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

Abstract

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 CO 2 kg −1 per day for non-fertilized and fertilized plots, respectively) and lowest in bare soil plots (5.0 and 9.4 mg CO 2 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.