Ali Nejidat

This study investigates the long-term effects of catastrophic phosphate mining effluent contamination on the biocrust microbial community structure in sections of the ephemeral Ashalim Stream, Negev Desert, Israel. Microbial communities were characterized using next-generation sequencing of 16S rRNA gene fragments, conducted 1.5 and 5 years after the contamination event, across five stream strips. Samples from the nearby, uncontaminated Gmalim Stream served as controls. Biocrusts from Ashalim showed higher relative abundances of the phyla Actinobacteria and Firmicutes compared to Gmalim, whereas Chloroflexi were more prevalent in the controls. At the genus level, Blastococcus, Bacillus, Massilia, and Noviherbaspirillum were more abundant in the Ashalim strips, while Flavisolibacter, Segetibacter, and Rhodocytophaga were more abundant in the controls. Notably, genera within the Cyanobacteria phylum accounted for only 0.0–2.0% of sequences in Ashalim samples versus 2.5–20% in controls. The filamentous Leptolyngbya, Tychonema, and Trichocoleus genera were the most dominant cyanobacteria in all samples. The Nitrogen-fixing cyanobacterial genera Scytonema and Nostoc were consistently detected in Gmalim, but only in trace numbers in certain Ashalim sites. The results from both sampling campaigns support the hypothesis that phosphate effluent contamination had a profound impact on biocrust microbial community structure and function. In particular, the marked reduction in Cyanobacteria suggests a long-lasting disruption that may substantially hinder the natural ecosystem rehabilitation.

At the spring, goat and sheep herds are transferred to planted forests, in a semi-arid region in the northern Negev Desert, Israel, to reduce herbaceous biomass and, fire risk. The herds are held overnight in corrals for about 4 months, enriching the soil with organic matter and nitrogen. This research examined the effect of these enrichments on soil bacterial community structure (BCS) and the abundance of tetracycline resistance genes (TRGs) in active and abandoned corrals (1–10-years-old). Based on 16S rRNA gene sequences, the Proteobacteria and Actinobacteria phyla dominated the soil of all corrals. The Actinobacteria were less abundant in the active and 1-year-old corrals (23–26%) than in the other corrals and the control (33–38%). A principal component analysis showed that, the BCS in the active and the 1-year-old abandoned corrals was significantly different from that in the older corrals and the control. The Firmicutes phylum constituted 28% of the BCS in the active corrals, 12.5% in the 1-year-old corrals and 2% in the older corrals and the control. In contrast, the Acidobacteria phylum was hardly detected in the active and 1-year-old abandoned corrals and constituted 10% of the BCS in the older corrals. Genes conferring resistance to tetracycline were detected in high numbers. The tetG and tetW genes were detected in the active and abandoned corrals (1–10 years). The tetQ gene was detected only in the active and 1-year-old abandoned corrals. None of the genes were detected in the control soil. The three genes were detected outside an active corral, in the downstream section of an ephemeral tributary. The results prove that abandoned and unobserved periodic animal corrals are an environmental reservoir for TRGs.

Among the factors that obstruct the application of anammox-based technology for nitrogen removal from mainstream municipal wastewater is the water’s high organic loads. We hypothesized that some anammox species can adapt and grow in mainstream wastewater in which a minimal temperature of 13–15 °C is maintained. Using the AMX368F and AMX820R PCR-primers, anammox bacteria were detected in influent wastewater (COD/N ratio > 13) and in the anaerobic, anoxic, and aerobic chambers of a full-scale municipal wastewater treatment plant, reaching 10⁷ copies/g VSS of the16S rRNA gene. Furthermore, anammox activity was demonstrated by ¹⁵N-isotopic tracing. The DNA sequences of clones randomly selected from a clone library were mainly clustered with Candidatus Brocadia flugida in addition to Ca. Brocadia sinica, Ca. Jettenia asiatica, and Ca. Anammoxoglobus propionicus. However, Ca. Brocadia was the only genus detected by high-throughput next-generation sequencing and denaturing gradient gel electrophoresis. The nitrite producers, ammonia-oxidizing archaea and bacteria, were both detected in the influent wastewater and the other chambers, while the nitrite consumers, Nitrospira nitrite oxidizers and the nirS-type denitrifiers, dominated all chambers. The results indicate the occurrence and potential activity of anammox bacteria in mainstream wastewater under certain conditions (proper temperature). The dominance of Brocadia flugida and Anammoxoglobus propionicus suggests a role for volatile fatty acids in selecting the anammox community in wastewater.

Ammonia-oxidizing archaea and bacteria (AOA, AOB) catalyze the first and rate-limiting step of nitrification. To examine their differential responses to the wetting of dry and salty arid soil, AOA and AOB amoA genes (encoding subunit A of the ammonia monooxygenase) and transcripts were enumerated in dry (summer) and wet (after the first rainfall) soil under the canopy of halophytic shrubs and between the shrubs. AOA and AOB were more abundant under shrub canopies than between shrubs in both the dry and wetted soil. Soil wetting caused a significant decrease in AOB abundance under the canopy and an increase of AOA between the shrubs. The abundance of the archaeal amoA gene transcript was similar for both the wet and dry soil, and the transcript-to-gene ratios were < 1 independent of niche or water content. In contrast, the bacterial amoA transcript-to-gene ratios were between 78 and 514. The lowest ratio was in dry soil under the canopy and the highest in the soil between the shrubs. The results suggest that the AOA are more resilient to stress conditions and maintain a basic activity in arid ecosystems, while the AOB are more responsive to changes in the biotic and abiotic conditions.

Ammonia oxidizers catalyze the first step of nitrification. Combined microbial nitrification–denitrification activities are essential for the removal

Besides water, nitrogen is the limiting factor for biomass production in arid ecosystems. Global climatic changes are exacerbating aridity levels, an

Unlined manure ponds are constructed on clay soil worldwide to manage farm waste. Seepage of ammonia-rich liquor into underlying soil layers contributes to groundwater contamination by nitrate. To identify the possible processes that lead to the production of nitrate from ammonia in this oxygen-limited environment, we studied the diversity and abundance of ammonia-transforming microorganisms under an unlined manure pond. The numbers of ammonia-oxidizing bacteria and anammox bacteria were most abundant in the top of the soil profile and decreased significantly with depth (0.5 m), correlating with soil pore-water ammonia concentrations and soil ammonia concentrations, respectively. On the other hand, the numbers of ammonia-oxidizing archaea were relatively constant throughout the soil profile (10⁷amoA copies per g_soil). Nitrite-oxidizing bacteria were detected mainly in the top 0.2 m. The results suggest that nitrate accumulation in the vadose zone under the manure pond could be the result of complete aerobic nitrification (ammonia oxidation to nitrate) and could exist as a byproduct of anammox activity. While the majority of the nitrogen was removed within the 0.5-m soil section, possibly by combined anammox and heterotrophic denitrification, a fraction of the produced nitrate leached into the groundwater.