Inhibitory activity of bacterial lipopeptides against Fusarium oxysporum f.sp. Strigae.

This study investigated the influence of bacterial cyclic lipopeptides (LP; surfactins, iturins, fengycins) on microbial interactions. The objective was to investigate whether the presence of bacteria inhibits fungal growth and whether this inhibition is due to the release of bacterial metabolites, particularly LP. Selected endophytic bacterial strains with known plant-growth promoting potential were cultured in the presence of Fusarium oxysporum f.sp. strigae (Fos), which was applied as model fungal organism. The extracellular metabolome of tested bacteria, with a focus on LP, was characterized, and the inhibitory effect of bacterial LP on fungal growth was investigated. The results showed that Bacillus velezensis GB03 and FZB42, as well as B. subtilis BSn5 exhibited the strongest antagonism against Fos. Paraburkholderia phytofirmans PsJN, on the other hand, tended to have a slight, though non-significant growth promotion effect. Crude LP from strains GB03 and FZB42 had the strongest inhibitory effect on Fos, with a significant inhibition of spore germination and damage of the hyphal structure. Liquid chromatography tandem mass spectrometry revealed the production of several variants of iturin, fengycin, and surfactin LP families from strains GB03, FZB42, and BSn5, with varying intensity. Using plate cultures, bacillomycin D fractions were detected in higher abundance in strains GB03, FZB42, and BSn5 in the presence of Fos. Additionally, the presence of Fos in dual plate culture triggered an increase in bacillomycin D production from the Bacillus strains. The study demonstrated the potent antagonistic effect of certain Bacillus strains (i.e., GB03, FZB42, BSn5) on Fos development. Our findings emphasize the crucial role of microbial interactions in shaping the co-existence of microbial assemblages.

Capacity of soil bacteria to reach the phyllosphere and convergence of floral communities despite soil microbiota variation.

Leaves and flowers are colonized by diverse bacteria that impact plant fitness and evolution. Although the structure of these microbial communities is becoming well-characterized, various aspects of their environmental origin and selection by plants remain uncertain, such as the relative proportion of soilborne bacteria in phyllosphere communities. Here, to address this issue and to provide experimental support for bacteria being filtered by flowers, we conducted common-garden experiments outside and under gnotobiotic conditions. We grew Arabidopsis thaliana in a soil substitute and added two microbial communities from natural soils. We estimated that at least 25% of the phyllosphere bacteria collected from the plants grown in the open environment were also detected in the controlled conditions, in which bacteria could reach leaves and flowers only from the soil. These taxa represented more than 40% of the communities based on amplicon sequencing. Unsupervised hierarchical clustering approaches supported the convergence of all floral microbiota, and 24 of the 28 bacteria responsible for this pattern belonged to the Burkholderiaceae family, which includes known plant pathogens and plant growth-promoting members. We anticipate that our study will foster future investigations regarding the routes used by soil microbes to reach leaves and flowers, the ubiquity of the environmental filtering of Burkholderiaceae across plant species and environments, and the potential functional effects of the accumulation of these bacteria in the reproductive organs of flowering plants.

Inoculation of Mimosa Pudica with Paraburkholderia phymatum Results in Changes to the Rhizoplane Microbial Community Structure.

Nitrogen fixing symbiosis between rhizobia and legumes contributes significant amounts of N to agricultural and natural environments. In natural soils, rhizobia compete with indigenous bacterial communities to colonize legume roots, which leads to symbiotic interactions. However, limited information is currently available on the effects of the rhizobial symbiont on the resident microbial community in the legume rhizosphere, rhizoplane, and endosphere, which is partly due to the presence of native nodulating rhizobial strains. In the present study, we used a symbiotic system comprised of Paraburkholderia phymatum and Mimosa pudica to examine the interaction of an inoculant strain with indigenous soil bacteria. The effects of a symbiont inoculation on the native bacterial community was investigated using high throughput sequencing and an analysis of 16S rRNA gene amplicons. The results obtained revealed that the inoculation induced significant alterations in the microbial community present in the rhizoplane+endosphere of the roots, with 13 different taxa showing significant changes in abundance. No significant changes were observed in the rhizospheric soil. The relative abundance of P. phymatum significantly increased in the rhizoplane+endosphere of the root, but significant decreased in the rhizospheric soil. While the rhizosphere, rhizoplane, and root endosphere contained a wide diversity of bacteria, the nodules were predominantly colonized by P. phymatum. A network analysis revealed that the operational taxonomic units of Streptomyces and Phycicoccus were positively associated with P. phymatum as potential keystone taxa. Collectively, these results suggest that the success of an inoculated symbiont depends on its ability to colonize the roots in the face of competition by other soil bacteria. A more detailed understanding of the mechanisms by which an inoculated strain colonizes its plant host is crucial for realizing the full potential of microbial inoculants in sustainable agriculture.

Fed-batch polyhydroxybutyrate production by Paraburkholderia sacchari from a ternary mixture of glucose, xylose and arabinose.

Polyhydroxybutyrate (PHB) is a biodegradable bioplastic that is comparable with many petroleum-based plastics in terms of mechanical properties and is highly biocompatible. Lignocellulosic biomass conversion into PHB can increase profit and add sustainability. Glucose, xylose and arabinose are the main monomer sugars derived from upstream lignocellulosic biomass processing. The sugar mixture ratios may vary greatly depending on the pretreatment and enzymatic hydrolysis conditions. Paraburkholderia sacchari DSM 17165 is a bacterium strain that can convert all three sugars into PHB. In this study, fed-batch mode was applied to produce PHB on three sugar mixtures (glucose:xylose:arabinose = 4:2:1, 2:2:1, 1:2:1). The highest PHB concentration produced was 67 g/L for 4:2:1 mixture at 41 h corresponding to an accumulation of 77% of cell dry weight as PHB. Corresponding sugar conversion efficiency and productivity were 0.33 g PHB/g sugar consumed and 1.6 g/L/h, respectively. The results provide references for process control to maximize PHB production from real sugar streams derived from corn fibre.

Delineation of a Subgroup of the Genus Paraburkholderia, Including P. terrae DSM 17804T, P. hospita DSM 17164T, and Four Soil-Isolated Fungiphiles, Reveals Remarkable Genomic and Ecological Features-Proposal for the Definition of a P. hospita Species Cluster.

The fungal-interactive (fungiphilic) strains BS001, BS007, BS110, and BS437 have previously been preliminarily assigned to the species Paraburkholderia terrae. However, in the (novel) genus Paraburkholderia, an as-yet unresolved subgroup exists, that clusters around Paraburkholderia hospita (containing the species P. terrae, P. hospita, and Paraburkholderia caribensis). To shed light on the precise relationships across the respective type strains and the novel fungiphiles, we here compare their genomic and ecophysiological features. To reach this goal, the genomes of the three type strains, with sizes ranging from 9.0 to 11.5 Mb, were de novo sequenced and the high-quality genomes analyzed. Using whole-genome, ribosomal RNA and marker-gene-concatenate analyses, close relationships between P. hospita DSM 17164T and P. terrae DSM 17804T, versus more remote relationships to P. caribensis DSM 13236T, were found. All four fungiphilic strains clustered closely to the two-species cluster. Analyses of average nucleotide identities (ANIm) and tetranucleotide frequencies (TETRA) confirmed the close relationships between P. hospita DSM 17164T and P. terrae DSM 17804T (ANIm = 95.42; TETRA = 0.99784), as compared with the similarities of each one of these strains to P. caribensis DSM 13236T. A species cluster was thus proposed. Furthermore, high similarities of the fungiphilic strains BS001, BS007, BS110, and BS437 with this cluster were found, indicating that these strains also make part of it, being closely linked to P. hospita DSM 17164T (ANIm = 99%; TETRA = 0.99). We propose to coin this cluster the P. hospita species cluster (containing P. hospita DSM 17164T, P. terrae DSM 17804T, and strains BS001, BS007, BS110, and BS437), being clearly divergent from the closely related species P. caribensis (type strain DSM 13236T). Moreover, given their close relatedness to P. hospita DSM 17164T within the cluster, we propose to rename the four fungiphilic strains as members of P. hospita. Analysis of migratory behavior along with fungal growth through soil revealed both P. terrae DSM 17804T and P. hospita DSM 17164T (next to the four fungiphilic strains) to be migration-proficient, whereas P. caribensis DSM 13236T was a relatively poor migrator. Examination of predicted functions across the genomes of the seven investigated strains, next to several selected additional ones, revealed the common presence of features in the P. hospita cluster strains that are potentially important in interactions with soil fungi. Thus, genes encoding specific metabolic functions, biofilm formation (pelABCDEFG, pgaABCD, alginate-related genes), motility/chemotaxis, type-4 pili, and diverse secretion systems were found.

Toxic responses of metabolites, organelles and gut microorganisms of Eisenia fetida in a soil with chromium contamination.

The toxic sensitivity in different physiological levels of chromium (Cr) contaminated soils with environmentally equivalent concentrations (EEC) was fully unknown. The earthworm Eisenia fetida was exposed to a Cr-contaminated soil at the EEC level (referred to as Cr-CS) to characterize the induced toxicity at the whole body, organ, tissue, subcellular structure and metabolic levels. The results showed that the survival rate, weight and biodiversity of the gut microorganisms (organ) had no significant difference (p > 0.05) between control and Cr-CS groups. Qualitative histopathological and subcellular evaluations from morphology showed earthworms obvious injuries. The organelle injuries combined with the metabolic changes provided additional evidence that the Cr-CS damaged the nucleus and probably disturbed the nucleic acid metabolism of earthworms. 2-hexyl-5-ethyl-3-furansulfonate, dimethylglycine, betaine and scyllo-inositol were sensitive and relatively quantitative metabolites that were recommended as potential biomarkers for Cr-CS based on their significant weights in the multivariate analysis model. In addition, the relative abundance of Burkholderiaceae, Enterobacteriaceae and Microscillaceae of the earthworm guts in the Cr-CS group significantly increased, particularly for Burkholderiaceae (increased by 13.1%), while that of Aeromonadaceae significantly decreased by 5.6% in contrast with the control group. These results provided new insights into our understanding of the toxic effects of the EEC level of Cr contaminated soil from different physiological levels of earthworms and extend our knowledge on the composition and sensitivity of the earthworm gut microbiota in Cr contaminated soil ecosystems. Furthermore, these toxic responses from gut microorganisms to metabolites of earthworms provided important data to improve the adverse outcome pathway and toxic mechanism of the Cr-CS if the earthworm genomics and proteomics would be also gained in the future.

Optimization of polyhydroxybutyrate production by experimental design of combined ternary mixture (glucose, xylose and arabinose) and process variables (sugar concentration, molar C:N ratio).

Conversion of lignocellulosic feedstocks to polyhydroxybutyrate (PHB) could make lignocellulosic biorefineries more profitable and sustainable. Glucose, xylose and arabinose are the main sugars derived from pretreatment and hydrolysis of herbaceous feedstocks. Burkholderia sacchari DSM 17165 is a bacterium that can convert these sugars into PHB. However, the effects of sugar ratio, sugar concentration, and molar C:N ratio on PHB production have not been studied. In this study, a seven-run mixture design for sugar ratio combined with a 32 full factorial design for process variables was performed to optimize PHB production. A polynomial model was built based on experimental data, and optimum conditions for different sugar streams were derived and validated. The highest PHB production (3.81 g/L) was achieved with arabinose at a concentration of 25.54 g/L and molar C:N ratio of 74.35. Results provide references for manipulation of sugar mixture and process control to maximize PHB production.

Poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) production from engineered Ralstonia eutropha using synthetic and anaerobically digested food waste derived volatile fatty acids.

Ralstonia eutropha Re2133/pCB81 is able to utilize various volatile fatty acids (VFAs) (acetate, butyrate, lactate, and propionate) for polyhydroxyalkanoates (PHAs) production. Acetate and lactate resulted in poly(3-hydroxybutyrate) P(3HB) production, butyrate in poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) P(3HB-co-3HHx), and propionate in poly(3-hydroxybutyrate-co-3-hydroxyvalerate) P(3-HB-co-3HV). Various biomass yields i.e. (Yx/s, 0.131 ±â€¯0.02 g/g acetate, 0.221 ±â€¯0.02 g/g butyrate, 0.222 ±â€¯0.05 g/g lactate, and 0.225 ±â€¯0.04 g/g propionate) and PHA yields (Yp/s, 0.01 ±â€¯0.001 g/g acetate, 0.11 ±â€¯0.004 g/g butyrate, 0.03 ±â€¯0.001 g/g lactate, and 0.18 ±â€¯0.005 g/g propionate) were observed with the different organic acids. When all the organic acids were mixed together R. eutropha Re2133/pCB81 had the following order of preference; lactate > butyrate > propionate > acetate. A response surface design study showed that in mixtures butyrate is the main organic acid involved in PHA production and acts as a precursor for HHx monomer units to produce copolymer P(3HB-co-3HHx). Food waste ferment (FWF) without any additional nitrogen source and precursors resulted in P(3HB-co-3HHx) accumulation (52 ±â€¯4% w/w with 18.5 ±â€¯3% HHx fraction).

Biofilm-Constructing Variants of Paraburkholderia phytofirmans PsJN Outcompete the Wild-Type Form in Free-Living and Static Conditions but Not In Planta.

Members of the genus Burkholderia colonize diverse ecological niches. Among the plant-associated strains, Paraburkholderia phytofirmans PsJN is an endophyte with a broad host range. In a spatially structured environment (unshaken broth cultures), biofilm-constructing specialists of P. phytofirmans PsJN colonizing the air-liquid interface arose at high frequency. In addition to forming a robust biofilm in vitro and in planta on Arabidopsis roots, those mucoid phenotypic variants display a reduced swimming ability and modulate the expression of several microbe-associated molecular patterns (MAMPs), including exopolysaccharides (EPS), flagellin, and GroEL. Interestingly, the variants induce low PR1 and PDF1.2 expression compared to that of the parental strain, suggesting a possible evasion of plant host immunity. We further demonstrated that switching from the planktonic to the sessile form did not involve quorum-sensing genes but arose from spontaneous mutations in two genes belonging to an iron-sulfur cluster: hscA (encoding a cochaperone protein) and iscS (encoding a cysteine desulfurase). A mutational approach validated the implication of these two genes in the appearance of variants. We showed for the first time that in a heterogeneous environment, P. phytofirmans strain PsJN is able to rapidly diversify and coexpress a variant that outcompete the wild-type form in free-living and static conditions but not in plantaIMPORTANCEParaburkholderia phytofirmans strain PsJN is a well-studied plant-associated bacterium known to induce resistance against biotic and abiotic stresses. In this work, we described the spontaneous appearance of mucoid variants in PsJN from static cultures. We showed that the conversion from the wild-type (WT) form to variants (V) correlates with an overproduction of EPS, an enhanced ability to form biofilm in vitro and in planta, and a reduced swimming motility. Our results revealed also that these phenotypes are in part associated with spontaneous mutations in an iron-sulfur cluster. Overall, the data provided here allow a better understanding of the adaptive mechanisms likely developed by P. phytofirmans PsJN in a heterogeneous environment.

Highly competitive fungi manipulate bacterial communities in decomposing beech wood (Fagus sylvatica).

The bacterial communities in decomposing wood are receiving increased attention, but their interactions with wood-decay fungi are poorly understood. This is the first field study to test the hypothesis that fungi are responsible for driving bacterial communities in beech wood (Fagus sylvatica). A meta-genetic approach was used to characterise bacterial and fungal communities in wood that had been laboratory-colonised with known wood-decay fungi, and left for a year at six woodland sites. Alpha-, Beta- and Gammaproteobacteria and Acidobacteria were the proportionally dominant bacterial taxa, as in previous studies. Pre-colonising wood with decay fungi had a clear effect on the bacterial community, apparently via direct fungal influence; the bacterial and fungal communities present at the time of collection explained nearly 60% of their mutual covariance. Site was less important than fungal influence in determining bacterial communities, but the effects of pre-colonisation were more pronounced at some sites than at others. Wood pH was also a strong bacterial predictor, but was itself under considerable fungal influence. Burkholderiaceae and Acidobacteriaceae showed directional responses against the trend of the bacterial community as a whole.

Enrichment of Verrucomicrobia, Actinobacteria and Burkholderiales drives selection of bacterial community from soil by maize roots in a traditional milpa agroecosystem.

Milpas are rain-fed agroecosystems involving domesticated, semi-domesticated and tolerated plant species that combine maize with a large variety of other crop, tree or shrub species. Milpas are low input and low-tillage, yet highly productive agroecosystems, which have been maintained over millennia in indigenous communities in Mexico and other countries in Central America. Thus, milpas may retain ancient plant-microorganisms interactions, which could have been lost in modern high-tillage monocultures with large agrochemical input. In this work, we performed high-throughput 16S ribosomal DNA sequencing of soil adjacent to maize roots and bulk soil sampled at 30 cm from the base of the plants. We found that the bacterial communities of maize root soil had a lower alpha diversity, suggesting selection of microorganisms by maize-roots from the bulk-soil community. Beta diversity analysis confirmed that these environments harbor two distinct microbial communities; differences were driven by members of phyla Verrucomicrobia and Actinobacteria, as well as the order Burkholderiales (Betaproteobacteria), all of which had higher relative abundance in soil adjacent to the roots. Numerous studies have shown the influence of maize plants on bacterial communities found in soil attached tightly to the roots; here we further show that the influence of maize roots at milpas on bacterial communities is detectable even in plant-free soil collected nearby. We propose that members of Verrucomicrobia and other phyla found in the rhizosphere may establish beneficial plant-microbe interactions with maize roots in milpas, and propose to address their cultivation for future studies on ecology and potential use.

Assessment of bacterial inoculant formulated with Paraburkholderia tropica to enhance wheat productivity.

Paraburkholderia tropica is an endophytic nitrogen-fixing bacterium isolated from the rhizosphere, rhizoplane, and internal tissues of sugarcane and corn plants in different geographical regions. Other plant-growth-promoting abilities, such as phosphate solubilization and antifungal activity, have also been reported for this bacterium. With an aim at investigating the potential use of P. tropica as an inoculant for improving the performance of wheat crop, in this work we evaluated an experimental inoculant formulated with P. tropica MTo-293 with respect to root colonization, the practical aspects of its application, and the effects under field conditions when applied to wheat seeds. Bacterial colonization was monitored by culture dependent techniques and the wheat yield determined by quantifying the total grain production in two different seasons. Rhizoplane and endophytic colonization in wheat roots was achieved efficiently (on average, 8 and 4 log colony-forming units/g fresh weight, respectively) even at relatively low concentrations of viable bacteria in the inoculum under controlled conditions. P. tropica was compatible with a widely used fungicide, maintained viability for 48 h once applied to seeds, and was also able to colonize wheat roots efficiently. Furthermore, we were able to formulate an inoculant that maintained bacterial viability for relatively long time periods. Preliminary field assays were realized, and even though the average yields values for the inoculated treatments remained above the uninoculated ones, no significant effects of inoculation were detected with or without fertilization. The correct physiologic behavior of P. tropica suggests the necessity to continue with field experiments under different conditions.

Effects of the deletion of hup genes encoding the uptake hydrogenase on the activity of hydrogen production in the purple photosynthetic bacterium Rubrivivax gelatinosus IL144.

The efficiency of hydrogen gas production by nitrogenase in bacteria has been improved by the inhibition of antagonistic activity by the uptake hydrogenase. In this study, a mutant lacking the gene coding for the uptake hydrogenase was generated from the photosynthetic beta-proteobacterium Rubrivivax gelatinosus IL144 to explore new ways of hydrogen gas production driven by light energy. The mutant cells produced 25-30% higher amounts of molecular hydrogen than the wild-type cells under nitrogen-deficient conditions under light. Furthermore, by the addition of 5 mM glutamate, the photosynthetic growth rate was greatly enhanced, and the hydrogen gas production activity reached 41.1 (mmol/l) in the mutant.

Strain-specific consumption and transformation of alga-derived dissolved organic matter by members of the Limnohabitans-C and Polynucleobacter-B clusters of Betaproteobacteria.

We investigated changes in quality and quantity of extracellular and biomass-derived organic matter (OM) from three axenic algae (genera Rhodomonas, Chlamydomonas, Coelastrum) during growth of Limnohabitans parvus, Limnohabitans planktonicus and Polynucleobacter acidiphobus representing important clusters of freshwater planktonic Betaproteobacteria. Total extracellular and biomass-derived OM concentrations from each alga were approximately 20 mg l-1 and 1 mg l-1 respectively, from which up to 9% could be identified as free carbohydrates, polyamines, or free and combined amino acids. Carbohydrates represented 54%-61% of identified compounds of the extracellular OM from each alga. In biomass-derived OM of Rhodomonas and Chlamydomonas 71%-77% were amino acids and polyamines, while in that of Coelastrum 85% were carbohydrates. All bacteria grew on alga-derived OM of Coelastrum, whereas only Limnohabitans strains grew on OM from Rhodomonas and Chlamydomonas. Bacteria consumed 24%-76% and 38%-82% of all identified extracellular and biomass-derived OM compounds respectively, and their consumption was proportional to the concentration of each OM compound in the different treatments. The bacterial biomass yield was higher than the total identifiable OM consumption indicating that bacteria also utilized other unidentified alga-derived OM compounds. Bacteria, however, also produced specific OM compounds suggesting enzymatic polymer degradation or de novo exudation.

Microdiversification of a Pelagic Polynucleobacter Species Is Mainly Driven by Acquisition of Genomic Islands from a Partially Interspecific Gene Pool.

Microdiversification of a planktonic freshwater bacterium was studied by comparing 37 Polynucleobacter asymbioticus strains obtained from three geographically separated sites in the Austrian Alps. Genome comparison of nine strains revealed a core genome of 1.8 Mb, representing 81% of the average genome size. Seventy-five percent of the remaining flexible genome is clustered in genomic islands (GIs). Twenty-four genomic positions could be identified where GIs are potentially located. These positions are occupied strain specifically from a set of 28 GI variants, classified according to similarities in their gene content. One variant, present in 62% of the isolates, encodes a pathway for the degradation of aromatic compounds, and another, found in 78% of the strains, contains an operon for nitrate assimilation. Both variants were shown in ecophysiological tests to be functional, thus providing the potential for microniche partitioning. In addition, detected interspecific horizontal exchange of GIs indicates a large gene pool accessible to Polynucleobacter species. In contrast to core genes, GIs are spread more successfully across spatially separated freshwater habitats. The mobility and functional diversity of GIs allow for rapid evolution, which may be a key aspect for the ubiquitous occurrence of Polynucleobacter bacteria. IMPORTANCE: Assessing the ecological relevance of bacterial diversity is a key challenge for current microbial ecology. The polyphasic approach which was applied in this study, including targeted isolation of strains, genome analysis, and ecophysiological tests, is crucial for the linkage of genetic and ecological knowledge. Particularly great importance is attached to the high number of closely related strains which were investigated, represented by genome-wide average nucleotide identities (ANI) larger than 97%. The extent of functional diversification found on this narrow phylogenetic scale is compelling. Moreover, the transfer of metabolically relevant genomic islands between more distant members of the Polynucleobacter community provides important insights toward a better understanding of the evolution of these globally abundant freshwater bacteria.

Monitoring the impact of bioaugmentation with a PAH-degrading strain on different soil microbiomes using pyrosequencing.

The effect of bioaugmentation with Sphingobium sp. AM strain on different soils microbiomes, pristine soil (PS), chronically contaminated soil (IPK) and recently contaminated soil (Phe) and their implications in bioremediation efficiency was studied by focusing on the ecology that drives bacterial communities in response to inoculation. AM strain draft genome codifies genes for metabolism of aromatic and aliphatic hydrocarbons. In Phe, the inoculation improved the elimination of phenanthrene during the whole treatment, whereas in IPK no improvement of degradation of any PAH was observed. Through the pyrosequencing analysis, we observed that inoculation managed to increase the richness and diversity in both contaminated microbiomes, therefore, independently of PAH degradation improvement, we observed clues of inoculant establishment, suggesting it may use other resources to survive. On the other hand, the inoculation did not influence the bacterial community of PS. On both contaminated microbiomes, incubation conditions produced a sharp increase on Actinomycetales and Sphingomonadales orders, while inoculation caused a relative decline of Actinomycetales. Inoculation of most diverse microbiomes, PS and Phe, produced a coupled increase of Sphingomonadales, Burkholderiales and Rhizobiales orders, although it may exist a synergy between those genera; our results suggest that this would not be directly related to PAH degradation.

Variations in Bacterial Community in a Temperate Lake Associated with an Agricultural Watershed.

Terrestrially derived carbon and nutrients are washed into lakes, providing nutritional drivers for both microbial heterotrophy and phototrophy. Changes in the quantity and diversity of carbon and nutrients exported from watersheds in response to alterations in long-term land use have led to a need for evaluation of the linkage between watershed-exported carbon and nutrients and bacterial community structure in watershed associated lakes. To learn more about these interactions, we investigated Muskrat Lake in Michigan, which has a well-defined moderately sized watershed dominated by agriculture. We measured the water chemistry, characterized the dissolved organic carbon, and determined the structure of the bacterial communities at the inlet and center of this lake (five depths per site) over the summer and fall of 2008. The lake had temporal and rain event-based fluctuations in water chemistry, as well as temporal and rain event-dependent shifts in bacterial communities as measured by terminal restriction fragment length polymorphism. Agricultural watershed inputs were observed in the lake during and after rain events. Terminal restriction fragment length polymorphism and 454 pyrosequencing of the bacterial communities indicated that there were differences over time and that the dominant phylotypes shifted between summer and late fall. Some populations (e.g., Polynucleobacter and Mycobacterium) increased during fall, while others (e.g., Gemmatimonas) diminished. Redundancy and partitioning analyses showed that water chemistry is highly correlated with variations in the bacterial community of the lake, which explained 34 % of the variations in the bacterial community. Dissolved organic carbon had the greatest effects on variations in the Muskrat Lake bacterial community (2 %). The results of this study provide information that will enable a better understanding of the interaction between the bacterial community of lakes and changes in chemical properties as a result of nutrient importation from the surrounding watershed.

Degradation pathway and kinetic analysis for p-xylene removal by a novel Pandoraea sp. strain WL1 and its application in a biotrickling filter.

In this study, a novel Pandoraea sp. strain WL1 capable of mineralizing p-xylene as sole carbon and energy source was isolated from the activated sludge of a pharmaceutical wastewater treatment plant. A nearly complete degradation of 16.6∼99.4 mg L(-1)p-xylene in the liquid-phase was achieved within 6∼18 h accompanied by 15.9∼56.3 mg dry cell weight (DCW)L(-1) for bacterial growth. A complete pathway for p-xylene degradation by strain WL1 was presented through identification of a major intermediate (p-toluic acid) and final products (2.193 gCO2 gp-xylene(-1) of CO2 production and 0.215 g DCW gp-xylene(-1) of bacterial yield). Kinetics of bacterial growth and p-xylene degradation were evaluated using Haldane-Andrews model and pseudo first-order model, respectively. Furthermore, a biotrickling filter (BTF) was employed to evaluate the application of strain WL1 on the removal of gas-phase p-xylene under gas flow rates of 0.41∼1.98 m(3)h(-1) for inlet loading rates of 5∼248 gm(-3)h(-1). The BTF inoculated with strain WL1 proved to be robust against fluctuations of gas flow rates and inlet p-xylene concentrations. All the results obtained highlight the potential of strain WL1 for the treatment of p-xylene.

Improving the growth of Rubrivivax gelatinosus cultivated in sewage environment.

Rubrivivax gelatinosus cultivated in wastewater environment can combine the biomass resource recycling for generating chemicals with sewage purification. However, low biomass accumulation restricts the exertion of this advantage. Thus, this paper investigated Fe(3+) advancement for biomass production in starch wastewater under light-anaerobic condition. Results showed that addition of Fe(3+) was successful in enhancing biomass production, which certainly improved the feasibility of biomass recycling in R. gelatinosus starch wastewater treatment. With optimal Fe(3+) dosage (20 mg/L), biomass production reached 4,060 mg/L, which was 1.63 times that of control group. Amylase activity was improved by 48 %. Both COD removal and starch removal reached 90 %. Hydraulic retention time was shortened by 25 %. Proper Fe(3+) dosage enhanced biomass production, but excess Fe(3+) was harmful for biomass accumulation.

Inhibition of co-colonizing cystic fibrosis-associated pathogens by Pseudomonas aeruginosa and Burkholderia multivorans.

Cystic fibrosis (CF) is a recessive genetic disease characterized by chronic respiratory infections and inflammation causing permanent lung damage. Recurrent infections are caused by Gram-negative antibiotic-resistant bacterial pathogens such as Pseudomonas aeruginosa, Burkholderia cepacia complex (Bcc) and the emerging pathogen genus Pandoraea. In this study, the interactions between co-colonizing CF pathogens were investigated. Both Pandoraea and Bcc elicited potent pro-inflammatory responses that were significantly greater than Ps. aeruginosa. The original aim was to examine whether combinations of pro-inflammatory pathogens would further exacerbate inflammation. In contrast, when these pathogens were colonized in the presence of Ps. aeruginosa the pro-inflammatory response was significantly decreased. Real-time PCR quantification of bacterial DNA from mixed cultures indicated that Ps. aeruginosa significantly inhibited the growth of Burkholderia multivorans, Burkholderia cenocepacia, Pandoraea pulmonicola and Pandoraea apista, which may be a factor in its dominance as a colonizer of CF patients. Ps. aeruginosa cell-free supernatant also suppressed growth of these pathogens, indicating that inhibition was innate rather than a response to the presence of a competitor. Screening of a Ps. aeruginosa mutant library highlighted a role for quorum sensing and pyoverdine biosynthesis genes in the inhibition of B. cenocepacia. Pyoverdine was confirmed to contribute to the inhibition of B. cenocepacia strain J2315. B. multivorans was the only species that could significantly inhibit Ps. aeruginosa growth. B. multivorans also inhibited B. cenocepacia and Pa. apista. In conclusion, both Ps. aeruginosa and B. multivorans are capable of suppressing growth and virulence of co-colonizing CF pathogens.