It’s hard to fathom what it’s like to live in the abyssal sea, miles below the sunlit world we experience. Dark, cold, high pressure, all the time. Living in such a habitat is so foreign to the way we interact with the world. Yet life in this deep-sea world is directly coupled to the world we know—life-supporting energy input to the deep sea arrives from above, in the form of sinking particles. These particles include dead and decaying organisms, fecal wastes, and discarded mucous-like webs used by marine invertebrates to catch their prey. The energy to make these particles can be traced back to harvesting of sunlight in the upper ocean by photosynthetic microorganisms. These particles gradually settle to the bottom of the sea, where they support the energetic needs of organisms that permanently reside on the ocean’s bottom.
The most abundant of these deep-sea organisms are microbes – tiny single-celled organisms too small to be seen without high-powered microscopes. At upwards of a billion cells per milliliter of seabed sediment, microbes are truly the invisible majority. Microorganisms are the oldest inhabitants of Earth, and over the course of billions of years, they have had a major role in shaping the habitability of our planet. They are enormously diverse, including all three domains of life: Archaea, Bacteria, and Eukaryotes. They range in size from submicron to a few microns; for perspective, the width of a human hair in ~100 microns, so hundreds of these microbes could be lined up, end-to-end, across a hair. Despite their vast numbers, we know little about who these organisms are, what they are doing, how fast they reproduce, or how they are distributed across deep-sea ecosystems.
Our research group, consisting of Drs. Emma Wear and Matthew Church from the Flathead Lake Biological Station at the University of Montana, is studying who these microorganisms are, what types of chemical reactions they catalyze, and how they interact with other organisms in the vast Clarion-Clipperton Zone (CCZ) ecosystem. We are harvesting microbes from seawater, sediments, and polymetallic nodules for subsequent analyses of nucleic acid sequences (DNA and RNA). We will use these samples to assess whether there are distinct communities of microbes in different habitats in the abyss and provide insight into the functioning of these ecosystems across the CCZ.
In many ways, our work is exploratory, obtaining new information on the role of microbes in sustaining life in one of Earth’s largest ecosystems – the abyssal seafloor. This cruise is our first experience working with deep-sea sediments—our past research has focused on microorganisms living in the seawater, so working in the mud presents exciting new challenges.
During the cruise, we have collected seawater samples and abyssal plain sediments. We collected seawater samples from the surface of the ocean down to five meters above the sediment. These samples will be used for analyses of nucleic acids to tell us what microbes are there and what they’re doing; cell abundances; and nutrient profiles to tell us about the environment the microbes are experiencing.
We sample seawater using an instrument package that measures temperature, salinity, and depth of the water. This instrument is deployed from the ship on a conducting wire, providing real-time data that allows us to examine the physical and chemical structure of the entire water column from the surface to the seabed.
This instrument package is also equipped with 24 ten-liter sampling bottles, which are open at both ends when deployed, but can be closed to capture water at up to 24 different depths. For sampling sediments, we use small coring tubes; the remotely operated vehicle pushes the tubes into the soft sediments, retrieving a vertical section of the mud.
Nucleic acids, DNA and RNA, are especially valuable for studying microorganisms. Very few marine microbes can be isolated and grown in the laboratory—as a result, our understanding of what these organisms are doing has required new approaches that do not rely on cultivation. The study of microbes has been transformed in recent decades by advances in nucleic acid sequencing technologies. DNA and RNA sequences have helped us to better understand which types of microorganisms are found in specific habitats and to identify key functions these organisms perform. These functions are driven by the action of proteins and the assembly manual life uses to make proteins is written in nucleic acid sequences. Hence, through sequencing this DNA, we have begun to identify the specific biochemical pathways these organisms use for reproduction and growth, acquisition of nutrition and energy, and strategies for defense and handling of waste products.
These sequencing approaches provide clues about how microbes have adapted to life in the energy-starved deep sea. Many feed on the organic matter contained in sinking particles as a source of energy and nutrition; such microbes are termed heterotrophs. Others are capable of growing on the waste products of heterotrophs, acquiring energy through oxidation of reduced molecules like ammonium, nitrite, and sulfide. Such microorganisms frequently also use carbon dioxide, similar to a plant, but using chemical energy rather than sunlight to fuel the process. The coordinated activities of these microorganisms sustain life in one of Earth’s largest ecosystems – the abyssal seafloor.