Glossary of Marine Deep Biosphere Terms

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An anaerobe is an organism that relies on an energy-producing metabolism or metabolisms that do not utilize oxygen (O2, specifically). Anaerobes can be divided into three types. Obligate, or strict, anaerobes cannot tolerate and are poisoned by oxygen; examples include Clostridium bacteria, one strain of which can cause botulism.  Aerotolerant anaerobes can tolerate oxygen but do not use it. Facultative anaerobes can grow with or without oxygen; examples include E. coli and yeast (or even human muscle cells).

Archaea are microbes that often resemble bacteria in size and shape but contain genes and metabolic pathways that are more similar to those of eukaryotes. They are, however, genetically distinct from both Bacteria and Eukarya, the other two domains of life on Earth. Archaea are found in a broad range of habitats, some very extreme, and are numerous in the ocean. They are important to the Earth’s carbon and nitrogen cycles. N.B. the term “Archaea” replaces the now-defunct term “archaeabacteria”.

Autotrophs, also known as self-feeders or primary producers, are organisms that produce complex organic compounds, such as carbohydrates, fats, and proteins, from carbon dioxide using light energy (photosynthesis) or inorganic chemical energy (chemosynthesis).

Bacteria are a large domain of microbes that are present in most habitats on Earth, including the ocean and crust, and encompass a tremendous diversity of metabolisms. Bacteria are genetically distinct from Archaea and Eukarya, the other two domains of life on Earth. N.B. “bacteria” is the plural form of “bacterium.”

Biomass is all of the physical material, alive and dead, of biological origin for a designated sample or system. Biomass can be calculated as wet (including water mass) or dry (without). It is sometimes calculated on a carbon-specific basis, that is, the mass of all of the carbon excluding hydrogen, oxygen, nitrogen or another element. For example, a 150-lb. human would amount to about 14 pounds of carbon. The term is often used to normalize (adjust values measured on different scales to a single common scale) between different organisms of varying size in the same study. For example, the weight of one bacterium is very different from one jellyfish, but they can be compared in relation to one another when viewed in terms of biomass.

A biosphere refers to all the life present in a given system, integrating all the communities there, and generally separated from other environments. Often used to refer to Earth’s life in its entirety, the term can also apply to any closed, self-regulating system, such as an ecosystem. The deep biosphere constitutes all the life found starting several feet below the seafloor and extending far below the crust. We don’t yet know how far, exactly.

Chemosynthesis is the biological conversion of nutrients and simple carbon compounds, usually carbon dioxide or methane, into organic matter using chemical energy. This is exemplified by the microbes that live off of sulfur and / or metals brought up from below the surface, whether by nature (e.g. hot springs) or humans (e.g. mine tailings). Chemosynthesis is distinct from photosynthesis, which does the same thing using light energy.

Oceanic crust is the uppermost layer of Earth’s rigid lithosphere layer beneath the ocean. It is thinner yet denser than continental crust, because it is made from basaltic rather than granitic rocks. Oceanic crust is formed from Earth’s mantle at mid-ocean spreading centers on the divergent margins of tectonic plates.

Deep (How deep is deep, anyway?) The average ocean depth is 4000 meters or 2.5 miles; the deepest part is about 11,000 meters or almost seven miles deep (deeper than Mt. Everest is high). The ocean bottom itself when first formed is rock several miles thick and is gradually covered by sediment. Most of the seafloor is sediment covered. This sediment can build up over time to layers many hundreds of feet, or even miles, thick. Thus, a typical location in the ocean has a couple of miles of water on top of hundreds of feet of sediment, all of which is on top of several miles of crust.

Demersal refers to the habitat at the bottom of oceans or lakes, on top of the sea floor or lake bed. Familiar demersal fish include flounder, halibut, and cod, among many others.

A DNA base pair is a single unit of genetic information coded by double-stranded DNA (deoxyribonucleic acid). “Base” refers to the variable component (Adenine, Citosine, Guanine, or Thymine, also know as A, C, G, or T) attached to the standard molecular backbone; “pair” is used because every A, C, G, or T is typically bonded to its complement on the opposite strand, to make a pair (A always bonds with T and C always bonds with G). The human genome is a little over 3 billion base pairs; one Japanese flower, Paris japonicum, has a 149 billion base pair genome; bacteria typically have less than 10 million base pairs.

A drillship is a specialized vessel for drilling into the mud and rock of the seafloor. Typically, drillships are large, require a skilled crew to operate, and are very expensive to operate (advanced commercial drillships can cost more than a half-million dollars a day). Many dozen drillships exist for commercial purposes such as oil and gas drilling, but only two dedicated scientific drillships currently operate: the American JOIDES Resolution and the Japanese Chikyu. See ODP/IODP.

Eukarya is a domain of organisms that contains both microbial and non-microbial members. Some eukaryotes are unicellular and some are multi-cellular. Eukaryotes are well known for the specialized compartments (organelles) and nuclei found in their cells. Members of the Eukarya include protists, fungi, animals, and plants. Eukarya are genetically distinct from Archaea and Bacteria, the other two domains of life on Earth.

An extremophile is an organism that thrives in physically or geochemically extreme conditions that are detrimental to most life on Earth. Many extremophiles are microorganisms within the domain Archaea.

A genome is all of the genetic information, or DNA, of a given organism. The term can refer to either the genetic information of several different individuals of the same species or to the genetic information of different species entirely. Genomic refers to all-inclusive sets of genetic information. This is different from almost all data sets produced in previous decades, which often focused on specific genes or chromosomes.

Geochemistry is the study of Earth using tools and principles of chemistry to explain the mechanisms behind major geological systems such as Earth’s atmosphere, crust and its oceans. This study may extend to the entire solar system.

Geophysics is the study of Earth’s shape, gravitational and magnetic fields, internal structure and composition, dynamics and their surface expression in plate tectonics, the generation of magmas, volcanism and rock formation. The term can also be applied to many other studies associated with the planetary dynamics, such as study of the hydrosphere, dynamics of the oceans and atmosphere, and inter-planetary studies.

A halophile is an extremophile that thrives in environments with very high concentrations of salt and is found anywhere with a concentration of salt five times greater than the salt concentration of the ocean.

A heterotroph is an organism that cannot convert carbon dioxide into organic matter and uses organic carbon for growth. Heterotrophs take in material produced by autotrophs as food and they depend on autotrophs for the energy and raw materials they need.

A hyperthermophile is an extremophile that thrives in extremely hot environments, from 60ºC (140ºF) upwards. Many are also able to withstand other environmental extremes such as high acidity. The most hardy hyperthermophiles discovered live on the superheated walls of deep-sea hydrothermal vents.

IODP/ODP (International Ocean Drilling Program/Ocean Drilling Program)  The Ocean Drilling Program (ODP) was an international cooperative effort to explore and study the composition, history and structure of the Earth’s ocean basins. It began in 1985, the successor of the Deep Sea Drilling Project initiated in 1968 by the United States. ODP used the drillship JOIDES Resolution to collect deep sea cores from major geological features located in the ocean basins of the world. In 2004, ODP transformed into the Integrated Ocean Drilling Program (IODP), an international marine research program using heavy drilling equipment mounted aboard ships to monitor and sample sub-seafloor environments. The IODP documents environmental change, Earth processes, the biosphere, solid earth cycles, and geodynamics.

Microbes are organisms generally too small to see with the naked eye, encompass Bacteria, Archaea, Eukarya (including some plants, animals, and fungi), and sometimes viruses. Microbes can be single- or multi-cellular. The term is often used interchangeably with microorganism. The term microbial refers to microbes or their processes.

A prokaryote is a single-celled microorganism that, typically, has no nucleus or organelles, including both Bacteria and Archaea. Since scientists now understand the latter to be more closely related genetically to eukaryotes, many experts consider the term prokaryote to be outdated.

Protists are a diverse group of eukaryotic microbes that are mostly unicellular, or multicellular without specialized tissues. Many protists, such as algae and plankton, are vital primary producers in ocean ecosystems.  N.B. protists and prokaryotes are completely different groups of organisms.

A rogue planet is a rocky or gaseous body that is too small to light up like a star but does not orbit a star either. These bodies can form like “regular” planets, but they get ejected from their parent system by gravitational forces–think of a slingshot; they escape their home star’s gravity and do not return. Since they do not have a star’s light to reflect, they are extremely dark and hard to see, but may be exceedingly common in the galaxy (http://www.nature.com/nature/journal/v473/n7347/full/nature10092.html).

Sediment is a loose unconsolidated deposit of particles. Sediment is transported by various means such as wind, water, ice, and gravity, to rest in places like river deltas and ocean floors. Sediments can come from many origins: land, biology, volcanoes, outer space, or even the water itself. Deep ocean sediments tend to be finer-grained.

Subseafloor refers to the environment below the interface between the ocean and the seafloor and includes both muddy (sediment) and rocky (crustal) environments.

Thermodynamics is the branch of science concerned with heat and its relation to other forms of energy and work.

A thermophile is an extremophile that thrives at relatively high temperatures, between 45 and 122°C (113 and 252 °F). Many thermophiles are Archaea and are found in various geothermally heated regions of Earth, such as deep sea hydrothermal vents.