Biotechnological Applications In Agriculture Research Articles

Characteristics of Stenotrophomonas rhizophila Lipopolysaccharide, a Representative of Antarctica

In 2002, Wolf described a new species of Stenotrophomonas, Stenotrophomonas rhizophila, which is a non-pathogenic plant inhabitant. The defining characteristics of the new species, in contrast to S. maltophilia, were the following: growth at 4 °C, but its absence at 37 °C; the use of xylose as a carbon source; low osmolytic tolerance. S. rhizophila is isolated exclusively from the rhizosphere or from the internal tissues of plants, in particular from the vascular tissues of the root and stem. In 2014, a number of authors, studying cultivated heterotrophic bacteria and yeasts, which dominate in plant samples collected from various terrestrial biotopes near the Ukrainian Antarctic station on Galindez Island in Marine Antarctica, isolated a number of bacterial isolates. The authors’ phylogenetic analysis using only BLAST analysis made it possible to determine the approximate phylogenetic affiliation of the bacterial isolate to the family Gammaproteobacteria (genus Stenotrophomonas, species S. rhizophila). It is known that many processes that determine the biological features of microorganisms, the nature of their relationships between them, as well as micro- and macroorganisms in biocenoses, are carried out with the participation of the surface structures of the bacterial cell, which are in direct contact with the environment. Among them, of particular interest are lipopolysaccharides (LPS), components of the outer membrane of Gram-negative bacteria. However, to date, we have not found any works devoted to the study of S. rhizophila lipopolysaccharides in the literature available to us. The aim of the work was to clarify the phylogenetic position of the 6p5m bacterial strain isolated from the Antarctic region by constructing dendrograms, to study some of its phenotypic properties, to isolate lipopolysaccharides and study chemical and component composition, serological, and biological properties. Methods. Identification was carried out via ribosomal phylogeny. A fragment of the 16S rRNA gene of bacterial strain 6p5m was amplified by PCR using primers 8F and 1492R. The phylogenetic position of the strains was determined by construction of dendrograms, which show the position of the investigated strains among closely related and typical species and type species (programs ClustalX 2.1, Mega v. 6.00). LPS was obtained from cells by water-phenol extraction, electrophoresis was carried out in polyacrylamide gel, monosaccharide and fatty acid composition was determined by chromato-mass spectrometry, antigenic activity was studied by immunodiffusion in agar. Results. Phylogenetic analysis of the nucleotide sequence of the 16S rRNA gene revealed a high level of homology (99.8%) of the bacterial strain 6p5m with typical strain S. rhizophila DSM 14405T from the GenBank database, which allows us to classify it. Comparing phylogenetic analysis with phenotypic data, we can assert that strain 6p5m belongs to the S. rhizophila species. When studying the biopolymer composition of LPS by specific reactions to each component, it was found that the carbohydrate content was relatively low and amounted to 27.42% and 13.34% for LPS1 and LPS2, respectively. The content of characteristic LPS components: heptose and 2-keto-3-deoxyoctonic (KDO) acid was 1.78% and 0.034%, as well as 5.38% and 0.09%, respectively, for LPS1 and LPS2. Analysis of the monosaccharide composition of LPS preparations showed that fucose (72.57%) is present as a dominant monosaccharide in LPS1 and rhamnose (65.04%) in LPS2. The main monosaccharides of the extracellular component were galactose (39.92%) and rhamnose (24.36%). Analysis of the lipid part of the studied LPS indicates significant differences between them. In the composition of lipid A LPS1 and LPS2 of S. rhizophila 6p5m, anti-iso-pentadecanoic acid (a-i-C15:0) was predominant (25.58% and 39.24%, respectively), and 3-hydroxydodecanoic acid (3-OH-C12:0) in LPS2 (26.21%), hexadecanoic acid (С16:0) (27.06% and 10.51%, respectively) for LPS1 and LPS2. Cyclic acids were present only in LPS1, while i-C15:0 and 9-C16:1 only in LPS2. Electrophoretic analysis showed heterogeneity characteristic of an LPS molecule, manifested by a plurality of bands in the form of a «ladder» when the gel was stained with silver ions, which is associated with the presence in the composition of LPS preparations of O-specific polysaccharide structures with different lengths of oligosaccharide chains, which determine their different molecular weight. On the electropherogram of LPS1 and LPS2, bands were not visualized in the upper part of the electrophoretic track, which indicates the absence of S-forms of LPS with long O-specific chains, but a significant predominance of SR-form molecules in the membrane LPS pool. S. rhizophila 6p5m LPS showed significantly higher pyrogenic activity compared to pyrogenal, a pharmaceutical preparation, an active ingredient of which is Shigella typhi LPS. The extracellular polymer did not exhibit pyrogenic activity. In the double immunodiffusion reaction in agar according to Ouchterlony, it was found that the studied LPSs in the homologous system exhibit antigen activity. The antigens present in both LPS1and LPS2 and the extracellular component are identical: the antigen present in each of the wells binds to all antibodies that can interact with the antigen from the other well. It was shown that pre-sowing treatment of seeds with LPS preparations of S. rhizophila 6p5m stimulates the energy of seed germination. LPS1 (+2.82 cm) showed the greatest impact in comparison with the control. A significant stimulatory effect of LPS1, LPS2, and extracellular polymer was observed when studying their effects on mustard seedlings. Conclusions. The taxonomic position of bacterial strain 6r5m of the ecosystems of the polar region (Antarctica) was determined via the phylogenetic analysis taking into account the phenotypic features of the strain. The bacterial strain is represented in the phylum Proteobacteria, class Gammaproteobacteria, family Xanthomonadaceae, genus Stenotrophomonas, species S. rhizophila. From S. rhizophila cells, LPS preparations were obtained, which differed in monosaccharide and fatty acid composition, but showed high pyrogenicity. S. rhizophila represents a promising alternative to S. maltophilia for applications in agricultural biotechnology and biological control due to its ability to both stimulate plant growth and protect roots from biotic and abiotic stresses.

Crystal structure and interconversion of monomers and domain-swapped dimers of the walnut tree phytocystatin

Biotechnological applications of phytocystatins have garnered significant interest due to their potential applications in crop protection and improve crop resistance to abiotic stress factors. Cof1 and Wal1 are phytocystatins derived from Coffea arabica and Juglans regia, respectively. These plants hold significant economic value due to coffee's global demand and the walnut tree's production of valuable timber and widely consumed walnuts with culinary and nutritional benefits. The study involved the heterologous expression in E. coli Lemo 21(DE3), purification by immobilized metal ion affinity and size exclusion chromatography, and biophysical characterization of both phytocystatins, focusing on isolating and interconverting their monomers and dimers. The crystal structure of the domain-swapped dimer of Wal1 was determined revealing two domain-swapped dimers in the asymmetric unit, an arrangement reminiscent of the human cystatin C structure. Alphafold models of monomers and Alphafold-Multimer models of domain-swapped dimers of Cof1 and Wal1 were analyzed in the context of the crystal structure. The methodology and data presented here contribute to a deeper understanding of the oligomerization mechanisms of phytocystatins and their potential biotechnological applications in agriculture.

CiteSpace-Based Review of Agricultural Biotechnology Applications

Agricultural biotechnology holds the potential to enhance crop productivity, improve food quality, and promote sustainable agricultural practices. With Web of Science (WoS) core collection as the data source, this study applies CiteSpace to visualize research frontiers, hot topics, and knowledge flow in agricultural biotechnology applications. The findings reveal an increasing number of publications and frequent regional collaborations between China, USA and India in this field from 2011 to 2023. It integrates diverse disciplines such as plant sciences, biotechnology, applied microbiology, genetics, and microbiology, encompassing a broad range of topics. CRISPR, CRISPR/Cas9, and strawberry emerge as the main knowledge sources in this domain. Additionally, the application of genetically modified crops using technologies like the CRISPR system, base editing, and prime editing may emerge as a novel research trend in the future, providing valuable insights and ideas for further exploration in the field of agricultural biotechnology applications.

WITHDRAWN: Crystal structure and interconversion of monomers and domain-swapped dimers of the walnut tree phytocystatin

Biotechnological applications of phytocystatins have garnered significant interest due to their potential applications in crop protection and improve crop resistance to abiotic stress factors. Cof1 and Wal1 are phytocystatins derived from Coffea arabica and Juglans regia, respectively. These plants hold significant economic value due to coffee's global demand and the walnut tree's production of valuable timber and widely consumed walnuts with culinary and nutritional benefits. The study involved the heterologous expression in E. coli Lemo 21(DE3), purification by immobilized metal ion affinity and size exclusion chromatography, and biophysical characterization of both phytocystatins, focusing on isolating and interconverting their monomers and dimers. The crystal structure of the domain-swapped dimer of Wal1 was determined revealing two domain-swapped dimers in the asymmetric unit, an arrangement reminiscent of the human cystatin C structure. Alphafold models of monomers and Alphafold-Multimer models of domain-swapped dimers of Cof1 and Wal1 were analyzed in the context of the crystal structure. The methodology and data presented here contribute to a deeper understanding of the oligomerization mechanisms of phytocystatins and their potential biotechnological applications in agriculture.

Whole-Genome Sequence Insight into the Plant-Growth-Promoting Bacterium Priestia filamentosa Strain AZC66 Obtained from Zygophyllum coccineum Rhizosphere.

This study aimed to isolate, screen the plant-growth-enhancing features, and explore the whole-genome sequence of AZC66 isolated from the rhizosphere of Zygophyllum coccineum and determine its biostimulating effects on the growth of cowpea under greenhouse conditions. Salkowski reagent was used to measure AZC66's indole acetic acid production. AZC66's inorganic phosphate solubility on Pikovskaya agar was evaluated using tricalcium phosphate. The results indicated the ability of AZC66 to fix nitrogen, produce IAA (66.33 ± 0.44 μg mL-1), solubilize inorganic phosphate, and exhibit the activity of ACC deaminase (278.40 ± 21 mol -ketobutyrate mg-1 h-1). Cowpea's root and shoot dry weights were also significantly increased after in vitro inoculation with AZC66. The identity of AZC66 was confirmed as Priestia filamentosa, and 4840 genes were predicted in its genome. The gene sequences were compared against the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, and the results showed that the top three pathways wherein the maximum number of genes are involved are signaling and cellular processes, genetic information processing, and carbohydrate metabolism. The genome sequencing of the strain AZC66 revealed a number of genes implicated in plant biostimulation activities such as nitrogen fixation (nifU), phytohormone synthesis (trpAB genes), phosphate solubilization (PhbCEF, pstABCS, and phoU), and siderophore formation (FbpA, feoAB, and fetB). The AZC66 genome contained numerous genes involved in nitrogen metabolism, nitrogen regulation, and the nitrate reduction pathway. The phenazine biosynthetic gene in AZC66 demonstrated biocontrol and soil survival properties. The trehalose synthesis genes in AZC66 may help plants resist osmotic and salt stress. The discovery of glycine betaine, cold shock, and heat shock protein genes demonstrated that AZC66 could withstand harsh conditions. AZC66 might be used to create robust, sustainable biological fertilizers for future agricultural use in Saudi Arabia. Furthermore, the predicted adaptable metabolic pathways might serve as the basis for potential biotechnological applications in agriculture and industry.

Unexploited Potentials of Endophytic Fungi: Patents Review on Endophytic Fungi Related to Secondary Bioactive Compounds

Pharmacognosy Research,2023,15,2,217-225.DOI:10.5530/pres.15.2.023Published:February 2023Type:Review ArticleAuthors:Priyatama V. Powar, and Shilpa Chaudhari Author(s) affiliations:Priyatama V. Powar*, Shilpa Chaudhari Department of Pharmaceutics, Dr. D. Y. Patil College of Pharmacy, Akurdi, Pune, Maharashtra, INDIA. Abstract:Endophytic fungi are various micro-organisms that inhabit intracellular or intercellular plant tissues in symbiotic association [at certain stages of their life cycles], without causing damage or morphological changes. The endophytes from medicinal plants are important resources for discovery of natural products and secondary bioactive metabolites having the potential biotechnological applications in agriculture, medicine, and allied sectors. The endophytic fungi such as Acremonium, Aspergillus, Fusarium, Trichoderma, Penicillium, Phomopsis, Pestalotiopsis, Pseudomassari, Quercina, Trichoderma genera have been reported from different medicinal plants with potential therapeutic activity. On the other hand, the endophytic fungi can also confer profound impacts on their host plants like improvement in growth, activation of systemic tolerances towards abiotic/biotic stresses, enhancement of nutrient solublization, biosynthesis of phytohormones and stimulating accumulation of secondary metabolites. Endophytic fungi have attracted much research interest because they have provided not only novel sources of Cytotoxic compounds, Antimicrobial agents, Bio-stimulants for essential oil biosynthesis, Anticancer agents, antioxidant agents, anti-diabetic agents, immunosuppressant and insecticidal compounds. The present review reveals the importance of endophytic fungi from medicinal plants as a source of bioactive compounds as well as landscape of patents related to the production of secondary metabolites through endophytic fungi and their application in pharmaceutical sectors. Keywords:Biological activity, Endophytic fungi, Patents, Phytohormones., Secondary metabolites, Symbiotic associationView:PDF (564.03 KB)

Nitric oxide-releasing nanomaterials: from basic research to potential biotechnological applications in agriculture.

Nitric oxide (NO) is a multifunctional gaseous signal that modulates the growth, development and stress tolerance of higher plants. NO donors have been used to boost plant endogenous NO levels and to activate NO-related responses, but this strategy is often hindered by the relative instability of donors. Alternatively, nanoscience offers a new, promising way to enhance NO delivery to plants, as NO-releasing nanomaterials (e.g. S-nitrosothiol-containing chitosan nanoparticles) have many beneficial physicochemical and biochemical properties compared to non-encapsulated NO donors. Nano NO donors are effective in increasing tissue NO levels and enhancing NO effects both in animal and human systems. The authors believe, and would like to emphasize, that new trends and technologies are essential for advancing plant NO research and nanotechnology may represent a breakthrough in traditional agriculture and environmental science. Herein, we aim to draw the attention of the scientific community to the potential of NO-releasing nanomaterials in both basic and applied plant research as alternatives to conventional NO donors, providing a brief overview of the current knowledge and identifying future research directions. We also express our opinion about the challenges for the application of nano NO donors, such as the environmental footprint and stakeholder's acceptance of these materials.

Achievements of agricultural biotechnology: An initiative to double the farmer’s income through cutting edge technology

The population of the world is increasing nearly exponentially over time. To feed this population following the environment conservation protocol, it is essential to enhance the agricultural productivity even in the synchronizing agrarian land use pattern. To enhance the quality and productivity in agriculture sector, introducing the cutting edge technology is need of the hour.From ancient times, traditional approaches like selective breeding, adoption of agronomic management practices and application of indigenous technical knowledge have been used to attain resilience against various abiotic and biotic stresses. However, these traditional approaches are not sufficient to tackle the increasing repercussions of climate change and feed quality food to the expanding population. Therefore, in order to address these issues of climate change, population explosion and malnutrition, biotechnological interventions can be a promising approach. In the past, biotechnology based approaches have given successful products like Herbicide-resistant Soybean, Pusa Basmati 1, Bt Cotton, Bt Brinjal, Flavr-Savr tomato, a therapeutically significant product of Lithospermum erythrorhizon and Panax ginseng. Besides that many more need based products are in pipeline which is under scrutiny of regulatory bodies, policymakers and environmentalists. It is profoundly expected that in the coming day’s agricultural biotechnology applications will bring revolutionary changes to existing agricultural scenario. Therefore, in this review, we have summarized the achievement of agricultural biotechnology that is assisting to enhance the agricultural produce to double the income of farmers. However, this much is not enough; hence full utilization of all the sustainable agricultural biotechnological tools must come into the existence that definitely will boost the agricultural productivity.

Genome Mining of Three Plant Growth-Promoting Bacillus Species from Maize Rhizosphere

Bacillus species genomes are rich in plant growth-promoting genetic elements. Bacillus subtilis and Bacillus velezensis are important plant growth promoters; hence, to further improve their abilities, the genetic elements responsible for these traits were characterized and reported. Genetic elements reported include those of auxin, nitrogen fixation, siderophore production, iron acquisition, volatile organic compounds, and antibiotics. Furthermore, the presence of phages and antibiotic-resistant genes in the genomes are reported. Pan-genome analysis was conducted using ten Bacillus species. From the analysis, pan-genome of Bacillus subtilis and Bacillus velezensis are still open. Ultimately, this study brings an insight into the genetic components of the plant growth-promoting abilities of these strains and shows their potential biotechnological applications in agriculture and other relevant sectors.

Attitude and application: Judge a crop on its potential and not breeding technology

In comparison with technological advancements in other fields, applications of biotechnology in agriculture elicit strong, divisive opinions. The polarizing debate over genetically modified organisms (GMOs), or transgenic crops, has spanned decades. Opponents have focused heavily on a single trait: herbicide tolerance. Public concern regarding the impacts of herbicides on human health and the environment has overshadowed other applications of genetic engineering, such as pest resistance, biofortification, and non-browning fruit (Abdallah et al., 2015).

Ageritin from Pioppino Mushroom: The Prototype of Ribotoxin-Like Proteins, a Novel Family of Specific Ribonucleases in Edible Mushrooms.

Ageritin is a specific ribonuclease, extracted from the edible mushroom Cyclocybe aegerita (synonym Agrocybe aegerita), which cleaves a single phosphodiester bond located within the universally conserved alpha-sarcin loop (SRL) of 23–28S rRNAs. This cleavage leads to the inhibition of protein biosynthesis, followed by cellular death through apoptosis. The structural and enzymatic properties show that Ageritin is the prototype of a novel specific ribonucleases family named ‘ribotoxin-like proteins’, recently found in fruiting bodies of other edible basidiomycetes mushrooms (e.g., Ostreatin from Pleurotus ostreatus, Edulitins from Boletus edulis, and Gambositin from Calocybe gambosa). Although the putative role of this toxin, present in high amount in fruiting body (>2.5 mg per 100 g) of C. aegerita, is unknown, its antifungal and insecticidal actions strongly support a role in defense mechanisms. Thus, in this review, we focus on structural, biological, antipathogenic, and enzymatic characteristics of this ribotoxin-like protein. We also highlight its biological relevance and potential biotechnological applications in agriculture as a bio-pesticide and in biomedicine as a therapeutic and diagnostic agent.

Potato Snakin-1: an antimicrobial player of the trade-off between host defense and development.

Snakin-1 (SN1) from potato is a cysteine-rich antimicrobial peptide with high evolutionary conservation. It has 63 amino acid residues, 12 of which are cysteines capable of forming six disulfide bonds. SN1 localizes in the plasma membrane, and it is present mainly in tissues associated with active growth and cell division. SN1 is active in vitro against bacteria, fungus, yeasts, and even animal/human pathogens. It was demonstrated that it also confers in vivo protection against commercially relevant pathogens in overexpressing potato, wheat, and lettuce plants. Although researchers have demonstrated SN1 can disrupt the membranes of E. coli, its integral antimicrobial mechanism remains unknown. It is likely that broad-spectrum antimicrobial activity is a combined outcome of membrane disruption and inhibition of intracellular functions. Besides, in potato, partial SN1 silencing affects cell division, leaf metabolism, and cell wall composition, thus revealing additional roles in growth and development. Its silencing also affects reactive oxygen species (ROS) and ROS scavenger levels. This finding indicates its participation in redox balance. Moreover, SN1 alters hormone levels, suggesting its involvement in the complex hormonal crosstalk. Altogether, SN1 has the potential to integrate development and defense signals directly and/or indirectly by modulating protein activity, modifying hormone balance and/or participating in redox regulation. Evidence supports a paramount role to SN1 in the mechanism underlying growth and immunity balance. Furthermore, SN1 may be a promising candidate in preservation, and pharmaceutical or agricultural biotechnology applications.

Salient Genetic Notes on Small-RNAs and their Applications in Agricultural Biotechnology

Small-RNAs are 20 to 27 nucleotides long non-protein-coding RNAs that act on either DNA or RNA to effect the regulation of gene expression. Small-RNAs are key in genetic and epigenetic regulation of diverse biological processes and pathways in response to biotic and abiotic environmental stresses. The gene regulatory functions of small-RNA molecules enhance healthy plant growth and normal development by controlling biological processes such as flowering programming, fruit development, disease and pests resistance. Small-RNAs comprise mainly microRNA and small interfering RNA species. MicroRNAs have been proven to primarily engage in posttranscriptional gene regulation while small interfering RNA have been implicated mainly in transcriptional gene regulation. This review covers the recent advancements in small-RNA research in plants, with emphasis on particularly microRNAs and small interfering RNA biogenesis, biological functions and their relevance in the regulation of traits of agronomic importance in plants. Also discussed extensively is the potential biotechnological applications of these small-RNAs for crop improvement.

Agrobiotechnology at The Nexus between Clientelism and The State’s Authority : The Indonesian Case

The impact of the Green Revolution in Indonesia over the past 50 years has entirely changed the social structure of the farming community. The state and its institutional apparatus once took a huge part in controlling the agricultural sector, yet this vital role has indeed declined dramatically over the past two decades in line with the political push to implement a democratic agenda due to the concerns with the society. However, in rural areas of Java the authoritarian mechanism of agricultural management was quickly replaced by a new type of patronage that no longer relied on land tenure, but rather controlled seeds and fertilizer. The link between the state and seeds as well as fertilizer companies in controlling the dynamics of the Javanese farmer community has led to every agricultural and polemic innovation that has shaped the state’s relationship with civil society for decades, which has not yet made the farmers an independent community. Regarding the issues concerning land tenure, a classic critique of patronage, now the shift over the meaning of patronage is more centered on the control of seeds and fertilizers as if these were still a critical effort that did not have adequate capacity on the part of farmers and those who stand for farmer justice. Criticism of the tacit application of agricultural biotechnology in East Java remains a secondary issue, and it faces no obstacles at all upon going through the clientelism structure driving the mechanism of agricultural management in rural areas.

Plant Genome Engineering for Targeted Improvement of Crop Traits.

To improve food security, plant biology research aims to improve crop yield and tolerance to biotic and abiotic stress, as well as increasing the nutrient contents of food. Conventional breeding systems have allowed breeders to produce improved varieties of many crops; for example, hybrid grain crops show dramatic improvements in yield. However, many challenges remain and emerging technologies have the potential to address many of these challenges. For example, site-specific nucleases such as TALENs and CRISPR/Cas systems, which enable high-efficiency genome engineering across eukaryotic species, have revolutionized biological research and its applications in crop plants. These nucleases have been used in diverse plant species to generate a wide variety of site-specific genome modifications through strategies that include targeted mutagenesis and editing for various agricultural biotechnology applications. Moreover, CRISPR/Cas genome-wide screens make it possible to discover novel traits, expand the range of traits, and accelerate trait development in target crops that are key for food security. Here, we discuss the development and use of various site-specific nuclease systems for different plant genome-engineering applications. We highlight the existing opportunities to harness these technologies for targeted improvement of traits to enhance crop productivity and resilience to climate change. These cutting-edge genome-editing technologies are thus poised to reshape the future of agriculture and food security.

An overview of genetically modified crop governance, issues and challenges in Malaysia.

The application of agricultural biotechnology attracts the interest of many stakeholders. Genetically modified (GM) crops, for example, have been rapidly increasing in production for the last 20 years. Despite their known benefits, GM crops also pose many concerns not only to human and animal health but also to the environment. Malaysia, in general, allows the use of GM technology applications but it has to come with precautionary and safety measures consistent with the international obligations and domestic legal frameworks. This paper provides an overview of GM crop technology from international and national context and explores the governance and issues surrounding this technology application in Malaysia. Basically, GM research activities in Malaysia are still at an early stage of research and development and most of the GM crops approved for release are limited for food, feed and processing purposes. Even though Malaysia has not planted any GM crops commercially, actions toward such a direction seem promising. Several issues concerning GM crops as discussed in this paper will become more complex as the number of GM crops and varieties commercialised globally increase and Malaysia starts to plant GM crops. © 2017 Society of Chemical Industry.

Complete genome sequence of endophyte Bacillus flexus KLBMP 4941 reveals its plant growth promotion mechanism and genetic basis for salt tolerance

Bacillus flexus KLBMP 4941 is a halotolerant endophyte isolated from the halophyte Limonium sinense. This strain can improve host seedling growth under salt stress conditions. We here report the complete genome information of endophyte KLBMP 4941. It has a circular chromosome and two plasmids for a total genome 4,104,242 bp in size with a G+C content of 38.09%. Genes related to plant growth promotion (PGP), such as those associated with nitrogen fixation, siderophore, spermidine, and acetoin synthesis were found in the KLBMP 4941 genome. Some genes responsible for high salinity tolerance, like genes associated with the Na+/H+ antiporter, glycine betaine transporter, and betaine-aldehyde dehydrogenase were also found in the KLBMP 4941 genome. The genome analysis will provide better understanding of the mechanisms underlying the promotion of plant growth in strain KLBMP 4941 under salt stress conditions and its ability to adapt to coastal salt marsh habitats, and provide a basis for its further biotechnological applications in agriculture.

Integration of Agrobacterium T-DNA into the Plant Genome.

Agrobacterium strains transfer a single-strand form of T-DNA (T-strands) and Virulence (Vir) effector proteins to plant cells. Following transfer, T-strands likely form complexes with Vir and plant proteins that traffic through the cytoplasm and enter the nucleus. T-strands may subsequently randomly integrate into plant chromosomes and permanently express encoded transgenes, a process known as stable transformation. The molecular processes by which T-strands integrate into the host genome remain unknown. Although integration resembles DNA repair processes, the requirement of known DNA repair pathways for integration is controversial. The configuration and genomic position of integrated T-DNA molecules likely affect transgene expression, and control of integration is consequently important for basic research and agricultural biotechnology applications. This article reviews our current knowledge of the process of T-DNA integration and proposes ways in which this knowledge may be manipulated for genome editing and synthetic biology purposes.

Classification of Isolates from the Pseudomonas fluorescens Complex into Phylogenomic Groups Based in Group-Specific Markers

The Pseudomonas fluorescens complex of species includes plant-associated bacteria with potential biotechnological applications in agriculture and environmental protection. Many of these bacteria can promote plant growth by different means, including modification of plant hormonal balance and biocontrol. The P. fluorescens group is currently divided into eight major subgroups in which these properties and many other ecophysiological traits are phylogenetically distributed. Therefore, a rapid phylogroup assignment for a particular isolate could be useful to simplify the screening of putative inoculants. By using comparative genomics on 71 P. fluorescens genomes, we have identified nine markers which allow classification of any isolate into these eight subgroups, by a presence/absence PCR test. Nine primer pairs were developed for the amplification of these markers. The specificity and sensitivity of these primer pairs were assessed on 28 field isolates, environmental samples from soil and rhizosphere and tested by in silico PCR on 421 genomes. Phylogenomic analysis validated the results: the PCR-based system for classification of P. fluorescens isolates has a 98.34% of accuracy and it could be used as a rapid and simple assay to evaluate the potential of any P. fluorescens complex strain.

Complete genome sequence of Serratia sp. YD25 (KCTC 42987) presenting strong antagonistic activities to various pathogenic fungi and bacteria

Serratia sp. YD25 (KCTC 42987) was originally isolated from rhizosphere soil in a continuous cropping tobacco-planting farm. Here, we show that its metabolites efficiently suppress the growth of various important pathogenic fungi and bacteria, causing infection in both plants and humans. In addition, Serratia sp. YD25 has a special trait of simultaneous production of both serrawettin W2 and prodigiosin, two important bioactive secondary metabolites produced by Serratia strains. Such co-production has not been reported in other Serratia strains. The complete genome sequence of Serratia sp. YD25 is presented, which is valuable for further exploration of its biotechnological applications in agriculture and medicine. The genome sequence reported here is also useful for understanding the unique regulatory mechanisms underlying biosynthesis of active compounds.