11:45 AM - 12:00 PM
[BCG07-11] Foraminifera-prokaryote biological interaction suggested by single-cell DNA and RNA amplicon sequencing analyses
Keywords:Co-extraction of DNA and RNA , Foraminifera, Amplicon sequence, ecto/endobionts
Amplicon sequence is a powerful tool to investigate the diversity of environments and reveals rare biosphere by discovering new unique species via multivariate analysis. DNA amplicon technique enables to uncover rare DNAs, though it involves both communities of living and dead cells as well as their remnants due to physical stability of DNAs. On the other hand, RNA amplicon only shows living community because RNAs degrade rapidly. Comparison of DNA and RNA amplicon study can give us clues on the living/dead community structure as well as the biodiversity. Thanks to the development of single-cell techniques, both DNAs and RNAs can be extracted efficiently from a single cell. A combination of single-cell DNA and RNA amplicon sequencing analyses have a potential to unveils a complex of micobiome in the single cell organisms.
Foraminifers are large single-cell eukaryotes, and some of them contain numerous prokaryotes in a cell. The presence of those prokaryotes has been argued as leftovers of food (bacterivore) or endobionts/ectobionts. Such state of prokaryotes in a foraminifera cell can be discriminate whether dead or alive, and whether derived from foods or endobionts/ectobionts, by using DNA and RNA amplicon sequencing analyses. We studied prokaryotic community of co-extracted DNAs and RNAs from a single cell Cyclammina cancellata which formed a small colony on a crustacean carcass in the Sagami Bay (750 m in depth). This species is a common benthic foraminifer in bathyal depth, but its ecology, in particular feeding habits, is unknown because its concrete agglutinated test prevents inner cell observation to find food source or endobionts. DNA and RNA amplicon analyses show us living/dead prokaryotic community structure in single cell. Analysis of composition of microbiomes (ANCOM) has shown different species communities in each of DNA or RNA assembly. Unique species found in RNA assembly showed living chemoautotrophic bacteria in/on C. cancellata, suggesting them as possible endobionts/ectobionts, because most of endobionts in deep-sea organisms are chemoautotrophic. Our analysis suggests co-extraction of DNAs and RNAs coupling with the amplicon technique open a new window to view the biological interactions with respect to living and dead community.
Foraminifers are large single-cell eukaryotes, and some of them contain numerous prokaryotes in a cell. The presence of those prokaryotes has been argued as leftovers of food (bacterivore) or endobionts/ectobionts. Such state of prokaryotes in a foraminifera cell can be discriminate whether dead or alive, and whether derived from foods or endobionts/ectobionts, by using DNA and RNA amplicon sequencing analyses. We studied prokaryotic community of co-extracted DNAs and RNAs from a single cell Cyclammina cancellata which formed a small colony on a crustacean carcass in the Sagami Bay (750 m in depth). This species is a common benthic foraminifer in bathyal depth, but its ecology, in particular feeding habits, is unknown because its concrete agglutinated test prevents inner cell observation to find food source or endobionts. DNA and RNA amplicon analyses show us living/dead prokaryotic community structure in single cell. Analysis of composition of microbiomes (ANCOM) has shown different species communities in each of DNA or RNA assembly. Unique species found in RNA assembly showed living chemoautotrophic bacteria in/on C. cancellata, suggesting them as possible endobionts/ectobionts, because most of endobionts in deep-sea organisms are chemoautotrophic. Our analysis suggests co-extraction of DNAs and RNAs coupling with the amplicon technique open a new window to view the biological interactions with respect to living and dead community.