| Candidatus Atelocyanobacterium thalassa | |
|---|---|
 | |
| Black arrow: the nitroplast insideB. bigelowii (motile phase) | |
Scientific classification | |
| Domain: | Bacteria |
| Kingdom: | Bacillati |
| Phylum: | Cyanobacteriota |
| Class: | Cyanophyceae |
| Order: | Chroococcales |
| Family: | Aphanothecaceae |
| Genus: | Ca. Atelocyanobacterium |
| Species: | Ca. Atelocyanobacterium thalassa |
| Binomial name | |
| Candidatus Atelocyanobacterium thalassa Thompson et al., 2012[1] | |
| Synonyms | |
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Candidatus Atelocyanobacterium thalassa, also referred to asUCYN-A, is anitrogen-fixing species ofcyanobacteria that exists exclusively as anobligate symbiont. Despite being found in measurable quantities throughout the world's oceans,A. thalassa is not known to be free-living in any environment.[1][2] Unlike typical cyanobacteria, its genome has undergone massive reduction, losing the genes forRuBisCO,photosystem II, and theTCA cycle.[3] Consequently, it possesses no independent means of fixing carbon or generating energy through photosynthesis, rendering it entirely dependent on its host (so far only known to beBraarudosphaera bigelowii and a closely-related unnamed species).[3]
This partnership is characterized by a strict metabolic exchange:A. thalassa fixes atmospheric nitrogen intoammonium for the host, while the host provides the essential carbon products the bacterium can no longer produce for itself.[4] While various sublineages are distributed across diverse marine niches—fromoligotrophic open waters to coastal regions—every known version ofA. thalassa remains confined within a host cell.[2]
In the more integrated form, specifically the UCYN-A2 sublineage[5] within the algaBraarudosphaera bigelowii, the relationship has progressed so far that the bacterium is now considered a trueorganelle, termed anitroplast.[6][7][a] In these cases, the "bacterium" is imported with nuclear-encoded proteins and its division is synchronized with the host, mirroring the evolutionary history ofmitochondria andchloroplasts.[6] This discovery of the first nitrogen-fixing organelle in aeukaryote has major implications foragricultural science, as it demonstrates a biological pathway for potentially engineering crops that do not require nitrogen fertilizer.[6]
Members ofA. thalassa are spheroid in shape and are 1-2 μm in diameter,[8] and providenitrogen to ocean regions by fixing non biologically available atmospheric nitrogen into biologically availableammonium that other marinemicroorganisms can use.[1] There are many sublineages ofA. thalassa that are distributed across a wide range of marine environments and host organisms.[2] It appears that some sublineages ofA. thalassa have a preference foroligotrophic ocean waters while other sublineages prefer coastal waters.[9] Much is still unknown about all ofA. thalassa's hosts and host preferences.[1]
In 1998, Jonathan Zehr, an ocean ecologist at theUniversity of California, Santa Cruz, and his colleagues found an unknown DNA sequence that appeared to be for an unknown nitrogen-fixingcyanobacterium in thePacific Ocean, which they calledUCYN-A (unicellular cyanobacterial group A).[10] At the same time, Kyoko Hagino, a paleontologist atKochi University, was working to culture the host organism,B. bigelowii.[11][8]
Nitrogen fixation, which is the reduction of N2 to biologically available nitrogen, is an important source of N for aquatic ecosystems. For many decades, N2 fixation was vastly underestimated.[citation needed] The assumption that N2 fixation only occurred viaTrichodesmium andRichelia led to the conclusion that in the oceans, nitrogen output exceeded the input.[citation needed] However, researchers found that thenitrogenase complex has variable evolutionary histories.[citation needed] The use of thepolymerase chain reaction (PCR), removed the requirement of cultivation or microscopy to identify N2 fixing microorganisms. As a result, marine N2-fixing microorganisms other thanTrichodesimum were found by sequencing PCR-amplified fragments of the gene nitrogenase (nifH). Nitrogenase is the enzyme that catalyzes nitrogen fixation, and studies have shown thatnifH is widely distributed throughout the different parts of the ocean.[12]
In 1989, a shortnifH gene sequence was discovered,[citation needed] and 15 years later it was revealed to be an unusual cyanobacterium that is widely distributed.[13] The microbe was originally given the name UCYN-A for "unicellular cyanobacteria group A". In research published in 1998,nifH sequences were amplified directly from water collected in the Pacific and Atlantic Oceans, and shown to be from bacterial, unicellular cyanobacterialnifH,Trichodesmium and diatom symbionts.[10] With the use of cultivation-independent PCR andquantitative PCR (qPCR) targeting thenifH gene, studies found thatA. thalassa is distributed in many ocean regions, showing that the oceanic plankton contain a broader range of nitrogen-fixing microorganisms than was previously believed.
The distribution ofA. thalassa is cosmopolitan and is found throughout the world's oceans including theNorth Sea,Mediterranean Sea,Adriatic Sea,Red Sea,Arabian Sea,South China Sea, and theCoral Sea.,[14] further reinforcing its significant role in nitrogen fixation.[14] AlthoughA. thalassa is ubiquitous, its abundance is highly regulated by various abiotic factors such as temperature and nutrients.[15] Studies have shown that it occupies cooler waters compared to otherdiazotrophs.[16]
There are four main defined sublineages ofA. thalassa, namely, UCYN-A1, UCYN-A2, UCYN-A3, and UCYN-A4 (see§ Diversity below); studies have shown that these groups are adapted to different marine environments.[2] UCYN-A1 and UCYN-A3 co-exist in open-ocean oligotrophic waters. while UCYN-A2 and UCYN-A4 co-exist in coastal waters.[2][9] UCYN-A2 is typically found in high latitude temperate coastal waters. In addition, it can also be found co-occurring with UCYN-A4 in the coastal bodies of water. UCYN-A3 was found to be in greater abundance in the surface of the open ocean in the subtropics. In addition, UCYN-A3 has only been found to co-occur with UCYN-A1 thus far.
Atelocyanobacterium thalassa is categorized as aphotoheterotroph. Complete genome analysis reveals a reduced-size genome of 1.44 megabases, and the lack of pathways needed for metabolic self-sufficiency common to cyanobacteria.[17]Genes are lacking forphotosystem II of thephotosynthetic apparatus,RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase), and enzymes of theCalvin andtricarboxylic acid (TCA) cycle.[18][19] Due to the lack of metabolically essential genes,A. thalassa requires external sources of carbon and other biosynthetic compounds.[17] As well,A. thalassa lacks thetricarboxylic acid cycle, but expresses a putative dicarboxylic-acid transporter.[17] This suggests thatA. thalassa fills its requirement for dicarboxylic acids from an external source.[17] The complete or partial lack of biosynthetic enzymes required for valine, leucine, isoleucine, phenylalanine, tyrosine and tryptophan biosynthesis further suggests the need for external sources of amino acids.[17] However,A. thalassa still possesses the Fe-III transport genes (afuABC), which should allow for the transport of Fe-III into the cell.[3]
Atelocyanobacterium thalassa is anobligate symbiote of the calcifyinghaptophyte algaBraarudosphaera bigelowii.[1] Stable isotope experiments revealed thatA. thalassa fixes15N2 and exchanges fixed nitrogen with the partner, while H13CO3- was fixed byB. bigelowii and exchanged toA. thalassa.A. thalassa receives ~16% of the total carbon of the symbiotic partner, and exchanges ~85 -95% of total fixed nitrogen in return.[1][20]
Atelocyanobacterium thalassa must live in close physical association with its metabolically dependent symbiosis partner; however, the details of the physical interaction are still unclear due to a lack of clear microscopy images.[3]Atelocyanobacterium thalassa may be a trueendosymbiont and fully enclosed within the host's cell membrane or has molecular mechanisms to allow for secure attachment and transfer of metabolites.[20] This symbiotic connection must not allow the passage of oxygen while maintaining an exchange of fixed nitrogen and carbon.[20] Such close symbiosis also requires signalling pathways between the partners and synchronized growth.[20]
A stable co-culture of UCYN-A2 and its host was obtained and subjected to imaging studies. The UCYN-A2 "nitroplast" lineage imports a wide variety proteins from the host, triggered by a unique signal sequence, making it subject to tight control by the host cell. Its light-dark cycle is kept in sync with the host cell by hostcryptochrome proteins. Several of its metabolic pathways are only complete with the help of host proteins.[7]
Atelocyanobacterium thalassa is unicellular, hence it does not have specialized cellular compartments (heterocysts) to protect thenitrogenase (nifH) from oxygen exposure. Other nitrogen-fixing organisms employ temporal separation by fixing nitrogen only at night-time, however,A. thalassa has been found to express thenifH gene during the daylight.[21][18] This is possible due to the absence ofphotosystem II and, therefore, oxygen and transcriptional control.[18][22] It is hypothesized that the day-time nitrogen-fixation is more energy-efficient than night-time fixation common in otherdiazotrophs because light energy can be used directly for the energy-intensive nitrogen fixation.[22]
The lifecycle ofA. thalassa is not well understood. As an obligate endosymbiont,A. thalassa is thought to be unable to survive outside of the host, suggesting its entire life cycle takes place inside of the host.[3] The division and replication ofA. thalassa are at least partially under the control of the host cell.[23] It is thought that a signal transduction pathway exists to regulate the amount ofA. thalassa cells within the host to ensure a sufficient amount ofA. thalassa cells are supplied to the host's daughter cell during cell division.[3]
UCYN-A2's cell division cadence is kept in sync with the host, like the mitochondria and the chloroplasts.[7]
Genomic analysis ofA. thalassa shows a wide variety ofnifH gene sequences. Thus, this group of cyanobacteria can be divided into genetically distinct sublineages, four of which have been identified and defined.Sequences belonging to A. thalassa have been found in nearly all oceanic bodies.[14]
The lineages ofA. thalassa are split by their determining oligotypes. There is a very high level of similarity between all sublineages in their amino-acid sequences, but some variance was found in theirnifH sequences. The oligotypes ofA. thalassa are based on its nitrogenase (nifH) sequences, and reveal thirteen positions of variance (entropy).[2] The variances would cause different oligotypes/sublineages ofA. thalassa to be found in different relative abundances and have different impacts on the ecosystems where they are found. Four main sublineages have been identified from oligotype analysis, and their respective oligotypes are: UCYN-A1/Oligo1, UCYN-A2/Oligo2, UCYN-A3/Oligo3, UCYN-A4/Oligo4. As many as 8 sublineages have been distinguished.[24]
UCYN-A1 was the most abundant oligotype found across the oceans.[2] The UCYN-A1 sublineage has an abundance of nitrogenase in a range of 104 – 107 copies ofnifH per litre.[25] UCYN-A1 and UCYN-A2 also have a significantly reduced genome size. UCYN-A2 differs from UCYN-A1 in that its oligo2 oligotyping has 10/13 differing positions of entropy from oligo1 (UCYN-A1). They also have different hosts. UCYN-A3 differs from UCYN-A1 with its oligo3 differing from oligo1 with an entropy position difference of 8/13. UCYN-A4 also differs from UCYN-A1 by 8/13 entropy positions in a different set.
| Lineage | Environment | Hosts | Other traits | Genome? |
|---|---|---|---|---|
| UCYN-A1 | Open ocean | UnnamedChrysochromulina sp.[26]: Fig.S7 (1–3 μm)[27] | GCA_000025125.1 (full) | |
| UCYN-A2 | Coastal | B. bigelowii (4–10 μm)[27] | Nitroplast | GCA_020885515.1 (full) |
| UCYN-A3 | Open ocean[26] | B. bigelowii | Unpublished (~13%) | |
| UCYN-A4 | Coastal | B. bigelowii genotype I[28] | Nitroplast-like (possibly more derived than A2)[28] | GCA_051971635.1 (near-full) |
Oligotypes are used becausenifH is more easily detected in an intact form environmental samples compared to fullmetagenomes that require a larger amount of samples as well as sequencing work. Where available, however, full genomes are able to show more information. Complete genomes of the A1 and A2 sublineages, combined with amolecular clock approach, show that the two lineages diverged in thelate Cretaceous (~90 million years ago), corroborated by fossil records ofB. bigelowii going back about 100 million years. These lineages have likely co-evolved with their hosts.[27]
As ofGTDB Release 10-RS226 (April 2025), the NCBI GenBank contains 8A. thalassa genomes of sufficient quality and completeness for analysis. GTDB assigns UCYN-A1 (GCA_000025125.1 + 5 others) and UCYN-A2 (GCA_020885515.1 + 1 other) to two separate species-level clusters.[29]
Cornejo‐Castilloet al, 2019.nifH, maximum likelihood. Taxonomy corrected per NCBI and GTDB where applicable.[26]
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Cornejo‐Castilloet al, 2019. Phylogenomic (165 protein-coding sequences), maximum likelihood. Taxonomy corrected per NCBI and GTDB where applicable.[26]: Fig.S6
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Pleurocapsa sp. PCC 7327 | |||||||||||||||||||||||||||||||||||||||||||
The phylogenomic result is considered more representative of the life-history of organisms than the single-locusnifH result.[26]
As other endosymbiotic organelles, nitroplast genome lost many genes and many essential biosynthetic pathways of them should be supported by the proteins produced in the nucleus.
After analyzing the genome and proteome in the nitroplast, scientists found that three types of proteins coexist in nitoplast, UCYN-1 encoded proteins,B. bigelowii encoded proteins (nucleus encoded), and the proteins encoded by both (“redundancies”).
EachB. bigelowii encoded protein contains a special sequence named uTP (UCYN transition peptide), an extension at 3’ end of functional regions, which make them much longer than orthologous proteins found in other species. The uTP sequences assist the transition of proteins from nucleus to nitroplast. Actually, someB. bigelowii encoded proteins were not detected in nitroplast, but the existence of uTP sequence suggested that they might be transported into nitroplast.
Some proteins, like PyrC in the pyrimidine biosynthesis pathway, are produced in both nucleus and nitroplast. The scientists said that such redundancies might be the key reason why UCYN-1 lost genes faster than chromatophore inPaulinella, whose endosymbiosis event happened in similar time.[7]
The discovery of nitroplasts challenges previous notions about the exclusivity of nitrogen fixation toprokaryotic organisms. Understanding the structure and function of nitroplasts opens up possibilities forgenetic engineering in plants.[6] By incorporating genes responsible for nitroplast function, researchers aim to develop crops capable of fixing their own nitrogen, potentially reducing the need for nitrogen-based fertilizers and mitigating environmental damage.[6]