Marine Archaea and the Nitrogen Cycle

by Douglas Bartlett

What is more stirring than to contemplate the cycles of matter in nature? We sense that we witness vital transactions of this planet’s metabolism, a fulfilling thought. Such matters speak particularly loudly to us microbiologists: not only do global fluxes concern the elements of life but are to a great extent driven by microbial activities. In this vein, here is some important news.

Analyses of the nitrogen budget in the oceans suggest that a whole lot more nitrogen is being fixed than was recognized. Who does this extra nitrogen fixation? A recent paper from the laboratory of Victoria Orphan at Cal Tech provides clues that may help balance the nitrogen budget. These researchers studied the syntrophic aggregate of archaea belonging to the ANME-2 group and bacteria belonging to the Desulfosarcina/Desulfococcus. These consortia are a big deal: they consume about 80% of the methane released from seeps in marine sediments. Intriguing here is that their metagenomic analysis revealed that they contain genes for nitrogenase, the key enzyme in nitrogen fixation. So, do these partnerships fix nitrogen? And, if so, does this contribute substantially to that arm of the nitrogen cycle? The answer seems to be yes to the first and, "well, to some extent,” to the second.

How these workers went about this research is instructive. They incubated marine sediment samples with methane and one of several ¹⁵N-labeled N sources and followed the enrichment of the consortia for ¹⁵N over a period of six months. They determined ¹⁵N/¹⁴N by secondary ion mass spectrometry (nanoSIMS) imaging of single cells labeled for bacterial and archeal fluorescent probes. Thus, they could tell the location of the isotopic label in each of the microbial partners. The consortia often consist of spherical cell aggregates having a bacterial shell and an archaeal core. Their data suggest that nitrogen fixation takes place in the archaeal interior and that the archaea use that nitrogen to make reduced nitrogen compounds that they export to the bacterial layer.

Magnitude and distribution of ¹⁵N incorporation in a ANME-2/DSS consortium from sediments incubated with CH₄ and either ¹⁵N₂ (A and E) or ¹⁵NH₄⁺ (I and V) as the nitrogen source. FISH used probes targeting ANME-2 (red) and Desulfobacteraceae (green). NanoSIMS images show the ¹²C ¹⁵N / ¹²C ¹⁴N ratios of the same microbial consortia to demonstrate the location of ¹⁵N incorporation. (The scale range varies between images, with the minimum consistently set to natural abundance ¹⁵N/¹⁴N.) Source.

Cells incubated without sufficient methane or under conditions that inhibit sulfate reduction did not incorporate ¹⁵N dinitrogen. PCR and sequence analyses of nitrogen fixation (nif) genes recovered from the DNA present in the ¹⁵N-labeled incubations displayed similarity to sequences from methanogenic archaea. The nif operon gene order also suggested an archaeal source.

An additional curious aspect of nitrogen fixation in this aggregate is that ANME-2 archaea generate less energy per mole of substrate oxidized than any other microbe known to undertake the energetically expensive process of nitrogen fixation. The consortium grew twenty times faster when provided with ammonium rather than nitrogen as a nitrogen source, but the cells maintained similar respiratory rates under both conditions, apparently adjusting to a lower growth rate when stressed with the need to use more ATP to fix their own nitrogen.

There is much more to be found out. The authors state: …our inventory of marine diazotrophs is incomplete and … we are only beginning to understand the extent and importance of benthic marine N₂ fixation. That may be so, but the trip to this destination will be nothing short of fascinating.

Doug Bartlett is Professor of Microbiology at the Scripps Institute of Oceanography, University of California at San Diego.

Comments

[mathgon]

I had the chance to meet Douglas Bartlett two years ago. One hour was enough to have a more interesting discussion than three years with me director... Archaea, the champions of energy conservation and recycling!

[Mark O. Martin]

What a nice surprise, to see such a fun post from the very nice (and very wise) Doug Bartlett! I particularly appreciated learning how different techniques come together to answer questions about "emergent properties" in the microbial world. Syntrophic relationships are fascinating! Wonderful stuff!