W5 Microbial Ecology

Question 1

why is direct counts of bacteria in natural samples typically much higher than those from viable plate counts

Answer 1

bacteria may require another bacteria to live: syntrophy

bacteria are dead

bacteria are virally infected and unable to form

bacteria are viable but nonculturable

the bacteria are cultural but we are not giving them the right food

Question 2

definition of core gene

Answer 2

housekeeping gene, the minimal gene set that includes all basic cellular processes required for life

Question 3

definition of auxiliary genes

Answer 3

non essential genes that are not shared by all members of the species > provide additional functions that enhance survival in certain environments

Question 4

what is 70s ribosome made of

Answer 4

small subunit: 30S, 16S rRNA and 21 proteins

large subunit: 50S, 5S rRNA, 23 rRNA and 31 proteins

Question 5

what features of the 16S rRNA gene make it the ‘gold standard’ in microbial ecology

Answer 5

conserved in all bacteria

conserved in all life although it is equivalent to 18S eukaryotes (16S in a archaea)

16S rRNA gene found in eukaryote mitochondrial and chloroplast genomes

useful for eukaryote phylogeny

Question 6

properties of 16S ribosomal DNA

Answer 6

it encodes RNA component of small subunit > every nucleotide under selection pressure since important to maintain ribosome structure

conserved regions: stretches of nt that remain the same over evolutionary time > allows sequence alignment and primer and probe design of larger phylogenetic groups

variable regions: segments that show variation among different species over evolutionary time

Question 7

what is species richness

Answer 7

the number of species within a group of individuals

Question 8

what is operational taxonomic unit

Answer 8

unit of diversity defined by method such as similarity sequence rather than species concept

Question 9

what is Shannon index

Answer 9

measures the entropy or uncertainty in the data

Question 9

what is Simpson’s diversity index

Answer 9

measures the true diversity in that not just the number, but the proportional distribution of the species is calculated

1-D where D=(n/N)^2
where n = total number of species
N = number of organisms from all species

Question 10

what is species evenness

Answer 10

how equally individuals are distributed among different species in a community

Question 11

definitions of community, community ecology, alpha, beta and gamma diversity

Answer 11

community: a group of interacting organisms constrained in time and space

community ecology: study of changes in community structure over time and variation between communities throughout space

alpha diversity: studies community diversity within a habitat

beta diversity: studies community diversity between habitats

gamma diversity: study of large scale landscape diversity (alpha and beta)

Question 12

biogeography definition

Answer 12

study of species geographical distribution

Question 13

vicariance definition

Answer 13

the separation of a continuously distributed ancestral population or species into separate populations due to development of a geographic or ecological barrier

Question 14

what is a Z slope

Answer 14

linear plot to see strength of relationship between species richness and area

high Z value: species richness very responsive to area (genetic bottleneck, speciation, population size, genetic redundancy, carrying capacity)

Question 15

definition of contiguous habitat

Answer 15

habitat where there are bridges between habitat

Question 16

definition of succession

Answer 16

the directional and predictable change which a community undergoes over time

these shifts are in presence and abundance of species

usually focused on plant species (habit forming species)

process driven by interaction between biotic and abiotic factors

Question 17

what are the types of succession

Answer 17

primary: occurs when new habitat is colonised > rate is slower as habitat needs to develop and niches are formed

secondary: occurs after a disturbance > disturbance acts to reduce the succession stage of a community and over time succession establishes the new climax community

Question 18

definition of climax community

Answer 18

the end state community form succession; should be stable and define the habitat

Question 19

definitions of bioindicators

Answer 19

can be a biological process, species or community

change in their size indicates change in an environmental parameter

usually anthropogenic but can also be natural

an indicator species will have physiology that is responsive to the environment variable

Question 20

why are microbes great indicators of biological processes

Answer 20

they do primary productivity, respiration and biogeochemistry