1.1.1 Incorporating Microbial Indicators of Hydrologic
Connectivity
One emerging field-based approach that may provide new insights into
connectivity is utilizing hydrologic information contained in
microbiomes. Recent work has demonstrated that analysis of
microorganisms can be a valuable tool in hydrologic research because
membership of aquatic microbiomes are intimately coupled with hydrologic
processes (Good et al., 2018; MartÃnez-Carreras et al., 2015; Pfister et
al., 2009). Microorganisms are passive dispersers in aquatic systems and
dispersal effects are primarily driven by the directional flow of water
(Nemergut et al., 2013). As a result, membership of downstream aquatic
microbiomes have been shown to be similar to the microbiomes within
shallow soils (Crump et al., 2012) and deeper groundwaters (Amalfitano
et al., 2014) that generate streamflow. However, as surface water
ecosystems become disconnected and residence times of aquatic systems
increase, community assembly is increasingly affected by ecological
dynamics (e.g., competition, predation) that result in changes in
membership of the site-specific microbiome (Crump et al., 2012;
Lindström et al., 2006). At any one point in time, aquatic microbiome
membership is the balance between immigration and emigration, which are
primarily regulated by hydrologic connectivity, and microbial growth and
mortality, which are affected by in situ environmental parameters
(e.g., resources and temperature) (Crump & Hobbie, 2005; Read et al.,
2014; Savio et al., 2015). As hydrologic flow states and aquatic network
structure also influence hydrologic connectivity, the membership of
aquatic microbiomes has the potential to reflect connectivity status.
The recent formalization of analytical techniques and bioinformatic
pipelines to characterize microbiome membership have made analyses of
environmental microbiomes more affordable and accessible to
non-specialists (Thompson et al., 2017). These increasingly routine
analyses of microbiome membership, coupled with the ubiquity of
microorganisms, make microbial analyses a potentially powerful tool for
assessments of hydrologic connectivity.