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Rhizobacterial communities can contribute to plant trait expression and performance, including plant tolerance against abiotic stresses such as drought. The conditioning of microbial communities related to disease resistance over generations has been shown to develop suppressive soils which aid in plant defense responses. Here, we applied this concept for the development of drought resistant soils. We hypothesized that soils conditioned under severe drought stress and tomato cultivation over two generations, will allow for plant selection of rhizobacterial communities that provide plants with improved drought resistant traits. Surprisingly, the plants treated with a drought-conditioned microbial inoculant showed significantly decreased plant biomass in two generations of growth. Microbial community composition was significantly different between the inoculated and control soils within each generation (i.e., microbial history effect) and for the inoculated soils between generations (i.e., conditioning effect). These findings indicate a substantial effect of conditioning soils on the abiotic stress response and microbial recruitment of tomato plants undergoing drought stress.

Insects are known plant pests, and some of them such as Trichoplusia ni feed on a variety of crops. In this study, Trichoplusia ni was fed distinct diets of leaves of Arabidopsis thaliana or Solanum lycopersicum as well as an artificial diet. After four generations, the microbial composition of the insect gut was evaluated to determine if the diet influenced the structure and function of the microbial communities. The population fed with A. thaliana had higher proportions of Shinella, Terribacillus and Propionibacterium, and these genera are known to have tolerance to glucosinolate activity, which is produced by A. thaliana to deter insects. The population fed with S. lycopersicum expressed increased relative abundances of the Agrobacterium and Rhizobium genera. These microbial members can degrade alkaloids, which are produced by S. lycopersicum. All five of these genera were also present in the respective leaves of either A. thaliana or S. lycopersicum, suggesting that these microbes are acquired by the insects from the diet itself. This study describes a potential mechanism used by generalist insects to become habituated to their available diet based on acquisition of phytochemical degrading gut bacteria.

Sustainable agricultural production requires an inclusive framework that concurrently considers the impacts of production methods on soil health, crop productivity, and crop nutritional quality. However, few studies have directly examined the potential associations among management impacts on soil health (SH), crop productivity, and crop quality. We evaluated these linkages in a continuous maize experiment with treatments varying in nitrogen (N) fertilizer amount and type (zero input control, inorganic N, and manure-based N treatment). We evaluated select SH indicators after six cropping years, and computed physical, chemical, biological, nutrient, and overall SH indices using the Soil Management Assessment Framework (SMAF). Crop yields, mineral nutrient concentrations (denoted with brackets), and nutrient uptake were analyzed in years six and seven. Manure application increased biological SH indicators compared to the control and inorganic N treatments and also increased available potassium (K), zinc (Zn), copper (Cu), and phosphorus (P). Overall SH indices were higher in the inorganic N and manure treatments than in the control but did not differ between the two N sources, despite the large exogenous sources of C, N, and nutrients applied via manure. The SMAF tool only directly considers P and K in terms of soil nutrients—other nutrient benefits of manure application (i.e., increases in total soil N, available Cu and Zn) were not accounted for, suggesting that the SMAF nutrient SH index should be modified to account for the impacts of management practices on nutrient availability. Crop yields were higher in treatments with higher overall SH, supporting the linkages between SH and crop productivity. Despite widely differing nutrient inputs and soil fertility levels, we found no yield differences between the two N sources. However, there were notable treatment impacts on crop quality. Grain [N] was 40% greater in the urea and manure treatments than in the control. Grain [P], [K], and [Mg], important elements in livestock nutrition, were 10% to 28% greater in the manure treatment than in the urea treatment. In addition, although a yield dilution of grain [Zn] occurred in the urea treatment, the dilution effect was mitigated in the manure treatment, likely due to increases in available Zn. Overarchingly, our results suggest that management practices that maintain or improve SH and nutrient availability also improve maize productivity and nutritional quality, which could have cascading positive impacts on animal and human nutrition.

Soil microbiome disruption methods are regularly used to reduce populations of microbial pathogens, often resulting in increased crop growth. However, little is known about the effect of soil microbiome disruption on non-pathogenic members of the soil microbiome. Here, we applied soil microbiome disruption in the form of moist-heat sterilization (autoclaving) to reduce populations of naturally occurring soil microbiota. The disruption was applied to analyze bacterial community rearrangement mediated by four crops (corn, beet, lettuce, and tomato) grown in three historically distinct agroecosystem soils (conventional, organic, and diseased). Applying the soil disruption enhanced plant influence on rhizosphere bacterial colonization, and significantly different bacterial communities were detected between the tested crops. Furthermore, bacterial genera showed significant abundance increases in ways both unique-to and shared-by each tested crop. As an example, corn uniquely promoted abundances of Pseudomonas and Sporocytophaga, regardless of the disrupted soil in which it was grown. Whereas the promotion of Bosea, Dyadobacter and Luteoliobacter was shared by all four crops when grown in disrupted soils. In summary, soil disruption followed by crop introduction amplified the plant colonization of potential beneficial bacterial genera in the rhizosphere.

Root-knot nematodes (RKN) such as Meloidogyne spp. are among the most detrimental pests in agriculture affecting several crops. New methodologies to manage RKN are needed such as efficient discovery of nematophagous microbes. In this study, we developed an in vitro high-throughput method relying on the free-living nematode Caenorhabditis elegans and the infection of those nematodes with a soil slurry containing a microbiome likely to house nematophagous microbes. Nematodes were monitored for presence of infection and sub-cultured repeatedly for the purpose of isolating pure cultures of the microbe responsible for conferring the nematicidal activity. Once soil microbes were confirmed to be antagonistic to C. elegans, they were tested for pathogenicity against Meloidogyne chitwoodi. Using this methodology, the fungal isolate Mortierella globalpina was confirmed to be pathogenic in vitro against M. chitwoodi by nematode trapping via hyphal adhesion to the cuticle layer, penetration of the cuticle layer, and subsequently digestion of its cellular contents. M. globalpina was also observed to reduce disease symptomology of RKNs in vivo via significant reduction of root-galls on tomato (Solanum lycopersicum var. Rutgers).

Soil microbiome disruption methods are regularly used to reduce populations of microbial pathogens, which often results in increase crop growth. However, little is known about the effect of soil microbiome disruption on non-pathogenic members within the soil microbiome. Here, we applied soil microbiome disruption, in the form of moist-heat sterilization (autoclaving) to reduce populations of naturally occurring soil microbiota. The disruption was applied to analyze bacterial community rearrangement mediated by four crops (corn, beet, lettuce, and tomato) grown in three historically distinct agroecosystem soils (conventional, organic, and diseased). Applying the soil disruption enhanced plant influence on bacterial colonization, and significantly different bacterial communities were detected between the tested crops. Furthermore, bacterial genera showed significant abundance increases both unique-to and shared-by each tested crop. As an example, corn uniquely promoted abundances of Pseudomonas and Sporocytophaga, regardless of the disrupted soil in which it was grown. Whereas the promotion of Bosea, Dyadobacter and Luteoliobacter was shared by all crops grown in all disrupted soils. In summary, soil disruption followed by crop introduction amplified plant-mediated selection of plant benefiting bacterial genera.

The following study investigates the timing and mechanism of impact of Swiss needle cast on Douglas-fir (Pseudotsuga menziesii) needle physiology (i.e. gas exchange). Swiss needle cast is a foliar disease caused by the fungus Phaeocryptopus gaeumannii, which occurs throughout the range of Douglas fir and until recently has been considered unimportant. However, recent surveys show the Swiss needle cast currently affects52611 ha of forested lands in western Oregon, USA, causing a reduction in growth of c. 23% or an implied growth loss of c. 3.2 m

Information about the establishment phase of Miscanthus sinensis Andersson as sterile procedure to avoid the contamination were few reported. The aim of this study was to evaluate different immersion sterilization procedures with and without the biocide, Plant Preservative Mixture (PPM?) on in vitro contamination of two Miscanthus genotypes. The plant material were canes from adult plants of two accessions PI 668371 and PI 668375 cultivated in the germplasm bank of USDA-ARS, Griffin, Georgia. Apical meristems were submitted to immersion sterilization procedures (70% isopropyl alcohol and 1.5, 5.0 or 8.25% NaOCl for different time periods, followed by rinsing three times with autoclaved distilled water. After that, the explants were inoculated on MS basal medium in the presence or absence of 1 mL L-1 PPM?. The experimental design was fully randomized in a 2 x 5 x 2 factorial scheme (genotypes x sterilization process x PPM?) with five replicates per treatment and five apical meristems per experimental unit. Aseptic treatments showed no differences for percentage of bacterial and fungal contaminations and percentage of explant survival. In the presence of PPM ? there was less bacterial contamination in the accessions (28%) than in the absence (100%). For the percentage of fungal contamination, PPM ? had no significant effect on PI 668371 accession. However, on PI 668375 accession there was a lower percentage of fungal contamination (16%). The biocide PPM ? may be an efficient agent to prevent bacterial contamination on in vitro cultures of Miscanthus spp and fungal contamination in PI 668375 accession. Made available in DSpace on 2020-12-23T09:04:29Z (GMT). No. of bitstreams: 1 16.-Ana-Ledo-Sterilization-procedures-and-plant.pdf: 541048 bytes, checksum: 0a107e45b3f2de53cb2e54dcde5369ac (MD5) Previous issue date: 2019

Sustaining or increasing micronutrient concentrations in food and feed is essential for human and animal health, yet little research has quantified the relative importance of nitrogen (N) fertilization on maize micronutrient concentrations. Nitrogen fertilization could dilute some micronutrients while increasing others (i.e., biofortification). Nitrogen fertilization also influences the amount of residue returned to the soil, potentially altering soil organic carbon (SOC) and micronutrients. While changes in soil micronutrients under long-term production are sometimes attributed to export via harvest or import via fertilization, available micronutrients are also influenced by soil organic matter — changes in SOC could impact available micronutrients. Our objectives were to (1) examine the long-term effects (14 years) of different N rates (0, 68, 120,173, 232 kg ha−1) on the concentration ([]), uptake, and cycling of N and micronutrients (Fe, Zn, Cu, Mn) in no-till continuous maize and (2) assess whether nutrient removal via grain harvest, or residue return have resulted in depletion or accumulation of SOC and available and total micronutrients. Results showed a positive impact of fertilization on stover [N], [Cu] and [Mn], and increased grain [N] and [Fe]. However, fertilization decreased [Zn] in all plant fractions, indicating that maize [Zn] is susceptible to yield dilution. Total and available soil micronutrients were not impacted by fertilization, despite widely differing rates of nutrient harvest and return. Available Cu and Mn followed changes in SOC, which declined in all depths except the surface 0–7.5 cm. Available Zn increased in the surface 0–7.5 cm, with slight increases in deeper depths. Available micronutrients appear to be closely regulated by SOC in this system. These findings give additional insights into how N fertilization impacts maize micronutrient concentrations, and suggest that SOC contributes to micronutrient availability, underscoring the role of SOC in sustaining long-term soil fertility.

Phosphorous (P) fertilization is critical to enhance plant P uptake and proper growth. Soil microorganisms play a key role in P cycle and mediating P availability to plants. However, it is presently unknown if its application may have detrimental effects on the soil bacterial community. Blueberries are sensitive to fertilization hinting to close relationships with beneficial microbes related to soil nutrition. Our study explored the effect of P fertilization amendments on soil bacterial community composition in two varieties of commercial blueberry (Vaccinium sp. var. “Misty” and “Biloxi”). Shifts in microbial community composition and diversity were found in response to P amendment. The rhizosphere microbiome was influenced by P level and differentiated based on low P (0 and 50 kg/ha) and high P (101 and 192 kg/ha) rates. Additionally, predictive microbial acid phosphatase activity decreased with increasing levels of decomposition and solubility of mineral P. Thus, our results suggest that P fertilization decreases the ability of P–solubilizing microbes to naturally provide P to the plant.

Drought stress is a major factor limiting wheat production in rain-fed areas around the world. Wheat tolerance to drought stress may be enhanced through genotypic selection, but recently, there has been interest in manipulating wheat-microbial interactions to promote drought tolerance. The prime objective of the study was to examine the effects of inoculation with 1-aminocyclopropane-1-carboxylic acid (ACC)-deaminase containing (ACC+) bacteria on different winter wheat genotypes (grown in 1 m tall × 10 cm diameter tubes) under water-stressed and well-watered conditions as determined by root length, above- and below-ground biomass, and leaf relative water content. The results of the present study revealed that under water stress, inoculation with ACC+ bacteria increased leaf relative water content (RWC) for genotypes RonL and OK06318 by 22%, compared with non-inoculated controls. Under water stress, length of roots with a diameter class of 0.75–1 mm increased by 129% in response to ACC+ bacteria in the deepest tube section (67–99 cm depth increment). Under well-watered conditions, inoculation increased above-ground biomass for RonL and TAM112 by 37% and 32%, respectively, as compared to non-inoculated controls. Inoculation also increased RonL root biomass by 150% in the deepest tube section, and increased the length of roots with a diameter class of 0.50–0.75 mm in the deepest tube section for TAM112 by 40%. The results further showed that, irrespective of irrigation regime, the genotype RonL appears to be a good plant model to study wheat interactions with ACC+ bacteria. Collectively, the results of the present study revealed that the growth response of winter wheat to inoculation with ACC+ bacteria was genotype dependent. The variation among wheat genotypes in their response to ACC+ bacteria might lead to innovative selection strategies for improved water stress tolerance.

Thatch management in turfgrass has been recommended as part of integrated pest management; however, there is limited understanding of the microbial community in thatch. Previous studies on the turfgrass phytobiome mostly focused on the soil; however, culture-based studies have suggested that the thatch layer of golf courses contains higher bacterial and fungal abundances than the soil. In our study, quantitative PCR was used to investigate total abundance of bacteria, fungi, and the turfgrass pathogen, Sclerotinia homoeocarpa (causal agent of dollar spot) in the thatch and soil of three golf courses on two sampling dates. Additionally, we compared the abundance of these organisms among roughs, fairways, and putting greens, which are under different management intensities. Our results demonstrate bacterial abundance was higher in May than in September, but not consistently higher in the thatch or soil among the three golf courses or management areas. Fungi, and specifically S. homoeocarpa, are more abundant in the thatch than in the soil. These results show the necessity for future turfgrass phytobiome studies to analyze both thatch and soil to obtain a complete picture of bacterial and fungal microbial community structure and dynamics on golf courses. Despite the differences in fungicide usage and management inputs, there were no differences in S. homoeocarpa abundance among the three management areas in the soil. S. homoeocarpa abundance was higher in the thatch on the conventional golf course fairway in September. These results may have important practical implications for development of integrated disease management strategies and for understanding the epidemiology of S. homoeocarpa on golf courses.

Soils are the keystone of healthy and vibrant ecosystems, providing physical, chemical, and biological substrates and functions necessary to support life. In particular, it's the extensive and elaborate matrix of soil microorganisms and other life forms that contributes to soil health and utility. But soils are under constant threat from heavy use, changing climate, and in some cases poor management (1, 2). In view of soil’s key role and threatened status, we believe that there is a need for the scientific community to undertake coordinated research and development efforts that will lead to a unique asset: a National Living Soil Repository (Fig. 1). Fig. 1. A National Living Soil Repository would store agricultural cryogenic and air-dried soil samples, analyze samples for microbial community composition, assess samples for microbial viability, and serve as a potential source of living organisms for various agricultural ecosystem services. Image courtesy of Jennifer Moore-Kucera (USDA Natural Resources Conservation Service) and Daniel Manter (USDA Agricultural Research Service). Already local and national soil archives have been shown to be of great utility for studying, analyzing, and documenting long-term environmental and ecological trends. For example, the historical soil archive at Hubbard Brook helped researchers discover the link between fossil fuels and acidification of rain and snow (3); the Rothamsted Sample Archive in the United Kingdom has shown a steady increase in dioxins during the last century (4). And yet, a soil repository/archive designed to preserve native biological diversity does not currently exist. Such an archive would provide the ability to acquire data on the current biological (e.g., soil health) state of soils around the country across soil types, cropping systems, and ecosystems and over time. Further, by maintaining soil archives and a catalog of their microbial communities, we will gain a better understanding of how soil organisms are distributed … [↵][1]1To whom correspondence should be addressed. Email: Jorge.Delgado{at}ars.usda.gov. [1]: #xref-corresp-1-1

Nematodes are an important component of the golf course ecosystem. Many species provide benefits to turfgrass, while others can cause significant damage. Previous studies on golf courses have focused only on herbivore nematodes, mostly on putting greens. This study aimed to characterize all nematode trophic groups and nematode maturity and ecological indices under different management intensities (depicted by roughs, fairways, and putting greens) of three golf courses representing conventional and organic management types over two seasons in 2013 and 2014. The putting greens on all three golf courses had lower diversity and herbivore (plant-parasitic) index (PPI) values than the other management areas. The relative abundance of herbivores, bacterivores, and structure index (SI) values differed among organic and conventional management. Canonical correspondence and multiple stepwise regression analyses revealed pH, phosphorous, and organic matter were positively related to increased herbivores and negatively related to increased bacterivores. The results of this study can be used to develop alternative management practices aimed at decreasing problematic herbivore populations on putting greens and increasing potentially beneficial bacterivores.

Some rhizosphere microbes, such as plant growth-promoting rhizobacteria (PGPR), can alleviate plant drought stress and improve water use efficiency and productivity under drought conditions. The aims of this study are: 1) isolation and characterization of PGPRs from the rhizosphere of Arabidopsis plants that could improve drought tolerance of Arabidopsis and maize; 2) studying the potential mechanisms of improved plant drought tolerance by the isolated bacteria. In this study, bacteria isolates were isolated from the rhizosphere of Arabidopsis plants subjected to water limitation. Subsequently, the isolates were cultured and screened for their ability to improve drought tolerance of Arabidopsis. Potential mechanisms of improved plant drought tolerance by these bacteria including bacterial exopolysaccharide and 1-aminocyclopropane-1-carboxylic acid deaminase production, plant root system architecture modification, and plant physiological responses were also explored. Two bacterial isolates that conferred the greatest drought tolerance to Arabidopsis were further characterized. Both bacteria exhibit 1-aminocyclopropane-1-carboxylic acid deaminase activity, which can promote drought tolerance by decreasing plant ethylene levels. In vitro study showed that both Mitsuaria sp. ADR17 and Burkholderia sp. ADR10 altered the root structure system of Arabidopsis. Moreover, inoculation of Zea mays L. with either strain reduced evapotranspiration (i.e., soil water loss), and changed the plant proline and malondialdehyde levels, antioxidant enzymes activity, and phytohormone contents under drought stress. These results indicate that both strains interact with plants in ways that allow them to alter root system architecture, plant physiological responses and phytohormone levels under drought conditions to alleviate stress and improve plant survival. The results also indicated that each individual isolate has a separate pleiotropic effect.

Pratylenchus neglectus and Meloidogyne chitwoodi are the main plant-parasitic nematodes in potato crops of the San Luis Valley, Colorado. Bacterial microbiome (16S rRNA copies per gram of soil) and nematode communities (nematodes per 200 g of soil) from five different potato farms were analyzed to determine negative and positive correlations between any bacterial genus and P. neglectus and M. chitwoodi. Farms showed differences in bacterial communities, percentage of bacterivorous and fungivorous nematodes, and numbers of P. neglectus and M. chitwoodi. The farm with the lowest population of P. neglectus and M. chitwoodi had higher abundances of the bacterial genera Bacillus spp., Arthrobacter spp., and Lysobacter spp., and the soil nematode community was composed of more than 30% of fungivorous nematodes. In contrast, the farm with higher numbers of P. neglectus and M. chitwoodi had a lower abundance of the abovementioned bacterial genera, higher abundance of Burkholderia spp., and less than 25% of fungivorous nematodes. The α-Proteobacteria Rhodoplanes, Phenylobacterium, and Kaistobacter positively correlated with M. chitwoodi, and the Bacteroidia and γ-Proteobacteria positively correlated with P. neglectus. Our results, based largely on co-occurrence analyses, suggest that the abundance of Bacillus spp., Arthrobacter spp., and Lysobacter spp. in Colorado potato soils is negatively correlated with P. neglectus and M. chitwoodi abundance. Further studies will isolate and identify bacterial strains of these genera, and evaluate their nematode-antagonistic activity.

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 and structure of oomycete and fungal communities associated with a rye cover crop, and to track their community dynamics in the first several weeks after herbicide was applied to terminate the cover crop. The dominant oomycetes associated with cereal rye roots were Pythium volutum, Pythium sp. F86 (an unknown species within clade B), and Lagena radicicola. Because P. volutum is sensitive to common additives in isolation media, and L. radicicola is an obligate intracellular parasite, a unique aspect of this work is to reveal the dominance of oomycete taxa that would have been missed entirely under a traditional cultivation-based approach. Based on first detection in an amplicon sequencing survey, we were able to isolate P. volutum and Pythium sp. F86. We demonstrate that both species are pathogenic on corn, and that corn seedlings grown in the field following a rye cover crop show elevated rates of infection by P. volutum, highlighting a potential disease risk associated with cover cropping. P. volutum and Pythium sp. F86 exhibited contrasting spatial patterns of abundance, with nearly complete turnover of the dominant species across the field site. In contrast to the strong spatial structuring and low diversity of oomycete communities, fungal communities associated with a cereal rye cover crop were more diverse and dynamic, with some displacement of basidiomycetes by ascomycetes over time. Several plant pathogens, as well as putative beneficial organisms, were detected among fungal communities associated with rye roots. This work sheds light on microbial community dynamics on dying host plants, highlights the power of culture-independent microbial community assessment to yield new insights, and suggests the need for informed management to reduce seedling disease risk in corn following rye cover crops.

Estrogen decline during menopause is associated with altered metabolism, weight gain and increased risk of cardiometabolic diseases. The gut microbiota also plays a role in the development of cardiometabolic dysfunction and is also subject to changes associated with age-related hormone changes. Phytoestrogens are plant-based estrogen mimics that have gained popularity as dietary supplements for the treatment or prevention of menopause-related symptoms. These compounds have the potential to both modulate and be metabolized by the gut microbiota. Hops (Humulus lupulus L.) contain potent phytoestrogen precursors, which rely on microbial biotransformation in the gut to estrogenic forms. We supplemented ovariectomized (OVX) or sham-operated (SHAM) C57BL/6 mice, with oral estradiol (E2), a flavonoid-rich extract from hops, or a placebo carrier oil, to observe effects on adiposity, inflammation, and gut bacteria composition. Hops extract (HE) and E2 protected against increased visceral adiposity and liver triglyceride accumulation in OVX animals. Surprisingly, we found no evidence of OVX having a significant impact on the overall gut bacterial community structure. We did find differences in the abundance of Akkermansia muciniphila, which was lower with HE treatment in the SHAM group relative to OVX E2 treatment and to placebo in the SHAM group.

Estrogen decline during menopause is associated with altered metabolism, weight gain and increased risk of cardiometabolic diseases. The gut microbiota also plays a role in the development of cardiometabolic dysfunction and is also subject to changes associated with age-related hormone changes. Phytoestrogens are plant-based estrogen mimics that have gained popularity as dietary supplements for the treatment or prevention of menopause-related symptoms. These compounds have the potential to both modulate and be metabolized by the gut microbiota. Hops (Humulus lupulus L.) contain potent phytoestrogen precursors, which rely on microbial biotransformation in the gut to estrogenic forms. We supplemented ovariectomized (OVX) or sham-operated (SHAM) C57BL/6 mice, with oral estradiol (E2), a flavonoid-rich extract from hops, or a placebo carrier oil, to observe effects on adiposity, inflammation, and gut bacteria composition. Hops extract (HE) and E2 protected against increased visceral adiposity and liver triglyceride accumulation in OVX animals. Surprisingly, we found no evidence of OVX having a significant impact on the overall gut bacterial community structure. We did find differences in the abundance of Akkermansia muciniphila, which was lower with HE treatment in the SHAM group relative to OVX E2 treatment and to placebo in the SHAM group.

There is evidence that shows that phosphorus (P) fertilization has a moderate effect on the rhizosphere microbial composition of cultivated crops. But how this effect is manifested on wild species of the same crop is not clear. This study compares the impact of phosphorus fertilization with rhizosphere bacterial community composition and its predicted functions, related to P-cycling genes, in both cultivated and non-cultivated potato (Solanum sp.) plants. It was found that the biomass of non-cultivated potatoes was more responsive to P fertilization as compared with cultivated plants. Differences in general bacterial community composition patterns under increasing P amendments were subtle for both potato groups. However, potato genotype significantly influenced community composition with several bacterial families being more abundant in the cultivated plants. In addition, the predicted phosphatases had lower abundances in modern cultivars compared with non-cultivated potatoes. In summary, despite higher accumulation of differentially abundant bacteria in the rhizosphere of cultivated plants, the responsiveness of these plants to increase P levels was lower than in non-cultivated plants.

The gut microbiota is increasingly recognized as an important modulator of human health. As such, there is a growing need to identify effective means of selectively modifying gut microbial communities. Bacteriophages, which were briefly utilized as clinical antimicrobials in the early 20th century, present an opportunity to selectively reduce populations of undesirable microorganisms. However, whether intentional consumption of specific bacteriophages affects overall gut ecology is not yet known. Using a commercial cocktail of Escherichia coli-targeting bacteriophages, we examined their effects on gut microbiota and markers of intestinal and systemic inflammation in a healthy human population. In a double-blinded, placebo-controlled crossover trial, normal to overweight adults consumed bacteriophages for 28 days. Stool and blood samples were collected and used to examine inflammatory markers, lipid metabolism, and gut microbiota. Reductions in fecal E. coli loads were observed with phage consumption. However, there were no significant changes to alpha and beta diversity parameters, suggesting that consumed phages did not globally disrupt the microbiota. However, specific populations were altered in response to treatment, including increases in members of the butyrate-producing genera Eubacterium and a decreased proportion of taxa most closely related to Clostridium perfringens. Short-chain fatty acid production, inflammatory markers, and lipid metabolism were largely unaltered, but there was a small but significant decrease in circulating interleukin-4 (Il-4). Together, these data demonstrate the potential of bacteriophages to selectively reduce target organisms without global disruption of the gut community.