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

Biolog® EcoPlatesTM (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® EcoPlatesTM 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.

[1]  L. Lanyon,et al.  Evaluating soil management with microbial community-level physiological profiles , 2005 .

[2]  J. Orlando,et al.  Environmental conditions shape soil bacterial community structure in a fragmented landscape , 2016 .

[3]  Éva Ujaczki,et al.  Influence of red mud on soil microbial communities: Application and comprehensive evaluation of the Biolog EcoPlate approach as a tool in soil microbiological studies. , 2017, The Science of the total environment.

[4]  Zhiwei Ge,et al.  Application and Optimization of Biolog EcoPlates in Functional Diversity Studies of Soil Microbial Communities , 2015 .

[5]  J. Deckers,et al.  Long-term consequences of tillage, residue management, and crop rotation on selected soil micro-flora groups in the subtropical highlands , 2008 .

[6]  Lynne Boddy,et al.  Analysis of microbial community functional diversity using sole-carbon-source utilisation profiles - a critique. , 2002, FEMS microbiology ecology.

[7]  C. Crecchio,et al.  Soil microbial diversity and activity in a Mediterranean olive orchard using sustainable agricultural practices , 2014 .

[8]  G. Braker,et al.  Diversity and Activity of Denitrifiers of Chilean Arid Soil Ecosystems , 2012, Front. Microbio..

[9]  Yan-xia Li,et al.  Effects of chlortetracycline on soil microbial communities: Comparisons of enzyme activities to the functional diversity via Biolog EcoPlates™ , 2015 .

[10]  Julie E. Jones,et al.  Interactions between crop residue and soil organic matter quality and the functional diversity of soil microbial communities , 2002 .

[11]  J. Orlando,et al.  Intrinsic factors of Peltigera lichens influence the structure of the associated soil bacterial microbiota. , 2016, FEMS microbiology ecology.

[12]  M. Willig,et al.  Functional diversity of microbial communities: A quantitative approach , 1994 .

[13]  C. Crecchio,et al.  The metabolic and genetic diversity of soil bacterial communities depends on the soil management system and C/N dynamics: The case of sustainable and conventional olive groves , 2019, Applied Soil Ecology.

[14]  Lin Zhao,et al.  The soil carbon/nitrogen ratio and moisture affect microbial community structures in alkaline permafrost-affected soils with different vegetation types on the Tibetan plateau. , 2014, Research in microbiology.

[15]  I. Allegretta,et al.  Leaf biochemical responses and fruit oil quality parameters in olive plants subjected to airborne metal pollution. , 2017, Chemosphere.

[16]  G. Celano,et al.  Genetic, Functional, and Metabolic Responses of Soil Microbiota in a Sustainable Olive Orchard , 2010 .

[17]  R. Calbrix,et al.  Analysis of the potential functional diversity of the bacterial community in soil: a reproducible procedure using sole-carbon-source utilization profiles , 2005 .

[18]  A. Mills,et al.  Classification and Characterization of Heterotrophic Microbial Communities on the Basis of Patterns of Community-Level Sole-Carbon-Source Utilization , 1991, Applied and environmental microbiology.

[19]  J. Orlando,et al.  Effect of Colletia hystrix (Clos), a pioneer actinorhizal plant from the Chilean matorral, on the genetic and potential metabolic diversity of the soil bacterial community , 2007 .

[20]  E. Puglisi,et al.  Changes in chemical and biological soil properties as induced by anthropogenic disturbance: A case study of an agricultural soil under recurrent flooding by wastewaters , 2006 .