| "Candidatus Scalindua" | |
|---|---|
Scientific classification  | |
| Domain: | Bacteria |
| Phylum: | Planctomycetota |
| Class: | Planctomycetia |
| Order: | Planctomycetales |
| Family: | Brocadiaceae |
| Genus: | "Ca.Scalindua" Schmid et al. 2003 |
| Species | |
See text | |
" Candidatus Scalindua" is a bacterial genus, and a proposed member of the order Planctomycetales. [1] These bacteria lack peptidoglycan in their cell wall and have a compartmentalized cytoplasm. They are ammonium oxidizing bacteria found in marine environments.
" Candidatus Scalindua" is a bacterial genus, member of the order Planctomycetales. These bacteria lack peptidoglycan in their cell wall and have a compartmentalized cytoplasm. [1] "Candidatus Scalindua" spp. can be further divided into three species: Scalindua brodae, Scalindua wagneri, and Scalindua sorokinii. They are ammonium oxidising bacteria found in marine environments. The genus "Ca. Scalindua" are the most abundant anammox bacteria in marine environments, so they are vital to the Earth's nitrogen cycle. [1]
Members of the proposed genus Scalindua are anaerobic anammox (ammonium oxidizing) bacteria. [2] The ammonium-oxidizing reaction composes a significant part of the global nitrogen cycle; by some estimates it is the cause of up to 50% of total nitrogen turnover in marine environments. [3] It consists of the oxidization of ammonium using nitrite as an electron acceptor (both are fixed nitrogen) and subsequent generation of nitrogen gas:
“NH4+ + NO2− = N2 + 2H2O (ΔG° = -357 kj mol-1)” [4]
This reaction uses nitrite (NO2−) as a terminal electron acceptor to produce nitric oxide (NO), which is then combined with ammonium (NH4+) to produce the intermediate hydrazine (N2H4) and water (H2O). Hydrazine, a very reactive molecule also used for rocket fuel, is then oxidized into nitrogen gas (N2). [5] The half reactions may be represented as:
“NO2− + 2H+ + e− = NO + H2O (E° = +0.38V)
NO + NH4+ + 2H+ + 3e− = N2H4 + H2O (E° = +0.06V)
N2H4 = N2 + 4H+ + 4e− (E° = -0.75V)” [4]
This metabolic pathway occurs anaerobically, something that was once considered impossible as ammonium was thought to be inert in the absence of oxygen. [6] In fact, the presence of oxygen over 2 μM inhibits the anammox pathway, which is why members of the proposed genus Scalindua respire anaerobically. [4]
These reactions occur in a large membrane-bound cellular organelle called the anammoxosome, which contains an electron transport chain and an ATPase that pumps protons back into the cytoplasm from the anammoxosome lumen. It functions much like a mitochondrion in eukaryotic cells. The anammoxosome membrane is invaginated (folded in upon itself) to increase its surface area. [7] The existence of membrane-bound cellular organelles is very unusual in prokaryotes, and appears to be limited to the members of the phylum Planctomycetota. [3]
Anammox bacteria, including those belonging to Ca. Scalindua, fix carbon using carbon dioxide as a carbon source. Metagenomic analysis has revealed the presence of genes responsible for the “reductive acetyl-CoA pathway (also known as the Wood-Ljungdahl pathway) which allows for the creation of the precursor molecule acetyl CoA from carbon dioxide. [8] [9]
Ammonium and methane are known to be relatively difficult to activate with reactions catalyzed by enzymes that make use of high-potential oxygen radicals, which are unavailable to anaerobic life, leading to the assumption that both compounds were effectively inactive in low oxygen environments. [6] Throughout the 1970s and 80s, results from several independent studies exploring relationships between methane and sulfate concentrations in marine sediments found indications that anaerobic methane oxidation was in fact a widespread occurrence. [6] It was not until 1999 that the existence of anaerobic ammonium oxidation was first discovered in a wastewater treatment plant in The Netherlands and given the name “anammox,” which would later prove to be a key player as part of the marine nitrogen cycle. [6] [10] [11] Some known anammox bacteria include Candidatus Scalindua, Kuenenia, Brocadia, Jettenia and Anammoxoglobus. [12] Of these bacteria, only Candidatus Scalindua spp. can be found in marine ecosystems. [12]
During the past, many microorganisms such as anammox bacteria may have escaped discovery due to their relatively low growth rates requiring very efficient biomass retention absent from classical methods of cultivation. [13] With the use of biofilms to improve the culturability of organisms that naturally occur in biofilms, combined with the use of biomass retention to study slowly growing microorganisms under substrate limitation, a technique using sequencing batch reactors (SBR) was developed for the long-term enrichment, cultivation, and quantitative analysis of a very slowly growing microbial community. [13] Phylogenetic analysis of the first anammox bacteria discovered concluded that the organisms branched deeply in the phylum, Planctomycetota, which was previously considered to be of limited environmental importance. [10] Nitrogen loses that could only be explained by the process of anammox continued to be discovered in freshwater waste-treatment facilities around the world including North America, Asia, and multiple regions throughout Europe. [14] The role of bacteria belonging to Ca. Scalindua in the marine nitrogen cycle has been found to be of important in the reduction of nitrate to atmospheric nitrogen in anoxic regions of the ocean. [11] Since primary productivity in the ocean is often limited by nitrogen availability, the removal of usable nitrogen in sediments through anammox by Ca. Scalindua may significantly affect biogeochemical cycles in anoxic waters. [11] In certain regions, such as the Golfo Dulce in Costa Rica, up to %35 of atmospheric nitrogen production in the water column can be attributed to Ca. Scalindua spp. [11] In other regions such as the Black Sea, the world's largest anoxic basin, characterized by a large gradient in ammonium concentrations (high levels in deep water tapering off to only trace amounts in the suboxic zone), the apparent ammonium sink in the suboxic zone was identified to be the result of anaerobic oxidation by bacteria belonging to Ca. Scalindua spp. [15]
Organisms within the genus “Candidatus Scalindua” are classified as gram-negative chemolithoautotrophic bacteria. [16] This means that their carbon and energy largely come from inorganic sources. Furthermore, bacteria in the genus Ca. Scalindua are obligate anaerobes, so they are unable live in oxygen-rich environments. [16] [1]
As with all other organisms within the order Planctomycetota, the cell wall does not contain peptidoglycan. [1] [17] The cells are spherical in shape, with a diameter of roughly one micrometer, and contain compartmentalized cytoplasms. [1] Furthermore, organisms within Ca. Scalindua have two inner membranes instead of one inner and one outer membrane surrounding the cell wall. [18] Cells within Ca. Scalindua wagenri are oriented into compact clusters, whereas Ca. Scalindua brodae's cells are more loosely packed. [1] All cells within Ca. Scalindua spp. contain unique organelles called anammoxosomes, which are membrane bound within the cytoplasm. [1] [19] Anammoxosomes are where anaerobic ammonium oxidation process occurs. The membrane that surrounds anammoxosomes in anammox bacteria contains unique lipids called “ladderane” lipids, which contain a series of cyclobutane ring structures. [19] However, all other membranes within anammox bacteria are similar to organisms within the order Planctomycetales.
According to Strous et al., anammox-capability is the result of a singular evolutionary event. All anammox bacteria are descendants of the same ancient Planctomycetota species that first evolved the anammox reaction. [6] Members of the proposed genus Ca. Scalindua are the most widespread of all the genera of anammox bacteria described so far. [1]
Currently, all anammox bacteria are thought to be members of the order Brocadiales. [20]
Members belonging to Candidatus Scalindua are close genetic relatives to other anammox bacteria within the order Planctomycetales, such as "Candidatus Brocadia" and "Candidatus Kuenenia". [1] Yet, members of Ca. Scalindua are quite different from other proposed genera of anammox bacteria in terms of their 16S ribosomal RNA sequences. [1] For example, Candidatus Scalindua and Candidatus Brocadia only share 85% similarity in their 16S rRNA sequences. [1] "Candidatus Scalindua" can be further divided into the following three species: "Ca. Scalindua brodae", "Ca. Scalindua wagneri", and "Ca. Scalindua sorokinii". [1] [21] Cells belonging to Ca. Scalindua spp. are the most abundant members of Anammox bacteria known to date, making it very important in the world's aquatic environments.
The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) [22] and National Center for Biotechnology Information (NCBI) [23]
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Species incertae sedis:
Candidatus Scalindua sp. is the only taxonomic group of ammonium-oxidizing bacteria found in the Black Sea, the Benguela Oxygen minimum zone off the coast of Namibia, and the estuary of the Randers Fjord, Denmark. [27] Globally, members of Candidatus Scalindua spp. have been discovered in all marine environments that have been studied; most other marine bacteria are not this wide spread. [27] [12]
The ideal environmental conditions, with regards to temperature, pH and salinity for “Candidatus Scalindua sp.” are as follows: 10 to 30 °C, 6.0 to 8.5 pH and 0.8% to 4.0% salinity. No ammonium oxidizing activity was observed when salinity was 0%. [28]
Marine sediments located in deep-sea methane seeps contain anammox bacteria associated with Candidatus Scalindua spp.; these bacteria likely have a substantial role in the nitrogen cycle in the sediments. [29]
Two types of anammox bacteria belonging to Ca. Scalindua (59% abundance) and Ca. Kuenenia (41% abundance), have been found in the non-rhizosphere area of the saltmarsh grass Spartina alterniflora while only Ca. Scalindua was present within the rhizosphere. Moreover, it was in 1.5 times greater abundance than for other anammox bacterial in the non-rhizosphere sediments. [30] Changing seasons do not affect the make-up of anammox-capable bacterial communities within the sediments in and around the rhizosphere; however, there was always a greater abundance of anammox bacteria within the rhizosphere that peaked in abundance during July and October when temperatures are warmest. [30] During the warmer parts of the year both communities of anammox bacteria within and outside of the rhizosphere are more active, and produce more N2 with the bacteria in the rhizosphere producing almost twice as much N2. [30]
Bacteria belonging to "Ca. Scalindua wagneri" are often used in wastewater treatment plants to reduce the adverse effects of nitrification and denitrification on the local environment. [31] The use of anammox bacteria in wastewater treatment plants has a drastically reduced cost compared to previous denitrification methods. Furthermore, it is a much more environmentally friendly method. [8]
The Planctomycetota are a phylum of widely distributed bacteria, occurring in both aquatic and terrestrial habitats. They play a considerable role in global carbon and nitrogen cycles, with many species of this phylum capable of anaerobic ammonium oxidation, also known as anammox. Many Planctomycetota occur in relatively high abundance as biofilms, often associating with other organisms such as macroalgae and marine sponges.
Anammox, an abbreviation for "anaerobic ammonium oxidation", is a globally important microbial process of the nitrogen cycle that takes place in many natural environments. The bacteria mediating this process were identified in 1999, and were a great surprise for the scientific community. In the anammox reaction, nitrite and ammonium ions are converted directly into diatomic nitrogen and water.
Methanotrophs are prokaryotes that metabolize methane as their source of carbon and chemical energy. They are bacteria or archaea, can grow aerobically or anaerobically, and require single-carbon compounds to survive.
Denitrifying bacteria are a diverse group of bacteria that encompass many different phyla. This group of bacteria, together with denitrifying fungi and archaea, is capable of performing denitrification as part of the nitrogen cycle. Denitrification is performed by a variety of denitrifying bacteria that are widely distributed in soils and sediments and that use oxidized nitrogen compounds such as nitrate and nitrite in the absence of oxygen as a terminal electron acceptor. They metabolize nitrogenous compounds using various enzymes, including nitrate reductase (NAR), nitrite reductase (NIR), nitric oxide reductase (NOR) and nitrous oxide reductase (NOS), turning nitrogen oxides back to nitrogen gas or nitrous oxide.
Microbial metabolism is the means by which a microbe obtains the energy and nutrients it needs to live and reproduce. Microbes use many different types of metabolic strategies and species can often be differentiated from each other based on metabolic characteristics. The specific metabolic properties of a microbe are the major factors in determining that microbe's ecological niche, and often allow for that microbe to be useful in industrial processes or responsible for biogeochemical cycles.
A lithoautotroph is an organism which derives energy from reactions of reduced compounds of mineral (inorganic) origin. Two types of lithoautotrophs are distinguished by their energy source; photolithoautotrophs derive their energy from light while chemolithoautotrophs (chemolithotrophs or chemoautotrophs) derive their energy from chemical reactions. Chemolithoautotrophs are exclusively microbes. Photolithoautotrophs include macroflora such as plants; these do not possess the ability to use mineral sources of reduced compounds for energy. Most chemolithoautotrophs belong to the domain Bacteria, while some belong to the domain Archaea. Lithoautotrophic bacteria can only use inorganic molecules as substrates in their energy-releasing reactions. The term "lithotroph" is from Greek lithos (λίθος) meaning "rock" and trōphos (τροφοσ) meaning "consumer"; literally, it may be read "eaters of rock". The "lithotroph" part of the name refers to the fact that these organisms use inorganic elements/compounds as their electron source, while the "autotroph" part of the name refers to their carbon source being CO2. Many lithoautotrophs are extremophiles, but this is not universally so, and some can be found to be the cause of acid mine drainage.
Nitrifying bacteria are chemolithotrophic organisms that include species of genera such as Nitrosomonas, Nitrosococcus, Nitrobacter, Nitrospina, Nitrospira and Nitrococcus. These bacteria get their energy from the oxidation of inorganic nitrogen compounds. Types include ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB). Many species of nitrifying bacteria have complex internal membrane systems that are the location for key enzymes in nitrification: ammonia monooxygenase, hydroxylamine oxidoreductase, and nitrite oxidoreductase.
In chemistry, a ladderane is an organic molecule containing two or more fused cyclobutane rings. The name arises from the resemblance of a series of fused cyclobutane rings to a ladder. Numerous synthetic approaches have been developed for the synthesis of ladderane compounds of various lengths. The mechanisms often involve [2 + 2] photocycloadditions, a useful reaction for creating strained 4-membered rings. Naturally occurring ladderanes have been identified as major components of the anammoxosome membrane of the anammox bacteria, phylum Planctomycetota.
"CandidatusScalindua brodae" is a bacterial member of the order Planctomycetales and therefore lacks peptidoglycan in its cell wall, has a compartmentalized cytoplasm. It is an ammonium oxidising bacteria.
CandidatusScalindua wagneri is a Gram-negative coccoid-shaped bacterium that was first isolated from a wastewater treatment plant. This bacterium is an obligate anaerobic chemolithotroph that undergoes anaerobic ammonium oxidation (anammox). It can be used in the wastewater treatment industry in nitrogen reactors to remove nitrogenous wastes from wastewater without contributing to fixed nitrogen loss and greenhouse gas emission.
Hydrazine oxidoreductase (EC 1.7.99.8, HAO (ambiguous)) is an enzyme with systematic name hydrazine:acceptor oxidoreductase. This enzyme catalyses the following chemical reaction
Nitrososphaera is a mesophilic genus of ammonia-oxidizing Crenarchaeota. The first Nitrososphaera organism was discovered in garden soils at the University of Vienna leading to the categorization of a new genus, family, order and class of Archaea. This genus is contains three distinct species: N. viennensis, Ca. N. gargensis, and Ca N. evergladensis. Nitrososphaera are chemolithoautotrophs and have important biogeochemical roles as nitrifying organisms.
Candidatus Brocadia fulgida is a prokaryotic species of bacteria that performs the anammox process. Fatty acids constitute an enrichment culture for B. fulgida. The species' 16S ribosomal RNA sequence has been determined. During the anammox process, it oxidizes acetate at the highest rate and outcompetes other anammox bacteria, which indicates that it does not incorporate acetate directly into its biomass like other anammox bacteria.
Dissimilatory nitrate reduction to ammonium (DNRA), also known as nitrate/nitrite ammonification, is the result of anaerobic respiration by chemoorganoheterotrophic microbes using nitrate (NO3−) as an electron acceptor for respiration. In anaerobic conditions microbes which undertake DNRA oxidise organic matter and use nitrate (rather than oxygen) as an electron acceptor, reducing it to nitrite, and then to ammonium (NO3− → NO2− → NH4+).
An oxygen minimum zone (OMZ) is characterized as an oxygen-deficient layer in the world's oceans. Typically found between 200 m to 1500 m deep below regions of high productivity, such as the western coasts of continents. OMZs can be seasonal following the spring-summer upwelling season. Upwelling of nutrient-rich water leads to high productivity and labile organic matter, that is respired by heterotrophs as it sinks down the water column. High respiration rates deplete the oxygen in the water column to concentrations of 2 mg/L or less forming the OMZ. OMZs are expanding, with increasing ocean deoxygenation. Under these oxygen-starved conditions, energy is diverted from higher trophic levels to microbial communities that have evolved to use other biogeochemical species instead of oxygen, these species include nitrate, nitrite, sulphate etc. Several Bacteria and Archea have adapted to live in these environments by using these alternate chemical species and thrive. The most abundant phyla in OMZs are Pseudomonadota, Bacteroidota, Actinomycetota, and Planctomycetota.
NC10 is a bacterial phylum with candidate status, meaning its members remain uncultured to date. The difficulty in producing lab cultures may be linked to low growth rates and other limiting growth factors.
CandidatusAnammoxoglobus propionicus is an anammox bacteria that is taxonomically in the phylum of Planctomycetota. Anammoxoglobus propionicus is an interest to many researchers due to its ability to reduce nitrite and oxidize ammonium into nitrogen gas and water.
Candidatus "Methylomirabilis oxyfera" is a candidate species of Gram-negative bacteria belonging to the NC10 phylum, characterized for its capacity to couple anaerobic methane oxidation with nitrite reduction in anoxic environments. To acquire oxygen for methane oxidation, M. oxyfera utilizes an intra-aerobic pathway through the reduction of nitrite (NO2) to dinitrogen (N2) and oxygen.
"Candidatus Brocadia" is a candidatus genus of bacteria, meaning that while it is well-characterized, it has not been grown as a pure culture yet. Due to this, much of what is known about Candidatus species has been discovered using culture-independent techniques such as metagenomic sequence analysis.
Anammox is a wastewater treatment technique that removes nitrogen using anaerobic ammonium oxidation (anammox). This process is performed by anammox bacteria which are autotrophic, meaning they do not need organic carbon for their metabolism to function. Instead, the metabolism of anammox bacteria convert ammonium and nitrite into dinitrogen gas. Anammox bacteria are a wastewater treatment technique and wastewater treatment facilities are in the process of implementing anammox-based technologies to further enhance ammonia and nitrogen removal.
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