Mid-term report for the CORE Organic II funded project. “Innovative cropping Practices to increase soil health of organic fruit tree orchards” BIO-INCROP

Activities performed in the first part of BIO-INCROP project concern five of the eight main objectives fixed in the project proposal. They are: Evaluation of soil borne pest and pathogens involved in replant disease Role of rhizospheric bacterial and fungal communities in plant health Selection of naturally available resources to increase microbial diversity and biomass Compost and organic amendments Evaluation of biologically active formulates The document reports main research results and shows main items of dissemination activity performed in the first part of the project

Application of COMPOCHIP Microarray to Investigate the Bacterial Communities of Different Composts

A microarray spotted with 369 different 16S rRNA gene probes specific to microorganisms involved in the degradation process of organic waste during composting was developed. The microarray was tested with pure cultures, and of the 30,258 individual probe-target hybridization reactions performed, there were only 188 false positive (0.62%) and 22 false negative signals (0.07%). Labeled target DNA was prepared by polymerase chain reaction amplification of 16S rRNA genes using a Cy5-labeled universal bacterial forward primer and a universal reverse primer. The COMPOCHIP microarray was applied to three different compost types (green compost, manure mix compost, and anaerobic digestate compost) of different maturity (2, 8, and 16 weeks), and differences in the microorganisms in the three compost types and maturity stages were observed. Multivariate analysis showed that the bacterial composition of the three composts was different at the beginning of the composting process and became more similar upon maturation. Certain probes (targeting Sphingobacterium, Actinomyces, Xylella/Xanthomonas/ Stenotrophomonas, Microbacterium, Verrucomicrobia, Planctomycetes, Low G + C and Alphaproteobacteria) were more influential in discriminating between different composts. Results from denaturing gradient gel electrophoresis supported those of microarray analysis. This study showed that the COMPOCHIP array is a suitable tool to study bacterial communities in composts

PhylArray: phylogenetic probe design algorithm for microarray

International audienceMOTIVATION: Microbial diversity is still largely unknown in most environments, such as soils. In order to get access to this microbial 'black-box', the development of powerful tools such as microarrays are necessary. However, the reliability of this approach relies on probe efficiency, in particular sensitivity, specificity and explorative power, in order to obtain an image of the microbial communities that is close to reality. RESULTS: We propose a new probe design algorithm that is able to select microarray probes targeting SSU rRNA at any phylogenetic level. This original approach, implemented in a program called 'PhylArray', designs a combination of degenerate and non-degenerate probes for each target taxon. Comparative experimental evaluations indicate that probes designed with PhylArray yield a higher sensitivity and specificity than those designed by conventional approaches. Applying the combined PhyArray/GoArrays strategy helps to optimize the hybridization performance of short probes. Finally, hybridizations with environmental targets have shown that the use of the PhylArray strategy can draw attention to even previously unknown bacteria

Aged-engineered nanoparticles effect on sludge anaerobic digestion performance and associated microbial communities

To investigate the potential effect of aged engineered nanoparticles (a-ENPs) on sludge digestion performance, 150 L pilot anaerobic digesters (AD) were fed with a blend of primary and waste activated sludge spiked either with a mixture of silver oxide, titanium dioxide and zinc oxide or a mixture of their equivalent bulk metal salts to achieve a target concentration of 250, 2000, and 2800 mg kg− 1 dry weight, respectively. Volatile fatty acids (VFA) were 1.2 times higher in the spiked digesters and significantly different (p = 0.05) from the control conditions. Specifically, isovaleric acid concentration was 2 times lower in the control digester compared to the spiked digesters, whereas hydrogen sulfide was 2 times lower in the ENPs spiked digester indicating inhibitory effect on sulfate reducing microorganisms. Based on the ether-linked isoprenoids concentration, the total abundance of methanogens was 1.4 times lower in the ENPs spiked digester than in the control and metal salt spiked digesters. Pyrosequencing indicated 80% decrease in abundance and diversity of methanogens in ENPs spiked digester compared to the control digester. Methanosarcina acetivorans and Methanosarcina barkeri were identified as nano-tolerant as their relative abundance increased by a factor of 6 and 11, respectively, compared to the other digesters. The results further provide compelling evidence on the resilience of Fusobacteria, Actinobacteria and the Trojan horse-like effect of ENPs which offered a competitive advantage to some organisms while reducing microbial abundance and diversity

Influence of a Conductive Material and Different Anaerobic Inocula on Biochemical Methane Potential of Substrates from Alcoholic Beverage Production

The impact of a conductive material as powdered activated carbon (PAC) on the biochemical methane potential of whisky pot ale (PA) and brewery spent yeast (SY) was investigated. The test was carried out with three different types of anaerobic inocula: manure inoculum (MI), sewage sludge (SS) and granular sludge (GR). Brewery spent yeast produced partial (in sewage and granular sludge) and total (in manure inoculum) methanogenesis inhibition due to the toxicity of some of its constituents (hops extract). The inhibition was overcome by the supplementation of PAC, that improved significantly the anaerobic digestion process for SY, allowing to reach biochemical methane potential values between 657-699 L CH4 kg-1 VS and it reduced redox potential from 369 to 398 mV. The activated carbon did not improve the methane yields from whisky PA since microorganisms did not have difficulties to process this substrate; in fact, the redox potential slightly increased from 355 to 330 mV