Effects of swine manure dilution with lagoon effluent on microbial communities and odor formation in pit recharge systems.

Pit recharge systems (PRS) control odor by managing organic solids in swine manure. However, there needs to be more understanding of PRS's effect on the microbiome composition and its impact on odor formation. A study was conducted to understand how recharge intervals used in PRS impact manure microbiome and odor formation. Bioreactors dynamically loaded simulated recharge intervals of 14, 10, and 4 days by diluting swine manure with lagoon effluent at varying ratios. Treatment ratios tested included 10:0 (control), 7:3 (typical Korean PRS), 5:5 (enhanced PRS #1), and 2:8 (enhanced PRS #2). Manure microbial membership, chemical concentrations, and odorant concentrations were used to identify the interactions between microbiota, manure, and odor. The initial microbial community structure was controlled by dilution ratio and manure barn source material. Firmicutes and Proteobacteria were the dominant microbial phyla in manure and lagoon effluent, respectively, and significantly decreased or increased with dilution. Key microbial species were Clostridium saudiense in manure and Pseudomonas caeni in lagoon effluent. Percentages of these species declined by 8.9% or increased by 17.6%, respectively, with each unit dilution. Microbial community composition was controlled by both treatment (i.e., manure dilution ratio and barn source material) and environmental factors (i.e., solids and pH). Microbiome composition was correlated with manure odor formation profiles, but this effect was inseparable from environmental factors, which explained over 75% of the variance in odor profiles. Consequently, monitoring solids and pH in recharge waters will significantly impact odor control in PRS.

Simulated nitrous oxide emissions from multiple agroecosystems in the U.S. Corn Belt using the modified SWAT-C model.

Agriculture is a major source of nitrous oxide (N2O) emissions into the atmosphere. However, assessing the impacts of agricultural conservation practices, land use change, and climate adaptation measures on N2O emissions at a large scale is a challenge for process-based model applications. Here, we integrated six N2O emission algorithms for the nitrification processes and seven N2O emission algorithms for the denitrification process into the Soil and Water Assessment Tool-Carbon (SWAT-C). We evaluated the different combinations of methods in simulating N2O emissions under corn (Zea mays L.) production systems with various conservation practices, including fertilization, tillage, and crop rotation (represented by 14 experimental treatments and 83 treatment-years) at five experimental sites across the U.S. Midwest. The SWAT-C model exhibited wide variability in simulating daily average N2O emissions across treatment-years with different method configurations, as indicated by the ranges of R2, NSE, and BIAS (0.04-0.68, -1.78-0.60, and -0.94-0.001, respectively). Our results indicate that the denitrification process has a stronger impact on N2O emissions than the nitrification process. The best performing N2O emission algorithms are those rooted in the CENTURY model, which considers soil pH and respiration effects that were overlooked by other algorithms. The optimal N2O emission algorithm explained about 63% of the variability of annual average N2O emissions, with NSE and BIAS of 0.60 and -0.033, respectively. The model can reasonably represent the impacts of agricultural conservation practices on N2O emissions. We anticipate that the improved SWAT-C model, with its flexible configurations and robust modeling and assessment capabilities, will provide a valuable tool for studying and managing N2O emissions from agroecosystems.

Nitrate losses and nitrous oxide emissions under contrasting tillage and cover crop management.

Agroecosystems in the upper Mississippi River Basin are highly productive but often contribute to deterioration of water quality and greenhouse gas emissions. Cover cropping and no-till are conservation strategies implemented to reduce the environmental impact of these agroecosystems. However, using multiple strategies can lead to systemwide interactions that are not fully understood. These interactions can affect not only environmental quality metrics, such as subsurface drainage nitrate losses or nitrous oxide (N2 O) emissions, but also may influence crop production potential. A field trial was initiated comparing nitrate losses, N2 O emissions, and crop production under systems with fall chisel plow tillage, fall chisel plow tillage with an oat (Avena sativa L.) cover crop (CP-oat), no-till (NT), no-till with a rye (Secale cereale L.) cover crop (NT-rye), and NT with zero N fertilizer. Pathways for nitrate losses and N2 O emissions did not appear linked and were not tied to cover crop or tillage practices. Nitrate losses were linked with drainage volumes, and cover crops and tillage had limited effect on cumulative drainage volumes. Notably, NT-rye altered the relationship between drainage volume and nitrate losses by reducing nitrate concentrations, lowering nitrate losses by 59 ±9% compared with CP-oat and 67 ± 9% compared with NT. Neither cover crop nor tillage consistently affected N2 O emissions or crop yield. Rather, N2 O emissions were closely tied with fertilizer N application and seasonal weather patterns. These findings indicate that nitrate leaching and N2 O emissions are regulated by separate mechanisms, so conservation management may require stacking multiple practices to be effective.

Both subsurface nitrate losses and nitrous oxide emissions were linked with weather. Subsurface nitrate losses were linked with cumulative annual drainage. Nitrous oxide emissions were linked with fertilizer N applications. Rye cover crop with no-till reduced nitrate losses with no yield declines.

Conserved and reproducible bacterial communities associate with extraradical hyphae of arbuscular mycorrhizal fungi.

Extraradical hyphae (ERH) of arbuscular mycorrhizal fungi (AMF) extend from plant roots into the soil environment and interact with soil microbial communities. Evidence of positive and negative interactions between AMF and soil bacteria point to functionally important ERH-associated communities. To characterize communities associated with ERH and test controls on their establishment and composition, we utilized an in-growth core system containing a live soil-sand mixture that allowed manual extraction of ERH for 16S rRNA gene amplicon profiling. Across experiments and soils, consistent enrichment of members of the Betaproteobacteriales, Myxococcales, Fibrobacterales, Cytophagales, Chloroflexales, and Cellvibrionales was observed on ERH samples, while variation among samples from different soils was observed primarily at lower taxonomic ranks. The ERH-associated community was conserved between two fungal species assayed, Glomus versiforme and Rhizophagus irregularis, though R. irregularis exerted a stronger selection and showed greater enrichment for taxa in the Alphaproteobacteria and Gammaproteobacteria. A distinct community established within 14 days of hyphal access to the soil, while temporal patterns of establishment and turnover varied between taxonomic groups. Identification of a conserved ERH-associated community is consistent with the concept of an AMF microbiome and can aid the characterization of facilitative and antagonistic interactions influencing the plant-fungal symbiosis.

Plant growth rate and nitrogen uptake shape rhizosphere bacterial community composition and activity in an agricultural field.

Plant-microbial interactions in the rhizosphere are an essential link in soil nitrogen (N) cycling and plant N supply. Plant phenotype and genotype interact with the soil environment to determine rhizosphere community structure and activity. However, the relative contributions of plant identity, phenology and soil resource availability in shaping rhizosphere effects are not well understood. Four summer annuals and a collection of maize hybrids were grown in a common garden experiment conducted at two levels of organic nutrient availability. Plant biomass, N accumulation, rhizosphere bacterial community composition, and rhizosphere potential extracellular enzyme activity were assessed at vegetative, flowering and grain-filling stages of maize. Plant N uptake was strongly coupled with protease activity in the rhizosphere. Temporal trends in rhizosphere community composition varied between plant species. Changes in rhizosphere community composition could be explained by variation in plant growth dynamics. These findings indicate that species-level variation in plant growth dynamics and resource acquisition drive variation in rhizosphere bacterial community composition and activity linked to plant N uptake.

Diverse Sorghum bicolor accessions show marked variation in growth and transcriptional responses to arbuscular mycorrhizal fungi.

Sorghum is an important crop grown worldwide for feed and fibre. Like most plants, it has the capacity to benefit from symbioses with arbuscular mycorrhizal (AM) fungi, and its diverse genotypes likely vary in their responses. Currently, the genetic basis of mycorrhiza-responsiveness is largely unknown. Here, we investigated transcriptional and physiological responses of sorghum accessions, founders of a bioenergy nested association mapping panel, for their responses to four species of AM fungi. Transcriptome comparisons across four accessions identified mycorrhiza-inducible genes; stringent filtering criteria revealed 278 genes that show mycorrhiza-inducible expression independent of genotype and 55 genes whose expression varies with genotype. The latter suggests variation in phosphate transport and defence across these accessions. The mycorrhiza growth and nutrient responses of 18 sorghum accessions varied tremendously, ranging from mycorrhiza-dependent to negatively mycorrhiza-responsive. Additionally, accessions varied in the number of AM fungi to which they showed positive responses, from one to several fungal species. Mycorrhiza growth and phosphorus responses were positively correlated, whereas expression of two mycorrhiza-inducible phosphate transporters, SbPT8 and SbPT9, correlated negatively with mycorrhizal growth responses. AM fungi improve growth and mineral nutrition of sorghum, and the substantial variation between lines provides the potential to map loci influencing mycorrhiza responses.

Plant Phylogeny and Life History Shape Rhizosphere Bacterial Microbiome of Summer Annuals in an Agricultural Field.

Rhizosphere microbial communities are critically important for soil nitrogen cycling and plant productivity. There is evidence that plant species and genotypes select distinct rhizosphere communities, however, knowledge of the drivers and extent of this variation remains limited. We grew 11 annual species and 11 maize (Zea mays subsp. mays) inbred lines in a common garden experiment to assess the influence of host phylogeny, growth, and nitrogen metabolism on rhizosphere communities. Growth characteristics, bacterial community composition and potential activity of extracellular enzymes were assayed at time of flowering, when plant nitrogen demand is maximal. Bacterial community composition varied significantly between different plant species and genotypes. Rhizosphere beta-diversity was positively correlated with phylogenetic distance between plant species, but not genetic distance within a plant species. In particular, life history traits associated with plant resource acquisition (e.g., longer lifespan, high nitrogen use efficiency, and larger seed size) were correlated with variation in bacterial community composition and enzyme activity. These results indicate that plant evolutionary history and life history strategy influence rhizosphere bacterial community composition and activity. Thus, incorporating phylogenetic or functional diversity into crop rotations may be a tool to manipulate plant-microbe interactions in agricultural systems.

Fine-root system development and susceptibility to pathogen colonization.

Root development may exert control on plant-pathogen interactions with soil-borne pathogens by shaping the spatial and temporal availability of susceptible tissues and in turn the impact of pathogen colonization on root function. To evaluate the relationship between root development and resistance to apple replant disease (ARD) pathogens, pathogen abundance was compared across root branching orders in a bioassay with two rootstock genotypes, M.26 (highly susceptible) and CG.210 (less susceptible). Root growth, anatomical development and secondary metabolite production were evaluated as tissue resistance mechanisms. ARD pathogens primarily colonized first and second order roots, which corresponded with cortical tissue senescence and loss in second and third order roots. Defense compounds were differentially allocated across root branching orders, while defense induction or stress response was only detected in first order and pioneer roots. Our results suggest disease development is based largely on fine-root tip attrition. In accordance, the less susceptible rootstock supported lower ARD pathogen abundance and altered defense compound production in first order and pioneer roots and maintained higher rates of root growth in both the ARD soil and pasteurized control compared to the more susceptible. Thus, this rootstock's ability to maintain shoot growth in replant soil may be attributable to relative replant pathogen resistance in distal root branches as well as tolerance of infection based on rates of root growth.