Biology subjects

Renteria, L.

Publications and source records attributed to Renteria, L..

8 recordsLinked to original sources

bioRxiv2025

Independent genomic trajectories shape adaptation to life on land across animal lineages

How animals repeatedly adapted to life on land is a central question in evolutionary biology. While terrestrialisation occurred independently across animal phyla, it remains unclear whether shared genomic mechanisms underlie these transitions. Here, we combine large-scale comparative genomics, machine learning, and multi-omics data, including proteomics and transcriptomics from stress experiments relevant to terrestrial environmental challenges in 17 species, to investigate the genomic basis of animal terrestrial adaptation. Gene co-expression networks reveal that genes relevant to stress are largely lineage-specific, yet converge in function through the co-option of gene families pre-dating terrestrialisation events. Phylogenomic and machine learning analyses support a dominant role for early-evolving genes, enriched in stress-related functions, paired with a higher gene loss than gain at terrestrialisation nodes. Our findings support a model of lineage-specific genomic changes involving mostly conserved genes that converged at the functional level during the independent transitions to terrestrial life.

evolutionary biology↗

bioRxiv2024

Sediment-associated processes drive spatial variation in ecosystem respiration in the Yakima River basin

Hyporheic zones (HZ) can contribute substantially to total stream ecosystem respiration (ERtot). HZ-focused process-based models may, therefore, effectively predict ERtot across sites, yet this remains untested under variable environmental conditions. Here we evaluate whether spatial variation in HZ respiration predicted via a process-based model explains spatial variation in field-estimates of ERtot across 33 sites in the Yakima River basin in Washington State, USA. We found that HZ respiration predictions did not explain spatial variation in field estimates of ERtot. To investigate further, we partitioned ERtot contributions into water column respiration (ERwc) and sediment-associated respiration (ERsed). ERsed contributed >50% of ERtot at 88% of sites, though relative contributions varied substantially. Despite this dominance, modeled HZ respiration explained neither spatial variation in ERtot nor in ERsed, suggesting that the HZ model alone does not capture the drivers of sediment-associated respiration across these sites. Instead, ERsed spatial variation was primarily explained by gross primary production, stream slope, velocity, and total dissolved nitrogen rather than median grain size, a primary control of HZ respiration predicted by the process-based model. Consistent with recent studies, our results indicate that improving basin-scale ERtot predictions requires integrating hydrologic and biogeochemical processes across hyporheic, benthic, and water column zones.

ecology↗

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↗

bioRxiv2021

Implications of sample treatment on characterization of the riverine environmental metabolome

High-resolution mass spectrometry techniques are widely used in the environmental sciences to characterize natural organic matter and, when utilizing these instruments, researchers must make multiple decisions regarding sample pre-treatment and the instrument ionization mode. To identify how these choices alter organic matter characterization and resulting conclusions, we analyzed a collection of 17 riverine samples from East River, CO (USA) under four PPL-based Solid Phase Extraction (SPE) treatment and electrospray ionization polarity (e.g., positive and negative) combinations: SPE (+), SPE (-), non-SPE (-), and non-SPE (+). The greatest number of formula assignments were achieved with SPE-treated samples due to the removal of compounds that could interfere with ionization. Furthermore, the SPE (-) treatment captured the most formulas across the widest chemical compound diversity. In addition to a reduced number of assigned formulas, the non-SPE datasets resulted in altered thermodynamic interpretations that could cascade into incomplete assumptions about the availability of organic matter pools for microbial heterotrophic respiration. Thus, we infer that the SPE (-) treatment is the best single method for characterizing environmental organic matter pools unless the focus is on lipid-like compounds, in which case we recommend a combination of SPE (-) and SPE (+) to adequately characterize these molecules. SynopsisWe provide data-driven sample treatment and ionization mode recommendations to researchers who aim to use high-resolution mass spectrometry to characterize environmental organic matter. Abstract Art O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

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

Disturbance Triggers Non-Linear Microbe-Environment Feedbacks

Conceptual frameworks linking microbial community membership, properties, and processes with the environment and emergent function have been proposed but remain untested. Here we refine and test a recent conceptual framework using hyporheic zone sediments exposed to wetting/drying transitions. Throughout the system we found threshold-like responses to the duration of desiccation. Membership of the putatively active community--but not the whole community--responded due to enhanced deterministic selection (an emergent community property). Concurrently, the thermodynamic properties of organic matter became less favorable for oxidation (an environmental component) and respiration decreased (a microbial process). While these responses were step functions of desiccation, we observed continuous monotonic relationships among community assembly, respiration, and organic matter thermodynamics. Placing the results in context of our conceptual framework points to previously unrecognized internal feedbacks that are initiated by disturbance, mediated by thermodynamics, and that cause the impacts of disturbance to be dependent on the history of disturbance.

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↗

bioRxiv2020

Carbon limitation leads to thermodynamic regulation of aerobic metabolism

Organic matter (OM) metabolism in freshwater ecosystems is a critical source of uncertainty in global biogeochemical cycles, yet aquatic OM cycling remains poorly understood. Here, we present the first work to explicitly test OM thermodynamics as a key regulator of aerobic respiration, challenging long-held beliefs that organic carbon and oxygen concentrations are the primary determinants of respiration rates. We pair controlled microcosm experiments with ultrahigh-resolution OM characterization to demonstrate a clear relationship between OM thermodynamic favorability and aerobic respiration under carbon limitation. We also demonstrate a shift in the regulation of aerobic respiration from OM thermodynamics to nitrogen content when carbon is in excess, highlighting a central role for OM thermodynamics in aquatic biogeochemical cycling particularly in carbon-limited ecosystems. Our work therefore illuminates a structural gap in aquatic biogeochemical models and presents a new paradigm in which OM thermodynamics and nitrogen content interactively govern aerobic respiration.

ecology↗