Detection and Community-Level Identification of Microbial Mats in the Mcmurdo Dry Valleys Using Drone-Based Hyperspectral Reflec
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Antarctic Science page 1 of 15 (2020) © Antarctic Science Ltd 2020 doi:10.1017/S0954102020000243 Detection and community-level identification of microbial mats in the McMurdo Dry Valleys using drone-based hyperspectral reflectance imaging JOSEPH LEVY 1, S. CRAIG CARY 2, KURT JOY 2 and CHARLES K. LEE 2 1Colgate University, Department of Geology, Hamilton, NY 13346, USA 2International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton 3240, New Zealand [email protected] Abstract: The reflectance spectroscopic characteristics of cyanobacteria-dominated microbial mats in the McMurdo Dry Valleys (MDVs) were measured using a hyperspectral point spectrometer aboard an unmanned aerial system (remotely piloted aircraft system, unmanned aerial vehicle or drone) to determine whether mat presence, type and activity could be mapped at a spatial scale sufficient to characterize inter-annual change. Mats near Howard Glacier and Canada Glacier (ASPA 131) were mapped and mat samples were collected for DNA-based microbiome analysis. Although a broadband spectral parameter (a partial normalized difference vegetation index) identified mats, it missed mats in comparatively deep (> 10 cm) water or on bouldery surfaces where mats occupied fringing moats. A hyperspectral parameter (B6) did not have these shortcomings and recorded a larger dynamic range at both sites. When linked with colour orthomosaic data, B6 band strength is shown to be capable of characterizing the presence, type and activity of cyanobacteria-dominated mats in and around MDV streams. 16S rRNA gene polymerase chain reaction amplicon sequencing analysis of the mat samples revealed that dominant cyanobacterial taxa differed between spectrally distinguishable mats, indicating that spectral differences reflect underlying biological distinctiveness. Combined rapid-repeat hyperspectral measurements can be applied in order to monitor the distribution and activity of sentinel microbial ecosystems across the terrestrial Antarctic. Received 11 June 2019, accepted 9 April 2020 Key words: Nostoc, Phormidium, remote sensing, spectroscopy Introduction McMurdo Dry Valleys (MDVs) (Fritsen et al. 2000, Moorhead et al. 2003, Hopkins et al. 2006). However, In ice-free terrestrial systems of Antarctica, there is currently no consensus concerning the drivers microorganisms are thought to be sentinel organisms: of the geographical distribution and extent of Antarctic organisms that rapidly respond to climate-driven cyanobacteria (Taton et al. 2003). Microbial mat changes in water, nutrient or sunlight availability in this heterogeneity is high, even over lengths scales of 1 m or oligotrophic cold desert environment (Stanish et al. less (Jungblut et al. 2005,Karret al. 2005, Zeglin et al. 2012, Tiao et al. 2012, Lee et al. 2018, Niederberger 2009). If different mat types (determined by the et al. 2019). Strong climate–organism connections are identity of characteristic cyanobacteria) respond inferred because the physical characteristics of stream rapidly and in environmentally diagnostic ways to habitats are thought to determine the occurrence of the changing physical conditions, then there is a need to be different microbial mats to a greater extent than able to monitor the extent and activity of Antarctic differences in water quality (McKnight et al. 2013). A microbial mats as a system proxy that would be useful strong relationship between species presence and activity for detecting regional changes in runoff and in microbial mats would be consistent with similar biogeochemistry in an environment that is on the brink relationships observed between mosses in the circum- of major climatic and hydrological change (Fountain Antarctic. For example, in the Windmill Islands, Lucieer et al. 2014, Levy et al. 2018). Critically, microbial mats et al. (2014) showed that the upstream area could serve in MDV streams respond rapidly, over days to weeks, to as a proxy for water availability from snowmelt, which in changes in water availability (McKnight et al. 1999). turn drove spatial patterns of moss activity. Changes in metabolic activity from dormant to active Cyanobacteria-dominated microbial mats are widely and growing are expressed via changes in pigmentation considered as a critical source of organic matter in the intensity and visibility, transitioning from 'cryptic' and otherwise ultra-oligotrophic ecosystem of the indistinguishable from background red-grey sediments 1 Downloaded from https://www.cambridge.org/core. University of Texas Libraries, on 19 May 2020 at 19:43:08, subject to the Cambridge Core terms of use, available at https://www.cambridge.org/core/terms. https://doi.org/10.1017/S0954102020000243 2 JOSEPH LEVY et al. Fig. 1. Location map and context. a. The location of Taylor Valley in the Ross Sea sector of Antarctica. b. The location of Canada Glacier (CG) and Howard Glacier (HG) in eastern Taylor Valley. c. The CG study site. d. The HG study site. Images in c. and d. are orthomosaics generated by UAS flights. b. is a Landsat 7 frame, courtesy of the United States Geological Survey. The green dot labelled P in c. shows the Phormidium mat community sampling site, while the red dot labelled N shows the Nostoc community mat sampling site. to orange and black colours apparent upon inspection Lucieer et al. (2014) have employed multispectral, (McKnight et al. 1999). filter-based sensors that provide superior spectral Based on research in warm desert environments, we resolution to orbital sensors (e.g. 10 nm full-width suggest that hyperspectral reflectance remote sensing half-maximum (FWHM) for drone-borne multispectral may serve as a sensitive tool for mapping the spatial sensors vs tens to hundreds of nanometre bandwidths for extent and species characteristics of cold desert orbital reflectance sensors). In contrasts, hyperspectral microbial mats in Antarctic cold deserts. For example, sensors can achieve FWHM values in the low single Schmidt & Karnieli (2000) used satellite hyperspectral digits, with spectral channel resolutions of < 1 nm observations of vegetation in the semi-arid Negev Desert (Burkart et al. 2013). The advantage of hyperspectral to distinguish biogenic crusts from sands and regolith, reflectance remote sensing over imaging alone is that it has even when during the dry season sands and biogenic been used extensively to discriminate between microbial crusts were nearly indistinguishable by visual inspection. species in both terrestrial (Bachar et al. 2008, Al-Najjar In Antarctica, biological communities typically have an et al. 2014) and marine/aquatic settings (Weaver & extremely small spatial footprint, forming in patches at the Wrigley 1994, Andrefouet et al. 2003, Kohls et al. 2010), metre to decametre scale. In order to capture these small provided that the sensors have the spectral resolution to biological communities, high-spatial-resolution imaging distinguish pigment-specific and organism-specific and reflectance remote sensing have been carried out in absorptions with a width of only a few tens of nanometres. order to study these limited biotic exposures using The goal of this work is to assess the following low-altitude unmanned aerial systems (UASs), also known questions: 1) how can hyperspectral remote sensing be as remotely piloted aircraft systems (RPASs), unmanned used to identify sentinel organisms for the terrestrial aerial vehicles (UAVs) or drones (Lucieer et al. 2014, Antarctic in order to monitor their distribution at Malenovsky et al. 2015, 2017). Prior studies such as change-relevant spatial scales over time? And 2) is it Downloaded from https://www.cambridge.org/core. University of Texas Libraries, on 19 May 2020 at 19:43:08, subject to the Cambridge Core terms of use, available at https://www.cambridge.org/core/terms. https://doi.org/10.1017/S0954102020000243 HYPERSPECTRAL CHARACTERIZATION OF MICROBIAL MATS 3 Fig. 2. Reflectance spectrum of an orange Phormidium mat collected using the STS-VIS from the ground. Spectrum is a 10 scan stack filtered through a 10 channel moving average. Grey shading indicates one standard deviation of the reflectance over the averaging window. a and b are spectral regions used in the calculation of the B6 index. Red and NIR indicate the wavelength regions averaged together to produce a partial NDVI equivalent parameter (NDVIp). possible to use point-sampled hyperspectral data to Canada Glacier (77.61°S, 163.03°E) (Fig. 1). Spectral resolve spatial differences in microbial mat type and measurements were made using an Ocean Optics location? Our guiding hypothesis is that mat-specific STS-VIS reflectance spectrometer with a 350–800 nm hyperspectral indices will have greater spatial and spectral range mounted on a UAS airframe for airborne spectral resolving power for determining the location, acquisition. The STS-VIS uses an ELIS1024 detector type and activity of microbial mats than broad-band with 1024 spectral channels and 50 μm slit size, vegetation indices such as the normalized difference producing a ∼0.4 nm spectral sampling interval per vegetation index (NDVI) (Rouse et al. unpublished data channel. Reflectance spectra were collected using two 1974). In order to confirm the general assumption that linked STS-VIS units, one looking upwards to collect visually distinct mats are dominated by different instantaneous downwelling irradiance and equipped cyanobacteria (Howard-Williams et al. 1986) and our with a direct-attach cosine corrector and the second specific assumption that spectrally distinct mats harbour