Environmental DNA Isolation, Validation, and Preservation Methods

Environmental DNA (eDNA) workflows contain many familiar molecular-lab techniques, but also employ several unique methodologies. When working with eDNA, it is essential to avoid contamination from the point of collection through preservation and select a meaningful negative control. As eDNA can be obtained from a variety of samples and habitats (e.g., soil, water, air, or tissue), protocols will vary depending on usage. Samples may require additional steps to dilute, block, or remove inhibitors or physically break up samples or filters. Thereafter, standard DNA isolation techniques (kit-based or phenol:chloroform:isoamyl [PCI]) are employed. Once DNA is extracted, it is typically quantified using a fluorometer. Yields vary greatly, but are important to know prior to amplification of the gene(s) of interest. Long-term storage of both the sampled material and the extracted DNA is encouraged, as it provides a backup for spilled/contaminated samples, lost data, reanalysis, and future studies using newer technology. Storage in a freezer is often ideal; however, some storage buffers (e.g., Longmires) require that filters or swabs are kept at room temperature to prevent precipitation of buffer-related solutes. These baseline methods for eDNA isolation, validation, and preservation are detailed in this protocol chapter. In addition, we outline a cost-effective, homebrew extraction protocol optimized to extract eDNA.

An Environmental DNA Primer for Microbial and Restoration Ecology

Environmental DNA (eDNA) sequencing-DNA collected from the environment from living cells or shed DNA-was first developed for working with microbes and has greatly benefitted microbial ecologists for decades since. These tools have only become increasingly powerful with the advent of metabarcoding and metagenomics. Most new studies that examine diverse assemblages of bacteria, archaea, protists, fungi, and viruses lean heavily into eDNA using these newer technologies, as the necessary sequencing technology and bioinformatic tools have become increasingly affordable and user friendly. However, eDNA methods are rapidly evolving, and sometimes it can feel overwhelming to simply keep up with the basics. In this review, we provide a starting point for microbial ecologists who are new to DNA-based methods by detailing the eDNA methods that are most pertinent, including study design, sample collection and storage, selecting the right sequencing technology, lab protocols, equipment, and a few bioinformatic tools. Furthermore, we focus on how eDNA work can benefit restoration and what modifications are needed when working in this subfield.

Rewilding in Miniature: Suburban Meadows Can Improve Soil Microbial Biodiversity and Soil Health

Lawns are a ubiquitous, human-made environment created for human enjoyment, leisure, and aesthetics. While net positive for carbon storage, lawns can have negative environmental impacts. Lawns require frequent mowing, which produces high levels of CO₂ pollution and kills off native plants. Lawn fertilizing creates its own environmental pollution. One (presumed) ecologically-friendly alternative to lawns is restoration, or rewilding, of these spaces as meadows, which need less maintenance (e.g., infrequent mowing). However, little work has compared lawns against small-scale meadows for biodiversity outside of pollinator studies. Here, we tested the hypotheses that compared to lawns, meadows have (1) unique and higher levels of soil microbial biodiversity and (2) different soil physical and chemical characteristics. We conducted bacterial (16S) and fungal (ITS2) metabarcoding, and found that both bacteria and fungi are indeed more diverse in meadows (significantly so for bacteria). Species composition between meadows and lawns was significantly different for both types of microbes, including higher levels of mycorrhizal fungi in meadows. We also found that chemistry (e.g., potassium and metrics relating to pH) differed significantly between lawns and meadows and was more optimal for plant growth in the meadows. We believe these differences are caused by the different organisms dwelling in these habitats. In summary, these findings point to notable-positive-shifts in microbial and chemical compositions within meadows, further indicating that meadow restoration benefits biodiversity and soil health.

Spatial modeling could not differentiate early SARS-CoV-2 cases from the distribution of humans on the basis of climate in the United States

The SARS-CoV-2 coronavirus is wreaking havoc globally, yet, as a novel pathogen, knowledge of its biology is still emerging. Climate and seasonality influence the distributions of many diseases, and studies suggest at least some link between SARS-CoV-2 and weather. One such study, building species distribution models (SDMs), predicted SARS-CoV-2 risk may remain concentrated in the Northern Hemisphere, shifting northward in summer months. Others have highlighted issues with SARS-CoV-2 SDMs, notably: the primary niche of the virus is the host it infects, climate may be a weak distributional predictor, global prevalence data have issues, and the virus is not in population equilibrium. While these issues should be considered, we believe climate's relationship with SARS-CoV-2 is still worth exploring, as it may have some impact on the distribution of cases. To further examine if there is a link to climate, we build model projections with raw SARS-CoV-2 case data and population-scaled case data in the USA. The case data were from across March 2020, before large travel restrictions and public health policies were impacting cases across the country. We show that SDMs built from population-scaled case data cannot be distinguished from control models (built from raw human population data), while SDMs built on raw case data fail to predict the known distribution of cases in the U.S. from March. The population-scaled analyses indicate that climate did not play a central role in early U.S. viral distribution and that human population density was likely the primary driver. We do find slightly more population-scaled viral cases in cooler areas. Ultimately, the temporal and geographic constraints on this study mean that we cannot rule out climate as a partial driver of the SARS-CoV-2 distribution. Climate's role on SARS-CoV-2 should continue to be cautiously examined, but at this time we should assume that SARS-CoV-2 will continue to spread anywhere in the U.S. where governmental policy does not prevent spread.

Spatial modeling could not differentiate early SARS-CoV-2 cases from the distribution of humans on the basis of climate in the United States

The SARS-CoV-2 coronavirus is wreaking havoc globally, yet, as a novel pathogen, knowledge of its biology is still emerging. Climate and seasonality influence the distributions of many diseases, and studies suggest at least some link between SARS-CoV-2 and weather. One such study, building species distribution models (SDMs), predicted SARS-CoV-2 risk may remain concentrated in the Northern Hemisphere, shifting northward in summer months. Others have highlighted issues with SARS-CoV-2 SDMs, notably: the primary niche of the virus is the host it infects, climate may be a weak distributional predictor, global prevalence data have issues, and the virus is not in population equilibrium. While these issues should be considered, we believe climate's relationship with SARS-CoV-2 is still worth exploring, as it may have some impact on the distribution of cases. To further examine if there is a link to climate, we build model projections with raw SARS-CoV-2 case data and population-scaled case data in the USA. The case data were from across March 2020, before large travel restrictions and public health policies were impacting cases across the country. We show that SDMs built from population-scaled case data cannot be distinguished from control models (built from raw human population data), while SDMs built on raw case data fail to predict the known distribution of cases in the U.S. from March. The population-scaled analyses indicate that climate did not play a central role in early U.S. viral distribution and that human population density was likely the primary driver. We do find slightly more population-scaled viral cases in cooler areas. Ultimately, the temporal and geographic constraints on this study mean that we cannot rule out climate as a partial driver of the SARS-CoV-2 distribution. Climate's role on SARS-CoV-2 should continue to be cautiously examined, but at this time we should assume that SARS-CoV-2 will continue to spread anywhere in the U.S. where governmental policy does not prevent spread.

Paleo-metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA

Fossil rodent middens are powerful tools in paleoecology. In arid parts of western North America, packrat (Neotoma spp.) middens preserve plant and animal remains for tens of thousands of years. Midden contents are so well preserved that fragments of endogenous ancient DNA (aDNA) can be extracted and analyzed across millennia. Here, we explore the use of shotgun metagenomics to study the aDNA obtained from packrat middens up to 32,000 C14 years old. Eleven Illumina HiSeq 2500 libraries were successfully sequenced, and between 0.11% and 6.7% of reads were classified using Centrifuge against the NCBI "nt" database. Eukaryotic taxa identified belonged primarily to vascular plants with smaller proportions mapping to ascomycete fungi, arthropods, chordates, and nematodes. Plant taxonomic diversity in the middens is shown to change through time and tracks changes in assemblages determined by morphological examination of the plant remains. Amplicon sequencing of ITS2 and rbcL provided minimal data for some middens, but failed at amplifying the highly fragmented DNA present in others. With repeated sampling and deep sequencing, analysis of packrat midden aDNA from well-preserved midden material can provide highly detailed characterizations of past communities of plants, animals, bacteria, and fungi present as trace DNA fossils. The prospects for gaining more paleoecological insights from aDNA for rodent middens will continue to improve with optimization of laboratory methods, decreasing sequencing costs, and increasing computational power.

Historical mitochondrial diversity in African leopards (Panthera pardus) revealed by archival museum specimens

Once found throughout Africa and Eurasia, the leopard (Panthera pardus) was recently uplisted from Near Threatened to Vulnerable by the International Union for the Conservation of Nature (IUCN). Historically, more than 50% of the leopard's global range occurred in continental Africa, yet sampling from this part of the species' distribution is only sparsely represented in prior studies examining patterns of genetic variation at the continental or global level. Broad sampling to determine baseline patterns of genetic variation throughout the leopard's historical distribution is important, as these measures are currently used by the IUCN to direct conservation priorities and management plans. By including data from 182 historical museum specimens, faecal samples from ongoing field surveys, and published sequences representing sub-Saharan Africa, we identify previously unrecognized genetic diversity in African leopards. Our mtDNA data indicates high levels of divergence among regional populations and strongly differentiated lineages in West Africa on par with recent studies of other large vertebrates. We provide a reference benchmark of genetic diversity in African leopards against which future monitoring can be compared. These findings emphasize the utility of historical museum collections in understanding the processes that shape present biodiversity. Additionally, we suggest future research to clarify African leopard taxonomy and to differentiate between delineated units requiring monitoring or conservation action.

Fine scale patterns of genetic partitioning in the rediscovered African crocodile, Crocodylus suchus (Saint-Hilaire 1807)

Landscape heterogeneity, phylogenetic history, and stochasticity all influence patterns of geneflow and connectivity in wild vertebrates. Fine-scale patterns of genetic partitioning may be particularly important for the sustainable management of widespread species in trade, such as crocodiles. We examined genetic variation within the rediscovered African crocodile, Crocodylus suchus, across its distribution in West and Central Africa. We genotyped 109 individuals at nine microsatellite loci from 16 sampling localities and used three Bayesian clustering techniques and an analysis of contemporary gene flow to identify population structure across the landscape. We identified up to eight genetic clusters that largely correspond to populations isolated in coastal wetland systems and across large distances. Crocodile population clusters from the interior were readily distinguished from coastal areas, which were further subdivided by distance and drainage basin. Migration analyses indicated contemporary migration only between closely positioned coastal populations. These findings indicate high levels of population structure throughout the range of C. suchus and we use our results to suggest a role for molecular tools in identifying crocodile conservation units for this species. Further research, including additional sampling throughout the Congo and Niger drainages, would clarify both the landscape connectivity and management of this species.

Noteworthy habitat and phylogeny updates for eastern US Ulota (Orthotrichaceae, Bryophyta)

The moss Ulota crispa is ubiquitous as an obligate epiphyte in eastern North America. Yet several specimens preliminarily identified as U. crispa were collected from the upper portions of boulders in the Shawangunks, NY. Mitochondrial (nad5) and chloroplast (rps4 and trnL-trnF) sequence data were produced for these specimens, confirming their status as the first record of rock-dwelling U. crispa in North America. The reviewed loci were then used to assess phylogenetic relationships of Northeastern US Ulota species, incorporating a species not yet reviewed, U. coarctata. Conforming to peristome morphology, Ulota hutchinsiae appears to be more closely related to U. crispa than to U. coarctata. Monophyly was recovered for U. crispa and U. coarctata. Although monophyly was not found for U. hutchinsiae, it is diagnosably distinct based on the reviewed loci. While almost identical in number of nucleotides sequenced, mitochondrial DNA held substantially less phylogenetically informative nucleotides than the chloroplast loci, but did have important indel information segregating U. coarctata from other species reviewed.

Integrating molecular, phenotypic and environmental data to elucidate patterns of crocodile hybridization in Belize

The genus Crocodylus comprises 12 currently recognized species, many of which can be difficult to differentiate phenotypically. Interspecific hybridization among crocodiles is known to occur in captivity and has been documented between some species in the wild. The identification of hybrid individuals is of importance for management and monitoring of crocodilians, many of which are Convention on International Trade in Endangered Species (CITES) listed. In this study, both mitochondrial and nuclear DNA markers were evaluated for their use in confirming a suspected hybrid zone between American crocodile (Crocodylus acutus) and Morelet's crocodile (Crocodylus moreletii) populations in southern Belize where individuals and nests exhibiting atypical phenotypic features had previously been observed. Patterns observed in both phenotypic and molecular data indicate possible behavioural and ecological characteristics associated with hybridization events. The results of the combined analyses found that the majority of suspected hybrid samples represent crosses between female C. acutus and male C. moreletii. Phenotypic data could statistically identify hybrids, although morphological overlap between hybrids and C. moreletii reduced reliability of identification based solely on field characters. Ecologically, C. acutus was exclusively found in saline waters, whereas hybrids and C. moreletii were largely absent in these conditions. A hypothesized correlation between unidirectional hybridization and destruction of C. acutus breeding habitats warrants additional research.