We are developing new molecular techniques to fill the gaps in the marine microbial ecosystem. For example, in marine virosphere, many studies have revealed the diversity and ecological functions of dsDNA viruses, however, those of ssDNA viruses and RNA viruses are still mostly unknown. To know the RNA viral diversity, we have developed fragmented and primer ligated dsRNA sequencing (FLDS) that can identify genetic diversity of both dsRNA and ssRNA viruses by targeting cellular long dsRNA molecule (Urayama et al. 2018). In addition, to know the significance of ssDNA viruses in marine virosphere, we have constructed a quantitative method of viral metagenomics (Yoshida et al. 2018). In the case of the deep-sea microbial ecology, geophysical control on microbial diversity and ecosystem has been discussed but there are issues in sampling and laboratory experiments. One of the major issues is the accessibility of the samples. However, if microbiologists can integrate with classical oceanography campaigns about ocean circulation we can join high-resolution sampling from the sea surface to just above the seafloor. Therefore, we have developed a procedure to construct shotgun metagenomic libraries from a few liters of deep-sea water that is identical to approximately 107 cells because only a few liters from each Niskin bottle are available in such collaborative work (Hirai et al. 2017). I will introduce our recent technological developments and the test studies.