Deep sea vent
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Description of Niche
Hydrothermal vents, also known as deepwater seeps, deep-sea springs, and deep sea vents are the aftermath of a volcanic eruption due to shifting of the plates that form the Earth’s crust . The shifting causes cracks to form when the earth’s plates are pulled apart along the Mid-Ocean Ridges. This allows water to seep directly into the cracks and become heated by the magma chambers up to around 400oC. Typical to these sites are the columnar chimneys, black and white smokers that are formed due to the high pressure at this depth and the temperature of the trapped water. The hot water is forced out of the cracks dissolving minerals and chemicals from the rocks, which forms a chemical plume.
Within a year, what flow through these now mature sulfide chimneys are high-temperature fluids. The chimneys form to a height of 10 to 20 meters. The black smokers emit fluids at 400oC or above causing it to emit chemicals such as sulfide, iron, copper and zinc. When the chemicals and the hot water interact with the low pH of the surrounding water, black precipitation occurs, giving black smokers its name. The white smokers emit fluids at 100-300oC in temperature. At the lower temperatures, the silica, anhydrite, and barite precipitate as white particles instead of black.
Hydrothermal-vent fields range from several hundred to several million square meters. It is also because of the larger range of the vent fields that allows for the low-temperature diffuse flows. It is the warm-water diffuse that allows for the sustainability of productive populations and organisms.
Although some hydrothermal vent organisms have adapted to the high temperatures, it is the chemistry of the fluids, which takes place because of the high temperature, that sustains the chemosynthetic basis of life at hydrothermal vent ecosystems.
Where located?
Physical Conditions?
What are the conditions in your niche? Temperature, pressure, pH, moisture, etc.
Influence by Adjacent Communities (if any)
Is your niche close to another niche or influenced by another community of organisms?
Conditions under which the environment changes
Do any of the physical conditions change? Are there chemicals, other organisms, nutrients, etc. that might change the community of your niche.
Who lives there?
Microbes Present
Many different kinds of archaea and chemolithotrophic bacteria live here. Studies have classified entire archaeal communities in deep-sea hydrothermal vent chimney structures. (http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=11472939) Scientists discovered deep-sea hydrothermal vents in 1979 and many microorganisms have been isolated from these deep-sea samples.
The majority of the microbes that live in this niche include hyperthermophiles and thermophiles from both the bacterial and archaeal domains. Recent studies have shown and increasing number of unclassified and uncultivated thermophiles. This leads scientists to believe that these communities are very phylogenetically diverse. Major types of bacteria that live near these vents are mesophilic sulfur bacteria. These bacteria are able to achieve high biomass densities due to their unique physiological adaptations. For example, Beggiatoa spp. is able to carry an internal store of nitrate as an electron acceptor that helps with the harvesting of free sulfide in the upper sediment region of the vents. Page 70
Some bacterial samples contained bacterial specific to the genera Thermotoga and Thermosipho. An analysis of a specific morphotype revealed that it was an anaerobic autotrophic sulfur and thiosulfate-reducing strain of bacteria but did not belong to any known phyla. It belongs to a branch between the orders Aquificales and Thermotogales. The new bacterium was named Desulfurobacterium thermolithotrophicum.
Recent studies have shown that large populations of extremely halophilic archaea inhabit the inside structures of black smoker chimneys. These bacteria belong to the genera Halomonas and Marinobacter. The existence of these halophilic archaea is probably due to the brines/salt deposits found in deep-sea hydrothermal systems. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=11472939
Based on microbiological, geochemical, and geophysical observations, some scientists believe that a whole new biosphere exists beneath active hydrothermal vents. This idea is supported by the detection of microbial rDNA in the black smoker vent water. However it is difficult to conclude if there is a true microbial population living under black smoker vents because deep ocean water is continuously being filtered underneath sea floor basalts and pumped out of black smoker vents. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=11472939
Are there any other non-microbes present?
Plants? Animals? Fungi? etc.
Microbe interaction with each other or other organisms
The hydrothermal vent tubeworm Riftia pachyptila is well-known for its symbiotic relationship with sulfide oxidizing chemoautotrophic bacteria found in the cells of its trophosome tissue. The tube worms have no gut so the bacteria live inside them. Tubeworms have red plumes which contain hemoglobin. The hemoglobin combines hydrogen sulfide and then gives this product to the bacteria. The bacteria, in return, give back carbon compounds to the worm. This interaction requires specific communications mechanism in both the bacteria and the worms. Scientists have found two classes of genes from Riftia symbionts that encode for environmental sensors, response regulators, and components of bacterial chemotaxis systems.
In detail, scientists have found functional genes encoding the following: members of the two-competent regulatory family, the methyl-accepting chemotaxis protein, and the flagellar C protein of the eubacterial flagellum. These functional genes strongly support the idea that these bacteria have a motile, free stage and are then acquired by Riftia each new generation. (page 71)
Do the microbes change their environment?
Do they alter pH, attach to surfaces, secrete anything, etc. etc.
Microbe metabolism affecting the environment
The primary source of metabolism for providing food is through animal-bacteria symbiosis. These bacteria are typically chemolithotrophic bacteria. In many worms, they have a layer of tissue called trophosome that fills the body cavity and allows these chemolithotrophic bacteria to live symbiotically in these trophosomes where they can oxidize sulfide. Enzymes in the trophosome also have the capacity to oxidize hydrogen sulfide. The energy produced can be used to drive net fixation of CO2 and to reduce nitrate to ammonia. A mechanism to avoid poisoning aerobic respiration by hydrogen sulfide is protected by sulfide binding proteins in the blood. The idea is to prevent as little free floating sulfide as possible.
Many invertebrates also show a range of O2 consumption that is similar to species that live closer to the surface. Besides a difference in thermal effects, there is no decline of O2 consumption, strongly indicating the importance of endosymbionts. Other organisms, such as deep sea pelagic animals will show a lower O2 consumption due to its inability to swim. If they lose the ability to swim, they can save that energy and lower their O2 consumption.
Current Research
1. Current research is being done to learn more about photosynthesis evolution. Some scientists believe that photosynthesis evolved from geothermal vents and then sunlight. This idea raises the possibility that photosynthesis originated from deep-ocean hydrothermal vents and then dispersed upwards to shallow-waters and more sunlight. The first photosynthetic bacteria to be found living at deep sea vents were discovered in 1998. The overall question was: what were the morphological and physiological properties of this new bacterium.
They addressed this question by extracting samples from non-buoyant regions of plumes emitted from the hydrothermal vents. The scientists then brought the samples on board the ship and stored them in sterile bottles at 4 degrees Celsius. The scientists plated the bacteria and incubated them aerobically at room temperature in the dark for 5 days. After the colonies were identified, the bacteria were incubated at 30 degrees Celsius for another 5 days. The bacteria’s capability for anaerobic photosynthetic growth was tested in screw-cap test tubes and in agar by using media for purple sulfur and non-sulfur bacteria. However, none of the strains tested were able to grow anaerobically in light.
This particular species had bacterial chlorophyll alpha and carotenoids. It is a member of the aerobic anoxygenic photosynthetic bacteria due to its following characteristics: the inability to grow anaerobically in the light, the small number of photosynthetic units it has, and its abundance of carotenoids. Aerobic anoxygenic photosynthetic bacteria belong under the subclass of Proteobacteria.
Aerobic anoxygenic photosynthetic bacteria are different in comparison to purple sulfur or non-sulfur bacteria, because they can utilize light as a source of energy for anaerobic growth. Photosynthetic activity in these bacteria is shown by the following three characteristics: the reversible photo-oxidation of cytochromes and the reversible photo-bleaching of bacterial chlorophyll, photo-inhibition of respiration, and light-stimulated increase in ATP pools which lead to an increase in growth rate and biomass production. The scientists concluded that light is a secondary source of energy for these bacteria.
2. α-Amylase is an enzyme that hydrolyzes starch by cleaving α-1,4-glucosidic linkages at random sites. This enzyme is widely used in starch-processing, brewing, alcohol production, textile, and other different industries. α-Amylase is one of the most important commercial enzymes. The most thermostable α-amylase that is used in industries is produced from a microbe called Bacillus licheniformis. The enzyme produced by this microbe operates optimally at 90°C and at a pH of 6.0, but it also requires addition of calcium ion, Ca2+, for maintaining its thermostability. Starch bioprocessing has two steps, liquefaction and saccharification. The most ideal conditions for these two steps are for them to be performed at 105°C and pH 4.5. However, the α-Amylase from Bacillus licheniformis is the best enzyme to use for the liquefaction step and the pH must be raised to 5.7-6.0 and calcium salt needs to be added for thermostability. Then the saccharification step uses a glucoamylase isolated from an Aspergillus sp. which requires the pH to return to 4.5 to work efficiently. These two modification steps increase chemical costs and create additional refining steps to remove the calcium salt from the final product. If an α-amylase that is able to work at pH 4.5 and 105°C without the addition of calcium is to be found then it would greatly reduce costs and simplify the process of starch bioprocessing. An extremely thermophilic anaerobic archaeon strain of Thermococcus, HJ21, was isolated from a deep-sea hydrothermal vent. This strain was found to be able to produce hyperthermophilic α-amylase named THJA (Thermococcus HJ21 amylase). The HJ21 strain was isolated and grown on different mediums to determine the optimal growth conditions. The genomic DNA was extracted and the 16S rRNA was amplified and sequenced. Protein purification of the α-amylase was performed to test the effects of pH and temperature on the activity and stability of THJA. The extracellular thermostable THJA is found to be most efficient at pH 5.0 and at a temperature of 95°C. This enzyme also did not require calcium ion for thermostability. This newly found enzyme opens the door of opportunity to find a much more efficient way to process starch. It can help reduce the cost and greatly reduce the amount of work needed in the bioprocessing of starch. This can lead to development for better efficiency in other industries that use α-amylase.
Wang, S., Lu, Z., Lu, M., Qin, S., Liu, H., Deng, X., Lin, Q., and Chen, J. “Identification of archaeon-producing hyperthermophilic α-amylase and characterization of the α-amylase”. Applied Microbiology and Biotechnology. 28 Jun 2008.
3. DNA bacteriophages lyse the host cell by using a two component lytic system consisting of two proteins, holin and lysin. Holins are small proteins without any known enzymatic function other than controlling the timing of lysis and to form pore in the cytoplasmic membrane of the host. These pores allow lysin to access the peptidoglycan layer of the host cell. Lysins are proteins with one of several muralytic activities, responsible for the destruction of the peptidoglycan. The destruction of peptidoglycan plays an important role in the infection of the bacteriophage. When the bacteriophage infects a host bacterium, the lysin of the bacteriophage digests the cell wall of the host from the outside. Then, the phage injects its genome into the host bacterial cell. A lot of lysins that have been found are obtained from bacteriophages that infect mesophiles. However, very few lysins are obtained from thermophilic bacteriophage. The thermophilic bacteriophages from deep-sea hydrothermal vents will greatly improve the study and understanding of the lysis mechanismof bacteriphages under thermophilic conditions. In a recent study, a lysin-encoding gene was cloned from a deep-sea thermophilic bacteriophage Geobacillus virus E2, GVE2. After recombination and expression of the lysin gene in E. coli the GVE2 lysin was purified. The lysin was highly active when enzyme inhibitors or detergents were present but was strongly inhibited by sodium dodecyl sulfate and ethylene di-amine tetra-acetic acid. The lysin’s enzymatic activity was also slightly stimulated by Na+ and Li+ but slightly inhibited by metal ions like Mg2+, Ba2+, Zn2+, Fe3+, Ca2+, and Mn2+. This study was the first time the characterization of lysin was obtained from deep-sea thermophilic bacteriophage. This can open up bacteriophage lysins as possible antimicrobial agents against gram-positive bacteria. There is also potential for the use of lysins as a prophylaxis and treatment of bacterial pathogens. Since peptidoglycan is not found in eukaryotic cells, lysins can be expected to be well tolerated by humans. This opens up opportunities for research to use lysin as antimicrobial agents in protecting plants and crops and even in food.
Ye, Ting and Zhang, Xiaobo. “Characterization of a lysin from deep-sea thermophilic bacteriophage GVE2”. Applied Microbiology and Biotechnology. Mar 2008. Volume 78: p. 635–641.
References
Edited by [Vicky Chen , Vicky Kuo , Ban Lam , Pan Lu , Tam Pham , Cassie Tom], students of Rachel Larsen
