David Ryan

Bio: David Ryan is an academic researcher from Institute of Technology, Carlow. The author has contributed to research in topics: Phytoremediation & Bioremediation. The author has an hindex of 18, co-authored 42 publications receiving 2802 citations. Previous affiliations of David Ryan include Solae.

Bacterial endophytes: recent developments and applications

Abstract: Endophytic bacteria have been found in virtually every plant studied, where they colonize the internal tissues of their host plant and can form a range of different relationships including symbiotic, mutualistic, commensalistic and trophobiotic Most endophytes appear to originate from the rhizosphere or phyllosphere; however, some may be transmitted through the seed Endophytic bacteria can promote plant growth and yield and can act as biocontrol agents Endophytes can also be beneficial to their host by producing a range of natural products that could be harnessed for potential use in medicine, agriculture or industry In addition, it has been shown that they have the potential to remove soil contaminants by enhancing phytoremediation and may play a role in soil fertility through phosphate solubilization and nitrogen fixation There is increasing interest in developing the potential biotechnological applications of endophytes for improving phytoremediation and the sustainable production of nonfood crops for biomass and biofuel production

Plant growth promotion induced by phosphate solubilizing endophytic Pseudomonas isolates

Abstract: The use of plant growth promoting bacterial inoculants as live microbial biofertilisers provides a promising alternative to chemical fertilisers and pesticides. Inorganic phosphate solubilisation is one of the major mechanisms of plant growth promotion by plant associated bacteria. This involves bacteria releasing organic acids into the soil which solubilise the phosphate complexes converting them into ortho-phosphate which is available for plant up-take and utilisation. The study presented here describes the ability of endophytic bacterial isolates to produce gluconic acid, solubilise insoluble phosphate and stimulate the growth of Pea plants (Pisum sativum). This study also describes the genetic systems within three of these endophyte isolates thought to be responsible for their effective phosphate solubilising abilities. The results showed that many of the endophytic isolates produced gluconic acid (14-169 mM) and have moderate to high phosphate solubilisation capacities (~ 400-1300 mg L-1). When inoculated to Pea plants grown in sand/soil under soluble phosphate limiting conditions, the endophyte isolates that produced medium to high levels of gluconic acid also displayed enhanced plant growth promotion effects.

Bacterial endophyte‐mediated naphthalene phytoprotection and phytoremediation

Abstract: Polyaromatic hydrocarbons (PAHs) are major and recalcitrant pollutants of the environment and their removal presents a significant problem. Phytoremediation has shown much promise in PAH removal from contaminated soil, but may be inhibited because the plant experiences phytotoxic effects from low-molecular-weight PAHs such as naphthalene. This paper describes the construction of a naphthalene-degrading endophytic strain designated Pseudomonas putida VM1441(pNAH7). This strain was found to be an efficient colonizer of plants, colonizing both the rhizosphere and interior root tissues. The inoculation of plants with P. putida VM1441(pNAH7) resulted in the protection of the host plant from the phytotoxic effects of naphthalene. When inoculated plants were exposed to naphthalene, both seed germination and plant transpiration rates were higher than those of the uninoculated controls. The inoculation of plants with this strain also facilitated higher (40%) naphthalene degradation rates compared with uninoculated plants in artificially contaminated soil.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

Plant–microbe interactions promoting plant growth and health: perspectives for controlled use of microorganisms in agriculture

Abstract: Plant-associated microorganisms fulfill important functions for plant growth and health. Direct plant growth promotion by microbes is based on improved nutrient acquisition and hormonal stimulation. Diverse mechanisms are involved in the suppression of plant pathogens, which is often indirectly connected with plant growth. Whereas members of the bacterial genera Azospirillum and Rhizobium are well-studied examples for plant growth promotion, Bacillus, Pseudomonas, Serratia, Stenotrophomonas, and Streptomyces and the fungal genera Ampelomyces, Coniothyrium, and Trichoderma are model organisms to demonstrate influence on plant health. Based on these beneficial plant–microbe interactions, it is possible to develop microbial inoculants for use in agricultural biotechnology. Dependent on their mode of action and effects, these products can be used as biofertilizers, plant strengtheners, phytostimulators, and biopesticides. There is a strong growing market for microbial inoculants worldwide with an annual growth rate of approximately 10%. The use of genomic technologies leads to products with more predictable and consistent effects. The future success of the biological control industry will benefit from interdisciplinary research, e.g., on mass production, formulation, interactions, and signaling with the environment, as well as on innovative business management, product marketing, and education. Altogether, the use of microorganisms and the exploitation of beneficial plant–microbe interactions offer promising and environmentally friendly strategies for conventional and organic agriculture worldwide.

Bacterial Endophytes and Their Interactions with Hosts

Abstract: Recent molecular studies on endophytic bacterial diversity have revealed a large richness of species. Endophytes promote plant growth and yield, suppress pathogens, may help to remove contaminants, solubilize phosphate, or contribute assimilable nitrogen to plants. Some endophytes are seed-borne, but others have mechanisms to colonize the plants that are being studied. Bacterial mutants unable to produce secreted proteins are impaired in the colonization process. Plant genes expressed in the presence of endophytes provide clues as to the effects of endophytes in plants. Molecular analysis showed that plant defense responses limit bacterial populations inside plants. Some human pathogens, such as Salmonella spp., have been found as endophytes, and these bacteria are not removed by disinfection procedures that eliminate superficially occurring bacteria. Delivery of endo-phytes to the environment or agricultural fields should be carefully evaluated to avoid introducing pathogens.

Bacterial endophytes: recent developments and applications

Abstract: Endophytic bacteria have been found in virtually every plant studied, where they colonize the internal tissues of their host plant and can form a range of different relationships including symbiotic, mutualistic, commensalistic and trophobiotic Most endophytes appear to originate from the rhizosphere or phyllosphere; however, some may be transmitted through the seed Endophytic bacteria can promote plant growth and yield and can act as biocontrol agents Endophytes can also be beneficial to their host by producing a range of natural products that could be harnessed for potential use in medicine, agriculture or industry In addition, it has been shown that they have the potential to remove soil contaminants by enhancing phytoremediation and may play a role in soil fertility through phosphate solubilization and nitrogen fixation There is increasing interest in developing the potential biotechnological applications of endophytes for improving phytoremediation and the sustainable production of nonfood crops for biomass and biofuel production