Hunting hidden archaeal viruses from the continental subsurface

Viruses are ubiquitous and are important microbial predators that not only influence global biogeochemical cycles but also drive microbial evolution. Moreover, viruses cause significant mortality in prokaryotic communities, can modify the host diversity and abundance, but also alter the genetic content of their hosts via horizontal gene transfer or by expression of viral-encoded genes during viral infection. However, little is known about the role of viruses in the deep terrestrial subsurface that contains a large reservoir of organic carbon and hosts a large fraction of all microbes on Earth. Compared to various investigations focusing on the bacterial diversity, studies on archaea in the deep terrestrial subsurface are very limited. Culture-independent methods such as metagenomics have shown that, archaea like Candidatus Altiarchaea can dominate this difficult to access ecosystem. Due to the limitations of conventional culture techniques, the microbial distribution, and the interaction of microorganisms with, e.g., viruses living in such an ecosystem, remain poorly understood. Studying viral infections can bolster our understanding in terms of the spatial and temporal distribution of viruses, the effects on the overall community composition, the microbial diversity, nutrient cycling, and carbon cycling in the deep biosphere.

The overarching objective of this study was to broaden the current knowledge on Ca. Altiarchaea and their microbial interactions within the deep subsurface. More specifically, this study focused on one specific sulfidic spring called the “Muehlbacher Schwefelquelle Isling (MSI)” located in Regensburg (Germany), that has been shown to harbor almost pure biofilms consisting of up to 95% of Candidatus Altiarchaeum hamiconexum (Ca.A. hamiconexum), a primary producer of the deep subsurface.

In this thesis, I report on one specific virus (here “Altivir_1_MSI”) hijacking Ca. A. hamiconexum and its respective viral lifestyle. This microbial “relationship” remained so far unexplored. Metagenomics coupled with fluorescence in situ hybridization (here “virusFISH”) enabled the investigation of this specific virus-host system in the deep subsurface. Moreover, this dissertation is the first one focusing on virus-host dynamics by using virusFISH in this rather difficult to access ecosystem at single-cell level. Analysis of the different infection stages using fluorescence microscopy revealed initial infections, advanced infections, as well as cell lysis of Ca. A. hamiconexum cells with the release of new virions. Through this linkage and the resulting stages of infection, a first indication of a lytic replication cycle of Altivir_1_MSI was received. In addition, the virusFISH results evidenced a stable virus-host relationship over four years.

Furthermore, it can be assumed that this lytic virus might jump-start heterotrophic carbon cycling in this ecosystem by acting as a potential top-down and bottom-up controller. By having different virusFISH images at hand, an accumulation of sulfate-reducing bacteria on spots where a successful lysis event of Ca. A. hamiconexum cells occurred, was observed. Through a constant viral lysis of the primary producer, this “microbial loop” of the deep subsurface seems to be activated by a release of possible nutrients that other microbes like sulfate-reducing bacteria can utilize.

Overall, the results and findings of these investigations that make up this thesis, have contributed significantly to today’s understanding of the interactions between archaeal viruses and their hosts, and their role in the deep subsurface. At the same time, this thesis is one of the first examples that showed how well these microbial interactions can be investigated by using today’s current state-of-the-art-techniques in an ecosystem that is difficult to access.


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