A comparative study of prokaryotic diversity and physicochemical characteristics of Devils Hole and the Ash Meadows Fish Conservation Facility, a constructed analog

<div><p>Devils Hole is the sole natural habitat of the critically endangered Devils Hole pupfish (<i>Cyprinodon diabolis</i>). To establish a backup population, the Ash Meadows Fish Conservation Facility (AMFCF), a full-scale replica of the uppermost 6.7 m of Devils Hole, was constructed by management agencies in the mid-2010s. Despite rigorous efforts to mimic the bathymetric and physical details of the Devils Hole environment, the biogeochemistry and microbiology of the AMFCF refuge tank remain largely unaddressed. We evaluated water physicochemistry and employed Illumina DNA sequencing of 16S rRNA gene libraries to evaluate planktonic and benthic bacterial and archaeal community composition within their respective physicochemical contexts in Devils Hole and AMFCF on the same day. Major ion concentrations were consistent between the two systems, but water temperature and dissolved oxygen dynamics differed. Bioavailable nitrogen (primarily nitrate) was 5x lower in AMFCF. Devils Hole and AMFCF nitrogen:phosphorus molar ratios were 107:1 and 22:1, indicative of different nutrient control mechanisms. Both sites are microbiologically diverse, with over 40 prokaryotic phyla represented at each, with 37 shared between them and nearly than half deriving from candidate divisions. The abundance and composition of predicted photosynthetic primary producers (Cyanobacteria) was markedly different between sites: Devils Hole planktonic and sediment communities were dominated by <i>Oscillatoria spp</i>. (13.2% mean relative abundance), which proved virtually undetectable in AMFCF. Conversely, AMFCF was dominated by a predicted heterotroph from the Verrucomicrobiaceae family (31.7%); which was comparatively rare (<2.4%) in Devils Hole. We propose that the paucity of bioavailable nitrogen in AMFCF, perhaps resulting from physical isolation from allochthonous environmental inputs, is reflected in the microbial assemblage disparity, influences biogeochemical cycling of other dissolved constituents, and may ultimately impact survivorship and recruitment of refuge populations of the Devils Hole pupfish.</p></div

Field sites.

<p>a) The top of the Devils Hole water table viewed looking north. The shallow shelf roughly corresponds to the area below the metal walkway (temporarily installed for this work) and was partially covered with algal mats on the day of sampling. The deep pool occupies the algae-free upper half of the submerged area. b) Refuge tank at the Ash Meadows Fish Conservation Facility, a full-scale bathymetric replica of the shelf at Devils Hole, on the day of sampling. As shown, the shelf occupies the area below the concrete ledge.</p

Relative abundances (mean and SD) of the top 5 differentially abundant operational taxonomic units identified by SIMPER analysis.

<p>Differentially abundant OTUs between <b>a)</b> planktonic samples and <b>b)</b> sediment samples between Devils Hole and Ash Meadows Fish Conservation Facility (AMFCF), along with OTU ID and taxonomy, are shown. Prefixes (p_, o_, f_ and g_) denote phylum, order, family, and genus level OTU identities. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194404#pone.0194404.s008" target="_blank">S6 Table</a> for the percent contribution of each OTU to the dissimilarity between each group of samples.</p

Major physicochemical characteristics of waters from Devils Hole (DH), Ash Meadows Fish Conservation Facility (AMFCF), and Well P-9.

<p>Major physicochemical characteristics of waters from Devils Hole (DH), Ash Meadows Fish Conservation Facility (AMFCF), and Well P-9.</p

Principal component analysis.

<p>Principal component analysis ordinations of a) pairwise abundance-unweighted UniFrac distances and b) pairwise abundance-weighted UniFrac distances for all samples show separation of samples by sample location and sample type (planktonic vs. sediment). Individual samples are colored according to sample type (planktonic vs. sediment: Devils Hole (DH) planktonic and sediment samples are shown as light blue and dark blue squares, respectively; Ash Meadows Fish Conservation Facility (AMFCF) planktonic and sediment samples are shown as yellow and red triangles, respectively; and the Well P-9 sample is shown as an asterisk.</p

Ancient human mitochondrial DNA and radiocarbon analysis of archived quids from the Mule Spring Rockshelter, Nevada, USA

<div><p>Chewed and expectorated quids, indigestible stringy fibers from the roasted inner pulp of agave or yucca root, have proven resilient over long periods of time in dry cave environments and correspondingly, although little studied, are common in archaeological archives. In the late 1960s, thousands of quids were recovered from Mule Spring Rockshelter (Nevada, USA) deposits and stored without consideration to DNA preservation in a museum collection, remaining unstudied for over fifty years. To assess the utility of these materials as repositories for genetic information about past inhabitants of the region and their movements, twenty-one quids were selected from arbitrary excavation depths for detailed analysis. Human mitochondrial DNA sequences from the quids were amplified by PCR and screened for diagnostic single nucleotide polymorphisms. Most detected single nucleotide polymorphisms were consistent with recognized Native American haplogroup subclades B2a5, B2i1, C1, C1c, C1c2, and D1; with the majority of the sample set consistent with subclades C1, C1c, and C1c2. In parallel with the DNA analysis, each quid was radiocarbon dated, revealing a time-resolved pattern of occupancy from 347 to 977 calibrated years before present. In particular, this dataset reveals strong evidence for the presence of haplogroup C1/C1c at the Southwestern edge of the US Great Basin from ~670 to 980 cal YBP, which may temporally correspond with the beginnings of the so-called Numic Spread into the region. The research described here demonstrates an approach which combines targeted DNA analysis with radiocarbon age dating; thus enabling the genetic analysis of archaeological materials of uncertain stratigraphic context. Here we present a survey of the maternal genetic profiles from people who used the Mule Spring Rockshelter and the historic timing of their utilization of a key natural resource.</p></div

Mule Spring Rockshelter site.

<p>Photograph of the Mule Spring Rockshelter opening and apron as it appeared in 2016.</p

Extant agave and prehistoric quid.

<p>Example of A) an agave plant (<i>Agave utahensis</i> var. <i>nevadensis</i>) photographed near Mule Spring Cave in 2016, and B) a quid before DNA extraction (this work).</p

Mule Spring Rockshelter quid haplogroups.

<p>Mule Spring Rockshelter quid haplogroups.</p