""How many cells are there in a human being?" It
sounds like a question from a nerdy pub quiz. It is also a profound
philosophical inquiry. One answer is around 37trn. This is the number, in a
typical adult weighing 70kg, that trace their descent from the fertilised egg
which brought that human into existence.
Look at it another way, though, and you arrive at a figure
roughly twice as large. That adds in the archaean, bacterial, fungal and
protist cells which occupy the mouth, gut, skin, lungs and almost every other
surface, nook and cranny of the human body. These cells contribute only about
0.3% to a person's body weight. But being, on the whole, much smaller than
"proper" human cells, they are almost equally numerous.
That human beings have this accompanying microbiome is not
news. Nor is it news that, while some of those extra cells are mere passengers,
others are actively beneficial. The idea of symbiosis, in which different
species live together intimately and collaboratively, goes back to the 19th
century.
Yet what started as a finite list of unusual cases has gradually grown
to the point where it is clear that almost every multicellular organism—and
even some single-celled ones—have symbionts.
This suggests to some biologists that the time is ripe for a
"paradigm shift"—a new way for scientists to look at the world. Out,
they say, with the old idea of plants and animals "having a
microbiome", and in with the idea that both are merely parts of a united
meta-organism whose components evolve in concert with each other. And in, too,
with a name for these communal critters: holobionts.
Holistic thinking
One believer in this way of thinking is Thomas Bell, head of
the Leverhulme Centre for the Holobiont at Imperial College, London, which
opened in January. Paradigm shifts have many causes. But one that has helped
tip the balance in this case is a technology called metagenomics. Dr Bell and
his colleagues plan to apply it to a wide range of known and potential holobionts.
Metagenomics analyses simultaneously the genomes of
everything in a sample—be it of soil, water, leaf litter or a mashed-up part of
a plant or animal. Before its invention, trying to work out which microbes were
present in such samples was tricky. Few bugs are amenable to being cultured in
a laboratory, so many were, in effect, invisible to science. These days you can
run a relevant extract of any organism you care to mention through the
metagenomics mill—and if you do so, it is likely to show up as a holobiont.
Dr Bell and his colleagues are looking, in particular, at
insects, amphibians and plants. Besides being eukaryotes—meaning their cells
have proper nuclei and contain complex structures called organelles—these have
little enough in common, evolutionarily speaking. Each group was picked for
study because viewing its members as holobionts rather than individual
creatures is illuminating.
Among insects, the centre is starting with bark beetles and
honeybees. Bark beetles' holobiont nature is emphasised by the fact that some
have evolved special structures called mycangia, which carry fungal spores. The
spores grow thin tendrils called hyphae that allow them to digest wood. That
releases nutrients which the beetles can metabolise. But if these fungi (one of
the best known of which causes Dutch elm disease) get out of hand, they can
devastate entire forests.
Honeybees, meanwhile, are important pollinators, a behaviour
that may result in hives exchanging microbiomes via flowers their members
visit. Some bee populations also show signs of being under stress, possibly
from insecticide use. Several of Dr Bell's colleagues suspect the explanation
for this lies not in the animal part of the holobiont, but rather in its
microbial part.
Amphibians are on the list because many are threatened with
extinction by skin fungi called chytrids, which have been spread from their
Asian homeland by humans. Along with researchers at London Zoo, the centre's
scientists are studying the diversity of amphibian skin microbiomes, and
whether this can give the meta-organism immunity to chytrid infection.
Plants find themselves in the centre's crosshairs because
most are accompanied by a "rhizosphere" of bacteria and fungi
attached to, or even penetrating their roots. The rhizosphere's biochemical
pathways increase the range of nutrients available to the holobiont as a whole.
The rhizosphere is sustained in turn by carbohydrates and other nutrients
synthesised by the holobiont's plant component.
A beneficial alliance
Work like Dr Bell's means the idea of holobionts as a
meaningful category is catching on (see chart). But for it to be accepted
fully, it needs to be disentangled and defined. As Scott Gilbert, a
developmental biologist at Swarthmore College, puts it, "This notion [of
holobionts] challenges and seeks to replace the concept of a monogenomic
individual whose essential identity arises during development, is maintained by
the immune system, and which is selected through evolution." That is a big
claim.
One possible stumbling block is individual continuity. For
organisms as conventionally classified, the link between parent and offspring
is clear. For putative holobionts, it can be less so. Rather than growing from
a single fertilised egg, holobionts have to be assembled. Sometimes the
components are passed between parents and offspring. Humans, for example, are
born with some microbes already in their guts. They pick up others during the
messy process of birth, and more from their mother's milk. In these circumstances
it is easy to see how the various components of a holobiont could co-evolve
into a single, functioning unit.
Plants tend to make their associations horizontally—forming
alliances with microbes already living in the soil in which they germinated. That
might be thought to weaken the case for the resulting alliances behaving as
single evolutionary units. In fact, calculations by Joan Roughgarden, an
evolutionary biologist at Stanford University, show that horizontal
transmission also supports co-evolution, and thus the emergence of true
holobionts.
One piece of evidence to suggest she is right comes from a
study of switchgrass by Thomas Juenger, a biologist at the University Texas,
Austin. If plants and their rhizospheres are evolutionary units, they might be
expected to collect a "core" microbiome that is encouraged into
existence by specific genes in the plant. Switchgrass has three genetically
distinct populations in North America. By comparing these and their associated
rhizospheres, Dr Juenger showed a relationship between a plant's genes,
particularly those associated with its immune system, and which bacteria
thrived in the resulting rhizosphere.
Sometimes, as with bark beetles and their mycangia, the
evolutionary integration of primary host and microbiome is obvious even without
a genetic analysis. Mastotermes darwiniensis, an Australian termite, relies on
gut microbes to break the tough wood it eats into molecules which the
holobiont's animal part can metabolise. Mixotricha paradoxa, one of those
fibre-digesting components, is itself a composite of a protist (a single-celled
eukaryote) and four types of bacteria. Lynn Margulis, the American biologist
who coined the term holobiont in 1991, called this critter "the beast with
five genomes".
Aphids are equally intriguing. All members of this group
carry bacteria of the genus Buchnera, a variety unknown anywhere else. In a
relationship reckoned to date back around 200m years, Buchnera live inside
specialised aphid cells called bacteriocytes. The bacteria are so cossetted
that they have shed most of the genes they started with, relying on their
animal partners to fill the biochemical gaps. In exchange, they synthesise
amino acids the insects are unable to make for themselves.
Nor does the story end there. Many aphids host a second bug,
Hamiltonella defensa, in their bacteriocytes. These critters, which also rely
on Buchnera for their supply of amino acids, kill the larvae of parasitic wasps
that would otherwise consume an aphid alive. But that, in turn, happens only in
the presence of a virus called APSE—an even smaller metaphorical flea in the
holobiont hierarchy.
All that is reminiscent of the most extreme case of
holobiontry: that of organelles called mitochondria and chloroplasts.
Mitochondria generate energy by metabolising glucose, and are found in all
eukaryotes. Chloroplasts engage in photosynthesis, and are restricted to algae
and plants. Both are the distant descendants of formerly free-living bacteria
that began their relationship with the cells they now call home over a billion
years ago. (It was these two cases which led Margulis to coin the term
holobiont.)
The holobionic man
The varying degrees of intimacy on display—from surface
passenger to vital cellular component—do raise the question of where, exactly,
the borders of the term "holobiont" lie. But biology is full of
concepts that are at once fuzzy and useful ("species" is one).
Perhaps the most important job of the concept is to act as a reminder to
biologists never to neglect a possible role for the microbiome in any
phenomenon they are trying to understand. For example, the study of the
evolution of pesticide resistance in insects usually involves the genome of the
insect itself. But resistance by pests called bean bugs to fenitrothion, an
insecticide, is conferred by bacteria of the genus Burkholderia which live in
their guts—important knowledge, if you want to counter that resistance.
And there are even stranger powers brought to holobionts by
their microbial parts. For example, certain bacteria are sensitive to magnetic
fields. Researchers suspect some may have formed alliances with creatures such
as turtles and birds, enabling these animal-based collectives to use Earth's
field to navigate. More familiarly, it is the holobiont nature of dogs (and
also hyenas and other carnivores with anal glands) that enables them to
communicate via scent marks. The odours they deposit this way are created by
bacterial degradation of secretions into these glands.
The best studied animal holobiont of all is Homo sapiens.
Topologically, a human being is a torus—a three-dimensional object with a hole
through the middle. The hole in question is the alimentary canal. Nearly the
whole surface of this torus is home to microbes, though different parts have
different inhabitants. By far the largest numbers of them live in the lower
gut.
These gut microbes extend the digestive capabilities of the
human holobiont in the same way (though not to the same degree) as happens in
termites, by breaking up fibrous plant polymers into smaller molecules that the
other 37trn cells can metabolise. But they produce lots of other molecules,
too, some of which send signals to the holobiont's animal cells. Those cells,
moreover, often signal back.
This signalling seems particularly influential over parts of
the nervous system. Among the molecules secreted by gut bacteria are serotonin,
GABA and catecholamines. All are neurotransmitters, chemicals which carry
impulses between nerve cells. The microbiome is thus an integral part of the
gut-brain axis, the constant neural chatter between the largest group of nerve
cells in the body (the central nervous system) and the second-largest (the
enteric nervous system).
The third big interaction between host and microbiome
involves the immune system. This brokers the deal that keeps the whole show on
the road by preventing any particular part of the microbiome running riot—a
task at least as important as fending off infectious diseases. In return, a
well-balanced microbiome assists the immune system by preventing pathogenic
bugs from multiplying in the intestines.
The gut microbiome is thus deeply integrated with the
mammalian part of the human holobiont—as can be seen when that integration goes
wrong. Dysbiosis, as this is known, is at least associated with, and in many
cases probably helps cause, obesity, diabetes, high blood pressure,
atherosclerosis, asthma, inflammatory bowel disease, some liver diseases,
various cancers, autism, Parkinson's disease and depression. And this is not an
exhaustive list.
Looking beyond the 37trn mammalian cells in this way can be
medically fruitful. A largely plant-based diet, for example, encourages
fibrolytic bugs, while a meat-rich one favours those that thrive on fat and
proteins. As a consequence, plant-based diets yield molecules such as butyric
and propionic acids which are known to regulate inflammation and other
immune-system functions. Meat-based ones result in branched-chain fatty acids,
and phenols and indoles, which have a range of bad effects, including being
risk factors for bad cardiovascular health.
Fixing things with holobionics
Crop breeders, too, are starting to take the holobiont
concept seriously. Field agents for Indigo Ag, in Boston, Massachusetts,
identify rare survivors in farmers' fields of events like droughts and
infestations, and send these plants in for study. The assumption is that there
is something special about such survivors. Indigo's foundational guess was that
this special something is often in the rhizosphere.
Pursuing that thought, the firm has found—and now
markets—rhizospheric bugs which confer drought-tolerance on cotton, maize,
soyabeans and wheat; improve resistance to fungi in maize, soyabeans and wheat;
guard against nematode attack; liberate phosphorus and potassium from the soil;
and "fix" atmospheric nitrogen by turning it into molecules such as
nitrates, which plants can use to make amino acids, the building blocks of
proteins.
Another firm, Pivot Bio of Berkeley, California, is
concentrating on nitrogen fixation. Pivot's researchers have edited the genes
of two types of nitrogen-fixing bacteria so that they continue to work even
when there is already plenty in the soil, and also turn out more fixed nitrogen
than they usually would. When planted alongside a crop such as maize, a
cocktail of these bugs provides an instant, nitrogen-fixing rhizosphere for
each seedling. That can reduce fertiliser use by a fifth.
Jean-Michel Ané of the University of Wisconsin-Madison, who
is, inter alia, a scientific adviser to Pivot, has two other nitrogen-fixing
ideas up his sleeve. One, observing that legumes grow special root nodules to
house nitrogen-fixing bacteria, is to reshape the roots of cereals (rice is the
main target) so that they grow similar nodules. He and his colleagues have
identified two leguminous genes that, when transplanted to poplars (a common
experimental plant) cause them to grow nodules too.
Dr Ané's other idea is based on unusual strains of maize and
sorghum that grow aerial roots which secrete a gel in which nitrogen-fixing
bacteria like to live. This gel then drips to the ground, where the fixed
nitrogen is absorbed by the plant's roots. In the case of maize, he and his
colleagues have managed to cross-breed plants carrying this trait with
commercial cultivars, and are now into the fifth generation of plants bearing
it.
Cattle and other livestock are also coming under scrutiny.
Their termite-like digestive systems generate more than 100m tonnes of methane
a year, about 6% of the greenhouse-gas emissions for which humans are
responsible. The bugs in question can be curbed by adding either of two
substances to cattle feed—a chemical called 3-nitrooxypropanol or a seaweed
called Asparagopsis taxiformis. Indeed, adding A. taxiformis not only curbs
methane output, but also increases the conversion rate of feed into milk or
meat.
Conservationists see promise in thinking of organisms as
holobionts, too. That is the motive for Dr Bell's work on amphibians. Others,
though, are looking to help entire ecosystems. Both forests and coral reefs are
temperature-sensitive and thus threatened by global warming. Viewing their
members as holobionts may allow ecologists to help them adjust.
Like Indigo's researchers, Cassandra Allsup, Isabelle George
and Richard Lankau, of the University of Wisconsin–Madison, have been looking
at soil microbes. They have sampled forests in their home state and in Illinois
to the south. Testing seedlings of various species grown near the north and
south of this span, which are 5.8 degrees of latitude apart, they found that
those grown in soil inoculated with bacteria from sites with similar climates
grew faster than those in soil given bugs from different ones. Though inoculating
entire forests is not practical, they hope that treating nursery-grown saplings
intended for local reforestation projects might help those trees' survival.
Like humans, corals are a particularly well-studied
meta-organisms. Their tourist-attracting colours come from photosynthetic
protists called zooxanthellae that live inside special cells in the sessile
animals responsible for secreting the limestone of which coral heads are
made—and it is these which provide the holobiont with most of its nutrition.
A weakness of this arrangement is that if zooxanthellae get
too hot, their photosynthetic mechanisms go haywire, generating toxic
oxygen-rich molecules called free radicals. The coral animals then expel them,
a phenomenon called bleaching. If conditions return to normal in time,
recolonisation may occur. But corals that remain bleached for too long will
die.
Some people are trying to inculcate resistance to rising
temperatures by tinkering with the genes of the animal part of the system. But
Madeleine van Oppen of Melbourne University, in Australia, and Raquel Peixoto
of King Abdullah University, in Saudi Arabia, are looking, in separate
projects, to tweak either the zooxanthellae, or some of the many bacteria which
are also part of the holobiont.
Such ecosystem engineering represents holobionic thinking on
a grand scale. Whether it will lead somewhere fruitful remains to be seen. But
the very fact that it is happening at all is, surely, testament to an idea
whose hour has come.” [1]
1. "The idea of 'holobionts' represents a paradigm shift
in biology." The Economist, 17 June 2023, p. NA.
