Biology subjects

Stoll, A.

Publications and source records attributed to Stoll, A..

6 recordsLinked to original sources

bioRxiv2026

Drowning in a sandy ocean: Epiarenic growth of Tillandsia in the hyperarid Atacama Desert

The Atacama Desert hosts a unique ecosystem formed by the sand-dwelling Tillandsia landbeckii, which extends over hundreds of square kilometers. This vegetation relies primarily on fog as its main water source; however, aeolian sand also plays a crucial role in the long-term persistence of both the species and the overall plant community. The terrain is sloped and exposed to the prevailing wind direction. Tillandsia forms regular banding patterns oriented orthogonally to these landscape features. In this study, we aim to elucidate the abiotic-biotic interactions between sand properties and vegetation characteristics through a comparative approach. Three populations - Caldera, Oyarbide and Arica -, each spanning several square kilometers in the southern, central, and northern regions of the Chilean Atacama Desert, were selected to compare wind regimes, terrain structure, sand and substrate properties, and vegetation structure in order to identify common principles that maintain vegetation integrity. Data were collected from six climate stations, 1,246 substrate samples, population genomic data from 718 individuals, as well as satellite imagery and digital terrain models. Our findings demonstrate that regional wind systems transport sand from distant source areas, while near the ground, Tillandsia vegetation reduces wind velocity and traps sand, leading to the formation of moderately sorted sandy substrates that are similar across all three populations. Sites lacking or containing dead Tillandsia individuals often differ significantly in substrate characteristics. Genetic analyses indicate that Tillandsia populations exhibit strong spatial structure albeit recruiting high genetic diversity and an excess of heterozygosity, reflecting adaptation to the dynamic environmental conditions. We conclude that sand represents an essential component of this ecosystem, while Tillandsia, as the dominant biotic factor, actively shapes and maintains this distinctive desert environment. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/707457v2_ufig1.gif" ALT="Figure 1"> View larger version (66K): org.highwire.dtl.DTLVardef@14529eforg.highwire.dtl.DTLVardef@1c42435org.highwire.dtl.DTLVardef@25147aorg.highwire.dtl.DTLVardef@639128_HPS_FORMAT_FIGEXP M_FIG C_FIG Generated based on own drawings and iterative improvements using ChatGPT while providing own peer-reviewed research contributions as input and baseline information (MAK). Short summaryWe exemplify unimodal regional wind systems facilitating sand transport toward Tillandsiales. Tillandsiales show a low-energy wind system allowing sand accumulation of predominant grain sizes available at each site. Thereby Tillandsia landbeckii modifies and maintains its own microenvironment. Genomic data reveal high clonality and excess of heterozygosity promoting fitness in a hyperarid environment, and abiotic factors drive the selection of diverse and adaptive Tillandsia phenotypes.

plant biology↗

bioRxiv2024

Soil biodiversity in the Atacama Desert shows distinct patterns at different diversity levels

Species diversity and distribution, in relation to how they interact with their environment is a major focus of ecological research. Particularly for soil ecosystems, information about geographical patterns of biota is scarce despite the pivotal role of soils as ecosystem service providers. The Atacama is the driest non-polar desert on earth: water is scarce, high salinity patches are frequent and water bodies have high concentrations of metals. It is believed that only specialized taxa can survive in this Desert. Accordingly, only some microbial life-forms and few plants, and vertebrates are present. Above ground invertebrates have been reported in the desert but its soils have not been comprehensively analyzed. By studying different areas in the Atacama, we aim to better understand resilience of soil organisms in times of global aridification. Nematodes are one of the most important groups of soil organisms in abundance and biodiversity. Here, we investigated diversity of soil nematodes at the genetic, taxonomic, community and life-cycle levels. We find distinct patterns and assemblages along the different habitats in the desert: dune systems, high altitude mountains, saline lakes, river valleys and fog oases. We also find that distribution of asexual taxa is more likely to occur at higher altitudes, and that the distribution of genera richness in the Atacama follows a latitudinal diversity gradient, as well as an increase with increasing precipitation. Our work shows that even under extreme environmental conditions stable, healthy soil communities can persist, but we see indicators of poor soil food webs.

ecology↗

bioRxiv2024

AnNoBrainer, an Automated Annotation of Mouse Brain Images using Deep Learning

Annotation of multiple regions of interest across the whole mouse brain is an indispensable process for quantitative evaluation of a multitude of study endpoints in neuroscience digital pathology. Prior experience and domain expert knowledge are the key aspects for image annotation quality and consistency. At present, image annotation is often achieved manually by certified pathologists or trained technicians, limiting the total throughput of studies performed at neuroscience digital pathology labs. It may also mean that less rigorous, less time-consuming methods of histopathological assessment are employed by non-pathologists, especially for early discovery and preclinical studies. To address these limitations and to meet the growing demand for image analysis in a pharmaceutical setting, we developed AnNoBrainer, an open-source software tool that leverages deep learning, image registration, and standard cortical brain templates to automatically annotate individual brain regions on 2D pathology slides. Application of AnNoBrainer to a published set of pathology slides from transgenic mice models of synucleinopathy revealed comparable accuracy, increased reproducibility, and a significant reduction ([~]50%) in time spent on brain annotation, quality control and labelling compared to trained scientists in pathology. Taken together, AnNoBrainer offers a rapid, accurate, and reproducible automated annotation of mouse brain images that largely meets the experts histopathological assessment standards (>85% of cases) and enables high-throughput image analysis workflows in digital pathology labs.

neuroscience↗

bioRxiv2024

Rhizospheric bacteria from the Atacama Desert hyper-arid core: cultured community dynamics and plant growth promotion

The Atacama Desert is the oldest and driest desert on Earth, with environmental conditions including great temperature variations, high UV-radiation, drought, high salinity, making it a natural laboratory to study the limits of life and resistance strategies. However, it shows great biodiversity harboring vast forms of adapted life and can be used as a model of desertification processes. While desertification is increasing as result of climate change and human activities, is necessary to optimize soil and water usage, where stress-resistant crops are possible solutions. As many studies have revealed the great impact of rhizobiome over plant growth efficiency and resistance to abiotic stress, we set up to explore the rhizospheric soils of Suaeda foliosa and Distichlis spicata from the Atacama Desert. By culturing these soils and using 16S rRNA amplicon sequencing, we address the community taxonomy composition dynamics, the stability through time and the ability to promote lettuce plants growth. The rhizospheric soil communities were dominated by the families Pseudomonadaceae, Bacillaceae and Planococcaceae for S. foliosa and Porphyromonadaceae and Haloferacaceae for D. spicata. Nonetheless, the cultures were completely dominated by the Enterobacteriaceae family (up to 98%). Effectively, lettuce plants supplemented with the cultures showed greater size and biomass accumulation, we identify 12 candidates that could be responsible of these outcomes, of which 5 (Enterococcus, Pseudomonas, Klebsiella, Paenisporosarcina and Ammoniphilus) were part of the built co-occurrence network, being Klebsiella a major participant. We aim to contribute to the efforts to characterize the microbial communities as key for the plants survival in extreme environments, and as a possible source of consortia with plant growth promotion traits aiming agricultural applications. IMPORTANCEThe current scenario of climate change and desertification represents a series of incoming challenges for all living organisms, also as the human population grows rapidly, so is rising the demand for food and natural resources; thus, it is necessary to make agriculture more efficient by optimizing soil and water usages thus ensuring future food supplies. Particularly, the Atacama Desert (northern Chile) is considered the most arid place on Earth as a consequence of geological and climatic characteristics, such as the naturally low precipitation patterns and high temperatures, which makes it an ideal place to carry out research that seeks to aid agriculture to the future sceneries, which are predicted to resemble these. The use of microorganism consortia from plants thriving under these extreme conditions to promote plant growth, improve crops and make "unsuitable" soils farmable is our main interest. TWEETCultures of rhizospheric soils from Atacama Desert resilient plants were enriched in Klebsiella, Bacillus and Brevibacillus which promoted lettuce growth

microbiology↗

bioRxiv2023

Genome-wide SNP data reveal recent population structure of Huidobria fruticosa (Loasaceae), a paleo-endemic lineage from the Atacama Desert

The Atacama Desert is a biodiversity hotspot of neo-endemic radiation, where long-term aridity and complex physiographic processes create a unique environmental setting. Current species assemblages are mainly concentrated in highly patchy loma formations, and plant populations occurring in these are often geographically isolated from each other. Despite a general consensus on long-term aridity in the Atacama, climatological and geological evidence points to repeated climate change, making the Atacama Desert an ideal system for studying population genetic processes in highly unstable habitats. We are analyzing the genetic structure within and between populations of Huidobria fruticosa, a paleo-endemic lineage of the Atacama Desert, to shed new light on its biogeographic history and broaden our understanding of the evolution of life in extreme aridity, as well as plant evolution in response to a changing environment. To do this, we analyzed SNP data from genotyping-by-sequencing of 354 individuals from 21 populations. Our results suggest that, despite being an ancient lineage, the current population structure of Huidobria fruticosa only reflects changing abiotic conditions over the last 2 million years. We therefore conclude that the present distribution, together with the evolutionary processes documented here, is the result of climatic fluctuations and prolonged periods of hyperaridity during the Pleistocene. Building on this understanding, our findings contribute to a global narrative that highlights the complex interplay between climate change and evolutionary dynamics, and emphasize the importance of deserts as living laboratories for deciphering how species have historically adapted to some of the most extreme habitats on Earth.

evolutionary biology↗

bioRxiv2023

Genetic diversity of the Atacama Desert shrub Huidobria chilensis in the context of geography and climate

Survival in hyperarid deserts is a major challenge for plant life, requiring the development of evolutionary strategies. The Atacama Desert presents harsh conditions such as limited rainfall, crusted soils, high soil salinity, high altitude, and intense solar radiation. These conditions, together with paleoclimatic variability since the past millions of years, have influenced the genetic structure and connectivity of plant populations, resulting in a diverse flora with high endemism. However, the diversification of most lineages appears to be relatively recent, in contrast to proposed age of the Atacama Desert and the onset, evolution and expansion of hyperarid conditions since the Late Oligocene and Early Miocene. A prominent exception is the Atacama paleoendemic Huidobria chilensis (Loasaceae), which is thought to be adapted to such conditions since the Eocene. Still, the environmental limits and thresholds for life in the Atacama remain poorly understood. To investigate the genetic structure in relation to the history of the Atacama Desert, we studied 186 individuals from 11 populations using genotyping-by-sequencing (GBS). Genome-wide single nucleotide polymorphisms (SNPs) were analyzed for population structure and genetic diversity. We identified three genetic clusters corresponding to geographic regions: the coastal region south of Tocopilla, the Coastal Cordillera around Chanaral, and the Copiapo watershed in the south. These clusters as well as genetic diversity were analyzed alongside rainfall, altitude, and landscape data. Although the genetic data generally supports isolation by distance as a major factor for genetic variation between populations, the study also reveals the influence of the topography on the distribution of H. chilensis and highlights the role of hydrologically connected watersheds and rivers in plant migration and colonization. This shapes the species evolutionary trajectory and genetic diversity. Understanding these patterns provides insights into the adaptation and survival strategies of plants in extreme desert environments such as the Atacama.

genetics↗