Flavobacterium sp. PS2 isolate:PS2 Genome sequencing

Water temperature in freshwater streams and lakes located in temperate zones fluctuate during the seasonal cycle. Bacteria are important players in biogeochemical cycles and water quality. Bacteria which inhabit such freshwater systems must cope with changing water temperature and the associated changes in water chemistry and nutrient resources. Metagenomic profiling of the prokaryotic community structure of a temperate river during a yearly cycle has identified discrete genera of bacteria whose abundance profiles changed markedly during the winter months. For example, the increased abundance of microbes during winter months were involved with nitrogen cycling, especially during ice cover. However, little is known about individual winter season species and even less about the how the genome is adapted to survive in cold seasons, as well as any potential matches with habitat chemistry during the winter months.Cold tolerance is often viewed as a generalist adaptation (broadening an originally mesophilic bacterium's temperature tolerance into psychrophilic ranges, often via horizontal gene transfer). However, as has been noted, generalism and specialism can exist along multiple different axes and is not necessarily related to temperature tolerance. This raises the question of whether cold tolerance is also correlated with other generalist properties, such as larger genome size, broader carbon acquisition capabilities, etc. A past study with Flavobacterium columnare has found that temperature generalism in the form of increased ability to survive at warmer temperatures was negatively associated with virulence.The origin of winter season bacterial species is not clear in part because they have only been studied at the genus level. Are they a unique species or are they simply polar bacteria which also happen to inhabit temperate zones? One study has indicated that a winter season marine Vibrio isolated from the intertidal zone near Virginia Beach was identical to a strain isolated from sea ice off the coast of Antarctica.To begin to address these questions, we cultured bacteria from the sediment beneath an ice-covered freshwater stream in western Pennsylvania (USA). Strains which grew after a two week period at a temperature of 4 degrees C were colony purified. Novel species were identified based on the sequence homology of their 16S rRNA to known reference species. Three potentially novel species were identified and whole genome sequences obtained using Oxford Nanopore sequence assembly polished with Illumina reads.