Complete genome of the switchgrass endophyte Enterobacter clocace P101

Humann, Jodi L.; Wildung, Mark R.; Pouchnik, Derek; Bates, Austin A.; Drew, Jennifer C.; Zipperer, Ursula N.; Triplett, Eric W.; Main, Dorrie; Schroeder, Brenda K.

doi:10.4056/sigs.4808608

Cited by 9 publications

(3 citation statements)

References 34 publications

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“…6 ). Enterobacter are endophytes, which have been associated with numerous plant species, including switchgrass [ 45 ]. These taxa have also been shown to metabolize cellulose and components of hemicellulose, such as xylose [ 46 – 48 ].…”

Section: Resultsmentioning

confidence: 99%

Utilization of lignocellulosic biofuel conversion residue by diverse microorganisms

Wadler

Wolters

Fortney

et al. 2022

Biotechnol Biofuels

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Background Lignocellulosic conversion residue (LCR) is the material remaining after deconstructed lignocellulosic biomass is subjected to microbial fermentation and treated to remove the biofuel. Technoeconomic analyses of biofuel refineries have shown that further microbial processing of this LCR into other bioproducts may help offset the costs of biofuel generation. Identifying organisms able to metabolize LCR is an important first step for harnessing the full chemical and economic potential of this material. In this study, we investigated the aerobic LCR utilization capabilities of 71 Streptomyces and 163 yeast species that could be engineered to produce valuable bioproducts. The LCR utilization by these individual microbes was compared to that of an aerobic mixed microbial consortium derived from a wastewater treatment plant as representative of a consortium with the highest potential for degrading the LCR components and a source of genetic material for future engineering efforts. Results We analyzed several batches of a model LCR by chemical oxygen demand (COD) and chromatography-based assays and determined that the major components of LCR were oligomeric and monomeric sugars and other organic compounds. Many of the Streptomyces and yeast species tested were able to grow in LCR, with some individual microbes capable of utilizing over 40% of the soluble COD. For comparison, the maximum total soluble COD utilized by the mixed microbial consortium was about 70%. This represents an upper limit on how much of the LCR could be valorized by engineered Streptomyces or yeasts into bioproducts. To investigate the utilization of specific components in LCR and have a defined media for future experiments, we developed a synthetic conversion residue (SynCR) to mimic our model LCR and used it to show lignocellulose-derived inhibitors (LDIs) had little effect on the ability of the Streptomyces species to metabolize SynCR. Conclusions We found that LCR is rich in carbon sources for microbial utilization and has vitamins, minerals, amino acids and other trace metabolites necessary to support growth. Testing diverse collections of Streptomyces and yeast species confirmed that these microorganisms were capable of growth on LCR and revealed a phylogenetic correlation between those able to best utilize LCR. Identification and quantification of the components of LCR enabled us to develop a synthetic LCR (SynCR) that will be a useful tool for examining how individual components of LCR contribute to microbial growth and as a substrate for future engineering efforts to use these microorganisms to generate valuable bioproducts.

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Section: Resultsmentioning

confidence: 99%

Utilization of lignocellulosic biofuel conversion residue by diverse microorganisms

Wadler

Wolters

Fortney

et al. 2022

Biotechnol Biofuels

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“…E . cloacae has been identified in the endosphere of pines, corn, switchgrass, cacao, spinach, and pepper and produces indole‐3‐acetic‐acid (IAA), solubilizes phosphate, and displays antagonistic activity against Fusarium moniliforme and Fusarium oxysporum (Hinton & Bacon, ; Humann et al, ; Leite et al, ; Madmony, Chernin, Pleban, Peleg, & Riov, ; Santoyo, Moreno‐Hagelsieb, Orozco‐Mosqueda, & Glick, ; Tsuda, Kosaka, Tsuge, Kubo, & Horino, ).…”

Section: Discussionmentioning

confidence: 99%

Smells from the desert: Microbial volatiles that affect plant growth and development of native and non‐native plant species

Camarena‐Pozos¹,

Flores‐Núñez²,

López³

et al. 2018

Plant Cell & Environment

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The plant microbiota can affect host fitness via the emission of microbial volatile organic compounds (mVOCs) that influence growth and development. However, evidence of these molecules and their effects in plants from arid ecosystems is limited. We screened the mVOCs produced by 40 core and representative members of the microbiome of agaves and cacti in their interaction with Arabidopsis thaliana and Nicotiana benthamiana. We used SPME‐GC‐MS to characterize the chemical diversity of mVOCs and tested the effects of selected compounds on growth and development of model and host plants. Our study revealed that approximately 90% of the bacterial strains promoted plant growth both in A. thaliana and N. benthamiana. Bacterial VOCs were mainly composed of esters, alcohols, and S‐containing compounds with 25% of them not previously characterized. Remarkably, ethyl isovalerate, isoamyl acetate, 3‐methyl‐1‐butanol, benzyl alcohol, 2‐phenylethyl alcohol, and 3‐(methylthio)‐1‐propanol, and some of their mixtures, displayed beneficial effects in A. thaliana and also improved growth and development of Agave tequilana and Agave salmiana in just 60 days. Volatiles produced by bacteria isolated from agaves and cacti are promising molecules for the sustainable production of crops in arid and semi‐arid regions.

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“…Enterobacter asburiae is a Gram-negative, facultative anaerobic, oxidase-negative, non-motile, and non-pigmented rod-shaped species belonging to the genus Enterobacter, which includes species that are difficult to identify with biochemical and phylogenetic tests [1][2][3]. The Enterobacter cloacae complex (ECC) is a group of common opportunistic pathogens consisting of Enterobacter asburiae, Enterobacter cloacae, Enterobacter hormaechei, Enterobacter kobei, Enterobacter ludwigii, Enterobacter mori, and Enterobacter nimipressuralis.…”

Section: Introductionmentioning

confidence: 99%

Isolation and draft genome sequence of Enterobacter asburiae strain i6 amenable to genetic manipulation

Kato

2024

J. Genomics

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Enterobacter asburiae is a species of Gram-negative bacteria that is found in soil, water, and sewage. E. asburiae is generally considered to be an opportunistic pathogen, but has also been reported as a plant growth-promoting bacterium (PGPB), which may have beneficial effects on plant growth and development. However, genetic analysis of E. asburiae has been limited, possibly due to its redundant enzymes that digest exogenous DNA in the cell. Here, an E. asburiae strain i6 was isolated from soil in Nara, Japan. This strain was amenable to transformation and the one-step gene inactivation method based on λ Red recombinase. The transformation efficiency of the i6 strain with the 10 kb plasmid DNA pCF430 was at least four orders of magnitude higher than that of the previously sequenced E. asburiae strain ATCC 35953, which could not be transformed with the same plasmid DNA. A draft genome sequence of the i6 strain was determined and deposited into the database, allowing several factors that may determine transformation efficiency to be perturbed and tested. Together with the amenability of the i6 strain to genetic manipulation, the information from the i6 genome will facilitate characterization and fine-tuning of the beneficial and detrimental traits of this species.

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Complete genome of the switchgrass endophyte Enterobacter clocace P101

Cited by 9 publications

References 34 publications

Utilization of lignocellulosic biofuel conversion residue by diverse microorganisms

Utilization of lignocellulosic biofuel conversion residue by diverse microorganisms

Smells from the desert: Microbial volatiles that affect plant growth and development of native and non‐native plant species

Isolation and draft genome sequence of Enterobacter asburiae strain i6 amenable to genetic manipulation

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