BACTERIA: 21 main phyla, with 147 important genera

16th April 2020

Translated from the original article in Catalan

If you want to go directly to the simplified phylogenetic tree (Figure 4) that I propose below, click here. Idem for the inventory of the 21 phyla, click here. Idem for the alphabetical list of bacterial genera, click here.

Purpose of this article

From time to time, students have told me that when in class or doing some bibliographic work, they come up with a name of a microbial genus that is not very familiar to them, they have no idea where to find which type of microorganism it is and what are its basic characteristics, besides using Wikipedia. Although there is plenty of bibliography, and for queries only for phylogenetic location of a particular genus I use the Taxonomy browser section of the National Center for Biotechnology Information (NCBI), it often happens that an easy and quick source of information is missing, and this source should not be too exhaustive.

This is the purpose of this post: to summarize the major bacterial phyla, with the list of the most important genera. These should be the ones that seem most relevant, especially for the environment or in food and other industrial applications, also some because of their characteristic metabolism, and also some of the more well-known pathogens.

Not to be too exhaustive, for the moment I limit myself to bacteria, and therefore are not considered archaea, eukaryotic microorganisms, or viruses.

Taxonomy and phylogeny of the Bacteria

Taxonomy is the science of naming, defining and classifying groups of living beings based on the characteristics they share. These groups are taxa, which are divided into hierarchical categories, which are (variable depending on the organisms): Domain, Kingdom, Phylum, Class, Order, Family, Gender and Species. The first taxonomic system was developed in the 18th century by Carl von Linné, who laid the foundations for binomial nomenclature (Genus + species).

After Linné, the taxonomy developed mainly thanks to Ernst Haeckel (19th century) and Robert Whittaker, who proposed the 5 kingdoms: 4 eukaryotes (Animals, Plants, Fungi and Protista) plus that of the Monera, prokaryotes, bacteria basically (Whittaker 1969).

Although taxonomic classifications could be established only on the basis of phenotypic characteristics (morphology, structures, metabolism, etc.), taxonomy is currently elaborated by looking at the kinship relationships between organisms and their evolutionary history, that is, phylogeny. Making phylogenetic trees, based on genetic similarities, can explain the evolution of organisms, both current and extinct ones.

Historically, before molecular knowledge, the bacterial classification or taxonomy presented many difficulties and mistakes, given their microscopic size and lack of easily distinguishable morphological features, unlike plants and animals. Classification was based on cell wall structure (Gram) and metabolism only, but a phylogenetic tree could not be performed.

This changed in the hands of Carl Richard Woese (1987), promoter of the molecular phylogenetic revolution, who classified all organisms (not just bacteria), based on ribosomal RNA sequences, first defining the Archaeabacteria (now Archaea), and thus introducing the concept of the three domains (Figure 1).

Fig 1 woese fig4

Figure 1. Universal phylogenetic tree of the 3 domains (Archaea, Bacteria and Eukaryotes), determined by comparing the sequences of rRNAs, where line lengths are proportional to the calculated distances for alignment (Woese 1987).

Regarding only the Bacteria, based on the rRNA, Carl Woese established 11 divisions (Figure 2).

Fig 2 woese fig11

Figure 2. Bacterial phylogenetic tree determined by comparing the sequences of 16S rRNAs, where line lengths are proportional to the calculated distances for 16S alignment, and the point of origin is an Archaea consensus sequence (Woese 1987).

Later on, after Woese’s phylogenetic tree, it has been modified, on the one hand, incorporating numerous groups of discovered bacteria, especially thermophiles, chemolithotrophs and others from extreme environments. On the other hand, the development of non-culture techniques has allowed numerous bacteria to be detected without isolating them. Among these techniques where the DNA of environmental samples can be directly analysed, we should point out the methods of metagenomics, which amplify and sequence fragments of the genes (16S or others) of all the bacteria present, and treat the data with bioinformatics programs to compare with others and deduce possible new species.

Coincidentally with Woese, the classification of all living beings was enhanced by Thomas Cavalier-Smith, especially at the protist level (Cavalier-Smith 1993). Some of the more complete recent bacterial trees have been based on comparing some more conserved genes, such as Lang et al (2016), which proposes different super branch models of 3000 prokaryotes sequenced on the basis of 24 genes.

Based on all this, one of the most recent phylogenetic trees is the one proposed by Hug et al. (2016), which has been compiled based on published sequences, including the genomic data of 1000 unknown and non-isolated organisms. This “tree of life” with the 3 domains of bacteria, archaea and eukaryotes reveals a predominance of bacterial diversification and underlines the importance of organisms of which there are no isolated representatives (Figure 3). For this tree, 30437 species genomes from the 3 domains available by September 2015 in the NCBI databases were used. Currently (March 2020) there are already 50159 species sequenced in the NCBI: 1724 archaea, 26467 bacteria, 4915 eukaryotes and 17053 viruses .

Fig 3 Hug-et-al-figure-1

Figure 3. Current view of the tree of life, encompassing the total diversity of sequenced genomes, with 92 bacterial phylum, 26 archaea, and the 5 eukaryotic supergroups (Hug et al. 2016).

By comparing the genetic sequences of many bacteria, we have seen the difficulty of producing evolutionary phylogenetic trees with branches as we always represent them, because horizontal gene transfer (HGT) is a common phenomenon in bacteria. By means of the mechanisms of transformation, viral transduction and conjugation, bacteria share many genes in their evolution and blur the branches, so that the representation should be more like a network. The representations of phyla in evolutionary branches should therefore be taken as a relative approximation.

The Bergey’s Manual has undoubtedly been the most important bibliographic resource for the determination, identification and systematization of all prokaryotic organisms, namely Bacteria and Archaea. Started in 1923 by David H. Bergey, it has logically had successive updates, while retaining the importance of being the Reference Manual for the description of all prokaryotic features. The latest paper version of the Bergey’s Manual of Systematic Bacteriology comprises 5 volumes in 7 books (2001-2012). More recently an online version has been published (Whitman, 2015).

Another valuable resource is the LPSN (List of Prokaryotic Names with Standing in Nomenclature) database (Parte 2014), which collects the online list of all prokaryotic names that have been validated by publication in the International Journal of Systematic and Evolutionary Microbiology, under the rules of the International Bacterial Nomenclature Code. The LPSN currently lists 15,974 taxa, distributed in 41 bacterial phyla plus 5 archaea ones. In addition, the LPSN includes the updated classification of prokaryotes, their nomenclature, and culture collections.

However, both Bergey and LPSN are either too exhaustive and impractical to search for a particular bacterial genus or to have a quick overview of phylogenetic relationships between various phyla.

My proposal of simplified phylogenetic tree of Bacteria

Based on the tree described by Hug et al (2016) (Figure 3), and limiting to bacteria, I dare to simplify it, doing without the almost not known phyla or the numerous branches without isolated representatives. With that said, here are the 21 main phyla we see in Figure 4.

As we see in Figure 4, Terrabacteria and Hydrobacteria are two higher taxonomic categories that comprise the vast majority of bacterial phyla, the 99% of bacteria. Terrabacteria would have evolved by acquiring resistance adaptations to terrestrial environmental conditions such as desiccation, UV radiation, high salinity, including a characteristic cell wall (Gram-positive), and others of them would have developed oxygen photosynthesis (cyanobacteria). Hydrobacteria would be the rest of the bacteria, most Gram-negative, that would have evolved in aqueous or humid environments, and which include the 2 superphyla FCB (Fibrobacter-Chlorobi-Bacteroides) and PVC (Planctomyces-Verrucomicrobia-Chlamydia), and the large group of Proteobacteria. The supertaxa Terrobacteria and Hydrobacteria would have diverged 3,000 million years ago, when the Terrabacteria would have begun to colonize the continents.

In the same Figure 4, I have indicated the protomitochondria and protochloroplasts, which emerged from the phyla Alfaproteobacteria and Cyanobacteria respectively, about 1500-2000 million years ago.

Fig 4 arbre bacteris

Figure 4. Simplified current view of the bacterial phylogenetic tree with 21 main phyla, based on the DNA sequence set of 16 ribosomal proteins (modified by Hug et al 2016). LUCA: Last Universal Common Ancestor.

The 21 main bacterial PHYLA: most important features and genera

I describe below in short, the 21 phyla (Figure 4), following the phylogenetic tree from right to left. For the most relevant taxa (class, order) that I comment in some phyla, I have followed the categories as they are in the NCBI (Taxonomy). I have summarized the descriptions based on the basic sources of Microbiology information, such as Brock (Madigan et al. 2017), Lengeler et al. (1999), Tortora et al. (2018), or the Prescott (Willey et al. 2017), and within the most common internet resources, in addition to WikipediaMicrobeWiki must be mentioned.

1. Aquificae

E.g., Aquifex or Hydrogenobacter, it is a phylum close to Thermotogae, and both are the closest bacteria to the archaea. They are gram-negative bacilli, hyperthermophiles, aerobic chemolithotrophs, they oxidize H2 to H2O, and are found in hot or volcanic waters.

2. Thermotogae

E.g., Thermotoga, it is a phylum close to Aquificae. They are hyperthermophilic, fermentative anaerobes, gram-negative bacilli with a “toga” type wrap, and are found in hot water and hydrothermal vents.

3. Deinococcus – Thermus

They are very resistant to extreme environments, therefore extremophiles, which includes 2 groups of which the most well-known genera are those giving the name to the phylum:

Deinococcus are gram-positive cocci with thick wall and a outer membrane, gamma-resistant, UV-resistant, and of pink color due to carotenoid deinoxanthin.

Thermus are hyperthermophilic gram-negative bacilli, found in hot springs, and also in composting. Th. aquaticus was isolated by Thomas D. Brock and H. Freeze, from Yellowstone geysers, and it is well known for Taq DNA polymerase, which is widely used in PCRs because it is not denatured at 95°C. Th. thermophilus, also with thermostable DNA-polymerases, is a model for genetic manipulation.

4. Cyanobacteria

Cyanobacteria were formerly known as “blue-green algae” or cyanophytes because they are filamentous and perform photosynthesis, such as algae and plants. Like these, they make non-cyclic photophosphorylation, with 2 photosystems and chlorophyll. In fact, they are the evolutionary origin of proto-chloroplasts, they “invented” oxygenic photosynthesis, are the only bacteria currently doing so, and they generated the atmosphere as we know it some 2700 million years ago. Fossil stromatolites made of cyanobacteria biofilms are the earliest signs of life on Earth. They are filamentous gram-negative, with inner membranes. Some attach N2 to thicker specialized cells (heterocysts), containing nitrogenase. They are found in many habitats, both terrestrial and aquatic, some are symbionts of plants, others make cyanotoxins, and they are the main cause of blooms in eutrophic waters. Some are edible (Spirulina), mainly used as a feed supplement. With very active secondary metabolism, they are also an interesting source of antiviral, antibiotic and antitumor agents. Other genera are: Anabaena, Chroococcus, Nostoc, Oscillatoria, Pleurocapsa and Synechococcus.

5. Firmicutes

They are a large phylum of gram-positive, bacilli or cocci, chemoheterotrophic, with a low G + C content in the DNA (most with <50%). It mainly includes 3 great classes, Bacilli, Clostridia and Negativicutes:

Bacilli with 2 orders, Bacillales and Lactobacillales:

Bacillales, that are aerobic or facultative, mainly with aerobic respiration. Important genera:

Bacillus, endospore-forming bacilli, ubiquitous in terrestrial environments, where together with Paenibacillus they favour plant crops (see my post). The most resistant sporulate is B. stearothermophilus, a model for thermal sterilization calculations. There are some pathogens such as B. anthracis (anthrax) and B. cereus (food poisoning). Other many species are of industrial interest: production of enzymes (such as amylase) or proteases (subtilisin of B. subtilis), peptide antibiotics, some are bird probiotics (see my post on Probiotic Bacillus), and B. thuringiensis is widely used as bioinsecticide for their Cry toxins and their genes incorporated in Bt genetically modified plants (cotton, corn and others).

Listeria, facultative non-endospore-forming anaerobic bacilli, saprophytes but also opportunistic pathogens (L. monocytogenes) and cold-resistant, are the leading cause of death among foodborne diseases.

Staphylococcus, cluster-shaped facultative anaerobic cocci, saprophytes living on the human skin and membranous mucosa. Some are pathogens due to coagulase formation.

Lactobacillales: they are the lactic acid bacteria (LAB). They are bacilli or cocci, aerotolerant anaerobes with a fermentative metabolism, producing mainly lactic acid from sugars. Not sporulated, they are present in decaying plants (mainly Lactobacillus) and dairy products (especially Lactococcus, Lactobacillus and Streptococcus). They are amongst the most important groups of microorganisms used in food industry: dairy and other lacto-fermented foods, such as vegetables, meats, fish, wines and beers, etc., where these bacteria contribute to conservation, by decrease of pH and production of bacteriocins, and give organoleptic qualities. They are generally considered GRAS (Generally Recognized as Safe). In addition, they also play a role in the healthy animal and human microbiota, both in the gastrointestinal tract and on the mucous surfaces. That is why some of them are the most common probiotics, especially Lactobacillus. On the other hand, Oenococcus is the exclusive genus of wines where malolactic fermentation takes place (here is a brief summary), a peculiar fermentation linked to ATPase. Other important BL genera are: Enterococcus (some may be pathogens and other probiotics), Leuconostoc, Pediococcus (present in beers, see my post), Weissella, Carnobacterium, Aerococcus, and Fructobacillus.

Clostridia

They are strict anaerobic bacilli that form endospores. They are saprophytes, mainly fermenting plant polysaccharides, and live mainly in soils. Some are opportunistic pathogens in the digestive (Clostridium difficile) or saprophytes that can cause gangrene (C. perfringens) and the worst produce some of the most dangerous toxins: C. tetani and C. botulinum. However, they are very abundant in the healthy gut microbiota (see my post) and therefore possible probiotics (Clostridium, Eubacterium, Coprococcus and Ruminococcus, producers of the beneficial butyrate and propionate, and especially Faecalibacterium prausnitzii or Christensenella, associated with low body index, and low fat.

Although of the same class as Clostridia and also sporulated anaerobes, the genus Heliobacteria are anoxygenic photoheterotrophs (with bacteriochlorophyll g, one photosystem and cyclic photophosphorylation), they are not grampositive and fix N2.

Negativicutes

They are sporulated anaerobes, phylogenetically close to Clostridia, but gram-negative, as they have an outer membrane similar to that of proteobacteria (possible horizontal gene transfer). Selenomonas is crescent-shaped, motile, present in the rumen of ruminants. Veillonella are cocci in the human gut, beneficial because they ferment lactose, giving acetate and propionate. Phascolarctobacterium is a pleomorphic bacillus that also produces these short-chain fatty acids in the gut, and therefore also beneficial.

6. Tenericutes

Phylum closely related to Firmicutes, but they have no cell wall. Unique class: Mollicutes. They are very small of size (0.2-0.3 µm) and genome (0.6 Mbp), because they are intracellular parasites of animals and plants, saprophytes and/or pathogens. Having no cell wall, they are resistant to many antibiotics. Variable form, they can live without oxygen. Mycoplasma are human pathogens that can cause pneumonia or sexually transmitted infections.

7. Chloroflexi

E.g., Chloroflexus, they are also called green non-sulphur bacteria or chlorobacteria, they are filamentous or gliding, with inner membranes (chlorosomes). They are anoxygenic photoheterotrophs (with bacteriochlorophyll cs, one photosystem and cyclic photophosphorylation). They are gram-negative but without outer membrane. The class Thermomicrobia includes those that are thermophilic (Thermomicrobium), some with pink pigment.

8. Actinobacteria

Another large phylum of gram-positive, heterotrophs, aerobic and anaerobic, with a high content of G+C in DNA (most with >50%), irregular in shape and some filamentous. They have very versatile catabolism and ubiquitous in terrestrial and aquatic environments. Includes these main orders:

Actinomycetales, such as Actinomyces, are facultative anaerobes, can make endospores, are filamentous but some are bacilli. They are economically important microorganisms in soils, both agricultural and forestry. They decompose organic matter, along with the fungi, which they resemble because they form filamentous mycelium.

Bifidobacteriales, anaerobes, they ferment carbohydrates. They are irregular bacilli, especially bifid, e.g. Bifidobacterium. They are important in the gut microbiota of mammals, in particular child in humans, and used as probiotics.

Corynebacteriales, aerobes, bacilli more or less irregular, some in the form of a club and others sometimes form hyphae. Abundant in different terrestrial environments, some are industrially important as amino acid producers, such as glutamic and lysine (Corynebacterium glutamicum). Others are pathogens: C. diphtheriae, Mycobacterium tuberculosis (see my post), M. leprae, and some opportunists with low virulence such as Nocardia.

Frankiales, filamentous, such as Frankia, live symbiotically fixing N2 in root nodules of many types of angiosperms.

Micrococcales, with genera such as: Micrococcus, cocci present in water and soil, saprophytes and opportunists, useful for biodegradation of contaminants and some in meat products, have very resistant cysts (see my post on microbial persistence); Cellulomonas, cellulose-degrading bacilli of soil, by glucanases; Arthrobacter (synonymous Siderocapsa) are common aerobic bacilli and cocci in the soil, some used for glutamic production and for bioremediation, some nylon degraders have even been described, and their DNA is the most persistent of permafrost, more 300,000 years (see my post); Brevibacterium linens is located on human skin, produces thioesters, the typical stink of feet, and is also used in cheeses (Munster, Limburger, etc.).

Propionibacteriales, such as Propionibacterium, anaerobic bacilli that synthesize propionic from sugars and from lactic acid. They may also use fumarate, by a peculiar fermentation with ATPase. Present in gut microbiota and animal skin, some of them are the cause of human acne (reclassified as Cutibacterium acnes) (see also my post). Others are important for the production of Vitamin B12 and dairy products, especially Swiss cheeses with “eyes” (Emmental and others).

Streptomycetales, with the important genus Streptomyces, are the most well-known Actinobacteria, with more than 500 species. Aerobes, form a complex mycelium of well-developed hyphae and are dispersed with aerial spores from structures comparable to mycelial fungi, but prokaryotic. Abundant in the soil and decaying vegetation, they produce geosmin and 2-methylisoborneol, which give the characteristic “ground” odour, invertebrate-attracting compounds that help bacteria disperse their spores. They have a complex secondary metabolism, which is why they are so important in industry: antibacterial antibiotics (streptomycin, neomycin, tetracycline, etc.), antifungals (nystatin), antiparasitic, anticancer, and also for the heterologous expression of eukaryotic proteins.

9. Fibrobacteres

Within the Hydrobacteria in Figure 4, together with Chlorobi and Bacteroidetes they belong to the FCB superphylum, formerly called Sphingobacteria by Cavalier-Smith. They are strict anaerobic gram-negative bacilli. They include some of the main cellulolytic bacteria in the rumen, such as Fibrobacter. They degrade beta-glucans, producing formate, acetate and succinate.

10a. Chlorobi

They are considered a single phylum together with Bacteroidetes, in the FCB superphylum. They are mainly green sulphur bacteria, gram-negative bacilli or cocci, strict photoautotrophic anaerobes that perform anoxygenic photosynthesis, with bacteriochlorophylls located in chlorosomes and the plasma membrane. They have one photosystem, and they use sulphides as electron donor. They fix CO2 through the reverse citric acid cycle. They can produce sulphates or accumulate elemental S outside the cell. Chlorobium is found on the seabed and lakes, and it is abundant for ex. in the Black Sea.

10b. Bacteroidetes

Also from the FCB superphylum and the same phylum as Chlorobi, they are non-sporulated strictly anaerobic gram-negative (outer membrane) bacilli, exclusive from the gastrointestinal tract of animals, where they are among the most abundant bacteria, notably Bacteroides and also Prevotella. They metabolize carbohydrates (polysaccharides especially) and other compounds such as bile salts, producing short chain fatty acids, beneficial for the host (see my post on Bacteroides). However, some of them can be pathogenic if they go outside the digestive tract. It seems that the Prevotella/Bacteroides ratio in humans is higher in high fibre diets and lower body weight. Flavobacterium is a known Bacteroidetes fish pathogen.

11. Planctomycetes

Of the PVC superphylum, e.g. Planctomyces, they are anaerobic gram-negative bacteria very particular: ovoid with a pseudo-stem appendix terminated in a substrate-adherent structure, with membrane invaginations reminiscent of eukaryotic cell structures, and cell wall with almost no glycopeptide. They reproduce by budding and generate free flagellate forms that then will be sessile. They live in waters, both sweet and marine. Some such as Brocardia contain a membranous structure, anammoxosome, where an important metabolism for the nitrogen cycle occurs: anaerobic ammonium oxidation (Anammox) with nitrite, producing N2.

12a. Verrucomicrobia

Also of the superphylum PVC, and considered of the same phylum with Chlamydiae, there are few described species. They are similar in shape to warts and are anaerobic gram-negative, isolated from soil, water and human faeces. Akkermansia, an aerotolerant, present in the human gut microbiota, has been linked to lower obesity and lower incidence of related diseases, thanks to maintaining the mucin-degrading mucosa, contributing to barrier function.

12b. Chlamydiae

Also of the superphylum PVC and of the same phylum with Verrucomicrobia, they are gram-negative cocci, obligate intracellular of eukaryotes, many animal pathogens and some protozoa symbionts. They have two forms (like viruses): the extracellular, particulate or elemental body, only 0.3 μm, which generates the intracytoplasmic reticular form of 0.5 μm by endocytosis. Chlamydia infections are the most common sexually transmitted bacterial disease.

13. Acidobacteria

Such as Acidobacterium, they are aerobic or facultative or anaerobic gram-negative bacilli, heterotrophic, many of them oligotrophic, most are acidophilic (pH 3-6), and they have capsules with a lot of exopolysaccharide. Although poorly isolated in culture, they are ubiquitous, especially in soils, where up to 50% of the present bacteria, where many are symbiotic in the rhizosphere of plants. Some are biodegraders of aromatic compounds (Holophaga) and / or metal scavengers (Geothrix).

14. Nitrospirae

Monophyletic phylum, they are gram-negative aerobic helical- or comma-shaped (vibrions). Hard to isolate, they are present in marine ecosystems forming biofilms but also in wet land or in activated sludge from sewage treatment plants, biofilters and others. They are nitrifying bacteria, making nitrite oxidation, e.g. Nitrospira.

Proteobacteria

As we see in in Figure 4, most of the remaining phyla contain this term. They are the largest and most metabolically diverse group of bacteria, and they have in common to be gram-negative with lipopolysaccharide outer membrane. They are almost half of the sequenced prokaryotes and include both phototrophs and heterotrophs with a common evolutionary origin, which are supposed to be anoxygenic phototrophs such as the purple bacteria (e.g. Rhodospirillum). For this reason and for having a phylogenetic relationship based on 16S rRNA, Woese (1987) called them “Purple and related bacteria” and established the first alpha, beta, gamma and delta subdivisions. Shortly after, Stackebrandt et al (1988) proposed the vocable Proteobacteria, based on the Greek god Proteus, by the analogy that it could take multiple forms.

15a. Deltaproteobacteria

Considered common phylum with Thermodesulfobacteria, they include two groups:

Mixobacteria (order Myxococcales), aerobes that live in soils, heterotrophs consuming insoluble organic matter, that move by gliding. They have very large genomes with respect to other bacteria, 10 Mbp, some up to 16 Mbp. The biological cycle (e.g. Myxococcus) is complex: vegetative forms are gliding bacilli that are grouped into fruiting bodies (by quorum sensing of contact) of different shapes and colours, and that give resistant spherical mixospores. Some are antibiotic producers and others like Sorangium, produce anti-tumour drugs.

The other large group is the strict anaerobic sulphur bacteria. The disassimilating reduction of sulphates in marine and water purification environments accounts for 50% of the mineralization of organic matter. They include these two orders:

Desulfovibrionales, the main sulphate reducing bacteria: Desulfovibrio, Desulfobacter and others. They are flagellate rods or curved bacilli that live in aqueous environments, where they degrade organic matter, by anaerobic respiration using sulphate as an electron acceptor. They produce SH2, which, in addition to stinking, reacts with metals, corrodes them, and produces e.g. FeS. They are considered ones of the oldest microbes on Earth and are very important in the S cycle.

Desulforomonadales reduce elemental S, also by anaerobic respiration, but they can also use other inorganic compounds such as nitrate, Fe3+ and other metals. They also produce SH2. Geobacter is one of the main genera, used for biodegradation and bioremediation of pollutants, and it is being studied for the design of microbial cells that generate electricity thanks to the conductivity of the biofilms they form.

15b. Thermodesulfobacteria

Same phylum as Deltaproteobacteria. They are sulphate reducers, thermophilic and hyperthermophilic, bacilli isolated from thermal sources, seabed and hydrothermal vents. The most known, Thermodesulfobacterium, has a membrane lipid (phosphoaminopentanotetrol) found only in the archaea. Geothermobacterium, isolated in Yellowstone, has an optimum temperature of 85-90°C, the highest of bacteria, and reduces Fe3+.

16. Oligoflexia

Phylogenetically related to Deltaproteobacteria, this phylum includes Bdellovibrio and other predators of gram-negative bacteria. They are small (about 1 µm) aerobic curved rods (vibrions), with a polar flagellum that allows them to swim over 100 times their body-length per second. In its biological cycle, the motile free form attaches to a bacterium prey, penetrates it, forms a spherical complex within the host, uses hydrolases to digest proteins and DNA from the host, and grows filamentous, the host is lysed and the filament is separated in 3-6 free daughter cells, all in 4 h.

17. Spirochaetes

Spirochetes are gram-negative bacteria with an outer membrane, and characteristic spiral or helical shape. They are rather long (3 to 200 µm), due to the axial filament, set of flagella, located in the periplasmic space. This filament shrinks, allowing motility. They are anaerobic heterotrophs or facultative of diverse aquatic environments. Spirochaeta is free-living and non-pathogenic, but other genera are pathogenic, such as Leptospira (leptospirosis), Borrelia (tick-borne Lyme disease), or Treponema (syphilis and tropical diseases).

18. Epsilonproteobacteria

They are gram-negative heterotrophic, most of them microaerophilic, motile and curved, spiral or helical. The most well-known are symbionts or pathogens in the digestive tract of animals, including humans. Campylobacter is a pathogen mainly of poultry, and in humans from eating contaminated food. Helicobacter is very common in the stomach causing ulcers and gastritis. Arcobacter is an emerging pathogen that, in addition to being found in the digestive tract of animals, can also be a seafood contaminant.

The phylum also includes quite a few non-pathogenic isolates isolated from deep-sea vents and marine sediments, such as Sulfurimonas.

19. Alphaproteobacteria

Large and very diverse phylum of gram-negative with outer membrane in the cell wall. Together with betaproteobacteria and gammaproteobacteria, they constitute a clear monophyletic group, of common origin, which are the most typical Proteobacteria (Figure 4). The whole of these 3 phyla was named Rhodobacteria by Cavalier-Smith in 1987.

Alphaproteobacteria include the following main orders:

Rhodobacterales, such as Rhodobacter, a study model for bacterial anoxygenic photosynthesis. They are the so-called non-sulphur purple bacteria (due to their color resulting from bacteriochlorophylls plus carotenes), to differentiate them from sulphur purple bacteria (Chromatiales, within Gammaproteobacteria). They have a wide variety of metabolisms: photosynthesis, lithotrophy and aerobic and anaerobic respiration, and are present in all aqueous environments.

Rhodospirillales, which also includes other non-sulphur purple bacteria (Rhodospirillum) with broad metabolic capabilities and a spiral shape. Others are acetic bacteria (Acetobacter, Gluconobacter, Gluconacetobacter, Komagataeibacter and others), aerobic bacilli well known for respiratory oxidative metabolism, oxidizing sugars and ethanol to acetic acid, producing the vinegars. Another is Magnetospirillum, a spiral-shaped microaerophile containing magnetosomes, organelles with magnetite (Fe3O4), that allow them to orient themselves with the geomagnetic field.

Caulobacterales, such as Caulobacter, curved rods, are oligotrophic in freshwater. They have a characteristic cell cycle with two differentiated forms: one with a peduncle attached to a substrate, which splitting asymmetrically generates a flagella free form that ends up in a pedunculate form.

Magnetococcales, with Magnetococcus, marine cocci with characteristics similar to Magnetospirillum, including magnetosomes.

Rhizobiales, with Rhizobium, the well-known N2 fixers, endosymbionts in the leguminous root nodules. In the same order are: Agrobacterium, which causes plant tumours by transferring its DNA, and for that reason it is widely used in genetic engineering (A. tumefaciens); Rhodopseudomonas, another photosynthetic non-sulphur purple bacterium of water and soil; Brucella, small coccobacilli pathogens of humans and other animals; and Nitrobacter, nitrifying chemolithotroph bacilli, which oxidize nitrite to nitrate.

Ricketssiales are obligate endosymbionts of eukaryotic cells, many pathogens, such as Rickettsia, pleomorphic human pathogen (cocci, bacilli, etc.) transmitted by arthropods, and Wolbachia, which infects many arthropods and nematodes. As shown in Figure 4, the phylogenetic relationship suggests that mitochondria (endosymbionts) developed from this group.

Sphingomonadales, such as Sphingomonas, are strict aerobic bacilli, with glycosphingolipids in the outer membrane, instead of the lipopolysaccharides of other gram-negatives, and with typical yellow colonies. Present in many different environments, where they survive with low nutrient concentrations and a versatile ability to biodegrade compounds, including aromatics and other xenobiotics. That is why they are used for bioremediation, and their extracellular polymers (sphingans) are used in the food industry. Zymomonas are facultative anaerobic bacilli, with the unique feature of bacteria doing alcoholic fermentation, in Mexican pulque, or African palm wine, degrading sugars to pyruvate by the Entner-Doudoroff pathway.

20. Betaproteobacteria

A diverse phylum of aerobic or facultative groups, of varied forms, with metabolic versatility, both heterotrophic and chemolithotrophic, and some phototrophic. The main orders are:

Burkholderiales, most are motile aerobic bacilli: Burkholderia and Bordetella, human and other animal pathogens; Ralstonia and Achromobacter are common in soils and are opportunistic pathogens; Alkaligenes are also opportunistic pathogens, and some produce polyhydroxybutyrate, a biopolymer; Oxalobacter is exceptionally anaerobic, found in the human microbiota and rumen of ruminants, where it degrades oxalic, benefitting the host, by peculiar fermentation with ATPase; Sphaerotilus natans are filamentous (up to 0.5 mm) heterotrophic aerobic growing within a long, tubular sheath, are present in contaminated water and prevent active sludge flocculation; Acidovorax, known pathogen of cucurbitaceous crops (pumpkin, zucchini, cucumber, watermelon, etc.); Ideonella sakaiensis is a degrader of PET plastic (see my post).

Neisseriales, nonmobile aerobic diplococci, colonize the mucosa of many animals without causing damage, and only two species are human pathogens: Neisseria meningitidis and N. gonorrhoeae.

Nitrosomonadales, diverse order with a few bacilli aerobic chemolithotrophs, such as Nitrosomonas, the most well-known of nitrifiers, which oxidize ammonium to nitrite, or Thiobacillus, the known sulphur (colourless) oxidizing bacteria and also of Fe2+, and Gallionella, helical and filamentous rods, which oxidizes iron but is microaerophilic. Methylophilus are (with other bacteria and fungi) methylotrophs, which use C1 compounds as a substrate, such as methanol, methane, and therefore are environmentally beneficial. Spirillum are spiral-shaped heterotrophic microaerophiles present in freshwater containing organic matter.

Rhodocyclales, as Zoogloea, are motile aerobic bacilli, relevant to aerobic wastewater treatments, mainly in activated sludge process, where they degrade organic matter and help to form biological flocs that settle down.

21. Gammaproteobacteria

The last big phylum of Proteobacteria includes many important groups scientifically, medically and environmentally, with these main orders:

Xanthomonadales, aerobic rods, most are phytopathogens such as Xanthomonas species that affect the crops of citrus fruits, tomatoes, rice and others, and Xylella in the vine. Some are opportunistic pathogens for humans.

Chromatiales, are the purple sulphur bacteria (Chromatium, Thiocapsa), which perform anoxygenic photosynthesis from sulphides or thiosulphate, producing elemental S. They have inner membranes with bacteriochlorophyll and carotenes and are present in the anoxic areas of lakes and other aquatic habitats such as intertidal areas.

Methylococcales, such as Methylococcus, are another large group of methylotrophs, which use methane as their source of energy and carbon, and which is oxidized to formaldehyde, and then this is assimilated by the ribulose monophosphate cycle, on inner disk-shaped membranes. perpendicular to the cell wall.

Thiotricales, are mainly chemolithotrophs, with cocci shape clustered into filaments, which accumulate sulphur granules. Beggiatoa lives in waters containing H2S, and oxidizes it to sulphur, but is also heterotrophic. Thiomargarita namibiensis, found in marine sediments, is the largest bacterium ever found, up to 0.7 mm in diameter, and accumulates S in the periplasm and nitrate in vacuoles, as it is also nitrifying.

Legionellae, with Legionella, aerobic pleomorphic bacilli, known pneumonia-causing pathogens (legionellosis), and other respiratory diseases. Most infections are due to poorly maintained cooling towers.

Oceanospirillales are a metabolically diverse group but all prefer or need a high salt content, such as Halomonas, motile aerobic rods.

Pseudomonodales include many motile bacilli or motile coccobacilli (with polar flagella), strict aerobic heterotrophs and oxidase positive. Pseudomonas is one of the most ubiquitous bacterial genera in many terrestrial and aquatic habitats, with some plant pathogens and other opportunists in humans, and causes food spoilage. Some of them (P. syringae) facilitate the nucleation of ice crystals causing plant tissue freezing or cloud condensation or artificial snow formation (see my post). On the other hand, their large and diverse aerobic catabolic ability makes them useful for wastewater treatment and bioremediation of hydrocarbons and other complex organic compounds. Azotobacter are cocci or oval-shaped, motile, with thick-walled cysts and extracellular lime strength, free-living in soils, with a relevant role in the N-cycle as Nfixers. Acinetobacter is also common in soils, where they mineralize aromatic compounds, and some are opportunistic pathogens, especially in hospitals. Moraxella are similar, commensals of animal mucosa but also some pathogens.

Aeromonadales, such as Aeromonas, facultatively anaerobic bacilli, morphologically similar to Enterobacterales, they are present in aqueous environments, and are a common cause of gastroenteritis and other water-borne infections or contaminated food.

Vibrionales, are vibrions or coccobacilli, motile facultative anaerobic, present in aqueous media, among which there are quite a few pathogens of humans, such as Vibrio cholerae, and of other animals, especially fish. However, it also includes most bioluminescent bacteria: Photobacterium, Aliivibrio and many Vibrio, from marine environments, many symbiotics of fish and other animals. The light produced (490 nm, cyan, blue-green) is due to luciferase-linked lux-flavin chromophores, reacting with oxygen and fatty acid reducing reactions.

Pasteurellales, they are bacilli or pleomorphic, without flagella, facultative anaerobes and oxidase positive (unlike Enterobacteriales), commensals at the mucosa surfaces of birds and mammals, and some are pathogens. Pasteurella are pleomorphic and zoonotic pathogens. Many Haemophilus are human pathogens, and H. influenzae was the first genome to be sequenced, by Craig Venter group in 1995.

Enterobacterales, it includes most of the well-known gram-negatives with outer membrane, some of them pathogens. They include the so-called enterobacteria, family Enterobacteriaceae, among which there are symbionts and pathogens, especially in the animals’ gut. They are facultative anaerobes, perform the mixed-acid fermentation and other metabolisms, have no cytochrome c oxidase, and most are motile bacilli or coccobacilli with peritrichous flagella. Of particular note is Escherichia coli, probably the most well-known bacterium and model organism for biochemical, genetic and molecular knowledge. Some E. coli are pathogens, other opportunists, many commensals, and some even beneficial members of the gut microbiota, and used as probiotics. The following are also Enterobacteriaceae: Salmonella, the intracellular pathogen of many animals by endotoxins, causing typhoid fever humans, food-borne infections, and other pathogens; Shigella, a pathogen in humans and other primates, also with endotoxins, it is a major cause of diarrhea; Yersinia pestis, coccobacillus pathogen well known for epidemics; Klebsiella, ubiquitous in many environments, is usual commensal of human mucosa and gut; Enterobacter are thermotolerant faecal coliforms (they grow at 44.5°C), opportunistic pathogens, and some are useful in dairy products; Citrobacter can use citrate as their only source of C, are also ubiquitous in many environments, and most are non-pathogenic

Of the same order Enterobacterales but of other families: Erwinia, pathogen of plants; Hafnia, commensal of the human gastrointestinal tract, used as a lactic ferment, and possible probiotic; Proteus, opportunistic pathogen; and finally, Thorsellia, present in the gut microbiota of the Anopheles mosquito, which could be used genetically modified against the mosquito to prevent malaria transmission.

Alphabetical LIST of 147 bacterial GENERA, with the corresponding Phyla

(link by clicking on the Phylum)

This is not a static, fixed list:  please, if you notice any other genera that you consider important, please tell me and I’ll incorporate it.

Genus Phylum
Acetobacter 19. Alphaproteobacteria
Achromobacter 20. Betaproteobacteria
Acidobacterium 13. Acidobacteria
Acidovorax 20. Betaproteobacteria
Acinetobacter 21. Gammaproteobacteria
Actinomyces 8. Actinobacteria
Aerococcus 5. Firmicutes
Aeromonas 21. Gammaproteobacteria
Agrobacterium 19. Alphaproteobacteria
Akkermansia 12a. Verrucomicrobia
Alcaligenes 20. Betaproteobacteria
Allivibrio 21. Gammaproteobacteria
Anabaena 4. Cyanobacteria
Aquifex 1. Aquificae
Arcobacter 18. Epsilonproteobacteria
Arthrobacter 8. Actinobacteria
Azotobacter 21. Gammaproteobacteria
Bacillus 5. Firmicutes
Bacteroides 10b. Bacteroidetes
Bdellovibrio 16. Oligoflexia
Beggiatoa 21. Gammaproteobacteria
Bifidobacterium 8. Actinobacteria
Bordetella 20. Betaproteobacteria
Borrelia 17. Spirochaetes
Brevibacterium 8. Actinobacteria
Brevibacterium 8. Actinobacteria
Brocardia 11. Planctomycetes
Brucella 19. Alphaproteobacteria
Burkholderia 20. Betaproteobacteria
Campylobacter 18. Epsilonproteobacteria
Carnobacterium 5. Firmicutes
Caulobacter 19. Alphaproteobacteria
Cellulomonas 8. Actinobacteria
Chlamydia 12b. Chlamydiae
Chlorobium 10a. Chlorobi
Chloroflexus 7. Chloroflexi
Christensenella 5. Firmicutes
Chromatium 21. Gammaproteobacteria
Chroococcus 4. Cyanobacteria
Citrobacter 21. Gammaproteobacteria
Clostridium 5. Firmicutes
Coprococcus 5. Firmicutes
Corynebacterium 8. Actinobacteria
Cutibacterium 8. Actinobacteria
Deinococcus 3. Deinococcus – Thermus
Desulfobacter 15a. Deltaproteobacteria
Desulphovibrio 15a. Deltaproteobacteria
Enterobacter 21. Gammaproteobacteria
Enterococcus 5. Firmicutes
Erwinia 21. Gammaproteobacteria
Escherichia 21. Gammaproteobacteria
Eubacterium 5. Firmicutes
Faecalibacterium 5. Firmicutes
Fibrobacter 9. Fibrobacteres
Flavobacterium 10b. Bacteroidetes
Frankia 8. Actinobacteria
Fructobacillus 5. Firmicutes
Gallionella 20. Betaproteobacteria
Geobacter 15a. Deltaproteobacteria
Geothermobacterium 15b. Thermodesulfobacteria
Geothrix 13. Acidobacteria
Gluconacetobacter 19. Alphaproteobacteria
Gluconobacter 19. Alphaproteobacteria
Haemophilus 21. Gammaproteobacteria
Hafnia 21. Gammaproteobacteria
Halomonas 21. Gammaproteobacteria
Helicobacter 18. Epsilonproteobacteria
Heliobacteria 5. Firmicutes
Holophaga 13. Acidobacteria
Hydrogenobacter 1. Aquificae1. Aquificae
Ideonella 20. Betaproteobacteria
Klebsiella 21. Gammaproteobacteria
Komagataeibacter 19. Alphaproteobacteria
Lactobacillus 5. Firmicutes
Lactococcus 5. Firmicutes
Legionella 21. Gammaproteobacteria
Leptospira 17. Spirochaetes
Leuconostoc 5. Firmicutes
Listeria 5. Firmicutes
Magnetococcus 19. Alphaproteobacteria
Magnetospirillum 19. Alphaproteobacteria
Methylococcus 21. Gammaproteobacteria
Methylophilus 20. Betaproteobacteria
Micrococcus 8. Actinobacteria
Moraxella 21. Gammaproteobacteria
Mycobacterium 8. Actinobacteria
Mycoplasma 6. Tenericutes
Myxococcus 15a. Deltaproteobacteria
Neisseria 20. Betaproteobacteria
Nitrosomonas 20. Betaproteobacteria
Nitrobacter 19. Alphaproteobacteria
Nitrospira 14. Nitrospirae
Nocardia 8. Actinobacteria
Nostoc 4. Cyanobacteria
Oenococcus 5. Firmicutes
Oscillatoria 4. Cyanobacteria
Oxalobacter 20. Betaproteobacteria
Paenibacillus 5. Firmicutes
Pasteurella 21. Gammaproteobacteria
Pediococcus 5. Firmicutes
Phascolarctobacterium 5. Firmicutes
Photobacterium 21. Gammaproteobacteria
Planctomyces 11. Planctomycetes
Pleurocapsa 4. Cyanobacteria
Prevotella 10b. Bacteroidetes
Propionibacterium 8. Actinobacteria
Proteus 21. Gammaproteobacteria
Pseudomonas 21. Gammaproteobacteria
Ralstonia 20. Betaproteobacteria
Rhizobium 19. Alphaproteobacteria
Rhodobacter 19. Alphaproteobacteria
Rhodopseudomonas 19. Alphaproteobacteria
Rhodospirillum 19. Alphaproteobacteria
Rickettsia 19. Alphaproteobacteria
Ruminococcus 5. Firmicutes
Salmonella 21. Gammaproteobacteria
Selenomonas 5. Firmicutes
Shigella 21. Gammaproteobacteria
Sorangium 15a. Deltaproteobacteria
Sphaerothilus 20. Betaproteobacteria
Sphingomonas 19. Alphaproteobacteria
Spirillum 20. Betaproteobacteria
Spirochaeta 17. Spirochaetes
Spirulina 4. Cyanobacteria
Staphylococcus 5. Firmicutes
Streptococcus 5. Firmicutes
Streptomyces 8. Actinobacteria
Sulfurimonas 18. Epsilonproteobacteria
Synechococcus 4. Cyanobacteria
Thermodesulfobacterium 15b. Thermodesulfobacteria
Thermomicrobium 7. Chloroflexi
Thermotoga 2. Thermotogae
Thermus 3. Deinococcus – Thermus
Thiobacillus 20. Betaproteobacteria
Thiocapsa 21. Gammaproteobacteria
Thiomargarita 21. Gammaproteobacteria
Thorsellia 21. Gammaproteobacteria
Treponema 17. Spirochaetes
Veillonella 5. Firmicutes
Vibrio 21. Gammaproteobacteria
Weissella 5. Firmicutes
Wolbachia 19. Alphaproteobacteria
Xanthomonas 21. Gammaproteobacteria
Xylella 21. Gammaproteobacteria
Yersinia 21. Gammaproteobacteria
Zoogloea 20. Betaproteobacteria
Zymomonas 19. Alphaproteobacteria

Bibliography

Bacterial phyla, Wikipedia

Bacterial taxonomy, Wikipedia

Cavalier-Smith T (1993) Kingdom protozoa and its 18 phyla. Microbiol Reviews 57, 953-94

Hug LA et al. (2016) A new view of the tree of life. Nat Microbiol. 1, 16048

Lang JM, Darling AE, Eisen JA (2013) Phylogeny of bacterial and archaeal genomes using conserved genes: Supertrees and supermatrices. PLoS ONE 8(4): e62510

Lengeler JW, Drews G, Schlegel HG (1999) Biology of the Prokaryotes. Blackwell Science.

Madigan M, Bender KS, Buckley DH, Sattley WM, Stahl DA (2017) Brock Biology of Microorganisms, 15th ed. Pearson.

MicrobeWiki: https://microbewiki.kenyon.edu/index.php/MicrobeWiki

NCBI, National Center for Biotechnology Information: https://www.ncbi.nlm.nih.gov

Parte AC (2014) LPSN – list of prokaryotic names with standing in nomenclature. Nucleic Acids Research 42, D1, D613-D616.

Stackebrandt E, Murray RGE, Trüper HG (1988) Proteobacteria classis nov., a name for the phylogenetic taxon that includes the “Purple bacteria and their relatives”. Int J Syst Bact 38, 321-325

Tortora GJ, Funke BR, Case CL, Weber D, Bair W. (2018) Microbiology: an Introduction. 13th ed. Pearson.

Whitman WB, ed. (2015) Bergey’s manual of systematics of archaea and bacteria. ISBN 9781118960608.

Whittaker RH (1969) New concepts of Kingdoms of organisms. Science 163, 150-160.

Wiley J, Sherwood L, Woolverton CJ (2017) Prescott’s Microbiology, 10th ed. McGraw Hill Education.

Woese CR (1987). Bacterial evolution. Microbiological Reviews 51(2): 221–71

About Albert Bordons

Professor at "Universitat Rovira i Virgili" in Tarragona. Born in Barcelona 1951. Scientific areas: microbiology, biochemistry, biotechnology, oenology. I like: nature, biological sciences, photography, mountains, ... Languages: catalan (first one), spanish, french, english and some italian.

Posted on 16/04/2020, in Bacteria, Evolution, Genetics and molecular biology, Microbiota and tagged , , , , , . Bookmark the permalink. 3 Comments.

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