Multiscale climate change impacts on plant diversity in the Atacama Desert

Interactive effects of grassland utilization and climatic factors govern the plant diversity-soil C relationship in steppe of North China

The relationship between plant diversity and the ecosystem carbon pool is important for understanding the role of biodiversity in regulating ecosystem functions. However, it is not clear how the relationship between plant diversity and soil carbon content changes under different grassland use patterns. In a 3-year study from 2013 to 2015, we investigated plant diversity and soil total carbon (TC) content of grasslands in northern China under different grassland utilization methods (grazing, mowing, and enclosure) and climatic conditions. Shannon-Wiener and Species richness index of grassland were significantly decreased by grazing and mowing. Plant diversity was positively correlated with annual precipitation (AP) and negatively correlated with annual mean temperature (AMT). AP was the primary regulator of plant diversity. Grazing and mowing decreased TC levels in grasslands compared with enclosures, especially in topsoil (0-20 cm). The average TC content was decreased by 58 % and 36 % in the 0-10 cm soil layer, while it was decreased by 68 % and 39 % in 10-20 cm soil layer. TC was positively correlated with AP and negatively correlated with AMT. Principal component analysis (PCA) showed that plant diversity was positively correlated with soil TC, and the correlation decreased with an increase in the soil depth. Overall, this study provides a theoretical basis for predicting soil carbon storage in grasslands under human disturbances and climate change impacts.

Effect of In Vitro Micropropagation on the Chemical, Antioxidant, and Biological Characteristics of Senecio nutans Sch. Bip., an Endemic Plant of the Atacama Desert Andean Region

The species Senecio nutans Sch. Bip., commonly called "chachacoma", is widely used as a medicinal plant by the Andean communities of Northern Chile. Ethanolic extracts of S. nutans and the main compound, 4-hydroxy-3-(3-methyl-2-butenyl) acetophenone, have shown interesting biological activity. However, due to the high-altitude areas where this species is found, access to S. nutans is very limited. Due to the latter, in this work, we carried out micropropagation in vitro and ex vitro adaptation techniques as an alternative for the massive multiplication, conservation, and in vitro production of high-value metabolites from this plant. The micropropagation and ex vitro adaptation techniques were successfully employed, and UHPLC-DAD analysis revealed no significant changes in the phenolic profile, with acetophenone 4 being the most abundant metabolite, whose antioxidant and antibacterial activity was studied. Independently of the applied culture condition, the ethanolic extracts of S. nutans presented high activity against both Gram-positive and Gram-negative bacteria, demonstrating their antimicrobial capacity. This successful initiation of in vitro and ex vitro cultures provides a biotechnological approach for the conservation of S. nutans and ensures a reliable and consistent source of acetophenone 4 as a potential raw material for pharmacological applications.

Genomics for monitoring and understanding species responses to global climate change

All life forms across the globe are experiencing drastic changes in environmental conditions as a result of global climate change. These environmental changes are happening rapidly, incur substantial socioeconomic costs, pose threats to biodiversity and diminish a species' potential to adapt to future environments. Understanding and monitoring how organisms respond to human-driven climate change is therefore a major priority for the conservation of biodiversity in a rapidly changing environment. Recent developments in genomic, transcriptomic and epigenomic technologies are enabling unprecedented insights into the evolutionary processes and molecular bases of adaptation. This Review summarizes methods that apply and integrate omics tools to experimentally investigate, monitor and predict how species and communities in the wild cope with global climate change, which is by genetically adapting to new environmental conditions, through range shifts or through phenotypic plasticity. We identify advantages and limitations of each method and discuss future research avenues that would improve our understanding of species' evolutionary responses to global climate change, highlighting the need for holistic, multi-omics approaches to ecosystem monitoring during global climate change.

Ecological and metabolic implications of the nurse effect of Maihueniopsis camachoi in the Atacama Desert

Plant-plant positive interactions are key drivers of community structure. Yet, the underlying molecular mechanisms of facilitation processes remain unexplored. We investigated the 'nursing' effect of Maihueniopsis camachoi, a cactus that thrives in the Atacama Desert between c. 2800 and 3800 m above sea level. We hypothesised that an important protective factor is thermal amelioration of less cold-tolerant species with a corresponding impact on molecular phenotypes. To test this hypothesis, we compared plant cover and temperatures within the cactus foliage with open areas and modelled the effect of temperatures on plant distribution. We combined eco-metabolomics and machine learning to test the molecular consequences of this association. Multiple species benefited from the interaction with M. camachoi. A conspicuous example was the extended distribution of Atriplex imbricata to colder elevations in association with M. camachoi (400 m higher as compared to plants in open areas). Metabolomics identified 93 biochemical markers predicting the interaction status of A. imbricata with 79% accuracy, independently of year. These findings place M. camachoi as a key species in Atacama plant communities, driving local biodiversity with an impact on molecular phenotypes of nursed species. Our results support the stress-gradient hypothesis and provide pioneer insights into the metabolic consequences of facilitation.

Climatic Niche Dynamics of the Astereae Lineage and Haplopappus Species Distribution following Amphitropical Long-Distance Dispersal

The tribe Astereae (Asteraceae) displays an American Amphitropical Disjunction. To understand the eco-evolutionary dynamics associated with a long-distance dispersal event and subsequent colonization of extratropical South America, we compared the climatic and geographic distributions of South American species with their closest North American relatives, focusing on the diverse South American Astereae genus, Haplopappus. Phylogenetic analysis revealed that two South American genera are closely related to seven North American genera. The climatic niche overlap (D = 0.5) between South and North America exhibits high stability (0.89), low expansion (0.12), and very low unfilling (0.04). The distribution of the North American species predicted the climatic and geographic space occupied by the South American species. In central Chile, Haplopappus showed a non-random latitudinal gradient in species richness, with Mediterranean climate variables mainly explaining the variation. Altitudinal patterns indicated peak richness at 600 m, declining at lower and higher elevations. These findings support climatic niche conservatism in shaping Haplopappus species distribution and diversity. Two major endemism zones were identified in central Chile and the southern region, with a transitional zone between Mediterranean and Temperate macro-bioclimates. Our results indicate strong niche conservatism following long-distance dispersal and slight niche expansion due to unique climatic variables in each hemisphere.

Simplified Genomic Data Revealing the Decline of Aleuritopteris grevilleoides Population Accompanied by the Uplift of Dry-Hot Valley in Yunnan, China

Understanding the evolutionary history of endangered species is crucial for identifying the main reasons for species endangerment in the past and predicting the changing trends and evolutionary directions of their future distribution. In order to study the impact of environmental changes caused by deep valley incision after the uplift of the Qinghai-Tibet Plateau on endangered species, we collected 23 samples belonging to four populations of Aleuritopteris grevilleoides, an endangered fern endemic to the dry-hot valleys (DHV) of Yunnan. Single-nucleotide variation sites (SNPs) were obtained by the genotyping-by-sequencing (GBS) method, and approximately 8085 SNP loci were identified. Through the reconstruction and analysis of genetic diversity, population structure, population dynamics, evolution time, and ancestral geographical distribution, combined with geological historical events such as the formation of dry-hot valleys, this study explores the formation history, current situation, reasons for endangerment and scientifically sound measures for the protection of A. grevilleoides. In our study, A. grevilleoides had low genetic diversity (Obs_Het = 0.16, Exp_Het = 0.32, Pi = 0.33) and a high inbreeding coefficient (Fis = 0.45). The differentiation events were 0.18 Mya, 0.16 Mya, and 0.11 Mya in the A. grevilleoides and may have been related to the formation of terraces within the dry-hot valleys. The history of population dynamics results shows that the diversion of the river resulted in a small amount of gene flow between the two clades, accompanied by a rapid increase in the population at 0.8 Mya. After that, the effective population sizes of A. grevilleoides began to contract continuously due to topographic changes resulting from the continuous expansion of dry-hot valleys. In conclusion, we found that the environmental changes caused by geological events might be the main reason for the changing population size of A. grevilleoides.

Testing the stress gradient hypothesis in soil bacterial communities associated with vegetation belts in the Andean Atacama Desert

BACKGROUND

Soil microorganisms are in constant interaction with plants, and these interactions shape the composition of soil bacterial communities by modifying their environment. However, little is known about the relationship between microorganisms and native plants present in extreme environments that are not affected by human intervention. Using high-throughput sequencing in combination with random forest and co-occurrence network analyses, we compared soil bacterial communities inhabiting the rhizosphere surrounding soil (RSS) and the corresponding bulk soil (BS) of 21 native plant species organized into three vegetation belts along the altitudinal gradient (2400-4500 m a.s.l.) of the Talabre-Lejía transect (TLT) in the slopes of the Andes in the Atacama Desert. We assessed how each plant community influenced the taxa, potential functions, and ecological interactions of the soil bacterial communities in this extreme natural ecosystem. We tested the ability of the stress gradient hypothesis, which predicts that positive species interactions become increasingly important as stressful conditions increase, to explain the interactions among members of TLT soil microbial communities.

RESULTS

Our comparison of RSS and BS compartments along the TLT provided evidence of plant-specific microbial community composition in the RSS and showed that bacterial communities modify their ecological interactions, in particular, their positive:negative connection ratios in the presence of plant roots at each vegetation belt. We also identified the taxa driving the transition of the BS to the RSS, which appear to be indicators of key host-microbial relationships in the rhizosphere of plants in response to different abiotic conditions. Finally, the potential functions of the bacterial communities also diverge between the BS and the RSS compartments, particularly in the extreme and harshest belts of the TLT.

CONCLUSIONS

In this study, we identified taxa of bacterial communities that establish species-specific relationships with native plants and showed that over a gradient of changing abiotic conditions, these relationships may also be plant community specific. These findings also reveal that the interactions among members of the soil microbial communities do not support the stress gradient hypothesis. However, through the RSS compartment, each plant community appears to moderate the abiotic stress gradient and increase the efficiency of the soil microbial community, suggesting that positive interactions may be context dependent.

Pre-Columbian cultivation of vegetatively propagated and fruit tree tropical crops in the Atacama Desert

South America is a megadiverse continent that witnessed the domestication, translocation and cultivation of various plant species from seemingly contrasting ecosystems. It was the recipient and supplier of crops brought to and from Mesoamerica (such as maize and cacao, respectively), and Polynesia to where the key staple crop sweet potato was exported. Not every instance of the trans-ecological expansion of cultivated plants (both domesticated and wild), however, resulted in successful farming. Here, we review the transregional circulation and introduction of five food tropical crops originated in the tropical and humid valleys of the eastern Andes—achira, cassava, ahipa, sweet potato, and pacay—to the hyper-arid coastal valleys of the Atacama Desert of northern Chile, where they have been found in early archeological sites. By means of an evaluation of the contexts of their deposition and supported by direct radiocarbon dating, stable isotopes analyses, and starch grain analysis, we evaluate different hypotheses for explaining their introduction and adaptation to the hyper-arid soils of northern Chile, by societal groups that after the introduction of cultigens still retained a strong dependence on marine hunting, gathering and fishing ways of life based on wide variety of marine coast resources. Many of the studied plants were part of a broader package of introduced goods and technological devices and procedures, linked to food, therapeutic medicine, social and ritual purposes that transformed previous hunter-gatherer social, economic, and ideological institutions. Based on archeological data, we discuss some of the possible socio-ecological processes involved in the development of agricultural landscapes including the adoption of tropical crops originated several hundred kilometers away from the Atacama Desert during the Late Holocene.

Phylogenomics and evolutionary history of Oreocnide (Urticaceae) shed light on recent geological and climatic events in SE Asia

Climate change and geological events have long been known to shape biodiversity, implying that these can likewise be viewed from a biological perspective. To study whether plants can shed light on this, and how they responded to climate change there, we examined Oreocnide, a genus widely distributed in SE Asia. Based on broad geographic sampling with genomic data, we employed an integrative approach of phylogenomics, molecular dating, historical biogeography, and ecological analyses. We found that Oreocnide originated in mainland East Asia and began to diversify ∼6.06 Ma, probably in response to a distinct geographic and climatic transition in East Asia at around that time, implying that the last important geological change in mainland SE Asia might be 1 Ma older than previously suggested. Around four immigration events to the islands of Malesia followed, indicating that immigration from the mainland could be an underestimated factor in the assembly of biotic communities in the region. Two detected increases of diversification rate occurred 3.13 and 1.19 Ma, which strongly implicated climatic rather than geological changes as likely drivers of diversification, with candidates being the Pliocene intensification of the East Asian monsoons, and Pleistocene climate and sea level fluctuations. Distribution modelling indicated that Pleistocene sea level and climate fluctuations were inferred to enable inter-island dispersal followed by allopatric separation, underpinning radiation in the genus. Overall, our study, based on multiple lines of evidence, linked plant diversification to the most recent climatic and geological events in SE Asia. We highlight the importance of immigration in the assembly and diversification of the SE Asian flora, and underscore the utility of plant clades, as independent lines of evidence, for reconstructing recent climatic and geological events in the SE Asian region.

Partners to survive: Hoffmannseggia doellii root-associated microbiome at the Atacama Desert

The discovery and characterization of plant species adapted to extreme environmental conditions have become increasingly important. Hoffmannseggia doellii is a perennial herb endemic to the Chilean Atacama Desert that grows in the western Andes between 2800 and 3600 m above sea level. Its growing habitat is characterized by high radiation and low water and nutrient availability. Under these conditions, H. doellii can grow, reproduce, and develop an edible tuberous root. We characterized the H. doellii soil-associated microbiomes to understand the biotic factors that could influence their surprising ability to survive. We found an increased number of observed species and higher phylogenetic diversity of bacteria and fungi on H. doellii root soils compared with bare soil (BS) along different sites and to soil microbiomes of other plant species. Also, the H. doellii-associated microbiome had a higher incidence of overall positive interactions and fungal within-kingdom interactions than their corresponding BS network. These findings suggest a microbial diversity soil modulation mechanism that may be a characteristic of highly tolerant plants to diverse and extreme environments. Furthermore, since H. doellii is related to important cultivated crops, our results create an opportunity for future studies on climate change adaptation of crop plants.

Predictive metabolomics of multiple Atacama plant species unveils a core set of generic metabolites for extreme climate resilience

Current crop yield of the best ideotypes is stagnating and threatened by climate change. In this scenario, understanding wild plant adaptations in extreme ecosystems offers an opportunity to learn about new mechanisms for resilience. Previous studies have shown species specificity for metabolites involved in plant adaptation to harsh environments. Here, we combined multispecies ecological metabolomics and machine learning-based generalized linear model predictions to link the metabolome to the plant environment in a set of 24 species belonging to 14 families growing along an altitudinal gradient in the Atacama Desert. Thirty-nine common compounds predicted the plant environment with 79% accuracy, thus establishing the plant metabolome as an excellent integrative predictor of environmental fluctuations. These metabolites were independent of the species and validated both statistically and biologically using an independent dataset from a different sampling year. Thereafter, using multiblock predictive regressions, metabolites were linked to climatic and edaphic stressors such as freezing temperature, water deficit and high solar irradiance. These findings indicate that plants from different evolutionary trajectories use a generic metabolic toolkit to face extreme environments. These core metabolites, also present in agronomic species, provide a unique metabolic goldmine for improving crop performances under abiotic pressure.

Two Sides of the Same Desert: Floristic Connectivity and Isolation Along the Hyperarid Coast and Precordillera in Peru and Chile

In this study we aim at refining our understanding of the floristic connectivity of the loma- and precordillera floras of southern Peru and northern Chile and the parameters determining vegetation cover in this region. We used multivariate analyses to test for floristic- and environmental similarity across 53 precordillera and loma locations in Peru and Chile. We propose the use of predictive modeling in estimating the extent of desert vegetation as a complementary method to remote sensing. We created habitat suitability models for the vegetation on the coast and in the precordillera based on a combination of latent bioclimatic variables and additional environmental predictors using Maxent. We found Peruvian and Chilean lomas to be strongly floristically differentiated, as are the Chilean precordillera and lomas. Conversely, there is clear connectivity between both the Peruvian loma- and precordillera floras on the one hand and the Peruvian and Chilean precordillera floras on the other. Divergent environmental conditions were retrieved as separating the precordillera and lomas, while environmental conditions are not differentiated between Peruvian and Chilean lomas. Peruvian and Chilean precordilleras show a gradual change in environmental conditions. Habitat suitability models of vegetation cover retrieve a gap for the loma vegetation along the coast between Peru and Chile, while a continuous belt of suitable habitats is retrieved along the Andean precordillera. Unsuitable habitat for loma vegetation north and south of the Chilean and Peruvian border likely represents an ecogeographic barrier responsible for the floristic divergence of Chilean and Peruvian lomas. Conversely, environmental parameters change continuously along the precordilleras, explaining the moderate differentiation of the corresponding floras. Our results underscore the idea of the desert core acting as an ecogeographic barrier separating the coast from the precordillera in Chile, while it has a more limited isolating function in Peru. We also find extensive potentially suitable habitats for both loma- and precordillera vegetation so far undetected by methods of remote sensing.

Climate change effects on desert ecosystems: A case study on the keystone species of the Namib Desert Welwitschia mirabilis

Deserts have been predicted to be one of the most responsive ecosystems to global climate change. In this study, we examine the spatial and demographic response of a keystone endemic plant of the Namib Desert (Welwitschia mirabilis), for which displacement and reduction of suitable climate has been foreseen under future conditions. The main aim is to assess the association between ongoing climate change and geographical patterns of welwitschia health, reproductive status, and size. We collected data on welwitschia distribution, health condition, reproductive status, and plant size in northern Namibia. We used ecological niche models to predict the expected geographic shift of suitability under climate change scenarios. For each variable, we compared our field measurements with the expected ongoing change in climate suitability. Finally, we tested the presence of simple geographical gradients in the observed patterns. The historically realized thermal niche of welwitschia will be almost completely unavailable in the next 30 years in northern Namibia. Expected reductions of climatic suitability in our study sites were strongly associated with indicators of negative population conditions, namely lower plant health, reduced recruitment and increased adult mortality. Population condition does not follow simple latitudinal or altitudinal gradients. The observed pattern of population traits is consistent with climate change trends and projections. This makes welwitschia a suitable bioindicator (i.e. a 'sentinel') for climate change effect in the Namib Desert ecosystems. Our spatially explicit approach, combining suitability modeling with geographic combinations of population conditions measured in the field, could be extensively adopted to identify sentinel species, and detect population responses to climate change in other regions and ecosystems.

Vulnerability of grassland seed banks to resource-enhancing global changes

Soil seed banks represent reservoirs of diversity in the soil that may increase resilience of communities to global changes. Two global change factors that can dramatically alter the composition and diversity of aboveground communities are nutrient enrichment and increased rainfall. In a full-factorial nutrient and rainfall addition experiment in an annual Californian grassland, we asked whether shifts in aboveground composition and diversity were reflected in belowground seed banks. Nutrient and rainfall additions increased exotic and decreased native abundances, while rainfall addition increased exotic richness, both in aboveground communities and seed banks. Under nutrient addition, forbs and short-statured plants were replaced by grasses and tall-statured species, both above and below ground, and whole-community responses to the treatments were similar. Structural equation models indicated that especially nutrient addition effects on seed banks were largely indirect via aboveground communities. However, rainfall addition also had a direct negative effect on native species richness and abundance of species with high specific leaf area (SLA) in seed banks, showing that seed banks are sensitive to the direct effects of temporary increases in rainfall. Our findings highlight the vulnerability of seed banks in annual, resource-poor grasslands to shifts in compositional and trait changes in aboveground communities and show how invasion of exotics and depletion of natives are critical for these above-belowground compositional shifts. Our findings suggest that seed banks have limited potential to buffer resource-poor annual grasslands from the community changes caused by resource enrichment.

Using paleo-archives to safeguard biodiversity under climate change

Strategies for 21st-century environmental management and conservation under global change require a strong understanding of the biological mechanisms that mediate responses to climate- and human-driven change to successfully mitigate range contractions, extinctions, and the degradation of ecosystem services. Biodiversity responses to past rapid warming events can be followed in situ and over extended periods, using cross-disciplinary approaches that provide cost-effective and scalable information for species' conservation and the maintenance of resilient ecosystems in many bioregions. Beyond the intrinsic knowledge gain such integrative research will increasingly provide the context, tools, and relevant case studies to assist in mitigating climate-driven biodiversity losses in the 21st century and beyond.

Isolation and Identification of Soil Bacteria from Extreme Environments of Chile and Their Plant Beneficial Characteristics

The isolation of soil bacteria from extreme environments represents a major challenge, but also an opportunity to characterize the metabolic potential of soil bacteria that could promote the growth of plants inhabiting these harsh conditions. The aim of this study was to isolate and identify bacteria from two Chilean desert environments and characterize the beneficial traits for plants through a biochemical approach. By means of different culture strategies, we obtained 39 bacterial soil isolates from the Coppermine Peninsula (Antarctica) and 32 from Lejía Lake shore soil (Atacama Desert). The results obtained from the taxonomic classification and phylogenetic analysis based on 16S rDNA sequences indicated that the isolates belonged to four phyla (Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes), and that the most represented genus at both sites was Pseudomonas. Regarding biochemical characterization, all strains displayed in vitro PGP capabilities, but these were in different proportions that grouped them according to their site of origin. This study contributes with microbial isolates from natural extreme environments with biotechnological potentials in improving plant growth under cold stress.

A balancing act: how plants integrate nitrogen and water signals

Nitrogen (N) and water (W) are crucial inputs for plant survival as well as costly resources for agriculture. Given their importance, the molecular mechanisms that plants rely on to signal changes in either N or W status have been under intense scrutiny. However, how plants sense and respond to the combination of N and W signals at the molecular level has received scant attention. The purpose of this review is to shed light on what is currently known about how plant responses to N are impacted by W status. We review classic studies which detail how N and W combinations have both synergistic and antagonistic effects on key plant traits, such as root architecture and stomatal aperture. Recent molecular studies of N and W interactions show that mutations in genes involved in N metabolism affect drought responses, and vice versa. Specifically, perturbing key N signaling genes may lead to changes in drought-responsive gene expression programs, which is supported by a meta-analysis we conduct on available transcriptomic data. Additionally, we cite studies that show how combinatorial transcriptional responses to N and W status might drive crop phenotypes. Through these insights, we suggest research strategies that could help to develop crops adapted to marginal soils depleted in both N and W, an important task in the face of climate change.

Plant life at the dry limit-Spatial patterns of floristic diversity and composition around the hyperarid core of the Atacama Desert

Extreme arid conditions in the Atacama Desert in northern Chile have created a unique vegetation almost entirely restricted to the desert margins along the coast of the Pacific Ocean and the Andean range. In this study we provide data on the desert vegetation along elevational gradients at four localities from the western Andean slopes, between 19° and 21° S. Additionally, zonation of floristic data was explored. Three altitudinal zones could be classified and described in detail for each locality. Conspicuously divergent floras in the Atacama Desert have been recorded in the coastal ‘lomas formations’ and in the Andean desert vegetation, separated by a narrow band of absolute desert. In this study, we investigate the floristic relationships between both regions by implementing similarity analyses for 21 localities from the coastal and Andean deserts in northern Chile. Our results show a drastic east-west divergence in pairwise floristic similarity, which is in stark contrast to a weaker north-south divergence. A biotic barrier, preventing plant exchange from east to west and vice versa, imposed by the hyperarid conditions of the absolute desert, is one possible explanation for this finding. Moreover, the coastal and Andean deserts likely represent ecologically divergent habitats, e.g., in rainfall seasonality. Essential differences in factors determining plant life between both regions have probably contributed to a divergent evolution of the floras. Both explanations–ecological divergence and ecogeographical isolation—are not mutually exclusive, but likely complementary. We also combined floristic data from northern Chile and southern Peru. Similarity analyses of this combined dataset provide first floristic evidence for the existence of a biotic north-south corridor along the western slope of the Andes. Sub-Andean distributions of several species are discussed in the light of floristic connectivity between the Peruvian and Chilean Andean floristic clusters.

A Paleogenomic Reconstruction of the Deep Population History of the Andes

There are many unanswered questions about the population history of the Central and South Central Andes, particularly regarding the impact of large-scale societies, such as the Moche, Wari, Tiwanaku, and Inca. We assembled genome-wide data on 89 individuals dating from ∼9,000-500 years ago (BP), with a particular focus on the period of the rise and fall of state societies. Today's genetic structure began to develop by 5,800 BP, followed by bi-directional gene flow between the North and South Highlands, and between the Highlands and Coast. We detect minimal admixture among neighboring groups between ∼2,000-500 BP, although we do detect cosmopolitanism (people of diverse ancestries living side-by-side) in the heartlands of the Tiwanaku and Inca polities. We also highlight cases of long-range mobility connecting the Andes to Argentina and the Northwest Andes to the Amazon Basin. VIDEO ABSTRACT.

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.