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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
34 Béjà et al., 2000
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)?