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Bacillati

Bacillati is a kingdom of bacteria proposed in 2024 to encompass a major monophyletic clade of primarily monoderm (Gram-positive-like) prokaryotes, reflecting phylogenetic relationships and cell envelope structures distinct from diderm bacteria.^[1] This kingdom, with Bacillus as the type genus, includes the phyla Bacillota (formerly Firmicutes), Actinomycetota (formerly Actinobacteria), Chloroflexota, Deinococcota (formerly Deinococcus-Thermus), and Mycoplasmatota (formerly Tenericutes).^[1] The etymology derives from the Latin bacillus (a small rod), combined with the suffix -ati to denote a kingdom, highlighting its naming after the rod-shaped bacterial forms prevalent in its type phylum.^[1] Previously known as the informal group "Terrabacteria," Bacillati was elevated to kingdom status by researchers Markus Göker and Aharon Oren to align bacterial taxonomy with contemporary genomic phylogenies and the International Code of Nomenclature of Prokaryotes (ICNP), which now formally recognizes kingdom-level categories.^[1] This subdivision places Bacillati alongside three other bacterial kingdoms—Fusobacteriati, Pseudomonadati, and Thermotogati—emphasizing evolutionary divergences in membrane architecture and ecological adaptations, such as terrestrial origins inferred for many of its members.^[1] The proposal underscores Bacillati's vast diversity, spanning free-living, pathogenic, and symbiotic species critical to biogeochemical cycles, human health, and biotechnology.^[1]

Taxonomy

Etymology and nomenclature

The name Bacillati derives from the genus Bacillus, the Latin term for "small rod" (or "little stick"), which alludes to the rod-shaped cells characteristic of many bacteria within this taxon; the suffix "-ati" is used to denote a kingdom-level grouping in prokaryotic nomenclature.^[2] This name was proposed as a kingdom within the domain Bacteria in 2024 by Oren and Göker to formally replace the informal supergroup "Terrabacteria," reflecting a reorganization of higher-level bacterial taxonomy based on phylogenetic and ecological coherence.^[2]^[3] The concept of Terrabacteria originated in 2004 with Battistuzzi et al., who identified a major clade of primarily terrestrial-adapted prokaryotes encompassing phyla such as Actinobacteria, Chloroflexi, and Deinococcus/Thermus, based on a genomic timescale analysis of 32 conserved proteins across 72 species.^[4] This group was expanded in 2009 by Battistuzzi and Hedges to include additional lineages like Cyanobacteriota and Bacillota (formerly Firmicutes), emphasizing ancient adaptations to land environments such as desiccation resistance and photoprotection, and comprising about two-thirds of known prokaryotic species.^[5] The transition to Bacillati was validated in 2024 through publication in the International Journal of Systematic and Evolutionary Microbiology, establishing it as a heterotypic synonym of Terrabacteria at the kingdom rank, with Bacillus designated as the type genus.^[2]^[3] As a kingdom, Bacillati employs the standard bacterial genetic code, known as Translation Table 11, which is shared across most prokaryotes and governs protein synthesis from messenger RNA.^[6] This taxonomic framework aligns with broader proposals to divide Bacteria into four kingdoms, prioritizing monophyletic groupings supported by molecular phylogenies.^[2]

Included phyla and classes

The kingdom Bacillati includes a diverse array of phyla, primarily comprising gram-positive bacteria and representing approximately two-thirds of all known prokaryotic species.^[1] This taxonomic grouping, formally established through the elevation and renaming of the informal "Terrabacteria" clade for nomenclatural stability, excludes the sister kingdom Pseudomonadati and focuses on lineages with shared terrestrial adaptations reflected in their phylogenetic clustering.^[1] The core phyla are Actinomycetota, Bacillota, Chloroflexota, Cyanobacteriota, Deinococcota, and Mycoplasmatota. Actinomycetota encompasses genera such as Actinomyces and Streptomyces. Bacillota includes genera like Bacillus and Clostridium, with key classes such as Bacilli and Clostridia. Chloroflexota comprises filamentous bacteria, Cyanobacteriota includes cyanobacteria, Deinococcota features radiation-resistant bacteria, and Mycoplasmatota includes wall-less bacteria such as Mycoplasma. Genomic data indicate potential inclusion of additional groups within Bacillati, such as the DST clade (encompassing Deinococcota, Synergistota, and Thermodesulfobacteriota) and the Candidate Phyla Radiation (CPR) group, a vast assemblage of mostly small-genome, uncultured lineages that may cluster closely with Chloroflexota.^[7]

Characteristics

Cell structure and morphology

Members of the Bacillati kingdom exhibit predominantly gram-positive characteristics due to the presence of a thick peptidoglycan layer in their cell walls, which retains the crystal violet stain during Gram staining procedures. This feature is particularly prominent in phyla such as Bacillota and Actinomycetota, where the peptidoglycan layer measures 20–80 nm in thickness, providing structural rigidity and protection against environmental stresses. However, variations exist across the clade; for instance, Cyanobacteriota possess a diderm envelope with an outer membrane, leading to gram-negative staining despite a comparably thick peptidoglycan layer (10–700 nm), which can sometimes result in ambiguous staining outcomes. Chloroflexota display a mix of gram-positive and gram-negative properties, with some lineages like Caldilineae featuring thinner peptidoglycan that correlates with gram-negative retention of the counterstain. Morphologically, Bacillati bacteria are diverse but often rod-shaped (bacilli), reflecting the etymological root of the name, as seen in genera like Bacillus in Bacillota and Corynebacterium in Actinomycetota. This rod form predominates in many aerobic and facultative anaerobic members adapted to terrestrial environments. Variations include cocci in some Bacillota species, filamentous structures in Chloroflexota such as Chloroflexus, and complex multicellular arrangements in Cyanobacteriota like Nostoc. Endospore formation is a notable feature in Bacillota, enabling dormancy and resistance to harsh conditions through the development of tough, dehydrated spores within the cell. These morphological traits contribute to the clade's versatility in nutrient acquisition and survival strategies. The cell wall of Bacillati is primarily composed of peptidoglycan, a polymer formed by alternating units of N-acetylglucosamine and N-acetylmuramic acid cross-linked by peptide bridges, which forms a mesh-like network essential for maintaining cell shape and integrity. In gram-positive members, this layer is augmented by teichoic acids—anionically charged polymers of glycerol or ribitol phosphate linked to the peptidoglycan—that facilitate ion binding, enzyme anchoring, and phage resistance, as exemplified in Bacillus subtilis. Protective adaptations such as S-layers, crystalline protein arrays on the cell surface, are common in certain Chloroflexota, enhancing resistance to desiccation and radiation by forming a paracrystalline lattice. These compositional elements underscore the clade's evolutionary adaptations while accommodating phylogenetic diversity.

Physiological adaptations

Members of Bacillati demonstrate exceptional physiological adaptations to desiccation and ultraviolet (UV) radiation, enabling survival in harsh terrestrial environments. Within Bacillota, endospore formation represents a primary mechanism for enduring these stresses. Endospores maintain a dehydrated core encased in multilayered structures, including peptidoglycan-rich cortex and protein coats, which limit water loss and block UV penetration. Small acid-soluble spore proteins bind spore DNA, converting it to an A-like form that resists UV-induced thymine dimer formation, thereby preserving genetic integrity during prolonged exposure.^[8] Photosynthetic adaptations in Bacillati highlight metabolic innovation for energy acquisition. Cyanobacteriota conduct oxygenic photosynthesis through coordinated action of photosystems I and II, where photosystem II oxidizes water to provide electrons for the electron transport chain, yielding oxygen, ATP, and NADPH for autotrophic growth. Conversely, Chloroflexota utilize anoxygenic photosynthesis via a type I reaction center akin to photosystem I, employing electron donors like organic compounds or sulfide without water splitting, thus supporting growth in low-oxygen settings.^[9]^[10] Metabolic diversity underpins the resilience of Bacillati, with aerobic respiration serving as the dominant energy pathway in many lineages, oxidizing substrates via the electron transport chain to maximize ATP production in oxygenated niches. Anaerobic alternatives persist, as seen in Clostridia fermentation, where pyruvate is metabolized to acetate, butyrate, or ethanol, generating energy through substrate-level phosphorylation in oxygen-free conditions. Pathogenicity in certain Actinomycetota, such as Mycobacterium species, involves cell wall components like mycolic acids and lipoarabinomannan, which act as virulence factors by inhibiting phagosome-lysosome fusion and modulating immune signaling.^[11]^[12]^[13] Salinity tolerance in Bacillati is facilitated by the synthesis of osmoprotectants, notably ectoine in halotolerant members like Brevibacterium species within Actinomycetota. This compatible solute stabilizes enzymes and membranes by maintaining hydration shells, countering osmotic stress without perturbing cellular metabolism. These adaptations often build upon the robust Gram-positive cell walls common in Bacillati, which provide a barrier against ionic influx.^[14]

Phylogeny and evolution

Molecular phylogeny

The molecular phylogeny of Bacillati establishes it as a monophyletic kingdom of predominantly monoderm (Gram-positive-like) bacteria within the domain Bacteria, supported by multi-gene and phylogenomic analyses that highlight its distinct evolutionary lineage. Early evidence came from the analysis of 53 protein-coding genes across 191 prokaryotic genomes, which identified a major clade encompassing approximately two-thirds of known prokaryotic species and characterized by adaptations to terrestrial environments; this group, originally termed Terrabacteria, forms the core of modern Bacillati.^[15] Within the broader subdomain Selabacteria—comprising 97% of prokaryotic species based on sequence data—Bacillati represents a well-supported monophyletic assemblage, validated through concatenated protein alignments that demonstrate robust branching patterns.^[15] As proposed in 2024 and adopted in major taxonomic resources as of 2025, recent phylogenomic studies using whole-genome sequences from thousands of bacterial genomes have further confirmed the monophyly and internal structure of Bacillati. Comprehensive taxonomic revisions drew on genome-based phylogenetic trees to formally name Bacillati as a kingdom, reflecting its cohesion among phyla such as Bacillota, Actinomycetota, Chloroflexota, and Cyanobacteriota, with high-confidence placements derived from relative evolutionary divergence metrics.^[1] These analyses, incorporating over 100 universal marker genes, show Bacillati as sister to the diderm kingdom Pseudomonadati within Selabacteria, with the combined clade accounting for the vast majority of bacterial diversity.^[1] Additionally, multi-gene trees position the Candidate Phyla Radiation (CPR, now Patescibacteria) as a deeply branching group affiliated with Bacillati, often as a sister lineage to Chloroflexota, underscoring reductive evolution within this kingdom.^[16] Phylogenetic markers for Bacillati include both the 16S rRNA gene for initial alignments and whole-genome datasets for higher-resolution inference, with methods like maximum likelihood yielding trees where critical nodes exhibit bootstrap support values greater than 90%, indicating strong statistical confidence in the clade's topology.^[16]

Evolutionary history

The Bacillati, also known as Terrabacteria, originated through a major divergence from the sister kingdom Pseudomonadati approximately 3 billion years ago during the Archean eon.^[4] This split coincided with the gradual rise in atmospheric oxygen levels and the initial colonization of terrestrial environments by prokaryotes, marking a pivotal transition from aquatic to land-based habitats.^[5] Molecular clock analyses place the common ancestor of Bacillati groups, including Actinomycetota, Chloroflexota, Cyanobacteriota, and Bacillota, around 3.05 billion years ago (95% confidence interval: 2.70–3.49 billion years ago), reflecting adaptations to increasingly oxygenated and desiccating conditions on early Earth.^[4] A key evolutionary event in Bacillati history was the development of oxygenic photosynthesis in the ancestors of Cyanobacteriota between 2.7 and 3.0 billion years ago. This innovation, evidenced by ancient biomarkers such as 2-methylhopanoids preserved in 2.7-billion-year-old sediments, enabled the use of water as an electron donor and produced oxygen as a byproduct, profoundly influencing global geochemistry. Following the Great Oxidation Event around 2.4 billion years ago, which elevated atmospheric oxygen concentrations, Bacillati lineages evolved gram-positive cell walls as a critical terrestrial adaptation. These thick peptidoglycan layers, unique to many Bacillati phyla, provided enhanced protection against desiccation, UV radiation, and oxidative stress on land surfaces, facilitating survival in arid and exposed environments.^[5] Subsequent expansions within Bacillati involved the incorporation of genetic material from Candidate Phyla Radiation (CPR) bacteria through horizontal gene transfer, enriching metabolic and stress-response capabilities.^[17] By the Proterozoic era (2.5–0.54 billion years ago), this diversification radiated into numerous phyla, driven by ongoing environmental changes and gene exchange, establishing Bacillati as dominant terrestrial prokaryotes with adaptations that persist today.^[4]

Ecology and distribution

Habitats and environmental roles

Members of the Bacillati clade are predominantly found in terrestrial environments, including soils and sediments, where they exhibit adaptations to challenging conditions such as aridity and high salinity.^[18] For instance, Bacillota and Actinomycetota thrive in these habitats, contributing to soil stability and nutrient cycling through their resilience to desiccation.^[19] Aquatic environments are primarily occupied by Cyanobacteriota, which are ubiquitous in oceans, freshwater systems, and even hypersaline waters, serving as key components of planktonic and benthic communities.^[20]^[21] Chloroflexota, meanwhile, are notable extremophiles often dominating microbial mats in geothermal hot springs, tolerating temperatures up to 70°C in anaerobic, reduced settings.^[22]^[23] Ecologically, Bacillati play critical roles in biogeochemical processes across their habitats. In terrestrial soils, certain Bacillota facilitate nitrogen fixation and the decomposition of organic matter, enhancing nutrient availability for ecosystems.^[24] Cyanobacteriota drive global primary production via oxygenic photosynthesis, historically transforming Earth's atmosphere and currently supporting food webs in aquatic and terrestrial settings.^[20] Actinomycetota contribute to bioremediation by degrading complex organic pollutants and producing antibiotics that influence microbial community dynamics in soils.^[18]^[25] Chloroflexota in hot springs aid in carbon and sulfur cycling through fermentative and phototrophic metabolisms.^[22] Bacillati exhibit a global distribution, encompassing diverse biomes from polar regions to tropics, and represent a major portion of bacterial diversity.^[2] Fossil records, particularly stromatolites formed by ancient Cyanobacteriota, provide evidence of their presence dating back about 2.5 billion years, marking early contributions to Earth's oxygenation.^[26]^[27]

Interactions with other organisms

Bacillati members engage in diverse interactions with eukaryotes and other microbes, ranging from pathogenic to symbiotic and commensal relationships that influence host health, microbial community dynamics, and ecosystem functions. Pathogenic interactions are prominent, particularly in human and animal diseases caused by Bacillota species. For example, Bacillus anthracis causes anthrax, a zoonotic disease that affects livestock and wildlife through spore inhalation, ingestion, or skin contact, and can be transmitted to humans via contaminated animal products, leading to severe systemic infections with high mortality if untreated.^[28] Similarly, Clostridium botulinum produces botulinum neurotoxin, resulting in botulism—a paralytic illness in humans and animals often linked to improperly preserved foods or wound infections, disrupting nerve function and potentially causing respiratory failure.^[29] In Actinomycetota, certain Streptomyces species act as plant pathogens; Streptomyces scabies, for instance, infects potato tubers and roots, producing thaxtomin toxins that induce common scab lesions, reducing crop yield and market value worldwide.^[30] Symbiotic and commensal associations further highlight Bacillati's ecological roles, especially in eukaryotic hosts. Within the human gut microbiota, Clostridia species such as Clostridium butyricum form mutualistic relationships by fermenting dietary fibers into short-chain fatty acids like butyrate, which supports intestinal epithelial health, modulates immune responses, and inhibits pathogens.^[31] Commensal Clostridia contribute to nutrient breakdown and microbiota stability without direct host harm, aiding in the prevention of dysbiosis-related conditions. In plant systems, Actinomycetota like Streptomyces spp. serve as mycorrhiza helper bacteria, enhancing arbuscular mycorrhizal symbioses by promoting fungal spore germination and root colonization, thereby improving plant nutrient uptake in nutrient-poor soils.^[32] Microbial interactions among Bacillati and other bacteria often involve chemical signaling and antagonism that shape community structures. Streptomyces species in Actinomycetota produce over 50% of clinically relevant antibiotics, such as streptomycin and tetracycline, which inhibit competing microbes in soil biofilms and rhizospheres, thereby influencing bacterial diversity and preventing overgrowth of sensitive taxa.^[33] In Bacillota, quorum sensing via autoinducer-2 (AI-2) in species like Bacillus subtilis coordinates biofilm formation and sporulation, facilitating cooperative behaviors in mixed microbial consortia and enhancing resilience against environmental stresses.^[34] Human relevance extends to beneficial applications leveraging these interactions. Bacillus subtilis spores are widely used as probiotics to restore gut microbiota balance, survive gastric acidity, and produce antimicrobial compounds that combat pathogens, with clinical trials showing reduced gastrointestinal symptoms in healthy adults.^[35] Industrially, Bacillota species provide enzymes like proteases and amylases for applications in detergents, food processing, and biofuels, owing to their stability and high yields in fermentation processes.^[36]

References

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Summary of each segment:
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