Deep Biosphere Sediment Microbiology - Center for Dark Energy ...

2011
DARK
ENERGY
BIOSPHERE
INSTITUTE
(DEBI)
RESEARCH
COORDINATION
NETWORK
(RCN)
MEETING
Deep
Biosphere
Sediment
Microbiology
March
7‐9,
2011
Carolina
Inn
and
UNC,
Chapel
Hill,
North
Carolina
The
 Dark
 Energy
 Biosphere
 Institute
 (DEBI)
 is
 pleased
 to
 announce
 the
 meeting
 "Deep
Biosphere
Sediment
Microbiology"
to
be
held
7‐9
March
2011
at
the
Carolina
Inn
and
University
of
 North
 Carolina
 in
 Chapel
 Hill,
 North
 Carolina.
 
 This
 meeting
 is
 a
 component
 of
 the
 NSF
Research
 Coordination
 Network
 (RCN)
 on
 the
 Deep
 Biosphere
 with
 co‐directors
 Katrina
Edwards
 and
 Jan
 Amend
 and
 the
 mission
 to
 help
 coordinate
 and
 support
 deep
 biosphere
research,
and
to
aid
in
the
transfer
of
information
regarding
the
deep
biosphere's
role
in
the
global
 Earth
 system.
 
 This
 meeting
 is
 supported
 by
 the
 US
 National
 Science
 Foundation
Research
 Coordination
 Network,
 the
 US
 Science
 Support
 Program
 associated
 with
 the
Integrated
 Ocean
 Drilling
 Program
 at
 the
 Consortium
 for
 Ocean
 Leadership,
 and
 the
 NASA
Astrobiology
Institute.
The
 theme
 of
 the
 UNC
 meeting
 is
 the
 application
 of
 novel
 culture‐independent
 and
 culturedependent
microbiological
 methods
 to
 marine
 sediments
 and
 their
 pore
 fluids.
 By
 necessity,
research
in
this
arena
often
focuses
on
enumerating
cells
and
cataloging
phylogenetic
diversity.
In
 the
 coming
 years,
 however,
 more
 emphasis
 will
 be
 placed
 on
 the
 active
 components
 of
microbial
 communities
 and
 the
 expression
 of
 functional
 genes.
 Accordingly,
 to
 diminish
misleading
 DNA
 signals
 from
 lysed
 and
 inactive
 cells,
 the
 more
 labile
 RNA
 molecules,
 which
occur
 in
 proportionally
 greater
 numbers
 in
 active
 cells
 (Sørensen
 and
 Teske
 2006),
 can
 be
targeted
through
both
molecular
and
microscopic
techniques.
The
standardization
of
molecular
(DNA
 and
 RNA‐dependent)
 techniques,
 and
 development
 of
 consistent
 protocols
 in
 sample
handling
and
analysis
become
increasingly
important
as
divergent
results
from
different
groups
and
 teams
 require
 cross‐checking
 and
 reconciliation
 (Schippers
 et
 al.
 2005
 vs.
 Lipp
 et
 al.).
Although
sequencing
capabilities
and
costs
permit
ever‐growing
genetic
databases
and
an
evergrowing
dependence
 on
 such
 data,
 culturing
 efforts
 are
 also
 experiencing
 a
 scientific
renaissance.
 As
 an
 example,
 the
 American
 Academy
 of
 Microbiology
 recently
 reported
 that
"most
 environmental
 microorganisms
 have
 yet
 to
 be
 isolated
 and
 identified,
 let
 alone
rigorously
 studies",
 and
 that
 research
 and
 technology
 must
 help
 overcome
 the
 barriers
 that
prevent
 the
 study
 of
 uncultivated
 microorganisms
 (Harwood
 and
 Buckley
 2008).
 Culturing
efforts
 must
 target
 individual
 species
 and
 microbial
 communities,
 as
 well
 as
 the
 "effects
 of
perturbation"
on
these
communities.
The
 training
 workshop
 at
 this
 meeting
 will
 highlight
 methods
 for
 extracting
 genetic
 material
from
sediment,
porewaters,
and
hydrothermal
fluids;
the
development
of
nucleotide
primers
for
functional
gene
analysis;
advances
in
cultivating
novel
and
dominant
members
of
microbial
communities;
 and
 ways
 to
 control
 for
 seawater
 contamination
 in
 sediments
 and
 associated
fluids.
 First,
 new
 methods
 for
 analyzing
 deep
 subsurface
 communities
 based
 on
 16S
 rRNA,

instead
of
16S
rRNA
genes
(i.e.
DNA),
will
be
made
available
to
the
DEBI
community
through
lectures,
 tutorials,
 and
 lab
 exercises;
 examples
 include
 extraction
 and
 analysis
 of
 16S
 rRNA,
instead
 of
 16S
 rRNA
 genes
 (i.e.
 DNA),
 and
 rRNA‐tag
 or
 randomly
 primed
 high‐throughput
pyrosequencing
techniques
(Sogin
et
al.
2006;
Huber
et
al.
2007).
Second,
expertise
in
practical
aspects
 of
 molecular
 surveys
 of
 deep‐subsurface
 communities
 will
 be
 shared.
 One
 obvious
example
 of
 many
 is
 primer
 development
 and
 functional
 gene
 analysis;
 published
 generic
primers
 are
 frequently
 insufficient
 for
 deep
 subsurface
 studies
 due
 to
 lineage‐specific
mismatches
 and
 inherent
 bias
 (Teske
 and
 Sorensen
 2008),
 and
 due
 to
 decreased
 sensitivity
owing
to
lineage‐specific
nucleotide
ambiguities;
using
multiple,
lineage‐specific
primers
allow
much
 more
 comprehensive
 analysis
 of
 deep
 subsurface
 functional
 gene
 cohorts
 (Lever
 and
Teske,
 2007).
 Third,
 novel
 approaches
 for
 the
 enrichment
 of
 specific
 functional
 and
phylogenetic
 groups
 will
 be
 discussed
 and
 also
 demonstrated
 as
 much
 as
 feasible.
 The
approaches
 include
 sediment
 microcosms,
 stable
 isotope
 probing,
 and
 in
 situ
 colonization
experiments.
New
culturing
efforts
are
relying
more
heavily
on
solid
substrates,
non‐traditional
redox
 pairs,
 micronutrients,
 chemical
 gradients,
 and
 symbiotic
 relationships.
 Fourth,
contamination
 monitoring
 with
 chemical
 tracers
 will
 be
 taught.
 An
 approach
 pioneered
 by
Smith
(Smith
et
al.
2000)
and
House
(House
et
al.
2003),
and
developed
further
on
IODP
leg
301
to
the
Juan
de
Fuca
Ridge
flanks,
can
now
be
applied
in
microbial
community
analyses
of
deep
sediments
continuing
into
basement
basalt
(Lever
and
Teske
2007).
Meeting
steering
committee:
Andreas
Teske
(Chair),
University
of
North
Carolina,
Chapel
Hill
Jen
Biddle,
University
of
Delaware
Matt
Schrenk,
East
Carolina
University
2011
DEBI
Meeting
Agenda
2

ACCOMMODATIONS
AND
MEETING
VENUE
The
Carolina
Inn
(http://www.carolinainn.com)
is
the
primary
meeting
venue
and
is
offering
a
special
room
rate
for
our
meeting
for
March
6‐10,
2011.

The
Carolina
Inn
is
a
historic
hotel
located
on
the
campus
of
the
University
of
North
Carolina,
on
South
Columbia
Street
in
downtown
Chapel
Hill
just
20
miles
west
of
the
Raleigh‐Durham
International
Airport
(RDU).
The
UNC
Department
of
Marine
Sciences
is
located
on
the
third
and
fourth
floors
of
Murray/New
Venable
Hall,
in
two
minute
walking
distance
to
the
Carolina
Inn
on
the
other
side
of
South
Columbia
Street.
The
main
entrance
opens
towards
Carroll
and
Gardner
Hall
on
the
Northeast
corner
of
Murray/New
Venable
Hall.

Wednesday
hands‐on
exercises
in
microscopy
and
cultivation
will
be
held
in
the
laboratories.
Underground Bar,
Tuesday Night BBQ
Carolina
Inn
UNC Marine Sciences,
Venable Hall Laboratories
2011
DEBI
Meeting
Agenda
3

The
Chapel
Hill
Underground
Bar
will
host
our
classic
North
Carolinan
BBQ
dinner
Tuesday
evening
and
is
located
at
157
E.
Rosemary
Street
in
downtown
Chapel
Hill.
HOTEL
SHUTTLE
We
will
provide
shuttle
service
between
Raleigh‐Durham
International
Airport
(RDU)
and
the
Carolina
Inn
before
(Sunday)
and
after
(Wednesday
afternoon)
the
meeting.

Other
options
include
Super
Shuttle
or
taxi
service.
POSTERS
The
Old
Well
Room
will
be
available
for
poster
set
up
beginning
Monday
(3/7)
during
the
coffee
break
at
4:00
PM.

The
poster
session
will
be
on
Monday
evening
at
6:00
–
9:00
PM.

Please
take
down
your
poster
immediately
afterwards.

Any
posters
left
up
will
be
discarded.
SUNDAY:
MARCH
6,
2011
6:00
–
8:00
PM
 Opening
reception
[Hill
Ballroom
South]
Welcome
to
DEBI,
the
RCN,
and
the
Deep
Sediment
Biosphere
workshop
(Andreas
Teske)
2011
DEBI
Meeting
Agenda
4

MONDAY:
MARCH
7,
2011
6:30
–
8:00
AM
 Continental
Breakfast
[Outside
Chancellors
Ballroom]
Deep
Sediment
Microbiology
Now
[Chancellors
Ballroom]
8:00

–
8:10
AM
 Welcome
and
introduction
(Andreas
Teske,
Jen
Biddle,
Matt
Schrenk)
8:10
–
9:00
AM
 Deep
sediment
microbiology
and
ODP:
An
overview
(Andreas
Teske)
9:00
–
9:30

 Energy
constraints
of
microbial
growth
and
survival
(Tori
Hoehler)
9:30
–
10:15
 ‘North
Pond’
and
‘South
Pacific
Gyre’
updates;
future
directions
(Wiebke
Ziebis)
10:15
–
10:45
 Coffee
break
Breakout
Session
I:
Fundamental
Microbiology
Questions
about
the
Deep
Biosphere
10:45
–
12:30
PM
Breakout
session
IA:
Genomics,
evolution
and
biogeography
Discussion
of
the
nature
of
microbial
ecology
in
the
deep
sediment
subsurface,
the
implications
for
microbial
genomes,
genome
evolution,
and
microbial
distributions.
[Chancellor
West]
(Leaders:
Eric
Boyd,
Billy
Brazelton,
Karla
Heidelberg)
10:45
–
12:30
PM
Breakout
session
IB:
Microbial
activity,
physiology,
metabolism
Discussion
of
the
biological
adaptations
that
may
be
specific
to
the
deep
subsurface
in
terms
of
energy
utilization,
growth,
and
survival.
[Chancellor
East]
(Leaders:
Karine
Alain,
Suzanna
Bräuer,
Alberto
Robador,
Daniel
Rogers)
12:30
–
2:00
 Lunch
[Old
Well
Room]
2:00
–
3:00
 Breakout
session
IA
review
[Chancellors
Ballroom]
3:00
–
4:00
 Breakout
session
IB
review
[Chancellors
Ballroom]
4:00
–
4:30
 Coffee
break
What
to
do
Better
the
Next
Time

[Chancellors
Ballroom]
4:30
–
5:30
PM
Sediment‐related
potential
projects
and
ideas
(Participant
mini‐presentations:
Karine
Alain/Maria
Ciobanu,
Jen
Biddle,
Brandon
Briggs,
Gaëtan
Burgaud,
Ginny
Edgcomb,
Jiasong
Fang,
Hector
Hernandez,
Heath
Mills)
Poster
Session
[Old
Well
Room]
6:00
–
9:00
PM
 Poster
session
with
finger
foods
2011
DEBI
Meeting
Agenda
5

TUESDAY:
MARCH
8,
2011
6:30
–
8:30
AM
 Continental
Breakfast
[Outside
Chancellors
Ballroom]
Technology
Challenges
and
Innovations

[Chancellors
Ballroom]
8:30
–
9:15
AM
 Detecting
and
probing
subseafloor
life:
New
technological
challenges
(Jens
Kallmeyer,
Yuki
Morono,
Axel
Schippers)
9:15
–
10:00

 Contamination
control,
NA
isolation,
amplification,
and
quantification
(Mark
Lever,
Karen
Lloyd)
10:00
–
11:00
 Technological
advances
in
cultivating
microbes
and
microbial
activity
measurement
(Mandy
Joye,
Karsten
Zengler)
11:00
–
11:30
 Coffee
break
Samples,
Ships,
and
the
System
[Chancellors
Ballroom]
11:30
–
12:00
PM
 Opportunities
with
DEBI
and
C‐DEBI
(Jan
Amend,
Rosalynn
Lee)
12:00
–
1:00
PM
Upcoming
IODP
cruises
and
how
to
get
involved/
Beyond
IODP
after
2013
(Geoff
Wheat)
1:00
–
2:00
 Lunch
[Old
Well
Room]
Breakout
Session
II:
New
Strategies
and
Technical
Innovation
2:00
–
3:30
PM
 Breakout
session
IIA:
Assessing
physiological
adaptations
and
energy
constraints
–
research
priorities
for
the
deep
sedimentary
biosphere
Discussion
of
the
current
state
of
knowledge
on
tools
available
to
study
microbiology
of
the
deep
subsurface,
their
limitations,
what
new
tools
might
be
employed,
and
what
needs
to
be
developed.
[Chancellor
West]
(Leaders:
Tom
McCollom,
Roy
Price,
Karyn
Rogers,
Everett
Shock)
2:00
–
3:30
 Breakout
session
IIB:
Sensitive
detection
and
identification
of
microbial
diversity
and
function:
Problems
and
solutions
Discussion
of
the
current
technologies
used
in
characterizing
the
microbiology
of
deep
subsurface
environments,
what
they
tell
us,
what
they
don’t,
and
where
we
need
to
focus
our
efforts.
[Chancellor
East]
(Leaders:
Ginny
Edgcomb,
D’Arcy
Meyer‐Dombard)
3:30
–
4:00
 Group
photo
and
coffee
break
4:00
–
6:00
 Group
discussions
focused
on
breakout
sessions
IIA
and
IIB
and
related
potential
projects
[Chancellors
Ballroom]
7:00
–
9:00
 Classic
North
Carolina
BBQ
[Chapel
Hill
Underground
Bar]
2011
DEBI
Meeting
Agenda
6

2011
DEBI
Meeting
Agenda
7
WEDNESDAY:
MARCH
9,
2011
6:30
–
8:00
AM
Continental
Breakfast
[Outside
Chancellors
Ballroom]
Hands
On
Activities
These
activities
run
in
three
major
sessions:
Microscopy,
Cultivation,
Sequence
Analysis.
Each
block
is
taught
three
times;
students
can
alternate,
or
repeat
the
same
block.
The
instructors
will

tag‐team
as
they
see
fit.
Exercises
in
Microscopy:
[UNC
Marine
Sciences
Laboratory
–
Room
3106]
Microscopy
in
sediments,
single
cells
and
substrate‐attached
biofilms,
automated
methods
(Jens
Kallmeyer,
Axel
Schippers,
Matthew
Schrenk,
Olympus
representatives)
Exercises
in
Cultivation:
[UNC
Marine
Sciences
Laboratory
–
Room
3106]
Novel
cultivation
techniques,
growth
and
activity
at
high
pressure
(Mandy
Joye/Marshall
Bowles,
Karsten
Zengler)
Exercises
in
Sequence
Analysis:
[Chancellors
Ballroom]
Pyrosequencing
data
analysis,
functional
genes,
and
guide
to
software
for
sequence
data
(Jennifer
Biddle,
Mark
Lever,
Karen
Lloyd)
8:00
–
10:00
AM
Session
I
10:00
–
10:30
 Coffee
break
[Chancellors
Ballroom,
UNC
Marine
Sciences
Break
Room]
10:30
–
12:30
PM
Session
II
12:30
–
2:00
 Lunch
[UNC
Marine
Sciences
Lobby]
2:00
–
4:00
 Session
III
Wrap
Up
[Chancellors
Ballroom]
4:00
–
4:30
PM
Workshop
recap
(Andreas
Teske)