Effects of Microhabitat and Land Use on Stream Salamander Abundance in the Southwest Virginia Coalfields S.E. Sweeten Department of Fisheries and Wildlife Conservation, Virginia Polytechnic Institute and State University, Blacksburg, VA W.M. Ford1 U.S. Geological Survey, Virginia Cooperative Fish and Wildlife Research Unit, Department of Fisheries and Wildlife Conservation, Virginia Polytechnic Institute and State University, Blacksburg, VA ABSTRACT Large‐scale land use practices such as residential wastewater discharge and coal mining, particularly surface coal extraction and associated valley fills, are of particular ecological concern in central Appalachia. Identification and quantification of alterations across scales are a necessary first‐step to mitigate negative consequences to biota. In central Appalachian headwater streams absent of fish, salamanders are the dominant, most abundant vertebrate predator providing a significant intermediate trophic role. Stream salamander species are considered to be sensitive to aquatic stressors and environmental alterations, and past research has shown linkages among microhabitat parameters, large‐ scale land use such as urbanization and logging with salamander abundances. However, little is known about these linkages in the coalfields of central Appalachia. In the summer of 2013, we visited 70 sites (sampled three times each) in the southwest Virginia coalfields to survey salamanders and quantify stream and riparian microhabitat parameters. Using an information‐theoretic framework we compared the effects of microhabitat and large‐scale land use on salamander abundances. Our findings indicate that dusky salamander (Desmognathus spp.) abundances are more correlated to microhabitat parameters such as canopy cover than to subwatershed land uses. Brook salamander (Eurycea spp.) abundances show strong negative associations to the suspended sediments and stream substrate embeddedness. Neither Desmognathus spp. nor Eurycea spp. abundances were influenced by water conductivity. These salamander microhabitat relationships suggest restoration of riparian habitats and erosion control are important conservations components for maintaining stream salamanders in the mined landscapes of central Appalachia. INTRODUCTION The extraction of Appalachian coal by mountaintop mining can be an efficient mining method, but may only be justified economically by high quantities and qualities of coal (Craynon et al. 2012). Although 1 This draft manuscript is distributed solely for purposes of scientific peer review. Its content is deliberative and pre‐decisional, so it must not be disclosed or released by reviewers. Because the manuscript has not yet been approved for publication by the U. S. Geological Survey (USGS), it does not represent any official USGS finding or policy. 1 mountaintop mining accounts for 37 % of coal production in Appalachia (National Mining Association 2012), it is controversial because of its large environmental footprint (Griffith et al. 2012). Along with direct physical stream loss from valley fills, mountaintop mining also alters watershed hydrology, stream chemistry, and biological communities through vegetation clearing, increases in impervious conditions and changes in area topography (Starnes and Gasper 1995; Pond et al. 2008; Simmons et al. 2008; Merriam et al. 2011; Griffith et al. 2012). Post‐mine flow regimes respond more quickly to rain events becoming “flashy”, and result in more frequent and intense stream flood events (Starnes and Gasper 1995; Price et al. 2006). These high flow events can lead to channelization of the stream along with eroded, unstable stream banks that continue to degrade habitat quality long after the cessation of mining (Baker 1985; Booth et al. 2004). Within the central Appalachian coalfields, efforts to minimize and mitigate environmental effects of surface coal mining have been complicated by incongruent restoration goals and poorly validated post‐ mine monitoring protocols that are unable to quantify ecosystem change relative to system recovery (Bernhardt and Palmer 2011; Zipper et al. 2011). Traditionally, aquatic ecosystem monitoring has focused on the effects of land use practices on water chemistry and macroinvertebrate assemblages (Pond et al. 2008; Northingham et al. 2011; USEPA 2011; Griffith et al. 2012). However, the ability to distinguish natural stream variability from the additive effects of anthropogenic influences on aquatic biotic communities is currently limited. Furthermore, more research is needed to examine the multiple temporal and spatial dynamics of the biological recovery of a degraded aquatic system (Harding et al. 1998; Adams et al. 2002; Niemi and McDonald 2004; Hartman et al. 2005; Milman and Short 2008; Simmons et al. 2008; Northingham et al. 2011). Adding to this uncertainly about natural variability and anthropogenic change interaction is the realization that even identifying and quantifying aquatic ecosystem structure and function of undisturbed systems can be very difficult (Simmons et al. 2008). As such, biological assessment using a suite of taxa may provide the most extensive view of aquatic changes including declines in stream health as well as stream recovery (Sweeten et al. 2013). In central Appalachian headwater streams absent of fish, salamanders are the dominant, most abundant vertebrate predator (Burton and Likens 1975; Hairston 1986; Davic and Welsh 2004). In undisturbed areas of central Appalachia, salamanders have been shown to have relatively stable populations with high densities of up to 1.4/m2 (Kleeberger 1984; Hairston and Wiley 1993). Stream salamander species are considered to be sensitive to both aquatic and environmental stressors, and low stream salamander abundance has been shown to be closely linked to anthropogenic terrestrial watershed alteration (Petranka et al. 1993; Willson and Dorcas 2003). Salamanders in central Appalachian headwater streams provide significant intermediate roles in trophic cycling, feeding on small prey such as benthic macroinvertebrates and in turn, are an important prey item for larger vertebrates (Petranka et al. 1993; Davic and Welsh 2004; OHEPA 2012). Research on salamanders related to land use in the eastern United States largely has focused on forestry practices. In the central and southern Appalachians, considerable data exist linking forest harvesting and younger stand age classes to declines in terrestrial salamander abundance at least in the short‐term (Ash 1988; Petranka et al. 1993; Ash 1997; Harper and Guynn 1999; Harpole and Haas 1999; Ford et al. 2002; Reichenbach and Sattler 2007; Crawford and Semlitsch 2008). Though less extensive, similar research in the central and southern Appalachians also suggest analogous links between stream salamander decline and forest harvesting and/or younger stand age (Moseley et al. 2008; Peterman and Semlitsch 2009). At smaller spatial scales, logging‐related alterations to riparian quality (such as decreases in canopy cover, leaf litter depth and soil moisture) along with declines in physical stream 2 conditions (such changed stream substrate class, greater substrate embeddedness, and reduced riffle/run/pool composition) are thought to negatively influence stream salamander populations (Crawford and Semlitsch 2008; Moseley et al. 2008; Peterman and Semlitsch 2009). Additionally, stream salamander abundance may be reduced, even to the point of local extirpation, by watershed land uses such as mining, urbanization, and timber harvesting that cause changes in pH, streambed sedimentation, suspended sediments, and water and soil temperature (Gore 1983; Willson and Dorcas 2003; Welsh et al. 2005; Moseley et al. 2008). These aquatic habitat changes underscore the need for understanding the dynamics among salamander abundance, land use, and microhabitat. Land managers and researchers have begun to examine stream salamander response to habitat alterations from either surface or underground coal mining; however, many environmental effects of coal mining on stream salamanders remain poorly quantified. Most of the amphibian research on mined lands has focused on constructed settling ponds and use and recolonization by pond salamanders such as those in the family Ambystomidae (Turner and Fowler 1981; Fowler et al. 1985; Lacki et al. 1992; Kirk 2000; Jansen et al. 2004; Loughman 2005). Some research has examined the effect of acid mine drainage on stream salamanders (Freda 1986; Middlekoop et al. 1998; Whiteleather 2001); however, acid mine drainage is not an issue throughout the entire Appalachian coalfields, such as in southwest Virginia (Herricks and Cairns 1974; Minear and Tschantz 1976). There has been limited research examining aquatic salamanders relative to coal mining. Generally community richness and abundance was lower in valley fill streams than reference streams (Hamilton 2002; Wood and Williams 2013a; Muncy et al. 2014). However, researchers did find evidence of recovery as Hamilton (2002) observed no difference in 18 year old valley fill streams with reference streams. Nonetheless complete examination linking microhabitat to landscape‐level conditions and stream salamanders generally has not occurred. The main objective of our study was to investigate relationships between aquatic salamander abundances and habitat parameters at both a microhabitat and a landscape‐level along a gradient of conditions in order to determine if more research is warranted for the development of a salamander index of biotic integrity