Journal: Environmental Microbiology

Abbreviation

Environ Microbiol,

Publisher

Wiley-Blackwell

Journal Volumes

ISSN

1462-2912
1462-2920

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Publications1 - 10 of 72
  • Effects of model root exudates on structure and activity of a soil diazotroph community
    Item type: Journal Article
    Bürgmann, Helmut; Meier, Stefan; Bunge, Michael; et al. (2005)
    Environmental Microbiology
  • Low-ammonia niche of ammonia-oxidizing archaea in rotating biological contactors of a municipal wastewater treatment plant
    Item type: Journal Article
    Sauder, Laura; Peterse, Francien; Schouten, Stefan; et al. (2012)
    Environmental Microbiology
  • The mechanics of bacterial cluster formation on plant leaf surfaces as revealed by bioreporter technology
    Item type: Journal Article
    Tecon, Robin; Leveau, Johan H.J. (2012)
    Environmental Microbiology
  • The secret life of plant-beneficial rhizosphere bacteria: insects as alternative hosts
    Item type: Review Article
    Pronk, Lotte J.U.; Bakker, Peter A.H.M.; Keel, Christoph; et al. (2022)
    Environmental Microbiology
    Root-colonizing bacteria have been intensively investigated for their intimate relationship with plants and their manifold plant-beneficial activities. They can inhibit growth and activity of pathogens or induce defence responses. In recent years, evidence has emerged that several plant-beneficial rhizosphere bacteria do not only associate with plants but also with insects. Their relationships with insects range from pathogenic to mutualistic and some rhizobacteria can use insects as vectors for dispersal to new host plants. Thus, the interactions of these bacteria with their environment are even more complex than previously thought and can extend far beyond the rhizosphere. The discovery of this secret life of rhizobacteria represents an exciting new field of research that should link the fields of plant-microbe and insect-microbe interactions. In this review, we provide examples of plant-beneficial rhizosphere bacteria that use insects as alternative hosts, and of potentially rhizosphere-competent insect symbionts. We discuss the bacterial traits that may enable a host-switch between plants and insects and further set the multi-host lifestyle of rhizobacteria into an evolutionary and ecological context. Finally, we identify important open research questions and discuss perspectives on the use of these rhizobacteria in agriculture.
  • Regulation of lactate metabolism in the acetogenic bacterium Acetobacterium woodii
    Item type: Journal Article
    Schölmerich, Marie; Katsyv, Alexander; Sung, Woung; et al. (2018)
    Environmental Microbiology
    Acetogenic bacteria compete in an energy-limited environment by coupling different metabolic routes to their central metabolism of CO2 fixation. The underlying regulatory mechanisms are often still not understood. In this work, we analysed how lactate metabolism is regulated in the model acetogen Acetobacterium woodii. Construction of a ΔlctCDEF mutant and growth analyses demonstrated that the genes are essential for growth on lactate. Subsequent bridging PCR and quantitative PCR analyses revealed that the lctBCDEF genes form an operon that was expressed only during lactate metabolism. The lctA gene was cloned, expressed in Escherichia coli and purified. LctA bound to the intergenic DNA region between lctA and the lct operon in electromobility shift assays, and binding was revoked in the presence of lactate. Further restriction site protection analyses consolidated the lactate-dependent binding of LctA and identified the binding site within the DNA. Cells grew mixotrophically on lactate and another energy source and showed no diauxic growth. From these data, we conclude that the catabolic lactate metabolism is encoded by the lct operon and its expression is negatively regulated by the DNA-binding repressor LctA.
  • Diversity of archaea and niche preferences among putative ammonia‐oxidizing Nitrososphaeria dominating across European arable soils
    Item type: Journal Article
    Saghaï, Aurélien; Saghaï, Aurélien; Banjeree, Samiran; et al. (2022)
    Environmental Microbiology
    Archaeal communities in arable soils are dominated by Nitrososphaeria, a class within Thaumarchaeota comprising all known ammonia-oxidizing archaea (AOA). AOA are key players in the nitrogen cycle and defining their niche specialization can help predicting effects of environmental change on these communities. However, hierarchical effects of environmental filters on AOA and the delineation of niche preferences of nitrososphaerial lineages remain poorly understood. We used phylogenetic information at fine scale and machine learning approaches to identify climatic, edaphic and geomorphological drivers of Nitrososphaeria and other archaea along a 3000 km European gradient. Only limited insights into the ecology of the low-abundant archaeal classes could be inferred, but our analyses underlined the multifactorial nature of niche differentiation within Nitrososphaeria. Mean annual temperature, C:N ratio and pH were the best predictors of their diversity, evenness and distribution. Thresholds in the predictions could be defined for C:N ratio and cation exchange capacity. Furthermore, multiple, independent and recent specializations to soil pH were detected in the Nitrososphaeria phylogeny. The coexistence of widespread ecophysiological differences between closely related soil Nitrososphaeria highlights that their ecology is best studied at fine phylogenetic scale.
  • Cloning of Baeyer-Villiger monooxygenases from Comamonas, Xanthobacter and Rhodococcus using polymerase chain reaction with highly degenerate primers
    Item type: Journal Article
    Beilen, J. B. van; Mourlane, F.; Seeger, M. A.; et al. (2003)
    Environmental Microbiology
    To clone novel type 1 Baeyer‐Villiger monooxygenase (BVMO) genes, we isolated or collected 25 bacterial strains able to grow on alicyclic compounds. Twelve of the bacterial strains yielded polymerase chain reaction (PCR) fragments with highly degenerate primers based on the sequences of known and putative BVMOs. All these fragments were found to encode peptides homologous to published BVMO sequences. The complete BVMO genes and flanking DNA were cloned from a Comamonas, a Xanthobacter and a Rhodococcus strain using the PCR fragments as probes. BVMO genes cloned from the first two strains could be expressed to high levels in Escherichia coli using standard expression vectors, and the recombinants converted cyclopentanone and cyclohexanone to the corresponding lactones. The Rhodococcus BVMO, a putative steroid monooxygenase, could be expressed after modification of the N‐terminal sequence. However, recombinants expressing this protein did not show activity towards progesterone. An esterase homologue located directly upstream of the Xanthobacter BVMO gene and a dehydrogenase homologue encoded directly downstream of the Comamonas sp. NCIMB 9872 BVMO gene were also expressed in E. coli and shown to specify lactone hydrolase and cyclohexanol dehydrogenase activity respectively.
  • NifA is required for maximal expression of denitrification genes in Bradyrhizobium japonicum
    Item type: Journal Article
    Bueno, Emilio; Mesa, Socorro; Sánchez, Cristina; et al. (2009)
    Environmental Microbiology
  • Generality of associations between biological richness and the rates of metabolic processes across microbial communities
    Item type: Journal Article
    Patsch, Deborah; van Vliet, Simon; Marcantini, Lorenzo Garbani; et al. (2018)
    Environmental Microbiology
  • Metabolite profiling and peptidoglycan analysis of transient cell wall-deficient bacteria in a new Escherichia coli model system
    Item type: Journal Article
    Cambré, Alexander; Zimmermann, Michael; Sauer, Uwe; et al. (2015)
    Environmental Microbiology
Publications1 - 10 of 72