Growth of a vortex polycrystal in type II superconductors

We discuss the formation of a vortex polycrystal in type II superconductors from the competition between pinning and elastic forces. We compute the elastic energy of a deformed grain boundary, which is strongly nonlocal, and obtain the depinning stress for weak and strong pinning. Our estimates for the grain size dependence on the magnetic field strength are in good agreement with previous experiments on NbMo. Finally, we discuss the effect of thermal noise on grain growth.

THE RESURRECTION PLANT TRIPOGON SPICATUS (POACEAE) HARBORS A DIVERSITY OF PLANT GROWTH PROMOTING BACTERIA IN NORTHEASTERN BRAZILIAN CAATINGA

Plant species that naturally occur in the Brazilian Caatinga(xeric shrubland) adapt in several ways to these harsh conditions, and that can be exploited to increase crop production. Among the strategic adaptations to confront low water availability, desiccation tolerance stands out. Up to now, the association of those species with beneficial soil microorganisms is not well understood. The aim of this study was to characterize Tripogon spicatusdiazotrophic bacterial isolates from the Caatingabiome and evaluate their ability to promote plant growth in rice. Sixteen bacterial isolates were studied in regard to their taxonomic position by partial sequencing of the 16S rRNA gene, putative diazotrophic capacity, in vitro indole-acetic acid (IAA) production and calcium phosphate solubilization, metabolism of nine different C sources in semi-solid media, tolerance to different concentrations of NaCl to pHs and intrinsic resistance to nine antibiotics. Finally, the ability of the bacterial isolates to promote plant growth was evaluated using rice (Oryza sativa) as a model plant. Among the 16 isolates evaluated, eight of them were classified as Enterobacteriaceae members, related to Enterobacter andPantoeagenera. Six other bacteria were related toBacillus, and the remaining two were related toRhizobiumand Stenotrophomonas.The evaluation of total N incorporation into the semi-solid medium indicated that all the bacteria studied have putative diazotrophic capacity. Two bacteria were able to produce more IAA than that observed for the strain BR 11175Tof Herbaspirillum seropedicae.Bacterial isolates were also able to form a microaerophilic pellicle in a semi-solid medium supplemented with different NaCl concentrations up to 1.27 mol L-1. Intrinsic resistance to antibiotics and the metabolism of different C sources indicated a great variation in physiological profile. Seven isolates were able to promote rice growth, and two bacteria were more efficient than the reference strainAzospirillum brasilense, Ab-V5. The results indicate the potential of T. spicatus as native plant source of plant growth promoting bacteria.

Calcineurin-Mediated Regulation of Hyphal Growth, Septation, and Virulence in Aspergillus fumigatus.

Calcineurin is a heterodimeric protein phosphatase complex composed of catalytic (CnaA) and regulatory (CnaB) subunits and plays diverse roles in regulating fungal stress responses, morphogenesis, and pathogenesis. Fungal pathogens utilize the calcineurin pathway to survive in the host environment and cause life-threatening infections. The immunosuppressive calcineurin inhibitors (FK506 and cyclosporine A) are active against fungi, making calcineurin a promising antifungal drug target. Here, we review novel findings on calcineurin localization and functions in Aspergillus fumigatus hyphal growth and septum formation through regulation of proteins involved in cell wall biosynthesis. Extensive mutational analysis in the functional domains of A. fumigatus CnaA has led to an understanding of the relevance of these domains for the localization and function of CnaA at the hyphal septum. An evolutionarily conserved novel mode of calcineurin regulation by phosphorylation in filamentous fungi was found to be responsible for virulence in A. fumigatus. This finding of a filamentous fungal-specific mechanism controlling hyphal growth and virulence represents a potential target for antifungal therapy.

Peptide vaccine induces enhanced tumor growth associated with apoptosis induction in CD8+ T cells.

CD8(+) CTLs play a critical role in antitumor immunity. However, vaccination with synthetic peptide containing CTL epitopes has not been generally effective in inducing protective antitumor immunity. In this study, we addressed the detailed mechanism(s) involved in this failure using a new tumor model of BALB/c transplanted tumors expressing NY-ESO-1, an extensively studied human cancer/testis Ag. Whereas peptide immunization with an H2-D(d)-restricted CTL epitope derived from NY-ESO-1 (NY-ESO-1 p81-88) induced NY-ESO-1(81-88)-specific CD8(+) T cells in draining lymph nodes and spleens, tumor growth was significantly enhanced. Single-cell analysis of specific CD8(+) T cells revealed that peptide immunization caused apoptosis of >80% of NY-ESO-1(81-88)-specific CD8(+) T cells at tumor sites and repetitive immunization further diminished the number of specific CD8(+) T cells. This phenomenon was associated with elevated surface expression of Fas and programmed death-1. When peptide vaccination was combined with an adjuvant, a TLR9 ligand CpG, the elevated Fas and programmed death-1 expression and apoptosis induction were not observed, and vaccine with peptide and CpG was associated with strong tumor growth inhibition. Selection of appropriate adjuvants is essential for development of effective cancer vaccines, with protection of effector T cells from peptide vaccine-induced apoptosis being a prime objective.

Immunoelectron microscopic localization of transforming growth factor alpha in rat colon

Transforming growth factor alpha (TGF alpha) is a polypeptide, which binds to the epidermal growth factor receptor to carry out its function related to cell proliferation and differentiation. The ultrastructural localisation of TGF alpha was studied in both the proximal and the distal colon. The columnar cells, lining the surface epithelium of the proximal colon, showed a strong immunoreactivity in the polyribosomes and in the interdigitations of the lateral membrane. The columnar cells of the crypts and the goblet cells in both the proximal and the distal colon showed the immunostaining in the cis and trans cisternae of the Golgi apparatus. TGF alpha seems to be processed differently in the surface columnar cells and in the crypt columnar cells and goblet cells. Moreover, it probably has different roles in proliferation and differentiation.

Early parenteral lipids and growth velocity in extremely-low-birth-weight infants.

BACKGROUND & AIMS: Whether early parenteral lipids improve postnatal growth of preterm neonates remains unclear. We aimed to assess the effects of parenteral lipids on growth velocity in extremely-low-birth-weight infants. METHODS: This retrospective cohort study included 121 extremely-low-birth-weight infants. The associations between parenteral lipids (cumulative intakes during the first week and delays in their introduction) and growth velocities (weight, head circumference and length) up to 28 days of life and to 36 weeks of corrected age were analysed using uni- and multivariate linear regression. RESULTS: Univariate analyses showed a significant positive association between the cumulative intakes of parenteral lipids during the first week and i) weight gain up to day 28; ii) weight gain up to 36 weeks of corrected age; iii) head circumference growth up to day 28. There was a negative correlation between the delay in parenteral lipid introduction and weight gain up to day 28. In multivariate analyses, the association between the cumulative intakes of parenteral lipids and weight gain up to 28 days was independent of gestational age at birth, birth weight, sex, smallness for gestational age, and enteral intakes (regression coefficient: 0.19; 95% CI: 0.01-0.38) and, up to 36 weeks, independent of gestational age, birth weight, sex, smallness for gestational age and parenteral glucose and amino acids (0.16; 95% CI: 0.04-0.27). CONCLUSIONS: Parenteral lipids during the first week were positively associated with weight gain in extremely-low-birth-weight infants and could improve early nutritional support of preterm neonates.

Organisation and role of actin microfilaments during cellular growth and morphogenesis in the moss Physcomitrella patens

ABSTRACT The network of actin cytoskeleton is composed of actin filaments (F-actin) that are made by polymerisation of actin monomers and actin binding proteins. It is required for growth and morphogenesis of eukaryotic cells. The labelling of F-actin with constitutively expressed GFP-Talin (Kost et al., 1998) reveals the organisation of cellular actin networks in plants. Due to the lack of information on actin cytoskeleton through gametophytic development of the model moss plant Physcornitrella patens, stable transgenic lines overexpressing GFP-Talin were generated to detect F-actin structures. It is shown that the 35S promoter driven expression is not suitable for F-actin labelling in all cells. When it is replaced by the inducible heat-shock promoter Gmhsp17.3 from soybean, one hour mild heat stress at 37°C followed by recovery at 25°C is enough to induce efficient and transient labelling in all tissues without altering cellular morphology. The optimal observations of F-actin structures at different stages of moss development can be done between 12-18 hours after the induction. By using confocal microscopy, we demonstrate that stellated actin arrays were densely accumulated at the growing tip in regenerating protoplasts, apical protonemal cells and rhizoids and connected with a fine dispersed F-actin mesh. Following three-dimensional growth, the cortical star-like structures are widespread in the meristematic cells of developing bud and young gametophores. On the contrary, undulating networks of actin cables are found at the final stage of cell differentiation. During redifferentiation of mature leaf cells into protonemal filaments the rather stagnant web of actin cables is replaced by diffuse actin meshwork. In eukaryotes, nucleation of the actin monomers prior to their polymerization is driven by the seven-subunit ARP2/3 complex and formins. We cloned the gene encoding the ARP3 subunit of P. patens and generated arp3 mutants of the moss through gene disruption. The knockout of ARP3 affects the elongation of chloronemal cells and blocks further differentiation of caulonemal cells and rhizoids, and the gametophores are slightly stunted compared to wild-type. The arp mutants were created in the heat-shock inducible GFP-Talin strains allowing us to visualise a disorganised actin network and a lack of star-like actin cytoskeleton arrays. We conclude that ARP2/3 dependent nucleation of actin filaments is critical for the growth of filamentous cells, which in turn influences moss colonization. In complementation assays, the overexpression of Physcomitrella and Arab idopsis ARP3 genes in the moss arp3 mutant results in full recovery of wild type phenotype. In contrast the ARP3 subunit of fission yeast is not able to complement the moss arp3 mutant of moss indicating that regulation of the ARP2/3 dependent actin nucleation diverged in different kingdoms. RESUME Le réseau d'actine est composé de filaments de F-actine et d'un ensemble de protéines s'y attachant (Actin binding proteins). Le réseau d'actine est nécessaire à la croissance et à la morphogenèse de toutes les cellules eucaryotes. Chez les plantes, le marquage ainsi que l'étude de l'organisation du réseau d'actine ont été réalisés en utilisant une fusion GFP-Talin (Kost et al., 1998) exprimée sous le control d'un promoteur constitutif. Afin d'étudier les structures F-actine dans les cellules de Physcomitrella Patens et pour combler le manque d'information sur le développement des gamétophores, des lignées transgéniques stables surexprimant GFP-Talin ont été crées. Nous avons démontré que l'utilisation du promoteur 35S est inadéquate pour le marquage complet et homogène des filaments d'actine dans toutes les cellules de P. patens. Par contre, l'utilisation du promoteur inductible Gmhsp17.3 nous a permis de réaliser un marquage transitoire et général dans tous les tissus de la mousse. Une heure de choc thermique à 37°C suivis d'un temps de récupération de 12-18h à 25°C sont les conditions optimales (sans dommages cellulaires) pour l'observation des structures F-actine à différentes étapes de développement de la mousse. En utilisant la microscopie confocale, nous avons observé l'existence de structures F-actine accumulées en forme d'étoiles. Ces structures, qui sont liées au réseau de microfilaments d'actine, ont été observées dans les protoplastes en régénération, les cellules des protonema apicales ainsi que dans les rhizoïdes. En suivant la croissance tridimensionnelle, ces structures en étoiles ont été observées dans les cellules meristématiques des bourgeons et des jeunes gamétophores. Par contre, dans les cellules différentiées ces structures laissent place à des réseaux de câbles épais. Nous avons également remarqué que durant la redifferentiation des cellules foliaires le réseau de câbles de F-actine est remplacé par un réseau de F-actine diffus. Dans les cellules eucaryotes, la nucléation des filaments d'actirie précédant leur polymérisation est contrôlé par sept sous unités du complexe ARP2/3 et par des formines. Nous avons isolé le gène codant pour la sous unité ARP3 de P. patens et nous avons crée des mutants arp3 par intégration ciblée (Knockout). L'élongation des cellules chloronema est clairement affectée dans les mutants arp3. La différentiation des caulonemata et des rhizoïdes est bloquée et les gametophores sont légèrement plus courts comparé au type sauvage. A fin d'étudier l'organisation des filaments d'actines dans les mutants arp3, nous avons aussi réalisé un arp3-knockout dans la lignée Hsp-GFP-Talin. La nouvelle lignée générée nous a permis de visualiser une désorganisation du réseau d'actine et une absence complète de structures de F-actine accumulée en forme d'étoiles. Les résultats obtenus nous amènent à conclure que la nucléation (ARP2/3 dépendante) des filaments d'actine est indispensable à la croissance des cellules filamenteuses. Par conséquent, les filaments d'actine semblent avoir un rôle dans la colonisation des milieux par les mousses. Nous avons également procédé à des essais de complémentation du mutant arp3. La surexpression des gènes ARP3 de Physcomitrella et d'Arabidopsis dans les cellules du mutant arp3 rétabli complètement le phénotype WT. Par contre, le gène ARP3 des levures n'est pas suffisant pour complémenter la même mutation dans les cellules de mousses. Ce résultat démontre que les mécanismes de régulation de la nucléation des filaments d'actine (ARP2/3 dépendante) sont différents entre les différents groupes d'eucaryotes.

Atomic Force Microscopy Stiffness Tomography on Living Arabidopsis thaliana Cells Reveals the Mechanical Properties of Surface and Deep Cell-Wall Layers during Growth.

Cell-wall mechanical properties play a key role in the growth and the protection of plants. However, little is known about genuine wall mechanical properties and their growth-related dynamics at subcellular resolution and in living cells. Here, we used atomic force microscopy (AFM) stiffness tomography to explore stiffness distribution in the cell wall of suspension-cultured Arabidopsis thaliana as a model of primary, growing cell wall. For the first time that we know of, this new imaging technique was performed on living single cells of a higher plant, permitting monitoring of the stiffness distribution in cell-wall layers as a function of the depth and its evolution during the different growth phases. The mechanical measurements were correlated with changes in the composition of the cell wall, which were revealed by Fourier-transform infrared (FTIR) spectroscopy. In the beginning and end of cell growth, the average stiffness of the cell wall was low and the wall was mechanically homogenous, whereas in the exponential growth phase, the average wall stiffness increased, with increasing heterogeneity. In this phase, the difference between the superficial and deep wall stiffness was highest. FTIR spectra revealed a relative increase in the polysaccharide/lignin content.

Potato crop growth as affected by nitrogen and plant density

Growth and development variables and dry matter characteristics were studied for cultivar Snowden of potato (Solanum tuberosum L.) to evaluate nitrogen and plant density influence. Disregarding ending of season plant stress, the average number of actives haulms per plant was five and it was not affected by plant spacing. However, seasonal and final number of active haulms per plant were increased at 200 kg/ha of nitrogen. Maximum stem elongation was reached quickly with double density and had the tendency to keep constant at the highest and lowest nitrogen levels after 70 days after planting. Specific stem mass defined as mass per unit stem length was established as an indirect measure of stem thickness and load capacity. Specific leaf mass position in plant was higher at upper stem leaves, increased as plant density increased and did not vary markedly over time throughout the season. The rate of leaf appearance increased drastically due to more branching caused by high nitrogen level, and increased above ground dry matter per plant. Canopy growth and development influenced main tuber yield components. The number of active tubers per haulm decreased after 60 days after planting showing that tuberization is reversible. Tuber growth functions were established allowing the estimate of dry biomass partitioning coefficients for each plant organ.

Igneous layering, fractional crystallization and growth of granitic plutons: The Dolbel batholith in SW Niger

This study reassesses the development of compositional layering during the growth of granitic plutons, with emphasis on fractional crystallization and its interaction with both injection and inflation-related deformation. The Dolbel batholith (SW Niger) consists of 14, kilometre-sized plutons emplaced by pulsed magma inputs. Each pluton has a coarse-grained core and a peripheral layered series. Rocks consist of albite (An(<= 11)), K-feldspar (Or(96 99), Ab(1) (4)), quartz, edenite (X(Mg)=0337-0.55), augite (X(Mg)=0.65-0.72) and accessories (apatite, titanite and Fe-Ti-oxides). Whole-rock compositions are metaluminous, sodic (K(2)O/Na(2)O=0.49-0.62) and iron-rich [FeO(tot)/(FeO(tot)+MgO)=0.65-0.82]. The layering is present as size-graded and modally graded, sub-vertical, rhythmic units. Each unit is composed of three layers, which are, towards the interior: edenite +/- plagioclase (C(a/p)), edenite+plagioclase+augite+quartz (C(q)), and edenite+plagioclase+augite+quartz+K-feldspar (C(k)). All phases except quartz show zoned microstructures consisting of external intercumulus overgrowths, a central section showing oscillatory zoning and, in the case of amphibole and titanite, complexly zoned cores. Ba and Sr contents of feldspars decrease towards the rims. Plagioclase crystal size distributions are similar in all units, suggesting that each unit experienced a similar thermal history. Edenite, characteristic of the basal C(a/p) layer, is the earliest phase to crystallize. Microtextures and phase diagrams suggest that edenite cores may have been brought up with magma batches at the site of emplacement and mechanically segregated along the crystallized wall, whereas outer zones of the same crystals formed in situ. The subsequent C(q) layers correspond to cotectic compositions in the Qz-Ab-Or phase diagram at P(H2O)=5 kbar. Each rhythmic unit may therefore correspond to a magma batch and their repetition to crystallization of recurrent magma recharges. Microtextures and chemical variations in major phases allow four main crystallization stages to be distinguished: (1) open-system crystallization in a stirred magma during magma emplacement, involving dissolution and overgrowth (core of edenite and titanite crystals); (2) in situ fractional crystallization in boundary layers (C(a/p) and C(q) layers); (3) equilibrium `en masse' eutectic crystallization (C(k) layers); (4) compaction and crystallization of the interstitial liquid in a highly crystallized mush (e. g. feldspar intercumulus overgrowths). It is concluded that the formation of the layered series in the Dolbel plutons corresponds principally to in situ differentiation of successive magma batches. The variable thickness of the Ck layers and the microtextures show that crystallization of a rhythmic unit stops and it is compacted when a new magma batch is injected into the chamber. Therefore, assembly of pulsed magma injections and fractional crystallization are independent, but complementary, processes during pluton construction.

A downstream mediator in the growth repression limb of the jasmonate pathway.

Wounding plant tissues initiates large-scale changes in transcription coupled to growth arrest, allowing resource diversion for defense. These processes are mediated in large part by the potent lipid regulator jasmonic acid (JA). Genes selected from a list of wound-inducible transcripts regulated by the jasmonate pathway were overexpressed in Arabidopsis thaliana, and the transgenic plants were then assayed for sensitivity to methyl jasmonate (MeJA). When grown in the presence of MeJA, the roots of plants overexpressing a gene of unknown function were longer than those of wild-type plants. When transcript levels for this gene, which we named JASMONATE-ASSOCIATED1 (JAS1), were reduced by RNA interference, the plants showed increased sensitivity to MeJA and growth was inhibited. These gain- and loss-of-function assays suggest that this gene acts as a repressor of JA-inhibited growth. An alternative transcript from the gene encoding a second protein isoform with a longer C terminus failed to repress jasmonate sensitivity. This identified a conserved C-terminal sequence in JAS1 and related genes, all of which also contain Zim motifs and many of which are jasmonate-regulated. Both forms of JAS1 were found to localize to the nucleus in transient expression assays. Physiological tests of growth responses after wounding were consistent with the fact that JAS1 is a repressor of JA-regulated growth retardation.

An SH2 domain-containing 5' inositolphosphatase inhibits insulin-induced GLUT4 translocation and growth factor-induced actin filament rearrangement.

Tyrosine kinase receptors lead to rapid activation of phosphatidylinositol 3-kinase (PI3 kinase) and the subsequent formation of phosphatidylinositides (PtdIns) 3,4-P2 and PtdIns 3,4, 5-P3, which are thought to be involved in signaling for glucose transporter GLUT4 translocation, cytoskeletal rearrangement, and DNA synthesis. However, the specific role of each of these PtdIns in insulin and growth factor signaling is still mainly unknown. Therefore, we assessed, in the current study, the effect of SH2-containing inositol phosphatase (SHIP) expression on these biological effects. SHIP is a 5' phosphatase that decreases the intracellular levels of PtdIns 3,4,5-P3. Expression of SHIP after nuclear microinjection in 3T3-L1 adipocytes inhibited insulin-induced GLUT4 translocation by 100 +/- 21% (mean +/- the standard error) at submaximal (3 ng/ml) and 64 +/- 5% at maximal (10 ng/ml) insulin concentrations (P < 0.05 and P < 0.001, respectively). A catalytically inactive mutant of SHIP had no effect on insulin-induced GLUT4 translocation. Furthermore, SHIP also abolished GLUT4 translocation induced by a membrane-targeted catalytic subunit of PI3 kinase. In addition, insulin-, insulin-like growth factor I (IGF-I)-, and platelet-derived growth factor-induced cytoskeletal rearrangement, i.e., membrane ruffling, was significantly inhibited (78 +/- 10, 64 +/- 3, and 62 +/- 5%, respectively; P < 0.05 for all) in 3T3-L1 adipocytes. In a rat fibroblast cell line overexpressing the human insulin receptor (HIRc-B), SHIP inhibited membrane ruffling induced by insulin and IGF-I by 76 +/- 3% (P < 0.001) and 68 +/- 5% (P < 0.005), respectively. However, growth factor-induced stress fiber breakdown was not affected by SHIP expression. Finally, SHIP decreased significantly growth factor-induced mitogen-activated protein kinase activation and DNA synthesis. Expression of the catalytically inactive mutant had no effect on these cellular responses. In summary, our results show that expression of SHIP inhibits insulin-induced GLUT4 translocation, growth factor-induced membrane ruffling, and DNA synthesis, indicating that PtdIns 3,4,5-P3 is the key phospholipid product mediating these biological actions.

In vitro activity of gallium maltolate against Staphylococci in logarithmic, stationary, and biofilm growth phases: comparison of conventional and calorimetric susceptibility testing methods.

Ga(3+) is a semimetal element that competes for the iron-binding sites of transporters and enzymes. We investigated the activity of gallium maltolate (GaM), an organic gallium salt with high solubility, against laboratory and clinical strains of methicillin-susceptible Staphylococcus aureus (MSSA), methicillin-resistant S. aureus (MRSA), methicillin-susceptible Staphylococcus epidermidis (MSSE), and methicillin-resistant S. epidermidis (MRSE) in logarithmic or stationary phase and in biofilms. The MICs of GaM were higher for S. aureus (375 to 2000 microg/ml) than S. epidermidis (94 to 200 microg/ml). Minimal biofilm inhibitory concentrations were 3,000 to >or=6,000 microg/ml (S. aureus) and 94 to 3,000 microg/ml (S. epidermidis). In time-kill studies, GaM exhibited a slow and dose-dependent killing, with maximal action at 24 h against S. aureus of 1.9 log(10) CFU/ml (MSSA) and 3.3 log(10) CFU/ml (MRSA) at 3x MIC and 2.9 log(10) CFU/ml (MSSE) and 4.0 log(10) CFU/ml (MRSE) against S. epidermidis at 10x MIC. In calorimetric studies, growth-related heat production was inhibited by GaM at subinhibitory concentrations; and the minimal heat inhibition concentrations were 188 to 4,500 microg/ml (MSSA), 94 to 1,500 microg/ml (MRSA), and 94 to 375 microg/ml (MSSE and MRSE), which correlated well with the MICs. Thus, calorimetry was a fast, accurate, and simple method useful for investigation of antimicrobial activity at subinhibitory concentrations. In conclusion, GaM exhibited activity against staphylococci in different growth phases, including in stationary phase and biofilms, but high concentrations were required. These data support the potential topical use of GaM, including its use for the treatment of wound infections, MRSA decolonization, and coating of implants.

Analysis of variance of primary data on plant growth analysis

Plant growth analysis presents difficulties related to statistical comparison of growth rates, and the analysis of variance of primary data could guide the interpretation of results. The objective of this work was to evaluate the analysis of variance of data from distinct harvests of an experiment, focusing especially on the homogeneity of variances and the choice of an adequate ANOVA model. Data from five experiments covering different crops and growth conditions were used. From the total number of variables, 19% were originally homoscedastic, 60% became homoscedastic after logarithmic transformation, and 21% remained heteroscedastic after transformation. Data transformation did not affect the F test in one experiment, whereas in the other experiments transformation modified the F test usually reducing the number of significant effects. Even when transformation has not altered the F test, mean comparisons led to divergent interpretations. The mixed ANOVA model, considering harvest as a random effect, reduced the number of significant effects of every factor which had the F test modified by this model. Examples illustrated that analysis of variance of primary variables provides a tool for identifying significant differences in growth rates. The analysis of variance imposes restrictions to experimental design thereby eliminating some advantages of the functional growth analysis.

Genome-wide analysis of Sphingomonas wittichii RW1 behaviour during inoculation and growth in contaminated sand.

The efficacy of inoculation of single pure bacterial cultures into complex microbiomes, for example, in order to achieve increased pollutant degradation rates in contaminated material (that is, bioaugmentation), has been frustrated by insufficient knowledge on the behaviour of the inoculated bacteria under the specific abiotic and biotic boundary conditions. Here we present a comprehensive analysis of genome-wide gene expression of the bacterium Sphingomonas wittichii RW1 in contaminated non-sterile sand, compared with regular suspended batch growth in liquid culture. RW1 is a well-known bacterium capable of mineralizing dibenzodioxins and dibenzofurans. We tested the reactions of the cells both during the immediate transition phase from liquid culture to sand with or without dibenzofuran, as well as during growth and stationary phase in sand. Cells during transition show stationary phase characteristics, evidence for stress and for nutrient scavenging, and adjust their primary metabolism if they were not precultured on the same contaminant as found in the soil. Cells growing and surviving in sand degrade dibenzofuran but display a very different transcriptome signature as in liquid or in liquid culture exposed to chemicals inducing drought stress, and we obtain evidence for numerous 'soil-specific' expressed genes. Studies focusing on inoculation efficacy should test behaviour under conditions as closely as possible mimicking the intended microbiome conditions.