Matthew G. Bakker

Matthew G. Bakker
University of Manitoba | UMN · Department of Microbiology

PhD

About

44
Publications
14,244
Reads
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2,795
Citations
Citations since 2017
19 Research Items
2195 Citations
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Introduction
My research investigates microbial ecology and species interactions, as connected to the productivity and sustainability of cropping systems. At present, most of our projects connect to Fusarium graminearum, a fungal pathogen of cereal crops.
Additional affiliations
July 2019 - present
University of Manitoba
Position
  • Professor (Assistant)
Description
  • For more information, please visit: https://matt-bakker.github.io/index.html
May 2016 - June 2019
USDA ARS
Position
  • Researcher
August 2013 - May 2016
USDA ARS
Position
  • Research Plant Pathologist
Education
July 2006 - June 2011
University of Minnesota Twin Cities
Field of study
  • Plant Pathology

Publications

Publications (44)
Article
Microbial ecology has been profoundly advanced by the ability to profile complex microbial communities by sequencing of marker genes amplified from environmental samples. However, inclusion of appropriate controls is vital to revealing the limitations and biases of this technique. ‘Mock community’ samples, in which the composition and relative abun...
Article
Due to health risks and economic losses associated with mycotoxins produced by plant pathogenic Fusarium species, there is a compelling need for improved understanding of these fungi from across diverse perspectives and disciplinary approaches. Phylogenetic studies have made tremendous progress in delineating the species that comprise the genus Fus...
Article
The dynamics of microbial communities associated with dying cover crops are of interest because of potential impacts on disease in a subsequent crop, and because of the importance of microbial activity on plant residue to soil organic matter dynamics and nutrient cycling. We used high throughput amplicon sequencing to characterize the composition a...
Article
Cover cropping is a prevalent conservation practice that offers substantial benefits to soil and water quality. However, winter cereal cover crops preceding corn may diminish beneficial rotation effects because two grass species are grown in succession. Here, we show that rye cover crops host pathogens capable of causing corn seedling disease. We i...
Article
Full-text available
Fusarium head blight (FHB) is a major fungal disease that causes severe yield and quality loss in wheat. Biological control can be integrated with other management strategies to control FHB. For this purpose, Trichoderma gamsii strain T6085 is a potential biocontrol agent to limit the infection of F. graminearum and F. culmorum in wheat. However, t...
Article
Full-text available
Mycotoxins such as deoxynivalenol introduce a health risk to the food supply and are costly to manage or avoid. Technologies for reducing or eliminating the toxicity of deoxynivalenol could be useful in a variety of processes, such as in preserving the value as animal feed of byproducts of ethanol production. We characterized transformation product...
Chapter
Plant diseases caused by soil-borne pathogens are a major limitation to crop production every year, and new tools are needed for more effective management. In this chapter, we argue for an expanded role for biological control, which involves the use of other living organisms to antagonize plant pathogens. Biological control approaches are complemen...
Article
Full-text available
Fusarium graminearum is the primary cause of Fusarium head blight (FHB), one of the most economically important diseases of wheat worldwide. FHB reduces yield and contaminates grain with the trichothecene mycotoxin deoxynivalenol (DON), which poses a risk to plant, human and animal health. The first committed step in trichothecene biosynthesis is f...
Article
Full-text available
Specialized metabolites constitute key layers of immunity that underlie disease resistance in crops; however, challenges in resolving pathways limit our understanding of the functions and applications of these metabolites. In maize (Zea mays), the inducible accumulation of acidic terpenoids is increasingly considered to be a defence mechanism that...
Article
Fusarium head blight (FHB) causes severe economic impacts by reducing yield and quality of small grain cereals, and poses health risks to both humans and animals via the accumulation of mycotoxins such as deoxynivalenol (DON). The use of endophytic fungi as potential biological control agents is an underexplored method for reducing the impact of FH...
Preprint
Specialized metabolites constitute key layers of immunity underlying crop resistance; however, challenges in resolving complex pathways limit our understanding of their functions and applications. In maize ( Zea mays ) the inducible accumulation of acidic terpenoids is increasingly considered as a defense regulating disease resistance. To understan...
Article
The fungal pathogen Fusarium graminearum causes Fusarium head blight (FHB) on wheat, barley and other grains. FHB results in yield reductions and contaminates grain with trichothecene mycotoxins, which threaten food safety and food security. Innovative mechanisms for controlling FHB are urgently needed. We have previously shown that transgenic toba...
Article
Characteristics or constituents of plant-associated microbiomes may assist in constraining disease development. To investigate this possibility for the wheat-Fusarium head blight pathosystem, we assessed seed weight, pathogen load, deoxynivalenol content, and microbiome profiles for individual wheat kernels collected over two years from a disease-c...
Article
Endophytic microbiota are potentially useful plant symbionts for conferring biotic or abiotic stress tolerance. Common approaches to identify putatively beneficial functions of endophytes rely on lab-based assays. However, if functional roles are context-dependent, lab-based assessments may not accurately represent functional outcomes under variabl...
Poster
Full-text available
The production and accumulation of trichothecene mycotoxins is responsible for much of the negative economic impact associated with Fusarium head blight. A variety of biochemical transformations to trichothecenes have been described, some of which result in a less toxic product. We expect that continued prospecting will reveal additional microbial...
Article
Full-text available
Corn seed is treated with various fungicide active ingredients that target several fungal and oomycete genera in the corn seedling disease complex. In this study, we investigated the effects of various combinations of fungicides as seed treatments on disease development, pathogen prevalence and seedling growth of corn planted after a winter cereal...
Article
Understanding how soil microbiomes respond to management is essential to maximizing soil health. We contrasted microbiomes in bulk soil under long-term organic and conventional management in a grain production setting. Management category significantly impacted the relative abundances of 17% of the most abundant taxa. Both conventional and organic...
Article
Plant breeders are increasing yields and improving agronomic traits in several perennial grain crops, the first of which is now being incorporated into commercial food products. Integration strategies and management guidelines are needed to optimize production of these new crops, which differ substantially from both annual grain crops and perennial...
Article
Cover crops can offer erosion protection as well as soil and environmental quality benefits. Cereal rye ( Secale cereale L.) is the most commonly used winter cover crop in corn–soybean rotations in the upper Midwest of the USA because of its superior winter hardiness and growth at cool temperatures. Cereal rye cover crops, however, can occasionally...
Article
Experiments were established in a controlled-growth chamber and in the field to evaluate the effect of the length of time intervals between winter rye cover crop termination and corn planting on corn seedling disease, corn growth, and grain yield in 2014 and 2015. Rye termination dates ranged from 25 days before planting (DBP) to 2 days after plant...
Article
Cover crops can improve the sustainability and resilience of corn (Zea mays L.) and soybean (Glycine max L. Merr.) production systems. At present, the most widely used cover crops in corn-soybean systems in the upper Midwest United States have been winter cereals. However, there have been isolated reports of corn yield reductions following winter r...
Article
In profiling the composition and structure of complex microbial communities via high throughput amplicon sequencing, a very low proportion of community members are typically sampled. As a result of this incomplete sampling, estimates of dissimilarity between communities are often inflated, an issue we term pseudo β-diversity. We present a set of to...
Conference Paper
Cover cropping is an expanding conservation practice that offers substantial benefits to soil protection, soil health, water quality, and potentially crop yields. Presently, winter cereals are the most widely used cover crops in the upper Midwest. However, winter cereal cover crops preceding corn, may dampen beneficial rotation effects by putting t...
Article
Background and aims: It has frequently been shown that plants interact with soils to shape rhizosphere microbiomes. However, previous work has not distinguished between effects of soil properties per se, and effects attributable to the resident microbial communities of those soils. We aimed to test whether differences in the structure of bulk soil...
Article
Plant species, plant community diversity can significantly impact soil microbial communities, yet there are few data on the interactive effects of plant species and plant community diversity on soil bacterial communities. We hypothesized that plant species and plant community diversity affect soil bacterial communities by setting the context in whi...
Article
Full-text available
Though traditionally perceived as weapons, antibiotics are also hypothesized to act as microbial signals in natural habitats. However, while subinhibitory concentrations of antibiotics (SICA) are known to shift bacterial gene expression, specific hypotheses as to how SICA influence the ecology of natural populations are scarce. We explored whether...
Article
A conceptual model emphasizing direct host-microbe interactions has dominated work on host-associated microbiomes. To understand plant-microbiome associations, however, broader influences on microbiome composition and functioning must be incorporated, such as those arising from plant-plant and microbe-microbe interactions. We sampled soil microbiom...
Article
Plant-soil feedbacks are important to productivity and plant community dynamics in both natural and managed ecosystems. Among soil bacteria, the Streptomyces possess particularly strong antagonistic activities and inhibit diverse plant pathogens, offering a clear pathway to involvement in plant-soil feedbacks.We hypothesized that feedback effects a...
Article
Diets shape the animal gut microbiota, although the relationships between diets and the structure of the gut microbial community are not yet well understood. The gut bacterial communities of Reticulitermes flavipes termites fed on four individual plant biomasses with different degrees of recalcitrance to biodegradation were investigated by 16S rRNA...
Chapter
Plants exert strong selective forces on rhizosphere microbes, largely through root exudates. Because root exudation is a dynamic process and influences important microbial functions, there is a possibility that plants may vary the selection they impose on soil microbial communities in ways that improve plant performance or alleviate plant stress. W...
Article
Full-text available
Plant roots constantly secrete compounds into the soil to interact with neighboring organisms presumably to gain certain functional advantages at different stages of development. Accordingly, it has been hypothesized that the phytochemical composition present in the root exudates changes over the course of the lifespan of a plant. Here, root exudat...
Article
It is known that environmental factors can affect the biosynthesis of leaf metabolites. Similarly, specific pairwise plant-microbe interactions modulate the plant's metabolome by stimulating production of phytoalexins and other defense-related compounds. However, there is no information about how different soil microbiomes could affect the plant gr...
Article
Rhizosphere microbial communities are impacted by resident plant species and have reciprocal effects on their host plants. We collected resident soil from five wild populations of Arabidopsis in the United States and Europe in an effort to characterize the impacts of natural soil microbiomes on Arabidopsis growth performance. The microbial communit...
Article
We investigated soil streptomycete communities associated with four host plant species (two warm season C4 grasses: Andropogon gerardii, Schizachyrium scoparium and two legumes: Lespedeza capitata, Lupinus perennis), grown in plant communities varying in species richness. We used actinobacteria-selective PCR coupled with pyrosequencing to character...
Article
Full-text available
The need to enhance the sustainability of intensive agricultural systems is widely recognized One promising approach is to encourage beneficial services provided by soil microorganisms to decrease the inputs of fertilizers and pesticides. However, limited success of this approach in field applications raises questions as to how this might be best a...
Article
Full-text available
There has been a rapid proliferation of approaches for processing and manipulating second generation DNA sequence data. However, users are often left with uncertainties about how the choice of processing methods may impact biological interpretation of data. In this report, we probe differences in output between two different processing pipelines: a...
Article
High densities of antagonistic Streptomyces are associated with plant disease suppression in many soils. Here we review use of inoculation and organic matter amendments for enriching antagonistic Streptomyces populations to reduce plant disease and note that effective and consistent disease suppression in response to management has been elusive. We...
Conference Paper
Both plant host and plant diversity have significant effects on rhizosphere microbial composition and diversity, yet it is difficult to distinguish the effects of plant diversity from the effects of individual plant hosts on soil microbes. To resolve this, we combined PCR with 454 sequencing targeting fungal communities, bacterial communities, and...
Article
This review explores a coevolutionary framework for the study and management of disease-suppressive soil microbial communities. Because antagonistic microbial interactions are especially important to disease suppression, conceptual, theoretical, and empirical work on antagonistic coevolution and its relevance to disease suppression is reviewed. In...
Article
Ecological factors that promote pathogen suppressive microbial communities remain poorly understood. However, plants have profound impacts on the structure and functional activities of soil microbial communities, and land-use changes which alter plant diversity or community composition may indirectly affect the structure and function of microbial c...
Conference Paper
Streptomycetes have been implicated in the control of soil-borne plant pathogens, and are known to produce an extensive array of antimicrobial secondary metabolites. We investigated the hypothesis that plants manipulate the production of secondary metabolites by streptomycetes. We tested a collection of diverse Streptomyces isolates for responses t...
Conference Paper
There is little understanding of the ecological and evolutionary factors that promote pathogen suppressive microbial communities. We hypothesize that high density and diversity microbial communities create a selective environment that gives rise to pathogen suppression. Because of the influence of plant inputs on rhizosphere microbial dynamics, red...

Questions

Questions (5)
Question
Does anyone know of a source for a carefully constructed fungal mock community to use as a control in high-throughput sequencing?
I know there is a bacterial mock community available from BEI Resources, but haven't found a corresponding product for fungi. Thanks!
Question
I can't find any estimates of genome size for Pythium sylvaticum or Pythium torulosum. Can anyone help with this?
Question
I'm wondering whether anyone has assembled a database of oomycetes and successfully used on the of high-throughput sequencing platforms to characterize the community structure of this group of organisms in soil.
Question
I have been consistently observing that corn seedling radicles are much more extensively damaged by pathogens, compared to the seminal roots of the same seedlings. Can anyone point me to some literature on why this might be the case?

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