Though microbial processes in the oxygen minimum zones (OMZs) of the Arabian Sea (AS) are well documented, prokaryote-virus interactions are less known. The present study was carried out to determine the potential physico-chemical factors influencing viral abundances and their life strategies (lytic and lysogenic) along the vertical gradient in the OMZ of the AS (southwest coast of India). Water samples were collected during the southwest monsoon (SWM) season in two consecutive years (2015 and 2016) from different depths, namely, the surface layer, secondary chlorophyll a maxima (~30–40 m), oxycline (~70–80 m), and hypoxic/suboxic layers (~200–350 m). The high viral abundances observed in oxygenated surface waters (mean ± SD = 6.1 ± 3.4 × 106 viral-like particles (VLPs) mL−1), drastically decreased with depth in the oxycline region (1.2 ± 0.5 × 106 VLPs mL−1) and hypoxic/suboxic waters (0.3 ± 0.3 × 106 VLPs mL−1). Virus to prokaryote ratio fluctuated in the mixed layer (~10) and declined significantly (p < 0.001) to 1 in the hypoxic layer. Viral production (VP) and frequency of virus infected cells (FIC) were maximum in the surface and minimum in the oxycline layer, whereas the viral lysis was undetectable in the suboxic/hypoxic layer. The detection of a high percentage of lysogeny in suboxic (48%) and oxycline zones (9–24%), accompanied by undetectable rates of lytic viral infection support the hypothesis that lysogeny may represent the major survival strategy for viruses in unproductive or harsh nutrient/host conditions in deoxygenated waters.

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El Niño, an interannual climate event characterized by elevated oceanic temperature, is a prime threat for coral reef ecosystems worldwide, owing to their thermal threshold sensitivity. Phytoplankton plays a crucial role in the sustenance of reef trophodynamics. The cell size of the phytoplankton forms the "master morphological trait" with implications for growth, resource acquisition, and adaptability to nutrients. In the context of a strong El Niño prediction for 2015-2016, the present study was undertaken to evaluate the variations in the size-structured phytoplankton of Kavaratti reef waters, a major coral atoll along the southeast coast of India. The present study witnessed a remarkable change in the physicochemical environment of the reef water and massive coral bleaching with the progression of El Niño 2015-2016 from its peak to waning phase. The fluctuations observed in sea surface temperature, pH, and nutrient concentration of the reef water with the El Niño progression resulted in a remarkable shift in phytoplankton size structure, abundance, and community composition of the reef waters. Though low nutrient concentration of the waning phase resulted in lower phytoplankton biomass and abundance, the diazotroph Trichodesmium erythraeum predominated the reef waters, owing to its capability of the atmospheric nitrogen fixation and dissolved organic phosphate utilization.