The second messenger cyclic diguanylate (c-di-GMP) is ubiquitously used by bacteria to modulate and shift between different phenotypes including motility, biofilm formation and virulence. Here we show that c-di-GMP-associated genes are widespread on plasmids and that enzymes that synthesize or degrade c-di-GMP are preferentially encoded on transmissible plasmids. Additionally, expression of enzymes that synthesize c-di-GMP was found to increase both biofilm formation and, interestingly, conjugative plasmid transfer rates.
Although bacteriophages are central entities in bacterial ecology and population dynamics, there is currently no literature on the genomes of bacteriophages isolated from groundwater. Using a collection of bacterial isolates from an aquifer as hosts, this study isolated, sequenced and characterised two bacteriophages native to the groundwater reservoir. Host phylogenetic analyses revealed that the phages targeted B. mycoides and a novel Pseudomonas species. these results suggest that both bacteriophages represent new genera, highlighting that groundwater reservoirs, and probably other subsurface environments as well, are underexplored biotopes in terms of the presence and ecology of bacteriophages. Despite metagenomics revealing that groundwater reservoirs harbour complex bacterial communities that are closely associated with biogeochemical cycling, much remains uncharted about their microbial ecology 1. In this context, it could be argued that bacteriophages (phages) have been studied to an even lesser extent, but they are generally considered to play a fundamental role in shaping bacterial communities and consequently influencing biogeochemical cycling 2, 3. While viruses (including phages) only constitute 0.04% of the earth's biomass 4 , they are widely regarded to constitute the largest and most diverse family of biological entities 5. Thus, mapping out their taxonomy, distribution and ecological role is a daunting task. Currently, there are no genome sequences of phages, isolated from groundwater systems, despite descriptions of phage abundances and viromes in these systems 6,7. This study isolated, sequenced and characterised two novel phages from a groundwater reservoir. To the authors' knowledge, this is the first report on groundwater phages that includes their sequenced genome and phylogenomic affiliation. The aim of the present study was to describe the first isolated groundwater bacteriophages that target actual bacterial isolates from the groundwater reservoir through isolation, genome sequencing, bioinformatics and protein characterisation. Predator-prey pairs are of relevance not only in the study of environmental microbiology, including the food webs of groundwater aquifers, but also in the context of bioaugmentation for purification of contaminated groundwater, where knowledge of indigenous enemies is crucial to the survival of introduced degrader bacteria. Results and discussion Phage isolation and phage host identification. Using a collection of natural bacterial groundwater isolates as hosts, two phages-Anath (Genbank accession MG983742.1) and Lana (Genbank accession MK473373.1)-were successfully obtained and their hosts identified as Bacillus mycoides and Pseudomonas sp., respectively, by means of the publicly available online tool for strain identification Type (Strain) Genome Server (TYGS) (https ://www.tygs.dsmz.de) 8. Besides being the first sequenced groundwater phages, this is also the
6As one of the only described degraders of the recalcitrant metabolite 2,6-dichlorobenzamide (BAM) of the 7 pesticide dichlobenil, Aminobacter sp. MSH1 has been intensively studied for its characteristics with regards 8 to physiology and its use in bioremediation. Two plasmid sequences from strain MSH1 have previously been 9 published, while the remaining genome sequence has been left uninvestigated. We here present the 10
Aminobacter sp. MSH1 (CIP 110285) can use the pesticide dichlobenil and its recalcitrant transformation product, 2,6-dichlorobenzamide (BAM), as sole source of carbon, nitrogen, and energy. The concentration of BAM in groundwater often exceeds the threshold limit for drinking water, requiring additional treatment in drinking water treatment plants or closure of the affected abstraction wells. Biological treatment with MSH1 is considered a potential sustainable alternative to remediate BAM-contamination in drinking water production. We present the complete genome of MSH1, which was determined independently in two institutes at Aarhus University and KU Leuven. Divergences were observed between the two genomes, i.e. one of them lacked four plasmids compared to the other. Besides the circular chromosome and the two previously described plasmids involved in BAM catabolism, pBAM1 and pBAM2, the genome of MSH1 contained two megaplasmids and three smaller plasmids. The MSH1 substrain from KU Leuven showed a reduced genome lacking a megaplasmid and three smaller plasmids and was designated substrain MK1, whereas the Aarhus variant with all plasmids was designated substrain DK1. A plasmid stability experiment indicate that substrain DK1 may have a polyploid chromosome when growing in R2B medium with more chromosomes than plasmids per cell. Finally, strain MSH1 is reassigned as Aminobacter niigataensis MSH1.
Aminobacter sp. MSH1 (CIP 110285) can use the pesticide dichlobenil and its transformation product, the recalcitrant groundwater micropollutant, 2,6-dichlorobenzamide (BAM) as sole source of carbon, nitrogen, and energy. The concentration of BAM in groundwater often exceeds the threshold limit for drinking water, resulting in the use of additional treatment in drinking water treatment plants (DWTPs) or closure of the affected abstraction wells. Biological treatment with MSH1 is considered a potential sustainable alternative to remediate BAM-contamination in drinking water production. Combining Illumina and Nanopore sequencing, we here present the complete genome of MSH1, which was determined independently in two different laboratories. Unexpectedly, divergences were observed between the two genomes, i.e. one of them lacked four plasmids compared to the other. Besides the circular chromosome and the two previously described plasmids involved in BAM catabolism pBAM1 (41 kb) and pBAM2 (54 kb), we observe that the genome of MSH1 contains two megaplasmids pUSP1 (367 kb) and pUSP2 (366 kb) and three smaller plasmids pUSP3 (97 kb), pUSP4 (64 kb), and pUSP5 (32 kb). The MSH1 substrain from KU Leuven showed a reduced genome lacking plasmids pUSP2 and the three smaller plasmids and was designated substrain MK1, whereas the variant with all plasmids 60 was designated as substrain DK1. Results of a plasmid stability experiment, indicate that strain MSH1 may have a polyploid chromosome when growing in R2B medium with more chromosomes than plasmids per cell. Based on phylogenetic analyses, strain MSH1 is reassigned as Aminobacter niigataensis MSH1.
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