pinaki sar department of biotechnology

64
Exploring microbial diversity and function within the granitic-basaltic deep crustal system of Koyna-Warna (India) region Pinaki Sar Department of Biotechnology Indian Institute of Technology Kharagpur India Collaborators Sufia K Kazy, National Institute of Technology Durgapur, India Sukanto Roy, National Geophysical Research Institute, Hyderabad, India

Upload: burke-sykes

Post on 30-Dec-2015

53 views

Category:

Documents


0 download

DESCRIPTION

Exploring microbial diversity and function within the granitic-basaltic deep crustal system of Koyna-Warna (India) region. Indian Institute of Technology Kharagpur India. Pinaki Sar Department of Biotechnology. Collaborators Sufia K Kazy, National Institute of Technology Durgapur, India - PowerPoint PPT Presentation

TRANSCRIPT

Page 1: Pinaki Sar Department of Biotechnology

Exploring microbial diversity and function within the granitic-basaltic deep crustal system of Koyna-Warna (India) region

Pinaki SarDepartment of Biotechnology

Indian Institute of Technology KharagpurIndia

CollaboratorsSufia K Kazy, National Institute of Technology Durgapur, India

Sukanto Roy, National Geophysical Research Institute, Hyderabad, India

Page 2: Pinaki Sar Department of Biotechnology

Deep biosphere within basaltic – granitic (igneous rocks) systems

Basalt

Granite

Image source : http://en.wikipedia.org/wiki/File:Igneous_rock_eng_text.jpg#file

Igneous rocks constitute ~95% of the Earth’s crust

Deep crustal system represents an Extreme Habitat for Life

Aphotic Devoid of Org C Subjected to high temperature/pressure at

some point in their history Oligotrophic

Page 3: Pinaki Sar Department of Biotechnology

Microbiology of deep, igneous crust seems more intriguing, though relatively less studied

Microbiology of basaltic/grantic deep subsurface (marine/terrestrial) are less studied and mostly unexplored

Some more reports for ocean crust than terrestrial habitats

Who are they ?What are their function

Biogeochemical importance;

Limits of life ? Newly generated (annually) and recycled (~

60 M yrs)

Upper (500 m), subseafloor basalts are significantly porous and permeable, hydrologically active

Largest potential microbial habitat

Unlike deep oceanic subsurface which may be partially dependent on organic C and energy derived from photosynthetic process, life within terrestrial crystalline rocks are independent to photosynthesis

Page 4: Pinaki Sar Department of Biotechnology

Bacterial communities in different (sub-)sea floor habitats, demonstrating that subsurface crustal bacteria are distinct from the bacteria in other deep-sea environments; Wang et al 2013; Edward et al 2011

What remained largely unexplored and poorly understood :

Distribution and diversity of microbes in terrestrial igneous rocks

Knowledge on their metabolic functions and their impact on global C and nutrient cycles

What remained largely unexplored and poorly understood :

Distribution and diversity of microbes in terrestrial igneous rocks

Knowledge on their metabolic functions and their impact on global C and nutrient cycles

Page 5: Pinaki Sar Department of Biotechnology

What powers deep microbiome ? Extent of microbial catabolic potential within

deep igneous crust

Abiogenic H2 driven metabolic pathways ? Role in C/N/nutrient cycling Rock weathering and climate change

Abiogenic H2 driven metabolic pathways ? Role in C/N/nutrient cycling Rock weathering and climate change

Page 6: Pinaki Sar Department of Biotechnology

Geomicrobial processes at a subsurface shale-sandstone interface; Fredrickson and Balkwill, 2006

XX

??Acetogenic –Methanogenic metabolism with

abiogenic H2

Acetogenic –Methanogenic metabolism with abiogenic H2

In igneous rock systemsIn igneous rock systems

Page 7: Pinaki Sar Department of Biotechnology

H2 driven system

Abiotic diagenetic formation of low mw compounds

Anaerobic lithoautotrophic metabolismSLiMEs (?)

Anaerobic lithoautotrophic metabolismSLiMEs (?)

Small Org compSmall Org compMethanogenMethanogenAbio

tic p

roce

sses

Tem

pera

ture

Abiotic geogenic H2

Anaerobic heterotrophic metabolism

Anaerobic heterotrophic metabolism

H2

N2 fixationN2 fixation

Denitrification/NH4 oxidation

Denitrification/NH4 oxidation

Radiolytic decomposition of waterWater-rock interactionDiffusion from deeper levels

Radiolytic decomposition of waterWater-rock interactionDiffusion from deeper levels

Page 8: Pinaki Sar Department of Biotechnology

The Deccan Traps

The Deccan Traps are a large igneous province, on the Deccan Plateau (west-central India (between 17–24N, 73–74E)

One of the largest volcanic features on Earth

Consist of multiple layers of solidified flood basalt [together >2,000 m thick and cover an area of 500,000 km2 and a volume of 512,000 km3 (123,000 cu mi)]

formed between 60 and 68 million years ago [end of the Cretaceous period] linked to the Cretaceous–Paleogene extinction event

Page 9: Pinaki Sar Department of Biotechnology

Seismic activity in deccan Trap at Koyna-Warna region

Reservoir triggered seismicity (RTS) record in past 38 years: >10 earthquakes of Mz5; >150 earthquakes of Mz4 >100,000 earthquakes of Mz0

soon after the impoundment of the Shivaji Sagar Lake created byKoyna Dam in Western India in 1962

Page 10: Pinaki Sar Department of Biotechnology

Drilling site at Koyna

JOUR.GEOL.SOC.INDIA, VOL.81, FEB. 2013

Drilling is proposed up to nearly 7 KM, so far ~1.5KM drilling is doneDrilling is proposed up to nearly 7 KM, so far ~1.5KM drilling is done

Cores recovered so far revealed :

Flood basalt pile with numbers of lava flow

Each flow has vesicular / amygdaloidal layer unde lined by massive basalt

Microbial presence (successful extraction of DNA and amplification of 16 S rRNA gene regions) from samples of 1300 M depth

Low C environment

Cores recovered so far revealed :

Flood basalt pile with numbers of lava flow

Each flow has vesicular / amygdaloidal layer unde lined by massive basalt

Microbial presence (successful extraction of DNA and amplification of 16 S rRNA gene regions) from samples of 1300 M depth

Low C environment

Core samples from borehole KBH-1 showing (a) massive basalt, (b) vesicular and amygdaloidal basalt with large vugs filled with quartz and/or calcite

Page 11: Pinaki Sar Department of Biotechnology

Major aim of the proposed work

Delineating the environmental limit of life within the terrestrial baslatic/granitic system

Understanding the processes that potentially define diversity /distribution of life in deep terrestrial crustal system

Possible modes of microbial interactions within such environment affecting C and nutrient cycle, rock weathering etc.

Page 12: Pinaki Sar Department of Biotechnology

ObjectivesAnalysis of microbial diversity and composition within the

basaltic-, granitic- and transition zones from deep subsurface environment of Koyna region: Combination of metagenome based sequencing techniques and enrichment/isolation of bacteria (include virus and fungi as well after this meeting )

Metabolic function and microbial role in biogeochemical cycling of carbon, rock microbiome interaction (weathering); effect –response of seismic activities: Metagenome and metatranscriptome analysis, WGS analysis of predominant isolates, metabolic modeling, getting ideas of novel metabolic routes running the biogeochemical reactions

Integration of geochemical/environmental data and comparative metagenomic analysis of deep basaltic-granitic biosphere with and without seismic activities: Assessment of the extent of microbial distribution and diversity, potential involvement in C cycle

Page 13: Pinaki Sar Department of Biotechnology

Work flow: implementaion

Drilling, sample collection and

analysis

Drilling, sample collection and

analysis

Analysis of microbial diversity, community structure, abundanceAnalysis of microbial diversity, community structure, abundance

Analysis of microbial functionAnalysis of microbial function

Elucidation of effect of seismic activity and crustal properties on microbial diversity and activity

Elucidation of effect of seismic activity and crustal properties on microbial diversity and activity

Data integration and modelingData integration and modeling

Time scale (year)0 5

Obj . I Obj . II Obj . III

Molecular genomic analysis

Molecular genomic analysis

Page 14: Pinaki Sar Department of Biotechnology

DeliverablesDeep carbon observatory goals :Elucidation of microbial diversity/distribution within carbon limited, dark, deep terrestrial crust

Better insight in understanding on survival strategies and role under deep subsurface igneous rocks

Delineation of limits for microbial deep life and their interaction with critical nutrient cycling

Global significance : Global primer site of RTS within basaltic/granitic crust

Microbial role in rock weatheringNutrient cycling, CO2 sequestration and other aspects of

climate changeBiomineralization; Bioremediation, Bioprospecting (Access of novel microbes and enzymes for industrial application)

Global significance : Global primer site of RTS within basaltic/granitic crust

Microbial role in rock weatheringNutrient cycling, CO2 sequestration and other aspects of

climate changeBiomineralization; Bioremediation, Bioprospecting (Access of novel microbes and enzymes for industrial application)

Page 15: Pinaki Sar Department of Biotechnology

Budget Details (five years)Particulars Cost in USD

(approx)

Equipment (NG Sequencer) 3,20,000

Accessory equipment 65,000Drilling 1,50,000

Chemicals/Consumables, contingency 2,00,000

Staff (01 PDF, 02 RF, 01 RA) 1,20,000International/domestic travel, material transport

45,000

Total 11,00,000

PDF: post doc fellow; RF: Research fellew /Ph D, RA: Research assistant

Page 16: Pinaki Sar Department of Biotechnology

Thank You

Page 17: Pinaki Sar Department of Biotechnology

Deep subsurface : the hidden and unexplored habitat for microbes

The largest potential ecosystem on Earth, estimated to harbour half of all the biomass; and 2/3 of all microbial biomass on Earth (2.5-3.5 X 1030)

Depth of distribution: Functionally and taxonomically diverse populations extending several kilometres underground

Adaptation : temperature limit 121oC, pressures of up to 1.6 Gpa

Function: fundamental role in global biogeochemical cycles over short and long time scale

(Itavaara et al., FEMS Microbiol Ecol 77 2012)

Page 18: Pinaki Sar Department of Biotechnology

The deep biosphere : an extreme habitat for microbes

Increasing temperature and pressureNutrient limitation, limited porosity and permeabilityDecreasing available carbon and energy sources

With increasing depth there are several constrains that affect composition, extent, life habitats, and the living conditions in deep subsurface

Rates of microbial activity in deep subsurface is slow (orders of magnitude over that in surface environments)With average generation times of hundreds to thousands of years

…and therefore defies our current understanding of the limits of life

Page 19: Pinaki Sar Department of Biotechnology

The deep biosphere

The huge size

Largely unexplored biogeochemcial process driving the deep biosphere

“Investigation of the extent and dynamics of subsurface microbial ecosystems an intriguing and relatively new topic in today’s geoscience research” ICDP, 2010

Page 20: Pinaki Sar Department of Biotechnology

Widely disseminated deep biosphere pose fundamental questions :

1. kind of microorganisms ? populate the deep subsurface?

2. their extension and limits? 3. metabolic processes ? carbon and energy sources ? 4. survival strategies? link to early life on Earth? 5. biological alteration of rock 6. impact on the global -biogeochemical cycle and -

climate?

ICDP 2010

1. Nature of microbial communities and their function in active seismogenic zone

2. Effect of fracturing (during earthquake) on microbial communities

3. Interrelation between geochemistry, microbiology and nature/location of fracture zones

IODP Nankai Trough Seismogenic Zone Experiment (NanTroSEIZE)

Natural Earthquake Laboratory at Focal Depth (DAFSAM-

NELSAM)

Taiwan Chelungpu Drilling Project (TCDP)

Lomonosov Ridge in the Central Arctic Basin

Outokumpu deep borehole, Fennoscandian Shield

Page 21: Pinaki Sar Department of Biotechnology

Requirements of microbes in deep biosphere

•Electron donor•Electron acceptor•Carbon source•thermodynamic potential of chemical reactions

•Electron donor•Electron acceptor•Carbon source•thermodynamic potential of chemical reactions

•Porosity•Permeability•Tectonostratigraphic setting

•Porosity•Permeability•Tectonostratigraphic setting

Page 22: Pinaki Sar Department of Biotechnology

Microbial metabolism within deep subsurface

Page 23: Pinaki Sar Department of Biotechnology

Scheme visualizing potential carbon and energy sources of deep microbial ecosystems

OM = organic matter, mw = molecular weightCH4

Acetate, CO2 and H2

Organic acids and

alcohols

Soluble monomers (sugar and amino

acids)

Complex polymers (CH2 O, proteins)

CH4

Acetate, CO2 and H2

Organic acids and

alcohols

Soluble monomers (sugar and amino

acids)

Complex polymers (CH2 O, proteins)

FermentationFermentation

Syntrophic fermentation

Syntrophic fermentation

MethanogenMethanogenOrganic matter

deposition

Bioti

c pr

oces

ses

Preserved OM (Kerogen, Bitumen,

Humics

Thermal activation

Abiotic diagenetic formation of low mw compounds

Anaerobic microbial

metabolism

Anaerobic microbial

metabolism

Abio

tic p

roce

sses

Tem

pera

ture

e accepto

r limited

Independent from primary microbial degradation

processes

Page 24: Pinaki Sar Department of Biotechnology

Extended known biosphere to 3 km, not limited by energy

Revealed biomass, biodiversity, unusual traits & microbes with indications of autotrophic ecosystems

Slow rates of deep subsurface microbial activity but linked with geological interfaces

Deep subsurface biosphere not linked to the surface (?)

Deep anaerobic communities fueled by subsurface abiotic energy sources (?)(Likely)

What have we learned? All Observations are consistent with the laws of

physics

Page 25: Pinaki Sar Department of Biotechnology

Objectives

Analysis of microbial abundance, diversity and composition within the deep subsurface environment of the seismic zone of Koyna-Warna region

Elucidation of functional role of indigenous microorganisms within the seismic zone

The effect of seismic activity on microbial community and function

Page 26: Pinaki Sar Department of Biotechnology

Work flow

Sample collection and analysis

Sample collection and analysis

Analysis of microbial diversity, community structure, abundanceAnalysis of microbial diversity, community structure, abundance

Analysis of microbial functionAnalysis of microbial function

Elucidation of effect of seismic activity and crustal properties on microbial diversity and activity

Elucidation of effect of seismic activity and crustal properties on microbial diversity and activity

Data integration and modelingData integration and modeling

Time scale (year)0 3

Obj . I Obj . II Obj . III

Molecular analysisMolecular analysis

Page 27: Pinaki Sar Department of Biotechnology

Work PlanObjective 1.: Analysis of microbial abundance, diversity and composition

Geochemical analysis

Geochemical analysis

Elemental analysis (XRF, ICP)Elemental analysis (XRF, ICP)

TOC, TC, TS, TP analysisTOC, TC, TS, TP analysis

Anion analysisAnion analysis

EPMA analysisEPMA analysis

Enumeration of cell countsEnumeration of cell counts

Analysis of community composition

Analysis of community composition

Sample collection from cores Sample collection from cores

Metagenome extractionMetagenome extraction

Amplification of 16S rRNA gene

Amplification of 16S rRNA gene

Library preparation

Library preparation

Sequencing [NGS]

Sequencing [NGS]

Sequence analysis

Sequence analysis

DGGE analysisDGGE

analysis

Sanger sequencing

Sanger sequencing

Community diversity and composition

Community diversity and composition

Page 28: Pinaki Sar Department of Biotechnology

Objective 2 Analysis of microbial communities’ function

Total communityTotal community

Analysis of metabolic diversity

Analysis of metabolic diversity

PM - Biolog systemPM - Biolog system

Analysis of genes related to S, Fe, C, N

cycles

Analysis of genes related to S, Fe, C, N

cycles

S cycle: dsrS cycle: dsr

Fe cycle: FurFe cycle: Fur

C cycle: mcrA, RuBisCO

C cycle: mcrA, RuBisCO

N cycle: nif, nirK, amoRN cycle: nif, nirK, amoR

NG sequencing of complete

metagenome

NG sequencing of complete

metagenome

Page 29: Pinaki Sar Department of Biotechnology

Objective 3 Effect of seismic activity on microbial community and function

Comparison of community structure across depth

Comparison of community function across depth

Integration of microbiological data with geochemical and other relevant data on seismic activity within the samples from various depths

Page 30: Pinaki Sar Department of Biotechnology

Expected out come1. Understanding the deep terrestrial biosphere with

seismogenic activity

2. Distribution, extent and composition of deep microbial communities within the basaltic-granitic subsurface

3. Impact of seismic activity and subsurface CO2, N2, and H2 production on microbial community structure and function, existence of SLiMEs?

4. Correlation of microbial activity, geochemistry/rock systems and seismic activity within the zone of RTS

Page 31: Pinaki Sar Department of Biotechnology

Recurring

Particulars 1st Year (Rs)

2nd Year (Rs)

3rd Year (Rs)

Total (Rs)

Manpower

Senior Research Fellow (01) 216000 216000 216000 648000

Technical Assistant (01) 144000 144000 144000 432000

Sub-Total 360000 360000 360000 1080000

Consumables 600000 800000 600000 2000000

Travel 200000 200000 100000 500000

Contingency 100000 100000 100000 300000

Overhead 752000 292000 232000 1276000

Sub-Total of Recurring 2012000 1752000 1392000 5156000

Grand Total (Non-Recurring + Recurring)

4512000 1752000 1392000 7656000

Page 32: Pinaki Sar Department of Biotechnology

Thank You

Page 33: Pinaki Sar Department of Biotechnology

Justification of Equipment

Fluorescence Microscope The fluorescent microscope is required for all microscopic enumeration of bacteria, cell counts, FISHT etc. This equipment is the major requirement for microbiological analysis related to the project.

Incubator shaker The temperature controlled shaker will be used for molecular biology work.

Gel electrophoresis systemwith accessories

The gel electrophoresis apparatus will be used for all routine DNA work.

Work station for bioinformatics with accessories

The computer will be required for all bioinformatics data analysis

Ultra deep fridge Ultra deep fridge will be used to store the samples from cores and other microbiological samples. Ion selective electrodes will be required for the Orion multiparameter meter to be used in the field.

Page 34: Pinaki Sar Department of Biotechnology

Real time PCR machine For all quantitative determination of rRNA and other genes; monitoring of expression levels of various functional genes this instrument is absolutely essential. In the present work transcriptional analysis of selected biogeochemical cycle relevant genes, abundance of specific microbial groups, -dynamics will be studied using this equipment. The proposed model is versatile and highly efficient. For this project this equipment is extremely essential

Page 35: Pinaki Sar Department of Biotechnology

Justification of Manpower

Senior Research Fellow One dedicated senior research fellow will be essential to assist the PI and co PI for carrying out the research work

Technical Assistant One TA will be essential or field work, sample collection, sample processing and other relevant activities of the project.

Page 36: Pinaki Sar Department of Biotechnology

Justification of Consumables

Consumables will be essential for carrying out culture independent RNA dependent and metagenomic analysis of microbial communities. Cost for RNA/DNA extraction kits, cDNA preparation, real time PCR reagents, primers, vectors and restriction enzymes, plasmid isolation kits, gel extraction and sequencing kits are all included. For real time based transcriptomic studies, cDNA kits and other reagents related to real time PCR (TaqMan probes, Syber green dye, etc.), nucleic acid quantification kits (pico green), etc. will be needed. For fluorescent microscopy and FISH analysis dedicated kite are required. Sequencing reagents, kits and other charges are included under this head. For all routine works general chemicals, glass and plastic ware are necessary. Bacterial type strains will be procured from National or international culture collection.

Page 37: Pinaki Sar Department of Biotechnology

Justification of travel

Field sampling and analysis; Project meeting

Several visits to fields and analytical labs for analysis; Project meeting, if any

Field work and project presentation; Seminar participation

Field work and project presentation at DBT, if any; Seminar participation

Travel to fields Several visits to fields for survey and sample collection

Travel to other laboratories Sample analysis

Page 38: Pinaki Sar Department of Biotechnology

Justification of Contingency

DNA sequencing, fatty acid analysis, GC content determination, Conference and meetings

DNA sequencing, fatty acid analysis, GC content determination, Conference and meetings

Field expenditures, photocopy, computational works, cost of gas for AAS, anaerobic station

Expenditures related to sample collections and other field work, cost of field labors, porters, gases for anaerobic workstation (N2 and mix gas), computational work, photocopying; charges for PLFA analysis, type strains and genomic DNA samples (from DSMZ or ATCC or MTCC), sequencing etc. and any unforeseen expenditures

Sample collection related costs, Conference and meeting related expenditures; DNA sequencing

Sample collection related costs, Conference and meeting related expenditures; Visit to other labs for analysis and data verification; Cost of DNA sequencing

Page 39: Pinaki Sar Department of Biotechnology

Extra slides

Page 40: Pinaki Sar Department of Biotechnology

Expedition to deep biosphere

Page 41: Pinaki Sar Department of Biotechnology

Map of DSDP, ODP, and IODP Legs (indicated by their numbers) considering microbial or deep microbial scientific objectives. b. Map showing completed and planned ICDP projects containing biogeochemical objectives. Black dots indicate ICDP projects where no biogeochemical objectives were included.

Page 42: Pinaki Sar Department of Biotechnology
Page 43: Pinaki Sar Department of Biotechnology

Microbial cells : the main biogeochemical engines of Earth

Microbes: the janitors of Earth

The most ubiquitous, abundant, most diverse live form on this planet

Occupy even most inhospitable niches

Vast metabolic and genetic repertoire

Responsible for many geobiochemical processes that take place deep in the Earth’s crust

Page 44: Pinaki Sar Department of Biotechnology

Global prokaryotic biomass distribution, given in cell numbers (after Whitman et al. 1998).

Page 45: Pinaki Sar Department of Biotechnology

•Tectonostratigraphic setting

•Distribution patterns, degree of sorting, lithology, etc.

•Porosity and permeability

•Subsidence, uplift and deformation of the basin fill control pressure (lithostatic, hydrostatic),

•Modification in porosity and permeability of lithotypes.

•Basin style and evolution control temperature gradient

Environmental parameters defining the dimensions of living space

Page 46: Pinaki Sar Department of Biotechnology

Living spacePore space; pore types and degree of interconnection are important factor controlling deep biosphere

microorganisms occupy only about one millionth of available porosity An adequate flux of liquids or gases through rock pores is required to sustain life and this is governed by pore throat dimensions.Permeability that regulates the pressure-driven transport of electron donors, electron acceptors, and nutrients to sustain living cells [Quartz arenites retain permeability to great depths and offer perhaps the most stable living accommodation for microorganisms while high reactivity

of unstable volcanogenic sandstones and their mechanical weakness make them susceptible to rapid porosity and permeability loss, in some cases at relatively low temperatures]

Fractures are orders of magnitude more permeable than pore systems and often allow microbial growth and activity

Page 47: Pinaki Sar Department of Biotechnology

Provision of food (electron donors) and oxidants (electron acceptor, e.g., O2) is controlled by the thermodynamic potential of chemical reactions, both organic and inorganic

The rate of microbially catalysed reactions can be up to 106

times higher compared to abiological rates

Depends on the rate of supply and removal of substrates and products, the concentration (above minimum thresholds and below toxic levels) and bioavailability of reactants and environmental conditions.

Supply of food

Page 48: Pinaki Sar Department of Biotechnology

Microbial distribution in geospheres

Extension of the biosphere on Earth

Greatest biomass inhabits within the surface/near surface lithosphere and shallow hydrosphere: reliance on photosynthesis / derived food chain

Microorganism make the major component of biosphere because they can grow under diverse conditions and have different metabolic pathways

Anaerobic organisms are dominant inhabitants of lithosphere .. generally decrease with increasing depth

Because, organic matters are too recalcitrant to be degraded or water, nutrients and TEAs can not be supplied or temporaries are too high

Surprisingly large bacterial populations with considerable diversity are present at depths near and over 1000m

Page 49: Pinaki Sar Department of Biotechnology

Out come of deep borehole studies by ICDP and/or IODP

The lower depth limit of the biosphere has not been reached in any borehole studies

and the factors that control the abundance and activities of microbes at depth and the lower depth limit of life are still poorly understood.

The largely unexplored deep biosphere must play fundamental role in global biogeochemical cycles over both short and longer time scales

To be added in end

Page 50: Pinaki Sar Department of Biotechnology

The original chemical composition of the sediment

Response of microbes and its organic and inorganic components to increasing temperature

Availability of liquid water

Potential limiting factors for microbes in deep biosphere

Increasing pressure during burial may not be a major limitation as some microorganisms can cope well with high pressure (>100 Mpa) and there is some evidence for metabolic activity at GPa pressures.

Page 51: Pinaki Sar Department of Biotechnology
Page 52: Pinaki Sar Department of Biotechnology

Molecular hydrogen, H2, is the key component to linkthe inorganic lithosphere with the subsurface biosphere.Geochemical and microbiological characterizations of naturalhydrothermal fields strongly suggested that H2 is an importantenergy source in subsurface microbial ecosystems because ofits metabolic versatility. One of the possible sources of H2has been considered as earthquakes: mechanoradical reactionson fault surfaces generate H2 during earthquake faulting.However it is unclear whether faulting can generateabundant H2 to sustain subsurface chemolithoautotrophicmicroorganisms, such as methanogens.

Microbiology of seismic zones

Page 53: Pinaki Sar Department of Biotechnology

Wanger et al 2007

Page 54: Pinaki Sar Department of Biotechnology
Page 55: Pinaki Sar Department of Biotechnology

Isolation of pure culture bacteria

(different enrichment cond., aerobic and anaerobic cond.)

Isolation of pure culture bacteria

(different enrichment cond., aerobic and anaerobic cond.)

Metabolic Characterization

Metabolic Characterization

Metal resistance and transformation

studies

Metal resistance and transformation

studies

Identification (16S rRNA gene, FAME, API, etc.)

Identification (16S rRNA gene, FAME, API, etc.)

Culture dependent analysis

Page 56: Pinaki Sar Department of Biotechnology

*SASFiG-9 (isolated)

Detected within a water-bearing dyke/fracture at 3.2 Km depth.

strictly anaerobic; iron-reducer

optimal growth temperature = 60 oC

virgin rock temp = ~ 45 oC

* SASFiG-1

SASFiG-2

SASFiG-3SASFiG-4

SASFiG-5

SASFiG-6

SASFiG-7SASFiG-9

SASFiG-8

*

image courtesy of Gordon Southam

What have we learned?Novel indigenous microbes and communitiesNovel and unusual deeply branched sequences may be indicative of ancestral linkages, (early life?), Novel products for biomed and biotech applications

Novel Bacterial lineages unique to the SA deep-subsurface:South Africa Subsurface Firmicutes Groups (SASFiG)

1 m

Page 57: Pinaki Sar Department of Biotechnology

Key Experiments: Culture-Independent Evidence for Deep Life

Could early life in the subsurface have survived the Hadean bombardment?

Genomic advancements Sequencing of a microbe required ~18

months in mid 90’s Currently >150 microbes have been

sequenced In 2004 TIGR discovers 1.2 million new

bacteria/archea genes in the Sargasso Sea By 2005 JGI could sequence 400 microbes per

year

Page 58: Pinaki Sar Department of Biotechnology

Earth’s subsurface microbial ecology

•The biosphere extends deep into the subsurface•Limited by geothermal gradient and nutrient flux•Biomass generally low relative to the surface•Distribution is very patchy and hetergenous•Rates of community metabolism very low•Volumetrically largest part of the biosphere

Page 59: Pinaki Sar Department of Biotechnology

Subsurface lithoautotrophic microbial ecosystems (SLiMEs)

Page 60: Pinaki Sar Department of Biotechnology

Basalt: - Forms on the surface of the earth - Because it forms on the surface it cools quickly and has a fine texture (mineral grains are too fine to see with the naked eye). - The source of this rock comes from partially melted material in the mantle. - It usually leaves the mantle at mid-ocean ridges, where new seafloor is being formed. That's why most of the ocean crust consists of basalt or gabbro (the intrusive version of basalt). - Because basalt comes from a mantle source, it's very mafic and consists of dark, dense minerals rich in iron and manganese (usually olivine and pyroxene).

Granite: - Forms underneath the surface of the earth. - Because it forms under the surface the magma cools slowly, grains have time to grow and therefore it has a coarse grained texture. Grains can be easily seen with the naked eye. - Granite forms when a part of the continental crust melts to form magma and solidifies again. The heat needed for this to happen can come from different sources, for example magma from the mantle which causes the crust to melt. - Because of the above granite will be found on the continental crust (mostly at least). - The crust consists of lighter minerals than deeper parts of the earth, and that is why the minerals you will find in granite will be lighter, less dense and richer in SiO2 than those found in basalt (granite is therefore a much more felsic rock). Minerals you will typically find is quartz, orthoclase and plagioclase

Page 61: Pinaki Sar Department of Biotechnology

Eon Era Period Extent, MillionYears Ago

Phanerozoic

Cenozoic

Quaternary (Pleistocene/Holocene)

2.588 - 0

Neogene (Miocene/Pliocene)

23.03 - 2.588

Paleogene (Paleocene/Eocene/Oligocene)

65.0 - 23.03

Mesozoic

Cretaceous 145.5 - 65.0

Jurassic 201.3 - 145.0

Triassic 252.17 - 201.3

Paleozoic

Permian 298.9 - 252.17

Carboniferous (Mississippian/Pennsylvanian)

358.9 - 298.9

Devonian 419.2 - 358.9

Silurian 443.4 - 419.2

Ordovician 485.4 - 443.4

Cambrian 541.0 - 485.4

Proterozoic

Neoproterozoic

Ediacaran 635.0 - 541.0

Cryogenian 850 - 635

Tonian 1000 - 850

Mesoproterozoic

Stenian 1200 - 1000

Ectasian 1400 - 1200

Calymmian 1600 - 1400

Paleoproterozoic

Statherian 1800 - 1600

Orosirian 2050 - 1800

Rhyacian 2300 - 2050

Siderian 2500 - 2300

Page 62: Pinaki Sar Department of Biotechnology

History[edit]The Deccan Traps formed between 60 and 68 million years ago,[2] at the end of the Cretaceous period. The bulk of the volcanic eruption occurred at the Western Ghats (near Mumbai) some 66 million years ago. This series of eruptions may have lasted less than 30,000 years in total.[3]

The original area covered by the lava flows is estimated to have been as large as 1.5 million km², approximately half the size of modern India. The Deccan Traps region was reduced to its current size by erosion and plate tectonics; the present area of directly observable lava flows is around 512,000 km2 (197,684 sq mi).Effect on climate and contemporary life[edit]The release of volcanic gases, particularly sulfur dioxide, during the formation of the traps contributed to contemporaryclimate change. Data points to an average drop in temperature of 2 °C in this period.[4]

Because of its magnitude, scientists formerly speculated that the gases released during the formation of the Deccan Traps played a role in the Cretaceous–Paleogene extinction event (also known as the K–Pg extinction), which included theextinction of the non-avian dinosaurs. Sudden cooling due to sulfurous volcanic gases released by the formation of the traps and localised gas concentrations may have contributed significantly to mass extinctions. However, the current consensus among the scientific community is that the extinction was triggered by the Chicxulub impact event in Central America (which would have produced a sunlight-blocking dust cloud that killed much of the plant life and reduced global temperature, called an impact winter).[5]

Page 63: Pinaki Sar Department of Biotechnology
Page 64: Pinaki Sar Department of Biotechnology

Core samples from borehole KBH-1 showing (a) massive basalt, (b) vesicular and amygdaloidal basalt with large vugs filled with quartz and/or calcite, (c) flow-top breccia, (d) red bole bed and overlying massive basalt, (e) vugs filled with zeolite, and (f) basement granite at 951 m depth.