The species composition and metabolic potential of microbial and viral communities are predictable and stable for most ecosystems. This apparent stability contradicts theoretical models as well as the viral-microbial dynamics observed in simple ecosystems, both of which show Kill-the-Winner behavior causing cycling of the dominant taxa. Microbial and viral metagenomes were obtained from four human-controlled aquatic environments at various time points separated by one day to 41 year. These environments were maintained within narrow geochemical bounds and had characteristic species composition and metabolic potentials at all time points. However, underlying this stability were rapid changes at the fine-grained level of viral genotypes and microbial strains. These results suggest a model wherein functionally redundant microbial and viral taxa are cycling at the level of viral genotypes and virus-sensitive microbial strains. Microbial taxa, viral taxa, and metabolic function persist over time in stable ecosystems and both communities fluctuate in a Kill-the-Winner manner at the level of viral genotypes and microbial strains.

Viruses, and more particularly phages (viruses that infect bacteria), represent one of the most abundant living entities in aquatic and terrestrial environments. The biogeography of phages has only recently been investigated and so far reveals a cosmopolitan distribution of phage genetic material (or genotypes). Here we address this cosmopolitan distribution through the analysis of phage communities in modern microbialites, the living representatives of one of the most ancient life forms on Earth. On the basis of a comparative metagenomic analysis of viral communities associated with marine (Highborne Cay, Bahamas) and freshwater (Pozas Azules II and Rio Mesquites, Mexico) microbialites, we show that some phage genotypes are geographically restricted. The high percentage of unknown sequences recovered from the three metagenomes (>97%), the low percentage similarities with sequences from other environmental viral (n = 42) and microbial (n = 36) metagenomes, and the absence of viral genotypes shared among microbialites indicate that viruses are genetically unique in these environments. Identifiable sequences in the Highborne Cay metagenome were dominated by single-stranded DNA microphages that were not detected in any other samples examined, including sea water, fresh water, sediment, terrestrial, extreme, metazoan-associated and marine microbial mats. Finally, a marine signature was present in the phage community of the Pozas Azules II microbialites, even though this environment has not been in contact with the ocean for tens of millions of years. Taken together, these results prove that viruses in modern microbialites display biogeographical variability and suggest that they may be derived from an ancient community.

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Abstract. The Tibetan Plateau (TP) is the largest alpine plateau on Earth and plays an important role in global climate dynamics. On the TP, climate change is happening particularly fast, with an increase in air temperature twice the global average. The particular sensitivity of this high mountain environment allows observation and tracking of abiotic and biotic feedback mechanisms. Closed lake systems, such as Nam Co on the central TP, represent important natural laboratories for tracking past and recent climatic changes, as well as geobiological processes and interactions within their respective catchments. This review gives an interdisciplinary overview of past and modern environmental changes using Nam Co as a case study. In the catchment area, ongoing rise in air temperature forces glaciers to melt, contributing to a rise in lake level and changes in water chemistry. Some studies base their conclusions on inconsistent glacier inventories, but an ever-increasing deglaciation and thus higher water availability have persisted over the last few decades. Increasing water availability causes translocation of sediments, nutrients and dissolved organic matter to the lake, as well as higher carbon emissions to the atmosphere. The intensity of grazing has an additional and significant effect on CO2 fluxes, with moderate grazing enhancing belowground allocation of carbon while adversely affecting the C sink potential through reduction of above-surface and subsurface biomass at higher grazing intensities. Furthermore, increasing pressure from human activities and livestock grazing are enhancing grassland degradation processes, thus shaping biodiversity patterns in the lake and catchment. The environmental signal provided by taxon-specific analysis (e.g., diatoms and ostracods) in Nam Co revealed profound climatic fluctuations between warmer–cooler and wetter–drier periods since the late Pleistocene and an increasing input of freshwater and nutrients from the catchment in recent years. Based on the reviewed literature, we outline perspectives to further understand the effects of global warming on geodiversity and biodiversity and their interplay at Nam Co, which acts as a case study for potentially TP-level or even worldwide processes that are currently shaping high mountain areas.