title: Microbial Profiling of a Suppressiveness-Induced Agricultural Soil Amended with Composted Almond Shells.
abstract: This study focused on the microbial profile present in an agricultural soil that becomes suppressive after the application of composted almond shells (AS) as organic amendments. For this purpose, we analyzed the functions and composition of the complex communities present in an experimental orchard of 40-year-old avocado trees, many of them historically amended with composted almond shells. The role of microbes in the suppression of Rosellinia necatrix, the causative agent of avocado white root rot, was determined after heat-treatment and complementation experiments with different types of soil. Bacterial and fungal profiles obtained from natural soil samples based on the 16S rRNA gene and ITS sequencing revealed slight differences among the amended (AS) and unamended (CT) soils. When the soil was under the influence of composted almond shells as organic amendments, an increase in Proteobacteria and Ascomycota groups was observed, as well as a reduction in Acidobacteria and Mortierellales. Complementary to these findings, functional analysis by GeoChip 4.6 confirmed these subtle differences, mainly present in the relative abundance of genes involved in the carbon cycle. Interestingly, a group of specific probes included in the "soil benefit" category was present only in AS-amended soils, corresponding to specific microorganisms previously described as potential biocontrol agents, such as Pseudomonas spp., Burkholderia spp., or Actinobacteria. Considering the results of both analyses, we determined that AS-amendments to the soil led to an increase in some orders of Gammaproteobacteria, Betaproteobacteria, and Dothideomycetes, as well as a reduction in the abundance of Xylariales fungi (where R. necatrix is allocated). The combination of microbial action and substrate properties of suppressiveness are discussed.
authors.affiliation: Departamento de Microbiología, Facultad de Ciencias, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas Málaga, Spain.
authors.forename: Carmen
authors.initials: C
authors.lastname: Vida
authors.affiliation: Departamento de Microbiología, Facultad de Ciencias, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas Málaga, Spain.
authors.forename: Nuria
authors.initials: N
authors.lastname: Bonilla
authors.affiliation: Departamento de Microbiología, Facultad de Ciencias, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas Málaga, Spain.
authors.forename: Antonio
authors.initials: A
authors.lastname: de Vicente
authors.affiliation: Departamento de Microbiología, Facultad de Ciencias, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas Málaga, Spain.
authors.forename: Francisco M
authors.initials: FM
authors.lastname: Cazorla
keywords: almond shells; amendment; microbial profiling; soil; suppressiveness
references.citation: Phytopathology. 2000 Feb;90(2):125-33
references.pmid: 18944600
references.citation: Annu Rev Phytopathol. 2002;40:309-48
references.pmid: 12147763
references.citation: Mol Ecol Resour. 2014 Sep;14(5):914-28
references.pmid: 24520909
references.citation: Appl Microbiol Biotechnol. 2013 Aug;97(15):7035-48
references.pmid: 23135227
references.citation: Annu Rev Phytopathol. 2012;50:133-53
references.pmid: 22920558
references.citation: Mol Plant Pathol. 2012 Apr;13(3):226-39
references.pmid: 22014332
references.citation: Appl Environ Microbiol. 2010 Feb;76(4):1088-94
references.pmid: 20038701
references.citation: J Hazard Mater. 2009 Aug 15;167(1-3):1203-8
references.pmid: 19272708
references.citation: Curr Opin Biotechnol. 2012 Feb;23(1):49-55
references.pmid: 22100036
references.citation: Bioresour Technol. 2011 Sep;102(17):8027-34
references.pmid: 21752637
references.citation: FEMS Microbiol Ecol. 2014 Jul;89(1):20-31
references.pmid: 24641321
references.citation: Persoonia. 2013 Jun;30:77-93
references.pmid: 24027348
references.citation: Appl Environ Microbiol. 2010 Jun;76(12):4063-75
references.pmid: 20435775
references.citation: FEMS Microbiol Ecol. 2005 Jul 1;53(2):245-53
references.pmid: 16329944
references.citation: BMC Microbiol. 2013 Mar 29;13:72
references.pmid: 23537200
references.citation: Appl Environ Microbiol. 2013 Sep;79(17):5291-301
references.pmid: 23811512
references.citation: Plant Dis. 1998 Oct;82(10):1088-1092
references.pmid: 30856767
references.citation: Front Microbiol. 2013 Jun 13;4:164
references.pmid: 23785368
references.citation: Front Microbiol. 2011 Nov 15;2:217
references.pmid: 22131985
references.citation: Appl Environ Microbiol. 2013 Feb;79(4):1284-92
references.pmid: 23241975
references.citation: Annu Rev Phytopathol. 1999;37:427-446
references.pmid: 11701830
references.citation: Sci Rep. 2015 May 06;5:10007
references.pmid: 25943705
references.citation: Science. 2010 Oct 8;330(6001):204-8
references.pmid: 20736401
references.citation: Mol Plant Microbe Interact. 2006 Apr;19(4):418-28
references.pmid: 16610745
references.citation: J Ginseng Res. 2016 Apr;40(2):127-34
references.pmid: 27158233
references.citation: Environ Microbiol. 2014 Jul;16(7):1949-60
references.pmid: 24650207
references.citation: Appl Environ Microbiol. 2015 May 15;81(10):3405-18
references.pmid: 25769825
references.citation: J Biotechnol. 1999 Oct 8;75(2-3):187-94
references.pmid: 10553657
references.citation: Curr Opin Microbiol. 2002 Jun;5(3):240-5
references.pmid: 12057676
references.citation: Fungal Genet Biol. 2009 Feb;46(2):137-45
references.pmid: 19100853
references.citation: Microbiol Mol Biol Rev. 1997 Jun;61(2):121-35
references.pmid: 9184007
references.citation: mBio. 2015 Mar 24;6(2):
references.pmid: 25805735
references.citation: PLoS One. 2013 Nov 21;8(11):e79512
references.pmid: 24278144
references.citation: Proc Natl Acad Sci U S A. 2007 Mar 6;104(10):3895-900
references.pmid: 17360449
references.citation: Appl Environ Microbiol. 2011 Feb;77(3):991-9
references.pmid: 21097602
references.citation: Science. 2011 May 27;332(6033):1097-100
references.pmid: 21551032
references.citation: Front Microbiol. 2014 Oct 02;5:516
references.pmid: 25324836
references.citation: J Appl Microbiol. 2010 Jul;109(1):65-78
references.pmid: 19961545
references.citation: Nat Methods. 2010 May;7(5):335-6
references.pmid: 20383131
references.citation: Trends Biotechnol. 2008 Nov;26(11):591-601
references.pmid: 18774191
references.citation: Phytopathology. 2001 Sep;91(9):847-55
references.pmid: 18944230
references.citation: J Appl Microbiol. 2007 Nov;103(5):1950-9
references.pmid: 17953605
references.citation: Phytopathology. 2002 Feb;92(2):181-9
references.pmid: 18943092
references.citation: Annu Rev Phytopathol. 2004;42:243-70
references.pmid: 15283667
references.citation: Proc Natl Acad Sci U S A. 2013 Apr 16;110(16):6548-53
references.pmid: 23576752