“ Candidatus  Macondimonas diazotrophica”, a novel gammaproteobacterial genus dominating crude-oil-contaminated coastal sediments

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Abstract

Modeling crude-oil biodegradation in sediments remains a challenge due in part to the lack of appropriate model organisms. Here we report the metagenome-guided isolation of a novel organism that represents a phylogenetically narrow (>97% 16S rRNA gene identity) group of previously uncharacterized, crude-oil degraders. Analysis of available sequence data showed that these organisms are highly abundant in oiled sediments of coastal marine ecosystems across the world, often comprising ~30% of the total community, and virtually absent in pristine sediments or seawater. The isolate genome encodes functional nitrogen fixation and hydrocarbon degradation genes together with putative genes for biosurfactant production that apparently facilitate growth in the typically nitrogen-limited, oiled environment. Comparisons to available genomes revealed that this isolate represents a novel genus within the Gammaproteobacteria, for which we propose the provisional name “ Candidatus Macondimonas diazotrophica” gen. nov., sp. nov. “ Ca. M. diazotrophica” appears to play a key ecological role in the response to oil spills around the globe and could be a promising model organism for studying ecophysiological responses to oil spills.

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Uncultivated microbes in need of their own taxonomy.

Konstantinos Konstantinidis, Ramon Rosselló-Mora, Rudolf Amann (2017)

The great majority of microbial species remains uncultured, severely limiting their taxonomic characterization and thus communication among scientists. Although Candidatus was devised as a provisional category to classify uncultured taxa, it has not been widely accepted owing to technical limitations and lack of priority of Candidatus names in the official nomenclature. High-throughput sequencing provides the potential for data-rich taxonomic descriptions of uncultivated microbes, comparable in quality to those of cultured organisms. In order to fully realize this potential, standards and guidelines on how to perform these descriptions are needed. Here we aimed to outline these standards and draw the roadmap for a new genome-based taxonomy that, at least initially, would be parallel but highly convergent to the one in existence for isolates. In particular, we recommend the use of DNA genome sequences, recovered by population binning or single-cell techniques, as the basis for (i) identification and phylogenetic placement, (ii) bioinformatics-based functional and thus phenotypic predictions, as well as (iii) type material. We also recommend the implementation of an independent nomenclatural system for uncultivated taxa, following the same nomenclature rules as those for cultured Bacteria and Archaea but with its own list of validly published names. If widely adopted, this system will not only facilitate a comprehensive characterization of the 'uncultivated majority', but also provide a unified catalogue of validly published names, thereby avoiding synonyms and confusion. We also suggest that a committee of experts, supported by an international microbiological society, should be formed to govern the new classification system.

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Extent and Degree of Shoreline Oiling: Deepwater Horizon Oil Spill, Gulf of Mexico, USA

Jacqueline Michel, Edward H. Owens, Scott Zengel … (2013)

The oil from the 2010 Deepwater Horizon spill in the Gulf of Mexico was documented by shoreline assessment teams as stranding on 1,773 km of shoreline. Beaches comprised 50.8%, marshes 44.9%, and other shoreline types 4.3% of the oiled shoreline. Shoreline cleanup activities were authorized on 660 km, or 73.3% of oiled beaches and up to 71 km, or 8.9% of oiled marshes and associated habitats. One year after the spill began, oil remained on 847 km; two years later, oil remained on 687 km, though at much lesser degrees of oiling. For example, shorelines characterized as heavily oiled went from a maximum of 360 km, to 22.4 km one year later, and to 6.4 km two years later. Shoreline cleanup has been conducted to meet habitat-specific cleanup endpoints and will continue until all oiled shoreline segments meet endpoints. The entire shoreline cleanup program has been managed under the Shoreline Cleanup Assessment Technique (SCAT) Program, which is a systematic, objective, and inclusive process to collect data on shoreline oiling conditions and support decision making on appropriate cleanup methods and endpoints. It was a particularly valuable and effective process during such a complex spill.

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Bacterial species may exist, metagenomics reveal.

Alejandro Caro-Quintero, Konstantinos Konstantinidis (2012)

Whether or not bacterial species exist remains an unresolved issue of paramount theoretical as well as practical consequences. Here we review and synthesize the findings emerging from metagenomic surveys of natural microbial populations and argue that microbial communities are predominantly organized in genetically and ecologically discernible populations, which possess the attributes expected for species. These sequence-discrete populations represent a major foundation for beginning high-resolution investigations on how populations are organized, interact, and evolve within communities. We also attempt to reconcile these findings with those of previous studies that reported indiscrete species and a genetic continuum within bacterial taxa and discuss the implications for the current bacterial species definition. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

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Author and article information

Contributors

Konstantinos T. Konstantinidis: kostas@ce.gatech.edu

Journal

Journal ID (nlm-ta): ISME J

Journal ID (iso-abbrev): ISME J

Title: The ISME Journal

Publisher: Nature Publishing Group UK (London )

ISSN (Print): 1751-7362

ISSN (Electronic): 1751-7370

Publication date (Electronic): 5 April 2019

Publication date (Print): August 2019

Volume: 13

Issue: 8

Pages: 2129-2134

Affiliations

[1 ] ISNI 0000 0001 2097 4943, GRID grid.213917.f, School of Civil and Environmental Engineering, , Georgia Institute of Technology, ; Atlanta, GA USA

[2 ] ISNI 0000 0001 2097 4943, GRID grid.213917.f, School of Biological Sciences, , Georgia Institute of Technology, ; Atlanta, GA USA

[3 ] ISNI 0000 0001 2097 4943, GRID grid.213917.f, School of Earth and Atmospheric Sciences, , Georgia Institute of Technology, ; Atlanta, GA USA

[4 ] ISNI 0000 0001 2112 2427, GRID grid.267436.2, Center for Environmental Diagnostics & Bioremediation, , University of West Florida, ; 11000 University Parkway, Pensacola, FL USA

[5 ] ISNI 0000 0004 0472 0419, GRID grid.255986.5, Department of Earth, Ocean and Atmospheric Sciences, , Florida State University, ; Tallahassee, FL USA

[6 ]IMEDEA (CSIC-UIB), Marine Microbiology Group, Esporles, Spain

[7 ] ISNI 0000 0004 0607 975X, GRID grid.19477.3c, Present Address: Faculty of Chemistry, Biotechnology and Food Science, , Norwegian University of Life Sciences (NMBU), ; 1432, Ås, Norway

Author information

Luis M. Rodriguez-R http://orcid.org/0000-0001-7603-3093

Markus Huettel http://orcid.org/0000-0003-4844-7525

Joel E. Kostka http://orcid.org/0000-0003-3051-1330

Article

Accession ID: PMC6776044 Pmcid ID: PMC6776044 Pmc-uid ID: 6776044 Publisher ID: 400

DOI: 10.1038/s41396-019-0400-5

PMC ID: 6776044

PubMed ID: 30952995

SO-VID: d681ac5e-763f-430d-8d35-13add10ff371

History

Date received : 19 October 2018

Date revision received : 2 March 2019

Date accepted : 6 March 2019

Funding

Funded by: FundRef https://doi.org/10.13039/100007240, Gulf of Mexico Research Initiative (GoMRI);

Award ID: 231611-00

Award Recipient : Smruthi Karthikeyan Luis M. Rodriguez-R Patrick Heritier-Robbins Minjae Kim Will A. Overholt Markus Huettel Joel E. Kostka Konstantinos T. Konstantinidis