Biology subjects

Danczak, R. E.

Publications and source records attributed to Danczak, R. E..

7 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

Spatial and temporal metagenomics of river compartments reveals viral community dynamics in an urban impacted stream

Although river ecosystems comprise less than 1% of Earths total non-glaciated area, they are critical modulators of microbially and virally orchestrated global biogeochemical cycles. However, most studies either use data that is not spatially resolved or is collected at timepoints that do not reflect the short life cycles of microorganisms. As a result, the relevance of microbiome interactions and the impacts they have over time on biogeochemical cycles are poorly understood. To assess how viral and microbial communities change over time, we sampled surface water and pore water compartments of the wastewater-impacted River Erpe in Germany every 3 hours over a 48-hour period resulting in 32 metagenomes paired to geochemical and metabolite measurements. We reconstructed 6,500 viral and 1,033 microbial genomes and found distinct communities associated with each river compartment. We show that 17% of our vMAGs clustered to viruses from other ecosystems like wastewater treatment plants and rivers. Our results also indicated that 70% of the viral community was persistent in surface waters, whereas only 13% were persistent in the pore waters taken from the hyporheic zone. Finally, we predicted linkages between 73 viral genomes and 38 microbial genomes. These putatively linked hosts included members of the Competibacteraceae, which we suggest are potential contributors to carbon and nitrogen cycling. Together, these findings demonstrate that microbial and viral communities in surface waters of this urban river can exist as stable communities along a flowing river; and raise important considerations for ecosystem models attempting to constrain dynamics of river biogeochemical cycles.

microbiology↗

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

Unification of Environmental Metabolomics with Metacommunity Ecology

Environmental metabolomics, enabled by high-resolution mass spectrometric techniques, have demonstrated the biogeochemical importance of the metabolites which comprise natural organic matter (NOM). However, significant gaps exist in our understanding of the spatiotemporal organization of NOM composition. We suggest that the underlying mechanisms governing NOM can be revealed by applying tools and concepts from metacommunity ecology to environmental metabolomics. After illustrating the similarities between metabolomes and ecological communities, we call this conceptual synthesis meta-metabolome ecology and demonstrate its potential utility using a freshwater mass spectrometry dataset. Specifically, we developed three relational metabolite dendrograms using combinations of molecular properties (i.e., aromaticity index, double-bond equivalents, etc.) and putative biochemical transformations. Using these dendrograms, which are similar to phylogenetic or functional trait trees in ecological communities, we illustrate potential analytical techniques by investigating relationally-informed -diversity and {beta}-diversity metrics (e.g., MPD, MNTD, UniFrac), and null model analyses (e.g., NRI, NTI, and {beta}NTI). Furthermore, we demonstrate that this synthesis allows ecological communities (e.g., microbes) and the metabolites they produce and consume using the same framework. We propose that applying this framework to a broad range of ecosystems will reveal generalizable principles that can advance our predictive capabilities regarding NOM dynamics.

ecology↗