Production of methane gas from the methane-hydrate-bearing layer below the deep-ocean floor is expected to be crucial in the future of energy resources worldwide. During the methane gas-production phase from the methane hydrate with the depressurisation method, the depressurising zone around the production well will lose strength, causing a potential geohazard. In this study, a bio-mediated treatment to reinforce the methane hydrate layers is proposed. A urease-producing bacterium, Sporosarcina newyorkensis, was isolated for the first time from a pressure core sampled from the Nankai Trough seabed methane-hydrate-bearing layer in Japan. This newly isolated species can survive deep-seabed environments and also enhance the population under nutrient-rich conditions. In addition, it is uniquely characterised with higher urease activities under low-temperature conditions in comparison to the well-known bacterium S. pasteurii. The results of triaxial tests suggest that this bacterium can catalyse the precipitation of calcium carbonate through urea hydrolysis, which enhances the soil strength below the ocean floor and hence reinforces the production well. This will not only make methane gas extraction safer but may also reduce sand production in the well, making extraction operations more efficient and cost effective.