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Forest and Rangeland Soil Biodiversity 5 Stephanie A Forest and Rangeland Soil Biodiversity 5 Stephanie A. Yarwood, Elizabeth M. Bach, Matt Busse, Jane E. Smith, Mac A. Callaham Jr, Chih-Han Chang, Taniya Roy Chowdhury, and Steven D. Warren Introduction animals utilize the same carbon (C) sources and mineralize at least a portion of that C to carbon dioxide (CO2), but Regardless of how soil is defined, soils are the most diverse within any soil ecosystem, specialized organisms break of all ecosystems. It is estimated that 25–30% of all species down lignin, transform nitrogen (N)-containing molecules, on Earth live in soils for all or part of their lives (Decaëns and produce methane (CH4). Few studies have systemati- et al. 2006). A single gram of soil is estimated to contain cally tested the role of biodiversity in maintaining both 1 × 109 microorganisms, roughly the same population size general and specialized functions, however. One study as the number of humans in Africa (Microbiology by reported a loss of N cycling functions when microbial bio- Numbers 2011). That same gram of soil likely contains mass was experimentally decreased using heat (Philippot 4000 species. They are only one part of a larger food web, et al. 2013b), but less drastic changes may also result in however, that includes roundworms (phylum Nematoda), functional shifts undetectable with some of our current springtails (order Collembola), and other fauna (Fig. 5.1). measurement methods, such as soil enzyme assays (Burns The soil fauna has equally astounding numbers (e.g., et al. 2013) or gas fluxes. Disturbance, development, and 40,000 springtails in 1 m2). Soil organisms, ranging from climate change may impact the functional capacity of for- microbes to moles (family Talpidae), promote crop growth est and rangeland soils, but currently we have little infor- and livestock production (Barrios 2007; Kibblewhite et al. mation on the resistance and resilience of soil communities 2008), produce antibiotics (Wall et al. 2015), control nutri- under these scenarios (Allison and Martiny 2008; Coyle ent loads in surface soils and groundwater (De Vries et al. et al. 2017) (Box 5.1). 2011), and regulate greenhouse gas emissions (Singh et al. Several studies have reported changes in soil biodiver- 2010). sity following disturbance. For example, bacterial diversity Understanding the processes governing soil community has been observed to increase in intermediate-aged soils size and composition and the functional implications of created by glacial retreat (Sigler and Zeyer 2004) and land biodiversity is challenging. Many microorganisms and soil uplift (Yarwood and Högberg 2017), and mature soils typi- S. A. Yarwood (*) M. A. Callaham Jr Department of Environmental Science and Technology, University U.S. Department of Agriculture, Forest Service, Southern Research of Maryland, College Park, MD, USA Station, Center for Forest Disturbance, Athens, GA, USA e-mail: [email protected] C.-H. Chang E. M. Bach Department of Environmental Science and Technology, University Global Soil Biodiversity Initiative, School of Environmental of Maryland, College Park, MD, USA Sustainability, Colorado State University, Fort Collins, CO, Department of Earth and Planetary Sciences, Johns Hopkins USA University, Baltimore, MD, USA M. Busse T. R. Chowdhury U.S. Department of Agriculture, Forest Service, Pacific Southwest Earth and Biological Sciences Division, Pacific Northwest Research Station, Davis, CA, USA National Laboratory, Richland, WA, USA J. E. Smith S. D. Warren Forestry Sciences Laboratory, U.S. Department of Agriculture, U.S. Department of Agriculture, Forest Service, Rocky Mountain Forest Service, Pacific Northwest Research Station, Research Station, Provo, UT, USA Corvallis, OR, USA © The Author(s) 2020 75 R. V. Pouyat et al. (eds.), Forest and Rangeland Soils of the United States Under Changing Conditions, https://doi.org/10.1007/978-3-030-45216-2_5 76 S. A. Yarwood et al. Fig. 5.1 Soil organisms are linked together in a multi- trophic food web. (Illustration by S. Yarwood, University of Maryland) largely unknown, but one model suggests that under- Box 5.1 Resistance and Resilience standing a loss of biodiversity requires not only under- Predicting how the community will react to distur- standing the functions of the ecosystem under the bance requires information on both the resistance and environmental conditions that existed at the time of resilience of the community. Resistance refers to the disturbance but also understanding how the commu- level of disturbance that a community can withstand nity functions under different environmental condi- before it is altered by the disturbance. In this case, pre- tions (Fetzer et al. 2015). In other words, a loss of disturbance and postdisturbance measurements along biodiversity may not have immediate impacts on func- a gradient, such as a fire intensity gradient, can be used tion, but changes may alter the functional capacity of to develop the metric (Cowan et al. 2016). A number of the soil and affect the response when environmental studies have been conducted on soil resistance conditions change. (reviewed in Griffiths and Philippot 2013). Measuring resilience, however, is more complex. Resilience is defined as the rate at which a community returns to its cally contain more soil fauna, a phenomenon explained by original state following disturbance (Allison and the intermediate disturbance hypothesis (Connell 1978; Martiny 2008). Whereas resistance can be measured Huston 2014). Soil detritivores also follow a successional between two time points, resilience requires monitor- pattern as plant litter decomposes, and such fine-scale tem- ing beyond the disturbance event for an often-unspeci- poral succession likely contributes to the high diversity fied timeframe. A disturbance may also lead to a new found in soils (Bastow 2012). Both conditions highlight the stable state that may even be functionally similar to the importance of site legacy and temporal change on deter- predisturbance condition, but this too is difficult to mining species richness. This begs the question: How do determine (Shade et al. 2012). we interpret the majority of studies that have only exam- The large amount of functional redundancy (high ined the soil biota at a single time point? biodiversity) of soils is thought to contribute to both To add another level of complexity, methods used to exam- resistance and resilience, but there are a number of ine the soil community have changed, and new methods have studies that have observed sensitivity of the soil com- been adopted for several decades. Following a long history of munity to disturbance (Shade et al. 2012). Whether culture-based and microscopic approaches, the use of bio- community changes lead to a change in function is markers such as lipids and nucleic acids has now become com- monplace. The use of high-throughput sequencing technology 5 Forest and Rangeland Soil Biodiversity 77 to sufficiently capture soil biodiversity has only existed for the Table 5.1 Estimated diversity and abundance of soil organisms. These last decade, however, and easily accessible computational estimates should be considered preliminary, as most soil species have not been described tools to analyze these data are still being developed. Trying to reconcile observations made using different methodologies Diversity per amount Abundance Taxon of soil or area (estimated) continues to be challenging but will hopefully become easier Prokaryotes 100–9000 4–20 × 109 cm−3 as the soil ecology community pushes for increased consis- Genome tency through the Earth Microbiome Project, the Global Litter equivalents cm−3 Invertebrate Decomposition Experiment (GLIDE) (Wall et al. Fungi 200–235 100 mg−1 2008), and other initiatives. Operational 1 Many emerging studies of soil biodiversity, particularly for taxonomic units g− 2 3 microorganisms and microfauna, target DNA (deoxyribonu- Arbuscular mycorrhizal 10–20 m− 81–111 m cm− fungi AMF (species) cleic acid) to capture the full community. However, this Protists 600–4800 104–107 m−2 approach can also be problematic because of dormancy. At sequences g−1 any time, 25–50% of all detected cells in soils may be dormant Nematodes (genera) 10–100 m−2 2–90 × 105 m−2 (Lennon and Jones 2011), and DNA includes both active and Enchytraeids 1–15 ha−1 12,000– inactive communities. Aside from dormancy, there is also a 311,000 m−2 growing recognition that soils contain extracellular relic DNA Collembola 20 m−2 1–5 × 104 m−2 2 4 2 (Carini et al. 2016; Dlott et al. 2015). Relic DNA complicates Mites (Orbatida) 100–150 m− 1–10 × 10 m− 2 2 our understanding of the current communities because it Isopoda 10–100 m− 10 m− Diplopoda −2 −2 simultaneously reflects current conditions as well as legacy 10–2500 m 110 m Earthworms 10–15 ha−1 300 m−2 conditions. In the case of relic DNA, treating soils with DNAse (Oligochaeta) before extractions may eliminate this inactive pool (Lennon Modified from Bardgett and van der Putten (2014), which includes et al. 2017), but this is not commonly done. It should also be additional references noted that relic DNA can be used to study soil animals such as earthworms (Ficetola et al. 2015). It is likely that relic DNA and inactive cells have hampered efforts to connect the bio- dry weight (Kimura et al. 2008). Current knowledge of soil logical community to targeted functions. At the end of the viruses is scarce, with only a handful of studies enumerating chapter, we will discuss other emerging methods that may pro- and characterizing them. Most of the literature describes vide better insights into structure-function relationships. soil viruses as bacteriophages, in part because bacteria are Before discussing new methods, this chapter will intro- numerous in soils and because bacteriophages have been the duce the various groups that compose the soil community, target of most studies. Currently there are only about 2000 with emphasis on the known trends for each group of organ- described soil viruses, a number too low to generate confi- isms in the forest and rangeland soils of the United States.
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