ECOLOGIA MICROBIANA (BIOL 4365) D r. A r t u r o M ... -...
Transcript of ECOLOGIA MICROBIANA (BIOL 4365) D r. A r t u r o M ... -...
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ECOLOGIA MICROBIANA (BIOL 4365)D r . A r t u r o M a s s o l D e y á
a r t u r o . m a s s o l @ u p r . e d uB-338 / Ext. 3956
H o r a s d e O f i c i n a : L & M 2 : 3 0 a 4 : 0 0 P M
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Tree of LifeCharles D
arwin
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Microbial communities in natural and engineered ecosystems:
How to analyze their diversity and
structure, and understand their
genetic interactions
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OrganismoGenes /
Genomas
Ambiente
GENOMICA
ECOLOGIAECOLO
GIA
DE GENES
Biol4365Dr. Arturo Massol
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MICROBIAL ECOSYSTEMS
Soils: 1 g : ca. 108 bacteria - 1 µm/cel
100 m bacteria
: 1 kg : 100 km
: 1 hectare: 300.000.000 km
> Distance Earth-Sun!
(150.000.000 km)
Enormous numbers:
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MICROBIAL ECOSYSTEMS
"Agriculture: + and - Bioremediation
"Water treatment/ hygiene"Air purification/ Transport
of pathogens
"Agriculture, food safety, health
Ecosystem Relevance/Applications
Chemical balance biosphere
Soil
WaterAir
Hosts: plants, animals,
humans
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ECOLOGIA MICROBIANA (BIOL 4365)
L i b r o d e T E X T O ( R e f e r e n c i a P r i m a r i a )
M i c r o b i a l E c o l o g y : F u n d a m e n t a l s a n d A p p l i c a t i o n sA t l a s & B a r t h a , 4 t a E d i c i ó n ( 1 9 9 8 )
. . . p e r o s u l i b r o d e t e x t o d e m i c r o b i o l o g í a g e n e r a l “ B i o l o g y o f M i c r o o r g a n i s m s ” p u e d e a s i s t i r l e s e n e l
s e m e s t r e
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¡Acceso a documentos de la clase!
• http://academic.uprm.edu/~amassol/biol4365/Pron4365(2009).pdf
• http://academic.uprm.edu/~amassol/biol4365/Propuesta.pdf
• http://academic.uprm.edu/~amassol/biol4365/Forney.pdf
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Universal Phylogenetic Treebased on rRNA sequences
From: Woese (2000) PNAS 97:8392-8396.
micro-organisms:largest diversity, mostly unknown
2 species: <70% similar
multicellular, macroscopic organisms:small branches in the Eucarya-domain:
Homo sapiens -chimpansee: 98.4% similar!
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Questions in Microbial Ecology
! Temporal Differences! Spatial Differences! Treatment Effects
! Measures of Diversity
1. ! = within site
2. " = between site
3. # = between regions! Descriptors of Diversity
1. species richness
2. species evenness
3. species composition
Diferencias TemporalesDiferencias EspacialesEfecto de Tratamientos
Medidas de Diversidad: 1. alfa-diversidad (dentro de un lugar) 2. beta-diversidad (entre lugares) 3. gama-diversidad (entre regiones)
Descripción de Biodiversidad: 1. Riqueza de especies 2. Equitabilidad de especies 3. Composición
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Environmental Complexity
Selection
Heterogeneous Environment
Homogeneous Environment
Few GenotypesSuccessful
Many GenotypesSuccessful
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‘Species’
Abundance
Richness Evenness Composition
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Sp. IISp. I
RECURSOS
Sp. II Sp. IISp. I Sp. I
Sp. I Sp. I Sp. I Sp. I
GANA Especie I
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Nutrientes
T (oC)
pH
bajo
alto
alto
alto
DNA
RNA
Proteínas
DogmaCENTRAL
Población 1
Población I1
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COMPETITIVE EXCLUSION PRINCIPLE
No two species can occupy precisely
the same ecological niche
✓ If two species coexist in a stable environment, they do so by niche differentiation.
✓ Niche differentiation occurs through adaptive evolution. ✓ If there is no niche differentiation, then one species will eliminate
or exclude the other.
Nutrientes
T (oC)
pH
bajo
alto
alto
alto
DNA
RNA
Proteínas
DogmaCENTRAL
Población 1
Población I1
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Sp. IISp. I
RECURSOS
Sp. II Sp. IISp. I Sp. I
InteraccionesMAYOR
DIVERSIDADSp. I Sp. I Sp. I Sp. I
ej. PATOGENOS/DEPREDADORES
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Effect of limiting substrate on growth
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Monod Growth Equation
µ = µmax
Survival under nutrient-limited conditions
SKs + S
µ = Growth rateµmax = Maximal growth rateS = Substrate concentrationKs = Substrate concentration where growth rate is one-half maximum rate
Growth of bacterial populations in the environment is typically limited by the availability of 1 or more nutrients
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µ and KS Relationships
B
For any D (= µ), the organism with the lowest KS will out-compete an organism with a higher KS.
PANEL A. At all D, KSA < KSB and A is more competitive, i.e., µA > µb.
PANEL B. At low [S] KSA < KSB and µA > µb ∴ organism A is more competitive; while at other [S] KSB > KSA and µb > µA ∴ organism B is more competitive.
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¿Quien eres y qué haces?
• Cultivo y caracterización
• Análisis de DNA (ej. 16S rRNA,
Phylochips)
• Microscopía/RAMAN
¿Cuán rápido trabajas?
• Process rate
• Enzyme activity
• RNA (no incubation necessary)
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Métodos de cultivo¿Por qué sólo recuperamos 0.1% o menos de la diversidad microbiana?
Platos de Agar (Siglo 19)R. Koch, Walter Hasse & esposa & Juliius Petri
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Cultivo de Microorganismos Fastidiosos
1. Agentes solidificantes
Agar y agentes inhibidores, uso de gellan gum como agente solidificante aumenta el número de microorganismos cultivables por un factor de 10.
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2. Factores de crecimiento desconocidos (ej. quorum sensing) Necesidad de factores de crecimiento o alguien que remueva ciertos desperdicios (Growth Factors Network).Cultivo con sobrenadante filtro-esterilizado de otros donde este organismo “aun no cultivado” está creciendo.
3. Sintrofismo (ej. H2 Transfer: sintrofomonas y metanogénicas)“Interspecies requirements for growth of microbes in natural communities”.Agitación puede ser fatal al dispersar agregados o disipar gradientes necesarios para crecimiento.Paciencia: Se necesitan más estudiantes graduados y subgraduados...
4. Concentración de nutrientes (ej. N & P en los océanos en escala de µM: DOC es 1000X menos en la naturaleza que en LB)
5. El tiempo de generación en la naturaleza es en escala de días, semanas, meses o años [no minutos como en cultivos domesticados] Paciencia: Se necesitan más estudiantes graduados y subgraduados...