Samenvatting Mariene wetenschappen 3 (III) B-B3MSCI05

What is a taxon?

Answer: A taxon is a group of organisms that share a number of features / traits as defined by the taxonomist.

Explain what a species is.

Answer: A species is the taxon of lowest taxonomic rank and the essential unit of genetic and ecological diversity.

In principal, how do you show that organisms are from two separate species?

Answer: To show that two organisms are from two separate species, one needs to show that they belong to two groups of organisms that are genetically isolated from each other (i.e. there is a barrier to gene flow between these two groups of organisms).

In practice, how are bacterial and archaeal species defined?

Answer: Considering that it is unpractical and often impossible providing limited time and resources to show that groups of organisms are genetically isolated from each other, bacterial and archaeal species are defined based on what is called on operational (ad hoc) criterion: one defines two species when the sequence of a taxonomic marker gene (i.e. the 16S rRNA gene) of two groups of organisms share less than 98.7% sequence identity.

Explain the concept of ‘the rare biosphere’.

Answer: The concept of the ‘rare biosphere’ refers to the idea that the vast majority of living species on earth and especially the vast majority of archaeal and bacterial species consist of rare organisms that are rarely / almost never observed.

If true, what is the challenge that the rare biosphere poses for studying the diversity and distribution of bacteria and archaea?

Answer: If most bacterial and archaeal species are rare, we may not learn about any of these rare organisms any time soon as detecting the presence of these organisms in environmental samples using current DNA sequencing technologies requires a volume of sequencing, which is beyond the capacity and budget of any sequencing facility and data processing center. For now, we may only learn about the most abundant species.

What is an organotroph?

Answer: An organotroph is an organism which uses an organic molecule as an electron donor.

Is an organotroph the same thing as a heterotroph? Explain your answer.

Answer: No an organotroph and a heterotroph are not the same thing. A heterotroph is an organism that uses an organic compound as carbon source. Heterotrophic organisms can be lithoheterotrophs for example meaning that they use an inorganic electron donor and therefore are not organotrophic. Similarly, some organotrophs can be organoautotrophs, meaning that they use CO2 (inorganic compound) as carbon source and therefore are not heterotrophic.

Define what is an aerobic chemolithoheterotroph and an anaerobic chemoorganoautotroph?

Answer: An aerobic chemolithoheterotroph is an organism, which uses chemical energy as driver of its metabolism, an inorganic compound as electron source, O2 as electron acceptor and an organic compound as a carbon source. An anaerobic chemoorganoautotroph is an organism, which uses chemical energy as driver of its metabolism, an organic compound as electron source, a compound other than O2 as electron acceptor and an inorganic carbon-containing compound (generally CO2) as carbon source.

A hypothetical organism was determined to grow in the dark by using acetate as carbon source, ferrous iron (Fe2+) as electron donor and nitrate (NO3-) as electron acceptor. In which category would you classify the metabolism of this organism? Explain your answer.

Answer: It is an anaerobic chemolithoheterotroph. Growing in the dark indicate that visible light is not an energy source and that the organism is a chemotroph. Ferrous iron is an inorganic substance meaning the organic is a lithotroph since it uses ferrous iron as electron donor. Acetate is an organic compound, meaning that the organism is an heterotroph since it uses acetate as carbon source. Nitrate is an inorganic ion, meaning the organism is an anaerobe since it uses nitrate as electron acceptor.