication of some sections of the stream ecosystem. Thus, the discharge of high nitrogen wastewater into desert streams should be done carefully as it may endanger the already fragile ecosystem.

Assessment of extraction methods with fowl manure for the production of liquid organic fertilizers

Supplementary nitrogen (N) side-dressing via the irrigation system is needed in organic cropping. The aim here was to improve N-extraction efficiency, by testing five extraction protocols with guano, layer and broiler manures. The manure-N released by the different methods and manures was mainly in the form of ammonia and ranged from 50% to 85% with no differences among extraction methods. Volatilised ammonia from the extract solution was trapped. At the end of the extraction period, the pH of the extract solution was raised and the rest of the volatilised ammonia was trapped. In the case of guano, about 89% of the manure-N that was mineralised to the extract solution volatilised (after a pH increase), whereas in the layer and broiler manures, 59% and 54% were volatilised, respectively. Extraction of ammonia, its volatilisation and entrapment could provide a significantly more efficient N source than using the extract solution as currently recommended.