The Harvard Forest Long Term Ecological Research site in Petersham, MA is home to long-term experimental soil warming sites heated continuously to 5° C above ambient temperature since 1991 (Prospect Hill), 2003 (Barre Woods) and 2006 (SWaN). The net short-term effect of warming on forest soil communities is increased microbial activity, which translates to increased CO2 flux to the atmosphere and lower soil organic carbon levels. Several challenges remain to directly link soil communities to changes in soil CO2 efflux. Consequently, it is essential that we develop alternative methods for analyzing community composition and function of active community members. Cells were labeled using SYBR green and separated by fluorescence activated cell sorting. To improve cost efficiency and throughput over single cells genomic methods, 360 subpools of 100 cells each were sequenced. This approach, termed mini-metagenomics, resulted in ~2,000 distinct genome bins. Phylogenomic analysis revealed a surprising diversity of microbial life. Sixteen new lineages of giant viruses were discovered for the first time in a forest soil ecosystem. Intracellular and host-dependent bacteria (Chlamydiae, Legionellales, Bacteriodetes, Rickettsiales and TM6/Dependentiae) were enriched in the data set relative to abundances in our traditional metagenomics data set of DNA extracted directly from the soil and further over-represented among high quality genome bins. Among the bins were several relatives of unusual parasitic vampire bacteria. This collection of mini-MAGs exposes a reservoir of genetic diversity in difficult to cultivate organisms, some of which are related to human pathogens.