Simon Bulman
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View article: Grapevines escaping trunk diseases in New Zealand vineyards have a distinct microbiome structure
Grapevines escaping trunk diseases in New Zealand vineyards have a distinct microbiome structure Open
Grapevine trunk diseases (GTDs) are a substantial challenge to viticulture, especially with a lack of available control measures. The lack of approved fungicides necessitates the exploration of alternative controls. One promising approach …
View article: Insect phylogeny structures the bacterial communities in the microbiome of psyllids (Hemiptera: Psylloidea) in Aotearoa New Zealand
Insect phylogeny structures the bacterial communities in the microbiome of psyllids (Hemiptera: Psylloidea) in Aotearoa New Zealand Open
The bacterial microbiome of psyllids has been studied for decades, with a strong focus on the primary and secondary endosymbionts capable of providing essential amino acids for the insects’ diet and therefore playing a key role in the inse…
View article: Rapid increases in soil pH solubilise organic matter, dramatically increase denitrification potential and strongly stimulate microorganisms from the<i>Firmicutes</i>phylum
Rapid increases in soil pH solubilise organic matter, dramatically increase denitrification potential and strongly stimulate microorganisms from the<i>Firmicutes</i>phylum Open
Rapid and transient changes in pH frequently occur in soil, impacting dissolved organic matter (DOM) and other chemical attributes such as redox and oxygen conditions. Although we have detailed knowledge on microbial adaptation to long-ter…
View article: Assessment of sampling and DNA extraction methods for identification of grapevine trunk microorganisms using metabarcoding
Assessment of sampling and DNA extraction methods for identification of grapevine trunk microorganisms using metabarcoding Open
For a deeper understanding of grapevine trunk disease (GTD) in New Zealand, a cheap, rapid, sensitive method for identifying within-vine microbial communities is required. Wood tissue from grapevine trunks was collected and three different…
View article: Rapid increase in soil pH solubilises organic matter, dramatically increases denitrification potential and strongly stimulates microorganisms from the <i>Firmicutes</i> phylum
Rapid increase in soil pH solubilises organic matter, dramatically increases denitrification potential and strongly stimulates microorganisms from the <i>Firmicutes</i> phylum Open
Rapid and transient changes in pH frequently occur in soil, impacting dissolved organic matter (DOM) and other chemical attributes such as redox and oxygen conditions. Although we have detailed knowledge on microbial adaptation to long-ter…
View article: DNA Barcoding Highlights Cryptic Diversity in the New Zealand Psylloidea (Hemiptera: Sternorrhyncha)
DNA Barcoding Highlights Cryptic Diversity in the New Zealand Psylloidea (Hemiptera: Sternorrhyncha) Open
The insect superfamily Psylloidea (Hemiptera) includes economically important biocontrol agents, pests and plant pathogen vectors, for which a rapid and accurate identification is fundamental for international biosecurity. Australasia is a…
View article: Rapid increase in soil pH solubilises organic matter, dramatically increases denitrification potential and strongly stimulates microorganisms from the <i>Firmicutes</i> phylum
Rapid increase in soil pH solubilises organic matter, dramatically increases denitrification potential and strongly stimulates microorganisms from the <i>Firmicutes</i> phylum Open
We used potassium hydroxide (KOH) to induce rapid soil pH changes and then observed microbial community change over 48 hours in anaerobic conditions before measuring denitrification enzyme activity (DEA). Soil pH was elevated from 4.7 to 6…
View article: Rapid increase in soil pH solubilises organic matter, dramatically increases denitrification potential and strongly stimulates microorganisms from the <i>Firmicutes</i> phylum
Rapid increase in soil pH solubilises organic matter, dramatically increases denitrification potential and strongly stimulates microorganisms from the <i>Firmicutes</i> phylum Open
Rapid and transient changes in pH frequently occur in soil, impacting dissolved organic matter (DOM) and other chemical attributes such as redox and oxygen conditions. Although we have detailed knowledge on microbial adaptation to long-ter…
View article: Not in your usual Top 10: protists that infect plants and algae
Not in your usual Top 10: protists that infect plants and algae Open
Summary Fungi, nematodes and oomycetes belong to the most prominent eukaryotic plant pathogenic organisms. Unicellular organisms from other eukaryotic lineages, commonly addressed as protists, also infect plants. This review provides an in…
View article: An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids
An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids Open
We have implemented an automated viral surveillance and diagnosis (VSD) bioinformatics toolkit that produces improved viruses and viroid sequence assemblies. The VSD toolkit provides several optimised and reusable workflows applicable to d…
View article: Additional file 11: of An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids
Additional file 11: of An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids Open
Summary of VirFind screening of small RNA-Seq datasets collected from quarantined plants. A) VirFind blastn results. Identified viruses/viroids were also identified using our VSD toolkit. B) VirFind blastx results. Identified viruses/viroi…
View article: Additional file 12: of An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids
Additional file 12: of An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids Open
VirFind BLASTX results for contigs with sequence simalrity to viruses or viroids. (XLSX 50Â kb)
View article: Additional file 4: of An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids
Additional file 4: of An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids Open
Paired sample t-test of contigs produced by SPAdes, Velvet, ABySS and SOAPdenovo assemblers. Our optimised ‘SPAdes K15-17-19_cap3’ (SPAdes assembly; dataset = 21–22 nt; kmer set =15,17 and 19; and scaffolded with CAP3) (SP22_K15-17-19_cap3…
View article: Additional file 1: of An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids
Additional file 1: of An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids Open
Adaptor clipped and quality trimmed read statistics of small RNA-Seq datasets. Clean reads = Adaptor clipped small RNA reads provided by BGI service provider; QC = Quality Control consisting of adaptor clipping and poor base call trimming;…
View article: Additional file 6: of An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids
Additional file 6: of An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids Open
Statistics of the viral sequences assembled using 21–25 nt, 21–22 nt and 24 nt small RNA subsets. *Virus name: GRSPaV = Grapevine rupestris stem pitting-associated virus; GVB = Grapevine virus B; GFkV = Grapevine fleck virus; GLRaV-3 = Gra…
View article: Additional file 14: of An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids
Additional file 14: of An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids Open
VirFind contigs annotated with hits to viruses were run through the Yabi VSD toolkit pipeline. Top BLASTX hits (Evalueâ =â < 1e-5) to a combined plant and virus protein database are reported. VirFind assembled contigs with a top hit to a p…