AbGradCon 2018: Lara Vimercati


my name is Larry McCarthy and I'm a PhD

student in the Schmidt lab a few Baldr

and our lab studies microbial diversity

and communities at extreme high

elevation and today I will talk to you

about how some of these environments in

particular the atacama volcanoes can be

represented and can represent some of

the best martian analogs here on earth

and tell you about what we have found

out of the life existing there through

different approaches that go from

microbial diversity community analysis

to genomics so terrestrial analogs of

the Martian surface of her insights on

its available Abbot's ability potential

and in the last decade extreme

environments that were thought to be

devoid of life have actually been shown

to be populated by various levels of

biodiversity supporting the notion that

pretty much at least on earth the life

always finds a way however we know that

no analogue is a perfect lips or the

representation of the Martian surface

but we argue that high elevation cold

desert soils are some of the best model

systems for life on Mars surface so this

type of Hilah vation cold deserts occur

worldwide on mountain ranges between the

upper boundary of land distribution and

the lower limit of permanently

ice-covered regions so that's

represented in this picture where we

have a relationship between latitude and

elevation and they would occur in they

would occur in this brown belt worldwide

and some of the highest peaks are also

shown as a reference so among these

environments the most extreme are

probably occur in the Dry Valleys and

slope of the Andean volcanoes

above 5000 meters of elevation so

conditions that life has to face there

is even more extreme that where we will

find in the Attic

desert so microbial life has to come to

cope with a complex interplay of

parameters that go from high UV flux

extreme 3 or no freeze-thaw cycles low

atmospheric pressure and pH and soils

and an extremely low nutrient content

and water activity so the highest of

this volcanoes is volcano yakko which is

also the highest archaeological site on

earth so close to a summit some of the

best the naturally preserved mummies

have been found and they're really

interesting on a microbiology

perspective because they pretty much

show no sign of decay after being very

there for more than 500 years without

preserving chemicals so this inspired

our first expeditions to decide to

address questions about the cold dry

limits to life on Earth so a first

analysis of the soils have shown that

there's nearly undetectable levels of

water organic carbon microbial biomass

and the extracellular enzyme activity

and it seems like only a very limited

spectrum of bacterial and fungal images

have been able to overcome the harshness

of this environment and possibly

functioning in the situ so when we look

at the distribution of like the main

phyla that we have in this environment

we see that they're completely dominated

by Laura flag sign up here and a tina

bacteria so we are also below the dry

limit of a photo on social fees there's

no photo scripts I've ever been found at

these elevations and they're probably

the soils that have the lowest microbial

diversity ever reported in the

terrestrial system especially if we

compare it to the Dry Valleys of

Antarctica and Himalaya there are

however some niches that are able to

mitigate some of this environmental

challenges for example fumaroles on

volcanoes are able to provide water and

warmth and the co2 through the gassing

and we have seen that they support some

way more complex communities especially

like they form uh some a very peculiar

math structure it's really close to the

summit and it is evident from the

rarefaction curves of our eukaryotic

communities the fumarole supports a much

more diverse community compared to the

dry soils that are just surrounding them

another Oasis is represented by the so


Nieves penitentes so these are ice

structures that are pretty common uh

along the high elevations of the Atacama

and they periodically release meltwater

around its soil so they're pretty much

the only semi-permanent sources of water

in this environment and again we've been

able to see that they are able to

support much richer communities and

especially important is that we found

photo tropes in the soils and the eye

structures themselves compared to the

dry soils where you would never find any

photo troops so the photo just found our

mainly the form of algae and

interestingly no cyanobacteria have been

retreated from here so it means that

penitentes and the fumaroles are the

only structures that allow the presence

of photo troops in this type of


another very harsh trait that has been

completely under studied but it's very

common in this high elevation

environment is the extreme diurnal three

cell cycle that occurs on the soils so

as we can see temperatures can fluctuate

starting from a - stand up to 30 degrees

within a 24 hour cycle so daily

temperature cycling across the freezing

point is a key challenge for microbial

growth and survival as it is known to

cause multiple damages on a multiple

level as it combines the stress of the

cold with the reduction in water

activity so the type of dry and cryo

philic environments it was assumed -

that the low biomass and diversity was

mainly due to the lack of water however

recent studies have challenged this by

showing for example the nutrient

additions in some

periglacial soils in Peru and the

Antarctic Dry Valleys

have a much stronger effect than water

additions on the community structures we

know that microbial in that soils and

you yaku have some of the lowest

nutrients available so it is entirely

possible at this point that microbial

life happens in the soils only if when

there is water availability also

nutrients are available

so given this premises I wondered how

would these extra food communities

respond if we partially elevated water

and mutual limitations in this

environment under the field the thermal

fluctuation so we assumed that the

communities law lay dormant for most of

the time and only come to life pretty

much when there are pulses of water and

the nutrients through snowfall events

which are pretty infrequent in this

environment and I only ended positions

of organic matter from the atmosphere so

the potential for this communities under

occasional favorable conditions remains

completely unknown to date so what I

decided to do was to apply experimental

water nutrient amendments in the street

events to soil to soil micro systems

micro cars and subject them to the

freeze-thaw cycles that we see in the

field so to do that I place the some

soils that we collected above 6000

meters on Union yahko in a temperature

control chamber that is able to mimic

that fluctuation in temperature that we

see also in the field and we had a two

type of treatment so we had microcosm

that were exposed to water additions to

simulate the snowfall events and then

three stop blast water and nutrients to

simulate also occasional aisle in

depositions in this soil

I also parsed out to be cumulative

effect of multiple watering events by

simulating three discrete snowfall

events we also allow

the soils to dry up to 90% before

applying a new water addition so that

they would simulate pretty much the the

moisture conditions that are normally

found in in this environment so after

extracting our DNA doing the sequencing

of the main 16s and 18s of the community

analyzing them what we saw is that the

community was significantly changing so

in here we have a pickup PCoIP lot of

the bacterial community and we see how

the community significantly changes when

treatments are applied both if it's just

the water addition or water plus

nutrient additions and the community

increases each time more with every

addition so which organ is are actually

allowing of this shift so we looked a

little bit and first of all we saw that

the there is a response to water input

even when nutrient limitations are not

alleviated so this may mean that water

availability allows this try adapted

communities to at least respond to the

very low nutrients that are available we

saw that one of the main orders that

responded to multiple wiring events were

was the Burkholder reality so this order

is very widespread in cryo philocan

oligotrophic environment so it may be

able to function in situ and take

advantage of this water and water in

impulses we saw an increase in the

action of mice italics especially when

you're providing them with nutrients and

with the first water addition there was

an increase in chloro sort of bacteria

so this group is interesting because it

has a potential to do photosynthesis

even if it's not demonstrated in our

soil and we saw pretty much like a

decrease in diversity

after the third event for both type of

treatments so this indicates probably

that only a very minor part of the

community would be active when

conditions allow for that and the rest

of the taxonomy that we see in this

soils is probably due to just like IO in

the position that they are dormant in

the soil a similar pattern is shown for

the eukaryotic community again we see

that multiple simulated snowfall events

and nutrient additions make the

community change and this is especially

more evidence for just like water

additions and interestingly we see that

freethought alone has an impact on the

community as we see here our starting

point cluster separately from our

freeze-thaw alone treatment so it may be

that some of this organizers are

actually responding just to the

FreeStore alone which microorganism

again like a responding to this so the

first and most interesting to us is the

Cryptococcus so this is very relevant in

our soil so it's one of the most

commonly we found and we saw that it

increases dramatically once you give the

first water and water plus nutrient

addition so it's possible that takes

advantage like very fast of this water

and nutrient impulses we see an increase

in the thea mindsets these are other

type of funds like they may not be as

fast of responders but they are known to

be well suited to low nutrient

environments and then the most dramatic

shift happened when just water was added

so we get one out of truck which is like

an algae and new cloris RC know that

starts becoming dominant and another

group of fans I mostly do my seeds that

again are well known that for being able

like to withstand a lot of stresses and

again like in the bacteria we see a

significant decrease in alpha diversity

with multiple water and nutrient

additions so we saw that a Cryptococcus

like becomes really dominant as soon as

like he provided with a little bit of

water and nutrients but interestingly it

does so even when it's just exposed the

tooth we saw dry condition so I'm

maybe that it's partially active when

there's an extremely low water content

so we isolated this organist and

cultured it and did a phylogenetic

analysis and we saw that it's extremely

closely related to another

Cryptococcus from the Dry Valleys

Cryptococcus trade money which is up

there were tolerant and in the lytic

type of Easton so cryptic Hachi have

been found like many times in many

glacial and extreme environments and

given its ubiquity in the south of

environments and the ability to

withstand three spell cycles it may be

an important functional component of

this environment so what I did next was

to try and figure out if the

Cryptococcus was not just a surviving

but if it was actively growing under

this condition so what I did is that I

set up called liquid cultures of it and

I placed them in that same thermal

chambers that allow fluctuations and

incredibly it was able to grow despite

freezing a solid every night so with a

doubling time of about two days so this

as far as we know is the first

demonstration of growth of an organized

during repeated extreme free cell cycles

and it supports even more our original

hypothesis that it has the capacity to

grow during this free cell cycles in the

environment mainly doing so when there

is higher soil moisture which is

provided by infrequent snowstorms in

this environment the next question that

we want to ask is which strategies does

they used to survive this multiple

challenges in this life limiting

environment and especially how does it

cope with free-stall so our plan is to

use a combined strategy of both genomics

and transcriptomics to figure out which

genes allow survival and metabolic

activity in this organism and the to

analyze its genome by seeing if it has

significant deviations from its men's

fellow counterpart so what we did was

culturing it an optimal temperature that

we found it to be 17 degrees and or we

extracted total DNA

sequence it and started its general

assembly and on rotation I'm sorry okay

I'm merely done okay yeah so very

briefly like the jeans that we're gonna

look for our metabolic gene so since we

suspect this to be like versatile

opportunity that is able to take

advantage of whatever the atmosphere

brings it on this high elevation we

expected to have many degrading pathways

we will look at genes associated with

oxidant and the somatic stress we still

don't know what kind of like stress

signal is generated with with pre cell

cycle cold adaptation genes genes

necessary to complete meiosis to see if

it's able to do with sexual reproduction

and then G's that allow through with

standfast temperature switches for

example related to membrane fluidity and

genes that allow it to live at water at

a low water activity so we have to keep

in mind that when there's low in this a

freezing environment there is extremely

low water activity so there are like

very similar to hyper saline

environments and the last step we'll do

to do a transcriptomic analysis of

specific time points within that thermal

cycle so the idea is to grow it and

sample at a different temperatures

within the daily thermal cycle do a

total RNA extraction and get its

transcriptome sequence to find out which

genes are up and down regulated under

the free stress compared to optimal

temperature and to see if it's active

during the whole free soft cycle so

all this work is relevant to the NASA

Astrobiology roadmap because it aims to

determine the physiological state of

microbial cells that are found in

extremely dry and temperature

fluctuating environments to get more

insight on the dynamics of survival of

my keurig and its possibly on the

surface of Mars and our work is the

first to explore adaptations to external

thermal fluctuation by analyzing the

genome and transcriptome of what at this

point can be called a poly external

philic yeast so given its unique ability

to withstand a lot of stressors it is a

potential model organs of astrobiology

and for stress resistance studies on

eukaryotes so I want to thank the

National Science Foundation's and the US

Air Force which gave up the grants to be

able to do this work and the Alpine and

microbial Observatory which is my lab

that has now become Arctic and Antarctic

as well so if you're interested in

looking at pretty pictures of all our

sites and our work this is our website

thank you thank you very much Laura we

have time for

perhaps one question

right so I noticed in one of your slides

you had something that you called plant

material going down when you added water

and nutrients and I was wondering if you

could explain that a little bit oh sure

so so when we look at this for example

like we see that our untreated

conditions so just like soils from

elevations have a lot of plant materials

that we know it's not growing there but

it's blown in so what we see is that

there's a reduction of that plant

material so we have two hypotheses about

how that's happening so one is that

Cryptococcus is actually taking

advantage of that and like actually like

degrading that plant material that is

blown in we also saw that it has like a

lot of genes that are able to degrade

some plant compounds some plant derived

compounds or the other option is that it

will simply be degraded as a as a result

of the free cell cycle itself because

it's known to damage a lot of cells so

it may be ethan alpha via the

Cryptococcus or it may be just like

degraded but in each case we suspect

that it will you know make advantage of

whatever new trend comes out of them

okay thank you very much Lauren thank