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

Enhanced Botrytis cinerea resistance of Arabidopsis plants grown in compost may be explained by increased expression of defense-related genes, as revealed by microarray analysis

Composts are the products obtained after the aerobic degradation of different types of organic matter waste and can be used as substrates or substrate/soil amendments for plant cultivation. There is a small but increasing number of reports that suggest that foliar diseases may be reduced when using compost, rather than standard substrates, as growing medium. The purpose of this study was to examine the gene expression alteration produced by the compost to gain knowledge of the mechanisms involved in compost-induced systemic resistance. A compost from olive marc and olive tree leaves was able to induce resistance against Botrytis cinerea in Arabidopsis, unlike the standard substrate, perlite. Microarray analyses revealed that 178 genes were differently expressed, with a fold change cut-off of 1, of which 155 were up-regulated and 23 were down-regulated in compost-grown, as against perlite-grown plants. A functional enrichment study of up-regulated genes revealed that 38 Gene Ontology terms were significantly enriched. Response to stress, biotic stimulus, other organism, bacterium, fungus, chemical and abiotic stimulus, SA and ABA stimulus, oxidative stress, water, temperature and cold were significantly enriched, as were immune and defense responses, systemic acquired resistance, secondary metabolic process and oxireductase activity. Interestingly, PR1 expression, which was equally enhanced by growing the plants in compost and by B. cinerea inoculation, was further boosted in compost-grown pathogen-inoculated plants. Compost triggered a plant response that shares similarities with both systemic acquired resistance and ABA-dependent/independent abiotic stress responses

Effects of mulching and fertilization on soil nutrients, microbial activity and rhizosphere bacterial community structure determined by analysis of TRFLPs of PCR-amplified 16S rRNA genes

Organic mulches such as recycled, ground wood pallets and composted yard waste are widely used in landscapes to suppress weeds, and improve plant health. However, little is known about how mulches affect soil or rhizosphere microbial communities. In a field microcosm study, we compared effects of mulching with composted yard waste, ground wood pallets, or a bare soil control, with or without chemical fertilizer on soil mineral, chemical, biological, and rhizosphere bacterial community properties. Both mulch treatments had significant effects on organic matter content, soil respiration, microbial biomass N, soil pH, cation-exchange capacity, and concentrations of essential plant nutrients. Microbial respiration rate was highest in soils mulched with composted yard wastes (17.2 and 15.3 mg CO2 kg-1 per day for non-fertilized and fertilized plots, respectively) and lowest in bare soil plots (5.0 and 9.4 mg CO2 kg-1 per day for non-fertilized and fertilized plots, respectively). In general, the other parameters were highest in plots mulched with composted yard waste and not affected by fertilization. Bacterial communities in the rhizosphere of cucumber (Cucumis sativus L. Straight Light) seedlings grown in the microcosms were analyzed using most probable number (MPN) analysis of culturable heterotrophic fluorescent pseudomonads in King's B medium as well as by analysis of terminal restriction fragment length polymorphisms (TRFLPs) of PCR amplified 16S rRNA genes. Populations of culturable heterotrophic bacteria and fluorescent pseudomonads in the rhizosphere were significantly greater in the composted yard waste plots than the bare soil fertilized mulched plots. TRFLP analysis of PCR amplified bacterial 16S rRNA genes from triplicate root tips grown in each treatment and digested with HhaI, MspI, and RsaI revealed that the TRFLP similarity was 0.81-0.91 among triplicate samples and 0.48-0.86 among different treatments. The TRFLP pattern of rhizosphere communities from the bare soil treatment were more similar (54-82%) to plots mulched with ground wood than to plots mulched with compost. Only 48-71% of TRFLP peaks detected in samples from the compost treatment were also detected in the bare soil control. The similarity in TRFLPs between the compost and ground wood pallet treatments was 56-80%. Although the community profiles showed differences in bacterial diversity, no significant difference in TRFLP-based diversity indices were observed. Unique TRF peaks detected among treatments suggest that specific subcomponents of the microbial communities differed. A higher number of TRFs corresponding with biocontrol organisms such as Pseudomonas and Pantoea spp. were observed in plots mulched with compost. However, the mulch treatments had more pronounced effects on soil chemical and microbial properties than on TRFLP based bacterial community structure on cucumber roots. Nonetheless, the data show clearly that mulching with compost strongly influenced the structure of the microbial rhizophere community. © 2002 Elsevier Science B.V. All rights reserved.http://deepblue.lib.umich.edu/bitstream/2027.42/191268/2/JA2-2002-PDF.pdfPublished versio

Isolation and Characterization of Rhizobacteria from Composts That Suppress the Severity of Bacterial Leaf Spot of Radish

Composts can induce systemic resistance in plants to disease. Unfortunately, the degree of resistance induced seems highly variable and the basis for this effect is not understood. In this work, only 1 of 79 potting mixes prepared with different batches of mature, stabilized composts produced from several different types of solid wastes suppressed the severity of bacterial leaf spot of radish caused by Xanthomonas campestris pv. armoraciae compared with disease on plants produced in a nonamended sphagnum peat mix. An additional batch of compostamended mix that had been inoculated with Trichoderma hamatum 382 (T382), which is known to induce systemic resistance in plants, also suppressed the disease. A total of 11 out of 538 rhizobacterial strains isolated from roots of radish seedlings grown in these two compostamended mixes that suppressed bacterial leaf spot were able to significantly suppress the severity of this disease when used as inoculum in the compost-amended mixes. The most effective strains were identified as Bacillus sp. based on partial sequencing of 16S rDNA. These strains were significantly less effective in reducing the severity of this disease than T382. A combined inoculum consisting of T382 and the most effective rhizobacterial Bacillus strain was less effective than T 382 alone. A drench applied to the potting mix with the systemic acquired resistance-inducing chemical acibenzolar-S-methyl was significantly more effective than T382 in several, but not all tests. We conclude that systemic suppression of foliar diseases induced by compost amendments is a rare phenomenon. Furthermore, inoculation of compost-amended potting mixes with biocontrol agents such as T382 that induce systemic resistance in plants can significantly increase the frequency of systemic disease control obtained with natural compost amendments. Raphanus sativus.http://deepblue.lib.umich.edu/bitstream/2027.42/191265/2/JA2-2003-PDF.pdfPublished versio