The soil microbiome is the key player regulating phosphorus cycling processes. Identifying phosphate-solubilizing bacteria and utilizing them for release of recalcitrant phosphate that is bound to rocks or minerals have implications for improving crop nutrient acquisition and crop productivity.

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Bacteria play a key role in phosphate solubilization, but related genome-centric research on agricultural microbiomes is scarce. Here, we reconstructed 472 metagenome-assembled genomes (MAGs) covering agricultural soils from six long-term field trials across China. A total of 79 MAGs contained gcd encoding quinoprotein glucose dehydrogenase (GCD), which is the key biomarker for phosphate solubilization. Our findings showed that all GCD-MAGs represent potentially novel species, with gcd copy numbers varying from 1 to 10 per genome. Large genome size, a high ratio of glycosyl hydrolase genes, and increased capacity for carbohydrate utilization were specific traits of GCD-MAGs. Notably, the gcd copy number showed a significant and positive correlation with genome size. Generated using a machine learning approach, our findings were validated in a dataset of 692 genotypes covering the 18 bacterial families to which the 79 GCD-MAGs belong. Our results improve the knowledge of both the diversity and the genetic composition of phosphate-solubilizing bacteria. In particular, they reveal a genomic link between phosphate solubilization capacity and increased potential for carbohydrate metabolism, which may accelerate targeted engineering and improve management practices for sustainable agriculture.

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Managing soil organic carbon (SOC) to maximize crop yield is a vital strategy to feed the world's growing population. However, the low SOC contents in agricultural soils limits the maximization of wheat yield. Here, we used modeling and a long‐term field experiment to determine whether improved crop management (IM) and an integrated procedure that combined IM with manure application (IMsoil) would close the yield gap while increasing SOC sequestration during wheat (Triticum aestivum L.) production in China. The yield of conventional farmers' practice (CM), operating with high fertilizer inputs, suboptimal management, and straw removal, was 5.3 Megagrams per hectare (Mg/ha), reaching 48% of yield potential (Yp, 11.0 Mg/ha) while reducing SOC sequestration during the year 2012–2019. The IM procedure with optimized density, planting dates, and nutrient management increased yield to 8.0 Mg/ha (i.e., 73% of Yp), and increased SOC sequestration. The IMsoil treatment further elevated wheat yield to 9.3 Mg/ha (i.e., 85% of Yp) by increasing spike number and pre‐anthesis dry matter accumulation. The SOC sequestration in the IMsoil increased by 15.4 Mg C/ha at a rate of 2.20  Mg C ha‐1 yr through large C inputs and high SOC transfer efficiencies compared with the beginning of this experiment. These results highlight the importance of combining optimized crop managements with soil amendment to close the yield gap with less fertilizer inputs while contributing to sustainable agriculture objectives.