Understanding soil–plant–microbe inter- and intra- interactions are essential for ensuring proper soil health, quality, and soil-mediated ecosystem services (e.g., nutrient cycling) required for human–plant–animal life. Intensive and unsustainable farming practices can decrease soil microbial biodiversity, fertility, and quality leading to soil degradation, impaired nutrient cycling, and the incapability of soil to support plant growth. Under such a context, soil biological fertility can appear as a regenerative component that has the potential to harmonize and improve soil’s physical, chemical, and biological parameters. This study defines and discusses the microbiome in the rhizosphere, microbial nutrient cycling, and biological soil crusts as the major components of soil biological fertility, and explores the answers to the following questions: (i) how does the rhizosphere promote plant growth, development, and nutrient cycling through soil microorganisms (e.g., bacteria, fungi)? (ii) How can soil microorganisms regulate macronutrient cycling and facilitate biocrust formation? This review reveals that soil biological fertility is crucial for increasing crop resilience and productivity as well as sustainability in agriculture. Additionally, the reintroduction of plant growth promoting rhizobacteria, a quantitative estimation of the root exudate’s composition, identifying the spatiotemporal dynamics of potassium solubilizing bacteria and establishing biological soil crusts in agricultural lands remain the major tasks for improving soil biological fertility and the transition towards regenerative agriculture.

It is evident that legume root nodules can accommodate rhizobial and non-rhizobial bacterial endophytes. Our recent nodule microbiome study in peanuts described that small nodules can harbor diverse bacterial endophytes. To understand their functional role, we isolated 87 indigenous endophytes from small nodules of field-grown peanut roots and characterized them at molecular, biochemical, and physiological levels. The amplified 16S rRNA genes and phylogenetic analysis of these isolates revealed a wide variety of microorganisms related to the genera Bacillus, Burkholderia, Enterobacter, Herbaspirillum, Mistsuaria, Pantoea, Pseudomonas, and Rhizobia. It was observed that 37% (100% identity) and 56% (>99% identity) of the isolates matched with the amplified sequence variants (ASVs) from our previous microbiome study. All of these isolates were tested for stress tolerance (high temperature, salinity, acidic pH) and phosphate (P) solubilization along with ammonia (NH₃), indole-3-acetic acid (IAA), 1-aminocyclopropane-1-carboxylate deaminase (ACCD), and siderophore production. The majority (78%) of the isolates were found to be halotolerant, thermotolerant, and acidophilic, and a few of them showed a significant positive response to the production of IAA, NH₃, siderophore, ACCD, and P-solubilization. To evaluate the plant growth promotion (PGP) activity, plant and nodulation assays were performed in the growth chamber conditions for the selected isolates from both the non-rhizobial and rhizobial groups. However, these isolates appeared to be non-nodulating in the tested conditions. Nonetheless, the isolates 2 (Pantoea), 17 (Burkholderia), 21 (Herbaspirillum), 33o (Pseudomonas), and 77 (Rhizobium sp.) showed significant PGP activity in terms of biomass production. Our findings indicate that these isolates have potential for future biotechnological applications through the development of biologicals for sustainable crop improvement.

Unique plant functional traits (morpho-physio-anatomical) may respond to novel environmental conditions to counterbalance elevated carbon dioxide (eCO₂) concentrations. Utilizing CO₂, plants produce photoassimilates (carbohydrates). A mechanistic understanding of partitioning and translocation of carbon/photoassimilates into different plant parts and soils under ambient and eCO₂ is required. In this study, we examine and present the intrinsic relationship between plant functional traits and eCO₂ and seek answers to (i) how do plant functional traits (morpho-physio-anatomical features) affect C storage and partitioning under ambient and eCO₂ in different plant parts? (ii) How do plant functional traits influence C transfer to the soil and rhizosphere services? Our study suggests that morpho-physio-anatomical features are interlinked, and under eCO₂, plant functional traits influence the quantity of C accumulation inside the plant biomass, its potential translocation to different plant parts, and to the soil. The availability of additional photoassimilates aids in increasing the above- and belowground growth of plants. Moreover, plants may retain a predisposition to build thick leaves due to reduced specific leaf area, thicker palisade tissue, and higher palisade/sponge tissue thickness. eCO₂ and soil-available N can alter root anatomy, the release of metabolites, and root respiration, impacting potential carbon transfer to the soil.

Optimizing cover crop termination timing (CCTT) is crucial for ensuring sustainable cover crop management under regenerative agriculture. This study investigated how early and delayed CCTTs interact with irrigation regimes to affect soil microbiomes, arbuscular mycorrhizal fungi (AMF) dynamics, and the root‐associated fungal biome in cotton roots. Field trials were conducted at two Texas A&M AgriLife Research sites in Lamesa and Chillicothe, TX. Treatments included (i) no cover (NC), ii) cover terminated at 6 weeks (CT6), and (iii) 2 weeks before cotton planting (CT2), each under base (60% ET replacement) and low (<7 cm) irrigation. Root‐associated soil (0–10 cm) and cotton root samples were collected before peak bloom to assess AMF colonization and spore density, phospholipid fatty acid (PLFA) profiles, and root mycobiome using high‐throughput amplicon sequencing. AMF root colonization (%) was significantly higher under CT6 at both sites. Spore density ranged from 4 to 9 g ^{− 1} soil in Lamesa and 5 to 8 g ^{− 1} in Chillicothe, with significantly higher spores under CT2 in Lamesa. No significant effects of CCTT on microbial community composition were observed based on PLFA analysis. However, base irrigation significantly increased the gram‐positive‐to‐gram‐negative bacterial ratio and the saturated‐to‐unsaturated fatty acid ratio, while low irrigation increased the monounsaturated‐to‐polyunsaturated fatty acid ratio. Ascomycota and Basidiomycota were the dominant fungal phyla across CCTT, with significantly higher Basidiomycota abundance under base irrigation at Lamesa. CCTT did not affect fungal alpha and beta diversity indices; however, alpha diversity was significantly greater under base irrigation at Lamesa. Overall, these results suggest that early termination sustains AMF dynamics while avoiding major shifts in the broader microbial community in cotton.