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1.  Complementarity in root architecture for nutrient uptake in ancient maize/bean and maize/bean/squash polycultures 
Annals of Botany  2012;110(2):521-534.
Background and Aims
During their domestication, maize, bean and squash evolved in polycultures grown by small-scale farmers in the Americas. Polycultures often overyield on low-fertility soils, which are a primary production constraint in low-input agriculture. We hypothesized that root architectural differences among these crops causes niche complementarity and thereby greater nutrient acquisition than corresponding monocultures.
Methods
A functional–structural plant model, SimRoot, was used to simulate the first 40 d of growth of these crops in monoculture and polyculture and to determine the effects of root competition on nutrient uptake and biomass production of each plant on low-nitrogen, -phosphorus and -potassium soils.
Key Results
Squash, the earliest domesticated crop, was most sensitive to low soil fertility, while bean, the most recently domesticated crop, was least sensitive to low soil fertility. Nitrate uptake and biomass production were up to 7 % greater in the polycultures than in the monocultures, but only when root architecture was taken into account. Enhanced nitrogen capture in polycultures was independent of nitrogen fixation by bean. Root competition had negligible effects on phosphorus or potassium uptake or biomass production.
Conclusions
We conclude that spatial niche differentiation caused by differences in root architecture allows polycultures to overyield when plants are competing for mobile soil resources. However, direct competition for immobile resources might be negligible in agricultural systems. Interspecies root spacing may also be too large to allow maize to benefit from root exudates of bean or squash. Above-ground competition for light, however, may have strong feedbacks on root foraging for immobile nutrients, which may increase cereal growth more than it will decrease the growth of the other crops. We note that the order of domestication of crops correlates with increasing nutrient efficiency, rather than production potential.
doi:10.1093/aob/mcs082
PMCID: PMC3394648  PMID: 22523423
‘Three sisters’; polyculture; root architecture; SimRoot; functional–structural model; nutrient deficiency; maize; bean; squash; niche complementarity; root competition
2.  Assess suitability of hydroaeroponic culture to establish tripartite symbiosis between different AMF species, beans, and rhizobia 
BMC Plant Biology  2009;9:73.
Background
Like other species of the Phaseoleae tribe, common bean (Phaseolus vulgaris L.) has the potential to establish symbiosis with rhizobia and to fix the atmospheric dinitrogen (N2) for its N nutrition. Common bean has also the potential to establish symbiosis with arbuscular mycorrhizal fungi (AMF) that improves the uptake of low mobile nutrients such as phosphorus, from the soil. Both rhizobial and mycorrhizal symbioses can act synergistically in benefits on plant.
Results
The tripartite symbiosis of common bean with rhizobia and arbuscular mycorrhizal fungi (AMF) was assessed in hydroaeroponic culture with common bean (Phaseolus vulgaris L.), by comparing the effects of three fungi spp. on growth, nodulation and mycorrhization of the roots under sufficient versus deficient P supplies, after transfer from initial sand culture. Although Glomus intraradices Schenck & Smith colonized intensely the roots of common bean in both sand and hydroaeroponic cultures, Gigaspora rosea Nicolson & Schenck only established well under sand culture conditions, and no root-colonization was found with Acaulospora mellea Spain & Schenck under either culture conditions. Interestingly, mycorrhization by Glomus was also obtained by contact with mycorrhized Stylosanthes guianensis (Aubl.) sw in sand culture under deficient P before transfer into hydroaeroponic culture. The effect of bean genotype on both rhizobial and mycorrhizal symbioses with Glomus was subsequently assessed with the common bean recombinant inbreed line 7, 28, 83, 115 and 147, and the cultivar Flamingo. Significant differences among colonization and nodulation of the roots and growth among genotypes were found.
Conclusion
The hydroaeroponic culture is a valuable tool for further scrutinizing the physiological interactions and nutrient partitioning within the tripartite symbiosis.
doi:10.1186/1471-2229-9-73
PMCID: PMC2713235  PMID: 19534785
3.  Optimizing reproductive phenology in a two-resource world: a dynamic allocation model of plant growth predicts later reproduction in phosphorus-limited plants 
Annals of Botany  2011;108(2):391-404.
Background and Aims
Timing of reproduction is a key life-history trait that is regulated by resource availability. Delayed reproduction in soils with low phosphorus availability is common among annuals, in contrast to the accelerated reproduction typical of other low-nutrient environments. It is hypothesized that this anomalous response arises from the high marginal value of additional allocation to root growth caused by the low mobility of phosphorus in soils.
Methods
To better understand the benefits and costs of such delayed reproduction, a two-resource dynamic allocation model of plant growth and reproduction is presented. The model incorporates growth, respiration, and carbon and phosphorus acquisition of both root and shoot tissue, and considers the reallocation of resources from senescent leaves. The model is parameterized with data from Arabidopsis and the optimal reproductive phenology is explored in a range of environments.
Key Results
The model predicts delayed reproduction in low-phosphorus environments. Reproductive timing in low-phosphorus environments is quite sensitive to phosphorus mobility, but is less sensitive to the temporal distribution of mortality risks. In low-phosphorus environments, the relative metabolic cost of roots was greater, and reproductive allocation reduced, compared with high-phosphorus conditions. The model suggests that delayed reproduction in response to low phosphorus availability may be reduced in plants adapted to environments where phosphorus mobility is greater.
Conclusions
Delayed reproduction in low-phosphorus soils can be a beneficial response allowing for increased acquisition and utilization of phosphorus. This finding has implications both for efforts to breed crops for low-phosphorus soils, and for efforts to understand how climate change may impact plant growth and productivity in low-phosphorus environments.
doi:10.1093/aob/mcr143
PMCID: PMC3143053  PMID: 21712299
Dynamic allocation budget; optimization; Arabidopsis thaliana; flowering phenology; root–shoot partitioning; phosphorus availability
4.  Is the Inherent Potential of Maize Roots Efficient for Soil Phosphorus Acquisition? 
PLoS ONE  2014;9(3):e90287.
Sustainable agriculture requires improved phosphorus (P) management to reduce the overreliance on P fertilization. Despite intensive research of root adaptive mechanisms for improving P acquisition, the inherent potential of roots for efficient P acquisition remains unfulfilled, especially in intensive agriculture, while current P management generally focuses on agronomic and environmental concerns. Here, we investigated how levels of soil P affect the inherent potential of maize (Zea mays L.) roots to obtain P from soil. Responses of root morphology, arbuscular mycorrhizal colonization, and phosphate transporters were characterized and related to agronomic traits in pot and field experiments with soil P supply from deficiency to excess. Critical soil Olsen-P level for maize growth approximated 3.2 mg kg−1, and the threshold indicating a significant environmental risk was about 15 mg kg−1, which represented the lower and upper levels of soil P recommended in current P management. However, most root adaptations involved with P acquisition were triggered when soil Olsen-P was below 10 mg kg−1, indicating a threshold for maximum root inherent potential. Therefore, to maintain efficient inherent potential of roots for P acquisition, we suggest that the target upper level of soil P in intensive agriculture should be reduced from the environmental risk threshold to the point maximizing the inherent potential of roots.
doi:10.1371/journal.pone.0090287
PMCID: PMC3940875  PMID: 24594677
5.  Lysigenous aerenchyma formation in maize root is confined to cortical cells by regulation of genes related to generation and scavenging of reactive oxygen species 
Plant Signaling & Behavior  2011;6(5):759-761.
To adapt to waterlogging, maize (Zea mays) forms lysigenous aerenchyma in root cortex as a result of ethylene-promoted programmed cell death (PCD). Respiratory burst oxidase homolog (RBOH) gene encodes a homolog of gp91phox in NADPH oxidase, and has a role in the generation of reactive oxygen species (ROS). Recently, we found that during aerenchyma formation, RBOH was upregulated in all maize root tissues examined, whereas an ROS scavengingrelated metallothionein (MT) gene was downregulated specifically in cortical cells. Together these changes should lead to high accumulations of ROS in root cortex, thereby inducing PCD for aerenchyma formation. As further evidence of the involvement of ROS in root aerenchyma formation, the PCD was inhibited by diphenyleneiodonium (DPI), an NADPH oxidase inhibitor. Based on these results, we propose a model of cortical cell-specific PCD for root aerenchyma formation.
doi:10.4161/psb.6.5.15417
PMCID: PMC3172858  PMID: 21502817
aerenchyma; ethylene; laser microdissection; maize (Zea mays); metallothionein; programmed cell death; reactive oxygen species; respiratory burst oxidase homolog
6.  Responses of root architecture development to low phosphorus availability: a review 
Annals of Botany  2012;112(2):391-408.
Background
Phosphorus (P) is an essential element for plant growth and development but it is often a limiting nutrient in soils. Hence, P acquisition from soil by plant roots is a subject of considerable interest in agriculture, ecology and plant root biology. Root architecture, with its shape and structured development, can be considered as an evolutionary response to scarcity of resources.
Scope
This review discusses the significance of root architecture development in response to low P availability and its beneficial effects on alleviation of P stress. It also focuses on recent progress in unravelling cellular, physiological and molecular mechanisms in root developmental adaptation to P starvation. The progress in a more detailed understanding of these mechanisms might be used for developing strategies that build upon the observed explorative behaviour of plant roots.
Conclusions
The role of root architecture in alleviation of P stress is well documented. However, this paper describes how plants adjust their root architecture to low-P conditions through inhibition of primary root growth, promotion of lateral root growth, enhancement of root hair development and cluster root formation, which all promote P acquisition by plants. The mechanisms for activating alterations in root architecture in response to P deprivation depend on changes in the localized P concentration, and transport of or sensitivity to growth regulators such as sugars, auxins, ethylene, cytokinins, nitric oxide (NO), reactive oxygen species (ROS) and abscisic acid (ABA). In the process, many genes are activated, which in turn trigger changes in molecular, physiological and cellular processes. As a result, root architecture is modified, allowing plants to adapt effectively to the low-P environment. This review provides a framework for understanding how P deficiency alters root architecture, with a focus on integrated physiological and molecular signalling.
doi:10.1093/aob/mcs285
PMCID: PMC3698383  PMID: 23267006
Low phosphate; phosphorus acquisition; primary root; lateral root; root hair; cluster root; sugars; auxins; ethylene; cytokinins; nitric oxide; reactive oxygen species
7.  Phosphate starvation of maize inhibits lateral root formation and alters gene expression in the lateral root primordium zone 
BMC Plant Biology  2012;12:89.
Background
Phosphorus (P) is an essential macronutrient for all living organisms. Maize (Zea mays) is an important human food, animal feed and energy crop throughout the world, and enormous quantities of phosphate fertilizer are required for maize cultivation. Thus, it is important to improve the efficiency of the use of phosphate fertilizer for maize.
Results
In this study, we analyzed the maize root response to phosphate starvation and performed a transcriptomic analysis of the 1.0-1.5 cm lateral root primordium zone. In the growth of plants, the root-to-shoot ratio (R/L) was reduced in both low-phosphate (LP) and sufficient-phosphate (SP) solutions, but the ratio (R/L) exhibited by the plants in the LP solution was higher than that of the SP plants. The growth of primary roots was slightly promoted after 6 days of phosphate starvation, whereas the numbers of lateral roots and lateral root primordia were significantly reduced, and these differences were increased when associated with the stress caused by phosphate starvation. Among the results of a transcriptomic analysis of the maize lateral root primordium zone, there were two highlights: 1) auxin signaling participated in the response and the modification of root morphology under low-phosphate conditions, which may occur via local concentration changes due to the biosynthesis and transport of auxin, and LOB domain proteins may be an intermediary between auxin signaling and root morphology; and 2) the observed retardation of lateral root development was the result of co-regulation of DNA replication, transcription, protein synthesis and degradation and cell growth.
Conclusions
These results indicated that maize roots show a different growth pattern than Arabidopsis under low-phosphate conditions, as the latter species has been observed to halt primary root growth when the root tip comes into contact with low-phosphate media. Moreover, our findings enrich our understanding of plant responses to phosphate deficits and of root morphogenesis in maize.
doi:10.1186/1471-2229-12-89
PMCID: PMC3463438  PMID: 22704465
Maize; Phosphate starvation; Root development; Transcriptomic analysis
8.  Heterogeneity in Spatial P-distribution and Foraging Capability by Zea mays: Effects of Patch Size and Barriers to Restrict Root Proliferation within a Patch 
Annals of Botany  2006;98(6):1271-1277.
• Background and Aims Localized proliferation of roots in nutrient-enriched patches seems to be an adaptive response in many plants, but its function is still debatable. To understand the efficiency and limitation of foraging behaviour, the impact of patch size and the presence or absence of a barrier to root proliferation within phosphorus (P)-enriched patches was examined.
• Methods In pots filled with P-poor soil, six treatments of heterogeneous P supply were prepared: three patch sizes with or without a root barrier between patches. In addition, a homogeneous P supply treatment was also prepared. Irrespective of these treatments, each pot received the same total amount of P. Maize (Zea mays) was grown in each pot for 45 d in a greenhouse.
• Key Results P content and biomass were greatest in plants grown in the largest patch due to successful root proliferation, and were higher in the presence of a root barrier. Interestingly, plants preferentially developed adventitious nodal roots projecting from the stem into the P-enriched soil, particularly in the largest patch with a root barrier. Removal of the barrier reduced the P-uptake capacity per unit root surface area or volume in P-enriched patches, revealing that the P-uptake capacity per root can be suppressed even in P-rich soil if other portions on the root axis encounter P-poor conditions.
• Conclusions The results suggest that the efficiency of root morphological plasticity is largely determined by the size of the P-enriched patch. Furthermore, the results imply a novel aspect of P-uptake physiology that roots in heterogeneous P cannot demonstrate their potential capacity, as would be observed in roots encountering P continuously; this effect is probably mediated by an internal root factor.
doi:10.1093/aob/mcl216
PMCID: PMC3292275  PMID: 17008353
Phenotypic plasticity; phosphate acquisition; resource foraging; root length; root surface area; root volume; Zea mays
9.  Nitrogen regulation of transpiration controls mass-flow acquisition of nutrients 
Journal of Experimental Botany  2013;65(1):159-168.
To test whether N regulates transpiration, Phaseolus vulgaris was grown with N placed at one of six distances behind a root-impenetrable mesh whilst control plants intercepted the N-source. N-availability regulated transpiration-driven mass-flow of nutrients from soil zones that were inaccessible
Transpiration may enhance mass-flow of nutrients to roots, especially in low-nutrient soils or where the root system is not extensively developed. Previous work suggested that nitrogen (N) may regulate mass-flow of nutrients. Experiments were conducted to determine whether N regulates water fluxes, and whether this regulation has a functional role in controlling the mass-flow of nutrients to roots. Phaseolus vulgaris were grown in troughs designed to create an N availability gradient by restricting roots from intercepting a slow-release N source, which was placed at one of six distances behind a 25 μm mesh from which nutrients could move by diffusion or mass-flow (termed ‘mass-flow’ treatment). Control plants had the N source supplied directly to their root zone so that N was available through interception, mass-flow, and diffusion (termed ‘interception’ treatment). ‘Mass-flow’ plants closest to the N source exhibited 2.9-fold higher transpiration (E), 2.6-fold higher stomatal conductance (g s), 1.2-fold higher intercellular [CO2] (C i), and 3.4-fold lower water use efficiency than ‘interception’ plants, despite comparable values of photosynthetic rate (A). E, g s, and C i first increased and then decreased with increasing distance from the N source to values even lower than those of ‘interception’ plants. ‘Mass-flow’ plants accumulated phosphorus and potassium, and had maximum concentrations at 10mm from the N source. Overall, N availability regulated transpiration-driven mass-flow of nutrients from substrate zones that were inaccessible to roots. Thus when water is available, mass-flow may partially substitute for root density in providing access to nutrients without incurring the costs of root extension, although the efficacy of mass-flow also depends on soil nutrient retention and hydraulic properties.
doi:10.1093/jxb/ert367
PMCID: PMC3883293  PMID: 24231035
Interception; phosphate; potassium; urea; water flux; water use efficiency.
10.  Combined inoculation with Glomus intraradices and Rhizobium tropici CIAT899 increases phosphorus use efficiency for symbiotic nitrogen fixation in common bean (Phaseolus vulgaris L.) 
This study compared the response of common bean (Phaseolus vulgaris L.) to arbuscular mycorrhizal fungi (AMF) and rhizobia strain inoculation. Two common bean genotypes i.e. CocoT and Flamingo varying in their effectiveness for nitrogen fixation were inoculated with Glomus intraradices and Rhizobium tropici CIAT899, and grown for 50 days in soil–sand substrate in glasshouse conditions. Inoculation of common bean plants with the AM fungi resulted in a significant increase in nodulation compared to plants without inoculation. The combined inoculation of AM fungi and rhizobia significantly increased various plant growth parameters compared to simple inoculated plants. In addition, the combined inoculation of AM fungi and rhizobia resulted in significantly higher nitrogen and phosphorus accumulation in the shoots of common bean plants and improved phosphorus use efficiency compared with their controls, which were not dually inoculated. It is concluded that inoculation with rhizobia and arbuscular mycorrhizal fungi could improve the efficiency in phosphorus use for symbiotic nitrogen fixation especially under phosphorus deficiency.
doi:10.1016/j.sjbs.2011.11.003
PMCID: PMC3730892  PMID: 23961175
Arbuscular mycorrhizal fungi; Glomus intraradices; Nitrogen fixation; Phaseolus vulgaris; Phosphorus; Rhizobia; Symbiosis
11.  High phosphate reduces host ability to develop arbuscular mycorrhizal symbiosis without affecting root calcium spiking responses to the fungus 
The arbuscular mycorrhizal symbiosis associates soil fungi with the roots of the majority of plants species and represents a major source of soil phosphorus acquisition. Mycorrhizal interactions begin with an exchange of molecular signals between the two partners. A root signaling pathway is recruited, for which the perception of fungal signals triggers oscillations of intracellular calcium concentration. High phosphate availability is known to inhibit the establishment and/or persistence of this symbiosis, thereby favoring the direct, non-symbiotic uptake of phosphorus by the root system. In this study, Medicago truncatula plants were used to investigate the effects of phosphate supply on the early stages of the interaction. When plants were supplied with high phosphate fungal attachment to the roots was drastically reduced. An experimental system was designed to individually study the effects of phosphate supply on the fungus, on the roots, and on root exudates. These experiments revealed that the most important effects of high phosphate supply were on the roots themselves, which became unable to host mycorrhizal fungi even when these had been appropriately stimulated. The ability of the roots to perceive their fungal partner was then investigated by monitoring nuclear calcium spiking in response to fungal signals. This response did not appear to be affected by high phosphate supply. In conclusion, high levels of phosphate predominantly impact the plant host, but apparently not in its ability to perceive the fungal partner.
doi:10.3389/fpls.2013.00426
PMCID: PMC3810610  PMID: 24194742
mycorrhiza; phosphate; symbiosis; molecular signaling; calcium spiking; chito-oligosaccharides
12.  Integration of root phenes for soil resource acquisition 
Suboptimal availability of water and nutrients is a primary limitation to plant growth in terrestrial ecosystems. The acquisition of soil resources by plant roots is therefore an important component of plant fitness and agricultural productivity. Plant root systems comprise a set of phenes, or traits, that interact. Phenes are the units of the plant phenotype, and phene states represent the variation in form and function a particular phene may take. Root phenes can be classified as affecting resource acquisition or utilization, influencing acquisition through exploration or exploitation, and in being metabolically influential or neutral. These classifications determine how one phene will interact with another phene, whether through foraging mechanisms or metabolic economics. Phenes that influence one another through foraging mechanisms are likely to operate within a phene module, a group of interacting phenes, that may be co-selected. Examples of root phene interactions discussed are: (1) root hair length × root hair density, (2) lateral branching × root cortical aerenchyma (RCA), (3) adventitious root number × adventitious root respiration and basal root growth angle (BRGA), (4) nodal root number × RCA, and (5) BRGA × root hair length and density. Progress in the study of phenes and phene interactions will be facilitated by employing simulation modeling and near-isophenic lines that allow the study of specific phenes and phene combinations within a common phenotypic background. Developing a robust understanding of the phenome at the organismal level will require new lines of inquiry into how phenotypic integration influences plant function in diverse environments. A better understanding of how root phenes interact to affect soil resource acquisition will be an important tool in the breeding of crops with superior stress tolerance and reduced dependence on intensive use of inputs.
doi:10.3389/fpls.2013.00355
PMCID: PMC3771073  PMID: 24062755
root architecture; phenomics; functional traits; ideotype; soil resources
13.  Expression of the ethylene biosynthetic machinery in maize roots is regulated in response to hypoxia 
Journal of Experimental Botany  2009;61(3):857-871.
Ethylene regulates plant growth in response to many adverse environmental conditions, including the induction of aerenchyma, i.e. the formation of air spaces, in flooded roots in an effort to maintain oxygen levels. In this work, quantitative RT-PCR and in situ RNA hybridization were used to determine how the expression of the ethylene biosynthetic machinery in maize roots is spatially and temporally regulated following exposure to 4% oxygen (i.e. hypoxia) for up to 24 h, conditions that induced aerenchyma formation in the fully-expanded region of the root and reduced cytoplasmic density throughout the root. Expression of ACC oxidase, the ethylene forming enzyme, was observed in the root cap, protophloem sieve elements, and companion cells associated with metaphloem sieve elements. Exposure to 4% oxygen induced ACC oxidase expression in these cell types as well as in the root cortex. ACC synthase, which generates the ethylene precursor, was expressed in the root cap and the cortex and its expression was induced in cortical cells following low oxygen treatment. The induction of expression of the ethylene biosynthetic machinery was accompanied by an induction of ethylene evolution and a reduced rate of root growth. These results suggest that maize roots respond to conditions of hypoxia by inducing the spatially restricted expression of the ethylene biosynthetic machinery, resulting in increased ethylene production.
doi:10.1093/jxb/erp362
PMCID: PMC2814119  PMID: 20008461
ACC oxidase; ACC synthase; ethylene; hypoxia; maize; root growth
14.  Pathogenicity of Pratylenchus penetrans to Navy Bean (Phaseolus vulgaris L.) 
Journal of Nematology  1985;17(2):81-85.
The pathogenicity of Pratylenchus penetrans (root-lesion nematode) to Phaseolus vulgaris (navy bean) was evaluated in greenhouse experiments. Shoot and root fresh weight of cv. Sanilac plants were increased 4 and 21%, respectively, by an initial population density (Pi) of 25 P. penetrans per 100 cm³ soil. Leaf area and shoot fresh and dry weights were decreased by a Pi of 50 or more P. penetrans per 100 cm³ soil. A significant positive linear relationship existed between initial soil population densities of P. penetrans and final soil and root population densities of this nematode. Three dry bean cultivars, Sanilac, Seafarer, and Tuscola, were susceptible to P. penetrans, and yields were reduced by 43-76% when plants were exposed to a Pi of 150 P. penetrans per 100 cm³ soil. P. penetrans also reproduced on bean cultivars Saginaw, Gratiot, and Kentwood, but did not decrease bean yields, suggesting that these cultivars were tolerant to this nematode.
PMCID: PMC2618433  PMID: 19294063
root-lesion nematode; bean yields; cultivars; population densities
15.  Population dynamics and identification of efficient strains of Azospirillum in maize ecosystems of Bihar (India) 
3 Biotech  2011;1(4):247-253.
Information on inoculum load and diversity of native microbial community is an important prerequisite for crop management of microbial origin. Azospirillum has a proven role in benefiting the maize (Zea mays) crop in terms of nutrient (nitrogen) supply as well as plant growth enhancement. Bihar state has highest average national maize productivity although fertilizer consumption is minimum, indicating richness of Azospirillum both in terms of population and diversity in soils. An experiment was planned to generate basic information on Azospirillum population variation in maize soils under different agricultural practices and soil types of Bihar, to identify suitable agricultural practices supporting the target microorganism and efficient Azospirillum strain(s). No tillage, growing traditional maize cultivar, land use history (diara soil having history of maize cultivation), soil organic carbon (>1%) and intercrop with oat supported prevalence of Azospirillum in maize rhizosphere. Native Azospirillum population varied from 1 million to 1 billion/g soil under diverse agricultural practices and soil types. Such richness, however, does not necessarily mean that artificial inoculation of Azospirillum is not required in Bihar soils as 92% of Azospirillum isolates (50 isolates) were poor in nitrogen-fixing ability and 88% were poor on IAA production. Efficient strains of Azospirillum based on growth (three), acetylene reduction assay (three), IAA production (three), broad range of pH (two) and temperature tolerance were identified. The findings suggested that maize crop in Bihar should be inoculated in universal mode rather than site-specific mode.
doi:10.1007/s13205-011-0031-7
PMCID: PMC3339590  PMID: 22558543
Azospirillum; Soil tillage; Soil type; Organic carbon; Biofertilizer; Chemistry; Stem Cells; Biotechnology; Biomaterials; Agriculture; Bioinformatics; Cancer Research
16.  Population dynamics and identification of efficient strains of Azospirillum in maize ecosystems of Bihar (India) 
3 Biotech  2011;1(4):247-253.
Information on inoculum load and diversity of native microbial community is an important prerequisite for crop management of microbial origin. Azospirillum has a proven role in benefiting the maize (Zea mays) crop in terms of nutrient (nitrogen) supply as well as plant growth enhancement. Bihar state has highest average national maize productivity although fertilizer consumption is minimum, indicating richness of Azospirillum both in terms of population and diversity in soils. An experiment was planned to generate basic information on Azospirillum population variation in maize soils under different agricultural practices and soil types of Bihar, to identify suitable agricultural practices supporting the target microorganism and efficient Azospirillum strain(s). No tillage, growing traditional maize cultivar, land use history (diara soil having history of maize cultivation), soil organic carbon (>1%) and intercrop with oat supported prevalence of Azospirillum in maize rhizosphere. Native Azospirillum population varied from 1 million to 1 billion/g soil under diverse agricultural practices and soil types. Such richness, however, does not necessarily mean that artificial inoculation of Azospirillum is not required in Bihar soils as 92% of Azospirillum isolates (50 isolates) were poor in nitrogen-fixing ability and 88% were poor on IAA production. Efficient strains of Azospirillum based on growth (three), acetylene reduction assay (three), IAA production (three), broad range of pH (two) and temperature tolerance were identified. The findings suggested that maize crop in Bihar should be inoculated in universal mode rather than site-specific mode.
doi:10.1007/s13205-011-0031-7
PMCID: PMC3339590  PMID: 22558543
Azospirillum; Soil tillage; Soil type; Organic carbon; Biofertilizer
17.  Two Common Bean Genotypes with Contrasting Response to Phosphorus Deficiency Show Variations in the microRNA 399-Mediated PvPHO2 Regulation within the PvPHR1 Signaling Pathway 
Crop production of the important legume, the common bean (Phaseolus vulgaris), is often limited by low phosphorus (P) in the soil. The genotypes, BAT477 and DOR364, of the common bean have contrasting responses to P starvation. Plants from the BAT477 P deficiency tolerant genotype showed higher phosphate content and root biomass as compared to the DOR364 plants under P starvation. The PvPHR1 transcription factor-signaling pathway plays an essential role in the response to P starvation. PvPHO2, a negative regulator of this pathway, encodes an ubiquitin E2 conjugase that promotes degradation of P-responsive proteins and is the target gene of PvmiR399. PvPHO2 is downregulated in BAT477 plants under P deficiency, while such a response is not observed in P-starved DOR364 plants. Five putative PvmiR399 binding sites were identified in the 5′ UTR region in both genotypes. While four sites showed an identical DNA sequence, the fifth (binding site of PvPHO2 one) showed three base changes and higher complementarity scores in DOR364 as compared to BAT477. Modified 5′RACE experiments indicated that PvmiR399 binding and/or processing was affected in DOR364 P-starved plants. We propose that a less efficient cleavage of the PvPHO2 mRNA directed by PvmiR399 would result in a higher PvPHO2-mediated degradation of P-responsive proteins in the DOR364 genotype with decreased P deficiency tolerance.
doi:10.3390/ijms14048328
PMCID: PMC3645745  PMID: 23591845
Phaseolus vulgaris; common bean; phosphorus deficiency; post-transcriptional regulation by microRNAs; PvPHR1/PvmiR399 signaling pathway
18.  Phosphorus and Nitrogen Regulate Arbuscular Mycorrhizal Symbiosis in Petunia hybrida 
PLoS ONE  2014;9(3):e90841.
Phosphorus and nitrogen are essential nutrient elements that are needed by plants in large amounts. The arbuscular mycorrhizal symbiosis between plants and soil fungi improves phosphorus and nitrogen acquisition under limiting conditions. On the other hand, these nutrients influence root colonization by mycorrhizal fungi and symbiotic functioning. This represents a feedback mechanism that allows plants to control the fungal symbiont depending on nutrient requirements and supply. Elevated phosphorus supply has previously been shown to exert strong inhibition of arbuscular mycorrhizal development. Here, we address to what extent inhibition by phosphorus is influenced by other nutritional pathways in the interaction between Petunia hybrida and R. irregularis. We show that phosphorus and nitrogen are the major nutritional determinants of the interaction. Interestingly, the symbiosis-promoting effect of nitrogen starvation dominantly overruled the suppressive effect of high phosphorus nutrition onto arbuscular mycorrhiza, suggesting that plants promote the symbiosis as long as they are limited by one of the two major nutrients. Our results also show that in a given pair of symbiotic partners (Petunia hybrida and R. irregularis), the entire range from mutually symbiotic to parasitic can be observed depending on the nutritional conditions. Taken together, these results reveal complex nutritional feedback mechanisms in the control of root colonization by arbuscular mycorrhizal fungi.
doi:10.1371/journal.pone.0090841
PMCID: PMC3946601  PMID: 24608923
19.  Nutrient and growth responses of cattail (Typha domingensis) to redox intensity and phosphate availability 
Annals of Botany  2009;105(1):175-184.
Background and Aims
In the Florida Everglades, the expansion of cattail (Typha domingensis) into areas once dominated by sawgrass (Cladium jamaicense) has been attributed to altered hydrology and phosphorus (P) enrichment. The objective of this study was to quantify the interactive effects of P availability and soil redox potential (Eh) on the growth and nutrient responses of Typha, which may help to explain its expansion.
Methods
The study examined the growth and nutrient responses of Typha to the interactive effects of P availability (10, 80 and 500 µg P L−1) and Eh level (−150, +150 and +600 mV). Plants were grown hydroponically in a factorial experiment using titanium (Ti3+) citrate as a redox buffer.
Key Results
Relative growth rate, elongation, root-supported tissue/root ratio, leaf length, lateral root length and biomass, as well as tissue nutrient concentrations, were all adversely affected by low Eh conditions. P availability compensated for the negative effect of low Eh for all these variables except that low P stimulated root length and nutrient use efficiency. The most growth-promoting treatment combination was 500 µg P L−1/ + 600 mV.
Conclusions
These results, plus previous data on Cladium responses to P/Eh combinations, document that high P availability and low Eh should benefit Typha more than Cladium as the growth and tissue nutrients of the former species responded more to excess P, even under highly reduced conditions. Therefore, the interactive effects of P enrichment and Eh appear to be linked to the expansion of Typha in the Everglades Water Conservation Area 2A, where both low Eh and enhanced phosphate availability have co-occurred during recent decades.
doi:10.1093/aob/mcp213
PMCID: PMC2794056  PMID: 19748907
Everglades; growth; nutrient; phosphorus; redox potential; Typha domingensis
20.  Phosphate solubilizers enhance NPK fertilizer use efficiency in rice and legume cultivation 
3 Biotech  2011;1(4):227-238.
It has been reported that phosphate solubilizing bacteria (PSB) are the most promising bacteria among the plant growth promoting rhizobacteria (PGPR); which may be used as biofertilizers for plant growth and nutrient use efficiency. Moreover, these soil micro-organisms play a significant role in regulating the dynamics of organic matter decomposition and the availability of plant nutrients such as nitrogen (N), phosphorus (P), potassium (K) and other nutrients. Through this study, the management of nutrient use efficiency by the application of PSB was targeted in order to make the applied nutrients more available to the plants in the rice (Oryza sativa) and yardlong bean (Vigna unguiculata) cultivation. Results have shown that the treatments with PSB alone or in the form of consortia of compatible strains with or without the external application of chemical NPK gave more germination index (G. I.) from 2.5 to 5 in rice and 2.7 to 4.8 in bean seeds. They also showed a higher growth in both shoot and root length and a higher biomass as compared to the control. This gives us an idea about the potentiality of these PSB strains and their application in rice and yardlong bean cultivation to get a better harvest index. Their use will also possibly reduce the nutrient runoff or leaching and increase in the use efficiency of the applied fertilizers. Thus, we can conclude that the NPK uptake and management can be improved by the use of PSB in rice and yardlong bean cultivation, and their application may be much more beneficial in the agricultural field.
doi:10.1007/s13205-011-0028-2
PMCID: PMC3339586  PMID: 22558541
Fertilizer; Phosphate solubilizing bacteria; Oryza sativa; Vigna unguiculata; Germination index; Plant growth; Chemistry; Stem Cells; Biotechnology; Biomaterials; Agriculture; Bioinformatics; Cancer Research
21.  Phosphate solubilizers enhance NPK fertilizer use efficiency in rice and legume cultivation 
3 Biotech  2011;1(4):227-238.
It has been reported that phosphate solubilizing bacteria (PSB) are the most promising bacteria among the plant growth promoting rhizobacteria (PGPR); which may be used as biofertilizers for plant growth and nutrient use efficiency. Moreover, these soil micro-organisms play a significant role in regulating the dynamics of organic matter decomposition and the availability of plant nutrients such as nitrogen (N), phosphorus (P), potassium (K) and other nutrients. Through this study, the management of nutrient use efficiency by the application of PSB was targeted in order to make the applied nutrients more available to the plants in the rice (Oryza sativa) and yardlong bean (Vigna unguiculata) cultivation. Results have shown that the treatments with PSB alone or in the form of consortia of compatible strains with or without the external application of chemical NPK gave more germination index (G. I.) from 2.5 to 5 in rice and 2.7 to 4.8 in bean seeds. They also showed a higher growth in both shoot and root length and a higher biomass as compared to the control. This gives us an idea about the potentiality of these PSB strains and their application in rice and yardlong bean cultivation to get a better harvest index. Their use will also possibly reduce the nutrient runoff or leaching and increase in the use efficiency of the applied fertilizers. Thus, we can conclude that the NPK uptake and management can be improved by the use of PSB in rice and yardlong bean cultivation, and their application may be much more beneficial in the agricultural field.
doi:10.1007/s13205-011-0028-2
PMCID: PMC3339586  PMID: 22558541
Fertilizer; Phosphate solubilizing bacteria; Oryza sativa; Vigna unguiculata; Germination index; Plant growth
22.  Contrasting arbuscular mycorrhizal communities colonizing different host plants show a similar response to a soil phosphorus concentration gradient 
The New Phytologist  2013;198(2):546-556.
High soil phosphorus (P) concentration is frequently shown to reduce root colonization by arbuscular mycorrhizal (AM) fungi, but the influence of P on the diversity of colonizing AM fungi is uncertain.We used terminal restriction fragment length polymorphism (T-RFLP) of 18S rDNA and cloning to assess diversity of AM fungi colonizing maize (Zea mays), soybean (Glycene max) and field violet (Viola arvensis) at three time points in one season along a P gradient of 10–280 mg l−1 in the field.Percentage AM colonization changed between sampling time points but was not reduced by high soil P except in maize. There was no significant difference in AM diversity between sampling time points. Diversity was reduced at concentrations of P > 25 mg l−1, particularly in maize and soybean. Both cloning and T-RFLP indicated differences between AM communities in the different host species. Host species was more important than soil P in determining the AM community, except at the highest P concentration.Our results show that the impact of soil P on the diversity of AM fungi colonizing plants was broadly similar, despite the fact that different plants contained different communities. However, subtle differences in the response of the AM community in each host were evident.
doi:10.1111/nph.12169
PMCID: PMC3798118  PMID: 23421495
colonization; diversity; maize (Zea mays); mycorrhizas; phosphorus (P); soybean (Glycene max); Viola arvensis (field violet)
23.  Phosphorus-mobilization ecosystem engineering: the roles of cluster roots and carboxylate exudation in young P-limited ecosystems 
Annals of Botany  2012;110(2):329-348.
Background
Carboxylate-releasing cluster roots of Proteaceae play a key role in acquiring phosphorus (P) from ancient nutrient-impoverished soils in Australia. However, cluster roots are also found in Proteaceae on young, P-rich soils in Chile where they allow P acquisition from soils that strongly sorb P.
Scope
Unlike Proteaceae in Australia that tend to proficiently remobilize P from senescent leaves, Chilean Proteaceae produce leaf litter rich in P. Consequently, they may act as ecosystem engineers, providing P for plants without specialized roots to access sorbed P. We propose a similar ecosystem-engineering role for species that release large amounts of carboxylates in other relatively young, strongly P-sorbing substrates, e.g. young acidic volcanic deposits and calcareous dunes. Many of these species also fix atmospheric nitrogen and release nutrient-rich litter, but their role as ecosystem engineers is commonly ascribed only to their diazotrophic nature.
Conclusions
We propose that the P-mobilizing capacity of Proteaceae on young soils, which contain an abundance of P, but where P is poorly available, in combination with inefficient nutrient remobilization from senescing leaves allows these species to function as ecosystem engineers. We suggest that diazotrophic species that colonize young soils with strong P-sorption potential should be considered for their positive effect on P availability, as well as their widely accepted role in nitrogen fixation. Their P-mobilizing activity possibly also enhances their nitrogen-fixing capacity. These diazotrophic species may therefore facilitate the establishment and growth of species with less-efficient P-uptake strategies on more-developed soils with low P availability through similar mechanisms. We argue that the significance of cluster roots and high carboxylate exudation in the development of young ecosystems is probably far more important than has been envisaged thus far.
doi:10.1093/aob/mcs130
PMCID: PMC3394658  PMID: 22700940
Actinorhizal species; carboxylates; cluster roots; phosphorus nutrition; Cyperaceae; ecosystem engineering; facilitation; Lupinus; Proteaceae
24.  Lysigenous aerenchyma formation involves non-apoptotic programmed cell death in rice (Oryza sativa L.) roots 
In waterlogged soil, deficiency of oxygen triggers development of aerenchyma in roots which facilitates gas diffusion between roots and the aerial environment. However, in contrast to other monocots, roots of rice (Oryza sativa L.) constitutively form aerenchyma even in aerobic conditions. The formation of cortical aerenchyma in roots is thought to occur by either lysigeny or schizogeny. Schizogenous aerenchyma is developed without cortical cell death. However, lysigenous gas-spaces are formed as a consequence of senescence of specific cells in primary cortex followed by their death due to autolysis. In the last stage of aerenchyma formation, a ‘spoked wheel’ arrangement is observed in the cortical region of root. Ultrastructural studies show that cell death is constitutive and no characteristic cell structural differentiation takes place in the dying cells with respect to surrounding cells. Cell collapse initiation occurs in the center of the cortical tissues which are characterized by shorter with radically enlarged diameter. Then, cell death proceeds by acidification of cytoplasm followed by rupturing of plasma membrane, loss of cellular contents and cell wall degradation, while cells nuclei remain intact. Dying cells releases a signal through symplast which initiates cell death in neighboring cells. During early stages, middle lamella-degenerating enzymes are synthesized in the rough endoplasmic reticulum which are transported through dictyosome and discharged through plasmalemma beneath the cell wall. In rice several features of root aerenchyma formation are analogous to a gene regulated developmental process called programmed cell death (PCD), for instance, specific cortical cell death, obligate production of aerenchyma under environmental stresses and early changes in nuclear structure which includes clumping of chromatin, fragmentation, disruption of nuclear membrane and apparent engulfment by the vacuole. These processes are followed by crenulation of plasma membrane, formation of electron-lucent regions in the cytoplasm, tonoplast disintegration, organellar swelling and disruption, loss of cytoplasmic contents, and collapse of cell. Many processes in lysing cells are structural features of apoptosis, but certain characteristics of apoptosis i.e., pycnosis of the nucleus, plasma membrane blebbing, and apoptotic bodies formation are still lacking and thus classified as non-apoptotic PCD. This review article, describes most recent observations alike to PCD involved in aerenchyma formation and their systematic distributions in rice roots.
doi:10.1007/s12298-011-0093-3
PMCID: PMC3550533  PMID: 23573035
Apoptosis; Cell death; Hypoxia; Lysigeny; Programmed cell death; Regulation; Rice
25.  Characterization of Two Inducible Phosphate Transport Systems in Rhizobium tropici 
Rhizobium tropici forms nitrogen-fixing nodules on the roots of the common bean (Phaseolus vulgaris). Like other legume-Rhizobium symbioses, the bean-R. tropici association is sensitive to the availability of phosphate (Pi). To better understand phosphorus movement between the bacteroid and the host plant, Pi transport was characterized in R. tropici. We observed two Pi transport systems, a high-affinity system and a low-affinity system. To facilitate the study of these transport systems, a Tn5B22 transposon mutant lacking expression of the high-affinity transport system was isolated and used to characterize the low-affinity transport system in the absence of the high-affinity system. The Km and Vmax values for the low-affinity system were estimated to be 34 ± 3 μM Pi and 118 ± 8 nmol of Pi · min−1 · mg (dry weight) of cells−1, respectively, and the Km and Vmax values for the high-affinity system were 0.45 ± 0.01 μM Pi and 86 ± 5 nmol of Pi · min−1 · mg (dry weight) of cells−1, respectively. Both systems were inducible by Pi starvation and were also shock sensitive, which indicated that there was a periplasmic binding-protein component. Neither transport system appeared to be sensitive to the proton motive force dissipator carbonyl cyanide m-chlorophenylhydrazone, but Pi transport through both systems was eliminated by the ATPase inhibitor N,N′-dicyclohexylcarbodiimide; the Pi transport rate was correlated with the intracellular ATP concentration. Also, Pi movement through both systems appeared to be unidirectional, as no efflux or exchange was observed with either the wild-type strain or the mutant. These properties suggest that both Pi transport systems are ABC type systems. Analysis of the transposon insertion site revealed that the interrupted gene exhibited a high level of homology with kdpE, which in several bacteria encodes a cytoplasmic response regulator that governs responses to low potassium contents and/or changes in medium osmolarity.
PMCID: PMC91779  PMID: 10618197

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