dear students until now we have studied about
microbial energetics so we know how one individual
cell will make sure it gets the electron acceptors
it requires the electron donors it requires
the energy it needs to survive in the environment
and thrive replicate and ah interact with
the environment now we are going to move on
to microbial ecosystems like we did in the
last lecture where we i introduced you to
the basic concepts in ecology so today we
are going to go little bit more in our advance
and look into terrestrial ecosystems which
is the ecology of microbes in terrestrial
ecosystems so lets start here
so microbes to live in an ecosystem they require
two things they should have all the resources
that they need and they should have the right
conditions to thrive so some of the resources
that microbes will require to thrive are carbon
some autotrophic microbes can utilize carbon
dioxide as source of carbon others require
organic carbon material so this is very important
for life as we know that carbon must be available
in the right form in the environment the other
thing we know is nitrogen is very essential
part of a cell so if you remember there is
dna the double helical structure that carries
the information on how cell would live for
proteins it would make how it would survive
and its activities
so nitrogen is very essential component of
the genetic material so nitrogen should be
available in its environment either in organic
form or inorganic form now some microbes can
actually fix inorganic form of nitrogen such
as nitrogen gas and they referred to as nitrogen
fixing bacteria others cannot so they would
require other assailable forms of nitrogen
such as nitrate nitrite ammonia or organic
form of nitrogen some cells also require other
micronutrients so remember the word here is
macronutrients not microbe so these are nutrients
that it requires in good quantities such as
sulfur for ah phosphorus potassium and magnesium
then there are micronutrients that i have
not put in this table that are also required
in trace amounts so we have talked about trace
elements before how they are essential for
making certain enzymes and amino acids so
we need them too got in very little amount
usually microbial communities have a way of
finding these micronutrients trapping them
and recycling them over and over so the environment
doesnt have to be rich in micronutrients but
definitely rich in carbon nitrogen and other
macronutrients also then environment should
have a good supply of electron acceptors and
electron donors because all life processes
are a redox reaction they are a reduction
in oxidation of ah electron acceptors and
electron donors so its important to have both
in the environment now when we talk of conditions
the conditions should be just right for the
microbe now the temperature that is right
for one microbe may not be correct for the
other microbe for example if we have a thermophilic
microbe that loves hot temperatures and we
put it in cold water it will die it has to
have just the right temperature that it requires
ranging from very cool like psychrophilic
microbes for example found in ice sheets of
antarctica and arctic and himalayas or we
can have thermophilic microbes that love to
be in hot water lakes or um undersea volcanic
vents
then the ph should be also right and in one
of the first lectures i talked about different
range of temperature and ph in which microbes
survive so a microbe that grows in acidic
lake will not survive in a neutral or mays
not survive in a neutral and alkaline lake
so the ph has to be correct too now thinking
of temperature and ph its very important to
note that human not only microbe but even
higher orders of life such as human beings
also require just the right temperature and
ph for example i cannot survive in extremely
cold environment such as minus one twenty
degree celsius or hot environments such as
seventy degree celsius or eight degree celsius
as we know it we cant survive and same is
true with ph if ph is very low in our environment
in our air we will get burned and we will
die of necrosis and other diseases similarly
if ph is very high we will have corrosive
burns
next is orp which stands for oxidation reduction
potential so basically ah a methanogen which
requires a very reduced environment to survive
will not survive in oxidized environment such
as so not only does methane methanogen a methane
producing bacteria it not require oxygen but
if it is exposed to oxygen it will die so
in this case we require just the right amount
of orp oxidation reduction potential of environment
the light should be correct too if there are
phototrophic bacteria and they are not getting
oxygen they will time in the osmotic conditions
if you remember we have talked in one of the
early lectures that cellular membrane is a
bi lipid in bacteria and ah it has hydrophilic
and hydrophobic end
so inside the cell there there is some osmotic
pressure relative to outside of the cell and
if there is change in external conditions
the osmotic pressure in external condition
the cell might either explode or implode for
example if i take microbes that live in hypersaline
environment like ocean and then put it in
a freshwater bowl or freshwater lake then
they are likely to ah they are likely to ah
lose their integrity same is true otherwise
if we take water from or if we take microbe
from a freshwater lake and put it into a saline
environment it will also lose its integrity
and not survive most probably
then another thing we need to understand so
this is microbe in a individual level we know
what microbes require on an individual level
what resources what conditions now lets look
at what microbes require when they we are
talking about many microbes present together
in an environment because there is hardly
any environment where theres just one microbe
sitting and you are looking at just one microbes
need usually its either a population gildo
community so now is a good time to introduce
you to the concept of population gildan community
i have sort of mentioned this before but let
me be very clear population is when many microbes
belonging to same species are together
so we might have population of eco live they
all belong to same species on the other hand
community is when different populations survive
together right so we might have ecoli we might
have pseudomonas aeruginosa we have some other
microbe acetobacterium (( )) pseudo bacterium
coming there so we have multiple populations
so we have a lot of microbes from different
species together they are interacting with
each other yeah this is community microbial
community and now the third word is guild
now guild is a group of microbes that are
same in their function and this i have talked
a lot about when i was talking about metabolism
of microbes in previous lectures that because
the orp or oxidation reduction potential of
an environment is bound to influence all the
microbes that are present in the community
they are likely to have similar functional
traits and we will go about this and i will
show you ah right away what we mean when we
talk about guilds
so students now lets take a look at population
guilds in communities within one particular
environment here we have a diagram of lake
a very rough schematic and what is in blue
and wavy is water and this is the sediment
and this is the control volume boundary that
i have drawn for the lake and this is the
cross section by the way of the lake so lets
look at the microbial community present in
the lake so where look here the red arrow
is showing you the depth until which light
can penetrate and its width gives you an idea
of the intensity of light that enters and
reaches at this particular depth
so until where the light can reach we can
have two kinds of microbes where in the first
microbial community we have oxygenic phototropes
so remember because this is towards the surface
of the lake we will have reaeration and aeration
going on and thus oxygen will also oxygen
will also be present in the top surface so
microbes that can utilize the light produce
food by consuming carbon dioxide as the source
of carbon they will be present here the other
kind of microbes that we will have here will
be facultative or obligate aerobes that require
oxygen as i mentioned oxygen will be present
here
so the first kind of microbial community now
remember i am calling this microbial community
so it implies that there is not just one oxygenic
phototropes but there are multiple species
of oxygenic phototropes that might be present
or in certain unique environments you might
only have one singular population of um oxygenic
a phototroph or facultative aerobes obligate
aerobes now in community one the ones that
is a phototroph they use light they use carbon
dioxide and water and produce glucose and
oxygen now facultative aerobe are in cooperation
with them they are very happy to live next
to the oxygenic phototrope because they are
producing oxygen and they are producing glucose
facultative aerobes and aerobes in general
can consume the glucose by using oxygen as
a electron acceptor and get tremendous amount
of energy from here so this is and produced
carbon dioxide which can be consumed by oxygen
in phototroph so this is an example of cooperation
between two different microbial communities
now in towards the sediment or towards the
bottom of the lake we have anoxic zones and
we might even have completely anaerobic zone
so anoxic zone has like trace amount of oxygen
present anaerobic zone no oxygen present so
in sediment for example we might have third
kind of community that is lives in anoxic
or anaerobic environment now in this part
of the community if you might have at the
top layer lets say there is some amount of
nitrate present now so the microbes that can
utilize the nitrate why did i say top layer
because lets say initially when the lake was
built lets say its a manmade lake there was
nitrate present here so microbes started utilizing
nitrate and as the nitrate depleted they moved
on ah to different ah electron acceptors and
they made a gradient of electron acceptors
over time
why would they be a gradient because remember
the oxygen is coming in from here and oxygen
as it comes in if nitrate has been denitrified
it will oxidize it again so there is higher
chances of nitrate to be present on the top
of this sediment layer than on the bottom
so one guild or one functional community of
microbes could be nitrifying bacteria so bacteria
or microbes they denitrify they are one functional
group and they are likely to be found in the
top layer next we have the second guild which
is ferric reducing bacteria so when lets say
nitrate got depleted and now we have ferric
ions present so microbes that can utilize
that reduce them and get energy will be present
here the third guilt and most probably below
it would be sulfate reducing bacteria followed
by sulfur ah reducing bacteria and then fermentated
microbes and then methanogenic and acidogenic
microbes
so you notice here that as the electron ah
acceptor gradient ah so we notice here that
the microbial community gradient follows the
electron acceptor gradient so here we have
oxygen then we have nitrate we have ferric
sulfate sulfur then we have fermentative condition
and then methanogenic and acidogenic conditions
so again is our microbes that have same function
so all microbes that are iron reducing microbes
they form one guild all microbes that are
iron oxidizing microbe their other guild now
they might have different populations within
them yeah so within guild too there might
be many different kinds of iron reducing bacteria
wherein sulfate reducing bacteria they might
be very different kinds of sulfate reducing
bacteria
so a guild might have singular population
or it might have a community but the unifying
factor for a guild is that their functional
characteristics are same now as i mentioned
before population you should remember is one
species only over all this together so a community
would be here you know the environment is
similar right their functions are sort of
similar multiple populations living and interacting
with each other so this is one community community
two community three within each community
there are multiple populations together they
make a meta community clear alrighty now note
here from top to bottom we have a gradient
of oxidation potential oxidation reduction
potential we have a gradient of um electron
acceptors therefore and we also have a gradient
of the kind of microbial communities we will
have no now because oxygen is energetically
most advantageous we also have a gradient
of energy yield
so if the microbes growing on the top of the
lake would have would get the highest energy
in yield and the ones on the bottom that are
methanogenic or acidogenic will have minimum
energy yield all righty so to revise we have
single cell physiology so we have single cells
and then we have local communities and population
remember population is microbe of same species
communities are different populations existing
together for example in this microbial frock
we have microbe stained red and microbe strained
blue all together this is a community then
we have meta communities and meta population
so a meta community and a meta population
the example would be the lake that we just
saw and then we have ecosystem so we have
um the entire region that includes aquatic
components terrestrial components and air
components
so the range in size also varies our single
cell can be anywhere from one to ten micrometer
the communities and population can be anywhere
up to thousand micrometer the meta community
is meta population and we will see some of
them today in lecture can be up to meter and
ecosystem more than meters many meters so
now let us look at environment in micro environment
of microbes their populations and their communities
so when we talk of environment and microenvironment
lets try to get an perspective of the area
or a microbe on distance
so for a human being a ten centimeter is not
a long distance yeah so ten centimeter we
can just approach it very easily but now think
from the perspective of a microbe that is
only a few micrometer in length for that microbe
three millimeter can be as long as it is as
two kilometers is for human being so within
two kilometer radii we can have different
um as we know we have different populations
of higher order of life we can have monkeys
dogs cats and rats and human beings again
human beings all following different practices
here different food habits similarly in for
microbes within three millimeter space its
a very small space from humans perspective
but its plenty from bacterial perspective
that we can have by microbes bacteria of very
different functions of very different populations
so if within three millimeter space we can
have very very diverse community as diverse
community and even more diverse community
than we have when we talk about higher order
of life like birds and animals and humans
and etcetera insects and etcetera within two
kilometer radius the other thing is within
three millimeter radius you might say well
its just three millimeter the environment
wont change a lot so the microbes within three
millimeters should not be very diverse but
the beauty here is that in the micro scale
we notice that the environment changes the
gradient of ah rate of change of environment
is very high
now on the right panel here i have a picture
and this is um a cartoon a schematic showing
you the oxygen levels in a soil micro pore
so you know soil has pores where through which
the air and water are transported now this
is a micro pores so even among pores its really
small and we notice that this is some ah twelve
millimeter in a diameter and now what you
are seeing in different colors is oxygen gradient
so in the brown you have the highest amount
of oxygen and it reduces that it goes to orange
and then lighter yellow and then blue then
a little bit slight purple and then dark purple
there is no oxygen left
so within this six ah into six milli so we
have twelve millimeter range we can go from
aerobic microbes to fermentative methanogenic
and acidogenic bacteria so think about it
this way and so if you look at even this is
too big a micro pool by the way even in pools
as small as three three millimeter we have
seen similar characteristics similar behavior
so in the dark purple region we might have
methanogens acidogens we might have sulfur
reduction sulfate reduction nitrate reduction
nitrate reduction and then obviously oxygen
reduction now now all this diversity in the
orp oxidation reduction potential of this
micro environment will result into diverse
function diversity of microbes which will
allow a very diverse community to grow in
this twelve millimeter by twelve millimeter
micro pore
now all these microbes of different kinds
they will compete for resources for example
in the aerobic region denoted here by dark
brown we not only have one singular kind of
aerobic bacteria or archaea or eukaryote but
we have different kinds of microbes and all
of them are competing for oxygen so the one
that can grasp oxygen fastest the one that
can degrade its electron donor fastest and
grow fastest is likely to out compete other
microbes but then there are other factors
also that influence ah microbial growth microbial
competition so now about microbial complete
competition because of this we notice that
over time the microbial communities undergo
succession
so initially we might have um ten different
aerobic microbes here and after some time
we notice we have eight because two have been
wiped out and lets say microbe population
number four was the most abundant initially
but now that might have been out competed
by microbial population number six so we notice
that microbial communities undergo succession
over time because of competition and on the
ah other end of the in the in the other end
of spectrum we have cooperation so microbes
cooperate with each other for example someones
waste product could be someones input and
in next few slides we will see how microbes
not only cooperate with each other but they
also cooperate with higher order of life such
as plants and such as humans and if you remember
this is one of the first things i talked about
in introductory lectures that we have more
non human cells in our body than we have human
cells begging the question how human we are
[laughter]
so for example in our gut we require certain
microbes to give us a healthy ah functioning
of gut and then that ah microbial balance
gets upset we have diseases such as diarrhea
and irritable bowel syndrome so microbes are
very important in terms of both competition
and cooperation um and by the way this diagram
should remind you of what we just studied
in the lake how um different kinds of functions
functional gradient can be found in um environment
ok so now lets look at surface in biofilms
until now we have not talked about how microbes
interact with the environment we know they
are there are they just sitting there are
they attached to where they are sitting or
are they floating in water yeah or flying
in the air
so lets start with understanding all microbes
interact with surface we know that many microbes
love to attach to a surface and there are
many advantages why they would love to attach
to a surface for example lets say we have
a stream with relatively low amount of organic
material low amount of electron donors and
electron acceptor it has good electron acceptor
oxygen so its a very healthy stream and it
is flowing down now as it flows down it interacts
with rocks and other surfaces where microbes
can attach so the microbes in water itself
dont have a lot of food to eat but once a
microbe attaches to the rock it now has a
perspective from which it can stay stationary
and capture all the nutrients from the flowing
water so attachment has an additional advantage
that microbe can capture nutrients in flowing
water instead of just flowing with um in in
an oligotrophic environment which means in
a nutrient deficient environment
so it is advantageous for microbes to attach
theres another reason why microbes would love
to attach to a surface when they attach to
a surface and they replicate they produce
ah daughter cells and the daughter cells also
attach to replicate over time what we might
have is accumulation of material so initially
we have um um just a plain surface with one
microbe attached microbe replicates produces
two daughter cells and so on and so forth
the application continues over time we have
a heap of microbes and now they are talking
about a singular population but then we can
also have communities complex communities
of microbes
now if microbes are faced with some problem
like a disinfectant then only the ones only
the microbes on the boundary would be affected
and the microbes closer in this accumulation
this heap of microbes will not be affected
thus surface attachment and growing this films
on a surface actually um ensures longevity
of microbes the other advantage of attaching
attaching to a surface and growing these films
they are referred to as biofilms by the way
so we have here the second term biofilm is
that these biofilms um microbes and biofilms
they secrete what is called as eps so these
are ah extracellular polymeric substances
that create a mesh in which those cells can
trap not only themselves but can also trap
nutrient so if there is any glucose molecule
floating in the water it will be trapped in
this matrix and then the cells can devour
it
so thus we see that biofilms can give a protection
to ah microbes and it can create a nutrient
rich environment in otherwise neutral deficit
environment so biofilms are very very beneficial
for microbes now um if you remember ah in
one of the first few lectures i talked about
plating of microbes and culturing so um in
plating what we have is we spread the inoculum
over a plate and we spread it in such diluted
amount that we expect that when they grow
from a singular microbe from a single bacterium
for example one colony will sprout up which
we can see the next day or the day after or
after some days so what the important take
home message is that the colony emerges emerged
from singular microbe singular micro bacteria
or some other microbe and it is visible to
eye
so we can actually count them right however
sometimes in oligotrophic environments such
as very clean streams in drinking water systems
the microbes do not grow into colonies in
sense that even though they are source from
a single microbe they grow make micro colonies
so the only thing is we cant see them so for
example let us look at this picture on the
right panel right bottom panel so this is
a hand of a person and we are noticing this
under dark light so this ah this is a special
technique where we can ask microbes to we
can make microscopes microbes to fluoresce
ah to give fluorescent signal under a particular
(( )) when lit by a particular light
so whatever you are seeing here ah giving
a fluorescent signal shining is actually microbial
micro colonies so on hand like mine which
i believe is pretty clean right now i cant
see micro colonies because they are too tiny
and only when i put my hand on a dark light
then i can see oh how this tiny colonies growing
that are otherwise invisible to naked eye
so structurally they are too small to be seen
but the signal can be seen by the eye now
ah microbes not only make micro colonies in
our body on our on our body and in our body
but also in other um in other surfaces for
example in the top right panel we have a plate
titled plants and fungi
so in the purple you have root the root of
a plant and in the green you have fungal sheath
so the fungus it has attached to the root
has entwined with it and is enjoying the nutrient
rich environment of the roots and hopefully
the root is also benefiting from the fungal
attachment to it so remember its not just
bacteria but fungus also attaches other microbes
also attached to surfaces here we have another
example where we have these microbes who have
attached to this surface and this is actually
a picture from a microbial mat so micro colonies
are very small we cant see them colonies we
can see there both a are ah their source is
singular microbe
the microbial mats are very interesting they
are ah microbes have populated so much they
have grown so much the biofilms that they
are centimeters thick and even meter thick
maybe and we can see them well i dont know
if me to think exists but definitely many
centimeter thick we can see them and we can
see the gradation so lets take a look at that
ah all righty before we take a look at that
let us go back to our root microbe interaction
and here we have a plant a tree and its making
um food from sunlight carbon dioxide water
and in its root its using roots to get water
and other resources that it requires and you
will notice that the roots provide a fixed
supply of carbon the yellow line or nutrients
to these microbes here and these microbes
in other on the other hand fix the nitrogen
and they provide nitrogen source to tree
so this is a very good example of symbiosis
all righty so now lets take a look at microbe
microbial growth on surfaces so the first
one we have here we want to understand how
biofilms grow and how microbes probably freight
in them later on we will be talking about
drinking water system and drinking water treatment
it is very important to understand how biofilms
will grow in our drinking water system and
this is a big challenge by the way so lets
get our fundamentals right here so in this
picture we have six different stages of biofilm
formation the first stage is substratum preconditioning
so initially this is our biotic or abiotic
surface so ah a biotic surface would be like
root or like a teeth or like my hand or hand
abiotic could be like a pipe material or a
wall right now or like a catheter when we
are talking about medical devices
so we have the (( )) bacteria they will grow
and they will attach to the surface and then
prepare the surface for better attachment
by like microbes so this is how bacteria have
attached and they have conditioned the substratum
the substratum is now ready to be sticky to
allow things to stick to it and now we have
this packed microbes in our yellow and purple
color there planktonic bacteria what means
they are free freely floating bacteria so
here we are imagining this blue environment
to be um water so they are freely flowing
bacteria and they are coming in all the surface
ready for attachment and then they get attached
when they get attached not only do they get
attached to the surface but they also get
attached to each other
so what we notice in the third step is cell
to cell adhesion so these microbes they start
talking to each other using chemicals so they
do bio signaling cell to cell signaling and
they tell i am here who else is here how many
of us are here ah are you are the others other
microbes present here or the enemies or their
friends are they going to compete are we going
to cooperate are we going to have predation
so they communicate with each other and then
they stick to each other according to whatever
serves them the best so they will stick to
the ones when sticking is beneficial so they
have um cell to cell adhesion cell to surface
adhesion and they have a very nice communication
network
now at this stage they also start producing
the exo polymer so this is eps which they
produce so this is a net that they cost so
if you see here dark blue darker shade of
blue here this background environment is the
eps that they have made so initially there
was no eps just the surface was ready to accept
microbe but now we have eps layer that will
trap both nutrients and trap the microbes
now in the next stage we have proliferation
so in proliferation this biofilm that has
grown and this ah eps structure that has grown
here so it has some microbes and lot of eps
structure they will start trapping food so
nutrient so diffusion of oxygen and nutrient
through biofilm because this is a pipe um
cut schematic showing how biofilms grow in
pipes
so we are talking about oxygen but if not
it does not have to be necessary oxygen as
we see later but the nutrients electron acceptor
electro donor and everything others else required
will start diffusing into these biofilms and
um the microbes will start proliferating which
means they will start growing in population
and then when they start growing in population
they produce more and more eps and they make
more complicated structures and this is maturation
so they are now secreting polysaccharide matrix
eps and now they are having more complex structures
and very diverse microbial community by normally
by this time
now note here they allow diffusion of oxygen
and nutrients lets say we have a disinfectant
in the environment now this disinfectant will
also diffuse but will only affect microbes
who are at the boundary and some microbes
here will survive and once the microbial community
in the biofilm becomes more and the biofilm
becomes more mature then the population surviving
microbes in face of disinfectant would be
much higher than microbes that dont survive
after a while when the biofilm grows too much
that it is structurally unstable and the microbes
are too populated they are ready to find new
avenues for attaching and for growing then
they would have dispersion
so this is where the biofilm releases itself
breaks how open and the microbes are released
back and they become planktonic bacteria now
this is where the problem is lets say there
was a pathogen hiding and proliferating here
some pathogens can proliferate in ah biofilms
many cant but some can or lets say just someone
was surviving here saving itself from the
disinfectant and getting the minimum nutrients
it requires to survive in such an oligotrophic
environment now in this stage when they are
released back into the water then this water
can be drunk by a human being or by some other
ah being
so when we open the tap and we get this planktonic
bacteria some of them could be pathogenic
and next thing we know we are falling sick
or the other fate of planktonic bacteria is
there nobody [laughter] drinks them but they
find more attachment surface and they attach
so you can see this is a cycle and they induce
each other so more biofilms produce more biofilms
one big its the other and next thing we know
that our drinking water system is afflicted
and with lot of biofilms so biofilms are rampant
in our water distribution system now this
is a picture you might think how will microbes
attach to something like a metal surface
this is a picture showing microbial attachment
to um stainless steel surface so we have stainless
steel surface in the background and all these
forces that you see here is from ah microbes
all righty and this is a picture of different
pipe material so in the right here pvc here
we have different kinds of ah metallic pipes
and we notice how biofilms develop and how
they aid in corrosion we wont get into depth
here but later on when we talk about drinking
water treatment i will talk more about this
the other example of biofilms would be our
teeth so remember this is not just all plaque
that forms in a teeth but now we have bio
from shining unity now lets talk about microbial
mats so as i said microbial mats can be multiple
centimeters so here we have um nearly nearly
two centimeter long deep microbial mat
so we have different layers and the beauty
of microbial mat is that they have different
layers so here we have four millimeter depth
of microbial mat lets look on the top we have
diatoms ok ah then we had their kind of special
kind of algae who are very highly sophisticated
and [laughter] i might say microscopically
very beautiful cell cell wall kind of structure
and then we have cyanobacteria then we have
purple sulphur bacteria and they are sulfate
reducing bacteria so you can see not only
do we have layer of microbe but we also have
a layer of functions and if you remember what
is a guild a guild is microbes of similar
functional nature so this these are guild
these are layer of guilds surface reducing
bacteria and you know they can be um different
they can belong to different phylum so they
can be very different but they are all same
function so this is a guild
now lets look at some very exciting ah microbial
mat usually found in the coastal regions of
chile and peru in south america and this is
a sulfur oxidizing chemolithotroph thioplaca
now thioplaca oxidizes sulfur and its a chemolithotroph
and it forms filamentous microbial mat that
can go up to five to ten centimeter below
the sediment so we are not just talking about
two centimeter here as we were talking here
but here we are talking five to ten centimeter
below the sediment and then they have these
hair like filaments that they have outside
these are sheath that actually ah allow that
whole thioplaca together so this is a microscopic
picture and these are indeed some other beautiful
pictures from chile and peru
now lets look at terrestrial environment as
promised now this is a well mature soil so
not just ah ok why would microbes form a gradient
why will they go from diatom or to all the
way to sulfate reducing bacteria as we saw
in this microbial mat because the environment
is changing this is oxygen rich and then oxygen
gets depleted as oxygen gets more and more
depleted and lets say for some reason the
reaeration is stopped then the sulfate reducing
bacteria will ah occupy more volume than the
other and when sulfate is gone then we have
fermentation or another ah of the electron
acceptor being reduced ok so its not just
microbes that form gradient but in nature
too we noticed that the environment is ah
has a gradient
so this is a fully mature soil and at the
bottom we have our zone our horizon which
is a hard bedrock then we have c horizon which
is a subsurface layer or soil forming parent
material this could be bearing material for
the soil this could be weathered raw unconsolidated
floodplain sediment or just loose and then
we have the b horizon here which is a subsurface
horizon which is showing depletion of organic
matter so we have rich organic matter dark
so rich organic matter gives soil dark color
but here the color has been lost we have a
lot of clay and we have um depleted organic
matter in a we have dark coloration because
organic matter has accumulated in the o we
have leaf litter so we have um lot of biomass
waiting to degrade and waiting to ah make
the soil darker in color and make it rich
as i talked earlier about micro environments
terrestrial environments are very complex
for many reasons because think of it this
way each pore in the soil and even in a small
handful or spoonful of soil you will have
so many pores each pore is a micro environment
and within this micro environment we have
gradient of nutrients we have gradient of
electron acceptors and even we have some pockets
within micro environment that will have waters
and will not have water as illustrated by
this schematic thus we can expect very diverse
microbial communities in each pore and you
know two pores adjacent to each other might
have very different microbial communities
flourishing one might be anaerobic the other
might be water loving aerobic
so lets look at this little micro pole we
have sand particles we have some silt we have
some clay small clay particles here its air
trapped so oxygen in this air would be utilized
until there is no oxygen left and then because
they might be nitrogen and other things we
might have a nitrogen fixing bacteria or the
kind of microbes now in each of these zones
we have micro niches that are perfect for
a particular kind of microbe to grow so microbes
that love binding to sand will probably stick
to sand and grow there the ones that would
love to grow between silt and sand or stick
on silt grow sticking on silt the ones that
love to grow in water will grow wherever they
find little trace amount of water within the
microbe pore and we are talking really small
environment here yeah
so we notice that there are a lot of m nutrient
um diversity and even you know as our air
gets consumed here initially we will have
aerobic microbes here then when air gets oxygen
gets consumed it will move on to um non oxygen
electron acceptor zones such as microbes that
use nitrate microbes that reduce sulfate or
sulfur and eventually to methanogen and fermentation
fermentation and methanogenesis so we will
see both electron acceptor gradient we will
see nutrient gradient and water gradient some
love water some like to like water but they
like to keep a distance so they would grow
in this region instead of going in this region
now um for example i here i showed you microbes
that love to stick to sand now there are microbes
that um what they do is and this is electron
um scanning ah this is a scanning electron
microscopy image that is showing you cyanobacteria
by the way and these are filaments and what
they are doing is um in this they the filaments
and the sand traps the microbes so the sand
is what is trapping the microbe here like
how this picture shows here the sand is what
this asking microbes come and stick to me
so this is what this picture is showing but
here we have a very different phenomena happening
we have no sand particles in desert and in
this particular example we have cyanobacteria
again like here and here we have algae and
they are binding the soil
so both the microbes can be trapped by the
soil can be trapped by the sand and then they
will proliferate they will grow they are or
undergo succession or they can actually change
their environment by binding the so here all
these sand particles are very ah they are
not attached to each other they can disperse
very easily but the algae has grown in and
around them and bound them together so next
thing we know the soil is very compact its
not loose you wont have sand blowing on your
face and similarly here is a desert in usa
where they conducted investigations intensive
comprehensive investigation and they found
that it was cyanobacteria that was actually
the binding the sand particles together and
thus changing the characteristics of soil
and changing the characteristic of vegetation
now within soil as you now notice that there
are different micro environments there are
different functional guilds and thus we notice
a very very diverse microbial communities
in our soil and this is just a snapshot of
some ah very ah basic eukaryotes archaea and
bacteria there have been known to found in
soil each of these kingdoms whether we go
to eukaryotes or bacteria or archaea each
of them are very very diverse so we cant say
that oh soil you have gram positive bacteria
spirochetes plantomyce plantomyces or proteobacteria
[laughter] you will have a lot of microbes
and within each of them for example proteobacteria
is a very very broad phylum within proteobacteria
we have alpha beta gamma delta and epsilon
proteobacteria and within each of them we
have very different um kinds of microbes for
example some delta delta proteobacteria are
sulfate ah reducers some are sulfur oxidizers
some are aerobic and they dont care about
sulfate reduction or sulfer oxidation so as
you notice microbial communities in soil interest
terra are very very diverse
so my dear students this is all for today
in next class we will move on to aquatic environments
and we see the ecology of aquatic environments
thank you
