Total soil C and N were strongly associated with EOC and EON, the soil C:N ratio, and POXC. These variables had negative values along axis 2 and thus contrasted with the pattern of soil inorganic N. Weak loading of AMT1.1, NRT2.1, Nii, and GS2 on the first two principal components reflects the lack of association of expression levels of these genes with biogeochemical and plant variables. Non-overlapping confidence ellipses for seven out of 13 fields on the PCA biplot indicated distinct N cycling patterns . Fields 1 and 2, with the highest values along axis 1, had low values of all variables included in the analysis. Field 4 had the highest values along axis 2 corresponding with higher soil NH4 + and NO3 – . Fields 10, 11, 12, and 13 were associated with high values of labile and total soil C and N. Overlapping confidence ellipses of fields 3, 5, 6, 7, 8, and 9 close to the origin indicate similar, moderate values of this suite of variables for these fields. Three groups of fields were identified by k-means cluster analysis of the same 28 variables included in the PCA . Group 1 included fields 1 and 2, which had low mean values for yield , the lowest mean soil C and N and soil inorganic N pools , and the lowest mean value of GS1 relative expression in roots. Groups 2 and 3 had similarly higher mean yield , shoot N, and petiole NO3 – than group 1, but these two groups differed substantially in their soil C and N pools. Group 2 had higher soil NH4 + and NO3 – pools as well as root expression of AMT1.2 while group 3 had higher total and labile soil C pools. Expression of GS1 was similar in both groups. Based on the relative magnitude of F-statistics calculated for each variable,vertical indoor hydroponic system soil C and N, EOC, EON, shoot N, and soil NO3 – at transplant and anthesis were most strongly differentiated across the three groups.
The high F-statistics of AMT1.2 and GS1 relative to other N metabolism genes indicate that root expression of these genes are most responsive to soil N cycling.This study confirms that working organic farms can produce high yields with tightly-coupled N cycling that minimizes the potential for N losses. Such farms had the highest soil C and N and used high C:N organic matter inputs coupled with labile N inputs that resulted in high soil biological activity, low soil inorganic N pools, high expression for a root N assimilation gene, adequate plant N, and high yields. Organic systems trials have previously shown crop N deficiencies that lead to less-than-ideal crop productivity; losses of N when Navail ability is poorly synchronized with crop N demand; or alternatively, that organic production can reduce N losses. But how working organic farms achieve yields competitive with high-input conventional production with low potential for N losses has not been demonstrated. Elevated expression of a key gene involved in root N assimilation, cytosolic glutamine synthetase GS1, in fields with tightly coupled N cycling confirmed that plant N assimilation was high when plant-soil-microbe N cycling was rapid and inorganic N pools were low, thus showing potential as a novel indicator of N availability to plants. Improving biologically-based farming systems will benefit from research that uses novel tools to uncover innovations happening on farms, especially if the research process helps facilitate knowledge exchange among farmers and researchers.To characterize the substantial variation in crop yield, plant-soil N cycling, and root gene expression across 13 fields growing the same crop on similar soil types, we propose three N cycling scenarios: “tightly-coupled N cycling”, “N surplus”, and “N deficient”.
Values of indicator variables suggest differing levels of provisioning, regulating, and supporting ecosystem services in each scenario . Fields in group 3 show evidence of tightly-coupled plant-soil N cycling, a desirable scenario in which crop productivity is supported by adequate N availability but low potential for N loss. Despite consistently low soil NO3 – pools in these fields, well below the critical mid-season level for conventional processing tomatoes in California, total above ground N concentrations were very close to or only slightly below the critical N concentration for processing tomatoes. Tomato yields were also above the county average . This discrepancy between low soil inorganic N pool sizes and adequate tomato N status is due to N pools that were turning over rapidly as a result of efficient N management, high soil microbial activity, and rapid plant N uptake. Composted yard waste inputs with relatively high C:N ratios in concert with limited use of labile organic fertilizers applied during peak plant N demand provided organic matter inputs with a range of N availability. A companion study showed how high potential activities of N-cycling soil enzymes but lower activities of C-cycling enzymes in this set of fields reflect an abundant supply of C but N limitation for the microbial community, thus stimulating production of microbial enzymes to mineralize N. Plant roots can effectively compete with microbes for this mineralized N, especially over time and when plant N demand is high. High root expression of GS1 in these fields indicates that root N assimilation was elevated and thus actual plant N availability and uptake was higher than low inorganic N pools would suggest . Fields from group 2 demonstrated N surplus, showing similar yields to group 3 but with lower total and labile soil C and N and a higher potential for N losses, given much higher soil inorganic N . While actual N losses depend on a host of factors , high soil NO3 – is considered an indicator for N loss potential. Results from a companion study support the idea that soil microbes were C rather than N-limited in these fields, showing higher potential activities of C-cycling soil enzymes but low activities of N-cycling soil enzymes, the inverse of group 3 .
An alternative multivariate clustering approach based on an artificial neural network suggests multiple potential drivers of higher inorganic N pools in these fields, including both management factors and soil characteristics . For instance, field 4 had strong indications of surplus N driven at least in part by a large application of seabird guano , a readily-mineralizable organic N fertilizer, at tomato transplanting when plant N demand is low. In contrast, higher inorganic N in field 8 was likely driven by low plant N demand based on very low soil P availability, which resulted in plant P limitation. These site-specific problems were identifiable due to the focus on variability across similar organic fields and illustrate the need for site-specific approaches to reduce N losses. Finally, the two fields included in group 1 were exemplary of N deficiency, in which low N availability compromises crop productivity but also likely limits N losses within the growing season. While low soil NH4 + and NO3 – concentrations were similar to group 3,vertical farming tower for sale low total and labile soil organic matter and poorly-timed organic matter inputs compromised microbial activity and likely limited N mineralization.Cytosolic glutamine synthetase GS1 encodes for the enzyme that catalyzes the addition of NH4 + to glutamate, the former resulting from either direct uptake of NH4 + from soil or reduction of NO3 – in roots. GS1 is thus the gateway for N assimilation in roots and is upregulated to increase root N assimilation capacity. Similar levels of GS1 expression in groups 2 and 3, in spite of large differences in soil NH4 + and NO3 – concentrations at the anthesis sampling, suggests that plant N availability is indeed higher in group 3 fields than would be expected based on measurement of inorganic N pools alone. The low levels of GS1 expression found in fields with clear N deficiency supports this idea. These results complement recent experimental approaches that showed rapidly increased expression of GS1 in tomato roots in response to a pulse of 15NH4 + -N on an organic farm soil, which was linked to subsequent increases in root and shoot 15N content, even when this pulse did not significantly change soil inorganic N pools. GS1 transcripts and glutamine synthetase enzyme activity also increased with increasing NH4 + and NO3 – availability in sorghum roots, suggesting this response may be widespread among plant species.
Interestingly, inclusion of soil GWC in multiple linear regression models increased the proportion of GS1 expression variability explained to nearly 30% ; soil water content increases microbial activity as well as the mass flow and diffusion of inorganic N to roots. Further research will undoubtedly show how other factors like crop physiological N demand relative to C fixation and P availability increase the interpretability of N uptake and assimilation gene expression in roots.The N cycling scenarios identified on this set of organic fields corresponded at least in part with landscape clusters based on landscape and soil characteristics . Fields that balanced high yields with low potential for N loss and high internal N cycling capacity were part of PAM cluster 1, which had the highest productive capacity rating . Landscape clusters encompassing more marginal soils included both low-yielding fields exhibiting N deficiency or high-yielding fields that used inputs of highly available N like seabird guano to alleviate N deficiency . But these inputs led to the highest soil NO3 – levels and thus came at the cost of higher potential for N loss. Long-term efforts to increase internal soil N cycling capacity would help alleviate both N deficiency and the need for such large inputs of labile N. Whether farmers are willing to invest in management to increase soil N cycling capacity depends in part on how likely they perceive the benefits to be, especially on marginal soils. The discussions that we had with each farmer in this study indicated genuine interest in adaptive management to further tighten plant-soil N cycling, but this may not always be the case. Indeed, the proportion of management vs. inherent soil characteristics responsible for driving differences in N cycling is challenging to untangle. Farmers may allocate more resources to more productive land and likewise fewer resources to more marginal land, or may selectively transition more marginal land to organic management. Documenting the multiple services provided by increases in soil quality and facilitating information exchange among organic growers such as through the landscape approach used here may help build momentum for efforts to improve soil quality and plant-soil-microbe N cycling.The so-called chelation strategy , which is mainly found in graminaceous plants, is based on the excretion of phytosideropores to the rhizosphere. Phytosideropores rapidly chelate Fe, to form Fe-PS chelates that are subsequently transported into the root cells through a specific transporter. The socalled reduction strategy relies on the coordinated action of a membrane bound Fe reductase, that reduces Fe to Fe, an Fe uptake transporter and an H+ -ATPase that lowers the pH of the rhizosphere, is mainly used by non graminaceous plants, including Beta vulgaris. The reduction strategy includes root morphological, physiological and biochemical changes that lead to an increased capacity for Fe uptake. Morphological changes include root tip swelling, development of transfer cells and an increase in the number of lateral roots, leading to an increase in the root surface in contact with the medium. Some plants are able to accumulate and/or release both reducing and chelating substances, such as phenolics and flavins, which may have a role in Fe acquisition. Iron has been shown to down-regulate riboflavin synthesis in flavinogenic yeast strains and some bacteria. In plants, Rbfl and derivatives are accumulated and/ or excreted in Fe-deficient roots and could act as a redox bridge for electron transport to the Fe reductase. Moreover, FRO2 belongs to a super family of flavocytochrome oxidoreductases, and a recent study confirmed that the FRO2 protein contains FAD sequence motifs on the inside of the membrane. Also, a connection between Fe deficiency perception and Rbfl excretion has been described to occur through basic helixloop-helix transcription factors in Arabidopsis thaliana. At the metabolic level, increases in the activity of phosphoenolpyruvate carboxylase and several enzymes of the glycolytic pathway and the tricarboxylic acid cycle have been found in different plant species grown under Fe deficiency.