Biology subjects

Foley, M. M.

Publications and source records attributed to Foley, M. M..

4 recordsLinked to original sources

bioRxiv2023

Improved characterization of soil organic matter by integrating FTICR-MS, liquid chromatography tandem mass spectrometry and molecular networking: a case study of root litter decay under drought conditions

Knowledge of the type of carbon contained in soils is important for predicting carbon fluxes in a warming climate, yet most soil organic matter (SOM) components are unknown. We used an integrated three-part approach to characterize SOM from decaying root-detritus microcosms subject to either drought or normal conditions. To observe broad differences in SOM compositions we employed direct infusion Fourier transform ion cyclotron resonance mass spectrometry (DI-FTICR-MS). We complemented this with liquid chromatography tandem mass spectrometry (LC-MS/MS) to identify components by library matching. Since libraries contain only a small fraction of SOM components, we also used fragment spectra cosine similarity scores to relate unknowns and library matches through molecular networks. This approach allowed us to corroborate DI-FTICR-MS molecular formulas using library matches and infer structures of unknowns from molecular networks to improve SOM annotation. We found matches to fungal metabolites, and under drought conditions, greater relative amounts of lignin-like vs condensed aromatic polyphenol formulas, and lower average nominal oxidation state of SOM carbon, suggesting reduced decomposition of carbon and/or microbes under stress. We propose this integrated approach as more comprehensive than individual analyses in parallel, with the potential to improve knowledge of the chemical composition and persistence of SOM. SynopsisStructural characterization and identifications are lacking for soil organic matter components. This study integrates molecular formula assignments and structural information from fragment ion spectra into molecular networks to better characterize unknown soil organic matter components. For Table of Contents Only O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=94 SRC="FIGDIR/small/545455v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@140a98org.highwire.dtl.DTLVardef@1c3b26forg.highwire.dtl.DTLVardef@f7b82aorg.highwire.dtl.DTLVardef@15c012f_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2022

Quantitative stable-isotope probing (qSIP) with metagenomics links microbial physiology and activity to soil moisture in Mediterranean-climate grassland ecosystems

The growth and physiology of soil microorganisms, which play vital roles in biogeochemical cycling, are likely dependent on current and prior soil moisture levels. Here, we developed and applied a genome-resolved metagenomic implementation of quantitative stable isotope probing (qSIP) to an H218O labeling experiment to determine which microbial community members, and with what capacities, are growing under in situ conditions. qSIP enabled measurement of taxon-specific growth because isotopic incorporation into microbial DNA requires production of new genome copies. We studied three Mediterranean grassland soils across a rainfall gradient to evaluate the hypothesis that historic precipitation levels are an important factor controlling trait selection. We used qSIP-informed genome-resolved metagenomics to resolve an active subset of soil community members and identify the ecophysiological traits that characterize them. Higher year-round precipitation levels correlated with higher activity and growth rates of flagellar motile microorganisms. In addition to bacteria that were heavily isotopically labeled, we identified abundant isotope-labeled phages suggesting phage-induced cell lysis likely contributed to necromass production at all three sites. Further, there was a positive correlation between phage activity and the activity of putative phage hosts. Contrary to our expectations, the capabilities to decompose the diverse complex carbohydrates common in soil necromass or oxidize methanol and carbon monoxide were broadly distributed across active and inactive bacteria in all three soils, implying that these traits are not highly selected for by historical precipitation.

microbiology↗

bioRxiv2021

Active communities and growth of soil microorganisms are framed by mean annual precipitation in three California annual grasslands

Earth system models project altered precipitation regimes across much of the globe; in California, the winter wet season is predicted to extend into spring, and the summer dry period to lengthen. How these precipitation trends will affect microbial traits and soil carbon (C) cycling is a key knowledge gap. Specifically, we do not have a mechanistic understanding of the linkages between soil moisture legacy effects, microbial population dynamics and soil C persistence. Using quantitative stable isotope probing (qSIP), we compared total and growing soil microbial communities across three California annual grasslands that span a rainfall gradient yet developed on similar parent material. We also assessed multiple edaphic variables, including the radiocarbon (14C) age of soil C, and found soil C turnover time increased with annual precipitation, but that soil microbes respired recently-fixed C regardless of site rainfall history. Samples were assayed in the wet season, when we expected environmental conditions would be most similar across sites. We hypothesized that growing communities would be more compositionally similar across the gradient than the total background microbiome. We also predicted that the long-term legacy effect of soil water limitation would be reflected in a lower community growth capacity at the driest site. We found that the proportion of the total community that was detected as growing was 28%, 48% and 58% at the wet, intermediate and dry sites, respectively. The composition of growing communities strongly resembled that of total communities, and growing communities were no more similar across the gradient than total communities, indicating a strong effect of climate of the structure of growing microbial communities. Members of three phyla, Acidobacteria, Actinobacteria, and Proteobacteria, were responsible for [~]79% of the cumulative 18O assimilation and 80% of all taxa that we defined as growers. Bacterial growth rates were low at the driest site relative to the intermediate and wettest sites. Reduced growth at the driest site was observed across major phyla, including the Actinobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes and Proteobacteria. Microbial communities at the driest site displayed phylogenetic clustering, suggesting that climate history impacts microbial growth through environmental filtering for slow growing taxa. Taxonomic identity was a strong predictor of growth, such that the growth rates of a taxon at one site predicted its growth rates at the others. This cross-site coherence in growth is likely a consequence of genetically determined physiological traits, and is consistent with the idea that evolutionary history influences growth rate.

ecology↗

bioRxiv2021

The Functional Significance of Bacterial Predators

Predation structures food webs, influences energy flow, and alters rates and pathways of nutrient cycling through ecosystems, effects that are well documented for macroscopic predators. In the microbial world, predatory bacteria are common, yet little is known about their rates of growth and roles in energy flows through microbial food webs, in part because these are difficult to quantify. Here, we show that growth and carbon uptake were higher in predatory bacteria compared to non-predatory bacteria, a finding across 15 sites, synthesizing 82 experiments and over 100,000 taxon-specific measurements of element flow into newly synthesized bacterial DNA. Obligate predatory bacteria grew 36% faster and assimilated carbon at rates 211% higher than non-predatory bacteria. These differences were less pronounced for facultative predators (6% higher growth rates, 17% higher carbon assimilation rates), though high growth and carbon assimilation rates were observed for some facultative predators, such as members of the genera Lysobacter and Cytophaga, both capable of gliding motility and wolfpack hunting behavior. Added carbon substrates disproportionately stimulated growth of obligate predators, with responses 63% higher than non-predators for the Bdellovibrionales and 81% higher for the Vampirovibrionales, whereas responses of facultative predators to substrate addition were no different from non-predators. This finding supports ecological theory that higher productivity increases predator control of lower trophic levels. These findings also indicate that the functional significance of bacterial predators increases with energy flow, and that predatory bacteria influence element flow through microbial food webs.

ecology↗