Ramsey, Buck

Seemann, Charlie

doi:10.1093/gmo/9781561592630.article.a2263029

Cited by 7 publications

(8 citation statements)

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“…Illumina MiSeq paired raw reads were subject to quality filtering using Sickle (Joshi and Fass, 2011) and assembled into contigs with MEGAHIT assembler (Li et al, 2015). PROKKA pipeline was used to find and annotate genes using the default settings (Seemann, 2014). Reads were mapped to contigs with Bowtie2 (Langmead and Salzberg, 2012) and counting was performed with HTSeq (Anders et al, 2015).…”

Section: Metagenome Sequencing and Analysismentioning

confidence: 99%

Microbial community and metagenome dynamics during biodegradation of dispersed oil reveals potential key-players in cold Norwegian seawater

Ribičić

Netzer

Hazen

et al. 2018

Marine Pollution Bulletin

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Oil biodegradation as a weathering process has been extensively investigated over the years, especially after the Deepwater Horizon blowout. In this study, we performed microcosm experiments at 5 °C with chemically dispersed oil in non-amended seawater. We link biodegradation processes with microbial community and metagenome dynamics and explain the succession based on substrate specialization. Reconstructed genomes and 16S rRNA gene analysis revealed that Bermanella and Zhongshania were the main contributors to initial n-alkane breakdown, while subsequent abundances of Colwellia and microorganisms closely related to Porticoccaceae were involved in secondary n‑alkane breakdown and beta‑oxidation. Cycloclasticus, Porticoccaceae and Spongiiabcteraceae were associated with degradation of mono- and poly-cyclic aromatics. Successional pattern of genes coding for hydrocarbon degrading enzymes at metagenome level, and reconstructed genomic content, revealed a high differentiation of bacteria involved in hydrocarbon biodegradation. A cooperation among oil degrading microorganisms is thus needed for the complete substrate transformation.

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Section: Metagenome Sequencing and Analysismentioning

confidence: 99%

Microbial community and metagenome dynamics during biodegradation of dispersed oil reveals potential key-players in cold Norwegian seawater

Ribičić

Netzer

Hazen

et al. 2018

Marine Pollution Bulletin

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“…56 For efficiency, TORMES also uses Parallel. 57 The TORMES pipeline also included ABRicate 58 to screen genomes for matches to VFDB 26 entries using ABRicate. The genus/species name based on Kraken 2.0.9beta prediction using the MiniKra-ken2_v1 database was used as the isolate name.…”

Section: ■ Methodsmentioning

confidence: 99%

From Natural Microbe Screening to Sustained Chitinase Activity in Exogenous Hosts

Chaulagain,

Shamabadi,

Leslie

et al. 2024

ACS Synth. Biol.

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Genetic parts and hosts can be sourced from nature to realize new functions for synthetic biology or to improve performance in a particular application environment. Here, we proceed from the discovery and characterization of new parts to stable expression in new hosts with a particular focus on achieving sustained chitinase activity. Chitinase is a key enzyme for various industrial applications that require the breakdown of chitin, the second most abundant biopolymer on the earth. Diverse microbes exhibit chitinase activity, but for applications, the environmental conditions for optimal enzyme activity and microbe fitness must align with the application context. Achieving sustained chitinase activity under broad conditions in heterologous hosts has also proven difficult due to toxic side effects. Toward addressing these challenges, we first screen ocean water samples to identify microbes with chitinase activity. Next, we perform whole genome sequencing and analysis and select a chitinase gene for heterologous expression. Then, we optimize transformation methods for target hosts and introduce chitinase. Finally, to achieve robust function, we optimize ribosome binding sites and discover a beneficial promoter that upregulates chitinase expression in the presence of colloidal chitin in a sense-and-respond fashion. We demonstrate chitinase activity for >21 days in standard (Escherichia coli) and nonstandard (Roseobacter denitrificans) hosts. Besides enhancing chitinase applications, our pipeline is extendable to other functions, identifies natural microbes that can be used directly in non-GMO contexts, generates new parts for synthetic biology, and achieves weeks of stable activity in heterologous hosts.

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“…Taxonomic classification of contigs was assigned by BLASTn 67 according to the taxonomy of the single-copy marker genes in contigs. SSU rRNA sequences in contigs were identified using Barrnap 68 and classified using VSEARCH 69 . The mapping, re-assembly, and rebinning process was repeated 5-7 times until the quality of the genomes could not be improved further.…”

Section: Genome Binning and Refinementmentioning

confidence: 99%

“…Genome annotation was conducted using Prokka v1.13 72 , eggNOG 73 , and BlastKoala 74 using the KEGG database. The functional assignments of genes of interest were also confirmed using BLASTp 68 against the NCBI RefSeq database. The metabolic pathways were reconstructed using KEGG Mapper 75 .…”

Section: Genome Annotationmentioning

confidence: 99%

A new abundant nitrite-oxidizing phylum in oligotrophic marine sediments

Zhao,

Jørgensen,

Babbin

2023

Preprint

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Nitrite-oxidizing bacteria (NOB) are important nitrifiers whose activity regulates the availability of nitrite and links reduced ammonium and oxidized nitrate in ecosystems. In oxic marine sediments, ammonia-oxidizing archaea (AOA) and NOB together catalyze the oxidation of ammonium to nitrate, but the observed abundance ratios of AOA to canonical NOB are significantly higher than the theoretical ratio predicted from microbial physiology, indicating that many novel NOBs are yet to be discovered. Here we report a new bacterial phylum Candidatus Nitrosediminicolota, members of which are more abundant than canonical NOBs and are widespread across global oligotrophic sediments. Ca. Nitrosediminicolota members have the functional potential to oxidize nitrite, in addition to other accessory functions such as urea hydrolysis and thiosulfate reduction. While one recovered species (Ca. Nitrosediminicola aerophilis) is generally confined within the oxic zone, another (Ca. Nitrosediminicola anaerotolerans) can additionally thrive in anoxic sediments. Counting Ca. Nitrosediminicolota as a nitrite-oxidizer resolves the apparent abundance imbalance between AOA and NOB in oxic marine sediments, and thus its activity may exert a critical control on the nitrite budget.

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Ramsey, Buck

Cited by 7 publications

References 0 publications

Microbial community and metagenome dynamics during biodegradation of dispersed oil reveals potential key-players in cold Norwegian seawater

Microbial community and metagenome dynamics during biodegradation of dispersed oil reveals potential key-players in cold Norwegian seawater

From Natural Microbe Screening to Sustained Chitinase Activity in Exogenous Hosts

A new abundant nitrite-oxidizing phylum in oligotrophic marine sediments

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