lecture 18 (4 5-2016) slides

Lecture 18: Everything is everywhere…?

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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)?

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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

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

Translated from the original Dutch:

"Alles is overal: maar het milieu selecteert”

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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

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Salinity is one of the strongest drivers of microbial community structure

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Compatible solutes are produced by microbes to combat osmotic stress

Organic compatible solutes Inorganic compatible solutes

K+Na+

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pH

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pH

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Temperature

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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

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Life history a.k.a. trophic strategy

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Maximum growth rate is phylogenetically conserved

Morrissey et al., ISME J 2016

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

Translated from the original Dutch:

"Alles is overal: maar het milieu selecteert”

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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…

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

• Genomics• Comparative

genomics• Stable isotope

probing and phylogenetics

• Metagenomics

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

• Genomics– e.g. bacteriorhodopsin

• Comparative genomics• Stable isotope probing

and phylogenetics • Metagenomics

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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

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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

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35 Béjà et al., 2000

36 Béjà et al., 2000

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

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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

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41 Horn et al., 2004

42 Horn et al., 2004

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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

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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

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Stable-isotope probing• Figure 22.4 Images

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

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NanoSIMS

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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

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Metagenomics

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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)?