Construction of Viable Soil Defined Media Using Quantitative Metabolomics Analysis of Soil Metabolites

Jenkins, Stefan; Swenson, Tami L.; Lau, Rebecca; Rocha, Andrea M.; Aaring, Alex; Hazen, Terry C.; Chakraborty, Romy; Northen, Trent

doi:10.3389/fmicb.2017.02618

Cited by 40 publications

(38 citation statements)

References 41 publications

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“…Likewise, similar to studies of root-associated metabolites [27][28][29], we too observed hydroxycinnamic acid derivatives, flavonoids, triterpenoids and other organic acids. Annotatable metabolites detected in our study differed significantly from annotatable metabolites described in prior untargeted analyses of agricultural soils [13,14], likely due to differences in metabolite extraction and instrumental protocols. Overlapping metabolites between the study of agricultural soil by Jenkins et al [13] and this study include valine and adenosine.…”

Section: Discussioncontrasting

confidence: 59%

“…For example, Ladd et al developed an untargeted LC-MS/MS method to analyze polar metabolites from an Arctic soil core [12]. Swenson et al implemented hydrophilic interaction liquid chromatography (HILIC)-MS, across 20 arid biocrust samples from a USA national park, relating metabolite profile following a wetting event to microbial growth [2], while Jenkins et al studied the metabolite profile of a single soil sample collected from the Oak Ridge Field Research Center by HILIC chromatography [13]. In contrast, Hewavitharana et al used reversed-phase liquid chromatography to assess the impact of a plant pathogen disinfestation method on an orchard metabolome [14].…”

Section: Introductionmentioning

confidence: 99%

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Local Phenomena Shape Backyard Soil Metabolite Composition

et al. 2020

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Soil covers most of Earth’s continental surface and is fundamental to life-sustaining processes such as agriculture. Given its rich biodiversity, soil is also a major source for natural product drug discovery from soil microorganisms. However, the study of the soil small molecule profile has been challenging due to the complexity and heterogeneity of this matrix. In this study, we implemented high-resolution liquid chromatography–tandem mass spectrometry and large-scale data analysis tools such as molecular networking to characterize the relative contributions of city, state and regional processes on backyard soil metabolite composition, in 188 soil samples collected from 14 USA States, representing five USA climate regions. We observed that region, state and city of collection all influence the overall soil metabolite profile. However, many metabolites were only detected in unique sites, indicating that uniquely local phenomena also influence the backyard soil environment, with both human-derived and naturally-produced (plant-derived, microbially-derived) metabolites identified. Overall, these findings are helping to define the processes that shape the backyard soil metabolite composition, while also highlighting the need for expanded metabolomic studies of this complex environment.

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Section: Discussioncontrasting

confidence: 59%

Section: Introductionmentioning

confidence: 99%

Local Phenomena Shape Backyard Soil Metabolite Composition

et al. 2020

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“…Here, R2A media was chosen as a generalist culture media. This media has been used to recover more than 300 phylogenetically diverse isolates from P. trichocarpa rhizosphere and endosphere samples, and so should permit co-culture of a large number of combinatorial strain mixtures within the microwell environment (40,41). While the YR343-GFP monoculture generated growth profiles across the array with relatively low variance (s 2 =3.55) according to final end-point fluorescence levels, mixed cultures generated a wider range of growth profiles, with final growth levels of higher variance (s 2 =17.55), indicating an impact due to the addition of the environmental isolates ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Simultaneous Discovery of Positive and Negative Interactions Among Root Microbiome Bacteria Using Microwell Recovery Arrays

Barua

Herken

Stern

et al. 2020

Preprint

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Understanding the consequences of microbe-microbe interactions is critical in efforts to predict the function of microbiomes and to manipulate or construct communities to achieve desired outcomes. The investigation of these interactions poses a significant challenge -in part due to the lack of suitable experimental tools. We present the Microwell Recovery Array, a high throughput approach designed to rapidly screen interactions across a microbiome and uncover higher-order combinations of strains that either inhibit or promote the function of a GFP-producing focal species. One experiment generates 10 4 unique microbial communities that contain a focal species combined with a unique combination of previously uncharacterized cells from plant rhizosphere. Cells are then sequentially extracted from individual co-culture wells that display highest or lowest levels of focal species function using a novel high-resolution photopolymer extraction system. Microbes present are subsequently identified and the putative interactions are validated. Using this approach, we screen the Populus trichocarpa rhizosphere for bacterial strains affecting the survival and growth of Pantoea sp. YR343, a plant growth promoting strain isolated from the P. trichocarpa rhizosphere. We were able to simultaneously isolate and validate multiple Stenotrophomonas strains that antagonize strain YR343 growth and a set of Enterobacter strains that promote strain YR343 growth. The latter demonstrates the unique ability of the platform to uncover multimembered consortia that generate emergent phenotypes. This knowledge will inform the development of beneficial consortia that promote the production of Populus biofuel feedstock, while the platform is adaptable to screening higher-order interactions in any microbiome of interest. Significance StatementAchieving a fundamental understanding of microbe-microbe interactions that occur within microbial communities is a grand challenge in microbiology due to the limited experimental tools available. In this report, we describe a new tool that enables one to screen microbial interactions across thousands of compositionally unique communities to discover collections of bacteria that antagonize or promote the survival and growth of bacteria with important functions. This approach has the unique ability to uncover higher-order combinations of bacteria that generate emergent

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“…The various substrates were sterilized, and incubated at 24°C for 8 hours with a 20 µm equimolar defined medium, encompassing a variety of chemical classes, among them amino acids, sugars, organic acids, and nucleotides (Jenkins et al, 2017). The sterility of the system was confirmed by plating an aliquot on LB plates, followed by a 3-day incubation.…”

Section: Methodsmentioning

confidence: 99%

“…A selection of different substrates (3 mm glass beads, 4 mm sand, 4 mm clay) was incubated with 50 times concentrated defined medium (50x DM, see: “Sorption test with defined medium” section, (Jenkins et al, 2017)) or with 0x DM (DM without carbon sources, but with vitamins and minerals) for 6 h at 23°C. The substrates were subsequently washed three times with water, to remove soluble metabolites.…”

Section: Methodsmentioning

confidence: 99%

Root morphology and exudate availability is shaped by particle size and chemistry in Brachypodium distachyon

Sasse

Jordan

Raad

et al. 2019

Preprint

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Keywords Brachypodium distachyonParticle chemistry Particle size Pseudomonas fluorescens Rhizosphere Root exudation Root morphology Abstract Root morphology and exudation define a plants sphere of influence in soils, and are in turn shaped by the physiochemical characteristics of soil. We explored how particle size and chemistry of growth substrates affect root morphology and exudation of the model grass Brachypodium distachyon. Root fresh weight and root lengths were correlated with particle size, whereas root number and shoot weight remained constant. Mass spectrometry imaging suggested that both, root length and number shape root exudation. Exudate metabolite profiles detected with liquid chromatography / mass spectrometry were comparable for plants growing in glass beads or sand with various particles sizes, but distinct for plants growing in clay. However, when exudates of clay-grown plants were collected by removing the plants from the substrate, their exudate profile was similar to sand-or glass beads-grown plants. Clay particles sorbed 20% of compounds exuded by clay-grown plants, and 70% of compounds of a defined exudate medium. The sorbed compounds belonged to a range of chemical classes, among them nucleosides/nucleotides, organic acids, sugars, and amino acids. Some of the sorbed compounds could be de-sorbed by a rhizobacterium (Pseudomonas fluorescens WCS415), supporting its growth. We show that root morphology is affected by substrate size, and that root exudation in contrast is not affected by substrate size or chemistry. The availability of exuded compounds, however, depends on the substrate present. These findings further support the critical importance of the physiochemical properties of soils are crucial to consider when investigating plant morphology, exudation, and plantmicrobe interactions. Plant roots shape their environment in various ways, and are in turn shaped by physiochemical properties of the surrounding soil. Roots shape soil by dislocating particles, by polymer production, and by release of a wide variety of compounds (root exudation). Root exudates alter pH and the chemical composition around roots. Overall, root presence in soils results in formation of larger soil aggregates and increases water-holding capacity (Six et al., 2004). The plant-induced changes in chemistry can lead to weathering of minerals (Uroz et al., 2015), and alter the composition of microbial communities (Carson et al., 2007).Soils are often characterized by their particle size and mineralogy. Typical soil particles range from small (< 50 µm) to large (> 2 mm), determining physical parameters such as water binding capacity (Six et al., 2004; Six and Paustian, 2014; Rellán-Álvarez et al., 2016). Differently sized sandstones are associated with different microbial numbers, with small sandstones (2 mm) being more densely populated by microbes than larger rocks (Certini et al., 2004). Minerals differ in their structure (e.g. accessible surface), and in their surface charge, determining if and how they interact wi...

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Construction of Viable Soil Defined Media Using Quantitative Metabolomics Analysis of Soil Metabolites

Cited by 40 publications

References 41 publications

Local Phenomena Shape Backyard Soil Metabolite Composition

Local Phenomena Shape Backyard Soil Metabolite Composition

Simultaneous Discovery of Positive and Negative Interactions Among Root Microbiome Bacteria Using Microwell Recovery Arrays

Root morphology and exudate availability is shaped by particle size and chemistry in Brachypodium distachyon

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