Melioribacter roseus

Domain: Bacteria
Phylum: Ignavibacteriae
Class: Ignavibacteria
Order: Ignavibacteriales
Family: Melioribacteraceae
Genus: Melioribacter
Species: M. roseus

Melioribacter roseus is a Gram-negative, rod-shaped bacterium first identified in a microbial mat coating the entrance to a thermal underwater spring in Western Siberia. It is motile only during exponential growth, using flagella to move through water, but loses its flagella and mobility during stationary growth. M. roseus cells tend to grow in aggregates or biofilms. The species name "roseus" comes from the observation that these biofilms appear pink under aerobic conditions. It grows most quickly under aerobic conditions but can thrive in oxygen-poor and completely anaerobic environments as well. M. roseus is the first and only identified species of the Melioribacter genus, and its discovery prompted reorganization of the Chlorobi-Ignavibacteriae-Bacteroidetes clade, shifting Ignavibacteria from "class" to "phylum" status.

Ecology

M. roseus was first isolated from a microbial mat growing on a plank of wood from an abandoned underwater oil-drilling site in Siberia. The mat was constantly exposed to flowing, warm, slightly alkaline water that was rich in hydrocarbons. In culture, it can grow at a temperature range from 35 to 60℃, pH range from 6 to 8.7, and salinity from 0 to 60 g/L. It grows best in warm (52 to 55℃), slightly alkaline (7.5), slightly salty (6 g/L) water like the environment where it was first isolated.

Since the initial identification, 16S rRNA sequencing has found Melioribacter species in marine, freshwater, sediment, and soil ecosystems. It is unclear whether M. roseus itself was represented in these environments from measuring 16S rRNA alone, but it is clear that this genus inhabits diverse environments.

Though it grows in a microbial mat, M. roseus accounts for a relatively small part of the community in which it was discovered. In a lab setting too, a Melioribacter species metabolically similar to M. roseus failed to thrive in the simulated ecosystem and did not contribute significantly to nutrient cycling interactions that supported the survival of other species in the culture. These findings suggest that M. roseus may not be native to the environment from which it was discovered. Since it is tolerant to high salinity and thrives in a range of levels of oxygen availability, scientists believe it originated from marine sediments.

Genome

The M. roseus genome is 3.3 Mbp in size and has a G+C content of 41.3%. The entire genome is contained in a single circular chromosome with no extrachromosomal genetic elements. 92% of the genome encodes proteins. 2133 of the 2838 protein coding genes have known or predicted functions but 272 sequences have unknown functions and no apparent orthologs in any other species.

Three CRISPR sites are present in the genome but the spacer regions do not contain sequences matching any known extrachromosomal sources like viruses or plasmids. Analysis of the CRISPR/cas sites themselves revealed a combination of Bacteroidetes-like sequences and Firmicutes-like sequences. Bacteroidetes homologs are likely conserved from a recent shared ancestor. However, the Firmicutes homolog likely arose from a horizontal gene transfer event between an M. roseus ancestor.

Phylogeny

Until the discovery of M. roseus, the only other known member of Ignavibacteriae, I. album, was thought to be the only heterotroph and non-photosynthesizer of the phylum Chlorobi. M. roseus and I. album are both heterotrophic facultative anaerobes, making them distinct from the next closest phyla--Chlorobi which is autotrophic and Bacteroidetes which is predominantly anaerobic and more distant based on genetic data. 16S rRNA and 23S rRNA sequencing further bolstered this change in phylogenetic organization. Its G+C content also lies between those of Chlorobi and Bacteroidetes.

Within its phylum, M. roseus is unique for its capacity to use Fe(III) oxide for respiration and use of cellulose as a carbon source. It also replicates much faster than I. album and only M. roseus forms biofilms.

Metabolism

M. roseus has adapted to acquire energy and nutrients from diverse sources. It is a chemo-organotroph with over 100 genes responsible for processing organic molecules for carbon acquisition. M. roseus generates ATP through oxidation of organic molecules through the Embden-Meyerhof-Parnas (EMP) pathway, oxidative TCA cycle, and electron transport chains. M. roseus can break down oligo- and polysaccharides including cellulose. It is the only known thermophilic facultative anaerobe of any phylum that can process cellulose.

M. roseus is also a facultative anaerobe. It has two varieties of cytochrome oxidase, one with moderate and one with strong affinity for oxygen. These serve as electron receptors under atmospheric and microaerobic conditions, allowing M. roseus to efficiently use aerobic respiration across a range of oxygen concentrations. Under anaerobic conditions, M. roseus performs fermentation of pyruvate which produces acetate, hydrogen gas, carbon dioxide, and a small amount of lactate as by-products. In anaerobic conditions when fermentable substances are scarce, M. roseus can also reduce nitrite, iron (III), and arsenate in place of oxygen, allowing it to perform anaerobic respiration in an even broader range of conditions.