Soil is a complex and dynamic ecosystem containing a diverse array of microorganisms, and plays a crucial and multifaceted role in various functions of the ecosystem. Substantial fluctuations in the environmental conditions arise from diverse global changes. The microbial shifts in the soil in concordance with the changing environmental factors, or a combination of these factors, are of high significance. Exploring the contribution of global change drivers to the microbial community to improve the predictions of the response of the microbial community to the functioning of the ecosystem is of prime importance. Promoting the health of soil microorganisms maintains the overall health and fertility of the soil, which in turn supports the health of terrestrial ecosystems and agricultural systems. The current review aims to assemble different abiotic factors or stressors that exist in the environment that affect the microbial community. More focus will be given to one of the stressors—antibiotics, a recent emerging pollutant. The effects on the soil microbial community and the future of soil health due to the presence of antibiotics will be addressed. The scope of the interaction of antibiotics with other pollutants like plastics and heavy metals (HMs) will be examined.

Antibiotic resistance (ABR) is a global concern, exacerbated by widespread antibiotics use in livestock, particularly in poultry systems where detection rates are high. This review systematically evaluates the literature, 71 studies (2014–2024) from NCBI, Google Scholar, and ScienceDirect, to assess the dynamics of ABR in agricultural soils using poultry manure. The analysis emphasizes the genetic landscape of ABR, soil's emerging contaminants like antibiotic resistance bacteria (ARB), and antibiotic resistance genes (ARGs). Tetracycline resistance was the most frequently reported, ranging from < 10% in chicken manure (China & Canada) to 98.28% in chicken fecal samples (Panama). β-lactams in manure spanned < 5% in Canada to > 93.65% in Uganda, followed by aminoglycoside resistance 10%-92.8% (chicken feces, China). Fluoroquinolone-carbenicillin-amoxicillin (FCA) varied from 2.5% (feces, China) to 90% (feces, Guangdong Province, China), Macrolides-lincosamide-streptogramin B (MLSB) and sulphonamide ranged from 5.7%-72.4% and 1.3%-66.7% respectively, with lower rates in chicken manure from China and higher rates in Israel. Over half of the 37 studies on multidrug resistance (MDR), originated from China, with Shandong Province revealing a high rate of 91.07%. The presence of microorganisms like E. coli , S. enterica , K. pneumoniae , Pseudomonas spp ., and Staphylococcus spp. highlights the threat of ESKAPEE ( Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter species, Escherichia coli ) pathogens. These MDR bacteria pose risks in clinical and agricultural settings, challenging healthcare and public health. Understanding ARG prevalence in the poultry sector is vital for developing strategies, including manure treatment technologies, probiotic and natural antimicrobial alternatives, and surveillance tools, alongside the global action plans to curb environmental spread.

Protists represent the largest proportion of eukaryotic diversity acting as a part of the soil microbiome. They play a significant role in mediating carbon and nitrogen cycles, influencing nutrient availability and overall soil health. However, their diversity is shaped by many factors, including plant species, bacterial microbiome, precipitation and organic matter. Here, we investigated protist diversity in date palm rhizosphere soils without and with different combinations of organic, bio-organic and chemical fertilizer treatments. Results showed that soil conductivity, salinity and total dissolved solids (TDS) correlated with the protist diversity. The highest protist diversity was found in the treatment using bio-organic fertilizers mixed with 30 % chemical fertilizer. Higher chemical fertilizer content on the other hand tended to decrease the protist diversity. The highest abundance of protist genera belonged to supergroups of Archaeaplastida , Alveolata, Rhizaria, Amoebozoa and Stramenopiles. The most abundant classes of protist were Filosa-Sarcomonadea, Colpodea, Variosea, Tubulinea and Chlorophyceae. Overall, our results suggest that balanced fertilization with organic matter inputs can enhance protist diversity, improve soil health, and contribute to sustainable crop productivity.

Protists represent a major component of eukaryotic diversity within the soil microbiome, playing critical roles in mediating carbon and nitrogen cycling and influencing nutrient availability and soil health. Their diversity is shaped by multiple factors, including temperature, pH, organic matter content, and land use. In this study, we investigated the protist diversity in rhizosphere soils from both wild and cultivated date palm varieties. Our results identified nitrate, nitrite, calcium, and carbon content as key soil factors significantly correlated with protist diversity. Only 9.2% (42) of operational taxonomic units (OTUs) were shared across all soil samples, suggesting that these taxa possess traits enabling adaptation to extreme environmental conditions. The dominant protist families belonged to Rhizaria, Alveolata, Amoebozoa, and Archaeplastida, primarily comprising bacterial consumers, alongside taxa from Stramenopiles, Opisthokonta, Hacrobia, and Excavata. At the class level, Filosa-Sarcomonadea, Colpodea, Variosea, Tubulinea, and Chlorophyceae were the most abundant. Filosa-Sarcomonadea and Colpodea were positively correlated with bacterial and fungal genera, suggesting their role as consumers, while Variosea showed a negative correlation with bacteria, reflecting predator-prey dynamics. Notably, the protist community composition in wild date palm rhizosphere soils was distinct from that in cultivated soils, with Opisthokonta being particularly abundant, likely reflecting adaptation to drought conditions. Overall, this study highlights the significant differences in protist diversity and community structure between wild and cultivated date palm ecosystems.