Xanthobacter-dominated biofilm as a novel source for high-value rhamnose

RedCorn, Raymond; Hillman, Ethan T.; Solomon, Kevin

doi:10.1007/s00253-019-09765-4

Cited by 7 publications

(5 citation statements)

References 76 publications

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“…As in previous microcosm studies, 68 the microbial community was then assessed by amplifying and sequencing the V4‐V5 region of the 16 S rRNA gene from the extracted DNA (primers: 515f—forward, 5′ GTGYCAGCMGCCGCGGTAA 3′; and 926r—reverse 5′ CCGYCAATTYMTTTRAGTTT 3′) 69 . 16 S rRNA gene PCRs were set up using Phusion Polymerase MasterMix (Thermo Fisher Scientific, Waltham, MA, USA) as follows PCR‐grade water (22 μl), Phusion mastermix (25 μl), forward primer (10 μM, 1.0 μl), reverse primer (10 μM, 1.0 μl), and template DNA (1.0 μl) in a total reaction volume of 50 μl; for samples that had very low template concentration up to 5 μl of DNA template was used and the water volume reduced to 17 μl.…”

Section: Methodsmentioning

confidence: 59%

“…As in previous microcosm studies, 68 the microbial community was then assessed by amplifying and sequencing the V4-V5 region of the 16 S rRNA gene from the extracted DNA (primers: 515f-forward, 5 0 GTGYCAGCMGCCGCGGTAA 3 0 ; and 926r-reverse 5 0 CCGYCAATTYMTTTRAGTTT 3 0 ). 69 Illumina MiSeq at the Purdue Genomics facilities.…”

Section: Dna Extraction Pcr Sequencing and Analysismentioning

confidence: 99%

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Top‐down enrichment of oil field microbiomes to limit souring and control oil composition during extraction operations

et al. 2022

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Microbial processes sour oil, corrode equipment, and degrade hydrocarbons at an annual global cost to the oil and gas industry of nearly $2 billion. However, top-down control of these microbial processes can reduce their damage and enhance oil recovery. Here, we screened microbial communities from five oil wells in the Illinois basin and evaluated nutrient injection strategies to control metabolism and community composition. Molasses with molybdate supplementation stimulated gas and organic acid production while suppressing corrosive H 2 S formation in samples from two wells. These changes were accompanied with significant reshaping of the microbiome community. Simulations of field operations via a lab-scale mini-coreflood validated that oil well microbiomes can be engineered to inhibit deleterious H 2 S and shape oil hydrocarbon composition in situ. These pilot studies validate the economic potential and sustainability of top-down approaches for microbiome engineering to control microbes in oil extraction and enhance the economic viability of oil recovery.comprehensive 2D-gas chromatography, cultivation screening, microbial enhanced oil recovery, microbiome engineering, miniature coreflood, top-down design | BACKGROUNDFossil fuels are likely to remain a significant energy source for at least the next 30 years 1 as economies transition globally toward more renewable energy sources. 2 Extracting trapped oil from aging wells can not only increase the overall production of existing wells but also minimize the need to drill new wells and, ultimately, decrease the cost of extracting oil from existing reservoirs. 3 Expensive polymer and/or surfactant/polymer formulations that require large amounts of funding and research effort are used to extract oil not recovered by primary extraction techniques. 4 Additionally, native and exogenous microbes have been harnessed as a more cost-effective 5 alternative for secondary and tertiary oil recovery-an approach coined microbial enhanced oil recovery (MEOR). 6 However, microbial activity in oil wells, can also be disruptive to oil recovery and/or alter its composition. 6 For example, microbes can degrade and sour oil, and produce metabolites that corrode the well casing, flowlines, and pipelines. 7

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Section: Methodsmentioning

confidence: 59%

Section: Dna Extraction Pcr Sequencing and Analysismentioning

confidence: 99%

Top‐down enrichment of oil field microbiomes to limit souring and control oil composition during extraction operations

et al. 2022

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“…Therefore, it is potentially a source of biologically active compounds, such as polymers endowed with better biological and functional properties than those already known. Depending on their nature, chemical composition, and structure, the biotechnological potential of the biofilm polymer can be considered in a wide range of uses, such as cryoprotectants, emulsifiers, heavy metal chelators, bioactives for human health and well-being, and as a source of high-value sugar monomers or enzymes [18][19][20]82].…”

Section: Discussionmentioning

confidence: 99%

“…For example, cellulose production has been described at the air-liquid interface of static liquid cultures of bacteria [6,17]. Biotechnological applications of carbohydrate polymers are strongly influenced by their structural features and they have been investigated in various fields, including human health and the production of valuable metabolites [18][19][20][21].Proteins in biofilms are the structural components of multimeric cellular appendages, such as flagella, pili, or fimbriae. They are involved in cell motility and in both the initial phase of biofilm formation and in its development [17].…”

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confidence: 99%

Characterization of Biofilm Extracts from Two Marine Bacteria

et al. 2019

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In the marine environment, biofilm formation is an important lifestyle for microorganisms. A biofilm is comprised of cells embedded in an extracellular matrix that holds them close together and keeps the biofilm attached to the colonized surface. This predominant lifestyle and its main regulation pathway, namely quorum-sensing (QS), have been shown to induce specific bioactive metabolites. In this study, we investigated the biofilm formation by two marine bacteria belonging to the Vibrio species to discover potentially innovative bioactive compounds. We proposed a protocol to isolate biofilm extracts, to analyze their biochemical composition, and to compare them to planktonic cell extracts. Cells were grown attached to a plastic surface; extracts were prepared in water, NaOH, or in ethyl acetate and analyzed. Extracellular matrix components featured carbohydrates, proteins, lipids, and low amount of DNA. Carbohydrates appeared to be the main constituent of biofilm but also of the planktonic cell supernatant. Moreover, antimicrobial and QS-signaling activities were evidenced in extracts.

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“…The improved bacterial fitness in biofilms contributes to issues in engineered or medical systems such as biofouling [104], biocorrosion [105], and clinical complications [106]. Nonetheless, biofilms are found useful for wastewater treatment [107][108][109], and production of economically valuable biomaterials [110,111].…”

Section: Eps In Biofilms For Bioadsorptionmentioning

confidence: 99%

Engineering biofilm matrix for efficient biofilm-mediated contaminant removal

Zaiden¹

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This graduate study has been a good character-building lesson. Never have I learn so much about my untapped capabilities. I am blessed to have worked with many brilliant minds throughout my research career. A huge appreciation to the many supervisors, and colleagues I have worked with since I was 20. All the good and bad events are the lifetime pointers that have pushed me to be better than yesterday. Thank you to my family and friends who provide me a listening ear when in times of need. Most especially to Myra Dew Baidah Ahmad, who instills grit each time I doubt myself. Lastly, I would like to acknowledge the graduate studies assistance, training opportunities, facilities and funding provided by SCELSE, Interdisciplinary Graduate Programme (IGP), National Research Foundation, and the Ministry of Education (MOE). vTable of Contents Statement of Originality……………………………………………………………………...i Supervisor Declaration Statement………………………………………………………….ii Acknowledgements .

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Xanthobacter-dominated biofilm as a novel source for high-value rhamnose

Cited by 7 publications

References 76 publications

Top‐down enrichment of oil field microbiomes to limit souring and control oil composition during extraction operations

Top‐down enrichment of oil field microbiomes to limit souring and control oil composition during extraction operations

Characterization of Biofilm Extracts from Two Marine Bacteria

Engineering biofilm matrix for efficient biofilm-mediated contaminant removal

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