The tidy story
Across the thirteen cores, the archaeal share of the DNA fell where the
nitrogen-fixing rhizobia rose. The correlation was strong - Spearman's
ρ = ,
ranking the cores rather than trusting their raw values - and the
two-group split between legume and non-legume patches was itself significant
(p = ).
Read forward, that is a mechanism: fixed nitrogen reaches the soil, the
archaea have less ammonia to oxidize, and their numbers fall. It is the kind
of result a paper is built around.
So ask the cheap question first. Would a number that strong turn up even if
the archaea were not answering to the legumes at all? Here it would, and the
rest of this page is why.
The result was real, but it was not specific
A correlation is only evidence for the story told about it if it is
specific to the players in that story. So the fixers' correlation
with the archaea was ranked against the same correlation computed for every
other reasonably abundant genus - all
that cleared a small
abundance and prevalence floor. If the nitrogen mechanism were doing the
work, the fixers should sit at the top of that ranking.
They did not. The nitrogen-fixers ranked
, and
unrelated genera - groups with no known part in nitrogen fixation -
tracked the archaea at least as closely, past a threshold of
ρ = .
A story that singles out the legumes cannot explain why so many groups that
have nothing to do with them follow the archaea just as faithfully.
Two duller explanations were ruled out before drawing that conclusion. The
first is compositional closure: in a fixed total of reads, a slice as large
and variable as the archaeal share
(% to
% here) pushes almost
everything else the other way by arithmetic alone. Re-run on centered
log-ratio abundances, which are free of that constraint, the association
survived
(ρ = ,
p = ), with
genera still
past the line. Closure did not manufacture it, so the association was
genuine. What failed was its specificity.
What the archaea were actually tracking
That negative result pointed at something. If dozens of
unrelated genera all follow the archaeal share, the simplest reason is that
the whole community varies along one dominant direction and the archaeal
share is simply a position along it. That is directly checkable. The leading
axis of the ordination - the same projection the home page plots -
accounted for % of the
variation between cores, and the archaeal share tracked it tightly:
ρ = ,
p = .
So the clover correlation and the fescue correlation and a dozen others were
not a dozen separate facts about a dozen plants. They were all the same fact:
the community sorted along a single axis, the plants sat at different places
on it, and the archaea rose and fell with the axis. The
legume signal was real because the legumes really did sit at one end - but
the mechanism the number seemed to name is not established, because the same
number fell out of the community's overall structure without any nitrogen
story at all.
And it was not a simple growth-strategy gradient either
The obvious next question is what that dominant axis is. One
standing candidate is a life-history gradient: soils are often described as
running from slow, resource-poor communities of oligotrophs to fast,
resource-rich communities of copiotrophs, and fast growers tend to carry more
copies of the 16S gene per genome.
If the axis were that gradient, community-weighted copy number should climb
along it.
Each core's community-weighted mean copy number was computed from
,
a published per-taxon database, covering
% of reads. It ranged
from to
copies per genome across the
thirteen cores, so there was real variation for the check to find.
It found very little. Copy number did not differ between legume and non-legume
cores
(p = ),
showed no clean gradient along the dominant axis, and barely tracked the
archaeal share
(ρ = ).
The same test ruled out the dull artifact it was first run to catch -
the archaea-to-bacteria ratio was not an effect of copy number - but it
does not name the axis. Whatever organizes this community, a plain
copiotroph-to-oligotroph reading is not it.