Potential Activity of Subglacial Microbiota Transported to Anoxic River Delta Sediments

The Watson River drains a portion of the SW Greenland ice sheet, transporting microbial communities from subglacial environments to a delta at the head of Søndre Strømfjord. This study investigates the potential activity and community shifts of glacial microbiota deposited and buried under layers of sediments within the river delta. A long-term (12-month) incubation experiment was established using Watson River delta sediment under anaerobic conditions, with and without CO2/H2 enrichment. Within CO2/H2-amended incubations, sulphate depletion and a shift in the microbial community to a 52% predominance of Desulfosporosinus meridiei by day 371 provides evidence for sulphate reduction. We found evidence of methanogenesis in CO2/H2-amended incubations within the first 5 months, with production rates of ~4 pmol g−1 d−1, which was likely performed by methanogenic Methanomicrobiales- and Methanosarcinales-related organisms. Later, a reduction in methane was observed to be paired with the depletion of sulphate, and we hypothesise that sulphate reduction out competed hydrogenotrophic methanogenesis. The structure and diversity of the original CO2/H2-amended incubation communities changed dramatically with a major shift in predominant community members and a decline in diversity and cell abundance. These results highlight the need for further investigations into the fate of subglacial microbiota within downstream environments

Upstream freshwater and terrestrial sources are differentially reflected in the bacterial community structure along a small Arctic river and its estuary

Glacier melting and altered precipitation patterns influence Arctic freshwater and coastal ecosystems. Arctic rivers are central to Arctic water ecosystems by linking glacier meltwaters and precipitation with the ocean through transport of particulate matter and microorganisms. However, the impact of different water sources on the microbial communities in Arctic rivers and estuaries remains unknown. In this study we used 16S rRNA gene amplicon sequencing to assess a small river and its estuary on the Disko Island, West Greenland (69°N). Samples were taken in August when there is maximum precipitation and temperatures are high in the Disko Bay area. We describe the bacterial community through a river into the estuary, including communities originating in a glacier and a proglacial lake. Our results show that water from the glacier and lake transports distinct communities into the river in terms of diversity and community composition. Bacteria of terrestrial origin were among the dominating OTUs in the main river, while the glacier and lake supplied the river with water containing fewer terrestrial organisms. Also, more psychrophilic taxa were found in the community supplied by the lake. At the river mouth, the presence of dominant bacterial taxa from the lake and glacier was unnoticeable, but these taxa increased their abundances again further into the estuary. On average 23% of the estuary community consisted of indicator OTUs from different sites along the river. Environmental variables showed only weak correlations with community composition, suggesting that hydrology largely influences the observed patterns

Exploring the Remarkable Diversity of Culturable <i>Escherichia coli</i> Phages in the Danish Wastewater Environment

Phages drive bacterial diversity, profoundly influencing microbial communities, from microbiomes to the drivers of global biogeochemical cycling. Aiming to broaden our understanding of Escherichia coli (MG1655, K-12) phages, we screened 188 Danish wastewater samples and isolated 136 phages. Ninety-two of these have genomic sequences with less than 95% similarity to known phages, while most map to existing genera several represent novel lineages. The isolated phages are highly diverse, estimated to represent roughly one-third of the true diversity of culturable virulent dsDNA Escherichia phages in Danish wastewater, yet almost half (40%) are not represented in metagenomic databases, emphasising the importance of isolating phages to uncover diversity. Seven viral families, Myoviridae, Siphoviridae, Podoviridae, Drexlerviridae, Chaseviridae, Autographviridae, and Microviridae, are represented in the dataset. Their genomes vary drastically in length from 5.3 kb to 170.8 kb, with a guanine and cytosine (GC) content ranging from 35.3% to 60.0%. Hence, even for a model host bacterium, substantial diversity remains to be uncovered. These results expand and underline the range of coliphage diversity and demonstrate how far we are from fully disclosing phage diversity and ecology

A New High-Throughput Screening Method for Phages:Enabling Crude Isolation and Fast Identification of Diverse Phages with Therapeutic Potential

Bacteriophage therapy and application of phages for biocontrol necessitate acquisition of suitable phages. The exclusivity of phage–host relations and the risk of phage resistance instigate a need to rapidly isolate and characterize novel phages and continually build sizeable phage libraries. Current methods for phage isolation are both laborious and time consuming, suitable for the isolation of a limited number of phages. The high-throughput screening method for phages upscales and organizes enrichment of phages for fast isolation and identification of potentially hundreds of distinct phages against single hosts. This enables screening of hundreds of samples, in multiple simultaneous setups with varying parameters, increasing the likelihood of isolating multiple distinct phages specific for the given conditions. The efficiency of the method is emphasized by our screening of 200 environmental samples, resulting in the identification of an abundance of unique phage species virulent to Escherichia coli, Salmonella enterica, Enterococcus faecalis, and Pseudomonas aeruginosa

Detection of preQ0 deazaguanine modifications in bacteriophage CAjan DNA using Nanopore sequencing reveals same hypermodification at two distinct DNA motifs

© 2020 The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. In the constant evolutionary battle against mobile genetic elements (MGEs), bacteria have developed several defense mechanisms, some of which target the incoming, foreign nucleic acids e.g. restriction-modification (R-M) or CRISPR-Cas systems. Some of these MGEs, including bacteriophages, have in turn evolved different strategies to evade these hurdles. It was recently shown that the siphophage CAjan and 180 other viruses use 7-deazaguanine modifications in their DNA to evade bacterial R-M systems. Among others, phage CAjan genome contains a gene coding for a DNA-modifying homolog of a tRNA-deazapurine modification enzyme, together with four 7-cyano-7-deazaguanine synthesis genes. Using the CRISPR-Cas9 genome editing tool combined with the Nanopore Sequencing (ONT) we showed that the 7-deazaguanine modification in the CAjan genome is dependent on phage-encoded genes. The modification is also site-specific and is found mainly in two separate DNA sequence contexts: GA and GGC. Homology modeling of the modifying enzyme DpdA provides insight into its probable DNA binding surface and general mode of DNA recognition