Methylated cycloalkanes fuel a novel genus in the Porticoccaceae family (Ca. Reddybacter gen. nov).

Cycloalkanes are abundant and toxic compounds in subsurface petroleum reservoirs and their fate is important to ecosystems impacted by natural oil seeps and spills. This study focuses on the microbial metabolism of methylcyclohexane (MCH) and methylcyclopentane (MCP) in the deep Gulf of Mexico. MCH and MCP are often abundant cycloalkanes observed in petroleum and will dissolve into the water column when introduced at the seafloor via a spill or natural seep. We conducted incubations with deep Gulf of Mexico (GOM) seawater amended with MCH and MCP at four stations. Within incubations with active respiration of MCH and MCP, we found that a novel genus of bacteria belonging to the Porticoccaceae family (Candidatus Reddybacter) dominated the microbial community. Using metagenome-assembled genomes, we reconstructed the central metabolism of Candidatus Reddybacter, identifying a novel clade of the particulate hydrocarbon monooxygenase (pmo) that may play a central role in MCH and MCP metabolism. Through comparative analysis of 174 genomes, we parsed the taxonomy of the Porticoccaceae family and found evidence suggesting the acquisition of pmo and other genes related to the degradation of cyclic and branched hydrophobic compounds were likely key events in the ecology and evolution of this group of organisms.

[1]  R. Prince,et al.  Deepwater Horizon 2010: Subsea dispersants protected responders from VOC exposure. , 2021, Marine pollution bulletin.

[2]  So-Jeong Kim,et al.  Verrucomicrobial methanotrophs grow on diverse C3 compounds and use a homolog of particulate methane monooxygenase to oxidize acetone , 2021, The ISME Journal.

[3]  D. Valentine,et al.  Microbial production and consumption of hydrocarbons in the global ocean , 2021, Nature Microbiology.

[4]  Karthik Anantharaman,et al.  Gammaproteobacteria mediating utilization of methyl-, sulfur- and petroleum organic compounds in deep ocean hydrothermal plumes , 2020, The ISME Journal.

[5]  Donovan H. Parks,et al.  A complete domain-to-species taxonomy for Bacteria and Archaea , 2020, Nature Biotechnology.

[6]  A. Arkin,et al.  Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity , 2020, Microbiome.

[7]  R. Malmstrom,et al.  Novel copper-containing membrane monooxygenases (CuMMOs) encoded by alkane-utilizing Betaproteobacteria , 2019, The ISME Journal.

[8]  Donovan H Parks,et al.  GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database , 2019, Bioinform..

[9]  Hiroyuki Ogata,et al.  KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold , 2019, bioRxiv.

[10]  A. von Haeseler,et al.  Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes , 2018, Nature Communications.

[11]  Pelin Yilmaz,et al.  25 years of serving the community with ribosomal RNA gene reference databases and tools. , 2017, Journal of biotechnology.

[12]  S. Socolofsky,et al.  Petroleum dynamics in the sea and influence of subsea dispersant injection during Deepwater Horizon , 2017, Proceedings of the National Academy of Sciences.

[13]  P. Pevzner,et al.  metaSPAdes: a new versatile metagenomic assembler. , 2017, Genome research.

[14]  D. Valentine,et al.  Persistence and biodegradation of oil at the ocean floor following Deepwater Horizon , 2016, Proceedings of the National Academy of Sciences.

[15]  S. Salzberg,et al.  Centrifuge: rapid and sensitive classification of metagenomic sequences , 2016, bioRxiv.

[16]  J. Fuhrman,et al.  Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. , 2016, Environmental microbiology.

[17]  Paul J. McMurdie,et al.  DADA2: High resolution sample inference from Illumina amplicon data , 2016, Nature Methods.

[18]  Ann Hayward Walker,et al.  Consensus Ecological Risk Assessment of Potential Transportation-related Bakken and Dilbit Crude Oil Spills in the Delaware Bay Watershed, USA , 2016 .

[19]  P. Furlan,et al.  Estimating diluted bitumen entrained by suspended sediments in river rapids using O2 absorption rate , 2016, International Journal of Environmental Science and Technology.

[20]  A. Solow,et al.  Natural and unnatural oil slicks in the Gulf of Mexico , 2015, Journal of geophysical research. Oceans.

[21]  Tom O. Delmont,et al.  Anvi’o: an advanced analysis and visualization platform for ‘omics data , 2015, PeerJ.

[22]  Connor T. Skennerton,et al.  CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes , 2015, Genome research.

[23]  R. Parsons,et al.  Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton , 2015 .

[24]  Yi Huang,et al.  Bacterial Community Features Are Shaped by Geographic Location, Physicochemical Properties, and Oil Contamination of Soil in Main Oil Fields of China , 2015, Microbial Ecology.

[25]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[26]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[27]  G. Andersen,et al.  Succession of hydrocarbon-degrading bacteria in the aftermath of the deepwater horizon oil spill in the gulf of Mexico. , 2013, Environmental science & technology.

[28]  Mary Ann Moran,et al.  Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill , 2013, The ISME Journal.

[29]  Sarah L. Westcott,et al.  Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform , 2013, Applied and Environmental Microbiology.

[30]  W. Ussler,et al.  Abundance and distribution of diverse membrane-bound monooxygenase (Cu-MMO) genes within the Costa Rica oxygen minimum zone. , 2013, Environmental microbiology reports.

[31]  Z. Shao,et al.  Enzymes and genes involved in aerobic alkane degradation , 2013, Front. Microbiol..

[32]  Alexey A. Gurevich,et al.  QUAST: quality assessment tool for genome assemblies , 2013, Bioinform..

[33]  Christoph Aeppli,et al.  Oil weathering after the Deepwater Horizon disaster led to the formation of oxygenated residues. , 2012, Environmental science & technology.

[34]  S. Tringe,et al.  Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill , 2012, The ISME Journal.

[35]  Lisa M McKenzie,et al.  Human health risk assessment of air emissions from development of unconventional natural gas resources. , 2012, The Science of the total environment.

[36]  Z. Shao,et al.  Genes involved in alkane degradation in the Alcanivorax hongdengensis strain A-11-3 , 2012, Applied Microbiology and Biotechnology.

[37]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[38]  H. Fuse,et al.  Isolation of Two Novel Marine Ethylene-Assimilating Bacteria, Haliea Species ETY-M and ETY-NAG, Containing Particulate Methane Monooxygenase-like Genes , 2012, Microbes and environments.

[39]  Senka Maćešić,et al.  Dynamic autoinoculation and the microbial ecology of a deep water hydrocarbon irruption , 2012, Proceedings of the National Academy of Sciences.

[40]  Sean R. Eddy,et al.  Accelerated Profile HMM Searches , 2011, PLoS Comput. Biol..

[41]  Karin L. Lemkau,et al.  Composition and fate of gas and oil released to the water column during the Deepwater Horizon oil spill , 2011, Proceedings of the National Academy of Sciences.

[42]  Eun-hee Lee,et al.  Novel biodegradation pathways of cyclohexane by Rhodococcus sp. EC1. , 2011, Journal of hazardous materials.

[43]  M. Klotz,et al.  A novel family of functional operons encoding methane/ammonia monooxygenase-related proteins in gammaproteobacterial methanotrophs. , 2011, Environmental microbiology reports.

[44]  David L. Valentine,et al.  Propane Respiration Jump-Starts Microbial Response to a Deep Oil Spill , 2010, Science.

[45]  Miriam L. Land,et al.  Trace: Tennessee Research and Creative Exchange Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification Recommended Citation Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification , 2022 .

[46]  Toni Gabaldón,et al.  trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses , 2009, Bioinform..

[47]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[48]  I. Rhee,et al.  Cloning and characterization of a cyclohexanone monooxygenase gene from Arthrobacter sp. L661 , 2008 .

[49]  W. Ludwig,et al.  SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB , 2007, Nucleic acids research.

[50]  A. Wentzel,et al.  Identification of Novel Genes Involved in Long-Chain n-Alkane Degradation by Acinetobacter sp. Strain DSM 17874 , 2007, Applied and Environmental Microbiology.

[51]  S. Giovannoni,et al.  The SAR92 Clade: an Abundant Coastal Clade of Culturable Marine Bacteria Possessing Proteorhodopsin , 2007, Applied and Environmental Microbiology.

[52]  W. Röling,et al.  Marine microorganisms make a meal of oil , 2006, Nature Reviews Microbiology.

[53]  T. Uchiyama,et al.  Isolation and Functional Analysis of Cytochrome P450 CYP153A Genes from Various Environments , 2005, Bioscience, biotechnology, and biochemistry.

[54]  Robert C. Edgar,et al.  MUSCLE: a multiple sequence alignment method with reduced time and space complexity , 2004, BMC Bioinformatics.

[55]  K. Kubota,et al.  Degradation pathways of cyclic alkanes in Rhodococcus sp. NDKK48 , 2004, Applied Microbiology and Biotechnology.

[56]  Owen P. Ward,et al.  Recent Advances in Petroleum Microbiology , 2003, Microbiology and Molecular Biology Reviews.

[57]  Richard B. Gaines,et al.  Resolving the unresolved complex mixture in petroleum-contaminated sediments. , 2003, Environmental science & technology.

[58]  P. Lau,et al.  Cloning and Characterization of a Gene Cluster Involved in Cyclopentanol Metabolism in Comamonas sp. Strain NCIMB 9872 and Biotransformations Effected by Escherichia coli-Expressed Cyclopentanone 1,2-Monooxygenase , 2002, Applied and Environmental Microbiology.

[59]  Richard B. Gaines,et al.  The West Falmouth oil spill after thirty years: the persistence of petroleum hydrocarbons in marsh sediments. , 2002, Environmental science & technology.

[60]  M. Sogin,et al.  Microbial Diversity of Hydrothermal Sediments in the Guaymas Basin: Evidence for Anaerobic Methanotrophic Communities , 2002, Applied and Environmental Microbiology.

[61]  Dennis R. Peterson,et al.  Calculating the aquatic toxicity of hydrocarbon mixtures , 1994 .

[62]  B. Fox,et al.  Eight histidine residues are catalytically essential in a membrane-associated iron enzyme, stearoyl-CoA desaturase, and are conserved in alkane hydroxylase and xylene monooxygenase. , 1994, Biochemistry.

[63]  J. Costerton,et al.  Biodegradation of cycloalkane carboxylic acids in oil sand tailings. , 1993, Canadian journal of microbiology.

[64]  R. Colwell,et al.  Microbial degradation of hydrocarbons in the environment , 1990 .

[65]  B. Simoneit,et al.  Hydrothermal oil of Guaymas Basin and implications for petroleum formation mechanisms , 1989, Nature.

[66]  M. Trower,et al.  Isolation and Characterization of a Cyclohexane-Metabolizing Xanthobacter sp , 1985, Applied and environmental microbiology.

[67]  R. Atlas.  Microbial degradation of petroleum hydrocarbons: an environmental perspective , 1981 .

[68]  M. Griffin,et al.  Microbial Metabolism of Alicyclic Hydrocarbons: Cyclohexane Catabolism by a Pure Strain of Pseudomonas sp. , 1980 .

[69]  J. Perry,et al.  Microbial metabolism of cyclic hydrocarbons and related compounds. , 1977, CRC critical reviews in microbiology.

[70]  R. J. Watkinson,et al.  Microbial Metabolism of Alicyclic Hydrocarbons: Isolation and Properties of a Cyclohexane-degrading Bacterium , 1977 .

[71]  J. Perry,et al.  Microbial Degradation and Assimilation of n-Alkyl-Substituted Cycloparaffins , 1974, Journal of bacteriology.

[72]  G. Tonge,et al.  Microbial metabolism of alicyclic hydrocarbons. Growth of Nocardia petroleophila (NCIB9438) on methylcyclohexane. , 1974, Journal of general microbiology.

[73]  R. B. Cain,et al.  Microbial metabolism of alkylbenzene sulphonates Enzyme system of a Bacillus species responsible for Β-oxidation of the alkyl side chain of alkylbenzene sulphonates , 1972, Antonie van Leeuwenhoek.

[74]  P. Trudgill,et al.  The metabolism of cyclopentanol by Pseudomonas N.C.I.B. 9872. , 1972, The Biochemical journal.

[75]  D. Anders,et al.  Cycloalkane constituents of the bitumen from Green River Shale , 1971 .

[76]  P. Trudgill,et al.  The degradation of alicyclic hydrocarbons by a microbial consortium , 1989 .