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good morning or good afternoon or good

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night depending on where you are it's my

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pleasure to talk to you today about the

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flexible genomes of halo archaea that

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live in hypersaline brines

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so i want to start off by introducing

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you to our field site which i find quite

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beautiful this is the south base salt

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works and it's a salt harvesting

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facility here in southern california in

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the san diego bay

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and so as you can see here in the top

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right we have the san diego bay

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um and that's the source of the the

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water which is channeled through a

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series of evaporative ponds

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within the the salt works

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and

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in those ponds the

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salts

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begin to accumulate via vapor

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and eventually they they reach

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saturation and they begin to precipitate

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at that point

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and so they can be harvested for

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commercial purposes

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but in the meantime

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these hyper saline brines serve as a

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habitat for a surprisingly diverse array

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of microbial life

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including uh the the halo archaea which

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are the um

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the organisms that produce these

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characteristic carotenoid pigments that

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that produce this beautiful red color um

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that's common in hyper saline systems

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um and so this field site is actually a

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really good analog for ancient mars as

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the planet transitioned from wet to dry

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because as you can see here on the left

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side of the map

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we have

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approximately seawater

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to hypersaline brines here on the right

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and we did manage to sample over over

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two field efforts we did manage to

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sample um

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an extensive gradient from from seawater

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to hyper saline brines uh and so we

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covered a broad gradient in 2019

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and in 2020 we decided to focus actually

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on

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this part of the gradient to fill in

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some of these gaps

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and so we sampled extensively

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between

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seawater here on the left to

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brines where the the sodium chloride has

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just reached saturation and is just

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beginning to precipitate out as halite

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and so here on the on the the bottom on

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the x-axis if you don't know water

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activity is a measure of um

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the free water molecules in a solution

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and so a water activity of one is as

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pure water

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and down here around point seven is

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beginning to be

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quite hyper saline brines

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and in our first field effort we did

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sample all the way down to

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water activity of 0.4

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which is well below the known water

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activity limit of life

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um and so i will talk a little bit about

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our um results from our uh a micro

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uh environmental investigation of the

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diversity within these brines

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from our 2019

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and this study was actually just

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published recently in environmental

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microbiology

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our key findings here

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was that this microbial succession from

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from seawater to

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presumably sterile brines is actually

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characterized by three phases

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stage one which is um between water

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activity of one and zero point seven

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which is already starting to be a

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hyper saline brine

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this stage is is characterized by a

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surge of of archaeal

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microdiversity and we called it

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microdiversity because

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here on the left we have a an estimate

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of the number of unique organisms

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within these brines which you can see is

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is increasing rapidly

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but on the right we can see that the

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total phylogen phylogenetic diversity is

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actually quite low and so

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this this surge in the number of unique

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taxa

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is is actually due to very very fine

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scale

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genetic diversity

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and

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um

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but uh uh this this first stage which is

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characterized by the proliferation of

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halo archaea um is uh uh followed by

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a a stage where the the increasing

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selection pressure due to the

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increasingly harsh um hyper saline

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conditions within the brines

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actually begins to drive down the

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diversity of halo archaea and

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at this stage the brines are dominated

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by only a few highly specialized

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halophilic taxa

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at some point the the the limit of life

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in these brines is reached and uh the

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the

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remaining brines we we assume are

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sterile or at the very least devoid of

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active life

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um and yet we do see that um nonetheless

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we we have an increase in bacterial

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diversity here um which we initially

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thought was somewhat unusual but we did

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show

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in this

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bacterial diversity is actually probably

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uh in fall or or exogenous genetic

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material on this coming from the

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surrounding environment it's falling

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into the brines and is getting preserved

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there so rather than a living active

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community what we're seeing here is a

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fossil community

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um but i do want to focus for the

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remainder of my presentation on this

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first stage here

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this is

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the stage in which we see a

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proliferation of halo archaea this surge

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of microdiversity and so

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in our 2020

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field effort and in our subsequent

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analyses we're trying to really zoom in

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on on that stage one and try to

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understand what are the sources of this

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diversity

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and what are the patterns of evolution

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that are are enabling

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this adaptation and specialization to

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hyper saline brine

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[Music]

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so

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we did take a metagenomics approach in

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this 2020 field study

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and we we began with using a

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bioinformatics pipeline

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uh that was developed by

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a member of my lab abhishek duta who

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i'll be sure to

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give an extra shout out to at the end

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um

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so one of the reasons that i'm

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particularly interested in taking this

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metagenomics approach

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is in order to look for evidence of

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horizontal gene transfer

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within this this succession from

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seawater to sodium chloride saturated

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brines

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and so

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uh

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horizontal gene transfer is fairly

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well studied in halo archaea it's been

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demonstrated that many families of halo

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archaea are quite promiscuous and have

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higher rates of horizontal gene transfer

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and

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recombination events

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and so i want to understand how

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does horizontal gene transfer drive

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these patterns and diversity the surge

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of diversity if at all

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so we begin by looking for some of the

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usual suspects um

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here i have the uh

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the the frequency of gene transfer agent

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proteins identified by rast within our

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metagenomes

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and it didn't take exactly the shape

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that i was expecting here we see that

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the the peak in

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gene transfer agent frequency actually

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uh anticipates the the surge of uh of

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microdiversity of of archaeal

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microdiversity

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and so that came as a bit of a surprise

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to us but we saw the exact same pattern

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emerge uh when we're looking at the the

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frequency of mobile element proteins um

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identified by rest

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and so um uh this this does lead us to

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to believe that what we have is actually

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a uh

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increase in horizontal gene transfer

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early on as the conditions begin to to

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to become a little bit more extreme but

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what we have then is a latent a latent

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diverse community

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which we weren't actually

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sequencing since the the

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the

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latent diversity might be quite rare

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and so

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that's that's our hypothesis for now

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but what we wanted to

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investigate now is okay so the the

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meta genomes are showing that there is

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quite a bit of change between

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seawater environment to the hyper saline

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brines but what is the function of this

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change what are the functional changes

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and so we're looking at the

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cog functions of the genes that were

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annotated

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by by rast

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and

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eggnog

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and a couple of patterns emerge the the

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first one is

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that quite clearly

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the the most common function is unknown

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and so

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that does tell us that there may be some

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more work that needs to be done in order

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to understand

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what those genes are that that we

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haven't

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but then

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here we did see a pattern emerge that

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actually quite closely corresponds to

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the uh

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pattern of um mobile gene mobile element

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proteins and gene transfer agents

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and so

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this this functional class

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is is cell wall membrane

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and envelope biogenesis proteins

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and uh

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so our uh our hypothesis here is that

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these these proteins might be the target

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of horizontal gene transfer somehow

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involved in horizontal gene transfer

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but then we do have a third major trend

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that's showing up here and that's um the

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the the cog

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l

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and so

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that might be a little bit closer to our

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original hypothesis we may be seeing

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that that that

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this is evidence of recombination

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driving

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some of this surge in microdiversity we

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can see that this maps fairly well onto

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microdiversity obviously these analyses

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are still quite exploratory

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i want to thank everybody for listening

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and in particular i want to thank

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my my team with oceans across space and

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time which has enabled this research um

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ocean's crossbasin time is funded by the

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nasa astrobiology program

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i also want to thank all of my uh

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collaborators at uh

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my my institution but also my

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collaborators at georgia tech and at

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stanford

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that made this research possible

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and finally i want to thank the jeff

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bowman lab at scripps

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that's my lab they've been really really

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great listening to me

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talk about my research

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and supporting me and helping me when

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possible

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and in particular i do want to thank

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abhishek duta who developed the

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metagenomics pipeline that i'm working

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with and has been an incredible help

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with all of my my uh struggles with um

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with the the bioinformatics side of

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things and

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um