Seed treatment with prodigiosin controls damping-off of cucumber caused by Pythium ultimum.

Ethanol extract of cell mass of Serratia marcescens strain N4-5, when applied as a treatment to cucumber seed, has been shown to provide control of the oomycete soil-borne plant pathogen Pythium ultimum equivalent to that provided by a seed-treatment chemical pesticide in some soils. Two dominant compounds in this extract, prodigiosin and the serratamolide serrawetin W1, were identified based on mass and collision induced dissociation mass fragmentation spectra. An additional four compounds with M+H masses (487, 541, 543, and 571) consistent with serratamolides reported in the literature were also detected.

Deciphering the Role of Trehalose in Tripartite Symbiosis Among Rhizobia, Arbuscular Mycorrhizal Fungi, and Legumes for Enhancing Abiotic Stress Tolerance in Crop Plants.

Drought is a critical factor limiting the productivity of legumes worldwide. Legumes can enter into a unique tripartite symbiotic relationship with root-nodulating bacteria of genera , , or and colonization by arbuscular mycorrhizal fungi (AMF). Rhizobial symbiosis provides nitrogen necessary for growth.

Soil Microbial Communities in Diverse Agroecosystems Exposed to the Herbicide Glyphosate.

Despite glyphosate's wide use for weed control in agriculture, questions remain about the herbicide's effect on soil microbial communities. The existing scientific literature contains conflicting results, from no observable effect of glyphosate to the enrichment of agricultural pathogens such as spp. We conducted a comprehensive field-based study to compare the microbial communities on the roots of plants that received a foliar application of glyphosate to adjacent plants that did not.

Comparative measurements of arbuscular mycorrhizal fungal responses to agricultural management practices.

Arbuscular mycorrhizal (AM) fungi are considered to be a key group of soil organisms for assessments of soil biological properties and developing relationships among crop production management practices, soil properties, crop performance, and ecosystem services. In a field study of cover crop treatments established during the transition from small grains to corn (Zea mays L), we assessed multiple measures of AM fungal responses to the management treatments: soil propagule numbers, biomass via lipid biomarkers, and root colonization extent. Our objectives were to determine response variables that reliably distinguished cover crop treatments and formed consistent relationships with grain yield, plant biomass, and mineral nutrient concentrations of the following corn crop.

Characterization of soil nematode communities in three cropping systems through morphological and DNA metabarcoding approaches.

We used complementary morphological and DNA metabarcoding approaches to characterize soil nematode communities in three cropping systems, conventional till (CT), no-till (NT) and organic (ORG), from a long-term field experiment. We hypothesized that organic inputs to the ORG system would promote a more abundant nematode community, and that the NT system would show a more structured trophic system (higher Bongers MI) than CT due to decreased soil disturbance. The abundance of Tylenchidae and Cephalobidae both showed positive correlations to soil organic carbon and nitrogen, which were highest in the ORG system.

Microbial community biomass and structure in saline and non-saline soils associated with salt- and boron-tolerant poplar clones grown for the phytoremediation of selenium.

Poplar trees (Populus spp.) are often used in bioremediation strategies because of their ability to phytoextract potential toxic ions, e.g.

Effects of growth temperature and carbon dioxide enrichment on soybean seed components at different stages of development.

Soybean plants were grown to maturity in controlled environment chambers and at the onset of flowering three temperature treatments were imposed that provided optimum [28/24 °C], low [22/18 °C] or high [36/32 °C] chamber air temperatures. In addition, plants were treated continuously with either 400 or 800 μmol mol CO. Seeds were harvested at 42, 53, 69 and 95 days after planting (i.

Belowground competition among invading detritivores.

The factors regulating soil animal communities are poorly understood. Current theory favors niche complementarity and facilitation over competition as the primary forms of non-trophic interspecific interaction in soil fauna; however, competition has frequently been suggested as an important community-structuring factor in earthworms, ecosystem engineers that influence belowground processes. To date, direct evidence of competition in earthworms is lacking due to the difficulty inherent in identifying a limiting resource for saprophagous animals.

Microbial rRNA:rDNA gene ratios may be unexpectedly low due to extracellular DNA preservation in soils.

We tested a method of estimating the activity of detectable individual bacterial and archaeal OTUs within a community by calculating ratios of absolute 16S rRNA to rDNA copy numbers. We investigated phylogenetically coherent patterns of activity among soil prokaryotes in non-growing soil communities. 'Activity ratios' were calculated for bacteria and archaea in soil sampled from a tropical rainforest and temperate agricultural field and incubated for one year at two levels of moisture availability and with and without carbon additions.

Yeasts associated with plums and their potential for controlling brown rot after harvest.

Bacterial and yeast antagonists isolated from fruit surfaces have been effective in controlling various post-harvest diseases, and several microbial antagonists have been developed into commercial products. Our knowledge of the fruit microbial community, with the exception of grapes, apples and some citrus fruit, is rudimentary and the potential of the resident yeasts for biocontrol remains largely unknown. We determined the occurrence of yeasts on plum surfaces during fruit development from the pre-hardening stage until harvest for 2 years.

Endophytic fungi from plums (Prunus domestica) and their antifungal activity against Monilinia fructicola.

Enophytic fungi were isolated from plum (Prunus domestica) leaves, identified with ITS1 and ITS4 primers, and their antagonistic activity was tested against Monilinia fructicola, which causes brown rot, blossom blight, and twig blight of stone fruits, and Colletotrichum gloeosporioides, which causes anthracnose on a variety of fruit crops. The production of antifungal compounds was determined in agar-diffusion and volatile inverted-plate tests. A total of 163 fungi were recovered from 30 plum trees, representing 22 cultivars.

Formulations of the endophytic bacterium Bacillus subtilis Tu-100 suppress Sclerotinia sclerotiorum on oilseed rape and improve plant vigor in field trials conducted at separate locations.

Sclerotinia sclerotiorum causes serious yield losses in crops in the People's Republic of China. Two formulations of oilseed rape seed containing the bacterium Bacillus subtilis Tu-100 were evaluated for suppression of this pathogen in field trials conducted at two independent locations. The pellet formulation significantly reduced disease (incidence and disease index) and increased plant dry mass, while the wrap formulation significantly reduced disease incidence and significantly increased plant dry mass at both field locations.

Culturable bacterial microflora associated with nectarine fruit and their potential for control of brown rot.

Microflora of fruit surfaces have been the best source of antagonists against fungi causing postharvest decay of fruit. However, there is little information on microflora colonizing surfaces of fruits other than grape, apple, and citrus. We characterized bacterial microflora on nectarine fruit surfaces from the early stage of development until harvest.

Isolation and partial characterization of Bacillus subtilis ME488 for suppression of soilborne pathogens of cucumber and pepper.

Environmentally friendly control measures are needed for suppression of soilborne pathogens of vegetable crops in the Republic of Korea. In vitro challenge assays were used to screen approximately 500 bacterial isolates from 20 Korean greenhouse soils for inhibition of diverse plant pathogens. One isolate, Bacillus subtilis ME488, suppressed the growth of 39 of 42 plant pathogens tested.

Role of sdhA and pfkA and catabolism of reduced carbon during colonization of cucumber roots by Enterobacter cloacae.

We have been using a mutational approach to determine how plant-beneficial bacteria such as Enterobacter cloacae 501R3 obtain carbon and energy for colonization of subterranean portions of cucumber and other plants. Reduced carbon detected in cucumber root exudate consisted of 73.3 % amino acids, 22.

Interpreting ecological diversity indices applied to terminal restriction fragment length polymorphism data: insights from simulated microbial communities.

Ecological diversity indices are frequently applied to molecular profiling methods, such as terminal restriction fragment length polymorphism (T-RFLP), in order to compare diversity among microbial communities. We performed simulations to determine whether diversity indices calculated from T-RFLP profiles could reflect the true diversity of the underlying communities despite potential analytical artifacts. These include multiple taxa generating the same terminal restriction fragment (TRF) and rare TRFs being excluded by a relative abundance (fluorescence) threshold.

Chromobacterium subtsugae sp. nov., a betaproteobacterium toxic to Colorado potato beetle and other insect pests.

Strain PRAA4-1(T), a motile, Gram-negative, violet-pigmented bacterium, was isolated from Maryland forest soil and found to be orally toxic to Colorado potato beetle larvae and other insects. Morphological, biological, biochemical and molecular characterization revealed that this strain was most similar to Chromobacterium violaceum, the type species and only currently recognized member of the genus Chromobacterium. DNA-DNA hybridization with C.

A mutation in an exbD gene reduces tagetitoxin production by Pseudomonas syringae pv. tagetis.

A mutant of Pseudomonas syringae pv. tagetis EB037 with limited ability to produce tagetitoxin was isolated after transposon mutagenesis and the mutation was characterized. The mutation occurred in a gene with a high degree of sequence identity to exbD.

Rapid and sensitive FAME analysis of bacteria by cold trap injection gas chromatography.

Whole cell fatty acid analysis is commonly used to identify bacteria. A cold trap, using a commercially available device that directs a stream of compressed air across a section of the GC column, is used to focus peaks at the head of the column. When combined with a rapid sample processing method that uses smaller volumes of solvents, it becomes possible to correctly identify bacteria from 1 to 2 mg of biomass.

Phylum- and class-specific PCR primers for general microbial community analysis.

Amplification of a particular DNA fragment from a mixture of organisms by PCR is a common first step in methods of examining microbial community structure. The use of group-specific primers in community DNA profiling applications can provide enhanced sensitivity and phylogenetic detail compared to domain-specific primers. Other uses for group-specific primers include quantitative PCR and library screening.

Endophytic bacteria in Coffea arabica L.

Eighty-seven culturable endophytic bacterial isolates in 19 genera were obtained from coffee plants collected in Colombia (n = 67), Hawaii (n = 17), and Mexico (n = 3). Both Gram positive and Gram negative bacteria were isolated, with a greater percentage (68%) being Gram negative. Tissues yielding bacterial endophytes included adult plant leaves, various parts of the berry (e.

Soil microbial communities associated with Bt and non-Bt corn in three soils.

The effects of expression of Cry endotoxin by Bt corn (transgenic corn engineered to express Bacillus thuringiensis toxin) on soil microbial community structure were assessed in a growth chamber experiment. Two lines of transgenic corn expressing different Cry endotoxins were compared with their respective non-transgenic isolines in three soil types with differing textures. Phospholipid fatty acid (PLFA) profiles from bulk soil and community-level physiological profiles (CLPP) from the rhizosphere community were used to assess community structure.

Improved fast gas chromatography for FAME analysis of bacteria.

Bacteria are frequently identified by fatty acid analysis. We previously reported on methods to speed up sample preparation and gas chromatography, resulting in greatly improved speed and throughput [J. Microbiol.