Diversity and functional traits of indigenous microbiome in Hilla agricultural soils: implications for biocontrol and bioremediation

Abstract

Indigenous bacterial and archaeal communities in agricultural soils were analyzed to provide a basis for biocontrol and bioremediation solutions to be reintroduced in affected areas. Samples from five agricultural soils in Hilla province, Iraq, were analyzed by inductively coupled plasma mass spectrometry for total and bioavailable metals. Bacterial community was identified using 16S rRNA metabarcoding and a cultivable approach. Plant growth-promoting, metal tolerance, and antifungal activities were evaluated on the established culture collection. Chemical analysis revealed elevated levels of nickel (Ni) and lithium (Li) among microelements, and sodium (Na) and phosphorus (P) among analyzed macroelements. 16S rRNA gene metabarcoding analysis showed significant differences in the composition and structure of bacterial and archaeal communities among samples. The most represented genera in the total bacterial community were Bacillus, Peribacillus, Acinetobacter, and Pseudomonas. The most abundant archaeal genera were Hallorussus, Halolamina, and Halarchaeum, detected only at the R5 site. Redundancy analysis indicated potential associations of taxa with micro- and macroelements, such as the positive correlation of Halomicrobium, Halorussus, Halomicrobiaceae, Natronomonas, Halolamina, Aliifodinibius, and Trabulsiella with Na and Fe. Based on the RDA, a negative correlation between Longimicrobiaceae and zinc (Zn) was detected for the first time, to the best of our knowledge. The culturable community was dominated by Bacillus, Mesobacillus, Arthrobacter, and Exiguobacterium. Among all isolates, Bacillus cabrialesii/inaquosorum R2-NA-6, Bacillus licheniformis R4-NA-3, Paenibacillus barcinonensis/taichungensis R4-TSA-5, Bacillus salacetis R4-NA-5, and Peribacillus simplex R2-TSA-2 showed in vitro the most promising combination of PGP traits, metal tolerance, and antifungal activity against most phytopathogenic fungi. The combination of beneficial traits makes these isolates excellent candidates for the further testing and potential development of multifunctional bioinoculants aimed at restoring degraded soils and reducing chemical pesticide use.