Some archaeal microorganisms have developed sophisticated nano-structures to capture their food: ammonia.
The earth's nitrogen cycle is a bit unheralded, but critical to life nonetheless. Gaseous nitrogen (N2) is all around us, but inert, given its extraordinary chemical stability. It can be broken down by lightning, but little else. It must have been very early in the history of life that the nascent chemical-biological life forms tapped out the geologically available forms of nitrogen, despite being dependent on nitrogen for countless critical aspects of organic chemistry, particularly of nucleic acids, proteins, and nucleotide cofactors. The race was then on to establish a way to capture it from the abundant, if tenaciously bound, dinitrogen of the air. It was thus very early bacteria that developed a way (heavily dependent, unsurprisingly, on catalytic metals like molybdenum and iron) to fix nitrogen, meaning breaking up the triple N≡N bond, and making ammonia, NH3 (or ammonium, NH4+). From there, the geochemical cycle of nitrogen is all down-hill, with organic nitrogen being oxidized to nitric oxide (NO), nitrite (NO2-), nitrate (NO3), and finally denitrification back to N2. Microorganisms obtain energy from all of these steps, some living exclusively on either nitrite or nitrate, oxidizing them as we oxidize carbon with oxygen to make CO2.
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| Nitrosopumilus, as imaged by the authors, showing its corrugated exterior, a layer entirely composed of ammonia collecting elements (can be hexameric or pentameric). Insets show an individual hexagonal complex, in face-on and transverse views. Note also the amazing resolution of other molecules, such as the ribosomes floating about. |
A recent paper looked at one of these denizens beneath our feet, an archaeal species that lives on ammonia, converting it to nitrite, NO2. It is a dominant microbe in its field, in the oceans, in soils, and in sewage treatment plants. The irony is that after we spend prodigious amounts of fossil fuels fixing huge amounts of nitrogen for fertilizer, most of which is wasted, and which today exceeds the entire global budget of naturally fixed nitrogen, we are faced with excess and damaging amounts of nitrogen in our effluent, which is then processed in complex treatment plants by our friends the microbes down the chain of oxidized states, back to gaseous N2.
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| Calculated structure of the ammonia-attracting pore. At right are various close-up views including the negatively charged amino acids (D, E) concentrated at the grooves of the structure, and the pores where ammonium can transit to the cell surface. |
The Nitrosopumilus genus is so successful because it has a remarkable way to capture ammonia from the environment, a way that is roughly two hundred times more efficient than that of its bacterial competitors. Its surface is covered by a curious array of hexagons, which turn out to be ammonia capture sites. In effect, its skin is an (relatively) enormous chemical antenna for ammonia, which is naturally at low concentration in sea water. These authors do a structural study, using the new methods of particle electron microscopy, to show that these hexagons have intensely negatively charged grooves and pores, to which positively charged ammonium ions are attracted. Within this outer shell, but still outside the cell membrane, enzymes at the cell surface transform the captured ammonium to other species such as hydroxylamine, which enforces the ammonium concentration gradient towards the cell surface, and which are then pumped inside.
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| Cartoon model of the ammonium attraction and transit mechanisms of this cell wall. |
It is a clever nano-material and micro-energetic system for concentrating a specific chemical- a method that might inspire human applications for other chemicals that we might need- chemicals whose isolation demands excessive energy, or whose geologic abundance may not last forever.
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