Rust (Puccinia emaculata) Management and Impact on Biomass Yield in Switchgrass

Rust, putatively caused by Puccinia emaculata, is a widespread and potentially damaging disease of switchgrass, a crop produced as feedstock for livestock and bioenergy. Azoxystrobin, chlorothalonil, and myclobutanil were applied at 1-, 2-, 3-, or 4-week intervals for 12 to 14 weeks to the vegetatively propagated switchgrass cultivar Cloud Nine to assess fungicide selection and application interval for the control of rust as well as the impact of this disease on switchgrass biomass yield. Although rust severity significantly differed among study years, azoxystrobin and myclobutanil were often equally and more effective than chlorothalonil at controlling rust, with superior disease control coming at shorter application intervals compared with extended application intervals. Year, product, application interval, and product × interval significantly impacted dry biomass yield, which was greatest in 2016 and lowest in 2014. Dry biomass yield protection was significantly better with azoxystrobin and myclobutanil applications than with chlorothalonil or no fungicide. Linear regression models with the final disease rating, as well as with the area under disease progress curve in each year, were significant, but coefficients of determination were low to moderate (0.21 < R² < 0.60), indicating that rust response and subsequent disease impact on dry biomass yield were impacted by other factors. From our models, an estimated 3 to 5% biomass decline was calculated for each 10% increment in rust-related leaf necrosis observed at the final September rating date. With rust-related leaf necrosis ≥80% by 1 September in each of 4 study years, biomass yield may be reduced by 24 to 40% if rust problems are not managed in switchgrass crops.

Drought stress and plant ecotype drive microbiome recruitment in switchgrass rhizosheath

The rhizosheath, a layer of soil grains that adheres firmly to roots, is beneficial for plant growth and adaptation to drought environments. Switchgrass is a perennial C4 grass which can form contact rhizosheath under drought conditions. In this study, we characterized the microbiomes of four different rhizocompartments of two switchgrass ecotypes (Alamo and Kanlow) grown under drought or well-watered conditions via 16S ribosomal RNA amplicon sequencing. These four rhizocompartments, the bulk soil, rhizosheath soil, rhizoplane, and root endosphere, harbored both distinct and overlapping microbial communities. The root compartments (rhizoplane and root endosphere) displayed low-complexity communities dominated by Proteobacteria and Firmicutes. Compared to bulk soil, Cyanobacteria and Bacteroidetes were selectively enriched, while Proteobacteria and Firmicutes were selectively depleted, in rhizosheath soil. Taxa from Proteobacteria or Firmicutes were specifically selected in Alamo or Kanlow rhizosheath soil. Following drought stress, Citrobacter and Acinetobacter were further enriched in rhizosheath soil, suggesting that rhizosheath microbiome assembly is driven by drought stress. Additionally, the ecotype-specific recruitment of rhizosheath microbiome reveals their differences in drought stress responses. Collectively, these results shed light on rhizosheath microbiome recruitment in switchgrass and lay the foundation for the improvement of drought tolerance in switchgrass by regulating the rhizosheath microbiome.

Improved node culture methods for rapid vegetative propagation of switchgrass (Panicum virgatum L.)

BACKGROUND

Switchgrass (Panicum virgatum L.) is an important bioenergy and forage crop. The outcrossing nature of switchgrass makes it infeasible to maintain a genotype through sexual propagation. Current asexual propagation protocols in switchgrass have various limitations. An easy and highly-efficient vegetative propagation method is needed to propagate large natural collections of switchgrass genotypes for genome-wide association studies (GWAS).

RESULTS

Micropropagation by node culture was found to be a rapid method for vegetative propagation of switchgrass. Bacterial and fungal contamination during node culture is a major cause for cultural failure. Adding the biocide, Plant Preservative Mixture (PPM, 0.2%), and the fungicide, Benomyl (5 mg/l), in the incubation solution after surface sterilization and in the culture medium significantly decreased bacterial and fungal contamination. In addition, "shoot trimming" before subculture had a positive effect on shoot multiplication for most genotypes tested. Using the optimized node culture procedure, we successfully propagated 330 genotypes from a switchgrass GWAS panel in three separate experiments. Large variations in shoot induction efficiency and shoot growth were observed among genotypes. Separately, we developed an in planta node culture method by stimulating the growth of aerial axillary buds into shoots directly on the parent plants, through which rooted plants can be generated within 6 weeks. By circumventing the tissue culture step and avoiding application of exterior hormones, the in planta node culture method is labor- and cost-efficient, easy to master, and has a high success rate. Plants generated by the in planta node culture method are similar to seedlings and can be used directly for various experiments.

CONCLUSIONS

In this study, we optimized a switchgrass node culture protocol by minimizing bacterial and fungal contamination and increasing shoot multiplication. With this improved protocol, we successfully propagated three quarters of the genotypes in a diverse switchgrass GWAS panel. Furthermore, we established a novel and high-throughput in planta node culture method. Together, these methods provide better options for researchers to accelerate vegetative propagation of switchgrass.

Exploring the Lignin Catabolism Potential of Soil-Derived Lignocellulolytic Microbial Consortia by a Gene-Centric Metagenomic Approach

An exploration of the ligninolytic potential of lignocellulolytic microbial consortia can improve our understanding of the eco-enzymology of lignin conversion in nature. In this study, we aimed to detect enriched lignin-transforming enzymes on metagenomes from three soil-derived microbial consortia that were cultivated on "pre-digested" plant biomass (wheat straw, WS1-M; switchgrass, SG-M; and corn stover, CS-M). Of 60 selected enzyme-encoding genes putatively involved in lignin catabolism, 20 genes were significantly abundant in WS1-M, CS-M, and/or SG-M consortia compared with the initial forest soil inoculum metagenome (FS1). These genes could be involved in lignin oxidation (e.g., superoxide dismutases), oxidative stress responses (e.g., catalase/peroxidases), generation of protocatechuate (e.g., vanAB genes), catabolism of gentisate, catechol and 3-phenylpropionic acid (e.g., gentisate 1,2-dioxygenases, muconate cycloisomerases, and hcaAB genes), the beta-ketoadipate pathway (e.g., pcaIJ genes), and tolerance to lignocellulose-derived inhibitors (e.g., thymidylate synthases). The taxonomic affiliation of 22 selected lignin-transforming enzymes from WS1-M and CS-M consortia metagenomes revealed that Pseudomonadaceae, Alcaligenaceae, Sphingomonadaceae, Caulobacteraceae, Comamonadaceae, and Xanthomonadaceae are the key bacterial families in the catabolism of lignin. A predictive "model" was sketched out, where each microbial population has the potential to metabolize an array of aromatic compounds through different pathways, suggesting that lignin catabolism can follow a "task division" strategy. Here, we have established an association between functions and taxonomy, allowing a better understanding of lignin transformations in soil-derived lignocellulolytic microbial consortia, and pinpointing some bacterial taxa and catabolic genes as ligninolytic trait-markers.

Draft genome sequence of Promicromonospora panici sp. nov., a novel ionizing-radiation-resistant actinobacterium isolated from roots of the desert plant Panicum turgidum

A novel strain of the genus Promicromonospora, designated PT9^T, was recovered from irradiated roots of the xerophyte Panicum turgidum collected from the Ksar Ghilane oasis in southern Tunisia. Strain PT9^T is aerobic, non-spore-forming, Gram- positive actinomycete that produces branched hyphae and forms white to yellowish-white colonies. Chemotaxonomic features, including fatty acids, whole cell sugars and polar lipid profiles, support the assignment of PT9^T to the genus Promicromonospora. The genomic relatedness indexes based on DNA-DNA hybridization and average nucleotide identity values revealed a significant genomic divergence between strain PT9^T and all sequenced type strains of the taxon. Phylogenomic analysis showed that isolate PT9^T was most closely related to Promicromonospora soli CGMCC 4.7398^T. Phenotypic and phylogenomic analyses suggest that isolate PT9^T represents a novel species of the genus Promicromonospora, for which the name Promicromonospora panici sp. nov. is proposed. The type strain is PT9^T (LMG 31103^T = DSM 108613^T).The isolate PT9^T is an ionizing-radiation-resistant actinobacterium (D₁₀ value = 2.6 kGy), with resistance to desiccation and hydrogen peroxide. The complete genome sequence of PT9^T consists of 6,582,650 bps with 71.2% G+C content and 6291 protein-coding sequences. This genome will help to decipher the microbial genetic bases for ionizing-radiation resistance mechanisms including the response to oxidative stress.

Complete genome sequence of the endophytic bacterium Cellulosimicrobium sp. JZ28 isolated from the root endosphere of the perennial desert tussock grass Panicum turgidum

Cellulosimicrobium sp. JZ28, a root endophytic bacterium from the desert plant Panicum turgidum, was previously identified as a plant growth-promoting bacterium. The genome of JZ28 consists of a 4378,193 bp circular chromosome and contains 3930 CDSs with an average GC content of 74.5%. Whole-genome sequencing analysis revealed that JZ28 was closely related to C. aquatile 3 bp. The genome harbors genes responsible for protection against oxidative, osmotic and salinity stresses, such as the production of osmoprotectants. It also contains genes with a role in the production of volatiles, such as hydrogen sulfide, which promote biotic and abiotic stress tolerance in plants. The presence of three copies of chitinase genes indicates a possible role of JZ28 as biocontrol agent against fungal pathogens, while a number of genes for the degradation of plant biopolymers indicates potential application in industrial processes. Genome sequencing and mining of culture-dependent collections of bacterial endophytes from desert plants provide new opportunities for biotechnological applications.

Nitrous oxide emissions associated with ammonia-oxidizing bacteria abundance in fields of switchgrass with and without intercropped alfalfa

The nitrogen (N) fertilizer required to supply a bioenergy industry with sufficient feedstocks is associated with adverse environmental impacts, including loss of oxidized reactive nitrogen through leaching and the production of the greenhouse gas nitrous oxide (N₂ O). We examined effects on crop yield, N fate and the response of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) to conventional fertilizer application or intercropping with N-fixing alfalfa, for N delivery to switchgrass (Panicum virgatum), a potential bioenergy crop. Replicated field plots in Prosser, WA, were sampled over two seasons for reactive nitrogen, N₂ O gas emissions, and bacterial and archaeal ammonia monooxygenase gene (amoA) counts. Intercropping with alfalfa (70:30, switchgrass:alfalfa) resulted in reduced dry matter yields compared to fertilized plots, but three times lower N₂ O fluxes (≤ 4 g N₂ O-N ha^-1 d^-1 ) than fertilized plots (12.5 g N₂ O-N ha^-1 d^-1 ). In the fertilized switchgrass plots, AOA abundance was greater than AOB abundance, but only AOB abundance was positively correlated with N₂ O emissions, implicating AOB as the major producer of N₂ O emissions. A life cycle analysis of N₂ O emissions suggested the greenhouse gas emissions from cellulosic ethanol produced from switchgrass intercropped with alfalfa cultivation would be 94% lower than emissions from equivalent gasoline usage.

One-time nitrogen fertilization shifts switchgrass soil microbiomes within a context of larger spatial and temporal variation

Soil microbiome responses to short-term nitrogen (N) inputs remain uncertain when compared with previous research that has focused on long-term fertilization responses. Here, we examined soil bacterial/archaeal and fungal communities pre- and post-N fertilization in an 8 year-old switchgrass field, in which twenty-four plots received N fertilization at three levels (0, 100, and 200 kg N ha^-1 as NH₄NO₃) for the first time since planting. Soils were collected at two depths, 0–5 and 5–15 cm, for DNA extraction and amplicon sequencing of 16S rRNA genes and ITS regions for assessment of microbial community composition. Baseline assessments prior to fertilization revealed no significant pre-existing divergence in either bacterial/archaeal or fungal communities across plots. The one-time N fertilizations increased switchgrass yields and tissue N content, and the added N was nearly completely removed from the soil of fertilized plots by the end of the growing season. Both bacterial/archaeal and fungal communities showed large spatial (by depth) and temporal variation (by season) within each plot, accounting for 17 and 12–22% of the variation as calculated from the Sq. root of PERMANOVA tests for bacterial/archaeal and fungal community composition, respectively. While N fertilization effects accounted for only ~4% of overall variation, some specific microbial groups, including the bacterial genus Pseudonocardia and the fungal genus Archaeorhizomyces, were notably repressed by fertilization at 200 kg N ha^-1. Bacterial groups varied with both depth in the soil profile and time of sampling, while temporal variability shaped the fungal community more significantly than vertical heterogeneity in the soil. These results suggest that short-term effects of N fertilization are significant but subtle, and other sources of variation will need to be carefully accounted for study designs including multiple intra-annual sampling dates, rather than one-time “snapshot” analyses that are common in the literature. Continued analyses of these trends over time with fertilization and management are needed to understand how these effects may persist or change over time.

Plant compartment and genetic variation drive microbiome composition in switchgrass roots

Switchgrass (Panicum virgatum) is a promising biofuel crop native to the United States with genotypes that are adapted to a wide range of distinct ecosystems. Various plants have been shown to undergo symbioses with plant growth-promoting bacteria and fungi, however, plant-associated microbial communities of switchgrass have not been extensively studied to date. We present 16S ribosomal RNA gene and internal transcribed spacer (ITS) data of rhizosphere and root endosphere compartments of four switchgrass genotypes to test the hypothesis that host selection of its root microbiota prevails after transfer to non-native soil. We show that differences in bacterial, archaeal and fungal community composition and diversity are strongly driven by plant compartment and switchgrass genotypes and ecotypes. Plant-associated microbiota show an enrichment in Alphaproteobacteria and Actinobacteria as well as Sordariales and Pleosporales compared with the surrounding soil. Root associated compartments display low-complexity communities dominated and enriched in Actinobacteria, in particular Streptomyces, in the lowland genotypes, and in Alphaproteobacteria, specifically Sphingobium, in the upland genotypes. Our comprehensive root analysis serves as a snapshot of host-specific bacterial and fungal associations of switchgrass in the field and confirms that host-selected microbiomes persist after transfer to non-native soil.

The culturable endophytic fungal communities of switchgrass grown on a coal-mining site and their effects on plant growth

Plants have a diverse endophytic microbiome that is functionally important for their growth, development, and health. In this study, the diversity and specificity of culturable endophytic fungal communities were explored in one of the most important biofuel crops, switchgrass plants (Panicum virgatum L.), which have been cultivated on a reclaimed coal-mining site for more than 20 years. The endophytic fungi were isolated from the surface-sterilized shoot (leaf and stem), root, and seed tissues of switchgrass plants and then cultured for identification. A total of 1339 fungal isolates were found and 22 operational taxonomic units (OTUs) were sequence identified by internal transcribed spacer (ITS) primers and grouped into 7 orders and 4 classes. Although a diverse range of endophytic fungi associated with switchgrass were documented, the most abundant class, order, and species were Sordariomycetes, Hypocreales, and Fusarium spp. respectively. About 86% of the isolated endophytic fungi were able to enhance the heights of the shoots; 69% could increase the shoot fresh weights; and 62% could improve the shoot dry weights after being reintroduced back into the switchgrass plants, which illustrated their functional importance. Through the Shannon Diversity Index analysis, we observed a gradation of species diversity, with shoots and roots having the similar values and seeds having a lesser value. It was observed that the switchgrass plants showing better growth performance displayed higher endophytic fungal species diversity and abundance. It was also discovered that the rhizosphere soil organic matter content was positively correlated with the fungal species diversity. All these data demonstrate the functional association of these beneficial endophytic fungi with switchgrass and their great potential in improving the switchgrass growth and biomass to benefit the biofuel industry by reducing chemical inputs and burden to the environment.

Transcriptome-based analyses of phosphite-mediated suppression of rust pathogens Puccinia emaculata and Phakopsora pachyrhizi and functional characterization of selected fungal target genes

Phosphite (Phi) is used commercially to manage diseases mainly caused by oomycetes, primarily due to its low cost compared with other fungicides and its persistent control of oomycetous pathogens. We explored the use of Phi in controlling the fungal pathogens Puccinia emaculata and Phakopsora pachyrhizi, the causal agents of switchgrass rust and Asian soybean rust, respectively. Phi primes host defenses and efficiently inhibits the growth of P. emaculata, P. pachyrhizi and several other fungal pathogens tested. To understand these Phi-mediated effects, a detailed molecular analysis was undertaken in both the host and the pathogen. Transcriptomic studies in switchgrass revealed that Phi activates plant defense signaling as early as 1 h after application by increasing the expression of several cytoplasmic and membrane receptor-like kinases and defense-related genes within 24 h of application. Unlike in oomycetes, RNA sequencing of P. emaculata and P. pachyrhizi did not exhibit Phi-mediated retardation of cell wall biosynthesis. The genes with reduced expression in either or both rust fungi belonged to functional categories such as ribosomal protein, actin, RNA-dependent RNA polymerase, and aldehyde dehydrogenase. A few P. emaculata genes that had reduced expression upon Phi treatment were further characterized. Application of double-stranded RNAs specific to P. emaculata genes encoding glutamate N-acetyltransferase and cystathionine gamma-synthase to switchgrass leaves resulted in reduced disease severity upon P. emaculata inoculation, suggesting their role in pathogen survival and/or pathogenesis.

Transgenic miR156 switchgrass in the field: growth, recalcitrance and rust susceptibility

Sustainable utilization of lignocellulosic perennial grass feedstocks will be enabled by high biomass production and optimized cell wall chemistry for efficient conversion into biofuels. MicroRNAs are regulatory elements that modulate the expression of genes involved in various biological functions in plants, including growth and development. In greenhouse studies, overexpressing a microRNA (miR156) gene in switchgrass had dramatic effects on plant architecture and flowering, which appeared to be driven by transgene expression levels. High expressing lines were extremely dwarfed, whereas low and moderate-expressing lines had higher biomass yields, improved sugar release and delayed flowering. Four lines with moderate or low miR156 overexpression from the prior greenhouse study were selected for a field experiment to assess the relationship between miR156 expression and biomass production over three years. We also analysed important bioenergy feedstock traits such as flowering, disease resistance, cell wall chemistry and biofuel production. Phenotypes of the transgenic lines were inconsistent between the greenhouse and the field as well as among different field growing seasons. One low expressing transgenic line consistently produced more biomass (25%-56%) than the control across all three seasons, which translated to the production of 30% more biofuel per plant during the final season. The other three transgenic lines produced less biomass than the control by the final season, and the two lines with moderate expression levels also exhibited altered disease susceptibilities. Results of this study emphasize the importance of performing multiyear field studies for plants with altered regulatory transgenes that target plant growth and development.

Toxicity of coal fly ash (CFA) and toxicological response of switchgrass in mycorrhiza-mediated CFA-soil admixtures

Increasing support for the use of Coal fly ash (CFA) in agriculture has necessitated a better understanding of the effects of the CFA in various cropping schemes. Experiments were conducted to assess mutagenic response of a mutant strain of Salmonella enterica serovar Typhimurium (TA100) to varying concentrations of CFA-water extracts, determine oxidative stress in switchgrass (Panicum virgatum L.) at varying levels of CFA-soil admixtures, and evaluate mycorrhiza-mediated modulation of oxidative stress responses of CFA-grown switchgrass. The TA100 exposed to 0%, 5%, 10%, 15%, 20% and 25% (w/v) CFA-water extracts elicited significant (p < 0.05) mutagenic responses at 20% and 25% extract levels but not below the 15% level. In greenhouse pot experiment, CFA-soil admixtures at 7.5% and 15% (w/w) significantly (p < 0.05) decreased the activities of superoxide dismutase (SOD) by 19.1% and 28.3% respectively, compared to control soil (0% w/w CFA/soil). Under the same conditions, activities of glutathione peroxidase (GPx) decreased by 75.9% and 66.9%. In contrast to the antioxidant enzyme activities, levels of malondialdehyde (MDA) an indicator of lipid peroxidation increased significantly (p < 0.05) by 30.49% and 38.38%. Inoculation of 7.5% and 15% CFA-soil admixtures with arbuscular mycorrhizal fungi (AMF), Rhizophaga clarus enhanced the activities of both SOD and GPx in the switchgrass, while it significantly (p < 0.05) reduced the levels of MDA. The study demonstrated that incorporation of CFA (at concentrations considered to be non-mutagenic against TA100) as soil amendment produced concentration-dependent oxidative stress responses in switchgrass; however, inoculation of the CFA-soil admixtures with AMF significantly modulated the oxidative stress responses.

Genome Assembly of the Fungus Cochliobolus miyabeanus, and Transcriptome Analysis during Early Stages of Infection on American Wildrice (Zizania palustris L.)

The fungus Cochliobolus miyabeanus causes severe leaf spot disease on rice (Oryza sativa) and two North American specialty crops, American wildrice (Zizania palustris) and switchgrass (Panicum virgatum). Despite the importance of C. miyabeanus as a disease-causing agent in wildrice, little is known about either the mechanisms of pathogenicity or host defense responses. To start bridging these gaps, the genome of C. miyabeanus strain TG12bL2 was shotgun sequenced using Illumina technology. The genome assembly consists of 31.79 Mbp in 2,378 scaffolds with an N50 = 74,921. It contains 11,000 predicted genes of which 94.5% were annotated. Approximately 10% of total gene number is expected to be secreted. The C. miyabeanus genome is rich in carbohydrate active enzymes, and harbors 187 small secreted peptides (SSPs) and some fungal effector homologs. Detoxification systems were represented by a variety of enzymes that could offer protection against plant defense compounds. The non-ribosomal peptide synthetases and polyketide synthases (PKS) present were common to other Cochliobolus species. Additionally, the fungal transcriptome was analyzed at 48 hours after inoculation in planta. A total of 10,674 genes were found to be expressed, some of which are known to be involved in pathogenicity or response to host defenses including hydrophobins, cutinase, cell wall degrading enzymes, enzymes related to reactive oxygen species scavenging, PKS, detoxification systems, SSPs, and a known fungal effector. This work will facilitate future research on C. miyabeanus pathogen-associated molecular patterns and effectors, and in the identification of their corresponding wildrice defense mechanisms.

[Composition diversity and metabolic characters of lactic acid bacteria community SGL]

OBJECTIVE

We aimed to select a stable lactic acid bacteria community from switchgrass silage, that was efficient in lactic acid production.

METHODS

We obtained the community by continuous restricted subcultivation in MRS broth, and analysed the composition diversity and stability of the community by 16S rRNA gene-based pyrosequencing and Denaturing Gradient Gel Electrophoresis (DGGE), respectively. In addition, we studied the effect of different nitrogen sources on growth and lactic acid production of the community, through adding different concentrations of yeast extraction, different nitrogen sources [yeast extract, peptone, urea and (NH4) 2SO4] and different proportions of (NH4)2SO4 and yeast extract leveled with elemental nitrogen 1.8 g/L.

RESULTS

The microbial composition of SGL became stable from the 8th generation according to the results of DGGE. The pH value of the MRS inoculated with SGL dropped to 3.7, and the concentration of lactic acid reached 26 g/L after 24 h cultivation. The result of the pyrosequencing showed that the major composition of SGL were Lactobacillus nantensis (78.78%), Lactobacillus plantarum (7.92%), Lactobacillus pantheris (5.27%), Bacillus coagulans (4.41%) and Lactococcus lactics (3.31%). The best supplementation of yeast extraction for SGL was 20 g/L. When the elemental nitrogen ratio of (NH4) 2SO4 to yeast extract was 1:4, the growth and lactic acid production were no significant difference with 0:5 (P < 0.05).

CONCLUSION

SGL had a great potential of application, as an efficient inoculant for ensilage or lactic acid production. This study would offer theoretical basis for cultivate and application of SGL in production.

Early growth promotion and leaf level physiology changes in Burkholderia phytofirmans strain PsJN inoculated switchgrass

Switchgrass (SG) is one of the most promising next generation biofuel crops in North America. Inoculation with bacterial endophytes has improved growth of several plant species. Our study demonstrated that Burkholderia phytofirmans strain PsJN, a well-studied plant growth promoting rhizo-bacterium (PGPR) significantly increased both aboveground and belowground biomass (DW) and promoted elongation of root, stem and leaf within 17 days following inoculation. Furthermore, the enhanced root growth in PsJN inoculated plants lagged behind the shoot response, resulting in greater allocation to aboveground growth (p = 0.0041). Lower specific root length (SRL, p = 0.0158) and higher specific leaf weight (SLW, p = 0.0029) were also observed in PsJN inoculated seedlings, indicating changes in development. Photosynthetic rates (Ps) were also significantly higher in PsJN inoculated seedlings after 17 days (54%, p = 0.0016), and this occurred initially without increases in stomatal conductance resulting in significantly greater water use efficiency (WUE, 37.7%, p = 0.0467) and lower non-stomatal limitation (LNS, 29.6%, p = 0.0222). These rapid changes in leaf level physiology are at least partially responsible for the growth enhancement due to PsJN.

Diversity of nitrogen-fixing bacteria associated with switchgrass in the native tallgrass prairie of northern Oklahoma

Switchgrass (Panicum virgatum L.) is a perennial C4 grass native to North America that is being developed as a feedstock for cellulosic ethanol production. Industrial nitrogen fertilizers enhance switchgrass biomass production but add to production and environmental costs. A potential sustainable alternative source of nitrogen is biological nitrogen fixation. As a step in this direction, we studied the diversity of nitrogen-fixing bacteria (NFB) associated with native switchgrass plants from the tallgrass prairie of northern Oklahoma (United States), using a culture-independent approach. DNA sequences from the nitrogenase structural gene, nifH, revealed over 20 putative diazotrophs from the alpha-, beta-, delta-, and gammaproteobacteria and the firmicutes associated with roots and shoots of switchgrass. Alphaproteobacteria, especially rhizobia, predominated. Sequences derived from nifH RNA indicated expression of this gene in several bacteria of the alpha-, beta-, delta-, and gammaproteobacterial groups associated with roots. Prominent among these were Rhizobium and Methylobacterium species of the alphaproteobacteria, Burkholderia and Azoarcus species of the betaproteobacteria, and Desulfuromonas and Geobacter species of the deltaproteobacteria.

Two-year field analysis of reduced recalcitrance transgenic switchgrass

Switchgrass (Panicum virgatum L.) is a leading candidate for a dedicated lignocellulosic biofuel feedstock owing to its high biomass production, wide adaptation and low agronomic input requirements. Lignin in cell walls of switchgrass, and other lignocellulosic feedstocks, severely limits the accessibility of cell wall carbohydrates to enzymatic breakdown into fermentable sugars and subsequently biofuels. Low-lignin transgenic switchgrass plants produced by the down-regulation of caffeic acid O-methyltransferase (COMT), a lignin biosynthetic enzyme, were analysed in the field for two growing seasons. COMT transcript abundance, lignin content and the syringyl/guaiacyl lignin monomer ratio were consistently lower in the COMT-down-regulated plants throughout the duration of the field trial. In general, analyses with fully established plants harvested during the second growing season produced results that were similar to those observed in previous greenhouse studies with these plants. Sugar release was improved by up to 34% and ethanol yield by up to 28% in the transgenic lines relative to controls. Additionally, these results were obtained using senesced plant material harvested at the end of the growing season, compared with the young, green tissue that was used in the greenhouse experiments. Another important finding was that transgenic plants were not more susceptible to rust (Puccinia emaculata). The results of this study suggest that lignin down-regulation in switchgrass can confer real-world improvements in biofuel yield without negative consequences to biomass yield or disease susceptibility.

Enrichment of specific bacterial and eukaryotic microbes in the rhizosphere of switchgrass (Panicum virgatum L.) through root exudates

Identification of microbes that actively utilize root exudates is essential to understand plant-microbe interactions. To identify active root exudate-utilizing microorganisms associated with switchgrass - a potential bioenergy crop - plants were labelled in situ with (13) CO2 , and 16S and 18S rRNA genes in the (13) C-labelled rhizosphere DNA were pyrosequenced. Multi-pulse labelling for 5 days produced detectable (13) C-DNA, which was well separated from unlabelled DNA. Methylibium from the order Burkholderiales were the most heavily labelled bacteria. Pythium, Auricularia and Galerina were the most heavily labelled eukaryotic microbes. We also identified a Glomus intraradices-like species; Glomus members are arbuscular mycorrhizal fungi that are able to colonize the switchgrass root. All of these heavily labelled microorganisms were also among the most abundant species in the rhizosphere. Species belonging to Methylibium and Pythium were the most heavily labelled and the most abundant bacteria and eukaryotes in the rhizosphere of switchgrass. Our results revealed that nearly all of the dominant rhizosphere bacterial and eukaryotic microbes were able to utilize root exudates. The enrichment of microbial species in the rhizosphere is selective and mostly due to root exudation, which functions as a nutrition source, promoting the growth of these microbes.

Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass

Thermophilic bacteria are a potential source of enzymes for the deconstruction of lignocellulosic biomass. However, the complement of proteins used to deconstruct biomass and the specific roles of different microbial groups in thermophilic biomass deconstruction are not well-explored. Here we report on the metagenomic and proteogenomic analyses of a compost-derived bacterial consortium adapted to switchgrass at elevated temperature with high levels of glycoside hydrolase activities. Near-complete genomes were reconstructed for the most abundant populations, which included composite genomes for populations closely related to sequenced strains of Thermus thermophilus and Rhodothermus marinus, and for novel populations that are related to thermophilic Paenibacilli and an uncultivated subdivision of the little-studied Gemmatimonadetes phylum. Partial genomes were also reconstructed for a number of lower abundance thermophilic Chloroflexi populations. Identification of genes for lignocellulose processing and metabolic reconstructions suggested Rhodothermus, Paenibacillus and Gemmatimonadetes as key groups for deconstructing biomass, and Thermus as a group that may primarily metabolize low molecular weight compounds. Mass spectrometry-based proteomic analysis of the consortium was used to identify >3000 proteins in fractionated samples from the cultures, and confirmed the importance of Paenibacillus and Gemmatimonadetes to biomass deconstruction. These studies also indicate that there are unexplored proteins with important roles in bacterial lignocellulose deconstruction.

Climate affects symbiotic fungal endophyte diversity and performance

PREMISE OF THE STUDY

Fungal endophytes are symbionts that inhabit aboveground tissues of most terrestrial plants and can affect plant physiology and growth under stressed conditions. In a future faced with substantial climate change, endophytes have the potential to play an important role in plant stress resistance. Understanding both the distributions of endophytes and their functioning in symbiosis with plants are key aspects of predicting their role in an altered climate.

METHODS

Here we characterized endophytes in grasses across a steep precipitation gradient to examine the relative importance of environmental and spatial factors in structuring endophyte communities. We also tested how 20 endophytes isolated from drier and wetter regions performed in symbiosis with grass seedlings under high and low soil moisture in the greenhouse.

KEY RESULTS

Environmental factors related to historical and current precipitation were the most important predictors of endophyte communities in the field. On average, endophytic fungi from western sites also reduced plant water loss in the greenhouse compared to fungi from eastern sites. However, there was substantial variability in how individual endophytic taxa affected plant traits under high and low water availability, with up to two orders of magnitude difference in the plasticity of plant traits conferred by the different fungal taxa.

CONCLUSIONS

While species sorting appears to largely explain local endophyte community composition, their function in symbiosis is not predictable from local environmental conditions. The development of a predictive framework for endophyte function will require further study of individual fungal taxa and genotypes across environmental gradients.

Screening for novel bacteria from the bioenergy feedstock switchgrass (Panicum virgatum L.)

Switchgrass is considered as a good candidate for biofuel, especially ethanol production due to its huge biomass output and high cellulose content. In a search for novel microorganisms capable of using and degrading switchgrass to produce sugars and ethanol, enrichment experiments were established to screen for microorganisms from soil samples obtained at the University of Tennessee Agricultural Research Station, Jackson, Tennessee. Three enrichments were prepared and incubated at different pH and temperatures: (1) 30 degrees C, pH 5, (2) 30 degrees C, pH 8 and (3) 60 degrees C, pH5. Bulk community DNA was directly extracted from the enrichments. Microbial community structures were determined by phylogenetic analysis of 16S rRNA gene sequences retrieved from the enrichment cultures containing switchgrass as the carbon source. The mesophilic enrichments were dominated by Sarcina, Anaerobacter, and Clostrium, which were not found in the thermophilic enrichment. The thermophilic enrichment selected for two types of bacteria belonging to the class Bacilli (Geobacillus and Saccharococcus). The thermophilic enrichments were dominated by the Geobacillus spp. (Firmicutes, class Bacilli), and Saccharococcus (Firmicutes, class Bacilli); both containing thermophilic microorganisms with some cellulolytic members. Enzymatic assays detected the presence of enzymes involved in cellulose (beta-glucosidase and cellobiohydrolase) and hemicellulose degradations (beta-xylosidase); and the activity tends to be higher in the enrichments incubated at 30 degrees C.

The insect-pathogenic fungus Metarhizium robertsii (Clavicipitaceae) is also an endophyte that stimulates plant root development

PREMISE OF THE STUDY

The soil-inhabiting insect-pathogenic fungus Metarhizium robertsii also colonizes plant roots endophytically, thus showing potential as a plant symbiont. Metarhizium robertsii is not randomly distributed in soils but preferentially associates with the plant rhizosphere when applied in agricultural settings. Root surface and endophytic colonization of switchgrass (Panicum virgatum) and haricot beans (Phaseolus vulgaris) by M. robertsii were examined after inoculation with fungal conidia.

METHODS

We used light and confocal microscopy to ascertain the plant endophytic association with GFP-expressing M. robertsii. Root lengths, root hair density, and lateral roots emerged were also observed.

KEY RESULTS

Initially, M. robertsii conidia adhered to, germinated on, and colonized roots. Furthermore, plant roots treated with Metarhizium grew faster and the density of plant root hairs increased when compared with control plants. The onset of plant root hair proliferation was initiated before germination of M. robertsii on the root (within 1-2 d). Plants inoculated with M. robertsii ΔMAD2 (plant adhesin gene) took significantly longer to show root hair proliferation than the wild type. Cell free extracts of M. robertsii did not stimulate root hair proliferation. Longer-term (60 d) associations showed that M. robertsii endophytically colonized cortical cells within bean roots. Metarhizium appeared as a mycelial aggregate within root cortical cells as well as between the intercellular spaces with no apparent damage to the plant.

CONCLUSIONS

These results suggest that M. robertsii is not only rhizosphere competent but also displays a beneficial endophytic association with plant roots that results in the proliferation of root hairs.

Enhancement of switchgrass (Panicum virgatum L.) biomass production under drought conditions by the ectomycorrhizal fungus Sebacina vermifera

Experiments were conducted to examine the effects of cocultivating the important bioenergy crop switchgrass with the ectomycorrhizal fungus Sebacina vermifera under severe drought conditions. Plants cocultivated with the fungus produced significantly higher biomass and had a higher macronutrient content than uninoculated control plants under both adequately watered and drought conditions.

Selection of conditions for cellulase and xylanase extraction from switchgrass colonized by Acidothermus cellulolyticus

Solid-state fermentation has been widely used for enzyme production. However, secreted enzymes often bind to the solid substrate preventing their detection and recovery. A series of screening studies was performed to examine the role of extraction buffer composition including NaCl, ethylene glycol, sodium acetate buffer, and Tween 80, on xylanase and cellulase recovery from switchgrass. Our results indicated that the selection of an extraction buffer is highly dependent on the nature and source of the enzyme being extracted. While a buffer containing 50 mM sodium acetate at pH 5 was found to have a positive effect on the recovery of commercial fungal-derived cellulase and xylanase amended to switchgrass, the same buffer had a significant negative effect on enzyme extraction from solid fermentation samples colonized by the bacterium Acidothermus cellulolyticus. Xylanase activity was more affected by components in the extraction buffers compared to cellulase. This study demonstrated that extraction followed by diafiltration is important for assessing enzyme recovery from solid fermentation samples. Reduction in activity due to compounds present in the switchgrass extracts is reversible when the compounds are removed via diafiltration.

Multiplex PCR-based strategy to detect contamination with mycotoxigenic Fusarium species in rice and fingermillet collected from southern India

BACKGROUND

The genus Fusarium comprises a diverse group of fungi including several species that produce mycotoxins in food commodities. In the present study, a multiplex PCR was standardised for the group-specific detection of fumonisin-producing and trichothecene-producing strains of Fusarium species. Primers for genus-level recognition of Fusarium spp. were designed from the internal transcribed spacer regions 1 and 2 of rDNA. Primers for group-specific detection were designed from the tri5 and tri6 genes involved in trichothecene biosynthesis and the fum1 and fum13 genes involved in fumonisin biosynthesis.

RESULTS

Among the various genera and their strains tested, all the 85 confirmed Fusarium strains were positive for rDNA gene and the rest stayed negative. From among the Fusarium strains, 15 had amplification for trichothecene- and 20 for fumonisin-encoding genes. All PCR positive trichothecene chemotypes of Fusarium species tested were positive for chemical analysis but in the case of fumonisins, of the 20 PCR positive cultures, only 13 showed positive for chemical analysis by HPTLC.

CONCLUSION

The assay described here provided a rapid and reliable detection of trichothecene- and fumonisin-producing Fusarium directly from natural food grains and the results were always comparable with a conventional HPTLC detection method. It can, therefore, be used by the food industry to monitor quality and safety.

Improvement of natural microbial remediation of petroleum-polluted soil using graminaceous plants

A 150-day pot experiment was conducted with graminaceous plants grown in natural soil contaminated with petroleum. The relationships among microbial activity, dehydrogenase activity, catalase activity, soil moisture, and the petroleum degradation rate were analyzed. All three plants accelerated the degradation of petroleum compared with unplanted soil. Plant roots improved the soil moisture by about 5% (from 15% in unplanted soil to 20% in soil containing plant roots), and the number of microorganisms in the rhizosphere increased by more than three orders of magnitude. The induction of the rhizosphere environment and the intimidation of the petroleum changed the abundance and activity of the microorganisms. Dehydrogenase activity in the rhizosphere was 1.54 to 1.87 times the value in the unplanted soil, but catalase activity was 0.90 to 0.93 times the value in unplanted soil. The petroleum degradation rates in the rhizosphere were 2.33 to 3.19 times higher than in the unplanted soil. The effect of rhizosphere degradation clearly changed the hydrocarbon composition, increasing the degradation of alkane hydrocarbons with low and moderate carbon contents. The rhizosphere environment promoted degradation of the high-carbon-content hydrocarbons into low-carbon-content hydrocarbons. At the same time, the Pr/nC(17), Ph/nC(18), and Pr/Ph values increased by 0.99 and 2.69 units, and decreased by 1.25 units, respectively, compared with the undegraded oil. The plants also accelerated the isomerization of alkane hydrocarbons.

Selecting, establishing, and managing switchgrass (Panicum virgatum) for biofuels

Switchgrass is being widely considered as a feedstock for biofuel production. Much remains to be learned about ideal feedstock characteristics, but switchgrass offers many advantages already and can perhaps be manipulated to offer more. When planning to grow switchgrass, select a cultivar that is well adapted to the location - generally a lowland cultivar for the southern United States and an upland cultivar at higher latitudes. Plant non-dormant seed after soils are well warmed, preferably with no-till methods and always with good weed control. Except for weeds, few pests appear to be widespread; but disease and insect pests could become more important as acreages increase. Fertilization requirements are relatively low, with 50 kg N/ha/year being a good "generic" recommendation where a single harvest is taken after plants have senesced; more will be needed if biomass is harvested while still green. Switchgrass should be harvested no more than twice per year and may generally be expected to produce 12 to >or=20 mg/ha/year across its usual range of distribution. A single harvest may provide for maximum sustainable yields - especially if the harvest is taken after tops die back at the end of the season. Several harvesting technologies are available, but the preferred technology may depend on logistics and economics associated with the local processing point, or biorefinery.

Degradation of phenanthrene and pyrene in rhizosphere of grasses and legumes

Phytoremediation is an emerging technology for the remediation of organic soil pollutants such as phenanthrene and pyrene (polycyclic aromatic hydrocarbons, PAHs). The PAH degradation ability of four native Korean plant species (Panicum bisulcatum, Echinogalus crus-galli, Astragalus membranaceus, and Aeschynomene indica) was compared in the greenhouse. During the 80-day experiment, soil samples were collected and analyzed periodically to determine the residual PAH content and microbial activity. More PAHs were dissipated in planted soil (i.e., with a rhizosphere) than in unplanted soil, and there were more obvious effects of plants on pyrene dissipation than on phenanthrene dissipation. After 80 days, >99 and 77-94% of phenanthrene and pyrene, respectively, had been degraded in planted soil, whereas 99% and 69% had been degraded in unplanted soil. This enhanced dissipation of PAHs in planted soils might be derived from increased microbial activity and plant-released enzymes. During the experimental period, a relatively large amount of phenolic compounds, high microbial activity, and high peroxidase activity were detected in planted soils.

Purification and characterization of proline/hydroxyproline-rich glycoprotein from pearl millet coleoptiles infected with downy mildew pathogen Sclerospora graminicola

Hydroxyproline-rich glycoproteins (HRGPs) are important plant cell wall structural components, which are also involved in response to pathogen attack. In pearl millet, deposition and cross-linking of HRGPs in plant cell walls was shown to contribute to the formation of resistance barriers against the phytopathogenic oomycete Sclerospora graminicola. In the present study, the purification and characterization of HRGPs that accumulated in coleoptiles of pearl millet seedlings in response to S. graminicola inoculation has been carried out. Periodic acid Schiff's staining revealed that the purified protein was a glycoprotein. The protein to carbohydrate ratio was determined to be 95.5%:4.5% (w/w). Proline amounted for 20 mol% of the total amino acids as indicated by amino acid composition analysis. The isolated protein had a pI of 9.8 and was shown to be composed of subunits of 27, 17, and 14 kDa. Cross reactivity with the monoclonal antibody MAC 265 and the presence of the signature amino acid sequence, PVYK, strongly suggested to classify the purified glycoprotein as a member of the P/HRGPs class. In the presence of horseradish peroxidase and H2O2 the purified glycoprotein served as a substrate for oxidative cross-linking processes.

Effect of heavy metals (Hg and Zn) on the growth and phosphate solubilising activity in halophilic phosphobacteria isolated from Manakudi mangrove

The diversity of phosphobacteria in Manakudi mangrove ecosystem of Tamil Nadu was carried out in root and rhizosphere soil samples. The counts of phosphobacteria were found higher in root samples than in soil samples particularly in Hymenachene acutigluma. The abundance of phosphobacterial diversity in Manakudi mangrove showed high degree of positive correlation with the content of phosphate in rhizosphere soil of all the mangrove and associated plant species. Nine phosphobacterial species belonging to 7 genera were reported from Manakudi mangrove ecosystem. All the identified bacterial species are sensitive to both the heavy metals (mercury and zinc) in terms of growth and physiology even at lower concentrations. The content of protein and total sugars were increased by the higher concentrations of heavy metals whereas decreased trend was noticed in lower concentrations of heavy metals.

Mycotoxins in Australia: biocontrol of aflatoxin in peanuts

The major mycotoxin problem in Australia is the formation of aflatoxins in peanuts by Aspergillus flavus and A. parasiticus. This is controlled by good farm management practice, segregation into grades on aflatoxin content at intake to shelling facilities, colour sorting and aflatoxin assays. A second problem is the potential presence of ochratoxin A in grapes and grape products, resulting from infection by Aspergillus carbonarius. Good quality control before and during wine making ensures ochratoxin A is kept to very low levels, but in dried vine fruit, ochratoxin A levels may be higher. Biocontrol by competitive exclusion has been developed as the most promising means of controlling aflatoxins in peanuts. Some details of the process are given, including some basic laboratory experiments.

Culture-independent analysis of the microbial composition of the African traditional fermented foods poto poto and dégué by using three different DNA extraction methods

The microbial composition of the traditional fermented foods poto poto (a maize dough from the Rep. of Congo) and dégué (a millet dough from Burkina Faso) was studied by a culture-independent approach using TTGE to separate the amplified target V3 region of the 16S rRNA gene from total microbial community, followed by DNA sequencing and homology search. Three different extraction methods were used. Guanidium thiocyanate-based DNA extraction provided better performance regarding purity and DNA yield, allowing the detection of a higher number of DNA bands by TTGE in poto poto. By contrast, all three methods yielded similar results for dégué samples, indicating that the performance of the DNA extraction method largely depends on the food composition. Sequencing of DNA bands from TTGE gels corresponding to poto poto samples revealed the presence of Lactobacillus gasseri, Enterococcus sp., Escherichia coli, Lactobacillus plantarum/paraplantarum, Lactobacillus acidophilus, Lactobacillus delbrueckii, Bacillus sp., Lactobacillus reuteri and Lactobacillus casei. The following bacteria were identified in dégué: L. gasseri, Enterococcus sp., E. coli, Lactobacillus fermentum, Lactobacillus brevis, and L. casei.

Spontaneously fermented millet product as a natural probiotic treatment for diarrhoea in young children: an intervention study in Northern Ghana

Indigenous lactic acid fermented foods may have potential as probiotic treatment for diarrhoea, due to high levels of lactic acid bacteria. In this study the effect of a millet drink, spontaneously fermented by lactic acid bacteria, as a therapeutic agent among Ghanaian children with diarrhoea, was assessed. Children below 5 years of age coming to Northern Ghana health clinics for treatment of diarrhoea were randomised to two groups. Children of both groups received treatment for diarrhoea given at the local clinic. The intervention group in addition received up to 300 ml fermented millet drink (KSW) daily for 5 days after enrolment. The clinical outcome of diarrhoea and reported well-being were registered every day for the 5-day intervention and again 14 days after diagnosis. Among 184 children (mean age 17.4, standard deviation 11.3 months) included, no effects of the intervention were found with respect to stool frequency, stool consistency and duration of diarrhoea. However, KSW was associated with greater reported well-being 14 days after the start of the intervention (P=0.02). The fact that no effect of KSW on diarrhoea was observed could be because many children had a mild form of diarrhoea, and many were treated with antibiotics. Either this could have affected the lactic acid bacteria, or the lactic acid bacteria in KSW had no probiotic effects. It is speculated that the effect after two weeks could be due to a preventing effect of KSW on antibiotic-associated diarrhoea which could help reducing persistent diarrhoea.

Origins of host-specific populations of the blast pathogen Magnaporthe oryzae in crop domestication with subsequent expansion of pandemic clones on rice and weeds of rice

Rice, as a widely and intensively cultivated crop, should be a target for parasite host shifts and a source for shifts to co-occurring weeds. Magnaporthe oryzae, of the M. grisea species complex, is the most important fungal pathogen of rice, with a high degree of host specificity. On the basis of 10 loci from six of its seven linkage groups, 37 multilocus haplotypes among 497 isolates of M. oryzae from rice and other grasses were identified. Phylogenetic relationships among isolates from rice (Oryza sativa), millet (Setaria spp.), cutgrass (Leersia hexandra), and torpedo grass (Panicum repens) were predominantly tree like, consistent with a lack of recombination, but from other hosts were reticulate, consistent with recombination. The single origin of rice-infecting M. oryzae followed a host shift from a Setaria millet and was closely followed by additional shifts to weeds of rice, cutgrass, and torpedo grass. Two independent estimators of divergence time indicate that these host shifts predate the Green Revolution and could be associated with rice domestication. The rice-infecting lineage is characterized by high copy number of the transposable element MGR586 (Pot3) and, except in two haplotypes, by a loss of AVR-Co39. Both mating types have been retained in ancestral, well-distributed rice-infecting haplotypes 10 (mainly temperate) and 14 (mainly tropical), but only one mating type was recovered from several derived, geographically restricted haplotypes. There is evidence of a common origin of both ACE1 virulence genotypes in haplotype 14. Host-haplotype association is evidenced by low pathogenicity on hosts associated with other haplotypes.

Characterization of a Novel Cr6+ Reducing Pseudomonas sp. with Plant Growth–Promoting Potential

The isolate RNP4 obtained from a long-term tannery waste contaminated soil was characterized and presumptively identified as Pseudomonas sp. The strain RNP4 tolerated concentrations up to 450 mg Cr(6+)/L on a Luria-Bartani (LB) agar medium and reduced a substantial amount of Cr(6+) to Cr(3+) in the LB liquid medium. The ability of performing multifarious activities in tandem suggested the uniqueness of isolate RNP4. The strain produced a substantial amount of indole acetic acid (IAA) in tryptophan-supplemented medium. The strain also exhibited the production of siderophore and solubilization of phosphorus in mineral salt medium and SRS1 medium, respectively. Concurrent production of IAA and siderophore and the solubilization of phosphorus revealed its plant growth promotion potential. Furthermore, the strain was able to promote the growth of black gram, Indian mustard, and pearl millet in the presence of Cr(6+). Thus, the innate capability of this novel isolate for parallel bioremediation and plant growth promotion has significance in the management of environmental and agricultural problems.

Factors affecting the sporulation capacity during long-term storage of the aphid-pathogenic fungus Pandora neoaphidis grown on broomcorn millet

Aphid-pathogenic fungus, Pandora neoaphidis, grown on broomcorn millet possesses greater sporulation capacity (C(s)) than aphid cadavers. The most sporulating cultures (32.0x10(4) spores millet(-1) grain) with water content (C(w)) of 48.7% were prepared by incubation at 20 degrees C for 15 days and used to study the effect of temperature and humidity on C(s) during long-term storage. Cultures were sealed with paper to retain ambient humidity, with parafilm for saturated humidity, or kept in 85% and 98% RH chambers. The C(w) and C(s) were monitored during 200-day storage at 5-20 degrees C. The paper-sealed cultures at 5 degrees C, associated with 21-25% of C(w), were best preserved and their 120-day C(s) was similar to that of the fresh cadavers. Consistently or variably high RH at 5 degrees C resulted in significantly higher C(w) and lower C(s) despite longer viability. The regimes at 10 degrees C preserved the cultures for 40 days. The observations fit well to the logistic model C(s)=35.28/{1+exp[-2.36+(-0.003C(w)+0.001C(w)T)t]} (r(2)=0.95) for all regimes of temperature (T) or C(s)=35.55/[1+exp(-2.33+0.001C(w)t)] (r(2)=0.93) at 5 degrees C only. The rate of decline of C(s) of -0.003C(w)+0.001C(w)T or 0.001 C(w) over days (t) highlights the primary effect of C(w). The daily C(s)-decline rates obtained for the best-stored cultures and air-dried cadavers stored at 5 degrees C were surprisingly identical. The results suggest a possible cheap method for preparing and storing large quantities of P. neoaphiodis inocula.

Rhizosheath of sinai desert plants is a potential repository for associative diazotrophs

Among 42 plant species representing the flora of north Sinai, two possessed sand grain sheath encasing the roots. They are Panicum turgidum Forssk. and Stipagrostis scoparia (Trin.and Rupr.) deWinter. Rhizosheaths, compared to surrounding free sand, accommodated higher population density of microorganisms including associative diazotrophs. Isolates secured belonged to the species of Bacillus circulans, Paenib. macerans (Bacillus macerans), Enterobacter agglomerans, Agrobacterium radiobacter and Chryseomonas luteola (Pseudomonos luteola). The rhizosheath potentiality in re-vegetating sand dunes and arid lands, through nitrogen fixation, plant-water relationship and root continuity for nutrient uptake, are discussed.

Microbiological characterization and probiotic potential of koko and koko sour water, African spontaneously fermented millet porridge and drink

AIMS

To identify and examine the diversity of predominant lactic acid bacteria (LAB) in koko and koko sour water (KSW) from different Ghanaian production sites with regard to pattern of fermentation (API 50 CHL), genotype, antimicrobial activity, and resistance to low pH and bile salts.

METHODS AND RESULTS

In total 215 LAB were isolated from koko and KSW. The isolates were identified using intergenic transcribed spacers (ITS)-PCR restriction fragment length polymorphism (RFLP), API 50 CHL, restriction enzyme analysis with pulsed-field gel electrophoresis (REA-PFGE) and sequencing of the 16S rRNA gene. The dominating micro-organisms in koko was found to be Weisella confusa and Lactobacillus fermentum, followed by Lact. salivarius and Pediococcus spp. Chemometric data analysis were used to link the LAB species to the different production stages and production sites. At intra-species level the isolates were found to have a great diversity. The isolates were investigated for antimicrobial activity using agar diffusion assays, and acid and bile tolerance. Most isolates showed low levels of antimicrobial activity towards the indicator strain Listeria innocua, but not towards the bacteriocin-sensitive Lact. sakei. Growth of all LAB isolates was unaffected by the presence of 0.3% (v/v) oxgall bile. The isolates were able to survive, but were not able to grow in growth medium adjusted to pH 2.5.

CONCLUSIONS

The dominating LAB of koko and KSW were W. confusa and Lact. fermentum showing a pronounced taxonomic biodiversity at sub-species level between stages within the production as well as between production sites. Other species observed in KSW were Lact. salivarius, Ped. pentosaceus, Ped. acidilactici and Lact. paraplantarum. They occurred in levels of 108 CFU ml-1 in fresh KSW and showed uniform antimicrobial activity, and acid and bile tolerance.

SIGNIFICANCE AND IMPACT OF THE STUDY

The present study gives a detailed picture of the taxonomy and diversity of LAB in an African-fermented millet product that may have potential as a probiotic product for the local population. The chemometric tools Principal Component Analysis and anova Partial Least Squares Regression were proven to be useful in the analysis of microbial groupings and associations with specific sites and stages in the production of koko and KSW.

Sourdough bread made from wheat and nontoxic flours and started with selected lactobacilli is tolerated in celiac sprue patients

This work was aimed at producing a sourdough bread that is tolerated by celiac sprue (CS) patients. Selected sourdough lactobacilli had specialized peptidases capable of hydrolyzing Pro-rich peptides, including the 33-mer peptide, the most potent inducer of gut-derived human T-cell lines in CS patients. This epitope, the most important in CS, was hydrolyzed completely after treatment with cells and their cytoplasmic extracts (CE). A sourdough made from a mixture of wheat (30%) and nontoxic oat, millet, and buckwheat flours was started with lactobacilli. After 24 h of fermentation, wheat gliadins and low-molecular-mass, alcohol-soluble polypeptides were hydrolyzed almost totally. Proteins were extracted from sourdough and used to produce a peptic-tryptic digest for in vitro agglutination tests on K 562(S) subclone cells of human origin. The minimal agglutinating activity was ca. 250 times higher than that of doughs chemically acidified or started with baker's yeast. Two types of bread, containing ca. 2 g of gluten, were produced with baker's yeast or lactobacilli and CE and used for an in vivo double-blind acute challenge of CS patients. Thirteen of the 17 patients showed a marked alteration of intestinal permeability after ingestion of baker's yeast bread. When fed the sourdough bread, the same 13 patients had values for excreted rhamnose and lactulose that did not differ significantly from the baseline values. The other 4 of the 17 CS patients did not respond to gluten after ingesting the baker's yeast or sourdough bread. These results showed that a bread biotechnology that uses selected lactobacilli, nontoxic flours, and a long fermentation time is a novel tool for decreasing the level of gluten intolerance in humans.

Pyrene degradation in the rhizosphere of tall fescue (Festuca arundinacea) and switchgrass (Panicum virgatum L.)

A growth chamber study was conducted to investigate the fate of pyrene in the rhizosphere of tall fescue (Festuca arundinacea) and switchgrass (Panicum virgatum L.). For this study, 14C-labeled pyrene was used, and distribution of 14C activity was assessed after plant establishment. After 190 days of incubation, 37.7 and 30.4% of 14C-pyrene was mineralized in the soil planted with tall fescue and switchgrass, respectively, while 4.3% mineralization was observed for the unplanted control. Only 7.6 and 8.7% of pyrene was recovered from the soil in the two planted treatments, while 31.5% of pyrene remained in the unplanted control. Significant amounts of 14C were observed for all treatments and controls in the humic/fulvic fraction of soil at the end of the experiment. This research indicates the potential for pyrene mineralization in planted systems, although the ultimate fate of degradation byproducts is uncertain.

Fate of isoxaben in a containerized plant rhizosphere system

Commercial production of ornamental plants is an important industry in the United States and involves a complex technology that includes the use of herbicides. Isoxaben[N-[3-(1-ethyl-1-methylpropyl)-5-isoxazolyl]-2,6-dimethoxybenzamide] is a pre-emergence herbicide used for controlling weeds in many areas including containerized ornamental plants. Degradation was studied in potting mix (80% bark, 20% sand) with three different regimes (sterile, bulk and rhizosphere). The rhizosphere regime contained Switch Grass (Panicum virgatum), and plants were allowed to grow for 14 days before adding isoxaben (10 microg/g potting mix). Isoxaben was degraded to 0.5 microg/g in 60 days giving a half-life of 7 days. Two degradation products were detected: 3-nitrophthalic acid in the rhizosphere and bulk regimes and 4-methoxyphenol in the sterile regime. Microbial population shifts were determined by fatty acid methyl ester profile analysis and were influenced by the introduction of a plant (rhizosphere regime) and by isoxaben addition.

Negative feedback within a mutualism: host-specific growth of mycorrhizal fungi reduces plant benefit

A basic tenet of ecology is that negative feedback on abundance plays an important part in the coexistence of species within guilds. Mutualistic interactions generate positive feedbacks on abundance and therefore are not thought to contribute to the maintenance of diversity. Here, I report evidence of negative feedback on plant growth through changes in the composition of their mutualistic fungal symbionts, arbuscular mycorrhizal (AM) fungi. Negative feedback results from asymmetries in the delivery of benefit between plant and AM fungal species in which the AM fungus that grows best with the plant Plantago lanceolata is a poor growth promoter for Plantago. Growth of Plantago is, instead, best promoted by the AM fungal species that accumulate with a second plant species, Panicum sphaerocarpon. The resulting community dynamic leads to a decline in mutualistic benefit received by Plantago, and can contribute to the coexistence of these two competing plant species.

Food as a vehicle of transmission of cholera

Cholera has been recognized as a killer disease since earliest time. Since 1817, six pandemics have swept over the world, and the seventh one is in progress. The disease is caused by infection of the small intestine by Vibrio cholerae O1 and O139 and is characterized by massive acute diarrhoea, vomiting, and dehydration: death occurs in severe, untreated cases. Cholera is a highly contagious disease, and is transmitted primarily by ingestion of faecally-contaminated water by susceptible persons. Besides water, foods have also been recognized as an important vehicle for transmission of cholera. Foods are likely to be faecally contaminated during preparation, particularly by infected food handlers in an unhygienic environment. The physicochemical characteristics of foods that support survival and growth of V. cholerae O1 and O139 include high-moisture content, neutral or an alkaline pH, low temperature, high-organic content, and absence of other competing bacteria. Seafoods, including fish, shellfish, crabs, oysters and clams, have all been incriminated in cholera outbreaks in many countries, including the United States and Australia. Contaminated rice, millet gruel, and vegetables have also been implicated in several outbreaks. Other foods, including fruits (except sour fruits), poultry, meat, and dairy products, have the potential of transmitting cholera. To reduce the risk of food-borne transmission of cholera, it is recommended that foods should be prepared, served, and eaten in an hygienic environment, free from faecal contamination. Proper cooking, storing, and re-heating of foods before eating, and hand-washing with safe water before eating and after defaecation are important safety measures for preventing food-borne transmission of cholera.

The nucleotide sequence of an infectious insect-transmissible clone of the geminivirus Panicum streak virus

The infectious genome of a Kenyan isolate of Panicum streak virus (PSV) has been cloned and sequenced. Infection of host plants was done using an Agrobacterium binary vector containing a partial repeat of the genome. Progeny virus from resultant infections proved to be transmissible by the leafhopper Cicadulina mbila (Naude). Comparisons of the amino acid sequences of PSV DNA-encoded proteins with those of previously characterized geminiviruses infecting monocotyledonous plants, including maize streak virus, revealed high levels of identity. The evolutionary relationship between PSV and other geminiviruses infecting monocotyledons is discussed.

Commercial milk products and indigenous weaning foods in a rural West African Environment: a bacteriological perspective

Two commercially available baby milks, one 'biologically acidified', the other 'non-acidified', and a traditional weaning food, millet gruel, were prepared and stored under village conditions in West Africa. Increases in total colony count and in number of Bacillus cereus, Clostridium welchii, Staphylococcus aureus and Escherichia coli were determined in these products when stored as commonly practised at ambient temperatures over a period of 8 h. Poor hygiene during preparation was indicated by readily detectable numbers of coliforms and E. coli in freshly prepared samples of each of the milks, though the cooked local gruel seemed less vulnerable in this respect. The rate of increase in the numbers of these organisms was lower in the acidified milk when prepared with unboiled water containing high numbers of coliforms and E. coli. Increases in total colony count and in numbers of Staph. aureus were also less marked in the acidified milk. When food was not eaten soon after preparation the problem of bacterial overgrowth was as great with the local gruel as with the considerably more nutritious reconstituted milks.