Thermomicrobia

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Thermomicrobia
Scientific classification
Domain:
Bacteria
Phylum:
Thermomicrobiota

Garrity and Holt 2021 [1]
Class:
Thermomicrobia

Garrity and & Holt 2002 [2]
Orders
Synonyms
  • Thermomicrobia:
    • "Thermomicrobia" Garrity and Holt 2001
    • "Thermomicrobiota" Whitman et al. 2018
    • "Thermomicrobaeota" Oren et al. 2015

The Thermomicrobia is a group of thermophilic green non-sulfur bacteria. Based on species Thermomicrobium roseum (type species) and Sphaerobacter thermophilus, this bacteria class has the following description: [3] [4]

Contents

The class Thermomicrobia subdivides into two orders with validly published names: ThermomicrobialesGarrity and Holt 2001 and SphaerobacteralesStackebrandt,Rainey and Ward-Rainey 1997. Gram negative. Pleomorphic, non-motile, non-spore-forming rods. Non-sporulating. No diamino acid present. No peptidoglycan in significant amount. Atypical proteinaceous cell walls. Hyper-thermophilic, optimum growth temperature at 70-75 °C. Obligatory aerobic and chemoorganotrophic. [note 1]

As thermophilic bacteria, members of this class are usually found in environments which are distant from human activity. [5] However, they have features like improved growth in antibiotics and CO oxidizing activity, making them interesting topics of research (e.g. for biotechnology application).

History

In 1973, a strain of rose-pink thermophilic bacteria was isolated from Toadstool Spring in Yellowstone National Park, which was later named Thermomicrobium roseum and proposed as a novel species of the novel genus Thermomicrobium. [6] At that time the genus was categorized under family Achromobacteraceae, but it became a distinct phylum by 2001. [3]

In 2004, it was proposed, on the basis of an analysis of genetic affiliations, that the Thermomicrobia should more properly be reclassified as a class belonging to the phylum Chloroflexota (formerly Chloroflexi). The bacteria Sphaerobacter thermophilus originally described as an Actinobacteria is now considered a Thermomicrobia. [4] [7] In the same year, another strain of rose-pink thermophilic bacteria was isolated from Yellowstone National Park, which was named Thermobaculum terrenum. [8] Later analysis based on genome put this species under Thermomicrobia class. [9] However, the current standing of Thermobaculum terrenum is disputed. [10]

In 2012, a thermo-tolerant nitrite-oxidizing bacterium was isolated from a bioreactor, which was named Nitrolancetus hollandica and proposed as a novel species later in 2014. [11] While it has nitrite-oxidizing activity, which is unique in the Thermomicrobia class, it is placed under the Thermomicrobia class based on 16s rRNA phylogeny. [12]

In 2014, two thermophilic, Gram-positive, rod-shaped, non-spore-forming bacteria (strains KI3T and KI4T) isolated from geothermally heated biofilms growing on a tumulus in the Kilauea Iki pit crater on the flank of Kilauea Volcano (Hawai'i) were proposed as representatives of new species based on 16s rRNA phylogeny. The KI3T strain, later named as Thermomicrobium carboxidum, is closely related to Thermomicrobium roseum. The KI4T strain, later named as Thermorudis peleae, was proposed as a type strain of new genus Thermorudis. [13]

In 2015, a thermophilic bacteria strain WKT50.2 isolated from geothermal soil in Waitike (New Zealand) was proposed to be a novel species, later named Thermorudis pharmacophila. Phylogenic analysis based on 16s rRNA place it within Thermomicrobia class, as close relative to Thermorudis peleae. [5]

Characteristics

Living environment

Members of the class Thermomicrobia are broadly distributed across a wide range of both aquatic and terrestrial habitats. Thermomicrobium roseum was found in geothermally heated hot springs, Thermorudis pharmacophila and Thermobaculum terrenum from heated soils, and Thermomicrobium carboxidum and Thermorudis peleae from heated sediments [13] [5] [14] In addition, Sphaerobacter thermophilus was found in sewage sludge that went through thermophilic treatment. [15] The common features of their habitats include temperature ranging from around 65~75 °C and a pH around 6.0~8.0 (except for Nitrolancea hollandica which grow around 40 °C [11] ).

Metabolism

Members of Thermomicrobia class have variation in their basic metabolism. Nitrolancetus hollandica has nitrifying activity that utilize NO2− as energy source, which is unique in the whole Chloroflexota phylum. [12] Thermomicrobium spp. and Sphaerobacter thermophilus have constitutive CO oxidizing not found in other species in this class. [13] [16] However, species of this class do share some features, as listed below:

Antibiotic resistance

Members of Thermomicrobia class exhibit certain level of resistance against metronidazole and/or trimethoprim, which are clinically relevant for humans. [17] [18] Thermomicrobium carboxidum and Thermorudis peleae show resistance against both of those antibiotics, while Sphaerobacter thermophilus shows resistance against only metronidazole. [5] Interestingly, Thermomicrobium roseum and Thermorudis pharmacophila have an increased growth in both metronidazole and trimethoprim, a rare trait even within antibiotic resistant bacteria. [5] The mechanisms behind are currently undocumented, and further study is required on this topic.

Cell envelope structure

Members of Thermomicrobia class have various Gram-staining results. Thermomicrobium roseum, Sphaerobacter thermophilus and Thermorudis pharmacophila are reported to be Gram-negative and have a typical layered diderm cell envelope structure. [3] [4] [5] However, their cell envelope composition are atypical compared to typical Gram-negative bacteria. Cell envelope of Thermomicrobium roseum lacks significant amount of peptidoglycan, which is fundamental for typical Gram-negative bacteria, while being rich in protein. [3] Membrane lipids of Thermomicrobium roseum are mostly long chain diols instead of glycerol-based lipids commonly found in bacteria. [19] The same feature was found in Sphaerobacter thermophilus and Thermorudis pharmacophila. [5] It was suggested that the high-protein and diol-based lipid composition are responsible for heat resistance of these bacteria. [4] [20]

Meanwhile, other members of Thermomicrobia class are reported to be Gram-positive and have typical monoderm cell envelope. [8] [12] [13] There are some possible explanations of the inconsistency of Gram-staining result within the class. For Thermorudis pharmacophila, a possible explanation suggested by Houghton et al. is that it is actually an atypical monoderm bacterium, because its cell envelope contains amino acids usually associated with Gram-positive bacteria, have reaction to KOH, vancomycin and ampicillin, and lacks genes responsible for diderm formation. [5] It is also suggested that further study is required to resolve this problem, since the inconsistent reports of cell envelope structure are found for the whole Chloroflexota phylum.

Phylogeny


16S rRNA based LTP_06_2022 [21] [22] [23] 120 marker proteins based GTDB 08-RS214 (28th April 2023). [24] [25] [26]
Thermomicrobia
Sphaerobacterales

Nitrolancea

Sphaerobacter

Thermomicrobiales

Thermomicrobium

Thermorudis

Thermomicrobiales
Thermomicrobiaceae

Nitrolancea

Sphaerobacter

Thermomicrobium

Thermorudis

Taxonomy

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) [27] and National Center for Biotechnology Information (NCBI). [28]

See also

Notes

  1. ↑ The above description does not take newly discovered species after 2004 into account.
  2. 1 2 Strain found at the National Center for Biotechnology Information (NCBI) but has no standing with the Bacteriological Code (1990 and subsequent Revision) as detailed by List of Prokaryotic names with Standing in Nomenclature (LPSN) as a result of the following reasons:

Related Research Articles

The Chloroflexia are a class of bacteria in the phylum Chloroflexota. Chloroflexia are typically filamentous, and can move about through bacterial gliding. It is named after the order Chloroflexales.

<span class="mw-page-title-main">Deinococcota</span> Phylum of Gram-negative bacteria

Deinococcota is a phylum of bacteria with a single class, Deinococci, that are highly resistant to environmental hazards, also known as extremophiles. These bacteria have thick cell walls that give them gram-positive stains, but they include a second membrane and so are closer in structure to those of gram-negative bacteria.

<span class="mw-page-title-main">Chlamydiota</span> Phylum of bacteria

The Chlamydiota are a bacterial phylum and class whose members are remarkably diverse, including pathogens of humans and animals, symbionts of ubiquitous protozoa, and marine sediment forms not yet well understood. All of the Chlamydiota that humans have known about for many decades are obligate intracellular bacteria; in 2020 many additional Chlamydiota were discovered in ocean-floor environments, and it is not yet known whether they all have hosts. Historically it was believed that all Chlamydiota had a peptidoglycan-free cell wall, but studies in the 2010s demonstrated a detectable presence of peptidoglycan, as well as other important proteins.

<i>Thermus</i> Genus of bacteria

Thermus is a genus of thermophilic bacteria. It is one of several bacteria belonging to the Deinococcota phylum. Thermus species can be distinguished from other genera in the family Thermaceae as well as all other bacteria by the presence of eight conserved signature indels (CSIs) found in proteins such as adenylate kinase and replicative DNA helicase as well as 14 conserved signature proteins (CSPs) that are exclusively shared by members of this genus.

Sulfur-reducing bacteria are microorganisms able to reduce elemental sulfur (S0) to hydrogen sulfide (H2S). These microbes use inorganic sulfur compounds as electron acceptors to sustain several activities such as respiration, conserving energy and growth, in absence of oxygen. The final product of these processes, sulfide, has a considerable influence on the chemistry of the environment and, in addition, is used as electron donor for a large variety of microbial metabolisms. Several types of bacteria and many non-methanogenic archaea can reduce sulfur. Microbial sulfur reduction was already shown in early studies, which highlighted the first proof of S0 reduction in a vibrioid bacterium from mud, with sulfur as electron acceptor and H
2 as electron donor. The first pure cultured species of sulfur-reducing bacteria, Desulfuromonas acetoxidans, was discovered in 1976 and described by Pfennig Norbert and Biebel Hanno as an anaerobic sulfur-reducing and acetate-oxidizing bacterium, not able to reduce sulfate. Only few taxa are true sulfur-reducing bacteria, using sulfur reduction as the only or main catabolic reaction. Normally, they couple this reaction with the oxidation of acetate, succinate or other organic compounds. In general, sulfate-reducing bacteria are able to use both sulfate and elemental sulfur as electron acceptors. Thanks to its abundancy and thermodynamic stability, sulfate is the most studied electron acceptor for anaerobic respiration that involves sulfur compounds. Elemental sulfur, however, is very abundant and important, especially in deep-sea hydrothermal vents, hot springs and other extreme environments, making its isolation more difficult. Some bacteria – such as Proteus, Campylobacter, Pseudomonas and Salmonella – have the ability to reduce sulfur, but can also use oxygen and other terminal electron acceptors.

Sphaerobacter is a genus of bacteria. When originally described it was placed in its own subclass (Spahaerobacteridae) within the class Actinomycetota. Subsequently, phylogenetic studies have now placed it in its own order Sphaerobacterales within the phylum Thermomicrobiota. Up to now there is only one species of this genus known. The closest related cultivated organism to S. Thermophilus is the Thermomicrobium Roseum and has an 87% sequence similarity which indicates that S. Thermophilus is one of the most isolated bacterial species.[4]

The Chloroflexota are a phylum of bacteria containing isolates with a diversity of phenotypes, including members that are aerobic thermophiles, which use oxygen and grow well in high temperatures; anoxygenic phototrophs, which use light for photosynthesis ; and anaerobic halorespirers, which uses halogenated organics as electron acceptors.

Hydrogenobacter thermophilus is an extremely thermophilic, straight rod (bacillus) bacterium. TK-6 is the type strain for this species. It is a Gram negative, non-motile, obligate chemolithoautotroph. It belongs to one of the earliest branching order of Bacteria. H. thermophilus TK-6 lives in soil that contains hot water. It was one of the first hydrogen oxidizing bacteria described leading to the discovery, and subsequent examination of many unique proteins involved in its metabolism. Its discovery contradicted the idea that no obligate hydrogen oxidizing bacteria existed, leading to a new understanding of this physiological group. Additionally, H. thermophilus contains a fatty acid composition that had not been observed before.

Thermoanaerobacter is a genus in the phylum Bacillota (Bacteria). Members of this genus are thermophilic and anaerobic, several of them were previously described as Clostridium species and members of the now obsolete genera Acetogenium and Thermobacteroides

Armatimonadota is a phylum of gram-negative bacteria.

Dehalococcoidia is a class of Chloroflexota, a phylum of Bacteria. It is also known as the DHC group.

There are several models of the Branching order of bacterial phyla, one of these was proposed in 1987 paper by Carl Woese.

Thermolithobacteria is a class of rod-shaped Gram-positive bacteria within phylum Bacillota. Species within this class are thermophilic lithotrophs isolated from sediment in Calcite Springs in Yellowstone National Park. Thermolithobacter ferrireducens strain JW/KA-2(T) metabolism consists of the oxidation of hydrogen gas and reduction of ferric oxide to magnetite. Thermolithobacter carboxydivorans strain R1(T) is hydrogenic and oxidizes carbon monoxide.

<i>Turicibacter</i> Genus of bacteria

Turicibacter is a genus in the Bacillota phylum of bacteria that has most commonly been found in the guts of animals. The genus is named after the city in which it was first isolated, Zurich, Switzerland.

Anaerolineaceae is a family of bacteria from the order of Anaerolineales. Anaerolineaceae bacteria occur in marine sediments. There are a total of twelve genera in this family, most of which only encompass one species. All known members of the family are Gram-negative and non-motile. They also do not form bacterial spores and are either mesophilic or thermophilic obligate anaerobes. It is also known that all species in this family are chemoheterotrophs.

Bellilinea is a thermophilic bacteria genus from the family of Anaerolineaceae with one known species. Bellilinea caldifistulae has been isolated from thermophilic digester sludge from Niigata in Japan.

Coprothermobacterota is a phylum of nonmotile, rod-shaped bacteria.

Coprothermobacteraceae is a bacterial family of rod-shaped microorganisms, belonging to the order Coprothermobacterales, class Coprothermobacteria of the phylum Coprothermobacterota.

Sulfobacillus thermosulfidooxidans is a species of bacteria of the genus Sulfobacillus. It is an acidophilic, mixotrophic, moderately thermophilic, Gram-positive, sporulating facultative anaerobe. As its name suggests, it is capable of oxidizing sulfur.

Ardenticatena is a Gram-negative, thermophilic and chemoheterotrophic genus of bacteria from the family of Ardenticatenaceae with one known species. Ardenticatena maritima has been isolated from iron-rich sediments from a coastal hydrothermal field from Kagoshima in Japan.

References

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  17. ↑ "Metronidazole Monograph for Professionals - Drugs.com". Drugs.com. Retrieved 2018-10-11.
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  21. ↑ "The LTP" . Retrieved 10 May 2023.
  22. ↑ "LTP_all tree in newick format" . Retrieved 10 May 2023.
  23. ↑ "LTP_06_2022 Release Notes" (PDF). Retrieved 10 May 2023.
  24. ↑ "GTDB release 08-RS214". Genome Taxonomy Database . Retrieved 10 May 2023.
  25. ↑ "bac120_r214.sp_label". Genome Taxonomy Database . Retrieved 10 May 2023.
  26. ↑ "Taxon History". Genome Taxonomy Database . Retrieved 10 May 2023.
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