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Unleashing the potential of the root hair cell as a single plant cell type model in root systems biology  [PDF]
Zhenzhen Qiao,Marc Libault
Frontiers in Plant Science , 2013, DOI: 10.3389/fpls.2013.00484
Abstract: Plant root is an organ composed of multiple cell types with different functions. This multicellular complexity limits our understanding of root biology because -omics studies performed at the level of the entire root reflect the average responses of all cells composing the organ. To overcome this difficulty and allow a more comprehensive understanding of root cell biology, an approach is needed that would focus on one single cell type in the plant root. Because of its biological functions (i.e., uptake of water and various nutrients; primary site of infection by nitrogen-fixing bacteria in legumes), the root hair cell is an attractive single cell model to study root cell response to various stresses and treatments. To fully study their biology, we have recently optimized procedures in obtaining root hair cell samples. We culture the plants using an ultrasound aeroponic system maximizing root hair cell density on the entire root systems and allowing the homogeneous treatment of the root system. We then isolate the root hair cells in liquid nitrogen. Isolated root hair yields could be up to 800 to 1000 mg of plant cells from 60 root systems. Using soybean as a model, the purity of the root hair was assessed by comparing the expression level of genes previously identified as soybean root hair specific between preparations of isolated root hair cells and stripped roots, roots devoid in root hairs. Enlarging our tests to include other plant species, our results support the isolation of large quantities of highly purified root hair cells which is compatible with a systems biology approach.
Screening of plant growth-promoting rhizobacteria and their promoting effects on maize

DENG Zhen-Shan,DANG Jun-Long,ZHANG Hai-Zhou,LI Jun,WEI Ge-Hong,

微生物学通报 , 2012,
Abstract: Objective] We used different root and rhizosphere soils in Weinan, Xianyang, Ankang, Shangluo and Yulin, Shaanxi province of China to isolate plant growth promoting rhizobacteria (PGPR), and then studied the mechanism why they can promote the growth of plants. Methods] Preliminary screening of PGPRs under the premises of PGPR may having the abilities of phosphate solubilization, N2-fixing, production of NH3 and indoleacetic acid (IAA) and antagonistic activity against three common pathogenic fungi. After that, multiple plant growth promoting activities were detected, maize growth enhancement by plant inoculation studies with these isolates alone individually and the mixture of each isolates under pot experiment conditions. Results] In total of 158 strains were isolated. 17 of which have mechanisms and a striking plant growth promoting activity with respect to various plant parameters. Under pot culture conditions, compared with the control, the results showed that the strain which inoculated in combination was significant increase than inoculated alone, which in shoot length, root length, stem length, average diameter of stem and plant dry weight, respectively. Conclusion] Isolates with multiple PGP activities can also be rhizospheric competent, providing promising isolates for PGPRs combination to resolve the challenges in field application of PGPR.
Why Some Plant Species Are Rare  [PDF]
G. W. Weiger Wamelink, Paul W. Goedhart, Josep Y. Frissel
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0102674
Abstract: Biodiversity, including plant species diversity, is threatened worldwide as a result of anthropogenic pressures such as an increase of pollutants and climate change. Rare species in particular are on the verge of becoming extinct. It is still unclear as to why some plant species are rare and others are not. Are they rare due to: intrinsic reasons, dispersal capacity, the effects of management or abiotic circumstances? Habitat preference of rare plant species may play an important role in determining why some species are rare. Based on an extensive data set of soil parameters we investigated if rarity is due to a narrow habitat preference for abiotic soil parameters. For 23 different abiotic soil parameters, of which the most influential were groundwater-table, soil-pH and nutrient-contents, we estimated species responses for common and rare species. Based on the responses per species we calculated the range of occurrence, the range between the 5 and 95 percentile of the response curve giving the habitat preference. Subsequently, we calculated the average response range for common and rare species. In addition, we designed a new graphic in order to provide a better means for presentation of the results. The habitat preferences of rare species for abiotic soil conditions are significantly narrower than for common species. Twenty of the twenty-three abiotic parameters showed on average significantly narrower habitat preferences for rare species than for common species; none of the abiotic parameters showed on average a narrower habitat preference for common species. The results have major implications for the conservation of rare plant species; accordingly management and nature development should be focussed on the maintenance and creation of a broad range of environmental conditions, so that the requirements of rare species are met. The conservation of (abiotic) gradients within ecosystems is particularly important for preserving rare species.
Distinct root-associated bacterial communities on three wild plant species growing in a common field  [PDF]
Kristin Aleklett,Jonathan W Leff,Noah Fierer,Miranda Hart
PeerJ , 2015, DOI: 10.7287/peerj.preprints.548v1
Abstract: Plant roots are known to harbor large and diverse communities of bacteria. It has been suggested that plant identity can structure these root-associated communities, but few studies have specifically assessed how the composition of root microbiota varies within and between plant species growing under natural conditions. We sampled endophytic and epiphytic bacteria in root tissues from a population of a wild, clonal plant (Orange hawkweed – Pilosella aurantiaca) as well as two neighboring plant species (Oxeye daisy – Leucanthemum vulgare and Alsike clover – Trifolium hybridum) to determine if plant species hosted unique root microbiota. Our results show that plants of different species host distinct bacterial communities in their roots. In terms of community composition, Betaproteobacteria (especially the family Oxalobacteraceae) were found to dominate in the root microbiota of L. vulgare and T. hybridum samples, whereas the root microbiota of P. aurantiaca had a more heterogeneous distribution of bacterial abundances where gamma Proteobacteria and Acidobacteria occupied a larger portion of the community. Whether all plant species host their own distinct root microbiota and plants more closely related to each other share more similar bacterial communities still remains to be explored.
Why Assembling Plant Genome Sequences Is So Challenging  [PDF]
Manuel Gonzalo Claros,Rocío Bautista,Darío Guerrero-Fernández,Hicham Benzerki,Pedro Seoane,Noé Fernández-Pozo
Biology , 2012, DOI: 10.3390/biology1020439
Abstract: In spite of the biological and economic importance of plants, relatively few plant species have been sequenced. Only the genome sequence of plants with relatively small genomes, most of them angiosperms, in particular eudicots, has been determined. The arrival of next-generation sequencing technologies has allowed the rapid and efficient development of new genomic resources for non-model or orphan plant species. But the sequencing pace of plants is far from that of animals and microorganisms. This review focuses on the typical challenges of plant genomes that can explain why plant genomics is less developed than animal genomics. Explanations about the impact of some confounding factors emerging from the nature of plant genomes are given. As a result of these challenges and confounding factors, the correct assembly and annotation of plant genomes is hindered, genome drafts are produced, and advances in plant genomics are delayed.
Advances in Plant Root Morphology Adaptability to Phosphorus Deficiency Stress

Hua Zhao,Fangsen Xu,Lei Shi,Yunhua Wang,

植物学报 , 2006,
Abstract: This paper summarizes the advances in studies of plant root morphology related to high efficient uptake and utilization of phosphorus (P), specifically, plant root morphological characters adapting to P deficiency stress and its possible mechanism regulated by phytohormones and the molecular biology of plant root systems adapting to low-P stress. Discussed are useful advanced biology approaches to develop similar studies.
Plant response to alternative matrices for in vitro root induction
G Gangopadhyay, SK Roy, KK Mukherjee
African Journal of Biotechnology , 2009,
Abstract: The quest for alternative matrices for plant tissue culture is a continuing process. This inquiry has two aspects. One being commercial for low cost tissue culture, and the other obviously is the better root induction vis-à-vis higher percentage of survival, particularly with respect to micropropagation. The advantage of alternative matrices raises the concomitant question of plant intelligence in sensing its environment. The present review apart from summarizing the works with alternative matrices, attempts to raise some issues related to plant sensitivity, which remain unanswered due to lack of present understanding in this area of plant biology.
Phenotypic plasticity of fine root growth increases plant productivity in pine seedlings
Rongling Wu, James E Grissom, Steven E McKeand, David M O'Malley
BMC Ecology , 2004, DOI: 10.1186/1472-6785-4-14
Abstract: The partitioning of biomass to fine roots is observed to reduce with increased nutrient availability. For the "mesic" ecotype, increased stem biomass as a consequence of more nutrients may be primarily due to reduced fine-root biomass partitioning. For the "xeric" ecotype, the favorable influence of the plasticity of fine root growth on stem growth results from increased allocation of biomass to foliage and decreased allocation to fine roots. An evolutionary genetic analysis indicates that the plasticity of fine root growth is inducible, whereas the plasticity of foliage is constitutive.Results promise to enhance a fundamental understanding of evolutionary changes of tree architecture under domestication and to design sound silvicultural and breeding measures for improving plant productivity.The use of chemical fertilizers has been responsible for dramatic increase in the stem wood production of forest trees [1-4]. In an 8-year-old stand of loblolly pine growing on an infertile site in Scotland County, North Carolina, for example, stem volume increment increased 152% after the fourth year of fertilization treatment [4]. However, little is known about the mechanistic basis for such favorable effects of fertilization. One hypothesis is that improved nutrient availability leads to increases in leaf area growth and photosynthetic capacity, thus producing more photosynthate that can be allocated to the stem wood. This hypothesis has been supported by a number of physiological studies [5-7] and used as a conceptual model for plant nitrogen acquisition and cycling [8]. However, forest trees can consume as much as 60–80% of annual net primary productivity in the turnover of fine roots [3]. Fine roots are a tissue with high maintenance respiration tissue whose primary function is to absorb and metabolize water and nutrients from the soil [9-12]. A number of previous studies have shown that the production of fine roots is sensitive to the availability and distribution of nutr
Sampling Date, Leaf Age and Root Size: Implications for the Study of Plant C:N:P Stoichiometry  [PDF]
Haiyang Zhang, Honghui Wu, Qiang Yu, Zhengwen Wang, Cunzheng Wei, Min Long, Jens Kattge, Melinda Smith, Xingguo Han
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0060360
Abstract: Plant carbon : nitrogen : phosphorus (C:N:P) ratios are powerful indicators of diverse ecological processes. During plant development and growth, plant C:N:P stoichiometry responds to environmental conditions and physiological constraints. However, variations caused by effects of sampling (i.e. sampling date, leaf age and root size) often have been neglected in previous studies. We investigated the relative contributions of sampling date, leaf age, root size and species identity to stoichiometric flexibility in a field mesocosm study and a natural grassland in Inner Mongolia. We found that sampling date, leaf age, root size and species identity all significantly affected C:N:P stoichiometry both in the pot study as well as in the field. Overall, C:N and C:P ratios increased significantly over time and with increasing leaf age and root size, while the dynamics of N:P ratios depended on species identity. Our results suggest that attempts to synthesize C:N:P stoichiometry data across studies that span regional to global scales and include many species need to better account for temporal variation.
Why Bacteriophage Encode Exotoxins and other Virulence Factors
Stephen T. Abedon,Jeffrey T. LeJeune
Evolutionary Bioinformatics , 2005,
Abstract: This study considers gene location within bacteria as a function of genetic element mobility. Our emphasis is on prophage encoding of bacterial virulence factors (VFs). At least four mechanisms potentially contribute to phage encoding of bacterial VFs: (i) Enhanced gene mobility could result in greater VF gene representation within bacterial populations. We question, though, why certain genes but not others might benefit from this mobility. (ii) Epistatic interactions—between VF genes and phage genes that enhance VF utility to bacteria—could maintain phage genes via selection acting on individual, VF-expressing bacteria. However, is this mechanism sufficient to maintain the rest of phage genomes or, without gene co-regulation, even genetic linkage between phage and VF genes? (iii) Phage could amplify VFs during disease progression by carrying them to otherwise commensal bacteria colocated within the same environment. However, lytic phage kill bacteria, thus requiring assumptions of inclusive fitness within bacterial populations to explain retention of phage-mediated VF amplification for the sake of bacterial utility. Finally, (iv) phage-encoded VFs could enhance phage Darwinian fitness, particularly by acting as ecosystem-modifying agents. That is, VF-supplied nutrients could enhance phage growth by increasing the density or by improving the physiology of phage-susceptible bacteria. Alternatively, VF-mediated break down of diffusion-inhibiting spatial structure found within the multicellular bodies of host organisms could augment phage dissemination to new bacteria or to environments. Such phage-fitness enhancing mechanisms could apply particularly given VF expression within microbiologically heterogeneous environments, ie, ones where phage have some reasonable potential to acquire phage-susceptible bacteria.
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