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Rationale: Fourier transform ion cyclotron resonance mass spectrometry (FT‐ICR‐MS) is a preferred technique for analyzing complex organic mixtures. Currently, there is no consensus normalization approach, nor an objective method for selecting one, for quantitative analyses of FT‐ICR‐MS data. We investigate a method to evaluate and score the amount of bias various normalization approaches introduce into the data. Methods: We evaluate the ability of the Statistical Procedure for the Analysis of Normalization Strategies (SPANS) to guide the selection of appropriate normalization approaches for two different FT‐ICR‐MS data sets. Furthermore, we test the robustness of SPANS results to changes in SPANS parameter values and assess the impact of using various normalization approaches on downstream statistical analyses. Results: The normalization approach identified by SPANS differed for the two data sets. Normalization methods impacted the statistical significance of peaks differently, underscoring the importance of carefully evaluating potential methods. More consistent SPANS scores resulted when at least 120 significant peaks are used, where larger sets of peaks were obtained by increasing the p‐value threshold. Interestingly, we show that total sum scaling and highest peak normalization, used in previous studies, underperformed relative to SPANS‐recommended normalization approaches. Conclusions: Although there is no single, best normalization method for all data sets, SPANS provides a mechanism to identify an appropriate normalization method for analyzing FT‐ICR‐MS data quantitatively. The number of peaks used in the background distributions of SPANS contributes more significantly to the reproducibility of results than the p‐value thresholds used to obtain those peaks. [ABSTRACT FROM AUTHOR]

The adaptability of soil microbial communities to prolonged periods of drought is influenced by their ability to produce extracellular polymeric substances (EPS) with sufficient water retention properties. Microbial EPS have been extensively investigated as water reservoirs during drought, but it remains unknown how carbon substrate accessibility to soil microbial communities will affect the chemical properties of the EPS they generate, and whether this in turn will alter their water retention characteristics. In this work, we observed that the accessibility of carbon substrates influenced microbial community structure and, consequently, the chemical properties of EPS produced by the microbial communities. Our results demonstrated that an insoluble carbon substrate (i.e., chitin), stimulated microbial communities to produce EPS with measurably better water retention properties in emulated soil microenvironments in comparison to a soluble carbon substrate (i.e., N-acetylglucosamine; NAG). In all, this study demonstrates the importance of carbon substrate accessibility by soil microorganisms in regulating the community structure and consequently, the EPS carbon chemistry, which in turn can greatly influence the adaptability of soil microbial communities to drought. • Carbon substrate accessibility regulates microbial community membership. • The properties of microbial community-produced EPS can be influenced by membership. • Soil microbial community membership influence EPS water retention properties. • Specific carbon substrates may affect microbial community EPS production and properties. [ABSTRACT FROM AUTHOR]

The microbial and molecular characterization of the ectorhizosphere is an important step towards developing a more complete understanding of how the cultivation of biofuel crops can be undertaken in nutrient poor environments. The ectorhizosphere of Setaria is of particular interest because the plant component of this plant-microbe system is an important agricultural grain crop and a model for biofuel grasses. Importantly, Setaria lends itself to high throughput molecular studies. As such, we have identified important intra- and interspecific microbial and molecular differences in the ectorhizospheres of three geographically distant Setaria italica accessions and their wild ancestor S. viridis. All were grown in a nutrient-poor soil with and without nutrient addition. To assess the contrasting impact of nutrient deficiency observed for two S. italica accessions, we quantitatively evaluated differences in soil organic matter, microbial community, and metabolite profiles. Together, these measurements suggest that rhizosphere priming differs with Setaria accession, which comes from alterations in microbial community abundances, specifically Actinobacteria and Proteobacteria populations. When globally comparing the metabolomic response of Setaria to nutrient addition, plants produced distinctly different metabolic profiles in the leaves and roots. With nutrient addition, increases of nitrogen containing metabolites were significantly higher in plant leaves and roots along with significant increases in tyrosine derived alkaloids, serotonin, and synephrine. Glycerol was also found to be significantly increased in the leaves as well as the ectorhizosphere. These differences provide insight into how C4 grasses adapt to changing nutrient availability in soils or with contrasting fertilization schemas. Gained knowledge could then be utilized in plant enhancement and bioengineering efforts to produce plants with superior traits when grown in nutrient poor soils. [ABSTRACT FROM AUTHOR]

Soil redox conditions exert substantial influence on biogeochemical processes in terrestrial ecosystems. Humid tropical forest soils are often characterized by fluctuating redox, yet how these dynamics affect patterns of organic matter decomposition and associated CO2 fluxes remains poorly understood. We used a 13C-label incubation experiment in a humid tropical forest soil to follow the decomposition of plant litter and soil organic matter (SOM) in response to four redox regimes—static oxic or anoxic, and two oscillating treatments. We used high-resolution mass spectrometry to characterize the relative composition of organic compound classes in the water extractable OM. CO2 production from litter and SOM showed different responses to redox treatments. While cumulative production of SOM-derived CO2 was positively correlated with the length of oxic exposure (r = 0.89, n = 20), cumulative 13C-litter-derived CO2 production was not linked to oxygen availability. Litter-derived CO2 production was highest under static anoxic conditions in the first half of the experiment, and later dropped to the lowest rate amongst the treatments. In anoxic soils, we observed depletion of more oxidized water-extractable OM (especially amino sugar-, carbohydrate-, and protein-like compounds) over the second half of the experiment, which likely served as substrates for anaerobic CO2 production. Results from two-pool kinetic modeling showed that more frequent anoxic exposure limited decomposition of a slow-cycling C pool, but not a fast-cycling pool. These results suggest that aerobic and anaerobic heterotrophs were equally effective at degrading labile substrates released from fresh plant litter in this humid tropical forest soil, while aerobic decomposers were more effective in breaking down the potentially refractory compounds found in SOM. [ABSTRACT FROM AUTHOR]

Most soil carbon (C) is in the form of soil organic matter (SOM), the composition of which is controlled by the plant–microbe–soil continuum. The extent to which plant and microbial inputs contribute to persistent SOM has been linked to edaphic properties such as mineralogy and aggregation. However, it is unknown how variation in plant inputs, microbial community structure, and soil physical and chemical attributes interact to influence the chemical classes that comprise SOM pools. We used two long‐term biofuel feedstock field experiments to test the influence of cropping systems (corn and switchgrass) and soil characteristics (sandy and silty loams) on microbial selection and SOM chemistry. Cropping system had a strong influence on water‐extractable organic C chemistry with perennial switchgrass generally having a higher chemical richness than the annual corn cropping system. Nonetheless, cropping system was a less influential driver of soil microbial community structure and overall C chemistry than soil type. Soil type was especially influential on fungal community structure and the chemical composition of the chloroform‐extractable C. Although plant inputs strongly influence the substrates available for decomposition and SOM formation, total C and nitrogen (N) did not differ between cropping systems within either site. We conclude this is likely due to enhanced microbial activity under the perennial cropping system. Silty soils also had a higher activity of phosphate and C liberating enzymes. After 8 years, silty loams still contained twice the total C and N as sandy loams, with no significant response to biofuel cropping system inputs. Together, these results demonstrate that initial site selection is critical to plant–microbe interactions and substantially impacts the potential for long‐term C accrual in soils under biofuel feedstock production. [ABSTRACT FROM AUTHOR]

Soil organic matter (SOM) dynamics are central to soil biogeochemistry and fertility. The retention of SOM is governed initially by interactions with minerals, which mediate the sorption of chemically diverse organic matter (OM) molecules via distinct surface areas and chemical functional group availabilities. Unifying principles of mineral-OM interactions remain elusive because of the multi-layered nature of biochemical-mineral interactions that contribute to soil aggregate formation and the heterogeneous nature of soils among ecosystems. This study sought to understand how soil mineralogy as well as nitrogen (N) enrichment regulate OM composition in grassland soils. Using a multi-site grassland experiment, we demonstrate that the composition of mineral-associated OM depended on the clay content and specific mineral composition in soils across the sites. With increasing abundance of ferrihydrite (Fh) across six different grassland locations, OM in the hydrophobic zone became more enriched in lipid- and protein-like compounds, whereas the kinetic zone OM became more enriched in lignin-like molecules. These relationships suggest that the persistence of various classes of OM in soils may depend on soil iron mineralogy and provide experimental evidence to support conceptual models of zonal mineral-OM associations. Experimental N addition disrupted the accumulation of protein-like molecules in the hydrophobic zone and the positive correlation of lignin-like molecules in the kinetic zone with Fh content, compared to unfertilized soils. These data suggest that mineralogy and clay content together influence the chemical composition not only of mineral-associated OM, but also of soluble compounds within the soil matrix. If these relationships are prevalent over larger spatial and temporal scales, they provide a foundation for understanding SOM cycling and persistence under a variety of environmental contexts. Unlabelled Image • Beyond clay content, mineralogy strongly controlled the composition of MAOM. • Ferrihydrite accumulated proteins and lipids in the hydrophobic zone of MAOM. • The mineral core influenced biochemical persistence of OM in the kinetic zone. • Nitrogen fertilization altered carbon chemistry and organo-mineral interactions. [ABSTRACT FROM AUTHOR]

The high-resolution and mass accuracy of Fourier transform mass spectrometry (FT-MS) has made it an increasingly popular technique for discerning the composition of soil, plant and aquatic samples containing complex mixtures of proteins, carbohydrates, lipids, lignins, hydrocarbons, phytochemicals and other compounds. Thus, there is a growing demand for informatics tools to analyze FT-MS data that will aid investigators seeking to understand the availability of carbon compounds to biotic and abiotic oxidation and to compare fundamental chemical properties of complex samples across groups. We present ftmsRanalysis, an R package which provides an extensive collection of data formatting and processing, filtering, visualization, and sample and group comparison functionalities. The package provides a suite of plotting methods and enables expedient, flexible and interactive visualization of complex datasets through functions which link to a powerful and interactive visualization user interface, Trelliscope. Example analysis using FT-MS data from a soil microbiology study demonstrates the core functionality of the package and highlights the capabilities for producing interactive visualizations. Author summary: High-resolution mass spectrometry instruments provide a mechanism for researchers to better understand the fundamental chemical composition of materials such as soil, plants, petroleum, and beverages. The large and complex data generated by analysis of these materials has led to a growing demand for software tools to aid researchers in processing, analyzing, and creating informative visualizations of these data. To move beyond existing software tools designed for specific purposes and visualizations of data from an individual sample, we present a software package, ftmsRanalysis, that provides researchers with a large collection of methods for streamlining the downstream processing high-resolution mass spectrometry data.ftmsRanalysis provides methods to compute useful chemical properties, filter data, define groups of samples, statistically compare sample groups, and make visualizations for many samples simultaneously. In this paper, we give an overview of ftmsRanalysis' general structure and capabilities. We then apply ftmsRanalysis to a soil microbiology dataset and present some of the results and visualizations generated by using the software package. [ABSTRACT FROM AUTHOR]