The tubeworm Lamellibrachia luymesi lives around hydrocarbon-releasing ocean floor seeps in the Gulf of
Mexico. It gets the sulfide it needs to survive from a
menagerie of bacteria and archaea that live in the sediments
surrounding the vent. (Credit: PLoS Biology)

The impulse to classify life seems hard-wired in our species, a relic perhaps of an ancient need to forage in landscapes rife with poisonous roots, fruits, shoots and fungi. Not that the need has disappeared. You get just once chance to mistake Amanita phalloides—aka the “death cap”—for the delectable paddy straw mushroom (Volvariella volvacea).

Linnaeus’ Systema Naturae
introduced the modern framework for classification, helping scientists categorize life as a first step to understanding it. Taxonomists have now described roughly 1.5 million species, just a fraction of the true measure of the planet’s biodiversity.

Figuring out how many species inhabit Earth remains one of science’s most enduring, and elusive, challenges. A recent census effort, published last summer, placed the estimate at around 8.7 million species on land and sea, with the vast majority still awaiting description.

The paper raised a stir, not least because its estimate of microbial diversity was so low (for bacteria, about 10,000 species), to the consternation of many, including UC Davis professor Jonathan Eisen, an evolutionary biologist and microbe ambassador. But I’ll return to that in a moment.

Taking stock of the number of species on the planet helps biologists predict how losing them might impact ecosystems. But we’re losing species faster than biologists can discover and describe them, let alone identify the conditions they need to survive.

As a somber report published a few years ago made clear, the Convention on Biological Diversity’s push to reduce the rate of biodiversity loss by 2010 has largely failed. Several categories of animals skirt the brink of extinction while threats to ecosystem health, from nitrogen pollution to overfishing, continue unabated.

Peter Kareiva, chief scientist for The Nature Conservancy, described our failure in an essay:

“Biodiversity on Earth continues its rapid decline. We continue to lose forests in Africa, Asia, and Latin America. There are so few wild tigers and apes that they will be lost forever if current trends continue. Simply put, we are losing many more special places and species than we're saving."

Kareiva’s point was not that we should all hang our heads in defeat, or dig in our heels and fence off more and more land from our ever-expanding ecological footprint. He suggested something more radical: recognize the resilience of nature—not “nature” with a capital “N” but nature as a complex system of physical forces and chemical processes—and our place in it.

Embrace your inner microbe

And here’s where microbes come in.

Consider this: by the numbers, you’re more microbe than human. Microbes outnumber you by at least 10 to 1. Your eyelashes, hair, saliva and skin offer prime habitat to a multitude of microorganisms. What looks like a body part to you looks like a niche to microbes. When you type, you leave a unique microbial fingerprint on your keyboard.

But the real action takes place in your gut, Microbe Megalopolis, population 100 trillion, give or take a few. And here’s where it gets interesting. Your gut microflora and mine differ. And these variations can spell the difference between health and disease.

David Relman, a Stanford microbiologist and “microbiome” pioneer, told a reporter that the diversity and individual variation of our gut microbial communities suggests that “one of the most important ecosystems on the planet might be the human body.”

B. thetaiotaomicron, a prominent human gut
bacterium, and the intestine. (Image: PLoS Biology)

Researchers have now implicated the microbiome in allergies, autoimmune disease, obesity, and a variety of other conditions. And it all started with one study that showed that when you transplant a microbial community from one mouse to another, the phenotype–traits associated with that community, in this case, obesity–goes with it, explains Eisen. “That changed everything. Until that paper came along no one had shown that microbes played that big a role.”

We know microbes are the most abundant life form on Earth. But that doesn’t mean we can take them for granted. Many of their natural habitats—both landscapes and organisms—are disappearing. When host organisms disappear, the microbes will go with them. The reverse could also be true.

Most captive breeding programs to restore endangered species to the wild concentrate on genetic diversity as the key to survival. “But no one’s really saying we need to worry about their microbes too,” says Eisen. “No one’s focusing on whatever we need to do to make sure they have the right microbial community with them.”

An improbable field guide

About 6,000 to 8,000 species of bacteria have been described so far, but biologists like Eisen think there may be hundreds of thousands or even billions of niches to exploit. Trying to count microbe species is a losing proposition, he thinks. But trying to characterize microbe diversity by thinking in terms of niches isn’t. Microbes exploit different niches just like any other organism, from Darwin’s finches to Arctic foxes.

A self-described “bird nerd” since he was 7 years old, Eisen thinks the best way to get a handle on the seemingly intractable diversity of microbial life on the planet is to think in terms of field guides. Document everything you know about different types of microbes, their niches, range, biology, genetics and ways to identify them. That becomes both a reference and an organizational framework for gathering and making sense of the mountains of data, mostly genetic, gathered from the places microbes live.

Using “metagenomic” tools, scientists sift through reams of genetic material extracted from environmental samples by matching gene sequences to known organisms or, if nothing matches, to something roughly similar.

DNA is obviously different from skeletons, bones and fossils, Eisen says, but the classification, clustering and taxonomy methods are no different from what ecologists, archeologists and paleontologists have been doing for thousands of years.

Even so, the microbe field guide is a tad more ambitious than any field guide to birds. The enormity of the task was perhaps best expressed by metagenomic pioneer Julian Davies in a quote beloved by microbe hunters: “Once the diversity of the microbial world is catalogued, it will make astronomy look like a pitiful science.”

It’s hard to overstate microbes’ importance to the planet. They drive the global carbon and nitrogen cycles that make life possible, regulate climate, purify groundwater and detoxify waste. If it weren’t for the ancient forebears of ocean-dwelling cyanobacteria, which pumped oxygen into Earth’s atmosphere after emerging some 3.5 billion years ago, we probably wouldn’t exist.

Dickcissel - a grassland bird. Photo Credit: Amy Larson

In an effort to improve the sustainability and health of their land, farmers are increasingly interested in taking a systems approach to farmland management. A systems approach acknowledges the key connections between ecological, economic, and social components. Given the ensuing complexity, measuring the health of a farm system requires good diagnostic tools. In addition, these tools need to be clear and straightforward.

Our current effort at the University of Nebraska Lincoln to develop a set of such indicators for farmers, the Healthy Farm Index, focuses on biodiversity and ecosystem services at the farm scale. One indicator in the index is the presences of a given set of birds on the farm. Birds are a popular indicator because they are sensitive to change in farm practices, found broadly in the environment, and are easy to detect by sight and sound.

The ability to detect birds by sound has spurred our research group to develop resources to aid farmers and other people interested in the songs and calls of farmland birds. As researchers, we use auditory detections of birds as one of our primary monitoring tools. With acoustic recorders, we have recorded the songs and calls of our local bird communities. Back in the lab, we use software to identify and isolate the best songs and calls. These vocalizations have been posted to our website, Farmland Birds of Nebraska, and distributed back to farmers and others interested on CDs. With the acoustic recordings, farmers can select a group of indicator species suitable for their area, learn its call, and listen for the bird while working in the field. This information can be used by the farmer in assessing their own farm or can be shared more broadly with researchers.

The recordings also allow farmers to share with consumers (many of whom are birders) an added environmental benefit of their farm. This spring we were able to take these recorded vocalizations back to one of our participating farms. In partnership with Common Good Farm, we hosted a “Birding on the Farm” tour. Local residents and other farmers spent the morning listening for and identifying the community of birds at the farm. New and experienced birders alike were surprised at the diversity found on the single farm.

In the coming months, we are expanding our network of recorders. This winter we will be monitoring winter bird communities on participating farms and testing the influences that road noise may have on bird vocalization and communication.

Photo credit: David McGuire, SeaStewards.org

Time passes slowly when days are full. It’s been nearly three weeks into the California Academy of Sciences' 2011 Philippines Biodiversity Expedition. With well over 1000 dives, 100 collection sites and as many new species we have barely scratched the surface of this amazing country of islands. With over 700 islands, volcanoes and rainforests, this island nation has many untold stories and species awaiting discovery and description.

Spending most of my time with the aquatic team, and having an aquatic bent, the undersea world is what I’m most familiar with on this expedition. While the botanists and entomologists are searching Mt. Makiling to the south (and scratching at leeches and mosquito bites), we are exploring the coral reefs, soft-coral forests and rubble pits for nudibranchs, sea urchins, bobbit woms, limpets, sea horses and representatives from the score of other phyla that live in the sea. While there are few insects, there are lionfish, blue-ring octopus and the beckoning spines of Dr. Mooi’s creatures of choice to navigate among.

Dr. Gossliner has upped his new nudibranch count is over 30 undescribed species, and the total number for this colorful and complex shell-less marine snail is over 800! Not to be out done, Chrissy Pietrowski is finding new species and possibly even genera of worms on her dives as she scours the rocks and dead coral. The reefs in this region, located on the Verde Island Passage are abundant and diverse. Scores of coral species color the reef system, enchanting octocorals – the eight-tentacled soft coral Dr. Gary Williams studies – flow and float like vespers in the current. One species common here called Xenia appears to be feeding as it closes and opens its eight-fingered flower-like tentacles. In fact, they are shading the Zooanthellae – the photosynthesizing symbiont who live in their tissues. Like us, too much sun is a bad thing, and this is how this organism protects itself from its own form of coral bleaching.

Another favorite are fire urchins: puffed up echinoderms with spines of electric blue which move around the bottom at amazing speed for an animal without muscles, a neurosystem or backbone. Endowed with small spines, a serious sting makes up for the lack of sticking power. Its cousin the Diadema is protected by wicked long spines which are painful when they embed the accidental hand or foot brushing up against them (and they do).

There is too much to describe and it is like being in school again being embedded with so many experts.
The footage I'm collecting along the way is as vivid and compelling as it is daunting to collect and review. Sometimes it's challenging like when a night dive was aborted due to a strong current that left me paralyzed with my big camera housing and weighted tripod. I sucked half my tank trying to keep up with the fish team. Spare parts are non-existent and as fasteners fall out, fittings get broken, my gear is starting to look more Frankensteinian each day.

Like developed countries, the Philippines has a number of challenges from human impacts. Over 100,000,000 people live in the islands, and like California, the preponderance live near the sea. The sea is everything here. Everyone fishes. Fish and rice are staples. Kids play in the warm waters and whole families pile aboard slender bamboo Bankhas to visit one another. The people here love the ocean. It’s in their stories, their daily lives and in their faces. But as elsewhere on the planet, modern technology and population expansion have made their mark on the land and seascape.

Sobering is the amount of plastic littering the reef, scattered along the shoreline and along the reef crest. Plastic bottles, bags and containers drift among the coconuts, broken bamboo mats and driftwood on the weathered coral shoreline. Debris lines of plastic mark the tidal currents and beneath the surface plastic threads itself into the mosaic of coral. This is a solvable problem, one we are struggling with at home. With a trillion single-use plastic bags used each year, we have our work cut out for us.

Also present are the scars from illegal fishing practices. Dynamite fishing has left coral rubble where there was once an undersea garden. A decade ago, Terry describes hearing dynamite percussions every dive. Here in Anilao, at least this destructive fishing practice seems to have been stopped. Intensive subsistence fishing is prevalent and all the top predators are gone. In response, Marine Protected Areas (MPAs) are being established by local townships to provide refuge for large fish and other heavily harvested species. In one of these MPAs, we saw more large fish than on all the other dives combined. Here in the field, time passes slowly but the need to explore, explain and protect natural systems like Philippine coral reef systems is urgent.

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California Academy of Sciences biologists Dr. Terrence Gossliner, Dr. Bob Van Syoc, Dave Catania. Credit: David McGuire, SaeStewards.org

It is midnight. The warm tradewind wafts onto the bamboo balcony as the gentle surf of the Philippine Sea splashes against the breakwall. The stars rotate on their steady cartwheel across the sky and the palm trees rustle their refrain. It is a lovely, romantic melody and it goes unheard by our team.

On Day 5 of the California Academy of Science’s 2011 Philippine Biodiversity Expedition, we completed a night dive observing and collecting specimens on what is affectionately known as a “muck dive.” We aren’t talking a colorful coral reef resplendent with fish and other marine life. It’s a silty shallow site near a pier with rubble and the occasional plastic bag. But in this habitat are undescribed worms, new species of nudibranchs and other invertebrates.

The tired divers have disembarked the Bangkha, disengaged from their dive gear, scarfed down a meal of rice and chicken and trooped to their microscopes, petri dishes, bags, jars and journals. Upstairs the scientists are counting worm segments, sorting sponges and writing the last of the day’s logs, as we download footage, make edits, charge batteries and repair gear before the morning’s dive. Science is hard work, and so is field documentation. We are sore, sunburned and exhausted, yet there is a real sense of satisfaction that what we are doing is important. If we don’t understand what is in nature, how will we know how to protect it, or why should we even care?

What makes us care about wildlife so much that we dedicate years of study, a hundred hours a week of time for little pay or even recognition? Why work so hard to understand, to describe the plants and animals of remote reefs? Even in this relatively untouched corner of the world, there are huge impacts on the world ocean. In the ever-growing battle against overfishing, habitat loss and over exploitation, we occasionally wonder why we do what we do.

Why not just get a regular job, sleep in a bed, forget the travel and insects and diseases? Forget the overwhelming sense of despair that even as we try to describe and explain and protect marine habitats like coral reefs we are losing the race to extinction, overfishing and declining coral reef habitat? To most of the expedition team it is not even a question; it is an imprinted devotion that has gone unasked for decades. There is no other thing a person can do but study, describe and try to share that knowledge in the interest that other people will grasp that love of knowledge and ultimately love that crusty barnacle, slithery sea slug or wandering worm. It’s about love of nature, the desire to explore and understand, to communicate and inculcate that same love to others.

For me the answer to the question is as simple as ABC: Adventure, Biology and Conservation. The excitement of exploration and entering the unknown underwater world is indescribable. Learning the details and then communicating the larger picture is the challenge. Appreciating and protecting the ocean is my mission.

The diversity of ocean life is just too important to let vanish. Forget the scientific explanations of interdependence, the benefit to humans through healthy fisheries, new medicines, our air and climate. To reduce it down to basics, the ocean is beautiful. And perhaps coral reefs like this system on the Verde Island Passage half an earth away from San Francisco is among the most beautiful and biodiverse. Like a complex tapestry, the threads combine into a larger more breathtaking work and we humans are just one of those threads. The Academy Team is working hard to understand how to keep the whole thing from unraveling.

In five hours it will be time to get up. The specimens are put away, my camera is ready, the batteries are charging, video is rendering, and the dive gear is prepared for the first dive at 8 AM. It's time to sleep and recharge my own batteries. But as I listen to the sound of the waves, the symphony of the reef serenades me. The fish and the corals and the sea snakes are calling. I can’t wait to get to work!

To learn more about the expedition,follow my posts on QUEST and read more on the project's website at the California Academy of Sciences.

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Getting to interview Edward O. Wilson was the pinnacle of my career so far.

How do you fit your hero into 2 minutes? Very, very carefully…!

All kidding aside, getting to interview Edward O. Wilson was the pinnacle of my career so far.  How often do you get to meet your hero, sit down face-to-face, and ask him questions about his life?  I still get goosebumps just thinking about it!

It probably sounds kind of silly – calling someone you’ve never met your “hero.”  But I think it’s important to have someone in your field of work that you can look up to, be inspired by, and who can challenge you to be a greater person.

The first time I heard E. O. Wilson speak, I was at the Jackson Hole Wildlife Film Festival.  He gave the keynote speech for the festival, in which he discussed the role of science and socio-biology in the future of western civilization.  This, of course, was many years ago, before the term “climate change” replaced “global warming;” before we really understood the impact modern man was creating on the globe; before the hopeless pessimists decided there was no turning back.  And yet, in EO Wilson, the eternal optimist had already been born.

I think it was his optimism that drew me in – I am constantly amazed at human nature, wondering WHY we do the things we do.  Throughout history, the studies of science and sociology were hopelessly at odds.  For hundreds of years, the pursuit of knowledge for these topics were on separate paths, since combining the two would essentially negate them both.  Enter Edward O Wilson, eager to learn, and unafraid to say “Nature AND Nuture.”  Needless to say, Wilson spent many years under attack by his colleagues, yet he managed to remain steadfast and optimistic, both about his own research, and about the future of science and biology.

Today, scientists generally agree that nature and nurture are not mutually exclusive.  In fact, E.O. Wilson continues to contribute valuable ideas, creating new ventures and collaborations that continue push the boundaries of modern science. His list of accolades is long: he has won the Pulitzer Prize (twice!); he created the Biodiversity Foundation; he has served on the Boards of Directors of The Nature Conservancy, Conservation International, and the American Museum of Natural History; and he conceived the idea of the Encyclopedia of Life – one of QUEST’s National Partners.  Recently, QUEST has been collaborating with local 5^th graders for the EOL Education and Learning group’s East Bay Regional Park District Bay Lab Project.

Perhaps the easiest way for me to show you how the world looks to someone like E.O. Wilson is to share this excerpt (which I absolutely LOVE, but unfortunately couldn’t squeeze it into a mere 2 minutes.

“The most common question I’m asked about ants is what do I do about the ones in my kitchen? And my answer is always to be the same – it is to feed them bits of honey and tuna, canned tuna fish. They love those particularly. Then watch where you step. Be careful of little lives. Get down and watch them closely, and you will see as they behave and communicate with one another, to come out and get those little bits of food, you will see behavior that is so strange to human beings, and so complex, that it might be what you would expect to see in life on another planet.”

Watch Why I Do Science: E.O. Wilson television story online.

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Some have dubbed it the "doomsday vault"; others, taking a more positive tone, call it a repository of biodiversity. However you look at it, the Global Seed Vault is a fortress. Buried under almost 500 feet of Arctic permafrost, secured against bomb blasts, earthquakes, and potential thieves, this massive seed bank, which will ultimately include samples of a large portion of the world's plant varieties, is our high-tech hope for preserving the genetic diversity that underlies the world's food supply. But despite its scope, the seed vault isn't enough.

Why a seed bank in the first place? Because industrial farming approaches have made what was once a plethora of diverse crops into something more like a set of monocultures, carefully bred to meet our standards for long distance travel, high yields, and resistance to bug and weed killers. Many scientists fear that climate change will threaten these crops, which provide us with a huge proportion of our food.

To keep growing enough food, we'll have to breed new plant varieties that fare better in higher temperatures, or in depleted soil, or under whatever challenging conditions a particular crop faces. For that, plant breeders will need to tap the genetic diversity that exists among the many varieties of any given plant. A gene that makes one kind of rice grow well in sandy soil, for example, can be transferred to another kind of rice. This is why preserving each and every variety of plant food is essential to securing our food supply.

But a seed bank, vital as it is, falls short. Why? Because how and what we eat is as much about who we are as it is about the seeds we put in the ground. We're missing something if we believe we're saving ourselves simply by saving seeds.

Don't get me wrong: Genetic diversity in edible plants is the toolbox nature gives us to feed ourselves with, and preserving it by saving seeds is central to our ability to grow and develop new crops. But, as Michael Pollan articulates in his latest book In Defense of Food, the way we eat is attached to our cultures, beliefs, languages, and rituals. We learn about growing and eating food from people who came before us, and that knowledge is as important as the food itself.

The (necessary) sterility of a seed bank doesn't capture the messy, many-threaded ways in which food and agriculture are incorporated into a society. A seed bank doesn't preserve the knowledge of how to grow its precious population, or how farming crops cooperatively might produce different results than farming them individually, or even how to make the plants into edible dishes.

If we want to ensure our food supply, we need to do more than freeze seeds. We need to also take careful notes about culture.

I began thinking about this several years ago, when I had the privilege of visiting a seed bank operated by a group called Native Seeds/SEARCHin Tucson, Arizona, when I was working on a piece about seed saving for our Science of Gardening Web site. Native Seeds/SEARCH Native Seeds/SEARCH (NS/S) was founded in 1983, when Native Americans in the region wanted to grow traditional crops and couldn't locate seeds. Since then, the organization has grown to include 4500 farmers and thousands of seed varieties developed by Native Americans in the Southwest.

NS/S doesn't just save seeds: they save the knowledge that goes with them. NS/S farmers continually plant and grow handfuls of the seed bank's reserve, refreshing the seed stock and passing along knowledge of how to best grow a particular plant. NS/S employees also collect stories from and share knowledge with Native people in the region.

Now, I'm no farmer, but it seems to me that safeguarding both the "agri-" and "-culture" of plant varieties will help us get the most out of the seeds we've saved. Otherwise, we end up seeing the security of our food as little more than a sterile set of seeds stored in a deep freeze, ready to be accessed for answers when our old farming technologies get us in trouble. But feeding ourselves is hardly a sterile affair: we grow, prepare, and consume food in a complex context of environment and humanity. I, for one, think our tendency to dismiss that larger picture is what's gotten us into this biodiversity problem in the first place.

Robin Marks is a journalist and science writer who current serves as a Multimedia Projects Developer for the Exploratorium in San Francisco, CA.