Biology subjects

Delgado-Baquerizo, M.

Publications and source records attributed to Delgado-Baquerizo, M..

17 recordsLinked to original sources

bioRxiv2025

Leaf microbiome assembly is linked to plant phylogeny

Background and AimsThe plant microbiome is considered as an extended part of the plant genome, and it provides key functions in regulating plant fitness, and stress tolerance. Plants and associated microbiomes have co-evolved over millennia, yet evidence for a strong influence of plant phylogeny in influencing their microbiomes is largely lacking. Our main aims was to identify key drivers of plant microbiome assembly. MethodsHere, we conducted a full factorial experiment that included three levels of soil microbial diversity, five plant species from three functional groups (C3, C4, and C3 nitrogen-fixing), and two moisture availability levels. ResultsOur results showed that host identity and plant functional group exerted the strongest effect on leaf microbial assembly, while root and soil microbiomes showed less sensitivity to host selection. The initial soil microbial diversity and community structure significantly impacted soil and root microbial composition, but not leaf microbiomes. Importantly, we observed significant positive linkage between host phylogeny distance and Bray-Curtis dissimilarity index in leaf microbiomes. This finding was further validated through analysis of microbiome data from seven plant species grown across different field and environmental conditions. Interestingly, there was no significant impact of short-term water stress on plant microbial communities. ConclusionsBy providing empirical evidence for important role of host selection in shaping plant microbiomes, this study advances our fundamental knowledge of plant-microbe interactions and their co-evolutionary relationships, and enhances our ability to develop future tools harnessing plant microbiome to improve plant health and productivity.

microbiology↗

bioRxiv2025

Aridity drives global convergence of desert microbiomes and biogeochemical activities

Deserts cover a third of the worlds surface, supporting unique biomes and ecosystem services. Yet, we lack a comprehensive assessment of what defines and drives the microbial communities that dominate life in these regions. Here, we conducted a standardized field survey in contrasting cold, hot, and polar deserts across the seven continents, and observed geographically distant deserts share similar structure, function, and activities. Desert communities are dominated by genomically streamlined Actinobacteriota and Chloroflexota, and compared with non-desert soils, are significantly enriched with stress tolerance genes, mobile genetic elements, and antiviral strategies, revealing previously unknown ecological and evolutionary dynamics. Metabolically, these communities exhibit reduced capacity for carbohydrate and protein degradation, and instead are enriched for chemosynthetic carbon fixation, continuous energy harvesting using atmospheric trace gases and sunlight, and energy reserve biosynthesis. All sampled soils mediated respiration, trace gas oxidation, and carbon fixation, with detectable activity even in hyper-arid Atacama and Antarctic soils at the margins of life. Driver analyses identified aridity as the primary overriding driver of the microbial communities and biogeochemical activities. Collectively, these findings suggest that aridity selects for metabolically self-sufficient taxa capable of continuously meeting energy and carbon needs independently of vegetation-derived inputs, while enduring physicochemical stressors and potentially elevated viral pressure. These new insights are integral to forecast the future of soils amid increasing desertification. Significance statementDesert soils occupy a vast and expanding portion of Earth, yet what defines and governs their dominant microbial life remains incompletely defined. By assessing the composition, capabilities, and activities of microbial communities across deserts on all seven continents, we identify unifying signatures of life under extreme water limitation. We show microbial communities are highly self-sufficient, capable of acquiring energy and carbon even where plant inputs are minimal. This planetary-scale understanding of the desert microbiome has important ramifications for forecasting potential shifts of microbial communities and the services they provide as desertification intensifies.

microbiology↗

bioRxiv2025

Lonely plants in arid land are functionally hyperdiverse

In Gross et al.1 we produced the largest ever standardized dryland plant trait database including 133,769 trait measurements from 301 perennial plant species surveyed across 326 plots and six continents. Our findings indicate that arid and hyper-arid drylands act as a global reservoir of plant phenotypic diversity, challenging the common assumption that harsh environmental conditions reduce plant trait diversity. Tordoni et al.2 speculate that the larger phenotypic diversity in harsh environments found in our study is overestimated and misinterpreted. The re-analyses presented here further confirm that the patterns we originally reported are robust, and thus that the concerns from Tordoni et al. are not well-founded and do not apply to our study. We stand for the main conclusions of our study and maintain that lonely plants in arid land are functionally hyperdiverse.

ecology↗

bioRxiv2023

Soil health is linked to primary productivity across Europe

A healthy soil is at the core of sustainable management and policy, but its importance for plant productivity across environmental gradients and land-use types remains poorly understood. To address this gap, we conducted a pan-European field study including 588 sites from 27 countries to investigate the link between soil health and primary productivity across three major land-use types: woodlands, grasslands, and croplands. We found that mean soil health (a composite index based on soil properties, biodiversity, and plant disease control) in woodlands was 31.4% higher than in grasslands, and 76.1% higher than in croplands. Soil health was positively linked to cropland and grassland productivity at the continental scale. Woodland productivity was best explained by climate. Among microbial diversity indicators, we observed a positive association between the richness of Acidobacteria, Firmicutes, and Proteobacteria and primary productivity. Among microbial functional groups, we found that nitrogen-fixing bacteria and mycorrhizal fungi positively related to primary productivity in croplands and grasslands, while plant pathogens showed a negative relationship. Together, our results point to the importance of soil biodiversity and soil health for maintaining primary productivity across contrasting land-use types.

ecology↗

bioRxiv2023

Complementary effects of above- and belowground biodiversity on ecosystem functions across global grasslands

Grasslands are integral to maintaining biodiversity and key ecosystem services under climate change. Plant and soil biodiversity, and their interactions, support the provision of multiple ecosystem functions (multifunctionality). However, whether plant and soil biodiversity explain unique, or shared, contributions to supporting multifunctionality across global grasslands remains virtually unknown. Here, we combine results from a global survey of 101 grasslands with a novel microcosm study, controlling for both plant and soil microbial diversity to identify their individual and interactive contribution to support multifunctionality under aridity and experimental drought. We found that, plant and soil microbial diversity independently predict a unique portion of variation in above- and belowground functioning, suggesting both types of biodiversity complement each other. Interactions between plant and soil microbial diversity regulated primary productivity, nutrient storage, and plant productivity. Our findings were also context dependent, since soil fungal diversity was strongly associated to multifunctionality in less arid regions, while plant diversity was strongly linked to multifunctionality in more arid regions. Our results highlight the need to conserve both above- and belowground diversity to sustain grassland multifunctionality in a drier world and indicate climate change may shift the relative contribution of plant and soil biodiversity to multifunctionality across global grasslands.

ecology↗

bioRxiv2023

Heritable maize microbiomes contribute to local adaptation and host stress resilience

Beneficial interactions with microorganisms are pivotal for crop performance and resilience. However, it remains unclear how heritable the microbiome is with respect to the host plant genotype and to what extent host genetic mechanisms can modulate plant-microbe interactions in the face of environmental stress. Here, we surveyed the root and rhizosphere microbiome of 129 accessions of locally adapted Zea mays, sourced from diverse habitats and grown under control and different stress conditions. We quantified treatment and host genotype effects on the microbiome. Plant genotype and source environment were predictive of microbiome composition. Genome wide association analysis identified host genetic variants linked to both rhizosphere microbiome composition and source environment. We identified transposon insertions in a candidate gene linked to both the abundance of a keystone microbe Massilia and source total soil nitrogen, finding mutant plants to show a reduction in lateral root density. We conclude that locally adapted maize varieties exert patterns of genetic control on their root and rhizosphere microbiomes that follow variation in their home environments, consistent with a role in tolerance to prevailing stress.

genetics↗

bioRxiv2022

Highly diverse and unknown viruses may enhance Antarctic endoliths' adaptability

Rock-dwelling microorganisms are key players in ecosystem functioning of Antarctic ice free-areas. Yet, little is known about their diversity and ecology. Here, we performed metagenomic analyses on rocks from across Antarctica comprising >75,000 viral operational taxonomic units (vOTUS). We found largely undescribed, highly diverse and spatially structured virus communities potentially influencing bacterial adaptation and biogeochemistry. This catalog lays the foundation for expanding knowledge of the virosphere in extreme environments.

microbiology↗

bioRxiv2022

The global distribution and environmental drivers of the soil antibiotic resistome

BackgroundLittle is known about the global distribution and environmental drivers of key microbial functional traits such as antibiotic resistance genes (ARGs). Soils are one of Earths largest reservoirs of ARGs, which are integral for soil microbial competition, and have potential implications for plant and human health. Yet, their diversity and global patterns remain poorly described. Here, we analyzed 285 ARGs in soils from 1012 sites across all continents, and created the first global atlas with the distributions of topsoil ARGs. ResultsWe show that ARGs peaked in high latitude cold and boreal forests. Climatic seasonality and mobile genetic elements, associated with the transmission of antibiotic resistance, were also key drivers of their global distribution. Dominant ARGs were mainly related to multidrug resistance genes and efflux pump machineries. We further pinpointed the global hotspots of the diversity and proportions of soil ARGs. ConclusionsTogether, our work provides the foundation for a better understanding of the ecology and global distribution of the environmental soil antibiotic resistome.

ecology↗

bioRxiv2022

Towards understanding diversity, endemicity and global change vulnerability of soil fungi

Fungi play pivotal roles in ecosystem functioning, but little is known about their global patterns of diversity, endemicity, vulnerability to global change drivers and conservation priority areas. We applied the high-resolution PacBio sequencing technique to identify fungi based on a long DNA marker that revealed a high proportion of hitherto unknown fungal taxa. We used a Global Soil Mycobiome consortium dataset to test relative performance of various sequencing depth standardization methods (calculation of residuals, exclusion of singletons, traditional and SRS rarefaction, use of Shannon index of diversity) to find optimal protocols for statistical analyses. Altogether, we used six global surveys to infer these patterns for soil-inhabiting fungi and their functional groups. We found that residuals of log-transformed richness (including singletons) against log-transformed sequencing depth yields significantly better model estimates compared with most other standardization methods. With respect to global patterns, fungal functional groups differed in the patterns of diversity, endemicity and vulnerability to main global change predictors. Unlike -diversity, endemicity and global-change vulnerability of fungi and most functional groups were greatest in the tropics. Fungi are vulnerable mostly to drought, heat, and land cover change. Fungal conservation areas of highest priority include wetlands and moist tropical ecosystems.

ecology↗

bioRxiv2022

Environmental thresholds in the functional mycobiome of global drylands

Fungi are major drivers of ecosystem functions. Increases in aridity are known to negatively impact fungal communities in dryland ecosystems globally, however, much less is known on the potential influence of other environmental drivers. To fill this knowledge gap, we reanalyzed fungal data from 912 soil samples, providing the largest and most complete fungal community dataset from global drylands. We used machine learning tools to examine geographical patterns in community composition and spatial, edaphic, and climatic factors driving them. Further, we determined critical thresholds of community turnover along those gradients. Our analysis identifies UV index, climate seasonality, and sand content as the most important environmental predictors of community shifts, harbouring greatest association with the richness of putative plant pathogens and saprobes. Important nonlinear relationships existed with each of these fungal guilds, with increases in UV and temperature seasonality above 7.5 and 900 SD, respectively, being associated with an increased probability of plant pathogens and unspecified saprotrophs occurrence. Conversely, these environmental parameters had a negative relationship with litter and soil saprotrophs richness. Consequently, these functional groups might be differentially sensitive to environmental changes, which might result in an inevitable disturbance of current plant-soil dynamics in drylands.

ecology↗

bioRxiv2022

Database-independent analysis of probable post-translational modifications of soil proteins across ecosystems

The identification rate of measured peptide spectra to proteins barely scratches 1% in best-case scenarios. Hundreds of thousands of valuable spectra are lost as no viable match in the database is found. Here, we apply the delta m/z plot that was previously implemented in MSnbase as tool for quality control to 63 soil samples from three ecosystems with different vegetation (39 forests, 11 grasslands, and 13 shrublands) with the aim to extract probable post-translational modifications (PTM) without the need of a reference database. The validity of the approach was verified with amino acids proposed for their respective 1 Da mass interval and compared to their relative abundance in proteins. We found that the average probable PTM and most known PTMs proposed for the mass intervals are similar across ecosystems. Otherwise, 11 mass intervals changed significantly in relative abundance in the three ecosystems but only for one an annotation could be proposed. Our approach not only highlights the opportunity of the database-independent analysis in soil metaproteomics but paves the way for targeted analysis of the yet unknown PTMs.

ecology↗

bioRxiv2021

Vegetation structure determines cyanobacterial communities during soil development across global biomes

O_LISoil cyanobacteria play essential ecological roles and are known to experience large changes in their diversity and abundance throughout early succession. However, much less is known about how and why soil cyanobacterial communities change as soil develops from centuries to millennia, and the effects of aboveground vegetation on these communities. C_LIO_LIWe combined an extensive field survey including 16 global soil chronosequences across contrasting ecosystems (from deserts to tropical forests) with molecular analyses to investigate how the diversity and abundance of soil cyanobacteria under vegetation change during soil development from hundreds to thousands of years. C_LIO_LIWe show that, in most chronosequences, the abundance, species richness and community composition of soil cyanobacteria were relatively stable as soil develops (from centuries to millennia). Regardless of soil age, forest chronosequences were consistently dominated by non-photosynthetic cyanobacteria (Vampirovibrionia), while grasslands and shrublands were dominated by photosynthetic cyanobacteria. Chronosequences undergoing drastic vegetation shifts during soil development (e.g. transitions from grasslands to forests) experienced significant changes in the composition of soil cyanobacteria communities. C_LIO_LIOur results advance our understanding of the ecology of cyanobacterial classes, specially the understudied non-photosynthetic ones and highlight the key role of vegetation as a major driver of their temporal dynamics as soil develops. C_LI

ecology↗

bioRxiv2020

Temperature increases soil respiration across ecosystem types and soil development, but soil properties determine the magnitude of this effect

Soil carbon losses to the atmosphere, via soil heterotrophic respiration, are expected to increase in response to global warming, resulting in a positive carbon-climate feedback. Despite the well-known suite of abiotic and biotic factors controlling soil respiration, much less is known about how the magnitude of soil respiration responses to temperature changes over soil development and across contrasting soil properties. Here, we investigated the role of soil development stage and soil properties in driving the responses of soil heterotrophic respiration to increasing temperatures. We incubated soils from eight chronosequences ranging in soil age from hundreds to million years, and encompassing a wide range of vegetation types, climatic conditions, and chronosequences origins, at three assay temperatures (5, 15 and 25{degrees}C). We found a consistent positive effect of assay temperature on soil respiration rates across the eight chronosequences evaluated. However, soil properties such as organic carbon concentration, texture, pH, phosphorus content, and microbial biomass determined the magnitude of temperature effects on soil respiration. Finally, we observed a positive effect of soil development stage on soil respiration that did not alter the magnitude of assay temperature effects. Our work reveals that key soil properties alter the magnitude of the positive effect of temperature on soil respiration found across ecosystem types and soil development stages. This information is essential to better understand the magnitude of the carbon-climate feedback, and thus to establish accurate greenhouse gas emission targets.

ecology↗

bioRxiv2019

A global survey of mycobacterial diversity in soil

Mycobacterium is a diverse bacterial genus ubiquitous in many soil and aquatic environments. Members of this genus have been associated with human and other animal diseases, including the nontuberculous mycobacteria (NTM), which are of growing relevance to public health worldwide. Although soils are often considered an important source of environmentally-acquired NTM infections, the biodiversity and ecological preferences of soil mycobacteria remain largely unexplored across contrasting climates and ecosystem types. Using a culture-independent approach by combining 16S rRNA marker gene sequencing with mycobacterial-specific hsp65 gene sequencing, we analyzed the diversity, distributions, and environmental preferences of soil-dwelling mycobacteria in 143 soil samples collected from across the globe. The surveyed soils harbored highly diverse mycobacterial communities that span the full-extent of the known mycobacterial phylogeny, with most soil mycobacteria belonging to previously undescribed lineages. While the genus Mycobacterium tended to have higher relative abundances in cool, wet, and acidic soil environments, several individual mycobacterial clades had contrasting environmental preferences. We identified the environmental preferences of many mycobacterial clades, including the clinically-relevant M. avium complex that was more commonly detected in wet and acidic soils. However, most of the soil mycobacteria detected were not closely related to known pathogens, calling into question previous assumptions about the general importance of soil as a source of NTM infections. Together this work provides novel insights into the diversity, distributions and ecological preferences of soil mycobacteria, and lays the foundation for future efforts to link mycobacterial phenotypes to their distributions. ImportanceMycobacteria are common inhabitants of soil, and while most members of the bacterial genus are innocuous, some mycobacteria can cause environmentally-acquired infections of humans and other animals. Human infections from nontuberculous mycobacteria (NTM) are increasingly prevalent worldwide, and some areas appear to be hotspots for NTM disease. While exposure to soil is frequently implicated as an important mode of NTM transmission, the diversity, distributions and ecological preferences of soil mycobacteria remain poorly understood. We analyzed 143 soils from across the globe and found that the genus Mycobacterium and lineages within the genus often exhibited predictable preferences for specific environmental conditions. Soils harbor large amounts of previously-undescribed mycobacterial diversity, and lineages that include known pathogens were rarely detected in soil. Together these findings suggest that soil is an unlikely source of many mycobacterial infections. The biogeographical patterns we documented lend insight into the ecology of this important group of soil-dwelling bacteria.

microbiology↗

bioRxiv2019

Ecological niche differentiation in soil cyanobacterial communities across the globe

Cyanobacteria are key organisms in the evolution of life on Earth, but their distribution and environmental preferences in terrestrial ecosystems remain poorly understood. This lack of knowledge is particularly evident for two recently discovered non-photosynthetic cyanobacterial classes, Melainabacteria and Sericytochromatia, limiting our capacity to predict how these organisms and the important ecosystem functions they perform will respond to ongoing global change. Here, we conducted a global field survey covering a wide range of vegetation types and climatic conditions to identify the environmental factors associated with the distribution of soil cyanobacterial communities. Network analyses revealed three major clusters of cyanobacterial phylotypes, each one dominated by members of one of the extant classes of Cyanobacteria (Oxyphotobacteria, Melainabacteria and Sericytochromatia), suggesting that species within these taxonomic groups share similar environmental preferences. Melainabacteria appear mostly in acidic and humid ecosystems, especially forests, Oxyphotobacteria are prevalent in arid and semiarid areas, and Sericytochromatia are common in hyperarid oligotrophic environments. We used this information to construct a global atlas of soil cyanobacteria. Our results provide novel insights into the ecology and biogeography of soil cyanobacteria and highlight how their global distribution could change in response to increased aridity, a landmark feature of climate change in terrestrial ecosystems worldwide. Significance statementCyanobacteria have shaped the history of life on Earth and can be important photosynthesizers and nitrogen fixers in terrestrial ecosystems worldwide. The recent discovery of two non-photosynthetic classes has advanced our understanding of their evolution, but their distribution and environmental preferences remain poorly described. Using a global survey conducted across 237 locations on six continents, we identified three main groups of soil cyanobacteria with contrasting environmental preferences: acidic and humid ecosystems, arid and semiarid areas, and hyperarid oligotrophic ecosystems. We then constructed the first global atlas of soil cyanobacteria, an important advance in our understanding of the ecology and biogeography of these functionally important organisms.

ecology↗

bioRxiv2018

Unraveling the effects of spatial variability and relic DNA on the temporal dynamics of soil microbial communities

Few studies have comprehensively investigated the temporal variability in soil microbial communities despite widespread recognition that the belowground environment is dynamic. In part, this stems from the challenges associated with the high degree of spatial heterogeneity in soil microbial communities and because the presence of relic DNA (DNA from non-living cells) may dampen temporal signals. Here we disentangle the relationships among spatial, temporal, and relic DNA effects on bacterial, archaeal, and fungal communities in soils collected from contrasting hillslopes in Colorado, USA. We intensively sampled plots on each hillslope over six months to discriminate between temporal variability, intra-plot spatial heterogeneity, and relic DNA effects on the soil prokaryotic and fungal communities. We show that the intra-plot spatial variability in microbial community composition was strong and independent of relic DNA effects with these spatial patterns persisting throughout the study. When controlling for intra-plot spatial variability, we identified significant temporal variability in both plots over the six-month study. These microbial communities were more dissimilar over time after relic DNA was removed, suggesting that relic DNA hinders the detection of important temporal dynamics in belowground microbial communities. We identified microbial taxa that exhibited shared temporal responses and show these responses were often predictable from temporal changes in soil conditions. Our findings highlight approaches that can be used to better characterize temporal shifts in soil microbial communities, information that is critical for predicting the environmental preferences of individual soil microbial taxa and identifying linkages between soil microbial community composition and belowground processes.\n\nImportanceNearly all microbial communities are dynamic in time. Understanding how temporal dynamics in microbial community structure affect soil biogeochemistry and fertility are key to being able to predict the responses of the soil microbiome to environmental perturbations. Here we explain the effects of soil spatial structure and relic DNA on the determination of microbial community fluctuations over time. We found that intensive spatial sampling is required to identify temporal effects in microbial communities because of the high degree of spatial heterogeneity in soil and that DNA from non-living microbial cells masks important temporal patterns. We identified groups of microbes that display correlated behavior over time and show that these patterns are predictable from soil characteristics. These results provide insight into the environmental preferences and temporal relationships between individual microbial taxa and highlight the importance of considering relic DNA when trying to detect temporal dynamics in belowground communities.

microbiology↗

bioRxiv2018

Ecological analyses of mycobacteria in showerhead biofilms and their relevance to human health

Bacteria within the genus Mycobacterium can be abundant in showerheads, and the inhalation of aerosolized mycobacteria while showering has been implicated as a mode of transmission in nontuberculous mycobacterial (NTM) lung infections. Despite their importance, the diversity, distributions, and environmental predictors of showerhead-associated mycobacteria remain largely unresolved. To address these knowledge gaps, we worked with citizen scientists to collect showerhead biofilm samples and associated water chemistry data from 656 households located across the U.S. and Europe. Our cultivation-independent analyses revealed that the genus Mycobacterium was consistently the most abundant genus of bacteria detected in residential showerheads, yet mycobacterial diversity and abundances were highly variable. Mycobacteria were far more abundant, on average, in showerheads receiving municipal versus well water, and in U.S. households as compared to European households, patterns that are likely driven by differences in the use of chlorine disinfectants. Moreover, we found that water source, water chemistry, and household location also influenced the prevalence of specific mycobacterial lineages detected in showerheads. We identified geographic regions within the U.S. where showerheads have particularly high abundances of potentially pathogenic lineages of mycobacteria and these hot spots generally overlapped with those regions where NTM lung disease is most prevalent. Together these results emphasize the public health relevance of mycobacteria in showerhead biofilms. They further demonstrate that mycobacterial distributions in showerhead biofilms are often predictable from household location and water chemistry, knowledge that advances our understanding of NTM transmission dynamics and the development of strategies to reduce exposures to these emerging pathogens.

microbiology↗