Monday, December 11, 2017

Secret Science Club Post-Lecture Recap: Oceans of Wonder, or Microbiome Del Mar

Last night, I headed down to the beautiful Bell House, in the Gowanus section of Brooklyn, for this month's Secret Science Club lecture featuring marine biologist and oceanographer Dr Ed DeLong of the University of Hawai`i at Manoa. Dr DeLong's lecture concerned the marine microbiome, and its effect on the Earth's biochemical systems.

Dr DeLong began his lecture by noting that microbes permeate everything, and have done so for the majority of Earth's history. Microbes move in a very different fashion than macroorganisms, their motions taking the form of a 'random walk'. Microbes must contend with a low Reynolds number, with viscous forces being stronger than inertial forces. Dr DeLong likened this to a human swimming in molasses, being able to stroke once per minute. A microbe 'runs' straight, then tumbles in a random direction, tumbling less near food sources (with a general movement toward food).

A common view of biodiversity tends to focus on macroorganisms, typically insects. There is an anecdote that the biologist J.B.S. Haldane (who first conceived of abiogenesis and a 'primordial soup' and first suspected that sickle-cell anemia was an adaptation to malaria), when asked to comment on God by a theologian, replied that God had an 'inordinate fondness for beetles'. This anecdote probably derived from a passage in Haldane's book What is Life?:

The Creator would appear as endowed with a passion for stars, on the one hand, and for beetles on the other, for the simple reason that there are nearly 300,000 species of beetle known, and perhaps more, as compared with somewhat less than 9,000 species of birds and a little over 10,000 species of mammals. Beetles are actually more numerous than the species of any other insect order. That kind of thing is characteristic of nature.

If the Creator has a fondness for beetles, it has even more fondness for microbes- in a teaspoon of seawater, there are about one million microbes and ten million viruses. It is estimated that here are about 1024 stars in the observable universe, and about 1030 microbes in the world's oceans. A Creator would seem to have a phenomenally inordinate fondness for oceanic microbes.

Microbes have been around for a long time. The Earth is considered to be over four billion years old and microbes are believed to have been around for 3.8 billion years. Microbes have had a profound effect on the planet's chemistry- phototrophic organisms evolved, some of them evolving into photosynthetic organisms, with some photosynthetic cyanobacteria being incorporated as plant organelles. The waste product of photosynthesis is oxygen, the production of which made eukaryotic life possible, setting the stage for us. Microbes play a critical role in biochemical cycles- perhaps the most important of which is the photosynthesis-respiration cycle. With increasing amounts of carbon dioxide being released into the atmosphere, it is possible that microbes might be able to store some of the carbon.

Life can exist in extreme conditions, such as boiling-hot geothermal vents and freezing polar conditions. Wherever there is water (hydrogen and oxygen), carbon, nitrogen, phosphorus, and energy, life can exist. Microbes drive Earth's biochemical cycles everywhere. One of the most important of these cycles is the microbial nitrogen cycle. The nitrogen cycle is crucial to the oceans, and nitrogen fixation, by which atmospheric nitrogen is converted into ammonia which can be used by other organisms, is a bacterial process- no microbes, no nitrogen cycling.

Dr DeLong noted that the 'forests of the sea' are microbial- while the primary photosynthetic organisms on land are macroorganisms, the plants, the primary photosynthetic organisms in the ocean are cyanobacteria, though diatoms and dinoflagellates are also important photosynthesizers. Approximately fifty percent of the oxygen we breathe comes from the ocean.

Dr DeLong gave a brief history of the 1872 HMS Challenger expedition, a four year voyage around the globe during which the Marianas Trench was discovered and numerous biological and geological samples were obtained. Among the biological specimens collected were many eukaryotic organisms now included in a supergroup known as the Rhizaria. Many of these organisms were beautifully depicted by Ernst Haeckel. The Rhizaria are an important carbon conduit to the deep sea- when they die, they sink, their calcium carbonate walls providing carbon to the depths.

Dr DeLong then played a video of satellite imagery of cyanobacteria blooms similar to this video:

Cyanobacteria blooms can occur due to factors such as upwellings of nutrients and discharges of sewage and fertilizer runoff. Cyanobacteria are massively parallel, broadly distributed engines of chemical processes.

Dr DeLong then turned to the topic of 'seeing the unseen'- it is hard to observe microbes, and it is especially hard to study them in nature. Studying microbes in a petri dish is like studying animals in a zoo- in limited environments, what we learn about organisms is limited. To understand organisms, it is important to study their interactions. Before 1980, wild microbes were invisible, unculturable, and unidentifiable. It is now possible to study them through epifluorescence microscopy, which involves staining microbial DNA with fluorescent dyes in order to make it visible under microscopes. The discovery of oceanic microbes really amped up in the 1970s, when Carl Woese applied quantitative molecular phylogenetics to all life. He used DNA/RNA sequencing to piece together an RNA phylogeny for all life. Differences in RNA can be used to calculate evolutionary distances. Dr Woese's RNA sequencing revealed a new view of life. Not only is all life related, sharing RNA sequences, but the 'tree of life' was upended with the discovery of the Archaea. Many of the Archaea live in extreme environments, such as hydrothermal vents and super-salty pools. Some of the RNA sequences characteristic to Archaea show that they are closer to us than to bacteria.

Before Woese's project, organisms were broadly divided into prokaryotes and eukaryotes, different prokaryotes could not be differentiated, and the Archaea were lumped in with bacteria. With Woese's techniques, differences could be characterized.

To study microbes in nature, a mixed population is collected, and the DNA 'bar codes' are extracted, sequenced, and phylogenies are constructed. Quantitative surveys are then conducted to determine the proportions among the organisms. Back in 1987, 11 bacterial phyla were known. By 2006, 100 phyla had been discovered, with numerous species in each phylum. There are difficulties in defining bacterial species, and there are possibly millions of billions of them.

There is a logical flow to hunting microbes- find the RNA, we may know 'who' the microbes are but not what they are doing. Is a microbe a heterotroph or a phototroph? How do the microbes interact? The discipline of metagenomics is a genomic approach to microbial ecology- get samples, extract the genetic material, build a 'library' of community genetic sequences.

Dr DeLong showed a cover from The Economist trumpeting MICROBES MAKETH MAN, noting that the human microbiome has entered into the popular consciousness. A microbiome is a community of microbes, a collective genome. Dr DeLong joked that every microbiologist is a microbiome. Dr DeLong showed two funny pictures of microbe-hunting (manual sampling, remote sensing, and in situ surveys- a picture of three guys in a rowboat and a picture of a small boy with muddy hands). The environment of a microbiome could be measured in microns or, in the case of the ocean, meters. New genes and new gene functions are being discovered- novel opsin genes, similar to the opsin genes in human eyes, were discovered in bacterial genomes. The bacterial opsins can make energy from light. Over fifty percent of bacteria at the ocean's surface have opsins to boost energy, even though they are heterotrophs. Dr DeLong likened them to hybrid cars- this energy boost can enhance the bacterial growth and survival rates.

Dr DeLong then focused on the University of Hawai'i's Station ALOHA, an oceanographic research center in the open ocean a half-day's steam north of Oahu. Station ALOHA, led by Dr David Karl, has been in operation for about thirty years, studying changes in the ocean, such as this pH curve:

As carbon dioxide is released into the atmosphere, some of it is absorbed by the ocean, which becomes more acidic, hence the lower pH.

Station ALOHA also surveys the oceanic microbiome, establishing a station gene catalog. Near the bright surface, there is a lot of life, such as bacteria and diatoms, but very few nutrients. At a depth of 125 meters, a chlorophyll maximum is reached- in the darker transition region, more chlorophyll 'antennae' are needed to make photosynthesis possible. Below this transition zone, the amount of nitrogen in the water increases. Below this zone is a genomic transition zone- where a microbe is influences the types of genes it has and the types of organisms they are. The genomic transition zone is at depths between 25 meters and 75 meters.

Dr DeLong gave us a brief refresher course on DNA, composed of the four nucleobases: adenine, cytosine, guanine, and thymine. Adenine forms a base pair with thymine, cytosine with guanine. The GC base pair can be used taxonomically- between 25 meters and 75 meters, there is a low incidence of GC base pairs. At 125 meters, GC base pairs increase, reaching a maximum at 200 meters, then declining. The increasing incidence of GC pairs corresponds to increasing nitrogen content. AT base pairs contain seven nitrogen molecules while GC base pairs contain eight.

Dr DeLong then briefly asked the question, where is the field heading? How are genomes related to environment, to metabolism, to ecology? The brief answer is that more sampling is needed so better models can be developed. Ultimately, the goal is to be able to predict the ocean's 'bio-weather', which is being increasingly affected by human activity. Humans are the only non-microbial organisms that can fix nitrogen, and we are adding additional nitrates to the oceans.

The lecture was followed by a Q&A session. The first question regarded post-Fukushima reactor findings- Dr DeLong indicated that they are tracking the situation closely but the results are not known yet. Another question regarded oceanic dead zones, or Oxygen Minimum Zones- nitrates can cause blooms of photosynthetic plankton which then die off and draw down the oxygen content of the water, in which fish cannot live, causing die-offs. There is a longstanding OMZ in the Gulf of Mexico- the Mississippi Plume, at the mouth of the river. A new OMZ has developed off the coast of Oregon. Another question regarded the shotgun hypothesis, which posits that warming waters could cause frozen methane clathrates at the bottom of the ocean to evaporate, releasing methane, which is a worse greenhouse gas than carbon dioxide. Another question regarded biodiversity- as the ocean becomes more eutrophic, certain organisms dominate, such as phytoplankton blooms. In another case, as fish are removed from the ocean, jellyfish populations bloom. Dr DeLong posed a conundrum- do microbe species go extinct?

Some bastard in the audience, keeping on the doom and gloom topic, asked about the effects of the Pacific Plastic Gyre on the ocean's biomes. Dr DeLong's immediate answer was 'Did you read our paper?' No... but I'm THAT guy. The plastic gyre in the mid-Pacific contains an average of one piece of plastic per cubic meter of seawater. The plastic is devastating to vertebrates, which ingest pieces of plastic. The pieces of plastic act as tiny reefs on which bryozoans and corals can colonize.

Other questions regarded the use of phytoplankton to absorb atmospheric carbon and sink it to the ocean bottom. By inducing blooms, uncontrolled systems result, which could cause problems. We can't control which species proliferate- geoengineering solutions are generally not viable. A question about how high GC organisms from high AT organisms elicited the response that genomes increase in size below the chlorophyll maximum. Steady surface conditions are conducive to low variability- as organisms follow each other in lockstep transferring nutrients, genomes can shrink. Deeper down, as conditions are more variable, stochastic environments, bigger genomes and more genetic diversity are conducive to success.

The lecture ended on a bit of a pessimistic note when an audience member asked Dr DeLong's opinion on the current political climate. The climate for climate science is not improving. Reports are held up, funding is decreasing. Dr DeLong brought up using a tactic of changing wording but keeping the same science to get by industry gatekeepers. He noted that science will move forward, and that scientists won't back down. Now, THAT is the Secret Science Club attitude this nation needs.

Once again, the SSC served up a fantastic lecture. Kudos to Dr DeLong, Margaret and Dorian, and the staff of the beautiful Bell House. On another happy note, my friend Sensei ____ came down to the lecture with her roommate, who just happens to be studying algae, albeit freshwater forms. High fives all around!

Here's a video of Dr DeLong discussing Station ALOHA:

Grab a beverage, and soak in that secret science, with a side of defiance.


mistah charley, ph.d. said...

i find my sense of wonder can still revive from time to time

i was a biology major for a semester, back in the '60s - i had to give it up when i dropped the intro biochem course

a lot has been discovered since then

maybe you would find this interesting:

Big Bad Bald Bastard said...

Thanks for the comment and the link, mc!

My mind is still blown by the whole 'AT/GC contrast' as a means of nitrogen conservation. You look at base pair diagrams and don't necessarily think about the implications of the extra N.