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Biofertilizers are promoted as a strategy for sustainable intensification of agriculture, but their efficacy varies widely among published studies and it is unclear whether they deliver the promised benefits. Studies are commonly conducted under controlled conditions prior to deployment in the field, yet the predictive value of such studies for field-scale productivity has not been critically examined. A meta-analysis was conducted using a novel host crop-specific approach to evaluate the agronomic potential of bacterial biofertilizers for maize. Yield increases tended to be slightly higher and more variable in greenhouse studies using field soil than in the field, and greenhouse studies poorly predicted the influence of moderating climate, soil and taxonomic variables. We found greater efficacy of Azospirillum spp. and lower efficacy of Bacillus spp. and Enterobacter spp. under field conditions. Surprisingly, biofertilizer strains with confirmed plant-growth-promoting traits such as phosphorus solubilization, nitrogen fixation and phytohormone production in vitro were associated with lower yields in the field than strains not confirmed to possess these traits; only 1-aminocyclopropane-1-carboxylate deaminase synthesis increased yields. These results indicate the need for a novel biofertilizer development framework that integrates information from native soil microbial communities and prioritizes field validation of results.

Agroecosystems are on both the receiving and contributing ends of increasingly demanding climatic and environmental conditions. Maintaining productive systems under resource scarcity and multiplicative stresses requires precise monitoring and systems-scale planning. By incorporating ecological resilience into agroecosystems research we can gain valuable insight into agroecosystem identity, change, responsivity, and performance under stress, but only if we move away from resilience as a mere touchstone concept. Using the productivity, stability, resistance, and recovery of system processes as a basic framework for resilience monitoring, we propose quantitative research approaches to tackle the continuing lack of biophysical, field-scale indicators needed to lend insight into dynamic resilience variables and mechanisms. We emphasize the importance of considering productive functions, sources of system regulation and disturbance, and cross-scale interactions when applying resilience theory to agroecosystems. Agroecosystem resilience research requires understanding of multiple scales and speeds of influence both above and below the focal scale. When these considerations are addressed, resilience theory can add tangible value to agroecosystems research, both for the purposes of monitoring current systems and of planning future systems that can reconcile productivity and sustainability goals.

A common agronomic recommendation is under-seeding red clover to wheat in the corn–soy–wheat rotation. As a leguminous cover crop, red clover boosts agro-ecological resilience and productivity through nitrogen fixation, as well as non-nitrogen-related contributions, such as soil temperature and moisture regulation; reduction of erosion, runoff, and leaching; weed suppression; and interruption of pest and disease cycles. The objective of this paper is to propose a system that extends red clover usage into the corn phase of the corn–soy–wheat rotation as a living mulch. The system incorporates strip-tillage, strip-mowing, as well as banded herbicide and fertilizer application in order to maximize productivity and minimize competition. We analyzed the feasibility of this proposal by examining red clover’s adequacy for the proposed system in comparison with other broadleaf, leguminous cover crops, and assessed potential agro-ecological benefits. We considered logistical components of the proposition, including the use of strip-tillage, the application of precision technology, as well as the opportunity for further technological developments. We found that the proposed system has potential to increase agro-ecological sustainability, resilience, and the overall productivity of this three-year rotation. Thus, this easily-implemented practice should be formally studied.

Continuously flooded rice systems are a major contributor to global rice production and food security. Allowing the soil to dry periodically during the growing season (such as with alternate wetting and drying irrigation - AWD) has been shown to decrease methane emissions, water usage, and heavy metal accumulation in rice grain. However, the effects of AWD on rice yields are variable and not well understood. A two-year study was established to quantify the impacts of a range of treatments differing in AWD severity (degree of soil drying between flooding events) on yield (as well as factors that may affect yields), soil hydrology in the soil profile, and grain arsenic (As) concentrations relative to a continuously flooded control (CF). Three AWD treatments of increasing severity were imposed between full canopy cover (around 45 days after sowing) and 50% heading: AWD-Safe (field was reflooded when the perched water table reached 15 cm below the soil surface) and AWD35 and AWD25 (field was reflooded when the soil volumetric water content at 0–15 cm depth reached 35% and 25%, respectively). During the drying periods, the 0–15 cm soil layer in the AWD-Safe remained saturated, whereas in AWD35 and AWD25 the soil dried to the desired volumetric water contents. In contrast, soil moisture at 25–35 cm below the soil surface was similar across all treatments. Yield was not reduced in any of the AWD treatments, compared to the CF control. There were no consistent differences in yield components, 13C discrimination, and N dynamics. Results suggest that the availability of water and the presence of roots at the 25–35 cm soil depth during the drying periods ensured that the crop did not suffer drought stress and thus yields were maintained. Grain As concentration in the AWD-Safe treatment was similar to that in the CF control but decreased by 56–68% in AWD35 and AWD25. AWD-Safe is often promoted as a means of practicing AWD without reducing yields; however, in this study this practice did not reduce grain As concentration because the soil did not reach an unsaturated state. These findings demonstrate that knowledge of surface and subsurface hydrology, and the root system are important for understanding the potential of AWD.

Many of the foods we eat today look very different than they did in the past. Corn, or maize, did not exist 10,000 years ago: it descended from a weedy grass with tiny hard-shelled seeds that we would not recognize as corn kernels. That wild ancestor of corn, called teosinte, grew in mixtures of many other plants, instead of grows in cornfields like today. Big changes between teosinte and corn that we can see aboveground lead us to think that there have been changes belowground too. Plants form partnerships with microbes, such as bacteria and fungi, to get the nutrients that they need to grow. Scientists are finding that microbes near the roots of teosinte are different than microbes that live around corn roots. Understanding how corn’s microbe partners have changed can help us make corn varieties that are better for the environment.

Diversifying rotations by including winter wheat and red clover in relay cropping provides several advantages to temperate cropping systems dominated by maize and soybean. To improve the environmental and economic benefits of introducing such relay systems, approaches toward wheat N fertilization that consider the negative impact of high N rates on the interseeded legume must be developed. We conducted experiments at 10 locations across Ontario over two years to quantify the effects of N fertilization on soft winter wheat–red clover relay cropping system yields and estimated the N rate at which maximum economic return to N can be achieved. Both crops responded inversely to N fertilization independently of site and year but the competition mechanisms involved were different between the two growing seasons. Whereas the balance between the two species was significantly adjusted to wheat growth response to N and the resulting decrease in radiation reaching the clover canopy in 2006, low precipitation in the summer of 2007 severely affected red clover biomass accumulation. Using economic assumptions to estimate N and forage values of red clover biomass, we show that relay cropping consistently increased the average return to N investment across the N fertility gradient. Under our conditions, N applications at the maximum economic rate (MERN) for wheat grain yield alone significantly decreased the economic benefits of red clover when the forage value of the clover biomass was considered. High N rates also increased the likelihood of non-uniform red clover stands, possibly decreasing red clover benefits and its value as a system component. We demonstrate that reduction in N rates can maximize economic returns from both wheat and red clover and that higher partial profits can be reached using lower N inputs.

The effect of domestication and modern breeding on aboveground traits in maize (Zea mays) has been well-characterized, but the impact on root systems and the rhizosphere remain unclear. The transition from wild ecosystems to modern agriculture has focused on selecting traits that yielded the largest aboveground production with increasing levels of crop management and nutrient inputs. Root morphology, anatomy, and ecophysiological processes may have been affected by the substantial environmental and genetic shifts associated with this transition. As a result, root and rhizosphere traits that allow more efficient foraging and uptake in lower synthetic input environments might have been lost. The development of modern maize has led to a shift in microbiome community composition, but questions remain as to the dynamics and drivers of this change during maize evolution and its implications for resource acquisition and agroecosystem functioning under different management practices. Better understanding of how domestication and breeding affected root and rhizosphere microbial traits could inform breeding strategies, facilitate the sourcing of favorable alleles, and open new frontiers to improve resource use efficiency through greater integration of root development and ecophysiology with agroecosystem functioning.

Examination of wild ancestors can identify which traits have been altered by selection as possible targets for genetic improvement. We investigated the whole plant response to low nitrogen (LN), especially below ground, by the wild ancestor of modern maize (Zea mays L.), Balsas teosinte (Zea mays subsp. parviglumis H. H. Iltis & Doebley). Teosinte responded to LN by reducing the shoot N concentration and increasing the root:shoot biomass ratio. The lengths of individual crown roots and the total lateral root length increased, compensated by reduced crown root number. Low N caused a decrease in total root hair (RH) length and increased expression of high affi nity nitrate transporters. To facilitate future mapping studies, these results were compared to a modern inbred (‘W22’) used as the parent in a modern maize × teosinte population and extensively employed in maize domestication studies. The adaptations to LN in teosinte and W22 were surprisingly conserved, but the strategies employed were often different. To reduce total RH length, teosinte reduced RH density whereas W22 reduced average RH length. To achieve reduced shoot biomass in response to LN, teosinte reduced tiller number and hence leaf number whereas W22 reduced average leaf size. Since tiller crown roots initiate from stem tissue, teosinte used tiller plasticity to reduce crown root number whereas modern maize reduced crown root number independently of tillering. We discuss the implications of these results for maize domestication.

There is interest in discovering root traits associated with acclimation to nutrient stress. Large root systems, such as in adult maize, have proven difficult to be phenotyped comprehensively and over time, causing target traits to be missed. These challenges were overcome here using aeroponics, a system where roots grow in the air misted with a nutrient solution. Applying an agriculturally relevant degree of low nitrogen (LN) stress, 30-day-old plants responded by increasing lengths of individual crown roots (CRs) by 63%, compensated by a 40% decline in CR number. LN increased the CR elongation rate rather than lengthening the duration of CR growth. Only younger CR were significantly responsive to LN stress, a novel finding. LN shifted the root system architectural balance, increasing the lateral root (LR)-to-CR ratio, adding ∼70 m to LR length. LN caused a dramatic increase in second-order LR density, not previously reported in adult maize. Despite the near-uniform aeroponics environment, LN induced increased variation in the relative lengths of opposing LR pairs. Large-scale analysis of root hairs (RHs) showed that LN decreased RH length and density. Time-course experiments suggested the RH responses may be indirect consequences of decreased biomass/demand under LN. These results identify novel root traits for genetic dissection.

Solanum tuberosum cultivars, Solanum tuberosum × Solanum tuberosum subsp. andigena hybrids and breeding clones with different time to maturity were screened for drought tolerance in field plots located in the coastal desert of Peru. Variation for drought tolerance was illustrated by clone-dependent differences in tuber yield and yield loss under drought conditions. Neither changes in stomatal conductance nor maximum quantum yield of chlorophyll fluorescence were quantitatively associated with yield or yield loss under drought. In contrast, relative vegetation index (reflectance at 800 nm / reflectance at 650 nm) and normalized difference vegetation index [(reflectance at 800 nm – reflectance at 650 nm) / (reflectance at 800 nm + reflectance at 650 nm)] on day 25 and day 40 after drought were correlated with yield. The vegetation indices are related to leaf area index and above ground biomass, which appeared to be major determinants for yield in the tested cultivars under drought. Nitrate reductase activity was significantly decreased in drought-exposed plants, but activity depletion was independent of yield or yield maintenance. Putative drought tolerance genes were differentially expressed in leaves of water stressed genotypes. Induction of the protein phosphatase 2C gene was positively associated with yield maintenance under drought. Furthermore, tolerant cultivars expressed DREB transcription factor to a higher extent than susceptible cultivars. By ranking 16 cultivars with respect to yield maintenance under drought, we identified canopy size and up-regulation of drought tolerance genes as contributors to drought tolerance.

Six potato varieties belonging to four different sub-species were submitted to drought stress during tuberization under controlled field conditions, resulting in contrasting responses of the genotypes to water stress with yield losses varying between 27 and 75%. In all clones free proline accumulated under drought, however, proline levels increased earlier in drought-susceptible varieties than in more tolerant ones. The expression of two key genes in proline metabolism, Δ1-pyrroline-5-carboxylate synthase and proline dehydrogenase, was monitored in the leaves of the experimental plants by real time PCR 23 and 42 days after drought onset. Expression of both enzymes did not correlate with the proline levels found in leaf tissue indicating that mechanisms other than transcription participate in the regulation of proline accumulation in potato leaves.

Cropping sequence diversification provides a systems approach to reduce yield variations and improve resilience to multiple environmental stresses. Yield advantages of more diverse crop rotations and their synergistic effects with reduced tillage are well documented, but few studies have quantified the impact of these management practices on yields and their stability when soil moisture is limiting or in excess. Using yield and weather data obtained from a 31-year long term rotation and tillage trial in Ontario, we tested whether crop rotation diversity is associated with greater yield stability when abnormal weather conditions occur. We used parametric and non-parametric approaches to quantify the impact of rotation diversity (monocrop, 2-crops, 3-crops without or with one or two legume cover crops) and tillage (conventional or reduced tillage) on yield probabilities and the benefits of crop diversity under different soil moisture and temperature scenarios. Although the magnitude of rotation benefits varied with crops, weather patterns and tillage, yield stability significantly increased when corn and soybean were integrated into more diverse rotations. Introducing small grains into short corn-soybean rotation was enough to provide substantial benefits on long-term soybean yields and their stability while the effects on corn were mostly associated with the temporal niche provided by small grains for underseeded red clover or alfalfa. Crop diversification strategies increased the probability of harnessing favorable growing conditions while decreasing the risk of crop failure. In hot and dry years, diversification of corn-soybean rotations and reduced tillage increased yield by 7% and 22% for corn and soybean respectively. Given the additional advantages associated with cropping system diversification, such a strategy provides a more comprehensive approach to lowering yield variability and improving the resilience of cropping systems to multiple environmental stresses. This could help to sustain future yield levels in challenging production environments.

Background There was ancient human selection on the wild progenitor of modern maize, Balsas teosinte, for decreased shoot branching (tillering), in order to allow more nutrients to be diverted to grain. Mechanistically, the decline in shoot tillering has been associated with selection for increased expression of the major domestication gene Teosinte Branched 1 (Tb1) in shoot primordia. Therefore, TB1 has been defined as a repressor of shoot branching. It is known that plants respond to changes in shoot size by compensatory changes in root growth and architecture. However, it has not been reported whether altered TB1 expression affects any plant traits below ground. Previously, changes in dosage of a well-studied mutant allele of Tb1 in modern maize, called tb1-ref, from one to two copies, was shown to increase tillering. As a result, plants with two copies of the tb1-ref allele have a larger shoot biomass than heterozygotes. Here we used aeroponics to phenotype the effects of tb1-ref copy number on maize roots at macro-, meso- and micro scales of development. Results An increase in the tb1-ref copy number from one to two copies resulted in: (1) an increase in crown root number due to the cumulative initiation of crown roots from successive tillers; (2) higher density of first and second order lateral roots; and (3) reduced average lateral root length. The resulting increase in root system biomass in homozygous tb1-ref mutants balanced the increase in shoot biomass caused by enhanced tillering. These changes caused homozygous tb1-ref mutants of modern maize to more closely resemble its ancestor Balsas teosinte below ground. Conclusion We conclude that a decrease in TB1 function in maize results in a larger root system, due to an increase in the number of crown roots and lateral roots. Given that decreased TB1 expression results in a more highly branched and larger shoot, the impact of TB1 below ground may be direct or indirect. We discuss the potential implications of these findings for whole plant coordination of biomass accumulation and maize domestication.

Numerous transgenes have been reported to increase rice drought resistance, mostly in small-scale experiments under vegetative-stage drought stress, but few studies have included grain yield or field evaluations. Different definitions of drought resistance are currently in use for field-based and laboratory evaluations of transgenics, the former emphasizing plant responses that may not be linked to yield under drought. Although those fundamental studies use efficient protocols to uncover and validate gene functions, screening conditions differ greatly from field drought environments where the onset of drought stress symptoms is slow (2-3 weeks). Simplified screening methods, including severely stressed survival studies, are therefore not likely to identify transgenic events with better yield performance under drought in the target environment. As biosafety regulations are becoming established to allow field trials in some rice-producing countries, there is a need to develop relevant screening procedures that scale from preliminary event selection to greenhouse and field trials. Multilocation testing in a range of drought environments may reveal that different transgenes are necessary for different types of drought-prone field conditions. We describe here a pipeline to improve the selection efficiency and reproducibility of results across drought treatments and test the potential of transgenic rice for the development of drought-resistant material for agricultural purposes.

A key strategy for climate change adaptation in the rain-fed northern Corn Belt is to decrease cropping system vulnerability to changes in precipitation patterns by building resilience. Using 50- year of county level yield and environmental data from Iowa and Ontario, we first demonstrate that sensitivity of corn yield to precipitation, particularly in July and August, has increased over the past five decades despite no changes in precipitation patterns. This can be attributed to steady improvement in corn yield potential and so plant water demand since the mid-20th century and removal of non-water constraints to crop production. Such vulnerability of corn-based cropping systems to water limitations is of increasing concern as climate change models predict higher summer temperatures and year-to-year variations in precipitations in this region. As suggested in the ecology literature, increasing agroecosystem temporal and spacial diversity is one of the key management strategies to deal with impending weather variability. Using yield and environmental data from a 30-year long-term rotation and tillage trial in Ontario, we show that diversification of short corn-based rotations using small grains and forage crops increases corn yield stability and resilience to both limiting and excess soil moisture1. We also demonstrate the importance of conservation tillage and measured the impact of rotation and tillage history on plants ability to access water resources, plant available soil water and their combined effects on timing of physiological water stress and grain yield when drought occurs at reproductive stages. Our results emphasize the growing importance of developing strategies for managing soil moisture in rain-fed regions and the significance of agroecological approaches to develop hardy agricultural systems and protect food and feed production against the upcoming extreme weather events.

Responses to prolonged drought and recovery from drought of two South American potato (Solanum tuberosum L. ssp. andigena (Juz & Buk) Hawkes) landraces, Sullu and Ccompis were compared under field conditions. Physiological and biomass measurements, yield analysis, the results of hybridisation to a potato microarray platform (44 000 probes) and metabolite profiling were used to characterise responses to water deficit. Drought affected shoot and root biomass negatively in Ccompis but not in Sullu, whereas both genotypes maintained tuber yield under water stress. Ccompis showed stronger reduction in maximum quantum yield under stress than Sullu, and less decrease in stomatal resistance. Genes associated with PSII functions were activated during recovery in Sullu only. Evidence for sucrose accumulation in Sullu only during maximum stress and recovery was observed, in addition to increases in cell wall biosynthesis. A depression in the abundance of plastid superoxide dismutase transcripts was observed under maximum stress in Ccompis. Both sucrose and the regulatory molecule trehalose accumulated in the leaves of Sullu only. In contrast, in Ccompis, the raffinose oligosaccharide family pathway was activated, whereas low levels of sucrose and minor stress-mediated changes in trehalose were observed. Proline, and expression of the associated genes, rose in both genotypes under drought, with a 3-fold higher increase in Sullu than in Ccompis. The results demonstrate the presence of distinct molecular and biochemical drought responses in the two potato landraces leading to yield maintenance but differential biomass accumulation in vegetative tissues.

Candidate traits for drought tolerance were targeted by analyzing water stress responses in two moderately drought-tolerant native Andean potato clones, SA2563 and Sullu (Solanum tuberosum L. subsp, andigena (Juz, Bukasov) Hawkes) under field conditions. SA2563 exhibited increased root growth under drought, while Sullu retained a higher relative leaf water content. Gene expression profiling using the TIGR 10 K microarray revealed 1713 significantly differentially expressed genes, 186 of these genes were up-regulated in both clones. In addition to these commonly up-regulated genes, each clone induced a specific gene set in response to drought. Gene expression and metabolite analysis pinpointed candidate traits for drought tolerance present either in one or both of the clones under investigation. These traits included osmotic adjustment, changes in carbohydrate metabolism, membrane modifications, strengthening of cuticle and cell rescue mechanisms, such as detoxification of oxygen radicals and protein stabilization. Many of the up-regulated genes have been identified previously in laboratory studies on model plants using shock treatments, and the present study confirms the importance of these factors under field conditions.

Resistance to antibiotics mediated by selectable marker genes remains a powerful selection tool for transgenic event production. However, regulatory agencies and consumer concerns favor these to be eliminated from food crops. Several excision systems exist but none have been optimized or shown to be functional for clonally propagated crops. The excision of the nptII gene conferring resistance to kanamycin has been achieved here using a gene construct based on a heat-inducible cre gene producing a recombinase that eliminates cre and nptII genes flanked by two loxP sites. First-generation regenerants with the Cre-loxP system were obtained by selection on kanamycin media. Following a heat treatment, second generation regenerants were screened for excision by PCR using nptII, cre, and T-DNA borders primers. Excision efficiency appeared to be at 4.7% depending on the heat treatment. The footprint of the excision was shown by sequencing between T-DNA borders to correspond to a perfect recombination event. Selectable marker-free sprouts were also obtained from tubers of transgenic events when submitted to similar heat treatment at 4% frequency. Spontaneous excision was not observed out of 196 regenerants from untreated transgenic explants. Biosafety concerns are minimized because the expression of cre gene driven by the hsp70 promoter of Drosophila melanogaster was remarkably low even under heat activation and no functional loxP site were found in published Solanum sequence database. A new plant transformation vector pCIP54/55 was developed including a multiple cloning site and the self-excision system which should be a useful tool not only for marker genes in potato but for any gene or sequence removal in any plant.