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In this book effect of nitrogen depletion on the cyanobacterium-Synechococcus-6301 primary processes of photosynthesis has been discussed. Nitrogen stress particularly affects the primary photochemistry of photosystem-II when compare that of PS-I. In photosystem-II, the light-harvesting complex namely phycobilisomes are a major target for nitrogen stress and impair energy transfers in PS-II. The enhanced lipid peroxidation in thylakoid membranes clearly demonstrates that nitrogen stress could be inducing free radicals that cause to the membrane.