User:Chibadi/Atelocyanobacterim Thalassa (previously known as UCYN-A)

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= History (Discovery) = 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 largely underestimated. It was assumed that N2 fixation only occurred via Trichodesmium and Richelia, leading to the conclusion that, in ocean, loss of N exceeded the input. However, researchers found that the nitrogenase fixation complex has variable evolutionary histories. With the discovery of new organisms, such as diverse cyanobacteria (including UCYN-A) and non-cyanobacterial diazotrophs, the N losses might be balanced by N input.

Normally, microorganisms that contain nitrogenase to fix nitrogen are archaea and bacteria, but not eukaryotes. However, with symbiotic interactions between Archaea or Bacteria, N2 fixation can be found in eukaryotes. With the utilization of polymerase chain reaction (PCR), the requirements of cultivation or microscopy to identify N2 fixing microorganism is no longer needed. As a result, marine N2-fixing microorganisms other than Trichodesimum were found by sequencing PCR-amplified nitrogenase gene (nifH) fragments.

In 1989, a short nifH gene sequence was discovered. Then, in the following 15 years, it was revealed to be an unusual cyanobacterium (UCYN-A) which is widely distributed. In the research published in 1998, nifH was amplified directly from oceanic waters in BAT and HOT sites as sequences from bacterial, unicellular cyanobacterial nifH, and Trichodesmium and diatom symbionts. According to this study, the oceanic plankton contains a wider range of nitrogen-fixing microorganisms than was previously believed. With the use of cultivation-independent PCR and quantitative PCR (qPCR) targeting the nifH gene, studies found that UCYN-A distributed in many ocean regions. In the study published in 2008, the utilization of generic UCYN PCR primers for FISH probes gave the first UCYN-A microscopic images.

There was an enigma about UCYN-A that remained a mystery for many years. Nitrogenase protein and enzyme activity can be inhibited by oxygen, so cyanobacteria normally separate photosynthesis and N2-fixation spatially or temporally. However, the uncultivated UCYN-A had the highest levels of nifH expression during the day when photosynthesis should be functional. Further research showed that the UCYN-A genome lacks PSII genes. Thus, unable to generate O2 could explain why UCYN-A expresses nitrogenase during the daytime. In 2010, the complete genome was closed. Besides PSII, the UCYN-A genome also lacks RuBisCO, TCA cycle, and other metabolic pathways.

With the lack of so many metabolic, it was likely that UCYN had a symbiosis relationship with other organisms that was not be found in the previous analysis. The reason was that the symbiosis was so fragile that the partners were separated during sample preparation. After changing sampling methods, the haptophyte partner was identified and visualized, and the partner cell was closely related to Braarudosphaera bigelowii. The name Candidatus Atelocyanobacterium thalassa was given to UCYN-A, meaning incomplete marine cyanobacterium. Following studies then revealed the pattern of symbiosis relationship between UCYN-A and haptophyte.

= Diversity = UCYN-A has been found in measurable amounts in all oceanic bodies. The lineages of UCYN-A are split by their determining oligotypes. There is a very high level of similarity between all sublineages in their amino acid sequencing but there was some variance found in their nifH sequences. The analyzed oligotype of UCYN-A is its nitrogenase (nifH) sequencing.After an oligotyping analysis of the nifH sequence, it was determined that there were thirteen positions of entropy. The variances would give different oligotypes/ sublineages which would have different impacts on the ecosystems they would be found in and relative abundance.

Oligotyping
There are four main sublineages that have arisen from oligotype analysis and their respective oligotype are: UCYN-A1/ Oligo1, UCYN-A2/Oligo2, UCYN-A3/Oligo3, UCYN-A4/Oligo4. UCYN-A1 was found to be the most abundant oligotyping found across the oceans. The UCYN-A1 sublineage has an abundance of nitrogenase in a range of 104 - 107 copies of nifH per litre. UCYN-A1 and UCYN-A2 also have a greatly 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). UCYN-A3 differs from UCYN-A1 with its oligo3 differing from oligo1 with a entropy position difference of 8/13. UCYN-A4 also differs from UCYN-A1 by 8/13 entropy positions but a different set.

Obligate photoheterotroph
UCYN-A is categorized as an obligate photoheterotroph. Complete genome assembly reveals a reduced size genome (only 1.44 megabases) and the lack of pathways needed for metabolic self-sufficiency. UCYN-A also lacks all genes for photosystem II and RuBisCO (ribulose-1,5-bisphosphate car­boxylase/oxygenase). Due to the lack of metabolically essential genes, UCYN-A requires external sources of carbon and other biosynthetic compounds. UCYN-A completely lacks the TCA cycle. This absence coupled with the presence of a putative dicarboxylic-acid transporter suggests that UCYN-A fills its requirement for dicarboxylic acids from an external source. 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. UCYN-A still possesses the Fe-III transport genes (afuABC) which allow Fe-III transport into the cell.

Obligate Symbiosis
UCYN-A has been discovered to be in symbiotic relationship with an algae, the calcifying haptophyte Braarudosphaera bigelowii. Stable isotope experiments revealed that UCYN-A fixed 15N2 and exchanged fixed nitrogen with the partner, while H13CO3- was fixed by B. bigelowii and exchanged to UCYN-A. UCYN-A receives ~16% of the total carbon of the symbiotic partner, and exchanges ~85 -95% of total fixed nitrogen in return.

UCYN-A 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. UCYN-A may be a true endosymbiont and fully enclosed within the host’s cell membrane or has molecular mechanisms to allow for secure attachment and transfer of metabolites. This symbiotic connection must not allow the passage of oxygen, while maintaining an exchange of fixed nitrogen and carbon. Such close symbiosis also requires signalling pathways between the partners and synchronized growth.

Daytime N-fixation
UCYN-A is unicellular, hence it cannot have specialized cellular compartments (heterocysts) to protect the nitrogenase (NifH) from oxygen exposure. Other nitrogen-fixing organisms employ temporal separation by fixing nitrogen only at night-time, however, UCYN-A has been found to express nifH gene during the day-time. This is possible due to the absence of photosystem II and, therefore, oxygen and transcriptional control. It is hypothesized that the day-time nitrogen-fixation is more energy-efficient than night-time fixation common in other diazotrophs.

Range
UCYN-A1 and UCYN-A2 can be found in coastal regions and are co-occurring. UCYN-A2 is normally found in high latitude temperate coastal waters. In addition it can 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 is only found to be co-occurring with UCYN-A1.