Seasonal Regime Shift in the Viral Communities of a Permafrost Thaw Lake

A Tale of Two Seasons: Distinct Seasonal Viral Communities in a Thermokarst Lake

Thermokarst lakes are important features of subarctic landscapes and are a substantial source of greenhouse gases, although the extent of gas produced varies seasonally. Microbial communities are responsible for the production of methane and CO₂ but the "top down" forces that influence microbial dynamics (i.e., grazers and viruses) and how they vary temporally within these lakes are still poorly understood. The aim of this study was to examine viral diversity over time to elucidate the seasonal structure of the viral communities in thermokarst lakes. We produced virus-enriched metagenomes from a subarctic peatland thermokarst lake in the summer and winter over three years. The vast majority of vOTUs assigned to viral families belonged to Caudovirales (Caudoviricetes), notably the morphological groups myovirus, siphovirus and podovirus. We identified two distinct communities: a dynamic, seasonal community in the oxygenated surface layer during the summer and a stable community found in the anoxic water layer at the bottom of the lake in summer and throughout much of the water column in winter. Comparison with other permafrost and northern lake metagenomes highlighted the distinct composition of viral communities in this permafrost thaw lake ecosystem.

Phage strategies facilitate bacterial coexistence under environmental variability

Bacterial communities are often exposed to temporal variations in resource availability, which exceed bacterial generation times and thereby affect bacterial coexistence. Bacterial population dynamics are also shaped by bacteriophages, which are a main cause of bacterial mortality. Several strategies are proposed in the literature to describe infections by phages, such as "Killing the Winner", "Piggyback the loser" (PtL) or "Piggyback the Winner" (PtW). The two temperate phage strategies PtL and PtW are defined by a change from lytic to lysogenic infection when the host density changes, from high to low or from low to high, respectively. To date, the occurrence of different phage strategies and their response to environmental variability is poorly understood. In our study, we developed a microbial trophic network model using ordinary differential equations (ODEs) and performed 'in silico' experiments. To model the switch from the lysogenic to the lytic cycle, we modified the lysis rate of infected bacteria and their growth was turned on or off using a density-dependent switching point. We addressed whether and how the different phage strategies facilitate bacteria coexistence competing for limiting resources. We also studied the impact of a fluctuating resource inflow to evaluate the response of the different phage strategies to environmental variability. Our results show that the viral shunt (i.e. nutrient release after bacterial lysis) leads to an enrichment of the system. This enrichment enables bacterial coexistence at lower resource concentrations. We were able to show that an established, purely lytic model leads to stable bacterial coexistence despite fluctuating resources. Both temperate phage models differ in their coexistence patterns. The model of PtW yields stable bacterial coexistence at a limited range of resource supply and is most sensitive to resource fluctuations. Interestingly, the purely lytic phage strategy and PtW both result in stable bacteria coexistence at oligotrophic conditions. The PtL model facilitates stable bacterial coexistence over a large range of stable and fluctuating resource inflow. An increase in bacterial growth rate results in a higher resilience to resource variability for the PtL and the lytic infection model. We propose that both temperate phage strategies represent different mechanisms of phages coping with environmental variability. Our study demonstrates how phage strategies can maintain bacterial coexistence in constant and fluctuating environments.

Possible Roles of Permafrost Melting, Atmospheric Transport, and Solar Irradiance in the Development of Major Coronavirus and Influenza Pandemics

Major pandemics involving respiratory viruses develop semi-regularly and require a large flux of novel viruses, yet their origination is equivocal. This paper explores how natural processes could give rise to this puzzling combination of characteristics. Our model is based on available data regarding the emergence of historic influenzas, early COVID-19 cases and spreading, the microbiome of permafrost, long-distance airborne transport of viruses reaching stratospheric levels, ultraviolet immunosuppression, sunlight variations, weather patterns, Arctic thawing, and global warming. Atmospheric conveyance is supported by hemispheric distribution disparities, ties of COVID-19 cases to air pollution particulate concentrations, and contemporaneous animal infections. The following sequence is proposed: (1) virus emergence after hot Arctic summers, predominantly near solar irradiance maxima or involving wildfires, indicates release of large amounts of ancient viruses during extensive permafrost melting, which are then incorporated in autumn polar air circulation, where cold storage and little sunlight permit survival. (2) Pandemics onset in winter to spring at rather few locations: from climate data on Wuhan, emergence occurs where the North Polar Jet stream hovers while intersecting warmer, moist air, producing rain which deposits particulates with the viral harvest on a vulnerable human population. (3) Spring and summer increases in COVID-19 cases link to high solar irradiance, implicating ultraviolet immune suppression as one means of amplification. (4) Viruses multiplied by infected humans at close range being incorporated in atmospheric circulation explains rapid global spread, periodic case surges (waves), and multi-year durations. Pollution and wind geography affect uptake and re-distribution. Our model can be tested, e.g., against permafrost stored in laboratories as well as Artic air samples, and suggests mitigating actions.