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Title: Genomic Mysteries of Giant Bacteria: Insights and Implications

Journal Article · · Genome Biology and Evolution
ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [3]; ORCiD logo [4]
  1. Leibniz Institute of Freshwater Ecology and Inland Fisheries, Neuglobsow (Germany)
  2. Laboratory for Research in Complex Systems, Menlo Park, CA (United States); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
  3. Laboratory for Research in Complex Systems, Menlo Park, CA (United States); Institut de Systématique, Evolution, Biodiversité (ISYEB), Pointe-à-Pitre (France)
  4. Institut de Systématique, Evolution, Biodiversité (ISYEB), Pointe-à-Pitre (France)

Bacteria and Archaea are traditionally regarded as organisms with a simple morphology constrained to a size of 2–3 µm. Nevertheless, the history of microbial research is rich in the description of giant bacteria exceeding tens and even hundreds of micrometers in length or diameter already from its early days, for example, Beggiatoa spp., to the present, for example, Candidatus Thiomargarita magnifica. While some of these giants are still being studied, some were lost to science, with merely drawings and photomicrographs as evidence for their existence. The physiology and biogeochemical role of giant bacteria have been studied, with a large focus on those involved in the sulfur cycle. With the onset of the genomic era, no special emphasis has been given to this group, in an attempt to gain a novel, evolutionary, and molecular understanding of the phenomenon of bacterial gigantism. The few existing genomic studies reveal a mysterious world of hyperpolyploid bacteria with hundreds to hundreds of thousands of chromosomes that are, in some cases, identical and in others, extremely different. These studies on giant bacteria reveal novel organelles, cellular compartmentalization, and novel mechanisms to combat the accumulation of deleterious mutations in polyploid bacteria. In this perspective paper, we provide a brief overview of what is known about the genomics of giant bacteria and build on that to highlight a few burning questions that await to be addressed.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
2281213
Journal Information:
Genome Biology and Evolution, Journal Name: Genome Biology and Evolution Journal Issue: 9 Vol. 15; ISSN 1759-6653
Publisher:
Society for Molecular Biology and EvolutionCopyright Statement
Country of Publication:
United States
Language:
English

References (71)

Epulopiscium fishelsoni N. G., N. Sp., a Protist of Uncertain Taxonomic Affinities from the Gut of an Herbivorous Reef Fish1 journal November 1988
Raman-guided subcellular pharmaco-metabolomics for metastatic melanoma cells journal September 2020
The Enigmatic Cytoarchitecture of Epulopiscium spp. book January 2006
Complex Diffusion in Bacteria book January 2020
How Clonal Is Clonal? Genome Plasticity across Multicellular Segments of a “Candidatus Marithrix sp.” Filament from Sulfidic, Briny Seafloor Sediments in the Gulf of Mexico journal August 2016
Filling the Gaps in the Cyanobacterial Tree of Life—Metagenome Analysis of Stigonema ocellatum DSM 106950, Chlorogloea purpurea SAG 13.99 and Gomphosphaeria aponina DSM 107014 journal March 2021
Two New Beggiatoa Species Inhabiting Marine Mangrove Sediments in the Caribbean journal February 2015
Small but Mighty: Cell Size and Bacteria journal June 2015
Complete, closed bacterial genomes from microbiomes using nanopore sequencing journal February 2020
Recombination and Replication in DNA Repair of Heavily Irradiated Deinococcus radiodurans journal March 2009
Size-independent symmetric division in extraordinarily long cells journal September 2014
Titanospirillum velox: A huge, speedy, sulfur-storing spirillum from Ebro Delta microbial mats journal September 1999
Polymorphic stages of the fresh water blue-green alga, Gomphosphaeria aponina journal September 2010
Metagenome Sequencing to Explore Phylogenomics of Terrestrial Cyanobacteria journal June 2021
Heterozygous, Polyploid, Giant Bacterium,Achromatium, Possesses an Identical Functional Inventory Worldwide across Drastically Different Ecosystems journal November 2020
Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus journal January 2017
Cave Thiovulum (Candidatus Thiovulum stygium) differs metabolically and genomically from marine species journal December 2022
First description of a new uncultured epsilon sulfur bacterium colonizing marine mangrove sediment in the Caribbean: Thiovulum sp. strain karukerense journal August 2017
The evolution of bacterial cell size: the internal diffusion-constraint hypothesis journal April 2017
Multicellular life cycle of magnetotactic prokaryotes journal November 2004
Candidatus Thiovulum sp. strain imperiosus: the largest free-living Epsilonproteobacteraeota Thiovulum strain lives in a marine mangrove environment journal January 2022
Cell Architecture of the Giant Sulfur Bacterium Achromatium oxaliferum: Extra-cytoplasmic Localization of Calcium Carbonate Bodies journal December 2019
In situ sequencing for RNA analysis in preserved tissue and cells journal July 2013
Scaling laws predict global microbial diversity journal May 2016
Symbiotic spirochetes in the termite hindgut: phylogenetic identification of ectosymbiotic spirochetes of oxymonad protists journal October 2000
A single-cell sequencing approach to the classification of large, vacuolated sulfur bacteria journal June 2011
Random Chromosome Partitioning in the Polyploid BacteriumThermus thermophilusHB27 journal April 2019
Phylogenetic characterisation of marine Chroococcus-like (Cyanobacteria) strains from the Pacific region journal September 2016
DNA Replication and Genomic Architecture of Very Large Bacteria journal October 2012
Evolutionary consequences of polyploidy in prokaryotes and the origin of mitosis and meiosis journal June 2016
Draft Genome Sequence of Chromatium okenii Isolated from the Stratified Alpine Lake Cadagno journal February 2019
Ecophysiology of Thioploca ingrica as revealed by the complete genome sequence supplemented with proteomic evidence journal October 2014
Direct‐geneFISH: a simplified protocol for the simultaneous detection and quantification of genes and rRNA in microorganisms journal July 2016
A Genomic Perspective Across Earth’s Microbiomes Reveals That Genome Size in Archaea and Bacteria Is Linked to Ecosystem Type and Trophic Strategy journal January 2022
Porphyrosiphon annulatus sp. nov. (Oscillatoriales, Cyanobacteria) isolated on moist soil in Suwon, Republic of Korea journal February 2022
MALDI Mass Spectrometry Imaging: A Potential Game-Changer in a Modern Microbiology journal December 2022
Biology of Microalgae book January 2018
Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi journal December 1997
Big Bacteria journal October 2001
Inside a living cell journal January 1991
Evolutionary tradeoffs in cellular composition across diverse bacteria journal April 2016
Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1T), reclassification of Spirochaeta caldaria, Spirochaeta stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema caldaria comb. nov., Treponema stenostrepta comb. nov., and Treponema zuelzerae comb. nov., and emendation of the genus Treponema journal April 2013
Long-distance electron transfer in a filamentous Gram-positive bacterium journal March 2021
Evolutionary scaling of maximum growth rate with organism size journal December 2022
Surface Area to Volume Ratio: A Natural Variable for Bacterial Morphogenesis journal October 2018
Filamentous bacteria transport electrons over centimetre distances journal October 2012
Genome architecture studied by nanoscale imaging: analyses among bacterial phyla and their implication to eukaryotic genome folding journal January 2004
High proportions of bacteria and archaea across most biomes remain uncultured journal August 2019
History of the Study of the Genus Thiothrix: From the First Enrichment Cultures to Pangenomic Analysis journal August 2022
Insights into the single cell draft genome of “Candidatus Achromatium palustre” journal March 2016
Extreme polyploidy in a large bacterium journal April 2008
Single-Cell (Meta-)Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity journal May 2016
Ploidy and gene conversion in Archaea journal January 2011
AnnoTree: visualization and exploration of a functionally annotated microbial tree of life journal April 2019
Interdependence of Cell Growth and Gene Expression: Origins and Consequences journal November 2010
Recombination contributes to population diversification in the polyploid intestinal symbiont Epulopiscium sp. type B journal January 2019
The ploidy level of Synechocystis sp. PCC 6803 is highly variable and is influenced by growth phase and by chemical and physical external parameters journal May 2016
Symbiosis and Insect Diversification: an Ancient Symbiont of Sap-Feeding Insects from the Bacterial Phylum Bacteroidetes journal December 2005
Atmospheric pressure MALDI mass spectrometry imaging of tissues and cells at 1.4-μm lateral resolution journal November 2016
Community-like genome in single cells of the sulfur bacterium Achromatium oxaliferum journal September 2017
Challenges Faced by Highly Polyploid Bacteria with Limits on DNA Inheritance journal March 2021
Etude de la structure, et plus spécialement de l'appareil nucléaire, de très grandes bactéries sporulantes journal January 1970
Phylogenetic Diversity, Distribution, and Cophylogeny of Giant Bacteria (Epulopiscium) with their Surgeonfish Hosts in the Red Sea journal March 2016
Formation and function of bacterial organelles journal July 2020
Quantification of Ploidy in Proteobacteria Revealed the Existence of Monoploid, (Mero-)Oligoploid and Polyploid Species journal January 2011
A centimeter-long bacterium with DNA contained in metabolically active, membrane-bound organelles journal June 2022
Morphological and ecological characteristics of Spirochaeta plicatilis journal January 1973
Horizontal Gene Transfer Can Rescue Prokaryotes from Muller’s Ratchet: Benefit of DNA from Dead Cells and Population Subdivision journal February 2014
The Genus Thiomargarita book January 2006
Filamentous Cyanobacteria book January 2015
The Dynamic Nature of Genomes across the Tree of Life journal February 2014