Browsing by Author "Ramond, Jean-Baptiste"

Now showing 1 - 12 of 12
  • Thumbnail Image
    Item
    Biogeographical survey of soil microbiomes across sub-Saharan Africa: structure, drivers, and predicted climate-driven changes
    (2022) Cowan, DA; Lebre, PH; Amon, CER; Becker, RW; Boga, HI; Boulangé, A; Chiyaka, TL; Coetzee, T; de Jager, PC; Ramond, Jean-Baptiste; Eckardt, F; Greve, M; Harris, MA; Hopkins, DW; Houngnandan, HB; Houngnandan, P; Jordaan, K; Kaimoyo, E; Kambura, AK; Kamgan-Nkuekam, G; Makhalanyane, TP; Maggs-Kölling, G; Marais, E; Mondlane, H; Nghalipo, E; Olivier, BW; Ortiz, M; Pertierra, LR; Dikinya, O; Seely, M; Sithole-Niang, I; Valverde, A; Varliero, G; Vikram, S; Wall, DH; Zeze, A
    Background: Top-soil microbiomes make a vital contribution to the Earth’s ecology and harbor an extraordinarily high biodiversity. They are also key players in many ecosystem services, particularly in arid regions of the globe such as the African continent. While several recent studies have documented patterns in global soil microbial ecology, these are largely biased towards widely studied regions and rely on models to interpolate the microbial diversity of other regions where there is low data coverage. This is the case for sub-Saharan Africa, where the number of regional microbial studies is very low in comparison to other continents. Results: The aim of this study was to conduct an extensive biogeographical survey of sub-Saharan Africa’s top-soil microbiomes, with a specific focus on investigating the environmental drivers of microbial ecology across the region. In this study, we sampled 810 sample sites across 9 sub-Saharan African countries and used taxonomic barcoding to profile the microbial ecology of these regions. Our results showed that the sub-Saharan nations included in the study harbor qualitatively distinguishable soil microbiomes. In addition, using soil chemistry and climatic data extracted from the same sites, we demonstrated that the top-soil microbiome is shaped by a broad range of environmental factors, most notably pH, precipitation, and temperature. Through the use of structural equation modeling, we also developed a model to predict how soil microbial biodiversity in sub-Saharan Africa might be affected by future climate change scenarios. This model predicted that the soil microbial biodiversity of countries such as Kenya will be negatively affected by increased temperatures and decreased precipitation, while the fungal biodiversity of Benin will benefit from the increase in annual precipitation. Conclusion: This study represents the most extensive biogeographical survey of sub-Saharan top-soil microbiomes to date. Importantly, this study has allowed us to identify countries in sub-Saharan Africa that might be particularly vulnerable to losses in soil microbial ecology and productivity due to climate change. Considering the reliance of many economies in the region on rain-fed agriculture, this study provides crucial information to support conservation efforts in the countries that will be most heavily impacted by climate change.
  • No Thumbnail Available
    Item
    Contribution of soil bacteria to the atmosphere across biomes
    (2023) Archer, Stephen D. J.; Lee, Kevin C.; Caruso, Tancredi; Alcami, Antonio; Araya, Jonathan G.; Cary, S. Craig; Cowan, Don A.; Etchebehere, Claudia; Gantsetseg, Batdelger; Gomez-Silva, Benito; Hartery, Sean; Hogg, Ian D.; Kansour, Mayada K.; Lawrence, Timothy; Lee, Charles K.; Lee, Patrick K. H.; Leopold, Matthias; Leung, Marcus H. Y.; Maki, Teruya; Mckay, Christopher P.; Al Mailem, Dina M.; Ramond, Jean-Baptiste; Rastrojo, Alberto; Santl-Temkiv, Tina; Sun, Henry J.; Tong, Xinzhao; Vandenbrink, Bryan; Warren-Rhodes, Kimberley A.; Pointing, Stephen B.
    The dispersion of microorganisms through the atmosphere is a continual and essential process that underpins biogeography and ecosystem development and function. Despite the ubiquity of atmospheric microorganisms globally, specific knowledge of the determinants of atmospheric microbial diversity at any given location remains unresolved. Here we describe bacterial diversity in the atmospheric boundary layer and underlying soil at twelve globally distributed locations encompassing all major biomes, and characterise the contribution of local and distant soils to the observed atmospheric community. Across biomes the diversity of bacteria in the atmosphere was negatively correlated with mean annual precipitation but positively correlated to mean annual temperature. We identified distinct non-randomly assembled atmosphere and soil communities from each location, and some broad trends persisted across biomes including the enrichment of desiccation and UV tolerant taxa in the atmospheric community. Source tracking revealed that local soils were more influential than distant soil sources in determining observed diversity in the atmosphere, with more emissive semi-arid and arid biomes contributing most to signatures from distant soil. Our findings highlight complexities in the atmospheric microbiota that are relevant to understanding regional and global ecosystem connectivity.
  • No Thumbnail Available
    Item
    Diamonds in the rough: Dryland microorganisms are ecological engineers to restore degraded land and mitigate desertification
    (2023) Marasco, Ramona; Ramond, Jean-Baptiste; Van Goethem, Marc W.; Rossi, Federico; Daffonchio, Daniele
    Our planet teeters on the brink of massive ecosystem collapses, and arid regions experience manifold environmental and climatic challenges that increase the magnitude of selective pressures on already stressed ecosystems. Ultimately, this leads to their aridification and desertification, that is, to simplified and barren ecosystems (with proportionally less microbial load and diversity) with altered functions and food webs and modification of microbial community network. Thus, preserving and restoring soil health in such a fragile biome could help buffer climate change's effects. We argue that microorganisms and the protection of their functional properties and networks are key to fight desertification. Specifically, we claim that it is rational, possible and certainly practical to rely on native dryland edaphic microorganisms and microbial communities as well as dryland plants and their associated microbiota to conserve and restore soil health and mitigate soil depletion in newly aridified lands. Furthermore, this will meet the objective of protecting/stabilizing (and even enhancing) soil biodiversity globally. Without urgent conservation and restoration actions that take into account microbial diversity, we will ultimately, and simply, not have anything to protect anymore.
  • 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
    Functional redundancy buffers the effect of poly-extreme environmental conditions on southern African dryland soil microbial communities
    (2024) Sauma-Sánchez, Tomás; Alcorta Loyola, Jaime Andrés; Tamayo Leiva, Javier Alejandro; Diez Moreno, Beatriz; Bezuidenhout, Hugo; Cowan, Don A.; Ramond, Jean-Baptiste
    Drylands' poly-extreme conditions limit edaphic microbial diversity and functionality. Furthermore, climate change exacerbates soil desiccation and salinity in most drylands. To better understand the potential effects of these changes on dryland microbial communities, we evaluated their taxonomic and functional diversities in two Southern African dryland soils with contrasting aridity and salinity. Fungal community structure was significantly influenced by aridity and salinity, while Bacteria and Archaea only by salinity. Deterministic homogeneous selection was significantly more important for bacterial and archaeal communities' assembly in hyperarid and saline soils when compared to those from arid soils. This suggests that niche partitioning drives bacterial and archaeal communities' assembly under the most extreme conditions. Conversely, stochastic dispersal limitations drove the assembly of fungal communities. Hyperarid and saline soil communities exhibited similar potential functional capacities, demonstrating a disconnect between microbial structure and function. Structure variations could be functionally compensated by different taxa with similar functions, as implied by the high levels of functional redundancy. Consequently, while environmental selective pressures shape the dryland microbial community assembly and structures, they do not influence their potential functionality. This suggests that they are functionally stable and that they could be functional even under harsher conditions, such as those expected with climate change., Salinity and aridity shape the assembly and structures, but not the potential functionality, of microbial communities from Southern African dryland soils.
  • No Thumbnail Available
    Item
    Rickettsia felis DNA recovered from a child who lived in southern Africa 2000 years ago
    (2023) Rifkin, Riaan F. F.; Vikram, Surendra; Alcorta, Jaime; Ramond, Jean-Baptiste; Cowan, Don A. A.; Jakobsson, Mattias; Schlebusch, Carina M. M.; Lombard, Marlize
    The Stone Age record of South Africa provides some of the earliest evidence for the biological and cultural origins of Homo sapiens. While there is extensive genomic evidence for the selection of polymorphisms in response to pathogen-pressure in sub-Saharan Africa, e.g., the sickle cell trait which provides protection against malaria, there is inadequate direct human genomic evidence for ancient human-pathogen infection in the region. Here, we analysed shotgun metagenome libraries derived from the sequencing of a Later Stone Age hunter-gatherer child who lived near Ballito Bay, South Africa, c. 2000 years ago. This resulted in the identification of ancient DNA sequence reads homologous to Rickettsia felis, the causative agent of typhus-like flea-borne rickettsioses, and the reconstruction of an ancient R. felis genome.
  • 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.
  • Thumbnail Image
    Item
    Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the ‘ancestral’ sub-Saharan African intestinal microbiome.
    (2020) Rifkin, Riaan F.; Ramond, Jean-Baptiste; Vikram, Surendra; Rey-Iglesia, Alba; Brand, Tina B.; Porraz, Guillaume; Val, Aurore; Hall, Grant; Woodborne, Stephan; Le Bailly, Matthieu
    Abstract Background The archaeological incidence of ancient human faecal material provides a rare opportunity to explore the taxonomic composition and metabolic capacity of the ancestral human intestinal microbiome (IM). Here, we report the results of the shotgun metagenomic analyses of an ancient South African palaeo-faecal specimen. Methods Following the recovery of a single desiccated palaeo-faecal specimen from Bushman Rock Shelter in Limpopo Province, South Africa, we applied a multi-proxy analytical protocol to the sample. The extraction of ancient DNA from the specimen and its subsequent shotgun metagenomic sequencing facilitated the taxonomic and metabolic characterisation of this ancient human IM. Results Our results indicate that the distal IM of the Neolithic ‘Middle Iron Age’ (c. AD 1460) Bantu-speaking individual exhibits features indicative of a largely mixed forager-agro-pastoralist diet. Subsequent comparison with the IMs of the Tyrolean Iceman (Ötzi) and contemporary Hadza hunter-gatherers, Malawian agro-pastoralists and Italians reveals that this IM precedes recent adaptation to ‘Western’ diets, including the consumption of coffee, tea, chocolate, citrus and soy, and the use of antibiotics, analgesics and also exposure to various toxic environmental pollutants. Conclusions Our analyses reveal some of the causes and means by which current human IMs are likely to have responded to recent dietary changes, prescription medications and environmental pollutants, providing rare insight into human IM evolution following the advent of the Neolithic c. 12,000 years ago. Video Abtract.
  • 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.
  • No Thumbnail Available
    Item
    Temporal dynamics of microbial transcription in wetted hyperarid desert soils
    (2024) Leon-Sobrino, Carlos; Ramond, Jean-Baptiste; Coclet, Clement; Kapitango, Ritha-Meriam; Maggs-Kolling, Gillian; Cowan, Don A.
    Rainfall is rare in hyperarid deserts but, when it occurs, it triggers large biological responses essential for the long-term maintenance of the ecosystem. In drylands, microbes play major roles in nutrient cycling, but their responses to short-lived opportunity windows are poorly understood. Due to its ephemeral nature, mRNA is ideally suited to study microbiome dynamics upon abrupt changes in the environment. We analyzed microbial community transcriptomes after simulated rainfall in a Namib Desert soil over 7 days. Using total mRNA from dry and watered plots we infer short-term functional responses in the microbiome. A rapid two-phase cycle of activation and return to basal state was completed in a short period. Motility systems activated immediately, whereas competition-toxicity increased in parallel to predator taxa and the drying of soils. Carbon fixation systems were downregulated, and reactivated upon return to a near-dry state. The chaperone HSP20 was markedly regulated by watering across all major bacteria, suggesting a particularly important role in adaptation to desiccated ecosystems. We show that transcriptomes provide consistent and high resolution information on microbiome processes in a low-biomass environment, revealing shared patterns across taxa. We propose a structured dispersal-predation dynamic as a central driver of desert microbial responses to rainfall.
  • No Thumbnail Available
    Item
    The plant rhizosheath-root niche is an edaphic "mini-oasis" in hyperarid deserts with enhanced microbial competition
    (2022) Marasco, Ramona; Fusi, Marco; Ramond, Jean-Baptiste; Van Goethem, Marc W.; Seferji, Kholoud; Maggs-Koelling, Gillian; Cowan, Don A.; Daffonchio, Daniele
    Plants have evolved unique morphological and developmental adaptations to cope with the abiotic stresses imposed by (hyper)arid environments. Such adaptations include the formation of rhizosheath-root system in which mutualistic plant-soil microbiome associations are established: the plant provides a nutrient-rich and shielded environment to microorganisms, which in return improve plant-fitness through plant growth promoting services. We hypothesized that the rhizosheath-root systems represent refuge niches and resource islands for the desert edaphic microbial communities. As a corollary, we posited that microorganisms compete intensively to colonize such "oasis" and only those beneficial microorganisms improving host fitness are preferentially selected by plant. Our results show that the belowground rhizosheath-root micro-environment is largely more hospitable than the surrounding gravel plain soil with higher nutrient and humidity contents, and cooler temperatures. By combining metabarcoding and shotgun metagenomics, we demonstrated that edaphic microbial biomass and community stability increased from the non-vegetated soils to the rhizosheath-root system. Concomitantly, non-vegetated soil communities favored autotrophy lifestyle while those associated with the plant niches were mainly heterotrophs and enriched in microbial plant growth promoting capacities. An intense inter-taxon microbial competition is involved in the colonization and homeostasis of the rhizosheath zone, as documented by significant enrichment of antibiotic resistance genes and CRISPR-Cas motifs. Altogether, our results demonstrate that rhizosheath-root systems are "edaphic mini-oases" and microbial diversity hotspots in hyperarid deserts. However, to colonize such refuge niches, the desert soil microorganisms compete intensively and are therefore prepared to outcompete potential rivals.
  • No Thumbnail Available
    Item
    With a pinch of salt: metagenomic insights into Namib Desert salt pan microbial mats and halites reveal functionally adapted and competitive communities
    (2023) Martinez-Alvarez, Laura; Ramond, Jean-Baptiste; Vikram, Surendra; Leon-Sobrino, Carlos; Maggs-Kolling, Gillian; Cowan, Don A.
    Salt pans or playas, which are saline-rich springs surrounded by halite evaporates in arid environments, have played an essential role in landscape erosion during the formation of the Namib Desert and are numerous in its central region. In this study, we used shotgun metagenomics to investigate the phylogenetic and functional capacities of the microbial communities from two salt pans (namely, Eisefeld and Hosabes) located in central Namib Desert, located in Southwest Africa. We studied the source and sink sediment mat communities of the saline streams, as well as those from two halites (crystallized structures on the stream margins). The microbial assemblages and potential functions were distinct in both niches. Independently from their localization (Eisfeld vs Hosabes and source vs sink), the sediment mat communities were dominated by members of the Alpha- and Gamma-proteobacteria classes, while halites were Archaea dominated and also contained high abundances of the extremely halophilic bacterium Salinibacter sp. (phylum Bacteroidota). Photoheterotrophy and chemoheterotrophy were the principal lifestyles in both niches, with halite communities having a reduced diversity of metabolic pathways. Intense microbial-virus interactions in both niches were implied by the widespread detection of CRISPR-Cas defense systems. We identified a putatively novel clade of type II CRISPR-Cas systems, as well as novel candidate viral lineages of the class Caudoviricetes and of Halobacteriales-infecting haloviruses. Putative gene transfer agent-like sequences within the Alphaproteobacteria were identified in the sediment mat communities. These horizontal gene transfer elements have the potential to drive genome plasticity and evolution of the Alphaproteobacteria in the Namib Desert salt pan microbiomes.IMPORTANCEThe hyperarid Namib Desert is one of the oldest deserts on Earth. It contains multiple clusters of playas which are saline-rich springs surrounded by halite evaporites. Playas are of great ecological importance, and their indigenous (poly)extremophilic microorganisms are potentially involved in the precipitation of minerals such as carbonates and sulfates and have been of great biotechnological importance. While there has been a considerable amount of microbial ecology research performed on various Namib Desert edaphic microbiomes, little is known about the microbial communities inhabiting its multiple playas. In this work, we provide a comprehensive taxonomic and functional potential characterization of the microbial, including viral, communities of sediment mats and halites from two distant salt pans of the Namib Desert, contributing toward a better understanding of the ecology of this biome.