Poribacteria are a
candidate phylum of
bacteria
Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micr ...
originally discovered
in the
microbiome
A microbiome () is the community of microorganisms that can usually be found living together in any given habitat. It was defined more precisely in 1988 by Whipps ''et al.'' as "a characteristic microbial community occupying a reasonably wel ...
of marine
sponge
Sponges or sea sponges are primarily marine invertebrates of the animal phylum Porifera (; meaning 'pore bearer'), a basal clade and a sister taxon of the diploblasts. They are sessile filter feeders that are bound to the seabed, and a ...
s (''Porifera''). Poribacteria are
Gram-negative
Gram-negative bacteria are bacteria that, unlike gram-positive bacteria, do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. Their defining characteristic is that their cell envelope consists ...
primarily
aerobic mixotrophs with the ability for
oxidative phosphorylation
Oxidative phosphorylation(UK , US : or electron transport-linked phosphorylation or terminal oxidation, is the metabolic pathway in which Cell (biology), cells use enzymes to Redox, oxidize nutrients, thereby releasing chemical energy in order ...
,
glycolysis
Glycolysis is the metabolic pathway that converts glucose () into pyruvic acid, pyruvate and, in most organisms, occurs in the liquid part of cells (the cytosol). The Thermodynamic free energy, free energy released in this process is used to form ...
, and autotrophic carbon fixation via the
Wood – Ljungdahl pathway.
Poribacterial heterotrophy is characterised by an enriched set of glycoside hydrolases, uronic acid degradation, as well as several specific sulfatases. This heterotrophic repertoire of poribacteria was suggested to be involved in the degradation of the extracellular sponge host matrix.
Genome
Single-cell
genomics
Genomics is an interdisciplinary field of molecular biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, ...
and
metagenomic shotgun sequencing approaches reveal a poribacterial
genome
A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as ...
size range between about 4.2 and 6.5
megabases encoding 4,254
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...
-coding genes, of which an unusually high 24% have no
homology to known
gene
In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...
s. Among the genes of identifiable homology, reconstructed pathways suggest that the poribacterial central metabolism is capable of
glycolysis
Glycolysis is the metabolic pathway that converts glucose () into pyruvic acid, pyruvate and, in most organisms, occurs in the liquid part of cells (the cytosol). The Thermodynamic free energy, free energy released in this process is used to form ...
,
tricarboxylic acid cycle,
pentose phosphate pathways,
oxidative phosphorylation
Oxidative phosphorylation(UK , US : or electron transport-linked phosphorylation or terminal oxidation, is the metabolic pathway in which Cell (biology), cells use enzymes to Redox, oxidize nutrients, thereby releasing chemical energy in order ...
, the
Entner-Doudoroff pathway, and
autotrophic carbon fixation
Biological carbon fixation, or сarbon assimilation, is the Biological process, process by which living organisms convert Total inorganic carbon, inorganic carbon (particularly carbon dioxide, ) to Organic compound, organic compounds. These o ...
via
Wood–Ljungdahl pathway. Further, Poribacteria seem to engage in assimilatory denitrification and ammonia scavenging with potential relevance in nitrogen re-cycling within the sponge holobiont. The poribacterial genome is also reported to contain an unusually high number of phage defence systems including
CRISPR-CAS and
restriction modification system
The restriction modification system (RM system) is found in bacteria and archaea, and provides a defense against foreign DNA, such as that borne by bacteriophages.
Bacteria have restriction enzymes, also called restriction endonucleases, which ...
s.
Cell compartmentalization
Cell compartmentalization into distinct
membrane-bound organelles is a universal and defining property of eukaryotes, but had not been observed in
prokaryote
A prokaryote (; less commonly spelled procaryote) is a unicellular organism, single-celled organism whose cell (biology), cell lacks a cell nucleus, nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Ancient Gree ...
s other than the
Planctomycetota. Poribacteria were previously thought to be distinguished from other microorganisms associated with marine
sponges
Sponges or sea sponges are primarily marine invertebrates of the animal phylum Porifera (; meaning 'pore bearer'), a basal clade and a sister taxon of the diploblasts. They are sessile filter feeders that are bound to the seabed, and ar ...
by such a distinctive morphology featuring a large membrane-bound cellular compartment that was suggested to contain DNA.
The distinctive poribacterial compartments were originally identified using
fluorescence in situ hybridization and
electron microscopy.
Genomic evidence suggests the presence of protein-bound organelles, but not for membrane-bound organelles.
More recently,
correlative light-electron microscopy, confirmed two elements of poribacterial subcellular compartmentation:
Firstly,
Bacterial microcompartments, atypically localized at the cell membrane. Secondly, spherical bipolar compartments which are discussed to be most likely carbon rich storage polymers such as
Polyhydroxybutyrate
Polyhydroxybutyrate (PHB) is a Polyhydroxyalkanoates, polyhydroxyalkanoate (PHA), a polymer belonging to the polyesters class that are of interest as bio-derived and biodegradable plastics. The poly-3-hydroxybutyrate (P3HB) form of PHB is probabl ...
.
Eukaryote-like proteins
Genomic analyses of poribacteria reveal several families of cell-surface repeat proteins that resemble those found in eukaryotes, and are infrequently found in prokaryotes. Examples include
ankyrin and
leucine-rich repeat
A leucine-rich repeat (LRR) is a protein structural motif that forms an α/β horseshoe tertiary structure, fold. It is composed of repeating 20–30 amino acid stretches that are unusually rich in the hydrophobic amino acid leucine. These Pr ...
domains,
as well as
tetratricopeptide
The tetratricopeptide repeat (TPR) is a structural motif. It consists of a degenerate 34 amino acid tandem repeat identified in a wide variety of proteins. It is found in tandem arrays of 3–16 motifs, which form scaffolds to mediate protein� ...
s.
Unusual
low-density lipoprotein receptor repeat proteins are also found, of unknown function. Most of these protein families are thought to be involved in surface interactions with the sponge host.
In addition, genetic infrastructure for
sterol
A sterol is any organic compound with a Skeletal formula, skeleton closely related to Cholestanol, cholestan-3-ol. The simplest sterol is gonan-3-ol, which has a formula of , and is derived from that of gonane by replacement of a hydrogen atom on ...
biosynthesis is observed in poribacterial genomes, otherwise found almost exclusively in eukaryotes and the planctomycete ''
Gemmata obscuriglobus''.
Ecological niche
Poribacteria are
symbionts of marine
sponge
Sponges or sea sponges are primarily marine invertebrates of the animal phylum Porifera (; meaning 'pore bearer'), a basal clade and a sister taxon of the diploblasts. They are sessile filter feeders that are bound to the seabed, and a ...
s, among the most abundant microorganisms in the highly diverse microbiome of the sponge
mesohyl
The mesohyl, formerly known as mesenchyme or as mesoglea, is the gelatinous matrix within a sponge. It fills the space between the external pinacoderm and the internal choanoderm. The mesohyl resembles a type of connective tissue and contains ...
.
They have been found in a large variety of sponge species from diverse geographic origins.
The composition of microorganisms in the sponge microbiome can be vertically inherited, with adult sponges transmitting their distinctive microbial communities to offspring.
References
{{Taxonbar, from=Q24975421
Bacteria
Candidatus taxa