Browsing by Author "Jordaan, Karen"

Now showing 1 - 6 of 6
  • No Thumbnail Available
    Item
    Diversity and functionality of soil prokaryotic communities in antarctic volcanic soils: insights from penguin-influenced environments
    (2024) Segura, Diego; Jordaan, Karen; Diez, Beatriz; Tamayo-Leiva, Javier; Doetterl, Sebastian; Wasner, Daniel; Cifuentes-Anticevic, Jeronimo; Casanova-Katny, Angelica
    In the nutrient-limited Antarctic terrestrial habitat, penguins transfer a significant amount of nutrients from the marine to the terrestrial ecosystem through their depositions (i.e., guano). This guano influences soil physicochemical properties, leading to the formation of ornithogenic soil rich in nutrients and organic matter. We hypothesize that soil prokaryotic communities will be strongly influenced by the contribution of nitrogenous nutrients from penguin rookeries, maintaining the influence over long distances. The objective was to establish how the soil prokaryotic diversity and community structure change with distance from a penguin colony, which provides large amounts of guano and nitrogenous compounds, and to study the effects of these nutrients on the functional role of these communities. Methods include volcanic soil sampling along a 1200 m transect from the penguin active rookery and the characterization of soil nutrient content and soil prokaryotic communities using 16S rRNA high-throughput amplicon sequencing. In contrast to our hypothesis, the results showed that the impact of guano from the penguin colony was restricted to the first 300 m. Probably because the penguin rookery was sheltered, strong wind and wind direction did not affect the transport of nutrients from the penguin rookery. Areas close to the penguin rookery were dominated by Proteobacteria and Bacteroidetes, while areas situated further away were dominated by Acidobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, Nitrospirae, and Planctomycetes. Beta diversity analysis among the soil prokaryotic communities revealed a high degree of community heterogeneity, strongly associated with N compound characteristics (NH4, NO3, and %N), C, and pH. Inferences from N metabolism genes suggest a high potential of the microbial community for dissimilatory nitrate reduction genes (DNRA) to ammonium, assimilatory nitrate reduction (ANR), and denitrification. Although it is assumed that the nitrogenous compounds of the penguin colonies reach long distances and affect the prokaryotic community, this effect can vary with wind directions or the morphology of the site, reducing the impact of the guano over long distances, as our results indicate. On the other hand, functional predictions give some clues about the main actors in nitrogen cycling, through processes like dissimilatory nitrate reduction, assimilatory nitrate reduction, and denitrification.
  • Thumbnail Image
    Item
    Documenting the diversity of the Namibian Ju|'hoansi intestinal microbiome
    (2024) Truter, Mia; Koopman, Jessica E.; Jordaan, Karen; Tsamkxao, Leon Oma; Cowan, Don A.; Underdown, Simon J.; Ramond, Jean-Baptiste; Rifkin, Riaan F.
    We investigate the bacterial and fungal composition and functionality of the Ju|'hoansi intestinal microbiome (IM). The Ju|'hoansi are a hunter-gatherer community residing in northeastern Namibia. They formerly subsisted by hunting and gathering but have been increasingly exposed to industrial dietary sources, medicines, and lifestyle features. They present an opportunity to study the evolution of the human IM in situ, from a predominantly hunter-gatherer to an increasingly Western urban-forager-farmer lifestyle. Their bacterial IM resembles that of typical hunter-gatherers, being enriched for genera such as Prevotella, Blautia, Faecalibacterium, Succinivibrio, and Treponema. Fungal IM inhabitants include animal pathogens and plant saprotrophs such as Fusarium, Issatchenkia, and Panellus. Our results suggest that diet and culture exert a greater influence on Ju|'hoansi IM composition than age, self-identified biological sex, and medical history. The Ju|'hoansi exhibit a unique core IM composition that diverges from the core IMs of other populations.
  • No Thumbnail Available
    Item
    Hydrogen-Oxidizing Bacteria Are Abundant in Desert Soils and Strongly Stimulated by Hydration
    (2020) Jordaan, Karen; Lappan, Rachael; Dong, Xiyang; Aitkenhead, Ian J.; Bay, Sean K.; Chiri, Eleonora; Wieler, Nimrod; Meredith, Laura K.; Cowan, Don A.; Chown, Steven L.; Greening, Chris
    How the diverse bacterial communities inhabiting desert soils maintain energy and carbon needs is much debated. Traditionally, most bacteria are thought to persist by using organic carbon synthesized by photoautotrophs following transient hydration events. Recent studies focused on Antarctic desert soils have revealed, however, that some bacteria use atmospheric trace gases, such as hydrogen (H-2), to conserve energy and fix carbon independently of photosynthesis. In this study, we investigated whether atmospheric H-2 oxidation occurs in four nonpolar desert soils and compared this process to photosynthesis. To do so, we first profiled the distribution, expression, and activities of hydrogenases and photosystems in surface soils collected from the South Australian desert over a simulated hydrationdesiccation cycle. Hydrogenase-encoding sequences were abundant in the metagenomes and metatranscriptomes and were detected in actinobacterial, acidobacterial, and cyanobacterial metagenome-assembled genomes. Native dry soil samples mediated H-2 oxidation, but rates increased 950-fold following wetting. Oxygenic and anoxygenic phototrophs were also detected in the community but at lower abundances. Hydration significantly stimulated rates of photosynthetic carbon fixation and, to a lesser extent, dark carbon assimilation. Hydrogenase genes were also widespread in samples from three other climatically distinct deserts, the Namib, Gobi, and Mojave, and atmospheric H-2 oxidation was also greatly stimulated by hydration at these sites. Together, these findings highlight that H-2 is an important, hitherto-overlooked energy source supporting bacterial communities in desert soils. Contrary to our previous hypotheses, however, H-2 oxidation occurs simultaneously rather than alternately with photosynthesis in such ecosystems and may even be mediated by some photoautotrophs.
  • No Thumbnail Available
    Item
    Modelling soil prokaryotic traits across environments with the trait sequence database ampliconTraits and the R package MicEnvMod
    (2024) Donhauser, Jonathan; Domenech-Pascual, Anna; Han, Xingguo; Jordaan, Karen; Ramond, Jean-Baptiste; Frossard, Aline; Romani, Anna M.; Prieme, Anders
    We present a comprehensive, customizable workflow for inferring prokaryotic phenotypic traits from marker gene sequences and modelling the relationships between these traits and environmental factors, thus overcoming the limited ecological interpretability of marker gene sequencing data. We created the trait sequence database ampliconTraits, constructed by cross-mapping species from a phenotypic trait database to the SILVA sequence database and formatted to enable seamless classification of environmental sequences using the SINAPS algorithm. The R package MicEnvMod enables modelling of trait - environment relationships, combining the strengths of different model types and integrating an approach to evaluate the models' predictive performance in a single framework. Traits could be accurately predicted even for sequences with low sequence identity (80 %) with the reference sequences, indicating that our approach is suitable to classify a wide range of environmental sequences. Validating our approach in a large trans-continental soil dataset, we showed that trait distributions were robust to classification settings such as the bootstrap cutoff for classification and the number of discrete intervals for continuous traits. Using functions from MicEnvMod, we revealed precipitation seasonality and land cover as the most important predictors of genome size. We found Pearson correlation coefficients between observed and predicted values up to 0.70 using repeated split sampling cross validation, corroborating the predictive ability of our models beyond the training data. Predicting genome size across the Iberian Peninsula, we found the largest genomes in the northern part. Potential limitations of our trait inference approach include dependence on the phylogenetic conservation of traits and limited database coverage of environmental prokaryotes. Overall, our approach enables robust inference of ecologically interpretable traits combined with environmental modelling allowing to harness traits as bioindicators of soil ecosystem functioning.
  • No Thumbnail Available
    Item
    Multiple energy sources and metabolic strategies sustain microbial diversity in Antarctic desert soils
    (2021) Ortiz, Maximiliano; Leung, Pok Man; Shelley, Guy; Jirapanjawat, Thanavit; Nauer, Philipp A.; Van Goethem, Marc W.; Bay, Sean K.; Islam, Zahra F.; Jordaan, Karen; Vikram, Surendra; Chown, Steven L.; Hogg, Ian D.; Makhalanyane, Thulani P.; Grinter, Rhys; Cowan, Don A.; Greening, Chris
    Numerous diverse microorganisms reside in the cold desert soils of continental Antarctica, though we lack a holistic understanding of the metabolic processes that sustain them. Here, we profile the composition, capabilities, and activities of the microbial communities in 16 physicochemically diverse mountainous and glacial soils. We assembled 451 metagenome-assembled genomes from 18 microbial phyla and inferred through Bayesian divergence analysis that the dominant lineages present are likely native to Antarctica. In support of earlier findings, metagenomic analysis revealed that the most abundant and prevalent microorganisms are metabolically versatile aerobes that use atmospheric hydrogen to support aerobic respiration and sometimes carbon fixation. Surprisingly, however, hydrogen oxidation in this region was catalyzed primarily by a phylogenetically and structurally distinct enzyme, the group 1l [NiFe]-hydrogenase, encoded by nine bacterial phyla. Through gas chromatography, we provide evidence that both Antarctic soil communities and an axenic Bacteroidota isolate (Hymenobacter roseosalivarius) oxidize atmospheric hydrogen using this enzyme. Based on ex situ rates at environmentally representative temperatures, hydrogen oxidation is theoretically sufficient for soil communities to meet energy requirements and, through metabolic water production, sustain hydration. Diverse carbon monoxide oxidizers and abundant methanotrophs were also active in the soils. We also recovered genomes of microorganisms capable of oxidizing edaphic inorganic nitrogen, sulfur, and iron compounds and harvesting solar energy via microbial rhodopsins and conventional photosystems. Obligately symbiotic bacteria, including Patescibacteria, Chlamydiae, and predatory Bdellovibrionota, were also present. We conclude that microbial diversity in Antarctic soils reflects the coexistence of metabolically flexible mixotrophs with metabolically constrained specialists.
  • No Thumbnail Available
    Item
    Soil organic matter properties drive microbial enzyme activities and greenhouse gas fluxes along an elevational gradient
    (2024) Han, Xingguo; Domenech-Pascual, Anna; Casas-Ruiz, Joan Pere; Donhauser, Jonathan; Jordaan, Karen; Ramond, Jean-Baptiste; Prieme, Anders; Romani, Anna M.; Frossard, Aline
    Mountain ecosystems, contributing substantially to the global carbon (C) and nitrogen (N) biogeochemical cycles, are heavily impacted by global changes. Although soil respiration and microbial activities have been extensively studied at different elevation, little is known on the relationships between environmental drivers, microbial functions, and greenhouse gas fluxes (GHGs; carbon dioxide [CO2], methane [CH4] and nitrous oxide [N2O]) in soils of different elevation. Here, we measured how in situ GHG fluxes were linked to soil properties, soil organic matter (SOM) quantity and composition (the proportion of humic-like vs. protein-like OM), microbial biomass, enzyme activities and functional gene abundances in natural soils spanning an elevational gradient of similar to 2400 m in Switzerland. Soil CO2 fluxes did not significantly vary from low (lowland zone) to higher (montane and subalpine zones) elevation forests, but decreased significantly (P<0.001) from the treeline to the mountain summit. Multivariate analyses revealed that CO2 fluxes were controlled by C-acquiring enzymatic activities which were mainly controlled by air mean annual temperature (MAT) and SOM quantity and composition. CH4 fluxes were characterized by uptake of atmospheric CH4, but no trend was observed along the elevation. N2O fluxes were also dominated by uptake of atmospheric N2O. The flux rates remained stable with increasing elevation below the treeline, but decreased significantly (P<0.001) from the treeline to the summit. N2O fluxes were driven by specific nitrifying and denitrifying microbial genes (ammonia-oxidizing amoA and N2O-producing norB), which were again controlled by SOM quantity and composition. Our study indicates the treeline as a demarcation point changing the patterns of CO2 and N2O fluxes along the elevation, highlighting the importance of SOM quantity and composition in controlling microbial enzyme activities and GHG fluxes.