Kari E. Dunfield

Inside the root microbiome: Bacterial root endophytes and plant growth promotion

Bacterial root endophytes reside in a vast number of plant species as part of their root microbiome, with some being shown to positively influence plant growth. Endophyte community structure (species diversity: richness and relative abundances) within the plant is dynamic and is influenced by abiotic and biotic factors such as soil conditions, biogeography, plant species, microbe-microbe interactions and plant-microbe interactions, both at local and larger scales. Plant-growth-promoting bacterial endophytes (PGPBEs) have been identified, but the predictive success at positively influencing plant growth in field conditions has been limited. Concurrent to the development of modern molecular techniques, the goal of predicting an organisms ability to promote plant growth can perhaps be realized by more thorough examination of endophyte community dynamics. This paper reviews the drivers of endophyte community structure relating to plant growth promotion, the mechanisms of plant growth promotion, and the current and future use of molecular techniques to study these communities.

Seasonal Changes in the Rhizosphere Microbial Communities Associated with Field-Grown Genetically Modified Canola (Brassica napus)

ABSTRACT The introduction of transgenic plants into agricultural ecosystems has raised the question of the ecological impact of these plants on nontarget organisms, such as soil bacteria. Although differences in both the genetic structure and the metabolic function of the microbial communities associated with some transgenic plant lines have been established, it remains to be seen whether these differences have an ecological impact on the soil microbial communities. We conducted a 2-year, multiple-site field study in which rhizosphere samples associated with a transgenic canola variety and a conventional canola variety were sampled at six times throughout the growing season. The objectives of this study were to identify differences between the rhizosphere microbial community associated with the transgenic plants and the rhizosphere microbial community associated with the conventional canola plants and to determine whether the differences were permanent or depended on the presence of the plant. Community-level physiological profiles, fatty acid methyl ester profiles, and terminal amplified ribosomal DNA restriction analysis profiles of rhizosphere microbial communities were compared to the profiles of the microbial community associated with an unplanted, fallow field plot. Principal-component analysis showed that there was variation in the microbial community associated with both canola variety and growth season. Importantly, while differences between the microbial communities associated with the transgenic plant variety were observed at several times throughout the growing season, all analyses indicated that when the microbial communities were assessed after winter, there were no differences between microbial communities from field plots that contained harvested transgenic canola plants and microbial communities from field plots that did not contain plants during the field season. Hence, the changes in the microbial community structure associated with genetically modified plants were temporary and did not persist into the next field season.

Chapter 4 Recent Advances in the Microbial Safety of Fresh Fruits and Vegetables

Foodborne illness outbreaks linked to fresh produce are becoming more frequent and widespread. High impact outbreaks, such as that associated with spinach contaminated with Escherichia coli O157:H7, resulted in almost 200 cases of foodborne illness across North America and >

Molecular Analysis of Carbon Monoxide-Oxidizing Bacteria Associated with Recent Hawaiian Volcanic Deposits

300 m market losses. Over the last decade there has been intensive research into gaining an understanding on the interactions of human pathogens with plants and how microbiological safety of fresh produce can be improved. The following review will provide an update on the food safety issues linked to fresh produce. An overview of recent foodborne illness outbreaks linked to fresh produce. The types of human pathogens encountered will be described and how they can be transferred from their normal animal or human host to fresh produce. The interaction of human pathogens with growing plants will be discussed, in addition to novel intervention methods to enhance the microbiological safety of fresh produce.

Influence of commercial inoculation with Glomus intraradices on the structure and functioning of an AM fungal community from an agricultural site

ABSTRACT Genomic DNA extracts from four sites at Kilauea Volcano were used as templates for PCR amplification of the large subunit (coxL) of aerobic carbon monoxide dehydrogenase. The sites included a 42-year-old tephra deposit, a 108-year-old lava flow, a 212-year-old partially vegetated ash-and-tephra deposit, and an approximately 300-year-old forest. PCR primers amplified coxL sequences from the OMP clade of CO oxidizers, which includes isolates such as Oligotropha carboxidovorans, Mycobacterium tuberculosis, and Pseudomonas thermocarboxydovorans. PCR products were used to create clone libraries that provide the first insights into the diversity and phylogenetic affiliations of CO oxidizers in situ. On the basis of phylogenetic and statistical analyses, clone libraries for each site were distinct. Although some clone sequences were similar to coxL sequences from known organisms, many sequences appeared to represent phylogenetic lineages not previously known to harbor CO oxidizers. On the basis of average nucleotide diversity and average pairwise difference, a forested site supported the most diverse CO-oxidizing populations, while an 1894 lava flow supported the least diverse populations. Neither parameter correlated with previous estimates of atmospheric CO uptake rates, but both parameters correlated positively with estimates of microbial biomass and respiration. Collectively, the results indicate that the CO oxidizer functional group associated with recent volcanic deposits of the remote Hawaiian Islands contains substantial and previously unsuspected diversity.

Mycorrhizal and Rhizobial Colonization of Genetically Modified and Conventional Soybeans

The use of commercial arbuscular mycorrhizal (AM) inoculants is growing. However, we know little about how resident AM communities respond to inoculations under different soil management conditions. The objective of this study was to simulate the application of a commercial AM fungal inoculant of Glomus intraradices to soil to determine whether the structure and functioning of that soil’s resident AM community would be affected. The effects of inoculation were investigated over time under disturbed or undisturbed soil conditions. We predicted that the introduction of an infective AM fungus, such as G. intraradices, would have greater consequences in disturbed soil. Using a combination of molecular (terminal restriction length polymorphism analysis based on the large subunit of the rRNA gene) and classical methods (AM fungal root colonization and P nutrition) we found that, contrary to our prediction, adding inoculant to soil containing a resident AM fungal community does not necessarily have an impact on the structure of that community either under disturbed or undisturbed conditions. However, we found evidence of positive effects of inoculation on plant nutrition under disturbed conditions, suggesting that the inoculant interacted, directly or indirectly, with the resident AM fungi. The inoculant significantly improved the P content of the host but only in presence of the resident AM fungal community. In contrast to inoculation, soil disturbance had a significant negative impact on species richness of AM fungi and influenced the AM fungal community composition as well as its functioning. Thus, we conclude that soil disturbance may under certain conditions have greater consequences for the structure of resident AM fungal communities in agricultural soils than commercial AM fungal inoculations with G. intraradices.

Evaluation of a biocontrol preparation consisting of Enterobacter asburiae JX1 and a lytic bacteriophage cocktail to suppress the growth of Salmonella Javiana associated with tomatoes.

ABSTRACT We grew plants of nine soybean varieties, six of which were genetically modified to express transgenic cp4-epsps, in the presence of Bradyrhizobium japonicum and arbuscular mycorrhizal fungi. Mycorrhizal colonization and nodule abundance and mass differed among soybean varieties; however, in no case was variation significantly associated with the genetic modification.

Relationships between dairy slurry total solids, gas emissions, and surface crusts.

A biocontrol preparation based on a combination of Enterobacter asburiae JX1 and a cocktail of five lytic bacteriophages was evaluated for control of Salmonella Javiana within the rhizosphere of plants and in pre- and postharvest tomatoes. The biocontrol preparation introduced into the rhizosphere of growing tomato plants reduced the persistence of Salmonella, although no synergistic action was observed between E. asburiae JX1 or the bacteriophage cocktail when used in combination. When the biocontrol preparation was coinoculated with Salmonella onto the blossom of tomato plants, the prevalence of the enteric pathogen both on the surface and in internal tissues of the subsequent tomatoes was significantly reduced compared with controls. Tomatoes derived from plants inoculated with Salmonella alone had a prevalence of 92% surface contamination (22 of 24 tomato batches were positive for Salmonella) and 43% internal contamination (31 of 72 batches positive). This Salmonella prevalence was reduced to 0% (0 of 38 positive) and 2% (1 of 57 positive), respectively, when the biocontrol preparation was applied. Although bacteriophages reduced the prevalence of internalized Salmonella, the main growth suppressing effect was via the antagonistic activity of E. asburiae JX1. No bacteriophages were recovered from tomatoes despite being introduced at 6 log PFU onto the blossom of plants. The biocontrol preparation was not effective for controlling the growth of Salmonella introduced onto postharvest tomatoes that were stored for 7 days at 15 degrees C. The application of E. asburiae JX1 is a promising approach for controlling Salmonella encountered in tomato production, and there was no evidence to suggest that the antagonistic activity could be enhanced by the coinoculation of bacteriophages.

Microbial population profiles of the microflora associated with pre‐ and postharvest tomatoes contaminated with Salmonella typhimurium or Salmonella montevideo

Livestock slurry storages are sources of methane (CH₄), nitrous oxide (NO₂), and ammonia (NH₃) emissions. Total solids (TS) content is an indicator of substrate availability for CH₄ and N₂O production and NH₃ emissions and is related to crust formation, which can affect these gas emissions. The effect of TS on these emissions from pilot-scale slurry storages was quantified from 20 May through 16 Nov. 2010 in Nova Scotia, Canada. Emissions from six dairy slurries with TS ranging from 0.3 to 9.5% were continuously measured using flow-through steady-state chambers. Methane emissions modeled using the USEPA methodology were compared with measured data focusing on emissions when empty storages were filled, and retention times were >30 d with undegraded volatile solids (VS) remaining in the system considered available for CH₄ production (VS carry-over). Surface crusts formed on all the slurries. Only the slurries with TS of 3.2 and 5.8% were covered completely for ∼3 mo. Nitrous oxide contributed <5% of total greenhouse gas emissions for all TS levels. Ammonia and CH₄ emissions increased linearly with TS despite variable crusting, suggesting substrate availability for gas production was more important than crust formation in regulating emissions over long-term storage. Modeled CH₄ emissions were substantially higher than measured data in the first month, and accounting for this could improve overall model performance. Carried-over VS were a CH₄ source in months 2 through 6. The results of this study suggest that substrate availability regulates emissions over long-term storage and that modifying the USEPA model to better describe carbon cycling is warranted.

Isolate identity determines plant tolerance to pathogen attack in assembled mycorrhizal communities.

Aims:  To determine the microflora profiles of pre‐ and postharvest tomatoes contaminated with Salmonella montevideo or S. typhimurium DT104.