A Standardized Method for Estimating the Functional Diversity of Soil Bacterial Community by Biolog® EcoPlatesTM Assay—The Case Study of a Sustainable Olive Orchard

Abstract

Biolog® EcoPlates™ (Biolog Inc., Hayward, CA, USA) were developed to analyse the functional diversity of bacterial communities by means of measuring their ability to oxidize carbon substrates. This technique has been successfully adopted for studying bacterial soil communities from different soil environments, polluted soils and soils subjected to various agronomic treatments. Unfortunately, Biolog® EcoPlates™ assay, especially working on soil, can be difficult to reproduce and hard to standardize due to the lack of detailed procedures and protocols. The main problems of this technique mainly regard soil preparation, bacterial inoculum densities and a correct definition of blank during the calculation of the diversity indices. On the basis of our previous research on agricultural soils, we here propose a standardized and accurate step-by-step method for estimating the functional diversity of a soil bacterial community by Biolog® EcoPlatesTM assay. A case study of soils sampled in a Mediterranean olive orchard managed accordingly to sustainable/conservation practices was reported for justifying the standardized method here used. The results of this methodological paper could be important for correctly evaluating and comparing the microbiological fertility of soils managed by sustainable/conservation or conventional/non-conservation systems.

The Status of Soil Microbiome as Affected by the Application of Phosphorus Biofertilizer: Fertilizer Enriched with Beneficial Bacterial Strains

“…One way to determine functional diversity is community level physiological profiling (CLPP) with the application of plates (BIOLOG ® , Hayward, CA, USA) coated with various carbon sources and dedicated to specific groups of microorganisms. As a result, a characteristic and unique utilization pattern of the C-substrates called "metabolic fingerprinting" is obtained [130,131]. For the evaluation of the catabolic abilities of soil bacterial and fungal communities, BIOLOG ECO and BIOLOG FF microplates were used, respectively [132].…”

Searching for New Beneficial Bacterial Isolates of Wild Raspberries for Biocontrol of Phytopathogens-Antagonistic Properties and Functional Characterization

“…Furthermore, carrying out tests considering two wavelengths of light allows us to draw more specific conclusions. This is because absorbances for those wavelengths depend on different factors: 750 nm stands for optical density, and 590 nm for substrate usage [ 67 ]. Based on this knowledge it is possible to calculate the ratio between them [ 68 ].…”

Sustainable Agriculture and Soil Conservation

“…This SI collects 12 original contributions focused on soil use and management, soil conservation, as well as on the impact of some pollutants on the soil. Specifically, the SI collects nine research papers [10][11][12][13][14][15][16][17][18], two reviews [19,20] and one methodological work [21]. Eight of the twelve manuscripts considered the effects of soil use and management (topic I) [10][11][12][13][14][15][16]21], while the remaining four [17][18][19][20] evaluated the impact of some soil contaminants (e.g., crude oil, tungsten, copper and polycyclic aromatic hydrocarbons) (topic II).…”

“…Sofo and Ricciuti [21] presented a standardized method, named Biolog ® EcoPlates™ (Biolog Inc., Hayward, CA, USA), to analyze the functional diversity of bacterial communities by means of measuring their ability to oxidize carbon substrates. Specifically, they reported a detailed methodological procedure which was easy to follow and reproduce (i.e., a detailed and step-by-step description of soil preparation, dispersion and dilution, optimal bacterial density of the inoculum and so on), based on previous data and experiments.…”