Community level physiological profiling of microorganisms in the rhizosphere of transgenic plants – A review

Since 1996, when the first genetically modified seeds were planted in field conditions, the commercial growing of genetically modified crops increased to over 134 millions of hectares in 2009 worldwide. Along with the great potential of transgenic plants for future agriculture, considerable concerns on their biosafety have been raised, including their potential impact on soil microbial communities. This review briefly summarizes the important features of soil microorganisms for plant health and ecosystem stability, the numerous methods available for microbial ecologists to study soil microbial diversity, with emphasis on the method of community level physiological profiling (CLPP) based on carbon substrate utilization patterning, and finally the use of CLPP for assessing the effects of transgenic crops on soil microbial communities.

Analysis of Bacterial Community level Physiological Profiling on the Fermentation of Traditional Pliek u using BIOLOG EcoPlates

Pliek u is an Acehnese traditional condiment made from fermented coconut (Cocos nucifera) endosperm. The traditional pliek u fermentation process typically involves a diverse bacterial community. This research aimed to discover the physiological profile of the bacterial community diversity in pliek u fermentation. BIOLOGTM EcoPlates was used to obtain the physiological functions of the bacterial community during the pliek u fermentation process. The bacteria were then isolated from EcoPlate substrate to determine the predominant microorganism. Results from the analysis showed that the value of the Average Well Colour Development (AWCD) increased during the EcoPlates incubation period. The AWCD values in sample IV were higher than the AWCD values in samples I, II, and III. PCA analysis showed that the use of EcoPlate substrate by the bacterial community at the beginning of the fermentation was correlated with the substrate groups of carbohydrate and polymer, and with the substrate groups of carbohydrate and the amino acid at the end of the fermentation. The phylogenetic analysis showed that EC1 had a close relation with Pseudomonas azotoformans strain NBRC, while EC3 had a close relation with Psedomonas lundensis strain ATCC 49968. In conclusion, there were changes in the use of EcoPlate substrate and the activities of the bacterial community during the pliek u fermentation process.

Application of Erythromycin and/or Raoultella sp. Strain MC3 Alters the Metabolic Activity of Soil Microbial Communities as Revealed by the Community Level Physiological Profiling Approach

Erythromycin (EM), a macrolide antibiotic, by influencing the biodiversity of microorganisms, might change the catabolic activity of the entire soil microbial community. Hence, the goal of this study was to determine the metabolic biodiversity in soil treated with EM (1 and 10 mg/kg soil) using the community-level physiological profiling (CLPP) method during a 90-day experiment. In addition, the effect of soil inoculation with antibiotic-resistant Raoultella sp. strain MC3 on CLPP was evaluated. The resistance and resilience concept as well as multifactorial analysis of data was exploited to interpret the outcomes obtained. EM negatively affected the metabolic microbial activity, as indicated by the values of the CLPP indices, i.e., microbial activity expressed as the average well-color development (AWCD), substrate richness (R), the Shannon–Wiener (H) and evenness (E) indices and the AWCD values for the six groups of carbon substrate present in EcoPlates until 15 days. The introduction of strain MC3 into soil increased the degradative activity of soil microorganisms in comparison with non-inoculated control. In contrast, at the consecutive sampling days, an increase in the values of the CLPP parameters was observed, especially for EM-10 + MC3-treated soil. Considering the average values of the resistance index for all of the measurement days, the resistance of the CLPP indices and the AWCD values for carbon substrate groups were categorized as follows: E > H > R > AWCD and polymers > amino acids > carbohydrates > miscellaneous > amines > carboxylic acids. The obtained results suggest a low level of resistance of soil microorganisms to EM and/or strain MC3 at the beginning of the exposure time, but the microbial community exhibited the ability to recover its initial decrease in catabolic activity over the experimental period. Despite the short-term effects, the balance of the soil ecosystem may be disturbed.

Potensi Metabolik Komunitas Bakteri Endofit dan Rhizosfer Ubi Jalar (Ipomoea batatas L.) Berdasarkan Analisis Community-Level Physiological Profiles (CLPP)

Aktivitas metabolik dari komunitas bakteri endofit dan rizosfir diukur untuk membandingkan tingkat community-level physiological profiling (CLPP) menggunakan Biolog Ecoplates. Hasil penelitian kami menunjukkan kepadatan bakteri meningkat dengan urutan: endofit<rhizosfer. Keragaman mikroba dinilai oleh kekayaan spesies, jumlah spesies dan indeks kesamaan. Aktivitas total mikroba tertinggi diamati pada mikroba rhizosfer. CLPP menunjukkan bahwa bakteri bisa memanfaatkan semua kelompok sumber karbon sebagai berikut karbohidrat, asam amino, asam karboksilat, polimer, amina/amida, dan senyawa fenolik. Karbohidrat yang paling dimanfaatkan. Total metabolic activity of endophytic and rhizosphere of bacterial community of sweet potato was measured to compare the community-level physiological profiles (CLPP) using by Biolog Ecoplates. Result of our study revealed that bacterial density increased in the following order: endophytes < rhizosphere. The microbial diversity assessed by species richness, the total number of species present and species evenness. The highest total microbial activity was observed for the rhizosphere. The CLPP revealed that the bacteria could differentially utilize all the groups of carbon sources as follows carbohydrate, amino acid, carboxilyc acid, polymer, amine/amide, and phenolic compound. Carbohydrate was most utilized.