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

Danczak, Robert E.; Goldman, Amy; Chu, Rosalie K.; Toyoda, Jason; Garayburu‐Caruso, Vanessa; Tolić, Nikola; Graham, Emily B.; Morad, Joseph W; Renteria, Lupita; Wells, Jacqueline; Herzog, Skuyler; Ward, Adam S.; Stegen, James C.

doi:10.1016/j.scitotenv.2021.147409

Cited by 24 publications

(43 citation statements)

References 68 publications

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“…Grouping molecular formula by either elemental composition categories or compound classes further revealed little consistent variation across wet-dry conditions suggesting that the OM meta-assemblage might be more impacted by ecosystem than treatment condition in this case (Figure 5). Similar patterns were observed in a headwater stream, where bulk environmental properties were conserved across ecosystem types despite divergent OM assemblages undergoing variable selection as a result of hypothesized thermodynamic redundancy (Danczak et al, 2021). Briefly, thermodynamic redundancy is like functional redundancy, where compositionally divergent OM assemblages have similar thermodynamic properties.…”

Section: Homologous Series Disproportionately Contribute To Convergen...supporting

confidence: 56%

“…Here, βNTI feat helps us examine whether this hypothesized redundancy exists across groups contributing to community structure. For example, in contrast to the thermodynamic behavior observed in Danczak et al (2021), we see that the nominal oxidation state of carbon (NOSC) significantly varies across those CHON and CHOP containing molecular formula which contribute to convergence/divergence (Mann-Whitney U test value of p < .05; Supplementary Figure 2). Specifically, we observe that CHOP formulas with less inferred structural complexity (e.g., lower aromaticity index and double-bond equivalents) and more inferred lability (e.g., lower NOSC) drove significant convergence; differences in the properties of CHON formulas appear to manifest more as variation in distributions (e.g., those formulas which contribute to convergence are more constrained).…”

Section: Homologous Series Disproportionately Contribute To Convergen...mentioning

confidence: 62%

“…significantly contribute to divergence across the entire dataset (Figure 4C). This might suggest that these more complex compounds may play variable roles depending on the situation; they could be a hallmark of differential nutrient limitation (i.e., the functional needs of the meta-assemblage are highly variable; Graham et al, 2018;Garayburu-Caruso et al, 2020;Danczak et al, 2021) or highlight divergent degradation potential (e.g., common metabolites might be processed through different pathways).…”

Section: Homologous Series Disproportionately Contribute To Convergen...mentioning

confidence: 99%

“…Evaluating the processes which govern community diversity is often the goal of ecological studies across all ecosystems (Swenson et al, 2006;Kraft et al, 2007;Gilbert and Bennett, 2010;Smith and Lundholm, 2010;Chase and Myers, 2011;George et al, 2011;Stegen et al, 2013;Herren and McMahon, 2017;Zhou and Ning, 2017;Danczak et al, 2020b). Analogously, researchers have also focused on understanding the processes governing the composition of organic molecules or metabolites within organic matter (OM) assemblages (Danczak et al, 2020a(Danczak et al, , 2021. While methods might vary in how researchers investigate these processes (e.g., variation partitioning, trait-based analyses, and null modeling), each study attempts to determine when, where, and how various ecological assembly processes give rise to specific community/ assemblage configurations.…”

Section: Introductionmentioning

confidence: 99%

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Inferring the Contribution of Microbial Taxa and Organic Matter Molecular Formulas to Ecological Assembly

et al. 2022

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Understanding the mechanisms underlying the assembly of communities has long been the goal of many ecological studies. While several studies have evaluated community wide ecological assembly, fewer have focused on investigating the impacts of individual members within a community or assemblage on ecological assembly. Here, we adapted a previous null model β-nearest taxon index (βNTI) to measure the contribution of individual features within an ecological community to overall assembly. This new metric, called feature-level βNTI (βNTIfeat), enables researchers to determine whether ecological features (e.g., individual microbial taxa) contribute to divergence, convergence, or have insignificant impacts across spatiotemporally resolved metacommunities or meta-assemblages. Using βNTIfeat, we revealed that unclassified microbial lineages often contributed to community divergence while diverse groups (e.g., Crenarchaeota, Alphaproteobacteria, and Gammaproteobacteria) contributed to convergence. We also demonstrate that βNTIfeat can be extended to other ecological assemblages such as organic molecules comprising organic matter (OM) pools. OM had more inconsistent trends compared to the microbial community though CHO-containing molecular formulas often contributed to convergence, while nitrogen and phosphorus-containing formulas contributed to both convergence and divergence. A network analysis was used to relate βNTIfeat values from the putatively active microbial community and the OM assemblage and examine potentially common contributions to ecological assembly across different communities/assemblages. This analysis revealed that P-containing formulas often contributed to convergence/divergence separately from other ecological features and N-containing formulas often contributed to assembly in coordination with microorganisms. Additionally, members of Family Geobacteraceae were often observed to contribute to convergence/divergence in conjunction with both N- and P-containing formulas, suggesting a coordinated ecological role for family members and the nitrogen/phosphorus cycle. Overall, we show that βNTIfeat offers opportunities to investigate the community or assemblage members, which shape the phylogenetic or functional landscape, and demonstrate the potential to evaluate potential points of coordination across various community types.

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Section: Homologous Series Disproportionately Contribute To Convergen...supporting

confidence: 56%

Section: Homologous Series Disproportionately Contribute To Convergen...mentioning

confidence: 62%

Section: Homologous Series Disproportionately Contribute To Convergen...mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Inferring the Contribution of Microbial Taxa and Organic Matter Molecular Formulas to Ecological Assembly

et al. 2022

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“…More specifically, Fudyma et al (2021) used the ultra-high mass resolution of Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) data (Marshall et al, 1998;Bahureksa et al, 2021) to infer putative abiotic and abiotic transformations of OM in a river corridor system. This extended previously-developed cheminformatics techniques (e.g., Breitling et al, 2006;Danczak et al, 2020Danczak et al, , 2021 to include abiotic transformations. Fudyma et al (2021) found that abiotic OM transformations, such as those driven by sunlight and photooxidation, may alter bioavailability of OM in groundwater and surface water.…”

Section: Introductionmentioning

confidence: 97%

Organic Matter Transformations are Disconnected Between Surface Water and the Hyporheic Zone

Stegen

Fansler

Tfaily

et al. 2022

Preprint

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Abstract. Biochemical transformations of organic matter (OM) are a primary driver of river corridor biogeochemistry, thereby modulating ecosystem processes at local to global scales. OM transformations are driven by diverse biotic and abiotic processes, but we lack knowledge of how the diversity of those processes varies across river corridors and across surface and subsurface components of river corridors. To fill this gap we quantified the number of putative biotic and abiotic transformations of organic molecules across diverse river corridors using ultra-high resolution mass spectrometry. The number of unique transformations is used here as a proxy for the diversity of biochemical processes underlying observed profiles of organic molecules. For this, we use public data spanning the contiguous United States (ConUS) from the Worldwide Hydrobiogeochemical Observation Network for Dynamic River Systems (WHONDRS) consortium. Our results show that surface water OM had more biotic and abiotic transformations than OM from shallow hyporheic zone sediments (1–3 cm depth). We observed substantially more biotic than abiotic transformations, and the number of biotic and abiotic transformations were highly correlated with each other. We found no relationship between the number of transformations in surface water and sediments, and no meaningful relationships with latitude, longitude, or climate. We also found that the composition of transformations in sediments was not linked with transformation composition in adjacent surface waters. We infer that OM transformations represented in surface water are an integrated signal of diverse processes occurring throughout the upstream catchment. In contrast, OM transformations in sediments likely reflect a narrower range of processes within the sampled volume. This indicates decoupling between surface water and sediment OM, which is surprising given the potential for hydrologic exchange to homogenize OM. We infer that the processes influencing OM transformations and the scales at which they operate diverge between surface water and sediments.

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Organic Carbon Cycling and Transformation

Martin,

Bianchi

2024

Treatise on Estuarine and Coastal Science (Second Edition)

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

Cited by 24 publications

References 68 publications

Inferring the Contribution of Microbial Taxa and Organic Matter Molecular Formulas to Ecological Assembly

Inferring the Contribution of Microbial Taxa and Organic Matter Molecular Formulas to Ecological Assembly

Organic Matter Transformations are Disconnected Between Surface Water and the Hyporheic Zone

Organic Carbon Cycling and Transformation

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