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The high-elevation cold deserts in Tibet and Himalaya are rich in soil cyanobacterial communities, which facilitate an initial establishment of vascular plants. During the following succession, the increasing cover of vascular plants modifies light intensity and nutrient availability for soil cyanobacterial community and other soil phototrophs. Despite the importance of soil phototrophic community for ecosystem functioning, surprisingly little is known about the actual interactions between vascular plants and soil phototrophs and about their variation along environmental gradients in high-elevation cold deserts. In this study, we disentangle the direct impact of vascular plants on soil phototrophic community, mainly on cyanobacteria, from indirect ones mediated through modification of soil chemistry and temperature stress along an unprecedented elevational gradient (5200-6000 m a.s.l.) using a combination of conditional inference trees, co-correspondence analysis and variation partitioning. We found that vascular plants and cyanobacteria substantially differ in their response to increasing elevation. While species richness, diversity and abundance of vascular plants decreased with elevation, the species richness, diversity and abundance of cyanobacteria growing below vascular plants did not change with elevation and the richness, abundance and diversity of cyanobacteria from bare soil increased with elevation. Cyanobacteria were generally more abundant and diverse in bare soil than in vegetated soil. This difference was caused mainly by the substantially higher abundance of cyanobacteria from orders Chroococales and Nostocales in bare soils. The diversity of cyanobacteria from vegetated-soil was unrelated to vascular plant cover, but the diversity of cyanobacteria from bare soil strongly declines with increasing plant cover. In vegetated soils, the composition of soil cyanobacterial communities was affected mainly by the species composition of vascular plants. In bare soil, the composition of soil cyanobacterial communities was driven mainly by the soil chemistry and elevation. Cyanobacterial assemblages were also indirectly affected by vascular plants through changes in soil texture and fertility, with finer and more nutrient rich soils hosting less diverse cyanobacterial communities. Our results shed light on the interactions between soil cyanobacteria and vascular plants in the high-elevation cold deserts and disentangle the role of different ecological filters in structuring soil phototrophic communities in the rapidly-warming Himalayas. (C) 2017 Elsevier Ltd. All rights reserved.