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introduction um I'll just see if I can
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share okay can you see that um
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PowerPoint
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presentation yep great yes all right um
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thank you again for that um nice
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presentation so I'm looking forward to
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talking to you all today about some of
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the research that um we do in my group
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here in Sydney in Australia
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and today I'm going to talk to you about
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Marine
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microorganisms and how their behavioral
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interactions can lead to um some quite
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profound implications for a variety of
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processes that occur in the ocean so the
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Marine microbes I'm going to focus on
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are those that live in this environment
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the pelagic ocean so plantonic microbes
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floating around out in the open water
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and these microbes are highly abundant
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they're also extremely diverse and they
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play a lot of really important roles in
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controlling the function of the
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ocean
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oops and among these roles is um their
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important um activities within the
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oceans biogeochemical cycles so to
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portray that what I'm showing here in
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this cartoon is the oceans um carbon
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nitrogen and sulfur Cycles um which are
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of course key parts of the um biogem
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chemical Cycles within the ocean and I
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know there's a lot going on in this
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image um so I'm not going to go into any
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of the specific detail except to say
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that the main take-home message is that
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it's different groups of microbes
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largely within the water column that
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control the chemical Transformations
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that make up these biogeochemical
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cycles and this is important because
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this ultimately influences things like
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nutrient cycling which controls the
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productivity of marine food webs
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and it also mediates the fluxes of um
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climatically important gases in and out
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of the ocean into the atmosphere and
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this is how the ocean can have an
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influence on our Global
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Climate now while all of these processes
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are important at Global ocean scales
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many of the chemical Transformations
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that build these biogeochemical cycles
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actually occur at much smaller SC scales
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really minute scales that in fact take
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up a fraction of an individual drop of
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seawater so these occur in specific
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micro environmental scenarios and
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ultimately play really important roles
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in the
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ocean and I'm just going to give you a
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couple of examples of some of these so
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if we zoom in on some of these um
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biogeochemical cycles like I said into
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what we're really talking about a
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fraction of a drop of seawat we can see
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that some important processes at Play
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that involve microbial Interac
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reactions so if we look over here um one
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of the microscale processes that um has
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a big impact on carbon cycling in the
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ocean is the way that microbes interact
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with um sinking organic particles which
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we often call Marine snow particles so
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as you know phop plankton in the upper
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ocean fix carbon dioxide into living
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biomass during
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photosynthesis but then many of these
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photop Plankton die or they're consumed
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by other plantonic organisms and this
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leads to the formation of these Marine
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snow particles which are rich in organic
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carbon and these particles um like you
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can see in this um image of a sinking
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Marine snow particle are responsible for
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a massive flux of carbon from the upper
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ocean to the deep sea about 10 gigatons
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of carbon every year are transported
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from the um sunlet part of the ocean to
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the deep ocean where some of this carbon
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is ultimately sequestered for up to
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hundreds or thousands of years so
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obviously this has a big effect on the
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amount of carbon that can be exchange
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between the upper Ocean and the
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atmosphere but microscale microbial
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processes have an influence on how much
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of this carbon actually exported to the
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deep sea so if we look at one of these
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Marine snow particles under a microscope
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after staining it with a nuclear acid
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stain we'll often see something that
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looks like this where all of these
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little blue dots are heterotrophic
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microbes including bacteria and ARA
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which heavily colonize these Marine snow
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particles because of their um rich
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source of organic carbon which that the
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microbes can consume these microbes use
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extracellular enzymes to break these
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particles down and consume the carbon
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and this can um recycle this carbon
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before it reaches the Deep potion and
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this of course has an influence on the
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ultimate amount of carbon that's export
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and like I said this is all occurring
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within a microscale scenario these
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particles are typically on the order of
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a fraction of a millimeter in diameter
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and they're colonized by these bacteria
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um which influence this carbon
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flux another example of these microscale
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processes are in the top left here um
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and this is what I'm going to focus a
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lot of my talk on today this is the
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interaction that occurs between um
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phototropic microbes phytoplankton and
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heterotrophic bacteria and there's
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evidence that these interactions are
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highly important for both groups of
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organisms and this can ultimately have a
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big influence on governing the
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productivity of um marine ecosystems as
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well as chemical Transformations at the
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base of the food web and there's growing
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evidence that many of these interactions
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are highly specific and might take place
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within a microscale context where we see
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these cellto cell interactions occurring
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an example of some of this is um what we
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can see in this video what we can see
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here is a seawater sample that we've
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taken and you can see there are two
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organisms within this there's a large
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organism with the spines looks a bit
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like an insect this is a a datom um it's
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a keros cell and you can see the little
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white dots buzzing around the cell and
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these are heterotrophic bacteria if you
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look closely it looks like many of these
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bacteria are trying to maintain their
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position close to the datom cell and
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this like I said before is going to be a
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big focus of what I talk about in my
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talk
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today so within my group we're
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interested in these type of types of
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microscale processes and we try to view
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the ocean from the perspective of a
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bacteria floating around in the seawater
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rather than looking at it from a a bulk
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scale and from this perspective what we
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think is what the ocean likely looks
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like to a a bacteria is not a
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homogeneous soup of substrates and
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resources but a structured environment
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where there's different microscale
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features which could each act as a a
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niche um full of resources for these
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microbes and within these um cartoon um
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or images that we've come up with to
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describe this um microbes view of the
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ocean what I'm going to be focusing on
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today is one particular feature and
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that's the interaction between
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phytoplankton and bacteria and how this
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occurs within this microscale scenario
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so photop Plankton as you know fix
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carbon dioxide into living biomass but a
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large proportion of this carbon that
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they fix ends up being released back
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into the seawater by the cells up to 50%
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or more of this carbon that they fix is
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released as dissolved organic carbon so
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it's leaked into the surrounding
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environment and within the region
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immediately surrounding each phyto Plank
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and cell within the area what we call
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the diffusion boundary layer where the
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effects of turbulent mixing are minor we
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expect to see chemical gradients
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emanating from the phytoplankton cell
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and these are often rich in carbon we
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know that um Marine bacteria obtain most
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of their carbon um from phytop planton
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in the environment so this produces an
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Environ or a micro environment um that
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bacteria might be able to take advantage
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of and this area has been called the fos
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spere which is this area surrounding an
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individual phop Plankton cell which is
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enriched in substrates and it could be
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the interface for interactions between
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bacterian
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phytoplankton so everything I talk about
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today is going to be focused on this
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idea of the fos spere and how bacteria
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and other microbes may be able to use
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behaviors to exploit this environment
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and this is important because it um
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leads to cycling of material released by
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The phytoplankton as I said it's a a
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major source of resources for bacteria
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in the ocean and more recently we're
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starting to understand that this is
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probably the interface for really
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important symbiotic relationships that
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take place between phytoplankton and
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heterotropic bacteria in the water
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column So within this idea of um these
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symbiotic or mutualistic relationships
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we're now starting to learn a lot about
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the interactions between phytoplancton
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and bacteria for a long time it's being
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known that bacteria and phytoplankton
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probably benefit from each other we as
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I've mentioned already phytoplankton
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release a lot of carbon into the water
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which the bacteria use as a key growth
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source and it had been thought that
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bacteria through the remineralization of
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this organic matter produce nutrients
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that the phytoplankton can then use but
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in more recent years we've got a much
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more sophisticated view on this whereby
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we see that specific bacteria and
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phytoplankton are likely to take part
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in mutualistic associations whereby
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really specific chemicals are um
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exchanged between them often in a
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reciprocal chemical exchange where they
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mutually benefit from these
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relationships and there's been a lot of
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work in recent years in laboratory
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situations showing that certain bacteria
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and phytoplankton really have a strong
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interdependence on each other now I'll
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talk more about some of these chemical
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exchanges later in my tour
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so if we think about these close
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relationships between the phytop planton
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and bacteria if a certain bacteria
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really relies on a given phop plankton
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for um certain chemicals then it makes
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sense that they probably should have
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close proximity to each other out within
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the vast expanses of the ocean where
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there's a Malo of different chemicals
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being mixed up but this often isn't as
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simple as it might sound so if we think
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about microbes out in the ocean even
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though I mentioned they're highly abant
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when we look at their abundance and look
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at the distances between individual
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cells these are often quite large so for
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marine bacteria the average distance if
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we think of the bacteria being uniformly
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distributed in sea water between two
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bacteria is typically around 100 cell
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lengths so they're quite um separated
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within the water
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column and the distance between one of
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these bacteria and a phytoplankton cell
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which they might be involved in one of
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these reciprocal chem IAL exchanges with
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are also quite large so if we think
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about a non-motile bacteria something
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like a sar 11 cell floating around in
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the ocean its chances of coming into
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contact with a phytoplankton cell are
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actually quite remote it'll typically
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come into contact with a f Plank and
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cell only once every 286 days so
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obviously this is an ideal if you want
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to be close to a particular pH Plankton
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partner however if we now consider that
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many Marine bacteria are motile so they
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can swim through the environment using
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helical floella which are these little
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tails that you can see on the bottom of
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this bacteria in the bottom right which
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they use for propulsion to swim around
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through the environment the in counter
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frequency between a phytol plant and a
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bacteria increases dramatically now one
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of these moole bacteria is likely to
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come into contact with a phytoplankton
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cell about nine times every day so you
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can see there's a big change just driven
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by this
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motility if we include another behavior
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um related to motility on top of this
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called chemot taxis which is the
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capacity of bacteria to direct their
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behavior according to chemical cues and
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chemical gradients in their environment
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then this means that the bacteria likely
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to come into contact with the fos spere
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and be able to maintain their position
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within it much greater so much so that
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we might expect to start to see bacteria
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clustering or maintaining their position
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close to a particular F Plankton host
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and that's what we think is happening in
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this image that in this video that I
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showed earlier where these bacteria are
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swimming close to this datom cell
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they're likely using chemotaxis to
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maintain that position close to this
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datom which is probably releasing
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organic carbon into the
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environment now this idea has been
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around for quite a long time it was
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first proposed um in the early 1970s in
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this paper by B and Mitchell where they
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showed that many Marine bacteria exhibit
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chemotaxis towards the chemical products
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produced from
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phytoplankton and they suggested that
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this bacterial chemot taxis probably
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helps the bacteria maintain itself close
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to this source of organic material which
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is the
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phytoplankton and they were the first
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people to come up with this term the
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phosphere which is this region
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surrounding an individual phytoplankton
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cell
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but since then although a lot of people
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have presumed this to be important and
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to play a role in the in um ecologically
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important interactions between
00:14:07
phytoplankton and bacteria there hasn't
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been a lot of real concrete evidence for
00:14:12
the fos spere and the role that behavior
00:14:14
might play in allowing bacteria to take
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advantage of
00:14:18
it so this is something that I've been
00:14:20
interested in for several years now and
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first started studying when um I was
00:14:25
doing my um postto in Roman stalkers lab
00:14:28
um at MIT about um 12 to 15 years ago
00:14:32
and at that time we wanted to come up
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with an approach to try to mimic this
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Ficus spere within a controlled
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experimental scenario so that we could
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really track the way that bacteria
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behavor within this micro environment so
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we used a technique called microfluidics
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which involves the fabrication of small
00:14:51
chips and on these chips we can etch
00:14:54
complex patterns and make things like
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micr channels within which we can
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control very carefully small volumes of
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fluid and create chemical gradients and
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in this photo you can see one of these
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microfluidic chips to give you an idea
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of its size that um in the background
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you can see that's the objective lens of
00:15:12
a microscope so this is a couple of cenm
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long and a few millimeters wide now we
00:15:18
use these microfluidic channels to try
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like I said to simulate the fosher and
00:15:23
using one of these systems what we did
00:15:25
was injected in bands of phytoplank and
00:15:28
produced to chemicals so we take phytop
00:15:30
planton cultures um extract the
00:15:33
chemicals that they exuded and inject
00:15:35
them into the channel and that's what
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you can see here this is a band of these
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phytoplankton exudates which we're
00:15:41
Imaging after adding a fluorescent stain
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this is about 100 micrometers wide in
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diameter and this diffuses across our
00:15:49
microfluidic Channel at at the same kind
00:15:52
of spatial and temporal scales you'd
00:15:54
expect to see in a real fosh in the
00:15:56
ocean we then put Marine bacteria into
00:15:59
this Channel and use video microscopy to
00:16:02
track their behaviors and that's what we
00:16:04
can see here these yellow lines of the
00:16:06
swimming Paths of individual bacteria
00:16:08
within the channel and they're swimming
00:16:10
around and you can start to see that
00:16:12
they're not uniformly distributed uh
00:16:15
across the channel they're maintaining
00:16:17
their position in the middle of the
00:16:18
channel where we had this um patch of
00:16:21
phytoplankton
00:16:22
exodites so this is some of the first
00:16:25
evidence that we had that bacteria could
00:16:28
use this ch ta tactic Behavior to hone
00:16:31
in on these microscale patches and
00:16:34
maintain their position within them
00:16:36
where they're going to be exposed to
00:16:37
higher levels of the organic substrates
00:16:39
released by The
00:16:41
phytoplankton we repeated these
00:16:43
experiments across a wide range of
00:16:46
different Marine bacteria and to
00:16:48
different phytoplankton exodites and
00:16:50
found that this was quite a common
00:16:52
feature amongst many Marine
00:16:55
bacteria but there are a few
00:16:56
shortcomings of this work um one being
00:16:59
that it was restricted to the laboratory
00:17:01
where we could perform it under a
00:17:02
microscope and this meant that we were
00:17:05
restricted to using um labor isolates of
00:17:08
marine bacteria so many of you probably
00:17:11
already learned that from natural
00:17:13
environments it's often difficult to
00:17:15
isolate um bacteria from the environment
00:17:19
and in environments like the ocean we
00:17:21
can usually only cultivate a small
00:17:23
fraction of all of the microbes that are
00:17:25
actually in the environment and that
00:17:27
means in these EXP experiments we were
00:17:29
using what you could describe as lab
00:17:31
rats in terms of the microbes in these
00:17:34
experiments and these were easily
00:17:36
cultivatable um bacteria which could
00:17:38
grow up on nutrient-rich media what it
00:17:41
also meant is that many of these
00:17:42
bacteria were highly motile and
00:17:44
chemotactic so this could these
00:17:46
experiments could be giving us a bias
00:17:48
view of the importance of this kind of
00:17:50
behavior because we're using these lab
00:17:51
rat type
00:17:53
organisms so our next step was to try to
00:17:56
look at this in a more realistic
00:17:57
framework and the goal was to take this
00:18:00
work back out into the ocean away from
00:18:03
these laboratory experiments and that
00:18:05
meant that we had to develop a new
00:18:07
experimental platform for trying to
00:18:10
understand chemotaxis in the natural
00:18:12
environment whereby we could look at
00:18:14
natural communities of marine bacteria
00:18:17
that we didn't have to grow up or
00:18:18
cultivate to start off with and to do
00:18:21
that we developed a new um piece of
00:18:24
technology called the insitu chemotaxis
00:18:27
assay or the
00:18:29
which you can see in this image now we
00:18:32
used our same microfluidic fabrication
00:18:35
approaches to make this system and to
00:18:37
give you an idea of its scale this is
00:18:39
about the size of a credit card and you
00:18:42
can see that it's a array of small
00:18:44
Chambers each one of these little
00:18:46
circles is a chamber that has a volume
00:18:48
of about 100 microliters and it's
00:18:50
enclosed from the external environment
00:18:53
with the exception of these two small
00:18:55
portals that you can see in each chamber
00:18:58
now can use these portals to inject in
00:19:01
chemicals and that's what we um use to
00:19:03
inject in our chemical um attractants or
00:19:06
chemo attractants and in the case I'm
00:19:09
going to be talking about today these
00:19:10
are chemicals that are released by
00:19:13
phytoplankton so we can fill this Isa
00:19:15
device up with these chemicals and then
00:19:17
we physically deploy it into the seawat
00:19:21
so we put it into the ocean where it's
00:19:23
exposed to natural
00:19:25
microbiomes and then what happens is the
00:19:27
chemicals that are in in these Wells
00:19:30
diffuse out of the well into the
00:19:32
surrounding seawater creating a chemical
00:19:34
gradient close to the surface of this
00:19:36
system emanating out into the seawater
00:19:39
where the microbes
00:19:41
are and if these microbes are motile and
00:19:44
chemotactic then they can potentially
00:19:47
swim up these chemical gradients into
00:19:50
the wells where the chemicals are coming
00:19:52
from so you could think of this as a
00:19:54
microbial trap where we're using
00:19:57
phytoplankton exodites as the bait and
00:19:59
the bacteria in the surrounding
00:20:01
environment if they like these chemicals
00:20:03
will swim in and they're captured Within
00:20:05
These Wells so what we're effectively
00:20:07
trying to do is simulate these fos
00:20:10
speres within the marine environment in
00:20:13
a way that we can capture the natural
00:20:15
communities of bacteria so we deploy
00:20:18
this Isa device in the environment for
00:20:20
30 minutes then we retrieve it we
00:20:23
perform flowetry on the sample so that
00:20:25
we can count how many bacteria swim into
00:20:27
the wells and understand the levels of
00:20:30
chemotaxis that have occurred and then
00:20:32
we perform DNA sequencing and in this
00:20:34
case we use shortgun metagenomic
00:20:36
sequencing to characterize the um
00:20:40
composition and potential function of
00:20:42
the microbes that are responding to our
00:20:44
different Cho
00:20:46
attractants so I'm going to talk about
00:20:48
some experiments that we've done to try
00:20:50
to test the hypothesis that different
00:20:52
fos speres or different phytoplankton
00:20:55
will attract discrete groups of microbes
00:20:58
that will um in end up in ecological
00:21:03
relationships with those phol
00:21:05
plantant so this is some work that was
00:21:07
led by my um postdoc um JB Rainer who's
00:21:10
worked in my lab for many years and he
00:21:12
was interested in this question of which
00:21:14
bacteria swim towards which
00:21:16
phytoplankton so what he did was he um
00:21:18
grew up cultures of phytoplankton
00:21:21
spanning all of the major groups of
00:21:22
phytoplankton that we find in the ocean
00:21:25
he made them made them axenic so removed
00:21:27
all of the bacteria that were living in
00:21:29
the cultures and then use the solvent
00:21:31
based approach to extract the chemicals
00:21:33
that these phop Plankton released into
00:21:35
the metor so these are the chemicals
00:21:37
that would be exuded into the fos
00:21:40
spere and he put these in our Isa and we
00:21:43
deployed it in the environment we did
00:21:45
this in a number of environments the
00:21:47
experiment I'm going to talk about today
00:21:49
is a deployment that we performed in
00:21:51
coastal seawater off of the coast of
00:21:53
Sydney which is where we live and we
00:21:55
tracked the response of bacteria in the
00:21:58
sea water to a suite of different phop
00:22:00
Plank and exodites that you can see
00:22:02
across the um x-axis in this plot now
00:22:05
the way we quantify the strength of
00:22:07
chemot taxis as I mentioned we perform
00:22:10
photometry and we quantify chemotaxis
00:22:13
using this chemotactic index which is
00:22:15
simply the numbers of cells that swim
00:22:17
into our different um Chambers
00:22:19
normalized to our control which in this
00:22:22
case is filtered seawater so the reason
00:22:25
we do this is because bacteria just
00:22:27
through random motility will potentially
00:22:29
end up in these Wells and so this is
00:22:31
what we see within our filed seawater
00:22:33
random motility um leading to small
00:22:36
number of cells but when we see a
00:22:39
significantly higher number of bacteria
00:22:41
within our treatments relative to this
00:22:43
controller indicates chemotaxis is
00:22:45
occurring and that's what we see we've
00:22:48
performed these experiments in a range
00:22:49
of different places and over different
00:22:51
seasons and we um find repeatedly that
00:22:55
natural communities of marine bacteria
00:22:57
exhibit chemotaxis towards a wide range
00:23:00
of different phytoplank and exdents like
00:23:02
you can see in this plot we see positive
00:23:05
chemot taxis in a number of these cases
00:23:07
it varies depending upon the phop
00:23:09
Plankton exodite but um we see that we
00:23:12
can answer this first question that it's
00:23:14
not just in the laboratory where we see
00:23:15
this Behavior natural communities of
00:23:18
marine bacteria can do this within the
00:23:21
environment so the next step if the next
00:23:24
question is if these communities are
00:23:26
doing this who amongst the communities
00:23:28
are performing chemot taxis and towards
00:23:31
what attractants and this is where we
00:23:33
start to use our metagenomic data where
00:23:36
we can characterize the taxonomy of the
00:23:38
microbial community in a moment I'm
00:23:40
going to show you a heat map showing you
00:23:42
the diversity of the responding bacteria
00:23:45
that have swam into these different
00:23:47
chambers which contain the phytoplank
00:23:49
and exit so on this case along the y-
00:23:52
axis here you can see colorcoded are our
00:23:54
different treatments which are the
00:23:56
phytoplankton exat taken from different
00:23:58
cultures we have five replicates and you
00:24:01
can see that we get good coherence
00:24:04
across our replicates and when we look
00:24:06
at the microbial Community which each
00:24:08
with each one of these cells within the
00:24:10
heat map indicative of a different um
00:24:12
procaryotic taxa we have bacteria as
00:24:15
well as ouria that responded to our um
00:24:18
chemo attractants there are two things
00:24:20
that you can see one is that across the
00:24:23
replicates for each treatment we see
00:24:25
good coherence generally and and you
00:24:29
then also see between our um different
00:24:32
treatments there's different patterns so
00:24:35
different parts of the community are
00:24:37
responding to different phytoplankton
00:24:39
exodites we don't just see one group of
00:24:41
bacteria that are responding to all of
00:24:43
the phytoplankton we're seeing discrete
00:24:45
populations responding to different
00:24:48
fosher we can look at this in another
00:24:50
way here we can see where we've used a
00:24:53
network analysis approach to show where
00:24:56
certain bacteria end up within our
00:24:59
different treatment so to walk you
00:25:01
through this in this network the large
00:25:03
circles with the um labels inside them
00:25:05
are our different treatments so there
00:25:08
are um phytoplank and exudates the small
00:25:11
circles are different um bacteria and
00:25:14
ARA that we find in our um isels the
00:25:19
lines between them or the edges between
00:25:21
them are indicative of finding one of
00:25:23
these bacteria or ARA within one of
00:25:26
these treatments now as you you can see
00:25:28
there are a lot of different um taxi
00:25:30
here and there are two different modes
00:25:32
of connection to these um treatments in
00:25:36
the middle you can see there's a lot of
00:25:37
bacteria that have multiple lines to
00:25:40
multiple um phytop plon exodites on the
00:25:43
outside you can see that there are some
00:25:45
that are only attached to a single
00:25:47
exodite so these are what we call our
00:25:50
generalist and specialist responses the
00:25:53
generalists are the organisms that are
00:25:55
responding to a wide range of different
00:25:57
phytoplankton and in this um change
00:26:00
version of the plot you can see these
00:26:01
are the colored organisms the different
00:26:04
colors correspond to how many um
00:26:06
different treatments the bacteria were
00:26:08
found in so you can see there's one in
00:26:10
the middle that was found in all 10 of
00:26:12
the treatments and then we can see the
00:26:14
gray circles on the outside are the
00:26:17
Specialists which are only found in one
00:26:18
or two of the
00:26:20
treatments if we look at the
00:26:22
distribution of these two different
00:26:24
modes of Association we find that most
00:26:27
of the bacteria that we found in these
00:26:30
um treatments um fell in the specialist
00:26:33
end of the um rain of the regime you can
00:26:37
see most what here on this plot you can
00:26:39
see our numbers correspond to the
00:26:41
numbers of um treatments the bacteria
00:26:44
were found in and you can see that most
00:26:47
were found in 1 two or three treatments
00:26:49
few were found in seven eight or nine
00:26:52
and so this indicates that the majority
00:26:55
of the bacteria we found in these
00:26:57
results were in the specialist
00:27:00
category so this answers one of these
00:27:03
other questions do we find specific
00:27:05
microbial assemblages associating
00:27:08
associating with um specific
00:27:12
phytoplankton and it gives us this
00:27:15
impression that within the seawater we
00:27:17
might have discrete FICO spere made up
00:27:19
of different microbiomes with specific
00:27:22
bacteria within them so I've now
00:27:24
answered a couple of questions can
00:27:25
Marine bacteria perform chemotaxis in
00:27:28
the environment towards fos speres and
00:27:30
do different communities respond to
00:27:32
different
00:27:33
phytoplankton the next thing we were
00:27:34
able to do is leverage our metagenomic
00:27:36
data to try to look at what some of the
00:27:38
repercussions of these responses are by
00:27:40
looking at the functional profiles in
00:27:43
these communities so I'm sure that
00:27:44
you've learned that metagenomics allows
00:27:46
us to look at the um predicted
00:27:48
functional capacity of bacteria within
00:27:51
samples and so that's what we've done
00:27:53
here now the first um set of functions
00:27:57
that we looked at um might seem obvious
00:27:59
to you and we did this purely as a
00:28:01
sanity check we look for genes involved
00:28:04
in chemotaxis so of course we'd expect
00:28:07
to see that within our chemotactic
00:28:10
experiment within the wells the um
00:28:12
bacteria would have um heighten capacity
00:28:15
for
00:28:16
chemotaxis and so we looked for genes
00:28:18
involved in the chemotaxis pathway and
00:28:21
what we can see in this First Column
00:28:23
here this is the bulk seawat outside of
00:28:25
our um experiment and then when We
00:28:28
compare it to what we see within our um
00:28:31
Isa Wells and you can see in this heat
00:28:33
map the color the heat corresponds to
00:28:36
the relative abundance of these genes
00:28:38
you can see there's an enrichment in
00:28:40
genes involved in chemotaxis within our
00:28:43
Chambers like said this is not
00:28:44
surprising at all we'd be worried if we
00:28:46
did not see this but it was a sanity
00:28:49
check to see that this approach was
00:28:51
going to provide us with any um
00:28:53
interesting
00:28:55
information so the next thing we we're
00:28:57
interested in looking at was whether
00:28:59
some of these bacteria that swim into
00:29:01
these um fos speres that we've made
00:29:05
might have the capacity to um establish
00:29:07
mutualistic Partnerships with the
00:29:09
phytoplankton so I showed an image
00:29:11
earlier which showed the many potential
00:29:14
um exchanges between phytop plon and
00:29:17
bacteria one of them was this exchange
00:29:19
here which has come from some work in a
00:29:22
number of Laboratories where they looked
00:29:24
at interactions between phytop plantant
00:29:26
and bacteria and shown that some
00:29:28
bacteria which benefit from the
00:29:30
production of organic material from the
00:29:32
phytoplankton can in turn um provide
00:29:35
benefits to the phanon by producing what
00:29:38
are called citores which are specialized
00:29:40
chemicals which are involved in binding
00:29:42
of iron IR many of you will probably
00:29:45
know is a limiting resource for a lot of
00:29:47
phylon and it's been shown that bacteria
00:29:50
that are enriched in the CIT fors um
00:29:53
help the phytoplankton assimilate iron
00:29:56
and this can lead to an in enhancements
00:29:58
of phytoplankton growth and it's been
00:30:00
proposed that um mutualistic
00:30:03
Partnerships between phytop planton and
00:30:04
bacteria are going to benefit from
00:30:07
bacteria which have this capacity or
00:30:09
have these um C
00:30:11
Force so we looked into the metagenomic
00:30:14
data to see whether the bacteria that
00:30:16
was swimming into our Chambers um showed
00:30:18
this capacity again I'm comparing it to
00:30:20
what we see in the external seawater and
00:30:22
here we're looking at genes involved in
00:30:24
the biosynthesis of citores by the
00:30:27
bacteria and we again found the
00:30:29
statistically significant over
00:30:31
enrichment of um these genes within our
00:30:35
different chambers so this indicates
00:30:37
that these bacteria that are swimming
00:30:39
into these fosher have this capacity to
00:30:41
help the um phytoplankton by producing
00:30:43
these CED
00:30:45
Force another example um of many
00:30:49
examples I only have time to show you
00:30:50
two today but we' saw many of these
00:30:52
examples where um bacteria had the
00:30:54
capacity to help phytop planton is in
00:30:56
the provision of um vitamins so some of
00:31:00
you might be aware that phytoplankton
00:31:02
require um B vitamins like vitamin B12
00:31:04
but many of them can't produce them
00:31:07
themselves so they rely on bacteria to
00:31:10
provide these um vitamins to the
00:31:12
phytoplankton and again this has been
00:31:14
shown to underpin interactions between
00:31:16
phytoplancton and bacteria whereby the
00:31:18
bacteria benefit from a range of
00:31:20
different organic substrates produced by
00:31:22
the phop Plankton and in return the
00:31:24
bacteria provide vitamin B12
00:31:28
so we look for genes involved in the
00:31:30
biosynthesis and transport of vitamin
00:31:32
B12 same story as we saw before we see a
00:31:36
significant enrichment in these geneses
00:31:37
so what we've seen across a number of
00:31:39
these different Pathways is that the
00:31:41
phytoplank the bacteria that swim into
00:31:43
these specialized um phytoplank and
00:31:46
enriched micro environments have a
00:31:49
number of um different functional
00:31:51
capacities that will benefit a
00:31:53
phytoplankton partner and you could come
00:31:55
up with a hypothesis that phytoplankton
00:31:57
are releas ing chemicals that actively
00:31:59
attract bacteria that are going to bring
00:32:02
these benefits towards them into their
00:32:04
fosh to establish these
00:32:08
interactions so now for the last few
00:32:10
minutes going to move away from these um
00:32:12
laboratory I mean these field-based
00:32:14
experiments with the ISA to um Target
00:32:17
some more of these potential
00:32:18
interactions um that we've done looked
00:32:20
at within a laboratory scenario one of
00:32:23
these is some work by one of my PhD
00:32:25
students Nan laroon who was interested
00:32:27
in their um interaction between the
00:32:29
Marine datom actinocyclus curve at tulus
00:32:32
and its microbiome Ted a range of
00:32:35
experiments including looking at um
00:32:37
bacteria bacteria that she'd isolated
00:32:39
from this um culture um capacity to
00:32:43
perform chemot taxis towards the datom
00:32:47
and she found that among these bacteria
00:32:49
one in particular Ultram monus
00:32:51
mediterania showed a strong chemotactic
00:32:54
response to the chemicals exuded by this
00:32:57
diom she performed this using the same
00:32:59
Isa device I've talked about before but
00:33:01
in a laboratory scenario she also
00:33:04
performed metabolomic analysis of the
00:33:06
chemicals released by this diet time and
00:33:08
used some of these chemicals within the
00:33:10
iscar and showed again that this
00:33:12
bacteria swam towards many of these So
00:33:15
within the system we know that this
00:33:17
bacteria can potentially swim towards
00:33:18
the fosher of this um datom she then
00:33:22
performed some co-growth experiments
00:33:24
after making the diom axenic and showed
00:33:27
that there's a istic benefit from the
00:33:29
association between these two the
00:33:31
bacteria um was able to grow um on the
00:33:35
carbon produced by the datom we see a
00:33:38
significant increase in bacterial growth
00:33:40
um when it's grown in co-culture with
00:33:42
the actinocyclus and similarly when we
00:33:45
grow um the um datom with the bacteria
00:33:49
we see an enhancement and growth of the
00:33:51
datom relative to an axenic situation so
00:33:54
there's this mutualistic partnership
00:33:56
which is underpinned initially by this
00:33:58
chemotactic migration of the bacteria
00:34:00
close to the
00:34:02
datom we wanted to understand more about
00:34:05
this so another PhD student in my lab
00:34:07
ABA khil using the same model system
00:34:10
started to um investigate what chemical
00:34:12
exchanges might be involved in this
00:34:14
relationship and she was particularly
00:34:16
interested in one group of chemicals
00:34:18
called plant growth promoting hormones
00:34:20
which has emerging evidence that many
00:34:23
bacteria can produce we know in
00:34:25
terrestrial systems that plants um
00:34:27
bacteria that are associated with plants
00:34:29
can provide these hormones to benefit
00:34:31
the plant and it's in there's evidence
00:34:34
that this is happening in phytoplank and
00:34:36
bacteria interactions as well so Bea
00:34:39
showed that this Ultram monus
00:34:41
mediterrania produces a large sweet of
00:34:44
different plant growth promoting
00:34:45
hormones often in quite high
00:34:47
concentrations which is surprising we
00:34:49
didn't expect a single bacteria to
00:34:51
produce so many hormones she then showed
00:34:55
using a technique where she knocked out
00:34:57
the Gene involved in the um biosynthesis
00:35:00
of one of these hormones called endol
00:35:02
atic acid or IAA um using a crisper C9
00:35:06
approach to knock out a gene involved in
00:35:09
its synthesis so she was able to make a
00:35:12
mutant of this bacteria which didn't
00:35:14
produce this plant growth promoting
00:35:16
hormone and then perform co-growth
00:35:19
experiments and she was able to show
00:35:21
that by eliminating the capacity of this
00:35:23
bacteria to produce these plant growth
00:35:25
promoting hormones it eliminat the
00:35:28
promotion effect that this bacteria had
00:35:30
so we think that there's good evidence
00:35:32
that this uronis Mediterranean is
00:35:35
benefiting this Daton by producing these
00:35:38
plant growth promoting hormones after
00:35:40
swimming into the fos
00:35:43
spere and for the final couple of
00:35:45
minutes I'm going to talk about one
00:35:46
final model system that we've looked at
00:35:48
within our laboratory this is worked by
00:35:50
another PhD student Marco giaden he was
00:35:53
helped by um our post um JB rener here
00:35:57
we were looking at the interactions
00:35:59
between a
00:36:00
picocyanobacteria coccus which is one of
00:36:03
the most important photot troes across
00:36:04
the ocean and heterotrophic bacteria
00:36:07
Marin marinera adherence and here we've
00:36:11
used a slightly different approach to
00:36:12
what I've talked about up until now
00:36:14
rather than looking at the growth
00:36:16
promotion we've looked more directly at
00:36:18
the chemical exchanges between these two
00:36:20
organisms and the way we've done this is
00:36:22
by using a technique called nanosims
00:36:24
which leverages um um imaging technology
00:36:28
that allows us to look at the transfer
00:36:30
of chemicals um when we use stable
00:36:33
isotope um um incubations of our
00:36:37
organisms so what we did in this
00:36:39
experiment was we grew our cnic coccus
00:36:42
the Picos bacteria in a media which um
00:36:46
included 15n as the source of nitrogen
00:36:49
so 15n is the stable isotope of nitrogen
00:36:53
so we grew this cnica coccus within the
00:36:55
stable isotope form of nitrogen which
00:36:57
meant we could then um visualize this
00:37:00
using our nanosims
00:37:02
approach we then C- grew the cnica
00:37:05
caucus and the marinoa together and we
00:37:08
found that the marinoa was able to
00:37:10
assimilate this 15n which was released
00:37:13
from the ca coccus likely in forms of
00:37:16
dissolved organic nitrogen so the
00:37:19
marinera benefited from this release of
00:37:22
nitrogen from the cnica caucus we then
00:37:25
went back to our idea of of whether
00:37:28
behavior is involved in this interaction
00:37:30
and here we took advantage of the fact
00:37:32
that we had some mutants for this
00:37:34
marinor as well including a chemotactic
00:37:37
deficient and a m motility deficient
00:37:39
mutant so we had a mutant where the um
00:37:42
Gene Ka was knocked out so this was a a
00:37:45
bacteria which didn't have the capacity
00:37:47
to perform chemotaxis and another one
00:37:50
where the fly C Gene was knocked out and
00:37:52
this is a fella assembly Gene meaning
00:37:54
that this bacteria was non-motile we
00:37:57
performed exactly the same experiment as
00:37:59
we did with the wild type and
00:38:01
interestingly what we found was that the
00:38:03
level of enrichment that we saw in the
00:38:05
marinor was heightened in the wild type
00:38:08
relative to the um two mutants so what
00:38:12
this tells us is that this capacity of
00:38:14
the bacteria to swim close to the
00:38:16
phytoplankton is important in this
00:38:18
uptake of the nutrients released by The
00:38:22
phytoplankton and the final part to this
00:38:24
story was that this Behavior was only
00:38:27
one part of this um reciprocal exchange
00:38:31
we also grew our marinoa up in a um
00:38:35
stable isotope in this case it was grown
00:38:37
up in a media containing 13c which is a
00:38:40
stable isotope of carbon and we're able
00:38:43
to show that this um 13c was transferred
00:38:46
from the marinoa to the CN coccus so we
00:38:49
know that cnic caucus can take up some
00:38:52
organic carbon from the environment and
00:38:54
here we're able to show that organic
00:38:55
carbon released by another bacteria was
00:38:58
assimilated by this C bacteria but
00:39:02
interestingly what we also found was
00:39:04
like we saw in the case with the marinor
00:39:07
taking up the chemicals released by The
00:39:09
cnic caucus we saw an increased amount
00:39:12
of um carbon taken up by the C caucus in
00:39:16
when we used the wild type of the
00:39:17
swimming marinor so this tells us that
00:39:20
the capacity of this Mariner Bor to swim
00:39:22
close to the cica caucus not only
00:39:25
benefited itself in bringing in
00:39:27
chemicals released by The cnic coccus
00:39:30
but it benefited the CN caucus cell by
00:39:32
maintaining position close by and
00:39:34
leading to um a reciprocal chemical
00:39:38
exchange so there are a few examples of
00:39:40
this little story that we're interested
00:39:42
in my group in how behavioral
00:39:45
interactions the swimming and chemotaxis
00:39:47
by bacteria can bring together
00:39:50
potentially mutualistic Partners in
00:39:52
particular the phytop plum bacteria so
00:39:55
hopefully today I've convinced you next
00:39:57
time you look at seawater it's not just
00:40:00
a homogeneous soup where everything's
00:40:02
uniformly mixed up it's a structured
00:40:05
environment where behaviors of some of
00:40:07
these microbes can facilitate
00:40:09
interactions between individual cells
00:40:11
and if we scale this up it can influence
00:40:14
things like the growth of whole
00:40:16
phytoplankton communities and important
00:40:18
chemical exchanges in the Marine
00:40:21
microbiome so with that obviously all of
00:40:23
this work has been done by people that
00:40:25
have worked in my group and other people
00:40:27
that that we've collaborated with so
00:40:29
thank all of these people and thank
00:40:31
Rachel for the invitation to speak to
00:40:34
you all and thank you for your attention
