Host population diversity as a driver of viral infection cycle in wild populations of green sulfur bacteria with long standing virus-host interactions

Abstract

Viral infections of bacterial hosts range from highly lytic to lysogenic, where highly lytic viruses undergo viral replication and immediately lyse their hosts, and lysogenic viruses have a latency period before replication and host lysis. While both types of infections are routinely observed in 15 the environment, the ecological and evolutionary processes that regulate these different viral dynamics are still not well understood. In this study, we identify and characterize the long-term dynamics of uncultivated viruses infecting green sulfur bacteria (GSB) in a model freshwater lake sampled from 2005-2018. Because of the additional requirements for the laboratory cultivation of anaerobes like GSB, viruses infecting GSB have yet to be formally identified, leaving their 20 diversity and impact on natural populations of GSB virtually unknown. In this study, we used two approaches to identify viruses infecting GSB; one in vitro based on flow cytometry cell sorting, the other in silico based on CRISPR spacer sequences. We then took advantage of existing bulk metagenomes derived from Trout Bog Lake covering the 2005-2018 period to examine the interactions between GSB hosts and their viruses across multiple years and seasons. From our 25 data, GSB populations in Trout Bog Lake were found to be concurrently infected with at least 2-8 viruses each, many of which were lysogenic viruses; one GSB host population in particular was consistently associated with two lysogens with a nearly 100% infection rate for over 10 years. We illustrate with a theoretical infection model that such an interaction can be stable over multiple years given a low, but persistent level of lysogen induction in host populations with already high 30 infection rates. Overall, our data suggest that single GSB populations are typically infected by multiple viruses at the same time, that lytic and lysogenic viruses can readily co-infect the same host population in the same ecosystem, and that host strain-level diversity might be an important factor controlling the lytic/lysogeny switch. 35

FreshwaterChlorobiaexhibit metabolic specialization among cosmopolitan and endemic populations

“…Most notably, for Lake Mekkojärvi (Finland), Chlorobium sequences comprised 57% of the community by relative abundance at some depths ( Figure 4G). These high levels are in line with previous studies showing that this class can constitute 12 -47% of reads in lake ecosystems (30,31,37,38). Our data shows one clear case in which multiple Chlorobium populations typically co-inhabit the same lake with spatially separated niches.…”

“…Specifically, mOTU02 and mOTU03 demonstrated differential depth preferences in August 2015 based on Lake Mekkojärvi samples ( Figure 4G). Similar findings were previously reported in Trout Bog, where one of the populations was recovered only in the lowermost 2 water layers (i.e., mOTU07, GSB-A/Chlorobium-111), whereas the other populations had broader distributions (e.g., mOTU58, GSB-B) (29,31). It has been previously postulated that such niche specialization may reflect distinct pigment absorbance profiles (31,39).…”

“…Most of these samples were collected with the objective of investigating depth-associated changes in taxonomic diversity in different water masses that capture oxic epilimnion, metalimnion, and anoxic hypolimnion conditions (28). MAGs available from previous studies (26,(29)(30)(31). In total, the dataset included 509 genomes including the MAGs, SAGs, and complete genomes of isolates (Table S1).…”