Michael Wisniewski

United States Department of Agriculture | USDA · Agricultural Research Service (ARS)

Fruits harbor abundant and diverse microbial communities that protect them from post‐harvest pathogens. Identification of functional traits associated with a given microbiota can provide a better understanding of their potential influence. Here, we focused on the epiphytic microbiome of apple fruit. We suggest that shotgun metagenomic data can indi...

With the introduction of new apple varieties, emerging diseases have been recorded including dry lenticel rot and white haze. Ramularia mali has been identified as the causal agent of dry lenticel rot, whereas species of Golubevia, Tilletiopsis and Entyloma have been associated to white haze, but the epidemiology of these pathogens remains unclear....

Reactive oxygen species (ROS) in harvested fruit wound tissues result in an oxidative microenvironment. The pretreatment of some antagonistic yeasts with stress-ameliorating compounds has been shown to enhance tolerance to subsequent exposure to oxidative stress and thus improves biocontrol performance. The effect of caffeic acid (CA) on ROS in Can...

Postharvest diseases of fruits and vegetables cause significant economic losses to producers and marketing firms. Many of these diseases are caused by necrotrophic fungal pathogens that require wounded or injured tissues to establish an infection. Biocontrol of postharvest diseases is an evolving science that has moved from the traditional paradigm...

Fungal decay, predominantly caused by Penicillium expansum, is the main cause of apple postharvest losses. To overcome this problem, synthetic fungicides are applied to fruit before storage. Public concern about this practice has raised interest in developing alternative biocontrol strategies for postharvest diseases. Debaryomyces hansenii F9D, a p...

Macadamia ( Macadamia integrifolia ) trees are an important source of revenue in rainforest ecosystems. Their nuts are rich in vitamins, minerals, fiber, antioxidants, and monounsaturated oils. The fungus Lasiodiplodia theobromae , however, is a major disease problem, causing kernel rot and other disease symptoms. In the present study, a dual confr...

Microbial communities associated with fruit can contribute to quality and pathogen resistance, but little is known about their assembly and dynamics during fruit development and storage. Three apple cultivars growing under the same environmental conditions were utilized to examine the apple carposphere microbiome composition and structure at differ...

Metagenomic sequencing and multi-omic technologies have greatly advanced our understanding of the microbiome of fruit crops and revealed the complex interactions that potentially occur between microbial communities and their host. Strong evidence exists for the involvement of multiple microorganisms in the onset and development of disease in plant...

Apple is the largest fruit crop produced in temperate regions and is a popular fruit worldwide. It is, however, susceptible to a variety of postharvest fungal pathogens, including Penicillium expansum, Botrytis cinerea, Botryosphaeria dothidea, Monilia spp., and Alternaria spp. Decays resulting from fungal infections severely reduce apple quality a...

The endophytic microbiome of plants is believed to have a significant impact on its physiology and disease resistance, however, the role of host genotype in determining the composition of the endophytic microbiome of apple root systems remains an open question that has important implications for defining breeding objectives. In the current study, t...

Plants evolved in association with a diverse community of microorganisms. The effect of plant phylogeny and domestication on host–microbiome co‐evolutionary dynamics are poorly understood. Here we examined the effect of domestication and plant lineage on the composition of the endophytic microbiome of 11 Malus species, representing three major grou...

Recently, increasing focus has been placed on exploring fruit microbiomes and their association with their hosts. Investigation of the fruit surface microbiome of apple has revealed variations in the composition and structure depending on management practices, phenological stages, and spatial distribution on the fruit itself. However, the fate of t...

Wheat grains are colonized by complex microbial communities that have the potential to affect seed quality and susceptibility to disease. Some of the beneficial microbes in these communities have been shown to protect plants against pathogens through antagonism. We evaluated the role of the microbiome in seed health: in particular, against mycotoxi...

To provide fruit throughout the whole year, maintain quality and reduce spoilage, apples and pears are stored at low temperature. However, the development of rots, caused mainly by Penicillium expansum, cannot be avoided. To prevent fruit losses, biological control has been proposed as a potential alternative. In this work, 16 psychrotrophic, non-p...

Fungi have been reported as common inhabitants of the maritime waters in Antarctica by studies based on culture-dependent methods. More recently, results obtained using DNA sequencing technologies, revealed that fungal diversity worldwide has been underestimated by culture methods. The present study provides the first characterization of fungal com...

Main conclusion Anatomical, metabolic and microbial factors were identified that contribute to sequential freezing in wheat leaves and likely contribute to supercooling in the youngest leaves and potentially meristematic regions. Abstract Infrared thermography (IR) has been used to observe wheat leaves freezing independently and in an age-related...

Kiwifruit is purchased by consumers worldwide and is increasing in demand. Unfortunately, kiwifruit is susceptible to postharvest decay caused by a variety of fungal pathogens, including Botrytis cinerea, Penicillium expansum, Alternaria alternata, Botryosphaeria dothidea, and Diaporthe spp. Among these pathogens, B. cinerea is the most prevalent a...

Plant-associated microbial communities form complex co-associations that play a role in promoting plant productivity and health, although the underlying mechanisms have not been fully elucidated. The functional role of the microbiome provides a new perspective on how we can potentially utilize the microbiome to maintain the postharvest quality and...

We present the first worldwide study on the apple (Malus × domestica) fruit microbiome that examines questions regarding the composition and the assembly of microbial communities on and in apple fruit. Results revealed that the composition and structure of the fungal and bacterial communities associated with apple fruit vary and are highly dependen...

Citrus fruit are highly susceptible to infection by several fungal pathogens during postharvest storage. Therefore, harvested citrus fruit receive a series of treatments in the packhouse such as initial drenching, washing and disinfection, immersion in heated solutions of chemical fungicides and waxing that also include fungicides to reduce the ino...

Globalization has a dramatic effect on the trade and movement of seeds, fruits and vegetables, with a corresponding increase in economic losses caused by the introduction of transboundary plant pathogens. Current diagnostic techniques provide a useful and precise tool to enact surveillance protocols regarding specific organisms, but this approach i...

While the environment is considered the primary origin of the plant microbiome, the potential role of seeds as a source of transmitting microorganisms has not received much attention. Here we tested the hypothesis that the plant microbiome is partially inherited through vertical transmission. An experimental culturing device was constructed to grow...

Background: Apple is one of the most highly consumed fruits worldwide and is the largest fruit crop produced in temperate regions. Fruit quality, safety and long-term storage are issues that are important to growers, distributors, and consumers. We present the first worldwide study on the apple fruit microbiome that examines questions regarding the...

Each plant has a microbiome that is consisted of epiphytic and endophytic microbial communities. The plant microbiome may play a prominent role in different functions such as growth, disease, suppressing pathogens and potential influence of the physiology of reproductive plant organs (e.g., fruit). Endophytic microbiomes of any plant organs have mu...

Penicillium expansum is a ubiquitous postharvest pathogen that infects a wide range of fruits, including pome and a variety of stone fruit. Virulence factors that mediate pathogenicity in postharvest-decay fungi have not been fully defined, especially in regard to if and how the pathogen is able to modulate fruit defense mechanisms, particularly at...

Accumulating evidence indicates that the composition of the microbiota inhabiting an organism (both endo- and epiphytically) can have a profound effect on host physiology and defense responses. The role of the microbiota in plant health and physiology, however, is poorly understood, and few studies have focused on temperate fruit trees. A global ef...

Malus sieversii is considered the progenitor of modern apple (Malus pumila) cultivars and to represent a valuable source of genetic diversity. Despite the importance of M. sieversii as a source of disease resistance, stress tolerance, and novel fruit traits, little is known about gene function and diversity in M. sieversii. Notably, a publicly anno...

Penicillium expansum is a destructive phytopathogen causing postharvest decay on many stored fruits. To develop effective and safe management strategies, it is important to investigate its pathogenicity-related mechanisms. In this study, a bioinformatic pipeline was constructed and 50 core effector genes were identified in P. expansum using multipl...

Microbial volatiles (MVOCs) are low molecular weight compounds synthesized by range of microbial strains including bacteria and fungi. The chemical diversity of volatiles is variable and strain specific. Although low boiling point, and high vapour pressure of volatiles make easy transition between soil particles associated water and environment, th...

In the recent past edible films and coatings have been extensively used as an alternative packaging system over conventional systems to enhance shelf life, fruit quality and antagonistic properties against phytopathogens. The coatings are composed of various materials including polysaccharides, lipids, and proteins along with some other additives,...

Plants are increasingly subjected to episodes of spring frost injury due to erratic weather patterns fostered by climate change. While many plant species undergo a seasonal cycle of cold acclimation and deacclimation, warm, late-winter temperatures induce plants to lose their frost tolerance and thus experience lethal injury when more seasonable fr...

There is growing recognition of the role that the microbiome plays in the health and physiology of many plant species. However, considerably less research has been conducted on the postharvest microbiome of produce and the impact that postharvest processing may have on its composition. Here, amplicon sequencing was used to study the effect of washi...

Background While the environment is considered the primary origin for establishing the microbiome of newly developing plants, the potential role of seeds as a source of transmitting microorganisms has not received much attention. Here we tested the hypothesis that the plant microbiome is at least partially inherited through vertical transmission. W...

Date palm (Phoenix dactylifera) is considered to be a highly important food crop in several African and Middle Eastern countries due to its nutritional value and health-promoting properties. Microbial contamination of dates has been of concern to consumers, but very few works have analyzed in detail the microbial load of the different parts of date...

Apple blue mold causes significant postharvest economic losses worldwide. A blue mold resistance locus, qM-Pe3.1, was previously identified on chromosome 3 of Malus sieversii PI 613981, a wild accession with inferior fruit quality. Introgression of the resistance allele into elite breeding germplasm is difficult and success of introgression and the...

Fungal pathogens in fruits and vegetables cause significant losses during handling, transportation, and storage. Biological control with microbial antagonists replacing the use of chemical fungicides is a major approach in postharvest disease control, and several products based on single antagonists have been developed but have limitations related...

Candida oleophila is an effective biocontrol agent used to control post-harvest diseases of fruits and vegetables. C. oleophila I-182 was the active agent used in the first-generation yeast-based commercial product, Aspire®, for post-harvest disease management. Several action modes, like competition for nutrients and space, induction of pathogenesi...

Plant-associated microorganisms play a crucial role in plant health and productivity. Belowground microbial diversity is widely reported as a major factor in determining the composition of the plant microbiome. In contrast, much less is known about the role of the atmosphere in relation to the plant microbiome. The current study examined the hypoth...

The CBF signal pathway is responsible for a significant portion of plant responses to low temperature and freezing. Overexpression of CBF genes in model organisms such as Arabidopsis thaliana enhances abiotic stress tolerance but also reduces growth. In addition to these effects, overexpression of the peach (Prunus persica [L.] Batsch) CBF1 gene in...

Biological control of postharvest diseases has been suggested as a viable alternative to synthetic chemicals and has been the focus of considerable research worldwide for the last 30 years by many scientists and several commercial companies. Microbiome-based research has opened a whole new frontier that will greatly expand our knowledge of postharv...

Penicillium expansum is a major postharvest pathogen that infects different fruits, mainly through injuries inflicted during harvest or subsequent handling after harvest. Several effectors were suggested to mediate pathogenicity of P. expansum in fruit tissue. Among these effectors Nep1-like proteins (NLPs), produced by various microorganisms with...

While the wheat-associated microbiome is of major agricultural importance, little is known about the alterations in wheat grain microbial community composition during storage. Characterization of the bacterial and fungal communities in stored wheat grains revealed the impact of phosphine fumigation, one of the most effective methods to eliminate in...

Blue mold caused by Penicillium expansum is a major postharvest disease of pome fruit. Several mechanisms possibly involved in P. expansum pathogenicity and virulence. However, factors that mediate pathogenicity and virulence are largely not yet characterized. In this work we analyzed P. expansum predicted secretome to reveal potential genes that h...

Antarctica and sub-Antarctic regions are characterized by extreme conditions for life such as low temperatures and nutrient availability, high solar irradiation, and dryness; however, microorganisms from the three domains of life have been found as common inhabitants of soils and waters from those zones. Despite bacteria being the most numerous mic...

Biological control of plant pathogens, although it has been a successful alternative that has allowed to select microorganisms for the generation of bioproducts and to understand multiple biological mechanisms, cannot be considered as a strategy defined only from the selection of a range of cultivable microorganisms, nor understood from interaction...

Ginger (Zingiber officinale Roscoe), a perennial herb, is one of the most economically valuable plants in the Zingiberaceae family. Gingerol, as the major constituents of ginger essential oil, contributes to the unique flavor and pharmaceutical value of ginger. However, the pathway of gingerol biosynthesis has not been verified and described in gin...

Dehydration-responsive element binding proteins are transcription factors that play a critical role in plant response to temperature stress. Over-expression of DREB genes has been demonstrated to enhance temperature stress tolerance. A series of physiological and biochemical modifications occur in a complex and integrated way when plants respond to...

Supporting information 1.

The yeast Metschnikowia fructicola was reported as an efficient biological control agent of postharvest diseases of fruits and vegetables, and it is the bases of the commercial formulated product "Shemer." Several mechanisms of action by which M. fructicola inhibits postharvest pathogens were suggested including iron-binding compounds, induction of...

Fasta file of transcripts of MF.

Fasta file of CDSs of MF.

fpkm expression data and statistical differences among conditions analyzed with RNAseq.

Fasta file of proteins of MF.

Annotation file of MF, produced by Blast2GO.

List of GO terms related to the mutation or repair of the DNA sequence.

Annotation of Mf transcripts.

Proteinortho analysis of M. fructicola, M. bicuspidata, C. auris and C. lusitaniae.

Vcf file, obtained by mapping the M. fructicola strain AP47 reads on the genome of strain 277.

CAZymes predicted in the M. fructicola 277 genome.

Background: High-throughput amplicon sequencing spanning conserved portions of microbial genomes (16s rRNA and ITS) was used in the present study to describe the endophytic microbiota associated with three apple varieties, "Royal Gala," "Golden Delicious," and "Honey Crisp," and two rootstocks, M.9 and M.M.111. The objectives were to (1) determine...