A Nitrogen Fixation

Nitrogen CycleWe return for November with a new Brian Thomas Creation Science Update, titled Newfound Nitrogen Harmony Saves Tropical Forest Trees. It is not a promising sign.

As should really be common knowledge, there’s no shortage of nitrogen in the atmosphere. This is, however, in the form of plain old N₂, which while it contains the right element is not very useful for life on Earth. This makes usable – “fixed” – nitrogen a major limiting factor for plant growth. Humans can fix nitrogen for fertiliser directly from the atmosphere via industrial-scale processes which aren’t readily available to the biosphere at large, but other sources do exist. Lightning, for example, is supposed to fix nitrogen into NO₂, but this probably isn’t an approach you can rely upon on the long term. Animals seem to have no difficulty in obtaining nitrogen for themselves – i.e. by eating other organisms – and in an unusual reversal of roles certain plants and fungi will actively capture and kill (small) animals for their nitrogen and other nutrients.

But probably the most important source of nitrogen are bacteria that are capable of fixing it for themselves. Many of these live freely in the soil, contributing to a background level of fixed nitrogen generally available in the ground, but some exist in a famous mutualistic relationship with some plants – mostly legumes – in which they provide the host plant nitrogen in exchange for other goods and services. The sum total of all these processes, plus the de-fixing of nitrogen by other bacteria and its return to the atmosphere, collectively makes the “nitrogen cycle.” We’ve known about this for a while, I should think.

That brings up to recent the paper in Nature, Key role of symbiotic dinitrogen fixation in tropical forest secondary succession, that is the inspiration for Thomas’ article. This paper observes that plants that are capable of fixing nitrogen via this mutualistic process are better able to sequester carbon dioxide, which has obvious implications re global warming. They looked at the composition of forests rebounding from clearance over time, and noted that nitrogen fixation rates dropped substantially, as did carbon sequestration:

We also observed a dramatic trend in N2 fixation across the forest chronosequence. Ecosystem nodulation and total N2 fixation increased steeply to a maximum in our 12-year forests (29 kg N ha−1 yr−1), and then decreased to low levels in 80-year forests. At 300 years, fixation recovered to 8% of maximum. Because our sampling was limited to specific forest ages, we cannot evaluate whether even higher fixation may have occurred between 5 and 30 years of forest age.

They asked whether this was due to nitrogen fixing plants ceased to be present in the forest or whether they simply wound down their fixation operations over time. They were able to determine that it was the latter that had occurred:

We further asked whether our observed fixation trend was generated by, first, N2-fixing species that always fix but are progressively excluded from the community as nitrogen is replenished (that is, obligate fixation); or, second, N2-fixing species that persist over time but that turn fixation on or off depending on their nitrogen balance (that is, facultative fixation). This distinction is significant because the first theory implies that the ecosystem capacity for fixation disappears over time, whereas the second theory implies that the capacity is functionally ensured throughout forest succession.

Our results support the second theory. The proportion of trees with confirmed ability to fix remained relatively stable in forests 12 years and older, yet the proportion that expressed fixation declined from 71% at 12 years to 23% at 80 years. Furthermore, even when fixing, individuals varied their investment in fixation and nodulation across at least two orders of magnitude independent of species, consistent with facultative fixation at the individual scale. These dynamics indicate that fixers can buffer forest nitrogen supply by upregulating fixation when nitrogen is low.

In other words, when nitrogen is high the plants did not bother investing resources in fixing it for themselves, while they retain the ability to start again should it drop.

Not done yet, the authors of the paper took a quick look at the feedback cycle that controls all this:

We evaluated the nitrogen feedback using a mass-balance model that captures the mechanisms of plant nitrogen demand (net leaf, wood and fine-root growth), plant–soil nitrogen recycling, nitrogen inputs (deposition and fixation) and nitrogen losses. When the model was run with the observed pattern of biomass carbon and nitrogen accumulation, it revealed, first, that the nitrogen demand imposed by vegetation growth greatly exceeded the capacity of internal recycling to supply plant nitrogen in the first approximately 25 years; second, that the resulting nitrogen deficit was highest when biomass accumulation was steepest in early succession, and declined as biomass accumulation decelerated over time; and, third, that the overall shape of the resulting nitrogen deficit recreated the observed changes in fixation across our plots. The field data indicated a lag in fixation in our youngest forests, compared to the model, probably caused by slow establishment and growth of the early tree community.

The fixers are responding in some manner to the lack of nitrogen in the soil in the early years, but as nitrogen ceases to be a precious resource what was once an advantage during a time of scarcity gradually becomes a waste of energy.

So where does Brian Thomas come in? Naturally he thinks that this is all a sign of God’s amazing handiwork:

The authors called this “facultative fixation” and wrote, “These dynamics indicate that fixers can buffer forest nitrogen supply by upregulating fixation when nitrogen is low.” In other words, these trees don’t just have simple on/off switches—they use more complicated self-adjusting dimmer switches connected to nitrogen detectors as a means to control the nitrogen manufacturing pace. “[This] implies that the capacity is functionally ensured throughout forest succession,” according to Nature.

Very little in biology seems to operate via “simple on/off switches,” or truly binary processes in general. Consider the common refrain of cleaning products, “Kills 99.99% of germs.” This isn’t just legal ass-covering – they really can’t guarantee that no germs whatsoever will survive contact with their chemical. In the realm of genetics when a gene is “switched off” – a process which I will have to remember is apparently “simple” for next time Jeff Tomkins tries to tell us how amazing and complex it is – they don’t really turn completely off, just “dimmed” really, really far down to the point that they may as well be. Enzymes massively increase the rate of reactions, but the reactions would have happened anyway – they just would have taken anything up to billions of years to do what a small number of enzymes can do in second, which does not a healthy organism make. In short, the notion that nitrogen fixation in plants is not an on/off system but one that can and will be ramped up and down is not the handiwork of God but an inescapable biological reality.

More generally, Thomas seems unable to grasp why the paper’s authors might be concentrating on scientific and usable results, rather than just signalling their amazement at the majesty of God’s creation and expecting to get published in Nature all the same:

Internal mechanisms—likely networks of biochemical machines—enable these trees to fix nitrogen, a suggestion with which the study authors would probably agree. And yet, they wrote, “The results imply that nitrogen limitation is the mechanism favouring fixers and fixation in young forests.”

Perhaps they intended to simply convey the idea that nitrogen is the key factor in the overarching ecological mechanism.

That would be an allusion to natural selection – nitrogen fixers do well when there is a shortage of nitrogen, which gives them and advantage over other plants – a process which previous posts have shown the Thomas is unable or unwilling to admit to understanding (these articles are so common that I have a post in my drafts folder right now in which I managed to write “Here’s your irregular reminder that Brian Thomas refuses to either” before giving up out of boredom).

Thomas concludes:

Their research focused on identifying environmental factors that affect forest regrowth. But this focus on external aspects may lead readers to quickly gloss over a more significant inference from their remarkable findings. These amazing trees work together over decades to regulate and maintain appropriate nitrogen levels in their own forest soils, showing an entire ecology organized to work in harmony and by design.

This paragraph ends with a ³ indicating a third footnote that from context is likely to be a bible quote, however at time of writing there is no number 3 in the list of footnotes at the bottom of the page. This is appropriate, as I don’t think there is any relevant verse to a process that was not known before the modern biblical canon came to be.

While we’re here, some work has been done on the evolution of the nitrogen fixation symbiosis. It’s not a settled question – we can be pretty confident that it evolved, but we don’t quite know how – but here’s a 2008 paper (press release) which explored the genetics of the interaction. There is a much more common type of symbiosis in plant roots, involving plants and fungi swapping sugars made via photosynthesis for the nutrients that fungi are better able to obtain, and it seems that a key gene involved in that process was lengthened and re-purposed for interaction with bacteria. That’s a scientific investigation of the process – standing around in awe is not.

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