The Microbial Anthropocene, Part 2
9/1/22 – The invisible transformation of life on Earth, continued
Hello everyone:
As always, please remember to scroll past the end of the essay to read some curated Anthropocene news.
Now on to this week’s writing:
Let’s not fool ourselves: Life on Earth planet is microbial, and has been for three and a half billion years. The big stuff like ferns and dinosaurs and tuna arrived much later and only by standing on microbial shoulders. Ocean and soil ecosystems, plants and animals: all visible life exists because of bacteria, archaea, fungi, viruses, and protists.
Until recently, humans were just another medium-sized newcomer, an odd hyper-conscious ape without much meaning in the continuum of the planet’s biodiversity. Suddenly, though, we’re the troubled kid drawing attention to ourselves as we throw lit matches everywhere amid the community of life.
When we talk about biodiversity, our bias for large visible life makes us think of the survival of charismatic plants and animals – polar bears, sequoias, frogs, wolves, mangroves – but nearly all living species are microscopic. Biodiversity, from any rational perspective, is mostly invisible to us. Or was, until recent science began to reveal it.
I wrote last week that we are driving microbial evolution. It would be more accurate to say we are forcing many species of microbes to respond to our rapid planetary disruption. Unless something changes, some of those responses will be essentially permanent – adjusting to an acidic ocean for thousands of years, for example – and cause a wide range of impacts that will in turn shape the planet’s future. Many other microbial species, though, are probably only slightly impacted so far, and would scarcely notice the disruption if we begin to repair and revitalize the Earth sooner than later.
Imagine the vast array of microbes associated with American bison, for example, both within the animals and spread through the other species, ecological relationships, and landscapes they shape. A couple centuries of cruel upheaval reduced a population of 30-60 million bison to fewer than 500, but if over the next century or so we manage to reverse climate change and rebuild a substantial bison population (currently about 500,000) which reinhabits a large portion of the West, the bison – as a keystone species – would likely reinvigorate much of that original network of macro- and microbiotic ecology. A few centuries are nothing in the history of microbial evolution on Earth, even when forced through a tiny population bottleneck.
Thus, I should be clear that we are not currently pushing the hundreds of billions of microbial species to the brink. As I said last week, this is their planet. We are reshaping and diminishing their world, and while there are plenty of losses and changes to worry about, especially if our litany of harms goes on unchecked, microbes will generally respond to a moderate Anthropocene like river water calming after minor turbulence. At least I hope so.
I closed last week with a promise to outline our substantial impacts on microbial life through three categories: Extinctions within Extinctions, Unnatural Selection, and Making Trouble. I may have made those categories a bit hastily… but let’s see if I can make them work.
Let’s start with extinctions. One way we’re transforming the microbiological world is of course by devastating the macrobiological one – animals, plants, and their visible ecosystems – which host innumerable microbes and live in complex relationships with them. Our devastation includes reducing populations of vertebrates, for example, by 60 percent on average since 1970. Only 4% of mammal biomass on Earth is wild; the other 96% is in humans and our livestock. Half of bird populations globally are in decline. In North America during the last fifty years, there’s been a population loss of three billion breeding birds.
Where the wild animals go, so go their associated microbes. Imagine the reduction in the diversity of digestive microbes when the guts of hundreds of wild animal species have been replaced with those of only a handful of antibiotic-infused domestics: poultry, pigs, cows, and sheep. And it’s not just the gut. Microbes live within and around each species in deeply-evolved relationships. A 2007 layman-friendly study titled “Extinction of Microbes” surveyed the possibilities and summarized them this way:
[E]ven free-living microbes have biogeographies and thus might be subject to at least local extinctions. Furthermore, some microbes do seem to be restricted to very particular environments and are endangered in as much as these environments are threatened. Finally, microbes intimately associated with other organisms share (partially) the biogeographies of their hosts. As far as they are species-specific, they could potentially become extinct along with their hosts. Overall, extinction rates typically reported are underestimates, since they do not take into account associated microorganisms which likely become extinct with the host organism, plant or animal.
That’s the extinctions within extinctions I was referring to. Perhaps the key idea here is not so much the loss of microbes but the loss of ecological relationships. The tapestry metaphor for ecology is overused, I suppose, but it works well enough here to remind us that a hole in the tapestry of life caused by extinction is actually made up of many small holes, each one a break in a larger number of threads.
We don’t really know much about microbial diversity, except that it’s vast. With one estimate of scientific identification of microbe species at about 0.001%, it’s safe to assume we don’t know a lot about what we’re losing (or changing) in the Anthropocene. To cite one large-scale example, imagine the loss in number and complexity of highly-evolved microscopic life when massive swathes of chemical-dependent agriculture replace forests and grasslands and wetlands, destroy soil communities, and poison insects.
Soil, we should remember, is alive. A National Geographic article out this month on the rich microbial life in forest soils notes that “a single gram of forest soil can contain as many as a billion bacteria, up to a million fungi, hundreds of thousands of protozoans, and nearly a thousand roundworms.” Imagine that forest cleared and turned into farmland – a process which is still a primary driver of deforestation – where the lack of a lush canopy of trees, shrubs, and plants above the soil means that the microbial life below also diminishes or dies off.
Furthermore, when industrial farm soils are depleted of nutrients, tilled constantly, allowed to erode, and soaked in herbicides and pesticides, they’re often bereft of these organisms which under normal conditions provide extraordinary benefits to the plants above. To what extent these soil communities are experiencing extinctions of some microbes, or extirpation in particular areas, or merely a reduction in numbers across all microbial species, is hard to say. But nothing in these scenarios is healthy. Good farming protects soil biodiversity.
I’ll move on to what I’m calling “unnatural selection.” I recognize that it’s a term you might swat down by reminding me that humans, for all of our weirdness, are as natural as clams and that our actions are also therefore natural. Point taken, but disregarded. Our Anthropocene actions – from genetic engineering to PFAS production – are extraordinarily unusual and their consequences are Earth-shaking.
Some of these planetary changes we’re making are within the normal range of microbial existence – higher temperatures, say – but some, like a flood of antibiotics and prescription drugs and petroleum products into natural systems, are not. And even the “normal” changes like warming the globe, increasing extinction rates, disrupting habitats, and acidifying the oceans are unusual by virtue of their incredible speed.
Whether evolution typically proceeds by slow and steady change over millions of years or by occasional ruptures in an otherwise stable equilibrium, assessment of previous mass extinctions on Earth suggests that if modern human activity continues unabated it will have only one real comparison: the asteroid which ended the Mesozoic era 66 million years ago. That comparison is still a wildly dramatic one, but not inaccurate. It’s a function of time, but only a matter of, say, a century or three, which is astonishingly quick in geologic terms and more akin to a sudden asteroid strike than, say, a million-year-long volcanic upheaval.
Which is all to say that human intervention in microbial evolution goes far beyond what we typically think of as our relationship with microbes: disease, and preventing disease. We’re forcing infectious viruses and bacteria to up their game as we challenge them with vaccines and antibiotics, sure, but there’s so much more going on in the shadow of our Anthropocene activities. And we don’t really know how the many, many microbial adjustments to the new conditions for life will pan out. It seems quite likely that in some cases they may not respond in the time frame or the manner we prefer.
Of the three categories I’m playing with here, selection pressure is by far the largest. Think of it as the full range of responses by microbes, other than extinction, to all of our strange and intense ecological disruptions. Some microbial populations will decline, others thrive. Some microbes will evolve rapidly to meet the new conditions of life we’re creating, while others will remain isolated in vestigial corners of a previously widespread habitat.
There’s far too much to detail here – I don’t claim to fully understand this category – but I’ll run through a handful of ideas that came to mind, just to provide a sense of the scale and depth of what’s happening. (I’d love to hear from anyone with ideas to add, corrections, etc. on our unnatural evolutionary pressure on microbes in the Anthropocene.) I’ll focus on aspects of the transformation related to the oceans:
The oceans are becoming warmer, more stratified, less oxygenated, and more acidic. I worry most about acidification, but they’re all connected. We’re lucky that the oceans have absorbed much of the atmospheric heat from our excess greenhouse gas emissions, but while we wipe our brows in relief that so much of our CO2 is being swept under the oceanic rug, what’s really happening is a degradation of the foundation of ocean food webs. See the picture above of pre- and post-acidified coccolithophores, a type of phytoplankton (which produce 40% of the planet’s oxygen) dissolving in low pH water like teeth in a glass of Coke. Studies are producing mixed results on the question of whether the Anthropocene oceans will produce less oxygen, but a decline is apparently the most likely result.
The erasure of coastal and deep ocean habitats means a radical shift in microbial life. By habitats I’m referring to the loss of fixed environments like mangroves, corals, and seagrass, but also to the 90% of large ocean predators that have disappeared, to the overharvested food fish species, and to those whale species which haven’t yet recovered from the slaughter. Squid and jellyfish populations are exploding, as are their associated microbes.
When we hear reports of corals bleaching, that’s a story of heat-driven loss of corals’ algae symbionts. (Algae feed the corals, which provide a home and nutrients for the algae.) The good news is that some corals are finding more heat-tolerant algae to take on the job, but again, this is a story of microbial selection by human activity.
The steady stream of oil spills from rigs and methane leaks from active and abandoned wells is creating an equally steady evolutionary pressure for microbes that can feed on petroleum products. To the extent that the oil products impact ocean ecosystems, they impact those associated microbes. The scale here is impressive: In U.S. federal waters alone, there are more than 55,000 wells, over half of which are abandoned with little oversight to assess methane leakage, etc.
The dead zones in coastal waters, as in the Gulf of Mexico, are microbial events fed by excess nutrients flowing off agricultural land upstream. Algae bloom as they feast on the nitrogen and phosphorus but then deprive the waters below of oxygen and sunlight. The resulting die-off uses up more oxygen as bacteria on the ocean floor decompose the dead matter.
Antibiotic-resistant bacteria are everywhere in the world now, especially downstream in coastal waters below intensive livestock operations. A 2017 study found up to 100 million antibiotic-resistant genes in each gram of mud pulled from Chinese estuaries. These come not just from feedlots and poultry farms but also from human waste. The antibiotics (like pharmaceuticals) pass through our bodies and out into streams and rivers, joining the industrial pollutants, heavy metals, and household chemicals which are also forcing microbes in coastal waters to adjust to a radically different world. The capacity for resistance is passed via horizontal gene transfer to an ever-increasing number of microbes, which in turn inhabit or interact with other life forms in the sea, many of which we eat.
One thing worth noting is that we’ve been pressuring microbes to change for quite a while, if on a smaller and sustainable scale. The genomes of bacteria and fungi used in our food production bear the signs of domestication also seen in our crops and livestock.
And one final note on all this: Our population, the sheer scale of our numbers – still increasing by about 80 million a year – makes everything we do, from shopping to gardening to flushing the toilet, a trauma on the landscape. There’s so much we can do to soften those impacts, but they’re still impacts. We’re the elephant in the room, because there’s no more room for the elephant.
I want to finish with a note on synthetic microbes, what one public health biologist suggests may well be “the primary hallmark of the Anthropocene.” This is my “making trouble” category. For some years now scientists have been creating GEMs (genetically engineered microorganisms) by rewriting part or all of microbial genomes to make them useful in medical research, agriculture, food production, and a host of other industries. They’re used to produce insulin, detergent enzymes, biofuels, and much more. They may soon be utilized to deliver drugs into your body and clean up toxic groundwater.
What can go wrong? Given the novelty and headlong development of DIY biology, the usual array of hazards to workers and the environment apply here, certainly, but there is something a bit more haunting, I think, in the power of synthetic life in the hands of the same people who, for example, produce thousands of toxic chemicals for huge profit while disregarding the health of people and nature.
There is plenty of discussion – though no firm legal framework – about ways to make the world safe from billions of tiny Frankenstein monsters, and I should be clear that much of what is in production now has little chance of running amok, but isn’t it just a matter of time? The nature of the Anthropocene is that our mistakes are nearly always presented initially as solutions. Every advance can become an advanced weapon, and every technological solution provides a new set of problems.
It’s not hard to imagine that with no more legal or cultural restrictions on synthetic microbes than exist now for pesticides, antibiotics, PFAS, or genetic modified organisms, the near future may be full of news about synthetic life passing on unwanted traits via HGT to natural microbes, or altering ecosystems they were meant to protect.
Experience tells me that we’re not smart or focused enough to manage our own worst behaviors, and that we’re absolutely not prepared to manage all the ways in which we’re rewriting the microbial relationship with the Earth. There’s already a tsunami of change building from our environmental destabilization, and now we’re rewriting genomes? Stay tuned…
If you’d like to read an excellent book on our microbiome and the role of microbes more generally, I highly recommend Ed Yong’s I Contain Multitudes.
To wrap up, the Anthropocene isn’t just the macro world we live in. There are numerous invisibilities in the world around us – our senses are weak, our biases are many – but arguably the greatest blank spot in our vision of the world is its microbiology, whose residents actually run this place. If nothing else, we need to remember that each manmade ecological problem we witness around us has a billion little shadows we don’t see. It’s not worth toting a sign in front of city hall that says “Save the Microbes,” but it is one more reason (a trillion more reasons?) to work quickly and effectively on the problems in front of us.
Thanks for sticking with me.
In other Anthropocene news:
Watch the winning short film “From Dreams to Dust” from the 2022 Yale Environment 360 Film Contest, which “shows how nickel mining has ravaged a seaside village in Indonesia, causing life-threatening landslides, polluting water supplies, and contaminating coastal waters.” The nickel is being mined for the batteries we’ll all need for our electric vehicles.
From Bitter Southerner, Down to the Tide Line, a short illustrated poetic note on paying attention to the land around us, particularly if we’re standing at the edge of the sea.
From Common Dreams, we really don’t need new reports and studies to tell us how bad conditions for life on Earth will become if we don’t radically curb emissions. Enough disturbing information is available already to motivate us, yet the reports keep coming because science doesn’t sleep. One of the latest to darken our doorstep is a Canadian study that examined the climate-enhanced risks to 35,000 marine species if we maintain current fossil fuel emissions. It found that “nearly 90% of marine species would be at high-to-critical risk of being wiped out and 85% of those species' native habitats would be affected, on average.”
From National Geographic, a series of maps identifying where in the U.S. we can best turn our attention to meet the goals of protecting 30% of our lands and waters by 2030. The goal here is to identify the most biodiverse areas most in need of protection so that we get the most of our conservation investments. Take a look and see what needs protecting in your state.
From the Times opinion section, a liberal critique of the way liberal environmentalists have for decades hobbled government’s ability to get important environmental projects built. What was used initially as an important restriction on environmentally harmful developments is now making it harder to make the massive transition necessary to combat and cope with climate change.
