Recent advancements in agricultural metagenomics allow for characterizing microbial indicators of soil health brought on by changes in management decisions, which ultimately affect the soil environment. Field-scale studies investigating the microbial taxa from agricultural experiments are sparse, with none investigating the long-term effect of crop rotation and tillage on microbial indicator species. Therefore, our goal was to determine the effect of rotations (continuous corn, CCC; continuous soybean, SSS; and each phase of a corn-soybean rotation, Cs and Sc) and tillage (no-till, NT; and chisel tillage, T) on the soil microbial community composition following 20 years of management. We found that crop rotation and tillage influence the soil environment by altering key soil properties, such as pH and soil organic matter (SOM). Monoculture corn lowered pH compared to SSS (5.9 vs. 6.9, respectively) but increased SOM (5.4% vs. 4.6%, respectively). Bacterial indicator microbes were categorized into two groups: SOM dependent and acidophile vs. N adverse and neutrophile. Fungi preferred the CCC rotation, characterized by low pH. Archaeal indicators were mainly ammonia oxidizers with species occupying niches at contrasting pHs. Numerous indicator microbes are involved with N cycling due to the fertilizer-rich environment, prone to aquatic or gaseous losses.

Soil microbial communities are essential in the cycling of nutrients that affect crop production. Our goal was to characterize the microbial community structure following 34 years of nitrogen (N) fertilization treatments in continuous maize production in highly fertile soils. Using 16S rRNA gene-based analysis of the V4 region via Illumina HiSeq2500 technology with downstream bioinformatics processing and analysis with QIIME 2.0, we aimed to characterize the prokaryotic communities under three increasing N fertilization rates. Factor analyses indicated that a high N level decreased the diversity of soil bacterial and archaeal communities and altered the relative abundance (RA) of the dominant (>1% RA) and minor (<1% RA) phyla. Among the 12 major phyla, we determined increases in Gemmatimonadetes, Proteobacteria, and Euryarchaeota, accompanied by reductions in Cyanobacteria, Chloroflexi, Firmicutes, and Planctomycetes with increasing N. Within the 29 minor phyla, N fertilization led to increases in Aquificae, WPS2, Parvarchaeota, AD3, FCPU426, Armatimonadetes, TM7, Chlamydiae, and OD1, along with reductions of Nitrospirae, WS3, Tenericutes, Lentisphaerae, OP3, Synergistetes, Thermotogae, and prokaryotes that could not be reliably assigned to a phylum (classified as Other).

Short‐term response of microbial respiration after treatment with different doses of the herbicides metsulfuron methyl (MET), 2,4‐D, and glyphosate (GLY) was studied in microcosms of soils collected in three agricultural sites of the Southern Pampas region, Buenos Aires, Argentina. The influence of diammonium phosphate [(NH₄)₂PO₄] on carbon dioxide (CO₂) evolution, when applied with the highest doses of the herbicides, was also investigated. MET had no effect on microbial respiration of an acidic soil of San Román (pH 6.06), even at the highest rate. However, MET inhibited microbial respiration in soils of Bordenave (pH 7.44), at a rate of 0.1 mg kg⁻¹ soil. Low application rates of GLY and 2,4‐D produced only transitory effects on CO₂ evolution, whereas the addition of high doses of these herbicides stimulated microbial activity. On the other hand, the addition of fertilizer to soil treated with a high dose of GLY temporarily inhibited CO₂ release.

Metagenomics in agricultural research allows for searching for bioindicators of soil health to characterize changes caused by management practices. Cover cropping (CC) improves soil health by mitigating nutrient losses, yet the benefits depend on the tillage system used. Field studies searching for indicator taxa within these systems are scarce and narrow in their scope. Our goal was to identify bioindicators of soil health from microbes that were responsive to CC (three levels) and tillage (chisel tillage, no-till) treatments after five years under field conditions. We used rRNA gene-based analysis via Illumina HiSeq2500 technology with QIIME 2.0 processing to characterize the microbial communities. Our results indicated that CC and tillage differentially changed the relative abundances (RAs) of the copiotrophic and oligotrophic guilds. Corn–soybean rotations with legume–grass CC increased the RA of copiotrophic decomposers more than rotations with grass CC, whereas rotations with only bare fallows favored stress-tolerant oligotrophs, including nitrifiers and denitrifiers. Unlike bacteria, fewer indicator fungi and archaea were detected; fungi were poorly identified, and their responses were inconsistent, while the archaea RA increased under bare fallow treatments. This is primary information that allows for understanding the potential for managing the soil community compositions using cover crops to reduce nutrient losses to the environment.