ELIXIR Germany (ELIXIR-DE) is the German National Node of ELIXIR Europe. By signing the ELIXIR Collaboration Agreement on 10 February 2020, the national node ELIXIR Germany is fully established. ELIXIR Germany is coordinated from Bielefeld University and is funded by the German government. The Administration Office of ELIXIR Germany is the central support entity for the German ELIXIR Node and for the Central Coordination Unit (CCU). ELIXIR Germany actively participates in the research activities of the ELIXIR platform, i. e. Data, Training, Compute, Interoperability, and Tools Platform. A remarkable contribution is highlighted by the involvement of the two databases, SILVA and BRENDA, in ELIXIR Data Platform as ELIXIR Core Data Resources. Within the Compute Platform, the Cloud of the German Network for Bioinformatics Infrastructure (de.NBI) has built connections to the European cloud infrastructures through its involvement in the EOSC-Life project and the adaptation of ELIXIR´s Authentication and Authorization Infrastructure (AAI) system. The members of ELIXIR Germany also make a decisive contribution in the current situation in COVID-19 research. The corona pandemic is a major challenge for our society and therefore requires special attention by the established scientific structures. It is important to advance molecular biological research of coronaviruses, especially of SARS-CoV-2, and to investigate both medical and epidemiological aspects of the infection process in COVID-19. These research areas generate large amounts of data requiring intensive bioinformatics analysis. Here, ELIXIR Germany provides a wide collection of analysis programs and the compute capacities of the network's own de.NBI cloud. For example, the GALAXY project provides workflows to analyze genomics, evolution and cheminformatics data related to COVID-19 and SARS-CoV-2. Both, analysis programs and compute capacities can be used free of charge by researchers in the life sciences. Overall, ELIXIR-DE channels efforts into the three pillars of ELIXIR´s COVID-19 response: 1. Connecting national COVID-19 data platforms to create federated European COVID-19 Data Spaces; 2. Fostering good data management to make COVID-19 data open, FAIR and reusable over the long term; 3. Providing open tools, workflows and computational resources to drive reproducible and collaborative science. Moreover, ELIXIR-DE reports all on-going and emerging community and national responses to the COVID-19 outbreak to ELIXIR Europe.

Pseudomonas pseudoalcaligenes CECT5344 tolerates cyanide and is also able to utilize cyanide and cyano-derivatives as a nitrogen source under alkaline conditions. The strain is considered as candidate for bioremediation of habitats contaminated with cyanide-containing liquid wastes. Information on the genome sequence of the strain CECT5344 became available previously. The P. pseudoalcaligenes CECT5344 genome was now resequenced by applying the single molecule, real-time (SMRT(®)) sequencing technique developed by Pacific Biosciences. The complete and finished genome sequence of the strain consists of a 4,696,984 bp chromosome featuring a GC-content of 62.34%. Comparative analyses between the new and previous versions of the P. pseudoalcaligenes CECT5344 genome sequence revealed additional regions in the new sequence that were missed in the older version. These additional regions mostly represent mobile genetic elements. Moreover, five additional genes predicted to play a role in sulfoxide reduction are present in the newly established genome sequence. The P. pseudoalcaligenes CECT5344 genome sequence is highly related to the genome sequences of different Pseudomonas mendocina strains. Approximately, 70% of all genes are shared between P. pseudoalcaligenes and P. mendocina. In contrast to P. mendocina, putative pathogenicity genes were not identified in the P. pseudoalcaligenes CECT5344 genome. P. pseudoalcaligenes CECT5344 possesses unique genes for nitrilases and mercury resistance proteins that are of importance for survival in habitats contaminated with cyano- and mercury compounds. As an additional feature of the SMRT sequencing technology, the methylome of P. pseudoalcaligenes was established. Six sequence motifs featuring methylated adenine residues (m6A) were identified in the genome. The genome encodes several methyltransferases, some of which may be considered for methylation of the m6A motifs identified. The complete genome sequence of the strain CECT5344 now provides the basis for exploitation of genetic features for biotechnological purposes.

A field study was conducted with genetically modified sinorhizobium meliloti strains L1 (RecA-) and L33 (RecA+), both tagged with the firefly luciferase luc gene as an identification marker. The strains' fate was studied over a time period of five years. Both strains were rapidly outcompeted for alfalfa nodulation by an indigenous population. In summary, this study demonstrates the usefulness of tagging bacteria designed for environmental releases by the firefly luciferase gene and the high resilience of soil bacteria to allow the establishment of foreign bacterial populations. This work was supported by grants of the German Federal Ministry of Education and Research (BMBF). We thank Penny Hirsch for valuable discussion concerning the preparation of the peat-based inoculants. The contribution of the Bayer-ische Staatsministerium fur Ernahrung, Landwirtschaft und Forsten for making available the field release site in Stras-smoos is gratefully acknowledged. We thank Rudolf Beck and the team of the Strassmoos experimental plant station for their excellent support during the field study.

The survival and vertical translocation of two isogenic, luciferase marker gene (luc)-tagged Sinorhizobum meliloti strains, L33 (RecA(+)) and L1 (RecA(-)) was studied under field conditions over a period of 2 years in a soil which was deficient in indigenous S, meliloti. Both strains were inoculated separately at the end of the growing season of 1994 onto replicate field lysimeters (diameter 32 cm) seeded with alfalfa (Medicago sativa). From an initial density of 10(6) cfu g(-1) soil in the A(p)-horizon (0-25 cm depth), populations of both strains declined during winter to 3 x 10(4) cfu g(-1) One year after the field release, a significantly increased titer of the RecA(+) strain was detected (P less than or equal to 0.05). Removal of the green parts of alfalfa from the lysimeters, 79 weeks after inoculation, resulted in a significant decline of the RecA- (2.3 x 10(3) cfu g(-1)) and a slight increase of the RecA(+) strain (9.0 x 10(3) cfu g(-1)). Throughout the whole monitoring period, marker gene-tagged cells were exclusively located in the A(p)-horizon and not below. No inoculated cells were detected in flow-through rain water (threshold of detection 10 cfu ml(-1)) even though each lysimeter was percolated with an average of 42.51 during this study. Single luciferase positive cells could be detected in the A(p)-horizons of non-inoculated lysimeters, which were located between the inoculated lysimeters using nodulation assays. Cultivation methods failed to detect these cells. The bioluminescent nodules were almost exclusively caused by strain L33 and not by L1, indicating that the RecA(-) strain was less competitive in alfalfa nodulation. Soil chemical properties and quantities of microbial populations, culturable on four different growth media, were not affected by the S. meliloti inoculations. This study demonstrates the usefulness of small scale lysimeter field releases to assess the performance and potential ecological effects of genetically modified bacterial inoculants, (C) 2000 Elsevier Science Ltd. All rights reserved.

The enterobacterial repetitive intergenic consensus (ERIC)-PCR method was employed to generate genomic amplification products of Sinorhizobium meliloti strain 2011. Eleven distinctive PCR fragments obtained in PCR reactions by using the ERIC2 primer were cloned and their partial or complete nucleotide sequences established. DNA sequences that extended past the ERIC2 primer region were not conserved among the 11 PCR fragments and showed no sequence similarity to the enterobacterial ERIC consensus sequence. Thus, repetitive ERIC or ERIC-like sequences seem not to be an integral part of the S. meliloti genome. An amplification product of S. meliloti 2011 was identified which was present in S. meliloti strains but absent in other rhizobial species. Based on the nucleotide sequence information, a pair of PCR primers was designed and used for PCR amplification of sequences of S. meliloti laboratory strains 2011, L5–30, AK631 and 102F34. Nucleotide sequence analysis of the amplification products revealed a 100% DNA sequence conservation. Database searches showed that the DNA fragment putatively encodes the C-terminal part of a protein displaying similarity to 2-hydroxyacid dehydrogenases of various organisms. The newly designed PCR primers should be useful for the rapid identification of S. meliloti isolates.