TY - JOUR AB - Modulating the soil microbiome by applying microbial inoculants has gained increasing attention as eco-friendly option to improve soil disease suppressiveness. Currently, studies unraveling the interplay of inoculants, root-associated microbiome, and plant response are lacking for apple trees. Here, we provide insights into the ability of Bacillus velezensis FZB42 or Pseudomonas sp. RU47 to colonize apple root-associated microhabitats and to modulate their microbiome. We applied the two strains to apple plants grown in soils from the same site either affected by apple replant disease (ARD) or not (grass), screened their establishment by selective plating, and measured phytoalexins in roots 3, 16, and 28 days post inoculation (dpi). Sequencing of 16S rRNA gene and ITS fragments amplified from DNA extracted 28 dpi from different microhabitat samples revealed significant inoculation effects on fungal β-diversity in root-affected soil and rhizoplane. Interestingly, only in ARD soil, most abundant bacterial amplicon sequence variants (ASVs) changed significantly in relative abundance. Relative abundances of ASVs affiliated with Enterobacteriaceae were higher in rhizoplane of apple grown in ARD soil and reduced by both inoculants. Bacterial communities in the root endosphere were not affected by the inoculants but their presence was indicated. Interestingly and previously unobserved, apple plants responded to the inoculants with increased phytoalexin content in roots, more pronounced in grass than ARD soil. Altogether, our results indicate that FZB42 and RU47 were rhizosphere competent, modulated the root-associated microbiome, and were perceived by the apple plants, which could make them interesting candidates for an eco-friendly mitigation strategy of ARD. KEY POINTS: • Rhizosphere competent inoculants modulated the microbiome (mainly fungi) • Inoculants reduced relative abundance of Enterobacteriaceae in the ARD rhizoplane • Inoculants increased phytoalexin content in roots, stronger in grass than ARD soil. AU - Hauschild, K.* AU - Orth, N.* AU - Liu, B.* AU - Giongo, A.* AU - Gschwendtner, S. AU - Beerhues, L.* AU - Schloter, M. AU - Vetterlein, D.* AU - Winkelmann, T.* AU - Smalla, K.* C1 - 70768 C2 - 55886 CY - One New York Plaza, Suite 4600, New York, Ny, United States TI - Rhizosphere competent inoculants modulate the apple root-associated microbiome and plant phytoalexins. JO - Appl. Microbiol. Biotechnol. VL - 108 IS - 1 PB - Springer PY - 2024 SN - 0175-7598 ER - TY - JOUR AB - The availability of bioresources is a precondition for life science research, medical applications, and diagnostics, but requires a dedicated quality management to guarantee reliable and safe storage. Anecdotal reports of bacterial isolates and sample contamination indicate that organisms may persist in liquid nitrogen (LN) storage tanks. To evaluate the safety status of cryocollections, we systematically screened organisms in the LN phase and in ice layers covering inner surfaces of storage tanks maintained in different biobanking facilities. We applied a culture-independent approach combining cell detection by epifluorescence microscopy with the amplification of group-specific marker genes and high-throughput sequencing of bacterial ribosomal genes. In the LN phase, neither cells nor bacterial 16S rRNA gene copy numbers were detectable (detection limit, 10(2) cells per ml, 10(3) gene copies per ml). In several cases, small numbers of bacteria of up to 10(4) cells per ml and up to 10(6) gene copies per ml, as well as Mycoplasma, or fungi were detected in the ice phase formed underneath the lids or accumulated at the bottom. The bacteria most likely originated from the stored materials themselves (Elizabethingia, Janthibacterium), the technical environment (Pseudomonas, Acinetobacter, Methylobacterium), or the human microbiome (Bacteroides, Streptococcus, Staphylococcus). In single cases, bacteria, Mycoplasma, fungi, and human cells were detected in the debris at the bottom of the storage tanks. In conclusion, the limited microbial load of the ice phase and in the debris of storage tanks can be effectively avoided by minimizing ice formation and by employing hermetically sealed sample containers. AU - Bajerski, F.* AU - Bürger, A. AU - Glasmacher, B.* AU - Keller, E.R.J.* AU - Müller, K.* AU - Mühldorfer, K.* AU - Nagel, M.* AU - Rüdel, H.* AU - Müller, T.* AU - Schenkel, J.* AU - Overmann, J.* C1 - 57604 C2 - 47858 CY - 233 Spring St, New York, Ny 10013 Usa SP - 131-144 TI - Factors determining microbial colonization of liquid nitrogen storage tanks used for archiving biological samples. JO - Appl. Microbiol. Biotechnol. VL - 104 IS - 1 PB - Springer PY - 2020 SN - 0175-7598 ER - TY - JOUR AB - The fungus Fusarium fujikuroi causes "bakanae" disease of rice due to its ability to produce gibberellins (GAs), a family of plant hormones. Recent genome sequencing revealed the genetic capacity for the biosynthesis of 46 additional secondary metabolites besides the industrially produced GAs. Among them are the pigments bikaverin and fusarubins, as well as mycotoxins, such as fumonisins, fusarin C, beauvericin, and fusaric acid. However, half of the potential secondary metabolite gene clusters are silent. In recent years, it has been shown that the fungal specific velvet complex is involved in global regulation of secondary metabolism in several filamentous fungi. We have previously shown that deletion of the three components of the F. fujikuroi velvet complex, vel1, vel2, and lae1, almost totally abolished biosynthesis of GAs, fumonisins and fusarin C. Here, we present a deeper insight into the genome-wide regulatory impact of Lae1 on secondary metabolism. Over-expression of lae1 resulted in de-repression of GA biosynthetic genes under otherwise repressing high nitrogen conditions demonstrating that the nitrogen repression is overcome. In addition, over-expression of one of five tested histone acetyltransferase genes, HAT1, was capable of returning GA gene expression and GA production to the GA-deficient Δlae1 mutant. Deletion and over-expression of HAT1 in the wild type resulted in downregulation and upregulation of GA gene expression, respectively, indicating that HAT1 together with Lae1 plays an essential role in the regulation of GA biosynthesis. AU - Niehaus, E.M.* AU - Rindermann, L.* AU - Janevska, S.* AU - Münsterkötter, M. AU - Güldener, U.* AU - Tudzynski, B.* C1 - 52238 C2 - 43882 CY - New York SP - 279–295 TI - Analysis of the global regulator Lae1 uncovers a connection between Lae1 and the histone acetyltransferase HAT1 in Fusarium fujikuroi. JO - Appl. Microbiol. Biotechnol. VL - 102 IS - 1 PB - Springer PY - 2017 SN - 0175-7598 ER - TY - JOUR AB - Green technologies are attracting increasing attention in industrial chemistry where enzymatic reactions can replace dangerous and environmentally unfriendly chemical processes. In situ enzymatic synthesis of peroxycarboxylic acid is an attractive alternative for several industrial applications although concentrated H2O2 can denature the biocatalyst, limiting its usefulness. Herein, we report the structure-guided engineering of the Pyrobaculum calidifontis esterase (PestE) substrate binding site to increase its stability and perhydrolysis activity. The L89R/L40A PestE mutant showed better tolerance toward concentrated H2O2 compared with wild-type PestE, and retained over 72% of its initial activity after 24-h incubation with 2 M H2O2. Surprisingly, the half-life (t1/2, 80 °C) of PestE increased from 28 to 54 h. The kcat/Km values of the mutant increased 21- and 3.4-fold toward pentanoic acid and H2O2, respectively. This work shows how protein engineering can be used to enhance the H2O2 resistance and catalytic efficiency of an enzyme. AU - Zhou, P.* AU - Lan, D.* AU - Popowicz, G.M. AU - Wang, X.* AU - Yang, B.* AU - Wang, Y.* C1 - 51242 C2 - 43083 SP - 5689-5697 TI - Enhancing H2O2 resistance of an esterase from Pyrobaculum calidifontis by structure-guided engineering of the substrate binding site. JO - Appl. Microbiol. Biotechnol. VL - 101 PY - 2017 SN - 0175-7598 ER - TY - JOUR AB - The rice pathogenic fungus Fusarium fujikuroi is known to produce a large variety of secondary metabolites. Besides the gibberellins, causing the bakanae effect in infected rice seedlings, the fungus produces several mycotoxins and pigments. Among the 47 putative secondary metabolite gene clusters identified in the genome of F. fujikuroi, the fumonisin gene cluster (FUM) shows very high homology to the FUM cluster of the main fumonisin producer Fusarium verticillioides, a pathogen of maize. Despite the high level of cluster gene conservation, total fumonisin FB1 and FB2 levels (FBx) produced by F. fujikuroi were only 1–10 % compared to F. verticillioides under inducing conditions. Nitrogen repression was found to be relevant for wild-type strains of both species. However, addition of germinated maize kernels activated the FBx production only in F. verticillioides, reflecting the different host specificity of both wild-type strains. Over-expression of the pathway-specific transcription factor Fum21 in F. fujikuroi strongly activated the FUM cluster genes leading to 1000-fold elevated FBx levels. To gain further insights into the nitrogen metabolite repression of FBx biosynthesis, we studied the impact of the global nitrogen regulators AreA and AreB and demonstrated that both GATA-type transcription factors are essential for full activation of the FUM gene cluster. Loss of one of them obstructs the pathway-specific transcription factor Fum21 to fully activate expression of FUM cluster genes. AU - Rösler, S.M.* AU - Sieber, C.M.K. AU - Humpf, H.U.* AU - Tudzynski, B.* C1 - 48155 C2 - 39989 CY - New York SP - 5869-5882 TI - Interplay between pathway-specific and global regulation of the fumonisin gene cluster in the rice pathogen Fusarium fujikuroi. JO - Appl. Microbiol. Biotechnol. VL - 100 IS - 13 PB - Springer PY - 2016 SN - 0175-7598 ER - TY - JOUR AB - Slow sand filtration (SSF) is an effective low-tech water treatment method for pathogen and particle removal. Yet despite its application for centuries, it has been uncertain to which extent pathogenic microbes are removed by mechanical filtration or due to ecological interactions such as grazing and competition for nutrients. In this study, we quantified the removal of bacterial faecal indicators, Escherichia coli and Enterococcus faecalis, from secondary effluent of a wastewater treatment plant and analysed the microbial community composition in compartments of laboratory model SSF columns. The columns were packed with different sand grain sizes and eliminated 1.6-2.3 log units of faecal indicators, which translated into effluents of bathing water quality according to the EU directive (<500 colony forming units of E. coli per 100 ml) for columns with small grain size. Most of that removal occurred in the upper filter area, the Schmutzdecke. Within that same zone, total bacterial numbers increased however, thus suggesting a specific elimination of the faecal indicators. The analysis of the microbial communities also revealed that some taxa were removed more from the wastewater than others. These results accentuate the contribution of biological mechanisms to water purification in SSF. AU - Pfannes, K. AU - Langenbach, K.M.* AU - Pilloni, G. AU - Stührmann, T. AU - Euringer, K. AU - Lueders, T. AU - Neu, T.R.* AU - Müller, J.A.* AU - Kästner, M.* AU - Meckenstock, R.U. C1 - 46573 C2 - 37705 SP - 10323-10332 TI - Selective elimination of bacterial faecal indicators in the Schmutzdecke of slow sand filtration columns. JO - Appl. Microbiol. Biotechnol. VL - 99 IS - 23 PY - 2015 SN - 0175-7598 ER - TY - JOUR AB - Sulfadiazine (SDZ) is an antibiotic frequently administered to livestock, and it alters microbial communities when entering soils with animal manure, but understanding the interactions of these effects to the prevailing climatic regime has eluded researchers. A climatic factor that strongly controls microbial activity is soil moisture. Here, we hypothesized that the effects of SDZ on soil microbial communities will be modulated depending on the soil moisture conditions. To test this hypothesis, we performed a 49-day fully controlled climate chamber pot experiments with soil grown with Dactylis glomerata (L.). Manure-amended pots without or with SDZ contamination were incubated under a dynamic moisture regime (DMR) with repeated drying and rewetting changes of >20 % maximum water holding capacity (WHCmax) in comparison to a control moisture regime (CMR) at an average soil moisture of 38 % WHCmax. We then monitored changes in SDZ concentration as well as in the phenotypic phospholipid fatty acid and genotypic 16S rRNA gene fragment patterns of the microbial community after 7, 20, 27, 34, and 49 days of incubation. The results showed that strongly changing water supply made SDZ accessible to mild extraction in the short term. As a result, and despite rather small SDZ effects on community structures, the PLFA-derived microbial biomass was suppressed in the SDZ-contaminated DMR soils relative to the CMR ones, indicating that dynamic moisture changes accelerate the susceptibility of the soil microbial community to antibiotics. AU - Reichel, R.* AU - Radl, V. AU - Rosendahl, I.* AU - Albert, A. AU - Amelung, W.* AU - Schloter, M. AU - Thiele-Bruhn, S.* C1 - 31122 C2 - 34130 CY - New York SP - 6487-6495 TI - Soil microbial community responses to antibiotic-contaminated manure under different soil moisture regimes. JO - Appl. Microbiol. Biotechnol. VL - 89 IS - 14 PB - Springer PY - 2014 SN - 0175-7598 ER - TY - JOUR AB - The plant microbial fuel cell (PMFC) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. Analysis and localisation of the microbial community is necessary for gaining insight into the competition for electron donor in a PMFC. This paper characterises the anode-rhizosphere bacterial community of a Glyceria maxima (reed mannagrass) PMFC. Electrochemically active bacteria (EAB) were located on the root surfaces, but they were more abundant colonising the graphite granular electrode. Anaerobic cellulolytic bacteria dominated the area where most of the EAB were found, indicating that the current was probably generated via the hydrolysis of cellulose. Due to the presence of oxygen and nitrate, short-chain fatty acid-utilising denitrifiers were the major competitors for the electron donor. Acetate-utilising methanogens played a minor role in the competition for electron donor, probably due to the availability of graphite granules as electron acceptors. AU - Timmers, R.A.* AU - Rothballer, M. AU - Strik, D.P.* AU - Engel, M. AU - Schulz, S. AU - Schloter, M. AU - Hartmann, A. AU - Hamelers, B.* AU - Buisman, C.* C1 - 7302 C2 - 29663 SP - 537-548 TI - Microbial community structure elucidates performance of Glyceria maxima plant microbial fuel cell. JO - Appl. Microbiol. Biotechnol. VL - 94 IS - 2 PB - Springer PY - 2012 SN - 0175-7598 ER - TY - JOUR AB - Production of lactic acid using Lactobacillus delbrueckii NRRL B445 recently renamed L. rhamnosus was studied in continuously recycled packed reactors at pH 6.3 and 42° C. Four inert adsorbent supports were used for immobilization: Raschig rings of sintered glass (Schott, FRG), beads of sintered glass (Schott), beads of porous glass (Poraver; Dennert, FRG) and irregular ceramic particles (Otto Feuerfest, FRG). The best support was found to be the beads of sintered glass, yielding the highest volumetric lactic acid productivity. Zeta potentials of L. rhamnosus showed the cells to be negatively charged at all pHs studied, the charge becoming less negative with increasing ionic strength. The surface charge did not control adhesion. A comparison between the immobilization carried out in batch and continuous tests with the different supports demonstrated that extrapolation from batch adsorption curves to continuous operation can introduce large errors. The effect of dilution rate was also stidied: a saturation concentration of adsorbed cells was achieved at all dilution rates, i.e., the immobilized cell component was almost invariant. Different diameters of Poraver beads were tested; clear evidence for mass transfer limitation was shown. Finally, the effects of pH and substrate concentration under immobilization were evaluated. The results indicate that pHs above or below the optimum for suspended cell systems can be used in the immobilized reactor while maintaining lactic acid productivity. To simplify downstream processing by keeping the glucose concentration close to zero in the effluent, the glucose concentration in the feed has to be chosen in conjunction with the dilution rate. AU - Gonçalves, L.M.D.* AU - Barreto, M.T.O.* AU - Xavier, A.M.R.B.* AU - Carrondo, M.J.T.* AU - Klein, J.D. C1 - 40608 C2 - 38761 SP - 305-311 TI - Inert supports for lactic acid fermentation -a technological assessment. JO - Appl. Microbiol. Biotechnol. VL - 38 IS - 3 PY - 1992 SN - 0175-7598 ER -