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Plant roots constantly secrete compounds into the soil to interact with neighboring organisms presumably to gain certain functional advantages at different stages of development. Accordingly, it has been hypothesized that the phytochemical composition present in the root exudates changes over the course of the lifespan of a plant. Here, root exudates of in vitro grown Arabidopsis plants were collected at different developmental stages and analyzed using GC-MS. Principle component analysis revealed that the composition of root exudates varied at each developmental stage. Cumulative secretion levels of sugars and sugar alcohols were higher in early time points and decreased through development. In contrast, the cumulative secretion levels of amino acids and phenolics increased over time. The expression in roots of genes involved in biosynthesis and transportation of compounds represented in the root exudates were consistent with patterns of root exudation. Correlation analyses were performed of the in vitro root exudation patterns with the functional capacity of the rhizosphere microbiome to metabolize these compounds at different developmental stages of Arabidopsis grown in natural soils. Pyrosequencing of rhizosphere mRNA revealed strong correlations (p

Summary It is known that environmental factors can affect the biosynthesis of leaf metabolites. Similarly, specific pairwise plant–microbe interactions modulate the plant's metabolome by stimulating production of phytoalexins and other defense-related compounds. However, there is no information about how different soil microbiomes could affect the plant growth and the leaf metabolome. We analyzed experimentally how diverse soil microbiomes applied to the roots of Arabidopsis thaliana were able to modulate plant growth and the leaf metabolome, as assessed by GC-MS analyses. Further, we determined the effects of soil microbiome-driven changes in leaf metabolomics on the feeding behavior of Trichopulsia ni larvae. Soil microbiomes differentially impacted plant growth patterns as well as leaf metabolome composition. Similarly, most microbiome-treated plants showed inhibition to larvae feeding, compared with unamended control plants. Pyrosequencing analysis was conducted to determine the soil microbial composition and diversity of the soils used in this study. Correlation analyses were performed to determine relationships between various factors (soil microbial taxa, leaf chemical components, plant growth patterns and insect feeding behavior) and revealed that leaf amino acid content was positively correlated with both microbiome composition and insect feeding behavior.

Soil microbial communities are comprised of a vast array of bacteria, fungi, nematodes, and other organisms. It is becoming increasingly clear that these communities are not passively determined but actively regulated by plants. This chapter discusses the role plant root exudates play in the active regulation of soil microbial communities. In addition, we discuss the potential role coadapted plant-soil microbial communities may play in agricultural sustainability and production. We suggest that minimal disruption in the plant microbial community should be maintained in order to achieve maximum long-term agricultural production by minimizing disease outbreaks and by reducing costly agricultural inputs such as pesticides and fertilizers.

Carbon storage in terrestrial ecosystems is contingent upon the natural resistance of plant cell wall polymers to rapid biological degradation. Nevertheless, certain microorganisms have evolved remarkable means to overcome this natural resistance. Lignocellulose decomposition by microorganisms comprises an essential step in closing the loop of the global carbon cycle as it facilitates the recycling of carbon reposited in the form of structural polymers in plant cell walls. The significance of microbial decomposition of lignocellulose has recently risen to greater heights with the revisitation of the potential of lignocellulosic biomass as a valuable and abundant feedstock for the renewable energy and bioproducts industry. The scope of this chapter is to succinctly touch upon the composition of lignocellulosic biomass, the major enzymes involved in decomposing lignocellulosic biomass, and the fungi and bacteria that secrete these enzymes.

Upon his first encounter with a neotropical rainforest, Alexander von Humboldt provided this description … the treetops, hung about with lianas, and crowned with great bushes of flowers, spread out like a great carpet, the dark green of which seemed to gleam in contrast to the light…. But more beautiful still than all the wonders individually is the impression conveyed by the whole of this vigorous, luxuriant and yet light, cheering and mild nature in its entirety (Kritcher 1999). Indeed, the first Europeans to encounter these forests must have been agape with wonder at the massive buttressed strangler figs, kapoks, and Brazil nut trees adorned with winding, snakelike lianas. While this diversity is easily noted and appreciated, an even greater wealth of organisms dominated by fungi, bacteria, algae, and protozoa remains largely unexplored. These organisms collectively referred to as microbes make up more than 50% of the earth’s biomass and as the oldest life forms on our planet have evolved an incredible array of diversity suitable for survival in every habitat imaginable.

A Gram-negative, yellow pigmented bacterium designated strain CA5(T) that reduced selenite to elemental red selenium was isolated from soil. 16S rRNA gene sequence alignment identified the isolate as a novel Pseudomonas species with P. argentinensis, P. flavescens, and P. straminea as its closest relatives. Sequence alignments show that the 16S rRNA gene of strain CA5(T) differed from that of P. argentinensis, P. flavescens, and P. straminea by 1.3, 1.5, and 1.7%, respectively. The G+C content was 62.8 mol%, similar to the 62.7-63 mol% reported for P. flavescens but slightly higher than the 62.5-62.6 mol% of P. straminea and significantly higher than the 57.5-58.0 mol% of P. argentinensis. The major cellular fatty acids present in the CA5(T) strain were C₁₈:₁ ω7c (41.1%), C₁₆:₁ ω6c and C₁₆:₁ ω7c (25.7%), C₁₆:₁ (12.0%), C₁₂:₀ (8.0%), C₁₂:₀ 3-OH (4.4%), and C₁₀:₀ 3-OH (2.9%). The cellular fatty acid profile, GC content, phenotypic properties, and biochemical characteristics were consistent with its placement within the genus Pseudomonas. The name P. seleniipraecipitatus is proposed for these bacteria.

In this study, we examined the bacterial endophyte community of potato (Solanum tuberosum) cultivar/clones using two different molecular-based techniques (bacterial automated ribosomal intergenic spacer analysis (B-ARISA) and pyrosequencing). B-ARISA profiles revealed a significant difference in the endophytic community between cultivars (perMANOVA, p0.001), and canonical correspondence analysis showed a significant correlation between the community structure and plant biomass (p = 0.001). Pyrosequencing detected, on average, 477 +/- 71 bacterial operational taxonomic units (OTUs, 97% genetic similarity) residing within the roots of each cultivar, with a Chao estimated total OTU richness of 1,265 +/- 313. Across all cultivars, a total of 238 known genera from 15 phyla were identified. Interestingly, five of the ten most common genera (Rheinheimera, Dyadobacter, Devosia, Pedobacter, and Pseudoxanthomonas) have not, to our knowledge, been previously reported as endophytes of potato. Like the B-ARISA analysis, the endophytic communities differed between cultivar/clones (integral-libshuff, p0.001) and exhibited low similarities on both a presence/absence (0.145 +/- 0.019) and abundance (0.420 +/- 0.081) basis. Seventeen OTUs showed a strong positive (r0.600) or negative (r-0.600) correlation with plant biomass, suggesting a possible link between plant production and endophyte abundance. This study represents one of the most comprehensive assessments of the bacterial endophytic communities to date, and similar analyses in other plant species, cultivars, or tissues could be utilized to further elucidate the potential contribution(s) of endophytic communities to plant physiology and production.

A Pseudomonas sp. that may be useful in bioremediation projects was isolated from soil. The strain is of potential value because it reduces selenite to elemental red selenium and is unusual in that it was resistant to high concentrations of both selenate and selenite. Exposure of the strain to 50, 100, and 150 mM selenite reduced growth by 28, 57, and 66%, respectively, while no change in growth was observed when the strain was exposed to 64 mM selenate, the highest level tested. Cells of the strain removed 1.7 mM selenite from the culture fluid during a 7-day incubation. A selenite reductase with a molecular weight of ~115 kD was detected in cell-free extracts and a protein with a molecular weight of ~700 kD was detected that reduced both selenate and nitrate. The bacterial isolate is a strict aerobe, reducing selenite to elemental red selenium under aerobic conditions only. Pseudomonas sp. strain CA5 might be useful as an inoculum for bioreactors used to harvest selenium from selenite-containing groundwater. 16S rRNA gene sequence alignment and fatty acid analysis were used to identify the bacterium as a novel species of Pseudomonas related to P. argentinensis, P. flavescens, and P. straminea.

Background Ecological, evolutionary and physiological studies have thus far provided an incomplete picture of why some plants become invasive; therefore we used genomic resources to complement and advance this field. In order to gain insight into the invasive mechanism of Centaurea stoebe we compared plants of three geo-cytotypes, native Eurasian diploids, native Eurasian tetraploids and introduced North American tetraploids, grown in a common greenhouse environment. We monitored plant performance characteristics and life cycle habits and characterized the expression of genes related to constitutive defense and genome stability using quantitative PCR. Results Plant origin and ploidy were found to have a significant effect on both life cycle characteristics and gene expression, highlighting the importance of comparing appropriate taxonomic groups in studies of native and introduced plant species. We found that introduced populations of C. stoebe exhibit reduced expression of transcripts related to constitutive defense relative to their native tetraploid counterparts, as might be expected based on ideas of enemy release and rapid evolution. Measurements of several vegetative traits were similar for all geo-cytotypes; however, fecundity of tetraploids was significantly greater than diploids, due in part to their polycarpic nature. A simulation of seed production over time predicts that introduced tetraploids have the highest fecundity of the three geo-cytotypes. Conclusion Our results suggest that characterizing gene expression in an invasive species using populations from both its native and introduced range can provide insight into the biology of plant invasion that can complement traditional measurements of plant performance. In addition, these results highlight the importance of using appropriate taxonomic units in ecological genomics investigations.

Plants are in constant contact with a community of soil biota that contains fungi ranging from pathogenic to symbiotic. A few studies have demonstrated a critical role of chemical communication in establishing highly specialized relationships, but the general role for root exudates in structuring the soil fungal community is poorly described. This study demonstrates that two model plant species ( Arabidopsis thaliana and Medicago truncatula ) are able to maintain resident soil fungal populations but unable to maintain nonresident soil fungal populations. This is mediated largely through root exudates: the effects of adding in vitro-generated root exudates to the soil fungal community were qualitatively and quantitatively similar to the results observed for plants grown in those same soils. This effect is observed for total fungal biomass, phylotype diversity, and overall community similarity to the starting community. Nonresident plants and root exudates influenced the fungal community by both positively and negatively impacting the relative abundance of individual phylotypes. A net increase in fungal biomass was observed when nonresident root exudates were added to resident plant treatments, suggesting that increases in specific carbon substrates and/or signaling compounds support an increased soil fungal population load. This study establishes root exudates as a mechanism through which a plant is able to regulate soil fungal community composition.

Molecular-based approaches to assess microbial biomass and diversity from soil and other ecosystems are rapidly becoming the standard methodology for analysis. While these techniques are advantageous, because they do not rely on the need to culture organisms, each technique may have its own biases and/or limitations when used to assess fungal diversity from mixed-template samples. In this study, we analyzed PCR specificity and efficiency of the ITS primers (ITS1F and ITS4) in a series of single- and mixed-template samples using a combined quantitative PCR-length heterogeneity analysis (LH-qPCR) approach. As expected, these primers successfully amplified all higher fungal species tested (10 ascomycetes, 6 basidiomycetes, and 4 zygomycetes) and no members of the oomycetes. Based on our results, and a search of the GenBank database, amplicons of the ITS1F and ITS4 primer set exhibit considerable variability (420 to 825 bp), but due to similarities in amplicon sizes of some fungal species, actual species diversity in environmental samples may be underestimated approximately two-fold. The addition of an initial qPCR step allowed for the accurate quantitation of total fungal DNA in mixed-template samples over five orders of magnitude (10(-)(1) to 10(3) pg microl(-)(1)). PCR biases between individuals in mixed-templates rendered it impossible to determine the absolute quantity of any individual within a population from its individual peak height. However, relative changes in individuals within a mixed-template sample could be determined due to a constant proportionality between peak heights and starting template concentration. Variability associated with the individual steps of the LH-qPCR analysis was also determined from environmental samples.

Microorganisms and insects use conifer tissue as a substrate and food source, which can result in damage and disease. Physiological changes and reduction in vigor of the host tissue resulting from microbial and insect activity could impair the ability of conifers to develop freezing tolerance. Freezing injury also damages cells and reduces tissue vigor, which could predispose conifers to pest damage and microbial infection. Therefore, there are potential interactions between freezing injury and conifer pests.

Bacillus anthracis plasmids pX01 and pX02, harboured by the Sterne and Pasteur strains, respectively, have been sequenced by random 'shotgun' cloning and high throughout sequence analysis. These sequences have been assembled (Sequencher) to generate a circulate pX01 plasmid containing 181 656 bp and a single linear (gapped) pX02 contig containing at least 93.479 bp. Initial annotation suggests that the two plasmids combined contain at least 200 potential open reading frames (ORFs) with < 40% having significant similarity to sequences registered in open databases. Collectively, only 118 566 bp of the pX01 DNA (65%) represent predicted coding regions. This value is similar to published gene densities for other plasmids and is indicative of the larger intergenic spaces in plasmids vs those found in the chromosomes of the parental microbes (85-93% gene density). A 70 kbp region including the toxin genes (cya, lef and pag) is distinct from the remainder of the pX01 sequence: (1) it has a lower gene density (58 vs 70%) than the remaining 111 kbp; (2) it contains all but one of the co-regulated transcriptional fusions identified by transposon mutagenesis (Hoffmaster & Koehler 1997) and (3) it contains a significantly higher proportion of positive BLAST scores (62 vs 20%) for putative ORFs. These data suggest different origins for the two regions of pX01.

Competition is a major determinant of plant community structure, and can influence the size and reproductive fitness of a species. Therefore, competitive responses may arise from alterations in gene expression and plant function when an individual is confronted with new competitors. This study explored competition at the level of gene expression by hybridising transcripts from Centaurea maculosa Lam., one of North America’s most invasive exotic plant species, to an Arabidopsis thaliana (L.) Heynh microarray chip. Centaurea was grown in competition with Festuca idahoensis Elmer, a native species that generally has weak competitive effects against Centaurea; Gaillardia aristata Pursh, a native species that tends to be a much stronger competitor against Centaurea; and alone (control). Some transcripts were induced or repressed to a similar extent regardless of the plant neighbour grown with Centaurea. Other transcripts showed differential expression that was specific to the competitor species, possibly indicating a species-specific aspect of the competitive response of Centaurea. These results are the first to identify genes in an invasive plant that are induced or repressed by plant neighbours and provide a new avenue of insight into the molecular aspects of plant competitive ability.