Effect of Contamination by Phosphate Mining Effluent on Biocrust Microbial Community Structure and Cyanobacterial Diversity in a Hot Dry Desert

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.