Lecture 18: Everything is everywhere…?

2

Objectives• What is the Baas-Becking hypothesis, and what is

its significance?• Define biogeography.• What causes a microbe to live in one place but not

another?• What environmental traits are the strongest drivers

of microbial communities?• What is a niche?• How do you link phenotype (function) and

phylotype (diversity of microbes)?

3

Baas Becking Hypothesis"Everything is everywhere, but the environment selects”

Translated from the original Dutch:

"Alles is overal: maar het milieu selecteert”

• published in the 1930s• Lourens Baas-Becking

was a Dutch botanist and microbiologist

• Based on his research in California's salt lakes, as well as work by others on salt lakes worldwide

5

Baas Becking Hypothesis"Everything is everywhere, but the environment selects”

Translated from the original Dutch:

"Alles is overal: maar het milieu selecteert”

6

What causes a microbe to live in one place but not another?

• Environment– The set of environmental parameters (including biotic

and abiotic factors) that describe permissive growth conditions for an organism is its niche

• Life history– the schedule and duration of key events in an

organism's lifetime are shaped by natural selection to produce the largest possible number of surviving offspring

– Changes to this schedule can affect evolution

7

Salinity is one of the strongest drivers of microbial community structure

9

Compatible solutes are produced by microbes to combat osmotic stress

Organic compatible solutes Inorganic compatible solutes

K+Na+

11

13

pH

15

pH

17

Temperature

19

What causes a microbe to live in one place but not another?

• Environment– The set of environmental parameters (including biotic

and abiotic factors) that describe permissive growth conditions for an organism is its niche

• Life history– the schedule and duration of key events in an

organism's lifetime are shaped by natural selection to produce the largest possible number of surviving offspring

– Changes to this schedule can affect evolution

20

Life history a.k.a. trophic strategy

22

Maximum growth rate is phylogenetically conserved

Morrissey et al., ISME J 2016

23

Baas Becking Hypothesis"Everything is everywhere, but the environment selects”

Translated from the original Dutch:

"Alles is overal: maar het milieu selecteert”

24

Biogeography

• The study of patterns of species distribution across geographical areas

• “...like plant and animal distributions, microbial distributions can be the result of both deterministic (environmental) and stochastic (dispersal) processes.”– Environment– Life history eg., dispersal limitation, past conditions

• Can explain traits observed in organisms – Gene sequence identity, gene content, genome size, and

more…

25

27

How do you link phenotype (function) and phylotype (diversity of microbes)?

• Genomics• Comparative

genomics• Stable isotope

probing and phylogenetics

• Metagenomics

29

How do you link phenotype (function) and phylotype (diversity of microbes)?

• Genomics– e.g. bacteriorhodopsin

• Comparative genomics• Stable isotope probing

and phylogenetics • Metagenomics

30

How do you link phenotype (function) and phylotype (diversity of microbes)?

• Sargasso sea, showing lines of sargassum, a genus of brown microalgae (seaweed)

• The waters are dominated by SAR86 group of Gammaproteobacteria, but at the time, their role in the ecology of the ocean was unknown

• Cosmid library sequences showed a link between the bacteria and photosynthesis

31

33

Fig. 1. (A) Phylogenetic tree of bacterial 16S rRNA gene sequences, including that encoded on the 130-kb bacterioplankton BAC clone (EBAC31A08) (16). (B) Phylogenetic analysis of proteorhodopsin with archaeal (BR, HR, and SR prefixes) and Neurospora crassa (NOP1 prefix) rhodopsins (16).Nomenclature: Name_Species.abbreviation_Genbank.gi (HR, halorhodopsin; SR, sensory rhodopsin;BR, bacteriorhodopsin). Halsod, Halorubrum sodomense; Halhal, Halobacterium salinarum (halobium); Halval, Haloarcula vallismortis; Natpha, Natronomonas pharaonis; Halsp, Halobacterium sp;Neucra, Neurospora crassa.

Béjà et al., 2000

34 Béjà et al., 2000

35 Béjà et al., 2000

36 Béjà et al., 2000

37 Béjà et al., 2000 Béjà et al., 2000

38

How do you link phenotype (function) and phylotype (diversity of microbes)?

• Genomics– e.g., bacteriorhodopsin

• Comparative genomics– e.g., chlamydia

• Stable isotope probing and phylogenetics

• Metagenomics

39

41 Horn et al., 2004

42 Horn et al., 2004

44

How do you link phenotype (function) and phylotype (diversity of microbes)?

• Genomics– e.g., bacteriorhodopsin

• Comparative genomics– e.g., chlamydia

• Stable isotope probing and phylogenetics – e.g., unicellular

eukaryotes • Metagenomics

45

Stable-isotope probing

• Feed a community isotopically-enriched substrates

• The biomass of the organism then becomes enriched

• The “heavy” DNA can be separated from the light DNA

• Sequencing each fraction separately tells which organisms took up the substrate

46

Stable-isotope probing• Figure 22.4 Images

of the unicellular eukaryotes identified in Moreno et al., AEM 2010

48

NanoSIMS

50

How do you link phenotype (function) and phylotype (diversity of microbes)?

• Genomics– e.g., bacteriorhodopsin

• Comparative genomics– e.g., chlamydia

• Stable isotope probing and phylogenetics – e.g., unicellular eukaryotes

• Comparative metagenomics– e.g., the Sargasso sea

microbiome

51

Metagenomics

52

53

54

55

Objectives• What is the Baas-Becking hypothesis, and what is

its significance?• Define biogeography.• What causes a microbe to live in one place but not

another?• What environmental traits are the strongest drivers

of microbial communities?• What is a niche?• How do you link phenotype (function) and

phylotype (diversity of microbes)?