Biology subjects

Garayburu-Caruso, V. A.

Publications and source records attributed to Garayburu-Caruso, V. A..

4 recordsLinked to original sources

bioRxiv2024

Meta-metabolome ecology reveals that geochemistry and microbial functional potential are linked to organic matter development across seven rivers

Rivers receive substantial dissolved organic matter (DOM) input from the land and transport it to the ocean. As DOM travels through watersheds, it undergoes biotic and abiotic transformations that impact biogeochemical cycles and any subsequent CO2 release into the atmosphere. While recent research has increased our mechanistic knowledge of DOM composition within watersheds, DOM development across broad spatial distances and within divergent biomes is under investigated. Here, we combined DOM characterization, geochemical analyses, and shotgun metagenomics to analyze samples from seven rivers ranging from the U.S. Pacific Northwest to Berlin, Germany. Initial analyses revealed that many DOM properties were distinguished by river type (e.g., wastewater, headwater) and that geochemistry often explained variation across rivers. At a global scale, analyses rooted in meta-metabolome ecology indicated that DOM was structured overwhelmingly by deterministic selection. When controlling for scale, however, analyses indicated that ecological assembly dynamics were again partially structured by river type. Finally, microbial analyses revealed that many riverine microbes from our systems shared core metabolic functional potential while differing in peripheral capabilities in across the rivers. Further analysis of the carbon degradation potential for recovered metagenomically assembled genomes indicated that the sampled rivers had strong taxonomically conserved niche differentiation and that carbon degradation potential diversity was significantly related to organic matter diversity. Together, these results help us uncover interconnections between the development of DOM, riverine geochemistry, and microbial functional potential.

ecology↗

bioRxiv2023

Genomic fingerprints of the world's soil ecosystems

Despite the explosion of soil metagenomic data, we lack a synthesized understanding of patterns in the distribution and functions of soil microorganisms. These patterns are critical to predictions of soil microbiome responses to climate change and resulting feedbacks that regulate greenhouse gas release from soils. To address this gap, we assay 1512 manually-curated soil metagenomes using complementary annotation databases, read-based taxonomy, and machine learning to extract multidimensional genomic fingerprints of global soil microbiomes. Our objective is to uncover novel biogeographical patterns of soil microbiomes across environmental factors and ecological biomes with high molecular resolution. We reveal shifts in the potential for (1) microbial nutrient acquisition across pH gradients; (2) stress, transport, and redox-based processes across changes in soil bulk density; and (3) greenhouse gas emissions across biomes. We also use an unsupervised approach to reveal a collection of soils with distinct genomic signatures, characterized by coordinated changes in soil organic carbon, nitrogen, and cation exchange capacity and in bulk density and clay content that may ultimately reflect soil environments with high microbial activity. Genomic fingerprints for these soils highlight the importance of resource scavenging, plant-microbe interactions, fungi, and heterotrophic metabolisms. Across all analyses, we observed phylogenetic coherence in soil microbiomes -- more closely related microorganisms tended to move congruently in response to soil factors. Collectively, the genomic fingerprints uncovered here present a basis for global patterns in the microbial mechanisms underlying soil biogeochemistry and help beget tractable microbial reaction networks for incorporation into process-based models of soil carbon and nutrient cycling. ImportanceWe address a critical gap in our understanding of soil microorganisms and their functions, which have a profound impact on our environment. We analyzed 1512 global soils with advanced analytics to create detailed genetic profiles (fingerprints) of soil microbiomes. This reveals novel patterns in how microorganisms are distributed across different soil environments. For instance, we discovered shifts in microbial potential to acquire nutrients in relation to soil acidity, as well as changes in stress responses and potential greenhouse gas emissions linked to soil structure. We also identified soils with putative high activity that had unique genomic characteristics surrounding resource acquisition, plant-microbe interactions, and fungal activity. Finally, we observed that closely related microorganisms tend to respond in similar ways to changes in their surroundings. Our work is a significant step towards comprehending the intricate world of soil microorganisms and its role in the global climate.

ecology↗

bioRxiv2020

Using Community Science to Reveal the Global Chemogeography of River Metabolomes

River corridor metabolomes reflect organic matter (OM) processing that drives aquatic biogeochemical cycles. Recent work highlights the power of ultrahigh-resolution mass spectrometry for understanding metabolome composition and river corridor metabolism. However, there have been no studies on the global chemogeography of surface water and sediment metabolomes using ultrahigh-resolution techniques. Here, we describe a community science effort from the Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) consortium to characterize global metabolomes in surface water and sediment that span multiple stream orders and biomes. We describe the distribution of key aspects of metabolomes including elemental groups, chemical classes, indices, and inferred biochemical transformations. We show that metabolomes significantly differ across surface water and sediment and that surface water metabolomes are more rich and variable. We also use inferred biochemical transformations to identify core metabolic processes shared among surface water and sediment. Finally, we observe significant spatial variation in sediment metabolites between rivers in the eastern and western portions of the contiguous United States. Our work not only provides a basis for understanding global patterns in river corridor biogeochemical cycles but also demonstrates that community science endeavors can enable global research projects that are unfeasible with traditional research models.

ecology↗

bioRxiv2020

Ecological theory applied to environmental metabolomes reveals compositional divergence despite conserved molecular properties

Stream and river systems transport and process substantial amounts of dissolved organic matter (DOM) from terrestrial and aquatic sources to the ocean, with global biogeochemical implications. However, the underlying mechanisms affecting the spatiotemporal organization of DOM composition are under-investigated. To understand the principles governing DOM composition, we leverage the recently proposed synthesis of metacommunity ecology and metabolomics, termed meta-metabolome ecology. Applying this novel approach to a freshwater ecosystem, we demonstrated that despite similar molecular properties across metabolomes, metabolite identity significantly diverged due to environmental filtering. We refer to this phenomenon as thermodynamic redundancy, which is analogous to the ecological concept of functional redundancy. We suggest that under thermodynamic redundancy, divergent metabolomes can support equivalent biogeochemical function just as divergent ecological communities can support equivalent ecosystem function. As these analyses are performed in additional ecosystems, potentially generalizable principles, like thermodynamic redundancy, can be revealed and provide insight into DOM dynamics.

ecology↗