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Qiao J.-Q.,Nanjing Agricultural University | Qiao J.-Q.,Jiangsu Academy of Agricultural Sciences | Wu H.-J.,Nanjing Agricultural University | Huo R.,Nanjing Agricultural University | And 3 more authors.
Applied Adhesion Science | Year: 2015

During the last decade, the use of plant-root colonizing bacteria with plant growth-promoting activity has been proven as an efficient and environmental-friendly alternative to chemical pesticides and fertilizers. Biofertilizer and biocontrol formulations prepared from endospore-forming Bacillus strains are increasingly applied due to their long shelf life, which is comparable with that of agrochemicals. Today, spore suspensions from natural representatives of mainly Bacillus amyloliquefaciens, Bacillus subtilis, and Bacillus pumilus are available. However, these biofertilizers, directly prepared from environmental strains, are sometimes hampered in their action and do not fulfill in each case the expectations of the appliers (Borriss R, Bacteria in agrobiology: plant growth responses, Springer, 2011, pp. 41-76). This review will focus on several ways to improve the action of B. amyloliquefaciens subsp. plantarum FZB42T, the type strain for the group of plant-associated B. amyloliquefaciens strains. We are focusing here on genomics and genetic engineering techniques as helpful tools for developing more powerful biofertilizer and biocontrol agents. © 2014, Qiao et al.; licensee Springer.

Fan B.,Nanjing Forestry University | Fan B.,Humboldt University of Berlin | Carvalhais L.C.,Humboldt University of Berlin | Becker A.,Albert Ludwigs University of Freiburg | And 4 more authors.
BMC Microbiology | Year: 2012

Background: Plant root exudates have been shown to play an important role in mediating interactions between plant growth-promoting rhizobacteria (PGPR) and their host plants. Most investigations were performed on Gram-negative rhizobacteria, while much less is known about Gram-positive rhizobacteria. To elucidate early responses of PGPR to root exudates, we investigated changes in the transcriptome of a Gram-positive PGPR to plant root exudates. Results: Bacillus amyloliquefaciens FZB42 is a well-studied Gram-positive PGPR. To obtain a comprehensive overview of FZB42 gene expression in response to maize root exudates, microarray experiments were performed. A total of 302 genes representing 8.2% of the FZB42 transcriptome showed significantly altered expression levels in the presence of root exudates. The majority of the genes (261) was up-regulated after incubation of FZB42 with root exudates, whereas only 41 genes were down-regulated. Several groups of the genes which were strongly induced by the root exudates are involved in metabolic pathways relating to nutrient utilization, bacterial chemotaxis and motility, and non-ribosomal synthesis of antimicrobial peptides and polyketides. Conclusions: Here we present a transcriptome analysis of the root-colonizing bacterium Bacillus amyloliquefaciens FZB42 in response to maize root exudates. The 302 genes identified as being differentially transcribed are proposed to be involved in interactions of Gram-positive bacteria with plants. © 2012 Fan et al.; licensee BioMed Central Ltd.

Carvalhais L.C.,University of Hohenheim | Carvalhais L.C.,Humboldt University of Berlin | Carvalhais L.C.,University of Queensland | Dennis P.G.,University of Queensland | And 9 more authors.
PLoS ONE | Year: 2013

Plants have developed a wide-range of adaptations to overcome nutrient limitation, including changes to the quantity and composition of carbon-containing compounds released by roots. Root-associated bacteria are largely influenced by these compounds which can be perceived as signals or substrates. Here, we evaluate the effect of root exudates collected from maize plants grown under nitrogen (N), phosphate (P), iron (Fe) and potassium (K) deficiencies on the transcriptome of the plant growth promoting rhizobacterium (PGPR) Bacillus amyloliquefaciens FZB42. The largest shifts in gene expression patterns were observed in cells exposed to exudates from N-, followed by P-deficient plants. Exudates from N-deprived maize triggered a general stress response in FZB42 in the exponential growth phase, which was evidenced by the suppression of numerous genes involved in protein synthesis. Exudates from P-deficient plants induced bacterial genes involved in chemotaxis and motility whilst exudates released by Fe and K deficient plants did not cause dramatic changes in the bacterial transcriptome during exponential growth phase. Global transcriptional changes in bacteria elicited by nutrient deficient maize exudates were significantly correlated with concentrations of the amino acids aspartate, valine and glutamate in root exudates suggesting that transcriptional profiling of FZB42 associated with metabolomics of N, P, Fe and K-deficient maize root exudates is a powerful approach to better understand plant-microbe interactions under conditions of nutritional stress. © 2013 Carvalhais et al.

Agency: European Commission | Branch: FP7 | Program: CP-TP | Phase: KBBE.2012.1.2-03 | Award Amount: 7.69M | Year: 2012

BIOFECTOR is an integrated project that develops alternative fertilisation strategies by the use of various bio-effectors (BEs, plant growth promoting microorganisms and natural extraction products). BEs stimulate root growth, solubilise and mineralise sparingly available nutrients, or protect plants from abiotic and biotic stresses. Novel BEs will be isolated, characterized and applied in strategic combination with alternative fertilisation strategies that include organic and low-input farming, use of waste recycling fertilizers, and fertiliser-placement technologies. Bio-effectors addressed comprise fungal strains of Trichoderma, Penicillium and Sebacinales, as well as bacterial strains of Bacillus and Pseudomonades with well-characterized root growth promoting and nutrient solubilising potential. Natural extraction products of seaweed, compost and plant extracts, as well as their purified active compounds are also tested in various combinations. Maize, wheat and tomato are chosen as representative crops. Laboratory and European-wide field experiments assure product adaptation to divers geo-climatic conditions. Viable alternatives to the conventional practice of mineral fertilisation are developed, towards environmental friendly agricultural practice with reduced agrochemical input.

Mariappan A.,Humboldt University of Berlin | Makarewicz O.,Universittsklinikum Jena | Makarewicz O.,Humboldt University of Berlin | Chen X.-H.,Humboldt University of Berlin | And 2 more authors.
Journal of Molecular Microbiology and Biotechnology | Year: 2012

The plant-growth-promoting-rhizobacteria Bacillus amyloliquefaciens FZB42 possess an enormous potential to synthesize a wide range of antimicrobial, antiviral and nematocidal compounds. One of them, the dipeptide antibiotic bacilysin, is synthesized by FZB42 during exponential growth. Here, we have demonstrated that bacilysin is positively regulated by the two-component response regulator DegU at the transcriptional level. In addition, ScoC (Hpr), a transition state regulator, negatively controlled expression of the bacA gene, which is the first gene within the bacilysin operon. Both DegU and ScoC were bound directly at the bacA promoter region. Furthermore, a monocistronic gene located in close vicinity of the bac operon and essential for bacilysin production, ywfH, was also regulated by DegU. Transcription of the bac operon and of the ywfH gene in B. amyloliquefaciens FZB42 was positively controlled by the DegU global regulator protein. The role of interactions within a ternary complex formed by the antagonistically acting regulators DegU and ScoC as well as the bacA promoter sequence remains to be elucidated. Copyright © 2012 S. Karger AG, Basel.

Agency: European Commission | Branch: H2020 | Program: MSCA-ITN-ETN | Phase: MSCA-ITN-2015-ETN | Award Amount: 3.91M | Year: 2015

We need to increase the crop yield while reducing pesticide and use of inorganic fertiliser to meet the challenges of world population growth and climate change. Plant endophytic microorganisms can improve plant yield and enhance plant tolerance to abiotic stress as well as to pathogens under experimental conditions, but these effects are often not sufficiently stable for practical application. How do we boost the stability and reliability of the positive effects of endophytes on plants? We need to understand the genetic basis of beneficial interactions between crops and endophytes and extent this basis exhibits phenotypic plasticity at all interaction levels from the cellular to the field environment. This requires increasing our knowledge of the molecular mechanisms underlying the effects of endophytes, including intra and inter-kingdom exchange and distribution of resources (nutrients), signalling and possibly regulation between and inside the partners, the mutual induced production of secondary metabolites and the environmental cues which influence crop-endophyte interactions. The genetic variation and its plasticity in host and microbe will be exploited in to establish crop breeding and inoculum production processes for boosting the establishment and stability of plant-microbe mutualisms to benefit crop development, stress tolerance, pathogen resistance and quality. In this project we will provide fundamental biological as well as practical knowledge about interactions between endophytes and plants. This improved understanding will pave the way for increased use of endophytes to improve sustainability and plant productivity in a reliable way. The participants in this project comprise many of the key institutions and industries working with these problems and provide a uniquely strong consortium to address the key issues. Furthermore, the consortium will train a new generation of scientists who have the insight and skills to continue this task in their careers.

Blom J.,Bielefeld University | Rueckert C.,Bielefeld University | Niu B.,China Agricultural University | Niu B.,Humboldt University of Berlin | And 3 more authors.
Journal of Bacteriology | Year: 2012

The genome of the rhizobacterium Bacillus amyloliquefaciens subsp. plantarum CAU B946 was 4.02 Mb in size and harbored 3,823 genes (coding sequences [CDS]). Nine giant gene clusters were dedicated to nonribosomal synthesis of antimicrobial compounds. Remarkably, strain CAU B946 possessed a gene cluster involved in synthesis of iturin A. © 2012, American Society for Microbiology.

Wibberg D.,Bielefeld University | Jelonek L.,Bielefeld University | Rupp O.,Bielefeld University | Hennig M.,Bielefeld University | And 8 more authors.
Journal of Biotechnology | Year: 2013

Anastomosis group AG1-IB isolates of the anamorphic basidiomycetous fungus Rhizoctonia solani Kühn affect various agricultural and horticultural important crops including bean, rice, soybean, figs, hortensia, cabbage and lettuce. To gain insights into the genome structure and content, the first draft genome sequence of R. solani AG1-IB isolate 7/3/14 was established. Four complete runs on the Genome Sequencer (GS) FLX platform (Roche Applied Science) yielding approx. a 25-fold coverage of the R. solani genome were accomplished. Assembly of the sequence reads by means of the gsAssembler software version 2.6 applying the heterozygotic mode resulted in numerous contigs and scaffolds and a predicted size of 87.1. Mb for the diploid status of the genome. 'Contig-length vs. read-count' analysis revealed that the assembled contigs can be classified into five different groups. Detailed BLAST-analysis revealed that most contigs of group II feature high-scoring matches to other contigs of the same group suggesting that distinguishable allelic variants exist for many genes. Due to the supposed diploid and heterokaryotic nature of R. solani AG1-IB 7/3/14, this result has been anticipated. However, the heterokaryotic character of the isolate is not really supported by sequencing data obtained for the isolate R. solani AG1-IB 7/3/14. Coverage of group III contigs is twice as high as for group II contigs which can also be explained by the diploid status of the genome and indistinguishable alleles on homologous chromosomes. Assembly of sequence data led to the identification of the rRNA unit (group V contigs) and the mitochondrial (mt) genome (group IV contigs) which is a circular molecule of 162,751. bp in size featuring a GC-content of 36.4%. The R. solani 7/3/14 mt-genome is one of the largest fungal mitochondrial genomes known to date. Its large size essentially is due to the presence of numerous non-conserved hypothetical ORFs and introns. Gene prediction for the R. solani AG1-IB 7/3/14 genome was conducted by the Augustus Gene Prediction Software for Eukaryotes (version 2.6.) applying the parameter set for the fungus Coprinopsis cinerea okayama 7#130. Gene prediction and annotation provided first insights into the R. solani AG1-IB 7/3/14 gene structure and content. In total, 12,422 genes were predicted. The average number of exons per gene is five. Exons have a mean length of 214. bp, whereas introns on average are 66. bp in length. Annotation of the genome revealed that 4169 of 12,422 genes could be assigned to KOG functional categories. © 2012 Elsevier B.V.

Chowdhury S.P.,Helmholtz Center for Environmental Research | Hartmann A.,Helmholtz Center for Environmental Research | Gao X.,Nanjing Agricultural University | Gao X.,Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects | And 2 more authors.
Frontiers in Microbiology | Year: 2015

Bacillus amyloliquefaciens subsp. plantarum FZB42 is a Gram-positive model bacterium for unraveling plant-microbe interactions in Bacilli. In addition, FZB42 is used commercially as biofertilizer and biocontrol agent in agriculture. Genome analysis of FZB42 revealed that nearly 10% of the FZB42 genome is devoted to synthesizing antimicrobial metabolites and their corresponding immunity genes. However, recent investigations in planta demonstrated that - except surfactin - the amount of such compounds found in vicinity of plant roots is relatively low, making doubtful a direct function in suppressing competing microflora including plant pathogens. These metabolites have been also suspected to induce changes within the rhizosphere microbial community, which might affect environment and plant health. However, sequence analysis of rhizosphere samples revealed only marginal changes in the root microbiome, suggesting that secondary metabolites are not the key factor in protecting plants from pathogenic microorganisms. On the other hand, adding FZB42 to plants compensate, at least in part, changes in the community structure caused by the pathogen, indicating an interesting mechanism of plant protection by beneficial Bacilli. Sub-lethal concentrations of cyclic lipopeptides and volatiles produced by plant-associated Bacilli trigger pathways of induced systemic resistance (ISR), which protect plants against attacks of pathogenic microbes, viruses, and nematodes. Stimulation of ISR by bacterial metabolites is likely the main mechanism responsible for biocontrol action of FZB42. © 2015 Chowdhury, Hartmann, Gao and Borriss.

Chowdhury S.P.,Helmholtz Center for Environmental Research | Dietel K.,ABiTEP GmbH | Randler M.,ABiTEP GmbH | Schmid M.,Helmholtz Center for Environmental Research | And 4 more authors.
PLoS ONE | Year: 2013

The soil-borne pathogen Rhizoctonia solani is responsible for crop losses on a wide range of important crops worldwide. The lack of effective control strategies and the increasing demand for organically grown food has stimulated research on biological control. The aim of the present study was to evaluate the rhizosphere competence of the commercially available inoculant Bacillus amyloliquefaciens FZB42 on lettuce growth and health together with its impact on the indigenous rhizosphere bacterial community in field and pot experiments. Results of both experiments demonstrated that FZB42 is able to effectively colonize the rhizosphere (7.45 to 6.61 Log 10 CFU g-1 root dry mass) within the growth period of lettuce in the field. The disease severity (DS) of bottom rot on lettuce was significantly reduced from severe symptoms with DS category 5 to slight symptom expression with DS category 3 on average through treatment of young plants with FZB42 before and after planting. The 16S rRNA gene based fingerprinting method terminal restriction fragment length polymorphism (T-RFLP) showed that the treatment with FZB42 did not have a major impact on the indigenous rhizosphere bacterial community. However, the bacterial community showed a clear temporal shift. The results also indicated that the pathogen R. solani AG1-IB affects the rhizosphere microbial community after inoculation. Thus, we revealed that the inoculant FZB42 could establish itself successfully in the rhizosphere without showing any durable effect on the rhizosphere bacterial community. © 2013 Chowdhury et al.

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