Statistical test for tolerability of effects of an antifungal biocontrol strain on fungal communities in three arable soils

Abstract

SummaryA statistical method was developed to test for equivalence of microbial communities analysed by next‐generation sequencing of amplicons. The test uses Bray–Curtis distances between the microbial community structures and is based on a two‐sample jackknife procedure. This approach was applied to investigate putative effects of the antifungal biocontrol strain RU47 on fungal communities in three arable soils which were analysed by high‐throughput ITS amplicon sequencing. Two contrasting workflows to produce abundance tables of operational taxonomic units from sequence data were applied. For both, the developed test indicated highly significant equivalence of the fungal communities with or without previous exposure to RU47 for all soil types, with reference to fungal community differences in conjunction with field site or cropping history. However, minor effects of RU47 on fungal communities were statistically significant using highly sensitive multivariate tests. Nearly all fungal taxa responding to RU47 increased in relative abundance indicating the absence of ecotoxicological effects. Use of the developed equivalence test is not restricted to evaluate effects on soil microbial communities by inoculants for biocontrol, bioremediation or other purposes, but could also be applied for biosafety assessment of compounds like pesticides, or genetically engineered plants.

Lime and ammonium carbonate fumigation coupled with bio‐organic fertilizer application steered banana rhizosphere to assemble a unique microbiome against Panama disease

“…Consistent with previous report that microbial community in rhizosphere could be shaped by microbiota in bulk soil (de Ridder‐Duine et al ., ), our result also revealed that the variation of soil microbiome in bulk soil could still exhibit a strong effect on rhizosphere microbial community. Unlike previous study that direct application of antifungal biocontrol strain into soil displayed a minor effect on fungal communities (Antweiler et al ., ), biofertilizer applied to fumigated soil displayed a strong influence on bacterial community composition both in bulk and rhizosphere soil even after banana re‐planted for couple of months. Thus, manipulation of the disturbed microbial community in bulk soil through lime and ammonium carbonate fumigation followed by biofertilizer application could assemble a healthy rhizosphere microbiome suppressive to banana Panama disease.…”

Impact of Long-Term Organic and Mineral Fertilization on Rhizosphere Metabolites, Root–Microbial Interactions and Plant Health of Lettuce

“…Barcode, primer and adapter trimming were performed based on a customized in-house perl script including the FASTX toolkit 5 followed by raw sequence merging using FLASH ( Magoč and Salzberg, 2011 ). Subsequently, the analysis of the resulting sequences was carried out with a local version of the GALAXY Bioinformatics Platform 6 based on a database-dependent strategy ( Antweiler et al, 2017 ) using UNITE database v7.2 ( UNITE Community, 2017 ) by applying the closed reference approach ( Carter et al, 2017 ). All sequences were aligned with the database (e-value 0.001) and only results with an alignment length >200 bp and a similarity >97% to the reference were kept.…”

“…All sequences were aligned with the database (e-value 0.001) and only results with an alignment length >200 bp and a similarity >97% to the reference were kept. Furthermore, BLAST-PARSER ( Antweiler et al, 2017 ) was used for taxonomic assignment based on the lowest e-value. The fungal OTU abundance table was generated by counting the sequences per assignment and using the SH-numbers from the database as identifier.…”

Free-Living Nematodes Together With Associated Microbes Play an Essential Role in Apple Replant Disease

“…Taxonomic affiliations were assigned by BlastN against the Silva SSU 128 database ( Quast et al, 2013 ). De-replication, singleton removal and clustering of sequences to operational taxonomic units (OTUs, >99% similarity) were performed using BLAST Parser ( Antweiler et al, 2017 ) implemented in a Galaxy workflow ( Cock et al, 2013 ). The multivariate analyses on the OTU abundance table were carried out with the R software version R3.1.3 2 with the packages vegan ( Oksanen et al, 2015 ), EdgeR ( Robinson et al, 2010 ), and LabDSV ( Roberts, 2016 ).…”