Microbial communities of thermal environments - possible analogues of early Earth ecosystems?

Microbial communities of Microbial communities of thermal environments - thermal environments - possible analogues of early possible analogues of early Earth ecosystems?Earth ecosystems?

E.A. Bonch-Osmolovskaya

Winogradsky Institute of Microbiology Russian Academy of Sciences

Archaean biosphere

Thermal habitats

Electron donors and acceptors

Metabolic diversity of thermophilic prokaryotes

Evidence for new metabolic groups

Carbon cycle in thermal ecosystems – is it closed?

SummarySummary

Archaean biosphere

Thermal habitats

Electron donors and acceptors

Metabolic diversity of thermophilic prokaryotes

Evidence for new metabolic groups

Carbon cycle in thermal ecosystems – is it closed?

SummarySummary

Georgy A. Zavarzin 1933-2011

Archaean biosphereArchaean biosphere

-4.0 - -2.5 billion years

Temperature: +70 - +100oC

Anaerobic

Reduced

Thermal habitatsThermal habitats

Thermophiles on the Tree of LifeThermophiles on the Tree of Life

H2

CH4

CO2

H2S

So

SO4-2

Methanogens, sulfur and sulfate reducersMethanogens, sulfur and sulfate reducers

MethanogensMethanogens, sulfur and sulfate reducers, sulfur and sulfate reducers

108 clones

Geyser Valley, KamchatkaHot spring 2012 (Т 58˚C, pH 5.7)

New methanogens in terrestrial hot springsNew methanogens in terrestrial hot springsAlexander Merkel

Methanogens, Methanogens, sulfursulfur and sulfate and sulfate reducersreducers

Methanogens, sulfur and Methanogens, sulfur and sulfate reducerssulfate reducers

Grows in the temperature range from 59-102oC with the optimum at 83oC and in pH range 3.5-6.5 with the optimum at 5.2

Isolated from the hot springs of Moutnovsky Volcano, Kamchatka

Sulfate reduction: Sulfate reduction: Vulcanisaeta moutnovskiaVulcanisaeta moutnovskia

Nikolai Chernyh

Maria Prokofeva

Evgeny Frolov

NikolayPimenov

Growth

SO4

H2S

mM

Cel

ls,

107/m

l

Time, hours

V. moutnovskya was found to be able to grow be sulfate reduction

Substrates are yeast extract, ethanol and glycerol


Growth

SO4

H2S

Pyrobaculum\Thermoproteus

dsrA Vmut_0501 Vulcanisaeta moutnovskia 768-28

Vulcanisaeta distributa DSM 14429

Caldivirga maquilingensis IC-167

Chlorobium

Magnetococcus marinus MC-1

Archaeoglobus

Thermodesulfovibrio

Desulfosporosinus

Desulfitobacterium dichloroeliminans

Desulfotomaculum

100

100

100

100

100

100

100

99

91

61

99

100

97

93

0.1

Crenarchaeal genes encoding sulfate reduction enzymes make a separate cluster, while those of Archaeoglobus are related to bacterial ones


H2

So

S2O3-2

H2S

SO4-2

H2O

CH4

CO2

H2S

So

SO4-2

Disproportionation of sulfur Disproportionation of sulfur compoundscompounds

Disproportionation - redox reaction in which compound with an intermediate oxidation state is simultaneously reduced and oxidized to form two different products

Electron donor and electron acceptor Inorganic sulfur fermentation

Disproportionation of sulfur compounds: sulfite, thiosulfate, elemental sulfur

Formation of sulfate and sulfide

4SO32- + H+ = 3SO4

2- + HS- 3:1 ΔG°’= -58.9 kJ mol-1 SO32-

S2O32- + H2O = SO4

2- + HS- + H+ 1:1 ΔG°’= -22.3 kJ mol-1 S2O32-

4S0 + 4H2O = SO42- + 3HS- + 5H+ 1:3 ΔG°’= +10.3 kJ mol-1 S0

Alexander Slobodkin

Galina Slobodkina

Thermosulfurimonas dismutansThermosulfurimonas dismutans

Isolated from the hydrothermal chimney of Lau Spreading Center, Pacific Ocean, depth 2060 m

Growth in the temperatures range from 50 to 92 oC, opt 74 oCObligate anaerobeObligate lithoautotrophNeeds Fe(III) for H2S scavenging (growth up to 108 cells/ml

Capable to grow with H2 reducing thiosulfate

Thermodesulfobacterium hveragerdense JSPT (X96725)

Thermodesulfobacterium thermophilum DSM 1276T (AF334601)

Thermodesulfobacterium commune YSRA-1T (AF418169)

Thermodesulfobacterium hydrogeniphilum SL6T (AF332514)

‘Geothermobacterium ferrireducens’ FW-1aT (AF411013)

Caldimicrobium rimae DST (EF554596)

Thermosulfurimonas dismutans S95T (JF346116)

Thermodesulfatator indicus CIR29812T (AF393376)

Thermodesulfatator atlanticus AT1325T (EU435435)

Thermosulfidibacter takaii ABI70S6T (AB282756)

100

100

100

58

100

100

58

0.02

Thermosulfurimonas dismutansThermosulfurimonas dismutans

New genus in Thermodesulfobacteria

‘Dissulfurimicrobium hydrothermalis’ Sh68

Dissulfuribacter thermophilus S69T (JQ414031)

Desulfobulbaceae

Syntrophaceae

Desulfobacca acetoxidans DSM 11109T (CP002629)

Desulfomonile

Syntrophobacteraceae

Deferrisoma camini S3R1T (JF802205)

Desulfuromonadaceae

100

100

100

100

100

97

69

70

59

29

52

0.02

New thermophilic New thermophilic Deltaproteobacteria Deltaproteobacteria capable of sulfur disproportionationcapable of sulfur disproportionation

Uzon Caldera, Kamchatka

Lau Spreading Center, Pacific Ocean

Genome size – 2.20 Mb Carbon metabolism - autotrophic CO2 fixation via reductive acetyl-CoA

pathway Identified genes: CO dehydrogenase/acetyl-CoA synthase, acetyl-CoA synthase subunit,

Acetyl-CoA synthase corrinoid iron-sulfur protein, large subunit; Acetyl-CoA synthase corrinoid activation protein NAD-dependent formate dehydrogenase alpha subunit 5,10-methylenetetrahydrofolate reductase Carbon monoxide dehydrogenase CooS subunit Methylenetetrahydrofolate dehydrogenase Formate--tetrahydrofolate ligase

Hydrogen metabolism – uptake [Ni/Fe] hydrogenase Identified genes: [Ni/Fe] hydrogenase, group 1, large subunit

[Ni/Fe] hydrogenase, group 1, small subunit Uptake hydrogenase large subunit Ni,Fe-hydrogenase I cytochrome b subunit Hydrogenase maturation protease [NiFe] hydrogenase metallocenter assembly protein HypC [NiFe] hydrogenase nickel incorporation protein HypA [NiFe] hydrogenase nickel incorporation-associated protein HypB [NiFe] hydrogenase metallocenter assembly protein HypF

Sulfur metabolism – complete pathway of sulfate reduction Identified genes:

Thiosulfate sulfurtransferase, rhodanase Dissimilatory sulfite reductase (desulfoviridin), alpha and beta subunits Tetrathionate reductase subunit A Sulfite reduction-associated complex DsrMKJOP protein DsrP (= HmeB) Sulfite reduction-associated complex DsrMKJOP iron-sulfur protein DsrO (=HmeA) Sulfite reduction-associated complex DsrMKJOP multiheme protein DsrJ (=HmeF) Sulfite reduction-associated complex DsrMKJOP protein DsrK (=HmeD) Sulfite reduction-associated complex DsrMKJOP protein DsrM (= HmeC) Tetrathionate reductase subunit C Tetrathionate reductase subunit B Anaerobic dimethyl sulfoxide reductase chain B Anaerobic dimethyl sulfoxide reductase, A subunit Polysulphide reductase, NrfD Adenylylsulfate reductase alpha-subunit Adenylylsulfate reductase beta-subunit Sulfate adenylyltransferase, dissimilatory-type Sulfite reductase, dissimilatory-type gamma subunit Sulfite reductase alpha subunit Sulfite reductase beta subunit Dissimilatory sulfite reductase clustered protein DsrD Octaheme tetrathionate reductase

Genome of Genome of Thermosulfurimonas Thermosulfurimonas dismutans dismutans

H2

CO So

S2O3-2

H2S

SO4-2

H2O

H2O

H2CH4

CO2

H2S

So

SO4-2

HCOOH

CO2

H2

H2O

Anaerobic CO and formate oxidationAnaerobic CO and formate oxidation


CO + H2O = CO2 + H2

CO

H2

Growth of Thermococcus barophilus Ch5 on CO

100% CO: phylogenetically diverse Firmicuteshyperthermophilic archaea of genus Thermococcus

45% CO:hyperthermophilic archaea of genus Thermofilum

5% CO:Thermophilic bacteria of genus Dictyoglomus

Tatyana Sokolova

AlexanderLebedinsky

Tatyana Kochetkova

(Svetlichny et al., 1991)

Daria Kozhevnikova

Carboxydothermus hydrogenoformans

cooA cooC cooM cooK cooL cooX cooU cooH hypA cooF cooS

“Thermofilum carboxydotrophus"

cooRa cooF cooS cooC 1/2 cooM cooU cooH cooY cooL cooK cooX

Thermococcus sp. AM4 T. barophilus MPT and Ch5T. onnurineus

cooRa cooF cooS cooC 1/2 cooM cooK cooU+cooH cooX cooL


Carboxydothermus hydrogenoformans

cooA cooC cooM cooK cooL cooX cooU cooH hypA cooF cooS

“Thermofilum carboxydotrophus"

cooRa cooF cooS cooC 1/2 cooM cooU cooH cooY cooL cooK cooX

Thermococcus sp. AM4 T. barophilus MPT and Ch5T. onnurineus

cooRa cooF cooS cooC 1/2 cooM cooK cooU+cooH cooX cooL

T. onnurineusT. gammatoleransT. barophilus Ch5

fdh cooF 1/2 cooM 1/2 cooM 1/2 cooM cooK cooU+cooH cooX cooL h f-tr


The energy of reaction:

HCOO- + H2O → HCO3- + H2 ΔG0' = +1.3 kJ/mol

was always considered to be insufficient to support microbial growth

In our experimental conditions ΔG0‘ varied from -8 to -20 kJ/mol

Kim et al., Nature, 2010, 467:352-355



Cells

H2

Formate

Thermococcus sp. able to grow on formate producing hydrogen:

T. barophilusT. gammatoleranceT. onnurineusthree new isolates from different deep-sea hydrothermal areas

H2

CO So

S2O3-2

H2S

SO4-2

H2O

H2O

H2CH4

CO2

H2S

So

SO4-2

HCOOH

CO2

H2

H2O


0,01

1

100

10000

Micrograms C l(-1)

day(-1)

65 70 85T, oC

Lithotrophic methanogenesis Acetoclastic methanogenesis Acetogenesis

Carbon assimilation Acetate oxidation

0,01

1

100

10000

1 2 3

Micrograms C l(-1) day(-1)

T, oC

Lithotrophic methanogenesis Acetoclastic methaogenesis Acetogenesis


0,01

1

100

10000

Micrograms C l(-1)

day(-1)

60 70 85T, oC



Radioisotopic tracing: detection of new metabolic groupsRadioisotopic tracing: detection of new metabolic groups


pH 7.0

pH 8.5

pH 3.5

Na14CO3

14C-acetate14C-products

In situ incubation

65 70 85

NikolayPimenov

0,01

1

100

10000

Micrograms C l(-1)

day(-1)

65 70 85T, oC



0,01

1

100

10000

1 2 3


T, oC



0,01

1

100

10000

Micrograms C l(-1)

day(-1)

60 70 85T, oC





pH 7.0

pH 8.5

pH 3.5

Na14CO3


In situ incubation

? ?

?

? ?

65 70 8565 70 85

H2

CO So

S2O3-2

H2S

SO4-2

H2O

H2O

H2CH4

CO2

H2S

So

SO4-2

HCOOH

CO2

H2

H2O


Acetate

0,01

1

100

10000

Micrograms C l(-1)

day(-1)

65 70 85T, oC



0,01

1

100

10000

1 2 3


T, oC



0,01

1

100

10000

Micrograms C l(-1)

day(-1)

60 70 85T, oC





pH 7.0

pH 8.5

pH 3.5

Na14CO3


In situ incubation

? ? ? ?

65 70 85

ConclusionsConclusions

• Microbial communities of thermal environments contain anaerobic lithoautotrophic microorganisms capable to use electron donors and acceptors of volcanic origin, and to assimilate inorganic carbon in cell material.

• C1 compounds of abiogenic origin can also fuel microbial ecosystems; no electron acceptor is required.

• Anaerobic thermophilic lithoautotrophs able to disproportionate sulfur compounds are phylogenetically diverse, widely spread and also could act as the primary producers in primary ecosystems of the Archaean Earth.

• New anaerobic lithotrophic thermophiles are still to be discovered.

• Microbial communities of thermal habitats are able to perform both primary production and complete mineralization of organic matter, thus, closing the carbon cycle in these environments.

Acknowledgements:

Financial support:Programs of RASRussian Foundation of Basic Research

Collaboration:Institute of Volcanology and Seysmology RAS (expeditions)IFREMER, France (expeditions)University of Portland, USA (expeditions)Center «Bioengineering» RAS (sequencing and annotation of genomes)KORDI, Republic of Korea (the genomics of formate-utilizing archaea)

Microbial communities of thermal environments - possible analogues of early Earth ecosystems?

Documents

Transcript of Microbial communities of thermal environments - possible analogues of early Earth ecosystems?