What is the fundamental nature of the *Aquificota* phylum?

The *Aquificota* phylum represents a diverse group of bacteria that are known for inhabiting harsh environmental conditions. These bacteria are a distinct lineage within the domain Bacteria, differentiating them from Archaea, which also thrive in extreme environments.

What does the name *Aquificota* signify, and from which genus was it derived?

The name *Aquificota* originates from an early genus identified within this group, *Aquifex*, which translates to 'water maker'. This name reflects the genus's ability to produce water through the oxidation of hydrogen.

What are the typical habitats where *Aquificota* bacteria are found?

*Aquificota* bacteria are commonly found in various harsh aquatic environments, including springs, pools, and oceans. Their presence in such extreme settings highlights their adaptability to challenging conditions.

How do *Aquificota* bacteria obtain their carbon, and what is their ecological role?

*Aquificota* bacteria are autotrophs, meaning they produce their own food from inorganic substances. They serve as the primary carbon fixers in their respective environments, playing a crucial role in converting inorganic carbon into organic compounds that can be used by other organisms.

What are the key morphological and cellular characteristics of *Aquificota* bacteria?

These bacteria are characterized as Gram-negative, which refers to their cell wall structure, and they are non-spore-forming rods. Their rod shape is a common bacterial morphology, and the absence of spores means they do not form dormant, resistant structures.

How are *Aquificota* distinguished from Archaea, despite often inhabiting similar extreme environments?

*Aquificota* are classified as true bacteria, belonging to the domain Bacteria, which distinguishes them from Archaea. While both groups can inhabit extreme environments, they represent two fundamentally different domains of life with distinct evolutionary histories and cellular characteristics.

Who is credited with the valid publication of the phylum *Aquificota* in 2021?

The valid publication of the phylum *Aquificota* was attributed to Reysenbach in 2021, as indicated in the scientific classification provided in the source material.

How many genera and species are currently recognized within the *Aquificota* phylum?

The *Aquificota* phylum currently encompasses 15 genera and 42 species that have been validly published. This indicates a relatively contained but distinct group within the bacterial domain.

What are the three main classes that comprise the *Aquificota* phylum?

The *Aquificota* phylum is composed of three distinct classes: Aquificia, Desulfurobacteriia, and Thermosulfidibacteria. Each of these classes contains its own respective order.

Which families belong to the order Aquificales within the *Aquificota* phylum?

The order Aquificales includes two families: Aquificaceae and Hydrogenothermaceae. These families represent groups of bacteria sharing common characteristics and evolutionary relationships within the order.

What is the sole family recognized within the Desulfurobacteriales order?

The Desulfurobacteriales order contains only one family, which is the Desulfurobacteriaceae. This indicates a more narrowly defined group within the phylum.

Why is *Thermosulfidibacter takaii* not assigned to a specific family within the *Aquificota* phylum, despite its classification?

*Thermosulfidibacter takaii* is not assigned to a specific family within the *Aquificota* phylum due to its phylogenetic distinctness from both the Aquificales and Desulfurobacteriales orders. Although it is currently classified as a member of Aquificales, it exhibits greater physiological similarity to the Desulfobacteriaceae.

What are some of the historical synonyms used for the *Aquificota* phylum?

Historically, the *Aquificota* phylum has been referred to by several synonyms, including 'Aquificae' (Reysenbach 2001), 'Aquithermota' (Cavalier-Smith 2020), 'Aquificota' (Whitman et al. 2018), and 'Aquificaeota' (Oren et al. 2015). These different names reflect changes in taxonomic understanding over time.

What are conserved signature indels (CSIs), and what is their significance for the *Aquificota* phylum?

Conserved signature indels (CSIs) are specific insertions or deletions in protein sequences that are maintained across a group of organisms. For the *Aquificota* phylum, CSIs have been identified through comparative genomic studies and serve as potential molecular markers, indicating shared evolutionary history and distinguishing features.

How do CSIs help differentiate between the Aquificales and Desulfurobacteriales orders?

Several CSIs found across different proteins are specific to either the Aquificales or Desulfurobacteriales orders, allowing for their distinction. These molecular markers provide a reliable way to differentiate between these two groups within the *Aquificota* phylum.

What physiological differences exist between members of the Desulfurobacteriales and Aquificales orders?

Members of the Desulfurobacteriales are strict anaerobes, meaning they cannot tolerate oxygen, and they exclusively oxidize hydrogen for energy. In contrast, members of the Aquificales are microaerophilic, capable of growing in low oxygen concentrations, and can oxidize various compounds like sulfur or thiosulfate in addition to hydrogen.

What unique molecular signature is shared by *Aquificota* and Thermotogales bacteria in the SecA preprotein translocase?

Both *Aquificota* and Thermotogales bacteria share a unique 51-amino-acid insertion in their SecA preprotein translocase. This specific sequence feature is a molecular signature found in these two groups.

What is the proposed reason for the independent development of the 51-amino-acid insertion in SecA in *Aquificota* and Thermotogales?

Phylogenetic studies suggest that the presence of the same 51-amino-acid insertion in SecA in these two unrelated groups of thermophilic bacteria is not due to lateral gene transfer, but rather developed independently in response to selective pressure. This indicates convergent evolution driven by similar environmental challenges.

How does the 51-amino-acid insertion in SecA contribute to the thermostability of *Aquificota* bacteria?

The 51-amino-acid insertion in SecA is located near the ADP/ATP binding site and forms a network of water molecules that create intermediate interactions with ADP molecules. This network helps stabilize the hydrogen bonds between ADP/ATP and the protein, thereby maintaining ATP/ADP binding at high temperatures and contributing to the bacteria's overall thermostability.

What evidence contradicts a deep branching position for *Aquificota* and a close relationship with Thermotogota?

Some phylogenetic studies, based on other gene/protein sequences and conserved signature indels (CSIs) in several highly conserved universal proteins (such as Hsp70, Hsp60, RpoB, and AlaRS), do not support a deep branching of *Aquificota* or a close relationship with Thermotogota. This suggests alternative phylogenetic placements based on different molecular markers.

Which bacterial phylum is suggested to have a specific relationship with *Aquificota* based on CSIs in important proteins?

Evidence from CSIs in a number of important proteins, including Hsp70, Hsp60, RpoB, and AlaRS, strongly supports the placement of *Aquificota* in proximity to the phylum Proteobacteria, particularly the Campylobacterota. This suggests a closer evolutionary link than previously thought by some methods.

What specific molecular evidence supports a relationship between *Aquificota* and Proteobacteria?

A specific relationship between *Aquificota* and Proteobacteria is supported by a two-amino-acid CSI found uniquely in the inorganic pyrophosphatase protein of species from both phyla. This shared molecular feature indicates a common ancestry or close evolutionary connection.

How do some authors explain the frequent grouping of *Aquificota* with Campylobacterota, despite other phylogenetic evidence?

Some authors explain the frequently observed grouping of *Aquificota* with Campylobacterota as a result of frequent horizontal gene transfer between these groups. This is attributed to their shared ecological niches, where genetic material can be exchanged more readily between different bacterial lineages.

What type of eubacteria are *Aquificota* and Thermotogota classified as, based on their temperature preference?

Both *Aquificota* and Thermotogota are classified as thermophilic eubacteria, meaning they thrive in high-temperature environments. This shared characteristic is a defining feature of these bacterial phyla.

According to the 16S rRNA based LTP_10_2024 phylogenetic tree, what are the main orders and families associated with the *Aquificota* phylum?

The 16S rRNA based LTP_10_2024 phylogenetic tree associates the *Aquificota* phylum with the Thermosulfidibacterales, which includes the Thermosulfidibacteraceae family. It also includes the Aquificales order, which further branches into the Desulfurobacteriaceae, Hydrogenothermaceae, and Aquificaceae families.

Based on the 120 marker proteins from GTDB 09-RS220, what is the hierarchical classification within the *Aquificota* phylum?

The 120 marker proteins based GTDB 09-RS220 classifies *Aquificota* into two main classes: Desulfurobacteriia and Aquificia. The Desulfurobacteriia class contains the order Desulfurobacteriales and the family Desulfurobacteriaceae. The Aquificia class includes the order Hydrogenothermales with the family Hydrogenothermaceae, and the order Aquificales, which encompasses 'Hydrogenobaculaceae' and Aquificaceae.

What is the domain classification of *Aquificota*?

The *Aquificota* belong to the domain Bacteria, indicating they are prokaryotic organisms with distinct cellular structures from Archaea and Eukaryota.

What kingdom is *Aquificota* classified under?

The *Aquificota* phylum is classified under the kingdom Pseudomonadati, according to the scientific classification provided.

When was the phylum *Aquificota* formally established by Reysenbach?

The phylum *Aquificota* was formally established by Reysenbach in 2021, as indicated by the scientific classification information.

What is the meaning of the term 'autotroph' in the context of *Aquificota* bacteria?

In the context of *Aquificota* bacteria, being an 'autotroph' means they are capable of producing their own food, typically by using light or chemical energy to convert inorganic substances into organic nutrients, rather than consuming other organisms.

What does 'Gram-negative' signify for *Aquificota* bacteria?

Being 'Gram-negative' means that *Aquificota* bacteria possess a cell wall structure that does not retain the crystal violet stain in the Gram staining procedure. This characteristic is due to their outer membrane and thinner peptidoglycan layer, which is a common feature used in bacterial classification.

What is the significance of *Aquificota* being 'non-spore-forming'?

The characteristic of *Aquificota* being 'non-spore-forming' means that these bacteria do not produce endospores, which are highly resistant, dormant structures that allow some bacteria to survive harsh conditions. This implies they rely on other mechanisms to endure environmental stresses.

What is the role of comparative genomic studies in understanding *Aquificota*?

Comparative genomic studies are essential in understanding *Aquificota* as they have been instrumental in identifying conserved signature indels (CSIs) specific to the phylum and its various clades. These studies provide molecular markers that help in classification and understanding evolutionary relationships.

What is a 'microaerophile' in the context of Aquificales?

A 'microaerophile' is an organism that requires oxygen to survive, but only at lower concentrations than are present in the atmosphere. For Aquificales, this means they can utilize oxygen but are sensitive to high levels of it, allowing them to thrive in specific low-oxygen niches.

What is 'lateral gene transfer' and why is it relevant to the SecA insertion in *Aquificota*?

Lateral gene transfer (LGT), also known as horizontal gene transfer, is the movement of genetic material between unicellular and/or multicellular organisms other than by 'vertical' transmission from parent to offspring. It is relevant to the SecA insertion in *Aquificota* because phylogenetic studies demonstrated that the shared 51-amino-acid insertion with Thermotogales was *not* due to LGT, but rather independent development under selective pressure.

What is 'selective pressure' and how did it influence the SecA insertion in *Aquificota*?

Selective pressure refers to any cause that reduces reproductive success in a portion of a population, exerting evolutionary force. In the case of *Aquificota*, selective pressure from high-temperature environments likely favored the independent development of the 51-amino-acid insertion in SecA, as this feature enhances thermostability and survival in such conditions.

What are 'hyperthermophilic organisms' and how do they relate to *Aquificota*?

Hyperthermophilic organisms are extremophiles that thrive in extremely hot environments, typically above 80°C. *Aquificota* are considered thermophilic eubacteria, and in some phylogenetic analyses (like 16S rRNA gene trees), they branch in proximity to other hyperthermophilic organisms like Thermotogota, indicating a shared adaptation to high temperatures.

What is the role of 16S rRNA gene trees in bacterial phylogeny?

16S rRNA gene trees are widely used in bacterial phylogeny because the 16S ribosomal RNA gene is highly conserved across bacteria, allowing for the inference of evolutionary relationships. In the context of *Aquificota*, these trees initially placed them near Thermotogota, suggesting a deep branching lineage.

What are 'informational genes' and why are they considered important for phylogenetic analyses of *Aquificota*?

Informational genes are those involved in information processing, such as replication, transcription, and translation, and are generally thought to be less prone to horizontal gene transfer compared to non-informational genes. For *Aquificota*, analyses based on informational genes often place Aquificales close to Thermotogales, suggesting a more reliable phylogenetic signal in these genes.

What is the significance of the 'archaeal-bacterial branch point' in the context of *Aquificota* phylogeny?

The 'archaeal-bacterial branch point' refers to the evolutionary divergence point between the domains Archaea and Bacteria. The placement of *Aquificota* near this point in 16S rRNA gene trees suggests they might represent one of the earliest diverging lineages within the Bacteria, indicating their ancient evolutionary origin.

What is inorganic pyrophosphatase, and how does it provide molecular evidence for *Aquificota*'s relationship with Proteobacteria?

Inorganic pyrophosphatase is an enzyme that catalyzes the hydrolysis of inorganic pyrophosphate into two molecules of inorganic phosphate. A specific two-amino-acid conserved signature indel (CSI) in this protein is uniquely found in species from both *Aquificota* and Proteobacteria, providing molecular evidence for a specific evolutionary relationship between these two phyla.

Who is Cavalier-Smith, and what was his suggestion regarding the *Aquificota*?

Cavalier-Smith is a prominent evolutionary biologist. He suggested that the *Aquificota* are closely related to the Proteobacteria, aligning with some phylogenetic studies based on molecular signatures that indicate a connection between these two groups.

What is the 'Genome Taxonomy Database' (GTDB) and how does it contribute to *Aquificota* taxonomy?

The Genome Taxonomy Database (GTDB) is a comprehensive database that provides a standardized bacterial and archaeal taxonomy based on comparative genomics, specifically using 120 marker proteins. It contributes to *Aquificota* taxonomy by offering an alternative phylogenetic view, as seen in the GTDB 09-RS220 tree, which can differ from 16S rRNA based classifications.

What is 'The All-Species Living Tree Project' (LTP) and its role in *Aquificota* classification?

The All-Species Living Tree Project (LTP) is a phylogenetic tree of all validly named prokaryotic species, primarily based on 16S rRNA gene sequences. Its role in *Aquificota* classification is to provide a phylogenetic framework, as exemplified by the LTP_10_2024 tree, which shows the evolutionary relationships of *Aquificota* based on this specific genetic marker.

What are the families included in the Aquificales order according to the infobox?

According to the infobox, the Aquificales order includes the families Aquificaceae and Hydrogenothermaceae. These are the primary taxonomic groupings at the family level within this order.

What is the family associated with the Desulfurobacteriales order in the infobox?

The Desulfurobacteriales order, as presented in the infobox, is associated with the family Desulfurobacteriaceae. This indicates it is the sole family within that order.

What is the significance of the term 'Pseudomonadati' as the kingdom for *Aquificota*?

The classification of *Aquificota* under the kingdom Pseudomonadati places it within a broader grouping of bacteria. This kingdom level classification helps organize diverse bacterial phyla based on shared fundamental characteristics, though specific details about Pseudomonadati itself are not provided in the source.

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What is Aquificota?

Pioneers of Harsh Realms

The Aquificota phylum encompasses a diverse array of bacteria uniquely adapted to thrive in extreme environmental conditions. These organisms are frequently discovered in geothermal springs, hydrothermal pools, and deep-sea oceanic vents, showcasing their remarkable resilience. As autotrophs, they play a critical role as primary carbon fixers within their ecosystems, forming the base of the food web in these otherwise desolate habitats.

The 'Water Makers'

The nomenclature Aquificota originates from an early genus identified within this group, Aquifex, meaning "water maker." This name aptly describes their metabolic prowess: these bacteria are capable of producing water through the oxidation of hydrogen. This distinctive metabolic pathway highlights their capacity for chemolithoautotrophy, utilizing inorganic compounds for energy.

Bacterial Extremophiles

Members of the Aquificota phylum are characterized as Gram-negative, non-spore-forming rods. Crucially, they are classified as true bacteria (within the Domain Bacteria), distinguishing them from Archaea, which also inhabit extreme environments but belong to a separate domain of life. Alongside the Thermotogota, Aquificota are recognized as prominent thermophilic eubacteria, flourishing at high temperatures.

Taxonomic Structure

Hierarchical Classification

The Aquificota phylum currently comprises 15 genera and 42 species that have been validly published. This phylum is further organized into three distinct classes, each containing its respective orders, reflecting a structured hierarchy within this ancient bacterial lineage.

Key Orders and Families

Within Aquificota, the primary orders and their constituent families are well-defined:

The order Aquificales includes the families Aquificaceae and Hydrogenothermaceae.
The order Desulfurobacteriales is represented by a single family, the Desulfurobacteriaceae.

This classification underscores the distinct evolutionary paths and physiological adaptations within the phylum.

Unique Cases: Thermosulfidibacter takaii

A notable exception in the family-level assignment is Thermosulfidibacter takaii. While currently classified as a member of Aquificales, its phylogenetic distinctness from both established orders prevents its assignment to a specific family within the phylum. Interestingly, it exhibits greater physiological similarity to the Desulfobacteriaceae, highlighting the complexities in bacterial taxonomy.

Molecular Signatures

Genetic Markers: Conserved Signature Indels (CSIs)

Comparative genomic analyses have revealed several Conserved Signature Indels (CSIs) that are uniquely present across all species within the Aquificota phylum. These specific insertions or deletions in protein sequences serve as robust molecular markers, aiding in the precise demarcation and identification of this group. Further CSIs differentiate the Aquificales from the Desulfurobacteriales, and additional markers distinguish Aquificota and Hydrogenothermaceae from other bacterial phyla.

Metabolic Divergence

The molecular distinctions observed through CSIs are paralleled by significant physiological differences between the orders:

Desulfurobacteriales: These are strict anaerobes, relying exclusively on hydrogen oxidation for their energy requirements.
Aquificales: In contrast, members of this order are microaerophilic, capable of oxidizing hydrogen as well as other compounds such as sulfur or thiosulfate, demonstrating a broader metabolic versatility.

SecA Translocase: A Thermostability Secret

A remarkable 51-amino-acid insertion has been identified in the SecA preprotein translocase, a protein crucial for protein secretion. This insertion is shared by all Aquificota members and also by the Thermotogales. Phylogenetic studies indicate that this shared feature is not a result of lateral gene transfer but rather an independent evolutionary adaptation driven by selective pressure in these thermophilic groups.

Molecular dynamic simulations have elucidated that this 51-amino-acid insertion is located on the surface of SecA, strategically positioned near the ADP/ATP binding site. It facilitates a network of water molecules that form intermediate interactions between the CSI residues and ADP molecules. This intricate network stabilizes the hydrogen bonds between ADP/ATP and the protein, thereby enhancing the protein's ability to bind ATP/ADP effectively at high temperatures and contributing significantly to the overall thermostability of the bacteria.

Phylogenetic Debates

The Phylogenetic Puzzle

The precise phylogenetic placement of Aquificota within the bacterial domain has been a subject of ongoing scientific debate. Different molecular analyses yield varying conclusions, highlighting the complexities inherent in reconstructing the deep evolutionary history of microbial life.

16S rRNA Perspective

Studies based on the 16S rRNA gene trees often position Aquificota species in close proximity to the phylum Thermotogota, another group of hyperthermophilic organisms. This placement suggests a deep branching point near the archaeal-bacterial divergence, implying an ancient lineage adapted to extreme heat.

Protein-Based Insights

Conversely, phylogenetic analyses utilizing other gene and protein sequences, along with CSIs in highly conserved universal proteins (such as Hsp70, Hsp60, RpoB, and AlaRS), present a different picture. These studies frequently support a closer relationship of Aquificota to the phylum Proteobacteria, particularly the Campylobacterota. This inference is further bolstered by a unique two-amino-acid CSI found in the inorganic pyrophosphatase protein, shared exclusively by species from these two phyla.

The high G+C content (over 62%) of Aquificota rRNAs is essential for maintaining the stability of their secondary structures at the high growth temperatures they endure. While this characteristic might suggest a deep-branching lineage, the protein-based evidence challenges this view, placing them closer to Proteobacteria. The observed grouping of Aquificota with Campylobacterota is often attributed to frequent horizontal gene transfer, a phenomenon common among bacteria sharing similar ecological niches, which can obscure true vertical evolutionary relationships.

Accepted Taxonomy and Phylogenetic Views

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

16S rRNA based (LTP_10_2024)	120 marker proteins based (GTDB 09-RS220)
Thermosulfidibacterales Thermosulfidibacteraceae Aquificales Desulfurobacteriaceae Hydrogenothermaceae Aquificaceae [incl. "Hydrogenobaculaceae"]	Thermosulfidibacterota Thermosulfidibacteria Thermosulfidibacterales Thermosulfidibacteraceae Chuvochina et al. 2024 Aquificota Desulfurobacteriia Desulfurobacteriales Desulfurobacteriaceae L'Haridon et al. 2006 Aquificia Hydrogenothermales Hydrogenothermaceae Eder and Huber 2003 Aquificales "Hydrogenobaculaceae" Aquificaceae Reysenbach 2002

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References

Reysenbach, A.-L. (2001) Phylum BII. Thermotogae phy. nov. In: Bergey's Manual of Systematic Bacteriology, pp. 369-387. Eds D. R. Boone, R. W. Castenholz. Springer-Verlag: Berlin.

Klenk, H. P., Meier, T. D., Durovic, P. and others (1999) RNA polymerase of Aquifex pyrophilus: Implications for the evolution of the bacterial rpoBC operon and extremely thermophilic bacteria. J Mol Evol 48: 528-541.

Gupta, R. S. (2000) The phylogeny of Proteobacteria: relationships to other eubacterial phyla and eukaryotes. FEMS Microbiol Rev 24: 367-402.

Ciccarelli, F. D., Doerks, T., von Mering, C., Creevey, C. J., Snel, B., and Bork, P. (2006) Toward automatic reconstruction of a highly resolved tree of life. Science 311: 1283-1287.

Di Giulio, M. (2003) The universal ancestor was a thermophile or a hyperthermophile: Tests and further evidence. J Theor Biol 221: 425-436.

Griffiths, E. and Gupta, R. S. (2004) Signature sequences in diverse proteins provide evidence for the late divergence of the order Aquificales. International Microbiol 7: 41-52.

Meyer, T. E. and Bansal, A. K. (2005) Stabilization against hyperthermal denaturation through increased CG content can explain the discrepancy between whole genome and 16S rRNA analyses. Biochemistry 44: 11458-11465.

Catalogue of Organisms: Standing the Heat

A full list of references for this article are available at the Aquificota Wikipedia page

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This is not professional scientific advice. The information provided on this website is not a substitute for professional microbiological research, taxonomic analysis, or expert consultation in the field of extremophile biology. Always refer to peer-reviewed scientific literature, official taxonomic databases, and consult with qualified researchers or professors for specific academic or research needs. Never disregard professional scientific consensus because of something you have read on this website.

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Aquificota: Architects of Extreme Ecosystems

💡 Dive in with Flashcard Learning! 💡

What is Aquificota? 🔥

🌋 Pioneers of Harsh Realms

💧 The 'Water Makers'

🦠 Bacterial Extremophiles

Taxonomic Structure 🌳

📊 Hierarchical Classification

🔬 Key Orders and Families

🧩 Unique Cases: Thermosulfidibacter takaii

Molecular Signatures 🧬

🏷️ Genetic Markers: Conserved Signature Indels (CSIs)

🧪 Metabolic Divergence

🌡️ SecA Translocase: A Thermostability Secret

Phylogenetic Debates 🤔

📜 The Phylogenetic Puzzle

🌿 16S rRNA Perspective

🔗 Protein-Based Insights

Accepted Taxonomy and Phylogenetic Views

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📜 Important Notice

Dive in with Flashcard Learning!

What is Aquificota?

Pioneers of Harsh Realms

The 'Water Makers'

Bacterial Extremophiles

Taxonomic Structure

Hierarchical Classification

Key Orders and Families

Unique Cases: Thermosulfidibacter takaii

Molecular Signatures

Genetic Markers: Conserved Signature Indels (CSIs)

Metabolic Divergence

SecA Translocase: A Thermostability Secret

Phylogenetic Debates

The Phylogenetic Puzzle

16S rRNA Perspective

Protein-Based Insights

Teacher's Corner

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Discover other topics to study!

References

Feedback & Support

Disclaimer

Important Notice