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At least 973 records · Page 54
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Microbial sensitivity to temperature and sulfate deposition modulates greenhouse gas emissions from peat soils

Abstract Peatlands are among the largest natural sources of atmospheric methane (CH 4 ) worldwide. Microbial processes play a key role in regulating CH 4 emissions from peatland ecosystems, yet the complex interplay between soil substrates and microbial communities in controlling CH 4 emissions as a function of global change remains unclear. Herein, we performed an integrated analysis of multi‐omics data sets to provide a comprehensive understanding of the molecular processes driving changes in greenhouse gas (GHG) emissions in peatland ecosystems with increasing temperature and sulfate deposition in a laboratory incubation study. We sought to first investigate how increasing temperatures (4, 21, and 35°C) impact soil microbiome–metabolome interactions; then explore the competition between methanogens and sulfate‐reducing bacteria (SRBs) with increasing sulfate concentrations at the optimum temperature for methanogenesis. Our results revealed that peat soil organic matter degradation, mediated by biotic and potentially abiotic processes, is the main driver of the increase in CO 2 production with temperature. In contrast, the decrease in CH 4 production at 35°C was linked to the absence of syntrophic communities and the potential inhibitory effect of phenols on methanogens. Elevated temperatures further induced the microbial communities to develop high growth yield and stress tolerator trait‐based strategies leading to a shift in their composition and function. On the other hand, SRBs were able to outcompete methanogens in the presence of non‐limiting sulfate concentrations at 21°C, thereby reducing CH 4 emissions. At higher sulfate concentrations, however, the prevalence of communities capable of producing sufficient low‐molecular‐weight carbon substrates for the coexistence of SRBs and methanogens was translated into elevated CH 4 emissions. The use of omics in this study enhanced our understanding of the structure and interactions among microbes with the abiotic components of the system that can be useful for mitigating GHG emissions from peatland ecosystems in the face of global change.

AminiTabrizi, Roya↗
DOE OSTI2021

Molecular Determination of Organic Adsorption Sites on Smectite during Fe Redox Processes Using ToF-SIMS Analysis

Turnover of soil organic carbon (SOC) is strongly affected by a balance between mineral protection and microbial degradation. However, the mechanisms controlling the heterogeneous and preferential adsorption of different types of SOC remain elusive, especially for humic substrates (HSs) and microbial carbon (MC), two hotly-debated forms of SOC prevalent in soils. In this work, the heterogeneous adsorption of HSs and MC on a clay mineral (nontronite NAu-2) during microbial-mediated Fe redox cycling was determined with the use of time-of-flight secondary ion mass spectrometry (ToF-SIMS). The results revealed that HSs pre-adsorbed on NAu-2 would partially inhibit the microbial Fe(III) reduction and structural modification of NAu-2, thus retarding the subsequent adsorption of MC. In contrast, NAu-2 without pre-coated HSs was adsorbed by a significant amount of MC from microbial polysaccharides as a result of Fe(III) reduction. This was attributed to the deposition of a thin Al-rich layer on clay surface, which provided active sites for MC adsorption. This study provides direct and detailed molecular evidence for the first time to explain the preferential adsorption of MC over HSs on the surface of clay minerals in the iron redox processes, which could be critical for the preservation of MC in soil. The results also indicate that ToF-SIMS is a unique tool for understanding complex organic-mineral-microbe interactions.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1980

Literature review of human microbes' interaction with plants

Human carried microorganisms, which cannot practically be excluded from human supporting agricultural systems of extra terrestrial stations, are considered. These microorganisms damage the plants on which the people depend for oxygen and food. The inclusion of carefully screened or constructed, but more or less normal, phylloplane and rhizosphere microbial communities is studied.

Maguire, B., Jr.↗
DOE OSTI2019

Microfluidics and Metabolomics Reveal Symbiotic Bacterial–Fungal Interactions Between Mortierella elongata and Burkholderia Include Metabolite Exchange

We identified two poplar ( Populus sp.)-associated microbes, the fungus, Mortierella elongata strain AG77, and the bacterium, Burkholderia strain BT03, that mutually promote each other’s growth. Using culture assays in concert with a novel microfluidic device to generate time-lapse videos, we found growth specific media differing in pH and pre-conditioned by microbial growth led to increased fungal and bacterial growth rates. Coupling microfluidics and comparative metabolomics data results indicated that observed microbial growth stimulation involves metabolic exchange during two ordered events. The first is an emission of fungal metabolites, including organic acids used or modified by bacteria. A second signal of unknown nature is produced by bacteria which increases fungal growth rates. We find this symbiosis is initiated in part by metabolic exchange involving fungal organic acids.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Nutrient Inputs Stimulate Mercury Methylation by Syntrophs in a Subarctic Peatland

Climate change dramatically impacts Arctic and subarctic regions, inducing shifts in wetland nutrient regimes as a consequence of thawing permafrost. Altered hydrological regimes may drive changes in the dynamics of microbial mercury (Hg) methylation and bioavailability. Important knowledge gaps remain on the contribution of specific microbial groups to methylmercury (MeHg) production in wetlands of various trophic status. Here, we measured aqueous chemistry, potential methylation rates (k meth ), volatile fatty acid (VFA) dynamics in peat-soil incubations, and genetic potential for Hg methylation across a groundwater-driven nutrient gradient in an interior Alaskan fen. We tested the hypotheses that (1) nutrient inputs will result in increased methylation potentials, and (2) syntrophic interactions contribute to methylation in subarctic wetlands. We observed that concentrations of nutrients, total Hg, and MeHg, abundance of hgcA genes, and rates of methylation in peat incubations (k meth ) were highest near the groundwater input and declined downgradient. hgcA sequences near the input were closely related to those from sulfate-reducing bacteria (SRB), methanogens, and syntrophs. Hg methylation in peat incubations collected near the input source (FPF2) were impacted by the addition of sulfate and some metabolic inhibitors while those down-gradient (FPF5) were not. Sulfate amendment to FPF2 incubations had higher k meth relative to unamended controls despite no effect on k meth from addition of the sulfate reduction inhibitor molybdate. The addition of the methanogenic inhibitor BES (25 mM) led to the accumulation of VFAs, but unlike molybdate, it did not affect Hg methylation rates. Rather, the concurrent additions of BES and molybdate significantly decreased k meth , suggesting a role for interactions between SRB and methanogens in Hg methylation. The reduction in k meth with combined addition of BES and molybdate, and accumulation of VFA in peat incubations containing BES, and a high abundance of syntroph-related hgcAsequences in peat metagenomes provide evidence for MeHg production by microorganisms growing in syntrophy. Collectively the results suggest that wetland nutrient regimes influence the activity of Hg methylating microorganisms and, consequently, Hg methylation rates. Our results provide key information about microbial Hg methylation and methylating communities under nutrient conditions that are expected to become more common as permafrost soils thaw.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Mercury Adsorption on Minerals and Its Effect on Microbial Methylation

Adsorbed or solid-phase inorganic mercury [Hg(II)] is commonly assumed immobile or less bioavailable for microbial uptake, although recent studies suggest that mineral-adsorbed Hg(II) is at least partially available for cell uptake and methylation. This study examined the adsorption of Hg(II) onto two reference minerals, hematite and montmorillonite, and evaluated Hg(II) uptake and methylation by a sulfate-reducing bacterium Desulfovibrio desulfuricans ND132 in laboratory incubations. Mineral-adsorbed Hg(II) on both hematite and montmorillonite was not only available for cell uptake and methylation but also resulted in a 2–3-fold increased methylmercury production compared to the mineral-free incubation. An optimal Hg(II) methylation was observed at a low to moderate mineral/solution ratio (1–5 g L–1) with fixed Hg(II) (25 nM) and cell concentrations. The result could be explained by decreased cellular immobilization of Hg(II) but enhanced close interactions between Hg(II) and cells both adsorbed or concentrated on mineral surfaces, leading to increased methylation. However, a high mineral/solution ratio inhibited Hg(II) methylation, likely as a result of a low Hg(II) coverage (per surface area) at high mineral loadings, which limit close contacts between Hg(II) and the cells. These results indicate that mineral-adsorbed Hg(II) may be directly available for microbial uptake or methylation, although whether the adsorption enhances or inhibits Hg(II) methylation may depend upon microniches, where Hg(II), microbes, and minerals co-exist in the natural environment. We suggest that future studies are performed to establish quantitative relationships of bioavailable Hg(II) with not only the dissolved but also adsorbed Hg(II) species to improve model predictions of Hg(II) fate and transformations.

Zhao, Linduo↗
DOE OSTI2021

Chapter 3: New Developments on Ionic Liquid-Tolerant Microorganisms Leading Toward a More Sustainable Biorefinery

The growing concerns about climate change and energy security are driving the development of bio-based technologies to produce renewable liquid fuels and chemicals. Ionic liquids (ILs) have demonstrated to be promising solvents to pretreat lignocellulosic residues, promoting efficient enzymatic hydrolysis of lignocellulosic carbohydrates into sugars, which can be further used by microorganisms to produce biofuels and other value-added chemicals. Despite their unique properties to effectively deconstruct plant cell walls, ILs show strong interactions with the pretreated biomass, and their presence is often inhibitory to cellulolytic enzymes and microorganisms. The most advanced biorefinery concepts based on IL pretreatments focus on the development of more biocompatible ILs and more robust microbial strains with higher tolerance to ILs. This chapter provides an overview and a discussion over the main efforts performed on the screening and development of IL-tolerant microbial strains, as well as in more biocompatible IL pretreatment methods. These early research advancements in this field offer a baseline and a platform for future research with the goal of improving the sustainability and economic viability of IL pretreatment-based biorefineries.

bioconversion↗
DOE OSTI2019

Synthetic Methane-Consuming Communities from a Natural Lake Sediment

The factors and processes that influence the behavior and functionality of ecosystems inhabited by complex microbiomes are still far from being clearly understood. Synthetic microbial communities provide reduced-complexity models that allow an examination of ecological theories under defined and controlled conditions. In this study, we applied a multiphasic approach to study synthetic methane-oxidizing communities and species interactions as proxies to the natural communities. Our results confirm that, under selective pressures, natural-sediment communities of high complexity simplify rapidly, selecting for several major functional guilds, the major partners in methane oxidation being the Methylococcaceae methanotrophs and the Methylophilaceae methylotrophs, along with minor but persistent partners, members of Burkholderiales and Flavobacteriales. As a proof of concept, we established minimalist synthetic communities that were representative of the four functional guilds to demonstrate the dependency of the non-methane-utilizing species on the methanotrophs as the primary carbon-providing species. We observed that in communities consisting of multiple representatives of the key guilds, members of the same guild appeared to compete for resources. For example, when two methanotrophs of the same family were present, the two expressed similar key methanotrophy pathways and responded similarly to changing environmental conditions, suggesting that they perform a similar keystone function in situ. Similar observations were made for the Methylophilaceae. However, differences were noted in the expression of auxiliary and unique genes among strains of the same functional guild, reflecting differential adaptation and suggesting mechanisms for competition. At the same time, differences were also noted in the performances of partners with specific metabolic schemes. For example, a mutant of Methylotenera mobilis impaired in nitrate utilization behaved as a more efficient cooperator in methane consumption, suggesting that the loss of function may lead to changes in communal behavior. Overall, we demonstrate the robust nature of synthetic communities built of native lake sediment strains and their utility in addressing important ecological questions while using a simplified model.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Plasma-induced inactivation of Staphylococcus aureus biofilms: The role of atomic oxygen and comparison with disinfectants and antibiotics

Microbial biofilms are of critical concern because of their recalcitrance to antimicrobials. Cold atmospheric plasmas (CAP) represent a promising biofilm remediation strategy as they generate reactive oxygen and nitrogen species (RONS), but mechanisms underpinning CAP-biofilm interactions remain unknown. We assess the impact of treatment modality on biofilm inactivation and show that CAP killing of Staphylococcus aureus biofilms is dependent on treatment conditions, including solution chemistry. In dry treatments, biofilms are locally ablated due to plasma-produced O flux. For saline-submerged biofilms, while we show that ClO – is generated at high concentrations in larger treatment volumes, CAP inactivation at low ClO – concentrations implicates other reaction pathways. Finally, we demonstrate CAP efficacy over conventional antimicrobials, underscoring its promise as a biofilm treatment approach.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

In Situ Detection of Amino Acids from Bacterial Biofilms and Plant Root Exudates by Liquid Microjunction Surface-Sampling Probe Mass Spectrometry

The plant rhizosphere is a complex and dynamic chemical environment where the exchange of molecular signals between plants, microbes, and fungi drives the development of the entire biological system. Exogenous compounds in the rhizosphere are known to affect plant-microbe organization, interactions between organisms, and ultimately, growth and survivability. The function of exogenous compounds in the rhizosphere is still under much investigation, specifically with respect to their roles in plant growth and development, the assembly of the associated microbial community, and the spatiotemporal distribution of molecular components. A major challenge for spatiotemporal measurements is developing a nondisruptive and nondestructive technique capable of analyzing the exogenous compounds contained within the environment. A methodology using liquid microjunction-surface sampling probe-mass spectrometry (LMJ-SSP-MS) and microfluidic devices with attached microporous membranes was developed for in situ, spatiotemporal measurement of amino acids (AAs) from bacterial biofilms and plant roots. Exuded arginine was measured from a living Pantoea YR 343 biofilm, which resulted in a chemical image indicative of biofilm growth within the device. Spot sampling along the roots of Populus trichocarpa with the LMJ-SSP-MS resulted in the detection of 15 AAs. Of note, variation in AA concentrations across the root system was observed, indicating that exudation is not homogeneous and may be linked to local rhizosphere architecture and different biological processes along the root.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem

Background: Viruses impact nearly all organisms on Earth, including microbial communities and their associated biogeochemical processes. In soils, highly diverse viral communities have been identified, with a global distribution seemingly driven by multiple biotic and abiotic factors, especially soil temperature and moisture. However, our current understanding of the stability of soil viral communities across time and their response to strong seasonal changes in environmental parameters remains limited. Here, we investigated the diversity and activity of environmental soil DNA and RNA viruses, focusing especially on bacteriophages, across dynamics’ seasonal changes in a snow-dominated mountainous watershed by examining paired metagenomes and metatranscriptomes. Results: We identified a large number of DNA and RNA viruses taxonomically divergent from existing environmental viruses, including a significant proportion of fungal RNA viruses, and a large and unsuspected diversity of positive single-stranded RNA phages ( Leviviricetes ), highlighting the under-characterization of the global soil virosphere. Among these, we were able to distinguish subsets of active DNA and RNA phages that changed across seasons, consistent with a “seed-bank” viral community structure in which new phage activity, for example, replication and host lysis, is sequentially triggered by changes in environmental conditions. At the population level, we further identified virus-host dynamics matching two existing ecological models: “Kill-The-Winner” which proposes that lytic phages are actively infecting abundant bacteria, and “Piggyback-The-Persistent” which argues that when the host is growing slowly, it is more beneficial to remain in a dormant state. The former was associated with summer months of high and rapid microbial activity, and the latter with winter months of limited and slow host growth. Conclusion: Taken together, these results suggest that the high diversity of viruses in soils is likely associated with a broad range of host interaction types each adapted to specific host ecological strategies and environmental conditions. As our understanding of how environmental and host factors drive viral activity in soil ecosystems progresses, integrating these viral impacts in complex natural microbiome models will be key to accurately predict ecosystem biogeochemistry.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Effects of hurricane disturbance and increased temperature on carbon cycling and storage of a Puerto Rican forest: a mechanistic investigation of above- and belowground processes (Final Technical Report)

The overall goal of the Tropical Responses for Altered Climate Experiment (TRACE) is to assess the effects of increasing temperature on tropical plant and soil carbon fluxes and storage as the forest recovers from major hurricane disturbance that occurred in September 2017. Ultimately, we aimed to reduce uncertainty and increase confidence with which tropical forests are represented in Earth System models to make more accurate global forecasts of future climate. We focused on both above- and belowground processes and explored temperature controls over critical aspects of carbon and nutrient cycling for tropical plants, soil, and microbes. TRACE is located in a wet tropical forest in the Luquillo Experimental Forest close to the USDA Forest Service Sabana Field Research Station in Luquillo, Puerto Rico. The warming treatment consists of six 4.7 m diameter plots. Three of the plots receive infrared warming and three have the same infrastructure but are not warmed (using ‘dummy’ heaters). Each plot was monitored from 2018-2023 to investigate two major questions: 1) Are there legacy effects of prior warming on forest recovery following hurricane disturbance? 2) Will the trajectory of forest recovery following disturbance be affected by warmer temperatures? Concurrent soil incubation experiments were conducted to enable more controlled mechanistic investigations of temperature response on microbial function. In sum, our goal was to use this novel climate manipulation experiment (the only of its kind in any tropical forest) and once-in-a-lifetime chance to assess how temperature and hurricane disturbance interact to affect coupled biogeochemical cycling in a tropical forest.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1992

Aquatic biofilms and their responses to disinfection and invading species

The control of microbial contamination is a primary concern in the development of a water reclamation system for long-duration manned space flights. This paper describes bench-scale experiments, using both static and recycling water systems, investigating the interaction of bacterial species in the development of a biofilm and their response to the introduction of a disinfectant or of additional species. The results showed that iodine concentrations as high as 15 to 20 mg/l I2 are necessary to completely disinfect a stable biofilm. When S. aueus and E. coli were introduced into a system containing natural mixed culture biofilms, their colonization in the biofilms increased their survival time, from 3 to 5 days as unattached cells to over 60 days when protected in the biofilms. While iodine concentrations of 0.5 to 1 mg/l were enough to eliminate these organisms from the bulk water, concentrations higher than 4.0 mg/l were necessary to completely eliminate these organisms from the biofilm.

Smithers, G. A.↗
NASA NTRS1985

From microbial communities to cells

The eukraotic cell, the unit of structure of protoctists, plants, fungi, and animals, is not at all homologous to prokaryotic cells. Instead the eukaryotic cell is homologous to communities of microorganisms such as those of the sulfuretum. This research is based on the hypothesis that at least four different interacting community members entered the original associations that, when stabilized, led to the emergence of eukaryotic cells. These are: (1) host nucleocytoplasm (thermoplasma like archaebacteria); (2) mitochrondria (paracoccus or bdellovibryo like respiring bacteria; and (3) plastids (cyanobacteria) and undulipodia. Tubulin like protein was found in the free living spirochete Spirochaeta bajacaliforniensis and in several other spirochetes. The amino acid sequence was to see if the spirochete protein is homologous to the tubulin of undulipodial and mitotic spindle microtubules.

Margulis, L.↗
DOE OSTI2024

Needle bacterial community structure across the species range of limber pine

Abstract Bacteria on and inside leaves can influence forest tree health and resilience. The distribution and limits of a tree species’ range can be influenced by various factors, with biological interactions among the most significant. We investigated the processes shaping the bacterial needle community across the species distribution of limber pine, a widespread Western conifer inhabiting a range of extreme habitats. We tested four hypotheses: (i) Needle community structure varies across sites, with site-specific factors more important to microbial assembly than host species selection; (ii) dispersal limitation structures foliar communities across the range of limber pine; (iii) the relative significance of dispersal and selection differs across sites in the tree species range; and (iv) needle age structures bacterial communities. We characterized needle communities from the needle surface and tissue of limber pine and co-occurring conifers across 16 sites in the limber pine distribution. Our findings confirmed that site characteristics shape the assembly of bacterial communities across the host species range and showed that these patterns are not driven by dispersal limitation. Furthermore, the strength of selection by the host varied by site, possibly due to differences in available microbes. Our study, by focusing on trees in their natural setting, reveals real needle bacterial dynamics in forests, which is key to understanding the balance between stochastic and deterministic processes in shaping forest tree-microbe interactions. Such understanding will be necessary to predict or manipulate these interactions to support forest ecosystem productivity or assist plant migration and adaptation in the face of global change.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Signatures of Mollicutes-related endobacteria in publicly available Mucoromycota genomes

ABSTRACT Mucoromycota fungi and their Mollicutes-related endobacteria (MRE) are an ideal system for studying bacterial–fungal interactions and evolution due to the long-term and intimate nature of their interactions. However, methods for detecting MRE face specific challenges due to the poor representation of MRE in sequencing databases coupled with the high sequence divergence of their genomes, making traditional similarity searches unreliable. This has precluded estimations on the diversity of MRE associated with Mucoromycota. To determine the prevalence of previously undetected MRE in fungal genome sequences, we scanned 389 Mucoromycota genome assemblies available from the National Center for Biotechnology Information for the presence of MRE sequences using publicly available tools to map contigs from fungal assemblies to publicly available MRE genomes. We demonstrate a higher diversity of MRE genomes than previously described in Mucoromycota and a lack of cophylogeny between MRE and the majority of their fungal hosts. This supports the late invasion hypothesis regarding MRE acquisition across most of the examined fungal families. In contrast with other Mucoromycota lineages, MRE from the Gigasporaceae displayed some degree of cophylogeny with their hosts, which may indicate that horizontal transmission is restricted between members of this family or that transmission is strictly vertical. These results underscore the need for a refined process to capture sequencing data from potential fungal endosymbionts to discern their evolution and transmission. Screens of fungal genomes for MRE can help improve the quality of fungal genome assemblies while identifying new MRE lineages to further test hypotheses on their origin and evolution. IMPORTANCE Mollicutes-related endobacteria (MRE) are obligate intracellular bacteria found within Mucoromycota fungi. Despite their frequent detection, MRE roles in host functioning are still unknown. Comparative genomic investigations can improve our understanding of the impact of MRE on their fungal hosts by identifying similarities and differences in MRE genome evolution. However, MRE genomes have only been assembled from a small fraction of Mucoromycota hosts. Here, we demonstrate that MRE can be present yet undetected in publicly available Mucoromycota genome assemblies. We use these newfound sequences to assess the broader diversity of MRE and their phylogenetic relationships with respect to their hosts. We demonstrate that publicly available tools can be used to extract novel MRE sequences from assembled fungal genomes leading to insights on MRE evolution. This work contributes to a greater understanding of the fungal microbiome, which is crucial to improving knowledge on the dynamics and impacts of fungi in microbial ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Clear as mud redefined: Tunable transparent mineral scaffolds for visualizing microbial processes below ground

Microbes inhabiting complex porous microenvironments in sediments and aquifers catalyze reactions that are critical to global biogeochemical cycles and ecosystem health. However, the opacity and complexity of porous sediment and rock matrices have considerably hindered the study of microbial processes occurring within these habitats. Here, we generated microbially compatible, optically transparent mineral scaffolds to visualize and investigate microbial colonization and activities occurring in these environments, in laboratory settings and in situ. Using inexpensive synthetic cryolite mineral, we produced optically transparent scaffolds mimicking the complex 3D structure of sediments and rocks by adapting a suspension-based, freeze-casting technique commonly used in materials science. Fine-tuning of parameters, such as freezing rate and choice of solvent, provided full control of pore size and architecture. The combined effects of scaffold porosity and structure on the movement of microbe-sized particles, tested using velocity tracking of fluorescent beads, showed diverse yet reproducible behaviors. The scaffolds we produced are compatible with epifluorescence microscopy, allowing the fluorescence-based identification of colonizing microbes by DNA-based staining and fluorescence in situ hybridization (FISH) to depths of 100 µm. Additionally, Raman spectroscopy analysis indicates minimal background signal in regions used for measuring deuterium and 13 C enrichment in microorganisms, highlighting the potential to directly couple D 2 O or 13 C stable isotope probing and Raman-FISH for quantifying microbial activity at the single-cell level. To demonstrate the relevance of cryolite scaffolds for environmental field studies, we visualized their colonization by diverse microorganisms within rhizosphere sediments of a coastal seagrass plant using epifluorescence microscopy. The tool presented here enables highly resolved, spatially explicit, and multimodal investigations into the distribution, activities, and interactions of underground microbes typically obscured within opaque geological materials until now.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Cross-Feeding of a Toxic Metabolite in a Synthetic Lignocellulose-Degrading Microbial Community

The recalcitrance of complex organic polymers such as lignocellulose is one of the major obstacles to sustainable energy production from plant biomass, and the generation of toxic intermediates can negatively impact the efficiency of microbial lignocellulose degradation. Here, we describe the development of a model microbial consortium for studying lignocellulose degradation, with the specific goal of mitigating the production of the toxin formaldehyde during the breakdown of methoxylated aromatic compounds. Included are Pseudomonas putida, a lignin degrader; Cellulomonas fimi, a cellulose degrader; and sometimes Yarrowia lipolytica, an oleaginous yeast. Unique to our system is the inclusion of Methylorubrum extorquens, a methylotroph capable of using formaldehyde for growth. We developed a defined minimal “Model Lignocellulose” growth medium for reproducible coculture experiments. We demonstrated that the formaldehyde produced by P. putida growing on vanillic acid can exceed the minimum inhibitory concentration for C. fimi, and, furthermore, that the presence of M. extorquens lowers those concentrations. We also uncovered unexpected ecological dynamics, including resource competition, and interspecies differences in growth requirements and toxin sensitivities. Finally, we introduced the possibility for a mutualistic interaction between C. fimi and M. extorquens through metabolite exchange. This study lays the foundation to enable future work incorporating metabolomic analysis and modeling, genetic engineering, and laboratory evolution, on a model system that is appropriate both for fundamental eco-evolutionary studies and for the optimization of efficiency and yield in microbially-mediated biomass transformation.

Methylorubrum extorquens↗