Table 4 Research works listed in chronological order where microbiome-assisted strategies are implemented by the high-throughput sequencing platforms for characterizing the soil microbiomes in sustainable agroecosystems

Soil bacterial community response to differences in agricultural management along with seasonal changes in a Mediterranean region

Terminal-restriction fragment

Length polymorphism

(T-RFLP)

Primer pair for the bacterial 16S rDNA gene:

Universal bacterial primers P0 and P6

63F (5′-AGGCCTAACACATGCAAGTC-3′)

518R (5′-ATTACCGCGGCTGCTGG-3′)

Bevivino et al. [19]

Organic farming induces changes in soil microbiota that affect agroecosystem functions

Amplicon sequencing of the V1–V3 regions of the bacterial 16S rRNA gene (520 bp) and a portion of the eukaryotic 18S rRNA gene region (436 bp) using Roche 454-pyrosequencing

Universal primers for the V1–V3 regions of the

16S rRNA gene

Primer pairs for the 18S rRNA gene portion:

580F (5′-ATTCCAKCTCCAAKAGCG-3′)

997R (5′-GACTACGAYGGTATCTIATC-3′)

Bonanomi et al. [26]

Organic amendment type and application frequency affect crop yields, soil, fertility, and microbiome composition

Amplicon sequencing of the V1–V3 regions of the bacterial 16S rRNA gene and a portion of the eukaryotic 18S rRNA gene region using Roche 454-pyrosequencing

Universal primers for the V1–V3 regions of the

16S rRNA gene

Primer pairs for the 18S rRNA gene portion:

580F (5′-ATTCCAKCTCCAAKAGCG-3′)

997R (5′-GACTACGAYGGTATCTIATC-3′)

Cesarano et al. [42]

Rhizosphere microbiome recruited from a suppressive compost improves plant fitness and increases protection against vascular wilt pathogens of tomato

T-RFLP

Universal primer pairs for the fungal rDNA ITS gene region:

ITS1F (5′-TCCGTAGGTGAACCTGCGG-3′)

ITS4R (5′-TCCTCCGCTTATTGATATGA-3′)

Primer pairs for the bacterial 16S rDNA gene:

27F (5′-AGAGTTTGATCMTGGCTCAG-3′)

907R (5′-CCGTCAATTCMTTTRAGTTT-3′)

Antoniou et al. [6]

Suppression of soil-borne Fusarium pathogens of peanut by intercropping with the medicinal herb Atractylodes lancea

Amplicon sequencing of the hypervariable V4 region of the bacterial 16S rRNA gene and the fungal ITS1 gene region using Roche 454-pyrosequencing

Universal primer pairs:

ITS5F/ITS4R (for fungi)

515F/806R (for bacteria)

Li et al. [134]

Activating Biochar by manipulating the bacterial and fungal microbiome through pre-conditioning

Amplicon sequencing of the bacterial 16S rRNA gene and the fungal ITS1 gene region using Illumina MiSeq sequencing

Universal primer pair 515F/806R for bacteria

Universal primer pair ITS1F/ITS2R for fungi

Jaiswal et al. [104]

Long-term coffee monoculture alters soil chemical properties and microbial communities

Amplicon sequencing of the V4 region of the bacterial 16S rRNA gene and the fungal ITS1 gene region using Illumina MiSeq sequencing

Universal primer pair for bacteria:

520F (5′-AYTGGGYDTAAAGNG-3′)

802R (5′-TACNVGGGTATCTAATCC-3′)

Universal primer pair for fungi:

ITS1F (5′-CTTGGTCATTTAGAGGAAGTAA-3′)

ITS2R (5′-GCTGCGTTCTTCATCGATGC-3′)

Zhao et al. [241]

Fungal community profiles in agricultural soils of a long-term field trial under different tillage, fertilization and crop rotation conditions

Analyzed by high-throughput its-amplicon

Sequencing

Amplicon sequencing of the fungal ITS1 and ITS2 gene regions using Illumina MiSeq sequencing

Primer pair sets for the ITS1 region:

ITS1F (5′-TAGAGGAAGTAAAAGTCGTAA-3′) and -ITS86R (5′-TTCAAAGATTCGATGATTCAC-3′)

Primer pair sets for ITS2 region:

ITS86F (5′-GTGAATCATCGAATCTTTGAA-3′) and

ITS4 (5′-TCCTCCGCTTATTGATATGC-3′)

Sommermann et al. [199]

Response of fungal communities and co-occurrence network patterns to compost amendment in black soil of Northeast China

Amplicon sequencing of the fungal ITS2 gene region using Illumina MiSeq sequencing

Forward primer gITS7F containing

a unique 12 nt barcode at the 5′ end for Miseq sequencing detection

Reverse primer ITS4R

Yang et al. [234]

Long-term organic farming manipulated rhizospheric microbiome and Bacillus antagonism against pepper blight (Phytophthora capsici)

Amplicon sequencing of the bacterial 16S rRNA gene using Illumina HiSeq 2500 sequencing

Universal primer pair:

515F (5′-GTGCCAGCMGCCGCGGTAA-3′)

909R (5′-CCCCGYCAATTCMTTTRAGT-3′)

with a 12 nt unique barcode

Li et al. [133]

Soil acidification in continuously cropped tobacco alters bacterial community structure and diversity via the accumulation of phenolic acids

Amplicon sequencing of the V4 region of the bacterial 16S rDNA gene using Illumina HiSeq 2500 sequencing

Universal primer pair:

515F (5′-GTGCCAGCMGCCGCGG-3′)

806R (5′-GGACTACHVGGGTWTCTAAT-3′)

Bai et al. [12]

Decoding wheat endosphere–rhizosphere microbiomes in Rhizoctonia solani-infested soils challenged by Streptomyces biocontrol agents

Amplicon sequencing of the V3–V4 regions of the bacterial 16S rRNA gene and the fungal ITS1 gene region using Illumina MiSeq sequencing

Universal primer pair:

341F/806R (for bacterial community)

ITS1F/ITS2 (for fungal community)

Araujo et al. [7]

Impacts of long-term plant residue management on soil organic matter quality, Pseudomonas community structure, and disease suppressiveness

Amplicon sequencing of the bacterial 16S rRNA gene fragments by a nested PCR using Illumina MiSeq sequencing

Primer pair for the first nested PCR:

F311Ps (5′-CTGGTCTGAGAGGATGATCAGT-3′)

R1459Ps (5′-AATCACTCCGTGGTAACCGT-3′)

Primer pair for the second nested PCR:

341F (5′-CCTAYGGGRBGCASCAG-3′)

and 806R (5′-GGACTACNNGGGTATCTAAT-3′)

Dignam et al. [65]

Deciphering differences in the chemical and microbial characteristics of healthy and fusarium wilt-infected watermelon rhizosphere soils

Amplicon sequencing of the V4 region of the bacterial 16S rRNA gene and the fungal ITS gene region using Illumina MiSeq sequencing

Universal primer pairs:

515F/907R (for bacterial community)

ITS1/ITS2 (for fungal community)

Meng et al. [158]

Rhizosphere bacteria assembly derived from fumigation and organic amendment triggers the direct and indirect suppression of tomato bacterial wilt disease

Amplicon sequencing of the V4 region of the bacterial 16S rRNA gene and the fungal ITS1 gene region using Illumina MiSeq sequencing

Universal primer pairs:

520F/802R (for bacteria)

ITS1f/ITS2 (for fungi)

Deng et al. [61]