William L. Kingery

Nitrogen (N) cycling in agroecosystems is a complex process regulated by both biological and agronomic factors, with ammonia-oxidizing archaea (AOA) and bacteria (AOB) playing pivotal roles in nitrification. Despite extensive fertilizer applications to achieve maximum crop yields, nitrogen use efficiency (NUE) remains less than ideal, with substantial losses contributing to environmental degradation. This review synthesizes current knowledge on plant-mediated and fertilization-induced shifts in ammonia-oxidizer communities and their implications on nitrogen cycling. We highlight the differential ecological niches of AOA and AOB, emphasizing their responses to plant community composition, root exudates, and allelopathic compounds. Fertilization regimes of inorganic nitrogen inputs and biological nitrification inhibition (BNI) are examined in the context of microbial adaptation and ammonia tolerance. Our review highlights the need for integrated nitrogen management strategies comprising optimized fertilization timing, nitrification inhibitors, and plant–microbe interactions in order to optimize NUE and mitigate nitrogen losses. Future research directions must involve applications of metagenomic and isotopic tracing techniques to unravel the mechanistic AOA and AOB pathways that are involved in regulating these dynamics. An improved understanding of these microbial interactions will inform the creation of more sustainable agricultural systems that aim to optimize nitrogen retention and reduce environmental footprint.

Conservation alternatives that include no-tillage (NT) and cover crops (CCs) reduce soil erosion in row-crop agroecosystems. However, little information is available about how these alternatives affect soil textural properties responsible for soil fertility. This study evaluated the soil particle size distribution and volumetric water content after three years of consistent management in a raised bed system. There were four treatment systems in a dryland maize/soybean rotation on a silt loam soil (Oxyaquic Fraglossudalfs) that included: NT + CCs, conventional tillage (CT) + CCs, CT + winter weeds, and CT + bare soil in winter in northwest Mississippi. The NT + CC system retained 62% more coarse sand in the furrow than the other systems (2.1% compared to 1.3%; p = 0.02). Regardless of the location, the NT + CC system (2.5%) retained 39% more fine sand than the CT + CC system (1.8%; p = 0.01), suggesting that coarse and fine sands were being trapped in furrows combining NT + CC systems, minimizing their off-site transport. In furrows, CCs increased soil volumetric water content by 47% compared to other winter covers. In beds, NT + CCs increased bed water contents by 20% compared to CT + CCs (17.1 to 14.3%; p < 0.01). Implementing conservation alternatives may promote the retention of sand fractions in silty loam soils that are important in supporting soil fertility and crop sustainability.

The metabolic diversity of soil microbiota embodies diverse functional capabilities that support ecosystem resilience, driving essential biogeochemical processes and facilitating the optimization of sustainable agricultural systems. Integrating cover crops into agricultural systems cultivates a diverse array of metabolic activities among soil microbes, synergistically enhancing ecosystem services and bolstering soil health for sustainable and productive farming practices. In an effort to gain deeper insights and expand our knowledge, we conducted a study examining the effects of cover crops and fertilizer sources, thereby shedding light on their combined impacts on the metabolic activity dynamics of soil microbial communities. In this investigation, we employed a split-plot design with two factors: (a) cover crop with three solo cover crop species—Cereal rye (Secale cereale), wheat (Triticum aestivum), hairy vetch (Vicia villosa), and one mixture of mustard (Brassica rapa) and cereal rye (Secale cereale) (CC-mix), (b) Fertilizer source includes poultry litter, chemical fertilizer, and no-fertilizer treatments. We assessed the metabolic potential of soil microbiota by using carbon substrates utilizing Biolog EcoPlates. The findings revealed that the plots with CC-mix treatment exhibited greater metabolic diversity compared to the other treatments, while among the fertilizer sources, poultry litter demonstrated higher metabolic activity. Furthermore, both treatment factors predominantly metabolized carbohydrates and polymers compared to other carbon substrate categories. The principal component analysis accounted for 46.4% of the variance, collectively represented by PC1 and PC2, emphasizing the substantial contributions of carbohydrates, amino acids, and carboxylic acids to the observed metabolic diversity. Canonical correspondence analysis revealed that pH had positively correlated with microbial functional diversity, whereas total carbon (TC), total nitrogen (TN), and water-stable aggregates (WSA) showed a negative correlation. In conclusion, cover cropping and type of fertilizer source had a notable impact on soil microbial functional diversity, with the cover crop mixture exhibiting a more pronounced influence than the individual cover crop treatments.

The abundance and distribution of soil microbial populations, i.e., microbial diversity is widely promoted as a key tenant of sustainable agricultural practices and/or soil health. A common approach to describing microbial diversity is phylogenetic analysis with high-throughput sequencing of microbial DNA. However, owing to the tremendous amounts of data generated, a continuing effort is required to better assess the effects of agricultural management systems on soil microbial diversity. Here, we report on the combined effects of management systems on bacterial and fungal diversity in a loessal agricultural soil located in north-central Mississippi, USA. Amplicon sequencing was performed using 16S rRNA-gene and ITS2 from soil samples collected from a three-year study with combinations of maize-soybean crop rotation, tillage practices, and winter vegetative covers. Differences were found in microbial fungal β-diversity among the management systems, with distinct clustering patterns for no-tillage combined with either winter weeds or bare-fallow. Management systems showed a significant influence on soil pH and bulk density, which were positively correlated with fungal community composition. Developments in the description and interpretation of soil microbial diversity will contribute to a more accurate understanding of its role in the various functions and processes important to agricultural soil management.

The response of soil microbial communities to management practices is composite, as it depends on the various environmental factors which contribute to a shift in the microbial communities. In this study we explored the impact of combinations of soil management practices on microbial diversity and community composition in a dryland soybean production system. Soil samples were collected from the experimental field maintained under no till, cover crops, and fertility treatments, at Pontotoc Ridge-Flatwoods Branch Experiment Station, MS, USA. Targeted amplicon sequencing of 16S rRNA and ITS2 genes was used to study the bacterial and fungal community composition. Poultry litter amendment and cover crops significantly influenced soil bacterial diversity. Fertilizer sources had significantly different bacterial communities, as specific microbial taxa were strongly influenced by the changes in the nutrient availability, while cover crops influenced the soil fungal community differences. Differential enrichment of advantageous bacterial (Proteobacteria, Actinobacteria and Acidobacteria) and fungal (Mortierellomycota) phyla was observed across the treatments. Soil pH and easily extractable glomalin-related soil proteins (EE-GRSP) were correlated with bacterial communities and aggregate stability (WSA) was influenced by the poultry litter amendment, thus driving the differences in bacterial and fungal communities. These findings suggest that a long-term study would provide more inferences on soil microbial community response to management changes in these dryland soybean production systems.

Our understanding on the effects of tillage intensity on the soil microbial community structure and composition in crop production systems are limited. This study evaluated the soil microbial community composition and diversity under different tillage management systems in an effort to identify management practices that effectively support sustainable agriculture. We report results from a three-year study to determine the effects on changes in soil microbial diversity and composition from four tillage intensity treatments and two residue management treatments in a corn-soybean production system using Illumina high-throughput sequencing of 16S rRNA genes. Soil samples were collected from tillage treatments at locations in the Southern Coastal Plain (Verona, MS, USA) and Southern Mississippi River Alluvium (Stoneville, MS, USA) for soil analysis and bacterial community characterization. Our results indicated that different tillage intensity treatments differentially changed the relative abundances of bacterial phyla. The Mantel test of correlations indicated that differences among bacterial community composition were significantly influenced by tillage regime (rM = 0.39, p ≤ 0.0001). Simpson’s reciprocal diversity index indicated greater bacterial diversity with reduction in tillage intensity for each year and study location. For both study sites, differences in tillage intensity had significant influence on the abundance of Proteobacteria. The shift in the soil bacterial community composition under different tillage systems was strongly correlated to changes in labile carbon pool in the system and how it affected the microbial metabolism. This study indicates that soil management through tillage intensity regime had a profound influence on diversity and composition of soil bacterial communities in a corn-soybean production system.

Soil biological properties are important for the stabilization and preservation of a good soil structure. Management practices can affect the diversity and population of microorganisms, which could beneficially change soil properties and promote a more sustainable dryland crop production. This study was established near Pontotoc, MS, USA (34°07′ N, 88°59′ W) on an Atwood silt loam (fine-silty, mixed, semiactive, thermic Typic Paleudalf) to evaluate the impacts of cover crops, planting dates and fertilizer sources (poultry litter, inorganic fertilizer and no fertilizer) on selected biologically related soil properties in a no-tillage, dryland soybean production. Soil analyses included total carbon and nitrogen, permanganate oxidizable carbon (POXC), easily extractable glomalin-related soil protein (EE-GRSP), water stable aggregate (WSA) and soil pH. Cover crop production and soybean yield were also determined. The results indicated that the fertilizer source had an impact on total nitrogen, EE-GRSP and soybean yield. Total N was 6% higher with poultry litter at the early planting date compared to no fertilizer (control) (p < 0.0018) and at the late planting date, when total N and EE-GRSP were increased by 11% and 13%, respectively, with poultry litter compared to no fertilizer. Additionally, soil pH was reduced by 0.25 units in the poultry litter-amended treatment. Soybean yield was increased by 68% and 51% in early-planted soybean and 42% and 40% in late-planted soybean with poultry litter and inorganic fertilizer, respectively, compared to no fertilizer. This study revealed that biological soil properties and soybean yield were influenced by poultry litter application. The results showed no significant effects of cover crops over the short time period of the study.

Understanding pollutant sorption, bioremediation of these pollutants, and their interactions with humic substances requires knowledge of molecular-level processes. New developments with nuclear magnetic resonance (NMR) experiments and labeled compounds have improved the overall understanding of these mechanisms. The advancements made with two-dimensional NMR show great promise, as structural information and hydrogen-carbon bond connectivity can be discerned. This communication presents the application of improved two-dimensional NMR methods, the double quantum filtered (DQF) correlation spectroscopy (COSY) and echo/anti-echo heteronuclear single quantum coherence (HSQC) experiments, for use in structural studies of humic substances. Both experiments were found to produce significant improvements over the conventional COSY and heteronuclear multiple quantum coherence (HMQC) experiments that have been previously employed in similar studies. The more sensitive echo/anti-echo HSQC experiment produced more cross-peaks with higher resolution when compared with the HMQC spectra. The DQF-COSY significantly suppressed the diagonal signals and allowed numerous signals previously hidden in the standard COSY experiment to be observed. These improvements will aid current characterization strategies of humic substances from soils, sediments, and water and their subsequent reactions with pollutants and microorganisms.

Various metals are added to poultry diets to facilitate weight increase and disease prevention. The large amounts of poultry waste produced annually are dispersed intensively over relatively small areas of land, resulting in accumulations that pose potential environmental risks to the surface and groundwater. The focus of this study was to assess the distribution of heavy metals among various solid-phase fractions in soil profiles from a 25-year poultry waste-amended soil. Copper and Zn accumulated close to the soil surface where the total amounts of Cu and Zn in waste-amended soils were significantly higher than in nonamended soils. The total metal concentrations in amended soils were not critically high. Copper in the amended soil was present mostly in the organic matter (OM) fraction (46.9%), whereas Zn was found in the easily reducible oxide (ERO) fraction (47.3%). This suggests that the Cu and Zn in this long-term amended soil are potentially bioavailable and mobile. We observed the mobility of Zn through much of the soil profile of the long-term waste-amended soil. Zinc in this soil profile was found primarily in forms of the residual (RES) and crystalline iron oxide bound (CryFe) fractions, followed by the organic matter-bound and exchangeable (EXC) fractions.