CHAPTER 1: SELF-STUDY QUESTIONS:

-What is the difference between global and local N-cycling?

Global N-cycling: The global nitrogen cycle is central to the biogeochemistry of the Earth, with large
natural flows of nitrogen from the atmosphere into terrestrial and marine ecosystems through
biological nitrogen fixation (BNF), in which the largely un-reactive molecular nitrogen is reduced to
ammonium compounds. Nitrogen gas (N2) makes up nearly 80% of the Earth's atmosphere, yet
nitrogen is often the nutrient that limits primary production in many ecosystems. Why is this so?
Because plants and animals are not able to use nitrogen gas in that form. For nitrogen to be available
to make proteins, DNA, and other biologically important compounds, it must first be converted into a
different chemical form (NH3; ammonia). The process of converting N2 into biologically available
nitrogen is called nitrogen fixation. This can happen in Oceans and Lakes and is influenced by many
factors including human activities.
Local N-cycling:
The nitrogen cycle also operates at a much smaller scale, cycling within an ecosystem whereby
nitrogen travels from the plants, back to the soil, and then back to the plants – we can think of this as
the local nitrogen cycle. Think of the N-cycle in the intestines whereby certain microbes can use NO
produced by the host under inflammatory situations.

-What is a biofilm and how does growing in a biofilm affect performance by bacteria?
Biofilms are the colonization of microorganisms on the solid surface of substratum or may form
complex aggregates without adhering to the surface. The biofilm can protect the bacteria from
antibiotics because by forming an aggregate and coating the surface with mucus/slime makes it
difficult to for the antibiotic to reach the bacteria deep within.

-Name the three different types of Horizontal Gene Transfer

Conjugation: a donor bacterial cell makes contact with a receptor bacterial cell via a (sex)pillus. This is
a small hollow tube that allows for the transfer of DNA, mainly via plasmids.
Transduction: bacteria can pick up ‘foreign’ or ‘non-self’ extra-chromosomal DNA after infection by
bacteriophage.
Transformation: in which a bacterial cell can take up DNA from the environment through the plasma
membrane.

-Explain how horizontal gene transfer can affect the bacteria and its interaction with the host, give an
example.
If a bacterium picks up a plasmid containing antibiotic resistance for example (trough conjugation or
transformation) or when a bacteriophage infects a bacteria and the bacteria survive it might have
introduced genes from other bacteria it has previously infected. In this way the bacteriophage
changes the DNA of the newly infected bacteria which thereby may obtain novel genes and have
increased fitness (or antibiotic resistance) as a result.

-Define the terms Microbiota, Metagenome and Microbiome

• Microbiota; the bacteria present within the biofilm or gut niche, characterized by their 16S rRNA
gene. (Some authors prefer to use the term ‘microbiota’ only to indicate bacteria and use the term
‘virome’ to refer to the collective of host-associated viruses, and to use the term ‘mycobiome’ to
refer to host-associated fungi including yeasts). In this reader, ‘microbiota’ is used to indicate host-
associated bacteria.
• Metagenome; represents all the genetic material present in the biofilm or specific niche: the
genomes of the bacterial species and the plasmids and bacteriophages which were present in that
biofilm at the time of sampling.
• Microbiome; the environment where microbes occur together with their (secreted and internal)
metabolites as well as with the host metabolites and proteins, some of which may have antimicrobial
activities.

-What is a ‘holobiont’ and what do CAZymes have to do with this?

The term ‘holobiont’ refers to the animal host together with all its microbial symbionts and can be
used to highlight that a multitude of metabolic processes are shared between host animals and
bacterial symbionts.
Rather than the host animal, specific gut bacteria contain so-called ‘polysaccharide utilisation loci’
(PUL) in their genomes, which code for genes that enable these bacteria to produce the
carbohydrate-active enzymes or ‘CAZymes’. These enzymes degrade the complex carbohydrates and
enable animals to grow on starch-based feeds. Specific bacteria usually degrade chemically related
polysaccharides, and different habitats contain different CAZymes producers, depending on the
substrate. This example highlights that the holobiont (animal and microbes together) can degrade
and utilise complex carbohydrates for its growth and development, whereas the complex-
carbohydrate-non-degrading host animal cannot manage this on its own.

-How many bacterial cells do we have approximately in each location? And how does that relate to
the number of cells humans have?
Different locations have different numbers of bacteria. They range from 103 in the stomach to
sometimes more than 1011 in the colon and for example on the skin. We have approximately 10x
more bacterial cells than human cells, but in terms of genes, together our bacteria contain about
100x more genes than our human DNA encodes for! These numbers keep changing, since we keep
uncovering more and more new species and genes.