We use next generation sequencing and LH-PCR to study the microbiome of cave and soil environments.  These studies help to determine changes in communities and community function caused by seasonal changes, environmental stress, and changing weather/climate patterns and changing  hydrological conditions. We have investigated microbial communities in shallow arsenic containing hydrothermal hotsprings in Papua New Guinea. We have also studied the global distribution of mesofaunal soil animals using 18S rRNA metagenomics, and are currently using 16S metagenomics to investigate microbial communities in cave systems in Florida and Italy. We have shown that bioinformatics of 16S rRNA gene sequence data can estimate community ecosystem function.