Table 2 Overview of the research questions and general approaches in the study of rare microbes
From: Where less may be more: how the rare biosphere pulls ecosystems strings
Research questions | Method | Critical issues | Options | References | |
|---|---|---|---|---|---|
Synthetic communities | |||||
Order of arrival | Vary order of arrival to test priority effects | Cultivation dependent | Selective/spatially structured media | ||
Density-dependent effects | Vary abundances to test effects of rare species | Cultivation dependent | Cell separation via microfluidic or flow cytometry | ||
Manipulation of natural communities | |||||
Removal | Consequence of rare species loss | Dilution-to-extinction | Equal biomass in all treatments | Incubation period for recovery of biomass | Philippot et al., 2013; Mallon et al., 2015; Hol et al., 2015a,2015b; Delgado-Baquerizo et al., 2016 |
Enrichment | Responders to changing conditions | Salinity, dry–rewet, predation, pollution, nutrient amendments | Molecular methods for composition (DNA) and activity (RNA) | DNA normalization; improve coverage rare biosphere via single-cell genomics | |
In situ | |||||
Microbial population dynamics | Time series | Availability of data sets | Increase sampling | ||
Genome recovery of rare species; predict metabolic pathways | Single-cell genomics | Selection of target | Labeling via FISH | ||
Function of rare species | SIP; Nano-SIMS | Low throughput | Combine with single-cell analysis | ||
