Victor Carrion

Victor Carrion
Leiden University | LEI · Institute of Biology Leiden

PhD

About

74
Publications
18,485
Reads
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2,001
Citations
Additional affiliations
November 2018 - present
Leiden University
Position
  • Professor (Assistant)
October 2012 - October 2018
Netherlands Institute of Ecology (NIOO-KNAW)
Position
  • PostDoc Position

Publications

Publications (74)
Preprint
A bstract With its candybar form factor and low initial investment cost, the MinION brought affordable portable nucleic acid analysis within reach. However, translating the electrical signal it outputs into a sequence of bases still requires high-end computer hardware, which remains a caveat when aiming for deployment of many devices at once or usa...
Article
Full-text available
Beneficial microorganisms are used to stimulate the germination of seeds; however, their growth-promoting mechanisms remain largely unexplored. Bacillus subtilis is commonly found in association with different plant organs, providing protection against pathogens or stimulating plant growth. We report that application of B. subtilis to melon seeds r...
Article
Full-text available
Microbiomes play a pivotal role in plant growth and health, but the genetic factors involved in microbiome assembly remain largely elusive. Here, we map the molecular features of the rhizosphere microbiome as quantitative traits of a diverse hybrid population of wild and domesticated tomato. Gene content analysis of prioritized tomato quantitative...
Article
Full-text available
Purpose Root inoculation of plants with beneficial microorganisms promotes plant growth and improves tolerance to biotic and abiotic stresses. In banana plants, microbial inoculation has shown promising effects on plant growth, but the effect on foliar diseases and on the resident native microbial community is yet unknown. We examined the effects o...
Article
Full-text available
A large part of the chemical space of bioactive natural products is derived from Actinobacteria . Many of the biosynthetic gene clusters for these compounds are cryptic; in others words, they are expressed in nature but not in the laboratory.
Article
Full-text available
Actinobacteria are a rich source of bioactive molecules, and genome sequencing has shown that the vast majority of their biosynthetic potential has yet to be explored. However, many of their biosynthetic gene clusters (BGCs) are poorly expressed in the laboratory, which prevents discovery of their cognate natural products. To exploit their full bio...
Article
Full-text available
Intensive cultivation with accompanying nitrogen fertilization leads to soil acidification in croplands of southern China, which in turn, imperils soil health, restricting the sustainability of agricultural production. Application of soil amendments is considered as a potential method for maintaining soil health; however, the underlying soil-health...
Preprint
Full-text available
Microbiomes play a pivotal role in plant growth and health, but the genetic factors involved in microbiome assembly remain largely elusive. Here, 16S amplicon and metagenomic features of the rhizosphere microbiome were mapped as quantitative traits of a recombinant inbred line population of a cross between wild and domesticated tomato. Gene content...
Article
Full-text available
Pseudomonas syringae is an important plant pathogen of many valuable crops worldwide, with more than 60 identified pathovars. The phytotoxins produced by these organisms were related to the severity of the damage caused to the plant. An emerging strategy to treat bacterial infections relies on interference with their signaling systems. In this stud...
Preprint
Full-text available
Actinobacteria are a rich source of bioactive molecules, and genome sequencing has shown that the vast majority of their biosynthetic potential has yet to be explored. However, many of their biosynthetic gene clusters (BGCs) are poorly expressed in the laboratory, which prevents discovery of their cognate natural products. To exploit their full bio...
Article
Full-text available
The cell wall is a stress-bearing structure and a unifying trait in bacteria. Without exception, synthesis of the cell wall involves formation of the precursor molecule lipid II by the activity of the essential biosynthetic enzyme MurG, which is encoded in the division and cell wall synthesis (dcw) gene cluster. Here, we present the discovery of a...
Article
Full-text available
Genomics and metabolomics are widely used to explore specialized metabolite diversity. The Paired Omics Data Platform is a community initiative to systematically document links between metabolome and (meta)genome data, aiding the identification of natural product biosynthetic origins and metabolite structures.
Preprint
Full-text available
Bacterial chromosome structure is organized by a diverse group of proteins collectively referred to as nucleoid-associated proteins (NAPs). Many NAPs have been well studied in Streptomyces, including Lsr2, HupA, HupS, and sIHF. Here, we show that SCO1839 represents a novel family of Actinobacteria NAPs and recognizes a consensus sequence consisting...
Article
Full-text available
Plant microbiome assembly is a spatial and dynamic process driven by root exudates and influenced by soil type, plant developmental stage and genotype. Genotype-dependent microbiome assembly has been reported for different crop plant species. Despite the effect of plant genetics on microbiome assembly, the magnitude of host control over its root mi...
Preprint
Full-text available
The cell wall is a stress-bearing structure and a unifying trait in bacteria. Without exception, synthesis of the cell wall involves formation of the precursor molecule Lipid II by the activity of the essential biosynthetic enzyme MurG, which is encoded in the division and cell wall synthesis ( dcw ) gene cluster. Here we present the discovery of a...
Preprint
Full-text available
Pseudomonas syringae is an important pathogen of many agriculturally valuable crops. Among the various pathovars described P. syringae pv. syringae (Pss) has a particularly wide host range, infecting primarily woody and herbaceous host plants. The ability of Pss to cause bacterial apical necrosis of mango trees is dependent on the production of the...
Preprint
Pseudomonas syringae is an important pathogen of many agriculturally valuable crops. Among the various pathovars described P. syringae pv. syringae (Pss) has a particularly wide host range, infecting primarily woody and herbaceous host plants. The ability of Pss to cause bacterial apical necrosis of mango trees is dependent on the production of the...
Preprint
div> Pseudomonas syringae is an important pathogen of many agriculturally valuable crops. Among the various pathovars described P. syringae pv. syringae (Pss) has a particularly wide host range, infecting primarily woody and herbaceous host plants. The ability of Pss to cause bacterial apical necrosis of mango trees is dependent on the production...
Article
Full-text available
Plants recruit specific microorganisms to live inside and outside their roots that provide essential functions for plant growth and health. The study of the microbial communities living in close association with plants helps in understanding the mechanisms involved in these beneficial interactions. Currently, most of the research in this field has...
Article
Full-text available
More than half of all antibiotics and many other bioactive compounds are produced by the actinobacterial mem-bers of the genus Streptomyces. It is therefore surprising that virtually no natural products have been described for its sister genus Streptacidiphilus within the Streptomycetaceae. Here, we describe an unusual family of spiro-tetronate pol...
Preprint
More than half of all antibiotics and many other bioactive compounds are produced by the actinobacterial members of the genus Streptomyces. It is therefore surprising that virtually no natural products have been described for its sister genus Streptacidiphilus within the Streptomycetaceae . Here, we describe an unusual family of spirotetronate poly...
Article
Protecting plants from the inside out Some soils show a remarkable ability to suppress disease caused by plant pathogens, an ability that is attributed to plant-associated microbiota. Carrión et al. investigated the role of endophytes, the intimate microbial community found within roots, in fungal disease suppression (see the Perspective by Tringe)...
Article
Full-text available
The production of biochemicals from renewables through biorefinery processes is important to reduce the anthropogenic impact on the environment. Chain elongation processes based on microbiomes have been successfully developed to produce medium-chain fatty acids (MCFA) from organic waste streams. Yet, the sustainability of chain elongation can still...
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Full-text available
Microorganisms colonizing plant surfaces and internal tissues provide a number of life-support functions for their host. Despite increasing recognition of the vast functional capabilities of the plant microbiome, our understanding of the ecology and evolution of the taxonomically hyperdiverse microbial communities is limited. Here, we review curren...
Article
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Background: Modern crop varieties are typically cultivated in agriculturally well-managed soils far from the centers of origin of their wild relatives. How this habitat expansion impacted plant microbiome assembly is not well understood. Results: Here, we investigated if the transition from a native to an agricultural soil affected rhizobacteria...
Article
Full-text available
Microorganisms associated with roots are thought to be part of the so-called extended plant phenotypes with roles in the acquisition of nutrients, production of growth hormones, and defense against diseases. Since the crops selectively enrich most rhizosphere microbes out of the bulk soil, we hypothesized that changes in the composition of bulk soi...
Article
Full-text available
Gaeumannomyces graminis var. tritici (Ggt) is the main soilborne factor that affects wheat production around the world. Recently we reported the occurrence of six suppressive soils in monoculture areas from indigenous “Mapuche” communities, and evidenced that the suppression relied on the biotic component of those soils. Here, we compare the rhizos...
Data
Standard curve of 10-fold serial dilutions of Gaeumannomyces graminis DNA (0.8 × 10-5 -0.8 ng μL-1) for absolute quantification of genomic DNA generated from pure culture of Ggt (A). Efficiency % (B) and dissociation curve (C), Phylogenetic tree showing the affiliation of Ggt (red letter) in relation to amplicons obtained by selected primers from s...
Data
Unspecific Melt curve of primers: (A) GgtEFF1 (5′-CCCTGCAAGCTCTTCCTCTTAG-3′) and GgtEFR1 (5′-GCATGCGAGGTCCCAAAA-3′, Keenan et al., 2015). (B) NS5 (5′-AACTTAAAGGAATTGACGGAAG-3′), and GGTRP (5′-TGCAATGGCTTCGTGAA-3′ (Fouly and Wilkinson, 2000).
Data
ITS region amplified with GGT2F-GGT168R primer pair tested by conventional polymerase chain reaction against: Lane M, 1-kb-plus ladder marker. Lane 1, Gaeumannonyces graminis. Lane 2, inoculum with Ggt (oat). Lane 3, inoculum without Ggt. Lane 4, Rhizosphere without Ggt. Lane 5, Rhizosphere with Ggt, Lane 6, roots without Ggt. Lane 7, roots with Gg...
Data
Pearson correlation between chemical parameters and biodiversity index of endosphere and rhizosphere samples. ∗Denote significant differences at p<0.05. ∗∗Denote significative differences at p < 0.01.
Data
Pearson correlation between endophytic ascomycete and different microbial groups of conducive and suppressive soils.
Data
Phylogenetic tree showing the affiliation of Ggt in relation to others strains which primers amplified. The neighbor-joining tree was constructed with representative ITS-2 gene sequences. Bootstrap analysis was performed with 1,000 interactions using uniform rates among sites and same (homogeneous) among lineages.
Article
In the past decade, various studies have described the effects of microbial volatiles on other (micro)organisms in vitro , but their broad-spectrum activity in vivo and the mechanisms underlying volatile-mediated plant growth promotion have not been addressed in detail. Here, we revealed that volatiles from root-associated bacteria of the genus Mic...
Article
Full-text available
Plants rely on their microbiome for a number of life-support functions including nutrient acquisition and protection against (a)biotic stress factors. For crop plants, however, the process of domestication may have adversely impacted the composition and functions of the associated microbiota, thereby undermining their benefi- cial effects on plant...
Article
Disease-suppressive soils are ecosystems in which plants suffer less from root infections due to the activities of specific microbial consortia. The characteristics of soils suppressive to specific fungal root pathogens are comparable to those of adaptive immunity in animals, as reported by Raaijmakers and Mazzola (Science 352:1392–3, 2016), but th...
Article
Full-text available
Wheat production around the world is severely compromised by the occurrence of “take-all” disease, which is caused by the soil-borne pathogen Gaeumannomyces graminis var. tritici (Ggt). In this context, suppressive soils are those environments in which plants comparatively suffer less soil-borne pathogen diseases than expected, owing to native soil...
Article
Full-text available
Beneficial soil microorganisms can affect plant growth and resistance by the production of volatile organic compounds (VOCs). Yet, little is known on how VOCs from soil-borne plant pathogens affect plant growth and resistance. Here we show that VOCs released from mycelium and sclerotia of the fungal root pathogen Rhizoctonia solani enhance growth a...
Article
Full-text available
Plant domestication was a pivotal accomplishment in human history, but also led to a reduction in genetic diversity of crop species compared to their wild ancestors. How this reduced genetic diversity affected plant–microbe interactions belowground is largely unknown. Here, we investigated the genetic relatedness, root phenotypic traits and rhizoba...
Article
Nature Microbiology 2 , 16197 (2016); published online 31 October 2016; corrected 23 January 2017 In the original version of this Article, co-author René De Mot's name was coded wrongly resulting in it being incorrect when exported to citation databases.
Article
Full-text available
Pseudomonads are cosmopolitan microorganisms able to produce a wide array of specialized metabolites. These molecules allow Pseudomonas to scavenge nutrients, sense population density and enhance or inhibit growth of competing microorganisms. However, these valuable metabolites are typically characterized one-molecule–one-microbe at a time, instead...
Article
Full-text available
In disease-suppressive soils, plants are protected from infections by specific root pathogens due to the antagonistic activities of soil and rhizosphere microorganisms. For most disease-suppressive soils, however, the microorganisms and mechanisms involved in pathogen control are largely unknown. Our recent studies identified Actinobacteria as the...
Article
Full-text available
The genome sequence of more than 100 Pseudomonas syringae strains has been sequenced to date; however only few of them have been fully assembled, including P. syringae pv. syringae B728a. Different strains of pv. syringae cause different diseases and have different host specificities; so, UMAF0158 is a P. syringae pv. syringae strain related to B72...
Article
Full-text available
Genome sequencing and annotation have revealed a putative cellulose biosynthetic operon in the strain Pseudomonas syringae pv. syringae UMAF0158, the causal agent of bacterial apical necrosis. Bioinformatics analyses and experimental methods were used to confirm the functionality of the cellulose biosynthetic operon. In addition, the results showed...
Article
Full-text available
Pseudomonas chlororaphis PCL1606 the antifungal antibiotic 2-hexyl, 5-propyl resorcinol, which is crucial for the biocontrol of fungal soil-borne pathogens. The genetic basis for HPR production lay in the dar genes, which are directly involved in the biosynthesis of HPR. In the present study, we elucidated the genetic features of dar genes. Reverse...
Article
Full-text available
The antimetabolite mangotoxin is a key factor in virulence of Pseudomonas syringae pv. syringae strains which cause apical necrosis of mango trees. Previous studies showed that mangotoxin biosynthesis is governed by the mbo operon. Random mutagenesis led to the identification of two other gene clusters that affect mangotoxin biosynthesis. These are...
Article
Full-text available
ABSTRACT Pseudomonas syringae pv. syringae, the causal agent of bacterial apical necrosis (BAN) in mango crops, has been isolated in different mango-producing areas worldwide. An extensive collection of 87 P. syringae pv. syringae strains isolated from mango trees affected by BAN from different countries, but mainly from Southern Spain, were initia...
Article
Full-text available
We describe the genetic organization of a copper resistant plasmid containing copG and cusCBA genes in the plant pathogen Pseudomonas syringae. Chromosomal variants of czcCBA and a plasmid variant of cusCBA were present in different P. syringae pathovar strains. Transformation of copper-sensitive Pseudomonas syringae pv. syringae FF5 strain with co...