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.

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.

Cover cropping has emerged as a pivotal strategy to enhance soil health and microbiome functionality across diverse agroecosystems. However, the extent to which cover crops reshape microbial diversity, composition, functional capacity, and ecological stability remains insufficiently understood, particularly within heterogenous environments like Mississippi. In this study, we conducted a comprehensive pooled analysis of 473 soil samples collected from multiple independent cover crop trials (2020-2024) across diverse cropping systems and edaphic contexts in Mississippi. Amplicon sequencing (16S rRNA and ITS2) coupled with machine learning, co-occurrence network modeling, and functional prediction tools were employed to evaluate microbial community responses to cover cropping. Results revealed that cover crops significantly elevated bacterial and fungal α-diversity, altered community composition, and enriched taxa associated with nitrogen fixation, organic matter turnover, and pathogen suppression. Notably, Proteobacteria, Acidobacteriota, and Chloroflexi were more abundant under cover cropping, whereas Firmicutes and Actinobacteriota dominated control plots. Fungal communities under cover cropping exhibited higher relative abundance of Rozellomycota and Chytridiomycota, indicating enhanced saprotrophic and decomposition potential. Functional predictions showed increased cellular and environmental processing functions in cover-cropped soils, alongside a marked reduction in KEGG pathways linked to human diseases and pathotroph dominance. Co-occurrence network analysis indicated increased connectivity, modularity, and robustness under cover cropping, suggested enhanced microbial interaction strength and ecological stability. Sloan's neutral model fitting and increased migration rates further revealed that stochastic processes played a greater role in microbial assembly under cover cropping. Random Forest model identified Bradyrhizobium, Bryobacter, and Solirubrobacter as top bacterial biomarkers enriched in cover-cropped soils, while Talaromyces, Purpureocillium, and Clonostachys were the most predictive fungal genera, known for their biocontrol and nutrient cycling roles. These findings underscore the ecological potential of cover crops to enhance soil microbial networks and sustainability within Mississippi production systems, while insights may inform similar humid, subtropical agroecosystems elsewhere.

Soil bacterial communities are vital for ecosystem functioning in the humid tropics, yet their response to land-use change remains poorly understood. This knowledge gap is exacerbated by the lack of long-term studies. We employed a space-for-time substitution approach to assess the effects of land-use intensification on soil bacterial communities across a gradient of anthropogenic disturbance in Trinidad. Three sub-watersheds (Arouca = pristine, Maracas = intermediate, Tacarigua = intensive) were selected, each containing adjacent forest, grassland, and agricultural land uses. We combined geophysical soil apparent electrical conductivity (ECa-directed) sampling with 16S rDNA gene amplicon sequencing to characterize bacterial communities and their relationships with soil and landscape properties. Soil properties were the primary determinant of bacterial community structure, explaining 56% of the variation (p < 0.001), with pH, clay content, hygroscopic water, and nutrient availability as key drivers. Bacterial α-diversity differed significantly among sub-watersheds (p < 0.01), with Tacarigua exhibiting lower richness and diversity compared to Arouca and Maracas, but not across land uses. While a core microbiome of ten bacterial families was ubiquitous across land uses, indicating a stable foundational community, land-use intensification significantly altered β-diversity (p < 0.01 among sub-watersheds). Agricultural soils showed the greatest divergence from forest soils (p < 0.05), with a marked decline in key Proteobacterial families (e.g., Xanthomonadaceae, Pseudomonadaceae) involved in nutrient cycling and plant growth promotion. Although inherent soil properties shape the core microbiome, land-use intensification acts as a strong secondary filter, shifting soil bacterial communities toward more stress-resistant Firmicutes with potentially less diverse functions. Our findings demonstrate the utility of integrating space-for-time substitution with molecular profiling to predict long-term microbial responses to environmental change in vulnerable tropical ecosystems.

Root-associated fungal communities play important roles in plant health and stress tolerance, yet their dynamics across developmental stages remain poorly understood. Here, we characterized rhizoplane fungal communities associated with cowpea genotypes (EpicSelect4 (ES4) and UCR369) under control and drought across four developmental stages. Drought affected richness, whereas Shannon diversity was influenced by genotype, drought, and growth stage. Fungal community composition was structured primarily by host genotype, with drought exerting a smaller but significant effect. Fungal richness showed a narrower response to drought, while fungal diversity displayed clearer genotype-dependent trajectories across growth stages. Community assembly analyses revealed a broad departure from neutral expectations, with weaker fit under drought and dominant homogeneous selection in both moisture regimes. Drought was associated with increased homogeneous selection and dispersal limitation, reduced drift, and a shift of ES4 toward stronger deterministic filtering. Co-occurrence network analysis further showed that drought was associated with reduced connectivity and increased modularity and predicted vulnerability, suggesting a more compartmentalized co-occurrence structure. Genotype effects on network organization were even more pronounced, as UCR369 exhibited a larger yet more fragile network compared to ES4. FUNGuild annotations showed drought increased ASVs in saprotrophic and mixed categories. Structural equation modeling revealed drought affected fungal diversity directly and via plant traits and soil pH. Host genotype was the main predictor of fungal composition, which positively associated with diversity. These findings indicate cowpea fungal communities respond to drought through changes in diversity, assembly, interaction, and function, with host genotype playing a key role during plant growth.