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Despite the extensive application of the Soil and Water Assessment Tool (SWAT) for water quality modeling, its ability to simulate soil inorganic nitrogen (SIN) dynamics in agricultural landscapes has not been directly verified. Here, we improved and evaluated the SWAT–Carbon (SWAT-C) model for simulating long-term (1984–2020) dynamics of SIN for 40 cropping system treatments in the U.S. Midwest. We added one new nitrification and two new denitrification algorithms to the default SWAT version, resulting in six combinations of nitrification and denitrification options with varying performance in simulating SIN. The combination of the existing nitrification method in SWAT and the second newly added denitrification method performed the best, achieving R, NSE, PBIAS, and RMSE of 0.63, 0.29, −4.7 %, and 16.0 kg N ha−1, respectively. This represents a significant improvement compared to the existing methods. In general, the revised SWAT-C model's performance was comparable to or better than other agroecosystem models tested in previous studies for assessing the availability of SIN for plant growth in different cropping systems. Sensitivity analysis showed that parameters controlling soil organic matter decomposition, nitrification, and denitrification were most sensitive for SIN simulation. Using SWAT-C for improved prediction of plant-available SIN is expected to better inform agroecosystem management decisions to ensure crop productivity while minimizing the negative environmental impacts caused by fertilizer application. 

ABSTRACT Root-associated microbes are key players in plant health, disease resistance, and nitrogen (N) use efficiency. It remains largely unclear how the interplay of biological and environmental factors affects rhizobiome dynamics in agricultural systems. In this study, we quantified the composition of rhizosphere and bulk soil microbial communities associated with maize ( Zea mays L.) and soybean ( Glycine max L.) in a long-term crop rotation study under conventional fertilization and low-N regimes. Over two growing seasons, we evaluated the effects of environmental conditions and several treatment factors on the abundance of rhizosphere- and soil-colonizing microbial taxa. Time of sampling, host plant species, and N fertilization had major effects on microbiomes, while no effect of crop rotation was observed. Using variance partitioning as well as 16S sequence information, we further defined a set of 82 microbial genera and functional taxonomic groups at the subgenus level that show distinct responses to treatment factors. We identified taxa that are highly specific to either maize or soybean rhizospheres, as well as taxa that are sensitive to N fertilization in plant rhizospheres and bulk soil. This study provides insights to harness the full potential of soil microbes in maize and soybean agricultural systems through plant breeding and field management. IMPORTANCE Plant roots are colonized by large numbers of microbes, some of which may help the plant acquire nutrients and fight diseases. Our study contributes to a better understanding of root-colonizing microbes in the widespread and economically important maize-soybean crop rotation system. The long-term goal of this research is to optimize crop plant varieties and field management to create the best possible conditions for beneficial plant-microbe interactions to occur. These beneficial microbes may be harnessed to sustainably reduce dependency on pesticides and industrial fertilizer. We identify groups of microbes specific to the maize or to the soybean host and microbes that are sensitive to nitrogen fertilization. These microbes represent candidates that may be influenced through plant breeding or field management, and future research will be directed toward elucidating their roles in plant health and nitrogen usage. 

Abstract Historically neglected by microbial ecologists, soil viruses are now thought to be critical to global biogeochemical cycles. However, our understanding of their global distribution, activities and interactions with the soil microbiome remains limited. Here we present the Global Soil Virus Atlas, a comprehensive dataset compiled from 2,953 previously sequenced soil metagenomes and composed of 616,935 uncultivated viral genomes and 38,508 unique viral operational taxonomic units. Rarefaction curves from the Global Soil Virus Atlas indicate that most soil viral diversity remains unexplored, further underscored by high spatial turnover and low rates of shared viral operational taxonomic units across samples. By examining genes associated with biogeochemical functions, we also demonstrate the viral potential to impact soil carbon and nutrient cycling. This study represents an extensive characterization of soil viral diversity and provides a foundation for developing testable hypotheses regarding the role of the virosphere in the soil microbiome and global biogeochemistry.