Archaea

Microbiology

Nameinstitution

Unit

Outline

Thepaper is organized into three major sections. The first sectionprovides an overview of the in context of microbiology. Thesection introduces the topic and provides a brief history on thestudy of archaea. It provides a discussion on various characteristicsof archaea such as their environment, how they reproduce, their DNAand how they differ from one another.

Animportant aspect critical in the study of archaea is their differentenvironments. This section is arguably longer than the rest as itexplains the two main categories of archea that have receivedconsiderable research attention to provide an understandable level ofknowledge

Thesecond section of the paper provides a summary and analysis to twomajor studies on the subject. One of the studies in by Baker andcolleagues which details the research into Gulf of California on acategory of archae that whose findings are summarized. The secondstudy addresses the Pacific to provide a point of reference to thefirst study that samples the waters of the Gulf of California.

Theseare phylogenetically coherent group of prokaryotes, meaning they haveno cell nucleus or any organelles within the membrane that enclosethe cell, that have a different organization than the bacteria. Thelineage of archaea was first discovered by Carl Woese in 1977 and by1996 together with other researchers published the first completegenome structure of an archaeon, Methanococcusjannaschii (De-Long,2003)

  • structure: cell wall, membranes and what is it made of?

Thereare three basic parts of archaeon cell cytoplasm, cell membrane andcell wall. This gives them the same structure as other organisms suchas bacteria but the main difference in that archaea build theirstructures from different chemical components. The cell membranecomprises of isoprene chains, L-glycerol and phosphate. In most casesthey are less than one micron long (Dos Santos 2012).

  • Where is archaea found

Initially,archaea were thought to survive in very extreme conditions such ashigh temperatures of 100◦C. There have been recorded cases wherethese organisms were found in environments that were previouslythought they could not support life. Further research however,revealed that they existed in diverse and less extreme environmentssuch as in soils and oceans (Leigh 2000). Their diversity and abilityto survive in extreme conditions has thus been very helpful toresearches keen to understand the bare minimum conditions that cansupport life.

  • Conditions in the deep ocean. How does archaea survive?

Conditionsin deep oceans are considerably extreme with no sunlight and nooxygen. However, archaea have managed to survive in these conditionsthat were previous thought could not support life. They manage tosurvive through sourcing energy from different sources. For one classof archaea, it surveys with no oxygen or sunlight by breaking downcarbon dioxide to methane (natural gas) with hydrogen being thereducing agent. For other in the class lithotrophs, they sourceenergy from inorganic compounds such as ammonia and sulfur (DosSantos 2012).

  • Nitrogen fixation(briefly)

    • Ammonia oxidizing cycle nitrogen and carbon

Ammoniafixation among the archaea is most abundant among the phylumThaumarchaeota commonly found in diverse environments. The archaeahas also developed a way of surviving i n nutrient limitedenvironment such as oceans. They assimilate inorganic carbon via amodified version of the autotrophic hydroxypropionate/hydroxybutyratecycle of Crenarchaeota and produces more energy as opposed to othermethods.

  • How is this archaea different than other archaea?

Therehave been observed to use a closely related cycle to nitrogen fixingbacteria. However, the methods are different in the sense thatnitrogen fixation in methanogenic Euryarchaeota only takes place inthe phylum Euryarchaeota.

Thegenetic composition of the archaea also influences the nitrogenfixation cycle. From afar, the archaea seems to share many genes withbacteria because of common proteins. However, there are keydifferences. The archaea have a singular gene carrying chromosome.The genetic composition of the different types of archaea determinestheir environment. For instance the DNA polymerase amino acid for onetype of archaea (Crenarchaeota) is thermal unstable and isinactivated at 40oC, forcing the organisms to reside in cooler anddeeper waters.

  • DNA

Genomesequence data has enabled more identification of Achaea through theirpotein component which is highly influenced by their environment. Inthe case of M.burtonii for instance, those which live in environmentsof 4°C, and 44 proteins have a different gene sequence from thoseliving in environments of 4°C and 23°C (Cavicchioli2006)

  • Different kinds at different depth?(from broad to 2 specific ones found in 2 different oceans)

Thereare two main types of Achaea found in oceans at different depthsCrenarchaeota (Marine group I) and Euryarchaeota(Marinegroup II).The Crenarchaeota survives better at deeper levels of more than 4000mbelow sea level while the Euryarchaeota survives better in 0-100mbelow sea level (Cavicchioli 2006). Among the many variants ofcrenarchaeotafound in deep waters,the Cenarchaeum symbiosum has been discovered to be living insidecoastal marine sponge Axinella Mexicana in a symbiotic relationshipand absent in surrounding waters. As a result of this symbioticrelationship, this specific crenarchaeotamanages to survive in environments way much warmer than what othercrenarchaeota would stand (DosSantos etal.2012).Inthe Euryarchaeotaphylum, there is more phenotypical diversity with eight classesrecognized. Three of the most common classes are methanobacteria,methanothermeaand methanopyri.A common species is methanopyruskandleriwhich can survive in temperatures of over 100C and even reproduce at122C with enough presence of hydrogen-carbon dioxide. However, thosecommon is salty oceans waters include the class halophiles with acommon species being halococcusdombrowskii commoninhighlysalty waters and lakes.

  • How abundant is deep ocean archaea

Theabundance of deep ocean archaea changes with depth. At about 1000mdeep, the MGI comprises about30% of the microbial organisms whichincreases to 35% at 3000m (DeLong 2003). Studies have also revealedthat in most environments bacteria exceeds archaea but this notalways the case Baker (2006) revels in his study in the Gulf ofCalifornia.

  • Metabolism and energy

Theseare different categories of archaea with the majority evolved to fitin with their environment. For archaea that sources its energy fromorganic components, they thrive best environments that supply suchmaterials. Others have adapted well to their environment to utilizeavailable sources of energy. For anaerobic arachea, they surveywithout oxygen by for instance making use of carbon dioxide. Forarchaea that suruvei on inorganic elements such as sulfur, they havedeveloped complex mechanisms to utilize such materials for energy. Toactivate key enzymes to carry out metabolic processes, catalysts mustbe present in the environment e.g. optimum pH or temperature. Some ofthese enzymes get denatured in extreme conditions such astemperatures thus limit distribution of archaea (Leigh 2000).

  • Photosynthesis?

Althoughsynonymous with multi-cellular plants, photosynthesis is also commonin some archaea called phototrophs.They utilizes energy from the sun in form light to anabolicallyconvert carbon dioxide into organic matter that can be metabolized toprovide energy. .

Reproduction

Asliving organisms archaea reproduce for survival. Given that they donot have gametes, they rely on binary fission to rapidly reproduce.It largely involves the single DNA molecule which holds thechromosome when it replicates following a complex sequentialprocesses. When the molecule divides, each part moves towards the endof the cell and through furrowing the cell divides itself into two(Leigh 2000).

Industrialuse

Archaesehave been applied in industries since the beginning of the 20thcentury. The first industrial application of archaea was as acatalyst for a detergent enzyme. In the modern word, archiase is moreapplied in the nutrition industry for developing enzymes for variouspurposes. The technology is also applied in industrial biochemicalprocesses. The same has also been applied in agriculture inproduction of organic manure.

1stresearch

Baker(2006). Genome-enabled transcriptomics reveals archaeal populationsthat drive nitrification in a deep-sea hydrothermal plume

Thisstudy examines distribution of Ammonia-oxidizing (AOA) in the ammoniums rich waters of Guaymas Basin (GB) inthe Gulf of California. The study involved collection of watersamples from the waters and transcription of novel genes to identifytheir genomic sequence as influenced by water environment. Genomicdata was also collected alongside the Nitrogenand energy metabolism of GBdata. Theresearch was also inspired by the need to understand the role andplace of archaea in the global climate change debate and greenhousegasses emissions.

Resultsindicated a large population of MGI in the study area with severalgenus identified. A total of seven MGI were identified with 16S rRNAgenes. The study sought to understand the distribution and role ofeach phylotype. MGI ammonia oxidizers archaea were dominant negatingprevious views that bacteria dominates environments with highammonium concentration

2ndresearch

Sato-Amano(2013). ldistribution and abundance in water masses of the Arctic Ocean,Pacific sector

Thestudy assesses the distribution and archaea in the Artic and Pacificoceans using catalyzed reporter deposition -Fluorescence in situhybridization (CARD-FISH) . The research was interested inunderstanding how environmental and climatic changes affected thedistribution of archaea in the water masses. The study sought to showthe seasonal variation in archaeal distribution, an aspect that isnot comprehensively addressed in other studies.

Thestudy collected water samples from 4-11 different depths in eachsampling station. The samples were tested for temperature, salinity,dissolved oxygen, nutrient concentrations (nitrate, nitrite,ammonium, phosphate, and chlorophyll fluorescence. The samples werelater probed for Thaumarchaeota, Euryarchaeota, Bacteria, or anegative control. Some stations recorded higher nutrient levels thanothers while salinity and water temperatures varied. A correlationanalysis test for each archaeal group to determine the level ofinfluence of the environmental factors on the distribution of thearchaea. No single geochemical factors was associated withthaumarchaeal relative abundance at the various depts. Intervals andstations. A multiple correlation analysis showed that ammoniaconcentration has the greatest influence in thaumarchaeal relativeabundance with chlorophyll fluorescence and oxygen playingcontributory roles. A second analysis using Canonical correspondenceanalysis gave clearer results. Thaumarchaeota concentration was highest in highly saline waters withhalocline layer and higher nutrient concentration. On the overall,Thaum archaeota concentration was negatively correlated with levelsof ammonium, dissolved oxygen, and chlorophyll fluorescence.

References

Baker(2006). Genome-enabled transcriptomics reveals archaeal populationsthat drive nitrification in a deep-sea hydrothermal plume

Cavicchioli,R. (2006). Cold-adapted archaea. NatureReviews Microbiology,.4(5).331-343

De-Long,J. (2003). Oceans of : Abundant oceanic Crenarchaeota appearto derive from thermophilic ancestors that invaded low-temperaturemarine environments. ASMNews69, (10)-503-511.

Leigh,J. (2000). Nitrogen Fixation In Methanogens: The lPerspective. Curr.Issues Mol. Biol.2(4): 125-131.

DosSantos, P., Fang, Z., Masonm Mason, S. Setubal, J. &amp Dixon, R.(2012). Distribution of nitrogen fixation and nitrogenase-likesequences amongst microbial genomes. BMCGenomics13:162

Sato-Amano,Akiyama, S., Uchida, M. &amp Shimda, K. (2013). ldistribution and abundance in water masses of the Arctic Ocean,Pacific sector. AquaticMicrobial Ecology.69: 101–112.