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What Lies Beneath? Fungal Diversity at the Bottom of Lake Michigan and Lake Superior

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What Lies Beneath? Fungal Diversity at the Bottom of Lake Michigan and Lake Superior Journal of Great Lakes Research 44 (2018) 263–270 Contents lists available at ScienceDirect Journal of Great Lakes Research journal homepage: www.elsevier.com/locate/jglr What lies beneath? Fungal diversity at the bottom of Lake Michigan and Lake Superior Hannah E. Wahl a,b, Daniel B. Raudabaugh a,b, Elizabeth M. Bach b,c, Tiffany S. Bone b, Mark R. Luttenton d, Robert H. Cichewicz e,AndrewN.Millerb,⁎ a Department of Plant Biology, University of Illinois, 265 Morrill Hall, 505 South Goodwin Avenue, Urbana, IL 61801, USA b Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA c Department of Biology, Colorado State University, 1878 Campus Delivery, Fort Collins, CO 80523, USA d Biology Department and Annis Water Resources Institute, Grand Valley State University, 1 Campus Drive, Allendale, MI 49401, USA e Natural Products Discovery Group, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, 101 Stephenson Parkway, Room 1000, University of Oklahoma, Norman, OK 73019-5251, USA article info abstract Article history: Fungi are phylogenetically diverse organisms found in nearly every environment as key contributors to the pro- Received 2 August 2017 cesses of nutrient cycling and decomposition. To date, most fungal diversity has been documented from terrestrial Accepted 21 December 2017 habitats leaving aquatic habitats underexplored. In particular, comparatively little is known about fungi inhabiting Available online 10 January 2018 freshwater lakes, particularly the benthic zone, which may serve as an untapped resource for fungal biodiversity. Advances in technology allowing for direct sequencing of DNA from environmental samples provide a new oppor- Communicated by Wendylee Stott tunity to investigate freshwater benthic fungi. In this study, we employed both culture-dependent and culture- Keywords: independent methods to evaluate the diversity of fungi in one of the largest freshwater systems on Earth, the Ascomycota North American Laurentian Great Lakes. This study presents the first comprehensive survey of fungi from sediment Aquatic fungi from Lake Michigan and Lake Superior, resulting in 465 fungal taxa with only 7% of sequence overlap between these Basidiomycota two methods. Additionally, culture-independent analyses of the ITS1 and ITS2 regions revealed 49% and 72%, re- Freshwater spectively, of the OTUs did not match a described fungal taxonomic group below kingdom Fungi. The low level of Great Lakes sequence overlap between methods and high percentage of fungal taxa that can only be classified at the kingdom Next-gen sequencing level suggests an immense amount of fungal diversity remains to be studied in these aquatic fungal communities. Systematics © 2018 International Association for Great Lakes Research. Published by Elsevier B.V. All rights reserved. Introduction as pathogens and decomposers of aquatic animals, insects, macro- phytes, and algae (Hyde et al., 1998; Wong et al., 1998). Fungi in aquatic Fungi are diverse organisms found in nearly every global environ- habitats can range from long-term residents that are adapted to com- ment as decomposers, pathogens, and symbionts. An estimated 1.5 mil- plete their lifecycle in water (e.g. Chytridiomycota, aquatic hyphomy- lion species of fungi inhabit the earth (Hawksworth, 1991), of which cetes, and some yeasts), to transient fungal species that reside as only 5% have been described to date (Mueller and Schmit, 2007). propagules in water transported from a terrestrial source. Much of the described fungal diversity has been documented from ter- Freshwater environments account for nearly 10% of all biological di- restrial environments leaving aquatic habitats seldom explored. Fungi versity (Strayer and Dudgeon, 2010), but in regards to fungal diversity, are essential to ecosystems as key drivers of nutrient recycling; so un- they remain grossly understudied. The dynamics of fungi in lotic sys- derstanding fungal diversity within aquatic ecosystems is paramount tems has been the focus of freshwater fungal research leaving freshwa- for understanding ecosystem processes (Shearer et al., 2007). ter lakes nearly unexplored (Wurzbacher et al., 2010). Freshwater lakes An estimated 3000–4150 species of fungi have been described from have unique habitats: littoral, pelagic, and benthic, each harboring aquatic habitats (Shearer et al., 2007; Jones et al., 2014), compared to unique communities of fungi (Wurzbacher et al., 2016). The littoral is 98,000 described from terrestrial environments (Kirk et al., 2008). subjected to high organic matter input leading to a diversity of fungi as- Fungi are found in diverse aquatic habitats including marine, brackish sociated with plants and decomposition, the pelagic zone is home to and freshwater environments, seas, wetlands, streams, and lakes. Simi- more specialized groups of fungi that can survive as saprobes or para- lar to their roles in terrestrial environments, fungi in aquatic systems act sites of plankton and algae, while the benthic zone is hypothesized to serve mainly as a reservoir for fungal spores (Wurzbacher et al., ⁎ Corresponding author. 2010). However, research in marine systems suggests fungal communi- E-mail address: [email protected] (A.N. Miller). ties exist and are active in the benthic region (Edgcomb et al., 2011; Orsi https://doi.org/10.1016/j.jglr.2018.01.001 0380-1330/© 2018 International Association for Great Lakes Research. Published by Elsevier B.V. All rights reserved. 264 H.E. Wahl et al. / Journal of Great Lakes Research 44 (2018) 263–270 et al., 2013). Although little overlap has been reported between fresh- DNA extraction and sequencing water and marine fungal species (Shearer et al., 2007), these results sug- DNA was extracted by adding 200 μl of a 0.5 M NaOH solution to fro- gest that the benthic zone of freshwater lakes is likely to contain active zen mycelium tissue, which was ground for approximately 1 min, incu- fungal communities and serve as a new resource for discovering unique bated between 0 and 4 °C for approximately 20 min, and centrifuged at fungi. 16,800 rcf for 2 min. Five microliters of supernatant was added to 495 μL One such region that holds great promise for describing fungal biodi- 100 mM Tris-HCL buffered with NaOH to pH 8.5–8.9 (Osmundson et al., versity is the North American Laurentian Great Lakes system, which 2013). PCR was performed using a Bio-Rad PTC 200 thermal cycler. A 25 holds approximately 18% of global surface freshwater (Fuller and μl reaction volume was used consisting of 12.5 μLGoTaq®GreenMaster Shear, 1995). To date, only 18 fungal species have been reported from Mix (Promega), 1 μl of each 10 μM primer ITS1F and ITS4 (Electronic Lake Michigan (Paterson, 1967; Kiziewicz and Nalepa, 2008). Paterson Supplementary material (ESM) Table S1), 3 μL Tris-HCL-DNA extraction (1967) used bait “traps” placed at 26–31 m depths to capture solution and 7.5 μL nuclease free water. The following thermal cycle pa- Chytridiomycota while Kiziewicz and Nalepa (2008) collected water rameters were used: 94 °C for 2 min for initial denaturing, followed by samples between 10 and 80 m to isolate Ascomycota, Chytridiomycota 30 cycles of 94 °C for 30 s, 55 °C for 45 s, 72 °C for 1 min with a final ex- and Zygomycota. The goal of this research was to survey the benthic tension step at 72 °C for 10 min. Gel electrophoresis was carried out fungal community in Lake Michigan and Lake Superior by using using a 1% TBE agarose gel with ethidium bromide to verify the presence culture-dependent and culture-independent techniques. Employing of PCR product prior to purification. The resulting PCR product was pu- these methods in tandem can provide a more detailed snapshot of fun- rified using the Wizard® SV Gel and PCR Clean-up System (Promega). A gal communities. This study offers the first systematic inventory of fungi BigDye® Terminator 3.1 cycle sequencing kit (Applied Biosystems Inc.) from sediments of two Great Lakes based on the use of both traditional was used to sequence the entire ITS (internal transcribed spacer) region culture-dependent techniques and current culture-independent envi- of nrDNA in one direction using the ITS5 (ESM Table S1) primer on an ronmental sequencing. Applied Biosystems 3730XL high-throughput capillary sequencer. Culture-independent Methods Sample selection Sample collection A total of 48 sediment samples collected from Lake Michigan (Fig. 1) and Lake Superior (Fig. 2) in 2015 were selected for culture- Sediment samples were collected during the summer months of independent environmental sequencing. Two negative controls were 2014, 2015, and 2016 from Lake Michigan (Fig. 1) and from Lake Supe- included for DNA extraction and sequencing. rior (Fig. 2) in 2015 and 2016. One hundred and forty-five samples were taken from depths between 30 and 272 m from Lake Michigan, while 20 DNA extraction and sequencing samples were taken from depths between 68 and 263 m from Lake Environmental DNA was extracted from approximately 0.5 g of sed- Superior using a Wildco Ponar® dredge. The depth of the sediment sam- iment using MoBio PowerSoil DNA isolation kits following the Earth ples ranged between 7 and 15 cm, but only the top 1 cm of the sediment Microbiome protocol (Gilbert et al., 2010). The ITS1 and ITS2 regions surface layer was collected for analysis. The dredge was thoroughly of the nuclear ribosomal DNA were used to identify fungal taxa washed and sanitized for at least 3 min in a 5% bleach solution between (Schoch et al., 2012). The high throughput Fluidigm Access Array each sample collection. All equipment was swabbed with sterile (Brown et al., 2016) was used to amplify the ITS1 and ITS2 regions of Copan™ swabs before sample collection. Samples and swabs were the environmental samples using fungal specificprimers(ESM stored on ice for up to four days before being sent overnight to the Illi- Table S1). Fluidigm Access Array amplicons were sequenced using the nois Natural History Survey.
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