Session Start: Sun Feb 03 10:52:22 2008
Session Ident: #micro08
03[10] * Now talking in #micro08
03[10] * Topic is 'Welcome to MACO - Reef Microbiology 2008'
03[10] * Set by wade on Wed Dec 31 19:00:01
[10] <walla2butterfly> morning
03[11] * Bob ([email protected]) has joined #micro08
01[11] <java> good morning
01[11] <java> now we're getting to the good stuff
[11] <Bob> good morning
01[11] <java> and hopefully understanding it differently now
01[11] <java> did people like the reading?
[11] <Bob> yes, very good
01[11] <java> good, thanks
[11] <walla2butterfly> yes
01[11] <java> areyou guys familiar with the controversy around sandbed depths?
[11] <walla2butterfly> yes that there is controversy
01[11] <java> the "DSB vs. BB" debates" and all that?
01[11] <java> ah
[11] <Bob> also plenum & no plenum
01[11] <java> yep
[11] <walla2butterfly> found that research interesting
[11] <walla2butterfly> about the no difference with the LR and critters
01[11] <java> yeah, it was a very interesting experiment and result
01[11] <java> both the experiments with and without animals
[11] <walla2butterfly> made me really think
[11] <walla2butterfly> about all that I thought I knew
01[11] <java> but now you know certain things about microbio that explain it
01[11] <java> explains
01[11] <java> the most significant, i think
01[11] <java> is that the n-cycle is "unbreakable"
01[11] <java> and will occur no matter what you do
[11] <walla2butterfly> which only made since
[11] <walla2butterfly> nature is nature
01[11] <java> but also makes one re-assess the risk associated with the jaubert plenum
[11] <walla2butterfly> remind me
01[11] <java> is it really necessary
01[11] <java> oops
01[11] <java> go ahead
[11] <walla2butterfly> still waking up out here in the west LOL
01[11] <java> shall i get into the jaubert method a little deeper? and what i meant?
[11] <walla2butterfly> if others are for it
01[11] <java> so as we all know the jaubert method is intended to provide an area of anaerobic environment
01[11] <java> by creating a space of very slow-circulating water under the sandbed
01[11] <java> typically eggcrate, plastic grids are used
01[11] <java> on the bottom of the tank, with a layer of fine mesh over it
01[11] <java> then the substrate is layered over that, to some significant depth
01[11] <java> the idea is that once you go to a certain depth in the substrate, anything under that will be anaerobic
01[11] <java> the risk involved
01[11] <java> is that water exchange will not occur at all
01[11] <java> because don't forget
01[11] <java> even though it may be annaerobic, that doesn't mean it doesn't have ANY water circulation
01[11] <java> so if the water stops circulating, nutrients can't get in, and wastes accumulate
01[11] <java> in the case of anaerobic respiration, a common end product is hydrogen sulfide
01[11] <java> which can be toxic if concentrations become too high
03[11] * Rob ([email protected]) has joined #micro08
01[11] <java> so getting back to biofilms
01[11] <java> and that they can slow water circulaiton in a poorly turned over sandbed
01[11] <java> one can see that the mesh used over the eggcrate
01[11] <java> may become clogged with bacterial biofilms over time
01[11] <java> slow water circulation, and end up crossing the threshold of too-little circulation
01[11] <java> because knowledge of the kinetics of denitrification is actually fairly new
01[11] <java> and the fact that facultative anaerobes participate is new as well
01[11] <java> makes one reassess the necessity of a plenum
01[11] <java> because if water circ is really low, that stagnant water can't be compartmentalized forever
01[11] <java> and you don't know if it's "bad" unless it's realeased
01[11] <java> so if one had to do a tank transfer or otherwise disrupt the apparatus
01[11] <java> you might be dealing with a nuking event
01[11] <java> so that research by toonen and wee was very useful
02[11] * mchia ([email protected]) Quit (Quit: mchia)
01[11] <java> in that it demonstrated that one does not need to take special pains
01[11] <java> to facilitate denitrification
02[11] * Bob ([email protected]) Quit (Ping timeout)
01[11] <java> what was fascinating was that even the shallow beds had significant denitrification
01[11] <java> all these things are still hotly debated today on various message boards and between hobby experts
01[11] <java> people still insist that denitrification simply CANNOT occur in a home aquarium
01[11] <java> because you need some massive anaerobic space
01[11] <java> obviously this article dispels that notion, fairly solidly
[11] <Rob> If you're one of those prior miss informed people what are the recommendaitons for an existing plenum?
01[11] <java> well, i'm actually a big fan of the "nothing is flat out incorrect" school of thought
01[11] <java> i don't think that there's anything inherently "wrong" about the plenum
01[11] <java> because those tanks still can work fine in terms of n-cycle
01[11] <java> but it jsut hass to be very carefully thought out
01[11] <java> during setup
01[11] <java> for one, don't make the mesh super-duper fine
01[11] <java> two, don't make the sandbed super thick, like 6 inches
01[11] <java> maybe 3 inches makes more sense for a sb depth
01[11] <java> possibly in one area, periodically disturb the sand down to the mesh to make sure there's at least one area which is "open"
01[11] <java> to circulation
01[11] <java> so it's jsut a little riskier
01[11] <java> and i don't want to dump on the method, because for it's time, and the existing knowledge, it was good work
01[11] <java> and can obviously be made to work
01[11] <java> but i think now it's been shown to be an unnecessary amount of effort
01[11] <java> with some extra unnecessary risk involved
01[11] <java> i'm curious - that means you have one set up?
[11] <Rob> yes
01[11] <java> tell me about it a little - how long have you had it, how big the tank, sb depth, plenum size, etc.
[11] <Rob> I've had it for a year. 240 gal tank. ~ 4 in of sand with two layers of window screen mess and an egg carton plenum.
01[11] <java> eggcrate about an inch thick?
[11] <Rob> The plenum depth is about 1/2"
01[11] <java> so proportionally it's not a HUGE plenum - i've seen some in smaller tanks which are proportionally much larger
01[11] <java> you ever notice gas bubbles coming out of the sandbed?
[11] <Rob> No
01[11] <java> look for that, it a high water circulation tank it may not be very noticeable
[11] <Rob> I have a trigger & puffer that like to dig into the sand
[11] <walla2butterfly> is that a bad sign
01[11] <java> oh, that'll mask it as well
01[11] <java> no - gas bubbles are good
01[11] <java> usually they are free nitrogen \
[11] <walla2butterfly> k
01[11] <java> N2, the final product of denitrification
01[11] <java> a lot of times if you look closely at live rock
01[11] <java> you'll notice timy bubbles on the surface, heree and there
01[11] <java> that's nitrogen from denitrification
[11] <walla2butterfly> have seen that
01[11] <java> so although i can't say whether rob most deffinitely SHOULD see as much bubbling as live rock
01[11] <java> i thought he might
01[11] <java> it's good that he has things stirring the sand on a big scale
01[11] <java> biofilms are jsut that - films
01[11] <java> very easily disrupted in sand
01[11] <java> has the plenum worked in terms of dentrification for you Rob?
[11] <Rob> Yes I don't see any problems with high levels of nitrates.
01[11] <java> sounds like you did a proper setup!
[11] <Rob> I had a problem with PO4 but it seemed to be short lived.
01[11] <java> interesting
01[11] <java> sort of mirrors the conclusions in the toonen paper
01[11] <java> plus your sandbed is on the deeper sidde
01[11] <java> how did you correct the PO4?
[11] <Rob> I wanted to experiment with something different.
01[11] <java> did it go away on it's own?
[11] <Rob> I had a GHA problem which was significantly reduced by turning off my MH's and kept removing it from the tank and it dropped.
01[11] <java> oh
01[11] <java> "removing" gha, lol
01[11] <java> nightmare!
[11] <Rob> I also added mangroves and spaghetti algae.
01[11] <java> there you go
01[11] <java> rob knows what he's doing
01[11] <java> which brings us to the only real difference in tank chemistry in the toonen papers
01[11] <java> phosphates
[11] <Rob> It's chat's like this that keep me on track.
01[11] <java> cool!
01[11] <java> so i was thinking about the phosphate difference in the tank setups in that paper
01[11] <java> i think it was a... not really the right term, but an "artifact"
01[11] <java> i think what toonen was seeing was the result of a highly artificial experimental settup
01[11] <java> not really a flaw, because i'm guessing he kept the tanks dark
01[11] <java> to make sure algae and photosynthsis didn't confound the results
01[11] <java> but since photosythesis on a natural reef is part of the overall nutrient cycling
01[11] <java> removing it from this experimental setup led to an accumulation of PO4
01[11] <java> in tanks with deeper sandbeds, which probably trapped more detritus and had slower detritus breakdown
01[11] <java> my theory, at least
01[11] <java> because as rob so perfectly demonstrated
01[11] <java> without enough photosynthesis going on
01[11] <java> or in his case, a more preferable form
01[11] <java> MAcro and mangroves over hair algae
01[11] <java> the PO4 accumulates and doesn't get cycled out
01[11] <java> jsut like the nitrogen cycle
01[11] <java> in nature there are other nutrient cycles
01[11] <java> one of them being the phosphate cycle
01[11] <java> it's not really discussed much in reef topics
01[11] <java> because the idea of a "cycle" is tied in our hobby to tank startup
01[11] <java> and some people get confused when it's used in terms of an ongoing phenomenon
01[11] <java> so the PO4 cycle gets left out
01[11] <java> but suffice to say, it rears an ugly head with algae, or in the case of this experiment
01[11] <java> can confound the results a bit, because it was a measured experimental variable
01[11] <java> although not really experimentally manipulated
01[11] <java> so i thought i'd touch on that since it was an unresolved part of the conclusions
[11] <walla2butterfly> k
01[11] <java> so tami, the take-home for the phosphate topic
01[11] <java> is that photosynthsis can take care of it
[11] <walla2butterfly> lol
01[11] <java> well, i only want to make sure everyone understands
01[11] <java> and only you and rob are here
[11] <walla2butterfly> "the take home" as in a test was how I read it...
01[11] <java> haha - maybe i should! anyhow - you'd rather remove phosphates with macroalgae
01[11] <java> than lest nuisance alge come in uninvited
01[11] <java> let
01[11] <java> because naturally SOMETHING will take advantage of the PO4
01[11] <java> sooner or later
[11] <walla2butterfly> by the way
01[11] <java> yes
[11] <walla2butterfly> how is it that the macro algae dominate over the univited algeas
[11] <walla2butterfly> oops
01[11] <java> i get it - it's thought that the macroalgaes are more efficient at removing nutrients
01[11] <java> so they "beat" the nuisance algaes to suspended nutrients
[11] <walla2butterfly> thought maybe that or have a higher demand
01[11] <java> that plays a role in cerrtain macros as well
01[11] <java> which is why Chaetomorpha - spaghetti algae
01[11] <java> is so desirable
01[11] <java> it adds mass so quickly
[11] <walla2butterfly> k
[11] <Rob> My experiment is to put the macros in a fuge and leave the light on more then the main tank. Make sense?
01[11] <java> hair algae, bryopsis, etc., can't compete
01[11] <java> R - yes
01[11] <java> because as long ass it's compartmentalized and under control
01[11] <java> as, oops
[11] <walla2butterfly> how would they work out in a cycling tank
01[11] <java> then you'd want it growing as fast as possible
01[11] <java> Tami - well, i'd slowly introduce macro to a cycling tank
01[11] <java> it's a nice idea to get ahead of PO4 before it becomes a problem
01[11] <java> and to start a cycle with some
01[11] <java> but photosynthesis also has an effeect on the diurnal pH swing, the change in pH over the course of 24 hrs
[11] <walla2butterfly> just a thought that crossed my mind while I was sitting here
01[11] <java> so without active respiration from other tank inhabitants
01[11] <java> pH might get a little swingy with too much
01[11] <java> no - i like that idea
01[12] <java> good idea, actually
01[12] <java> just something that has to be felt out
01[12] <java> in order to allow a stable environment establish over the period of the cycle
[12] <walla2butterfly> what would the effect of ammonia, etc that you would have from a traditional cycle have on them
01[12] <java> it depends on what you're using
[12] <walla2butterfly> (because you know that some people will never move away from that type
01[12] <java> some macroalgae incorporate ammonia as well
01[12] <java> caulerpa takes up nitrogenous wasstes
01[12] <java> so whilw it might be "good" to get rid of the ammonia
01[12] <java> and might be useful in a "spike" event
01[12] <java> it will outcompete your denitrifying bacteria
[12] <walla2butterfly> k
01[12] <java> and your microbial denitrification capacity might not be able to mature as well without it
[12] <walla2butterfly> so would make the cycling take longer'
01[12] <java> theoretically, it might. (lol)
[12] <walla2butterfly>
01[12] <java> hard to say, because the toonen papers demonstrate something else really really imnportant
01[12] <java> really really
01[12] <java> that theory only gets you so far
01[12] <java> and you never really knwo until you do the experiment
01[12] <java> biology on this level is so weblike, with so many processes intertwining
[12] <walla2butterfly> I was thinking that just a few min ago
01[12] <java> that focusing on one and making hypothesis and accurate predictions is very difficult
[12] <walla2butterfly> almost a which came first the chicken or the egg mentality
01[12] <java> yeah - so i think your idea of exploring the role of macroalgae in initial cycling is really interesting
[12] <walla2butterfly> could be
01[12] <java> because it might be a useful tool in something like a soft-cycle
01[12] <java> to keep ammonia spike down
01[12] <java> spikes
[12] <walla2butterfly> can see that
01[12] <java> but it might affect bacterial populations.... *shrug!
[12] <walla2butterfly> that too
[12] <walla2butterfly> "oh, the pain"
01[12] <java> lol
01[12] <java> but that's what makes this hobby so interesting to me
[12] <walla2butterfly> problem solving can be fun
01[12] <java> so many variables that interact, so many things to tweak
[12] <walla2butterfly> and the "what ifs"
01[12] <java> the best part is that nature tends to balance things out in the end
01[12] <java> so a lot of time patience solves a lot
01[12] <java> not everything, but usually in terms of the n-cycle it does
[12] <walla2butterfly> yea, had a friend with a hair algae problem for 2 years
[12] <walla2butterfly> time finally took care of it when her lights burnt out and she didnt replace them, she really shouldnt have a tank
01[12] <java> ouch - phosphate is a whole 'nother animal
01[12] <java> yes, there are some people who certainly should try something else
[12] <walla2butterfly> or get a job to support your hobby
01[12] <java> particualrly when corals are involved, i mean, fish too, but corals... ouch
[12] <walla2butterfly> anyway back to the subject
01[12] <java> i hate seeing threads ont eh forums with nice wild-caught specimens RTNing or otherwise jsut getting toasted
[12] <walla2butterfly> LRWfO
01[12] <java> yes
01[12] <java> FOWLR
[12] <walla2butterfly> still early here, my excuse and I sticking with it
01[12] <java> lol
[12] <Rob> Can you elaborate on using Xenia for the N cycle?
[12] <walla2butterfly> ( I was actually in my mind thinking what she had it in and typeing
01[12] <java> wow - i wass just typing that up
01[12] <java> you were tight on time with the phosphates too
01[12] <java> right
01[12] <java> Ron Shimek did an experiment a few years ago
[12] <walla2butterfly> sorry for the tangent ROb
[12] <Rob> always good to hear about other things
01[12] <java> similar to toonens, in terms of a water column with a certain amount of DOCs
01[12] <java> and he assayed the absorption of nitrogenous wastes
01[12] <java> he found that Xenia actually removed more nitrogen from the water by weight than caulerpa
01[12] <java> give me a moment, i'll find the article and link it here
01[12] <java> http://www.reefkeeping.com/issues/2002- ... /index.php
01[12] <java> he found that Xenia is an extremely efficient exporter of nitrogenous waste in the form of ammonia.
01[12] <java> By weight, it removes ammonia and total kjeldahl nitrogen more efficiently than Caulerpa.
01[12] <java> FYI, total kjeldahl nitrogen [TKN] is the total of organic nitrogen)
01[12] <java> in that article, the relevant data is in table 5
01[12] <java> and one other thing about that article
01[12] <java> the last couple of tables show that although xenia grows only 1/4 the rate of caulerpa in terms of biomass
01[12] <java> it is much richer in organics by weeight
[12] <walla2butterfly> will have to read that
01[12] <java> and is more efficient at removing heavy metals such as copper
[12] <Rob> I did some googling and found that raising Xenia can be unpredictable. Any tips?
01[12] <java> some people claim it can get out of control like some macro
01[12] <java> but i don't know - it's still a coral, and jsut isn't as aggressively growing as macro
[12] <Rob> I heard its dependent on iodine.
01[12] <java> i think it's really really pretty, and the pulsing action is cool lol
01[12] <java> yeah, one might have to dose iodine, but only if water changes were infrequent
[12] <walla2butterfly> does the article imply any type is better then another
01[12] <java> not really, it's all preferences
[12] <walla2butterfly> k
01[12] <java> recently i've heard people throwing around the idea of using a xenia bed in their sump
01[12] <java> to replace the macroalgae
01[12] <java> figuring it does the same, plus removing heavy metals
01[12] <java> but it can be kept in the display, i would, at least
01[12] <java> because i really like xenia
01[12] <java> but since it has been reported to overgrow sections of tanks
01[12] <java> and if one had a high nutrient load
01[12] <java> so it grew faster than a low nutrient tank
01[12] <java> keeping it in the sump might not be a bad idea
01[12] <java> anyhow, check out the article if you're interested
01[12] <java> it's nice to see actual data on things like this
01[12] <java> which are usually anecdotal
01[12] <java> any other questions?
01[12] <java> i'm thinkinig 10 min break
[12] <walla2butterfly> great see you in a few
[12] <Rob> good for me
01[12] <java> k
[12] <walla2butterfly> made it
[12] <Rob> i'm here
[12] <walla2butterfly> Don't recall ever being able to run and take a quick shower during a 10 min class break
[12] <walla2butterfly> a first for sure
01[12] <java> wow that's impressive
01[12] <java> first for one of my students ass well lol
[12] <walla2butterfly> the dripping wet hair will make me think more about the ocean
01[12] <java> ok, so i wanted to talk a bit about the other papers assigned
[12] <walla2butterfly> k
01[12] <java> first, the jensen and revsbech
01[12] <java> "estimation of nitrification and denitrification...
01[12] <java> so sorry if these are a little teechnical
01[12] <java> but i like people to be able to see with their own eyes
01[12] <java> get the papers in hand
01[12] <java> ratehr than just take my word for it
[12] <walla2butterfly> trying
01[12] <java> well i'll point out what i think are the immportant items
[12] <Rob> got it
01[12] <java> one - the oxic/anoxic boundary in marine sediments is only 1-2 centimeters down
01[12] <java> mind you, this is in a natural setting
01[12] <java> they're looking at oxygen levels in nature, not a tank where flow may be hiigher
01[12] <java> i didn't expect you to deccipher the data panels
01[12] <java> but there is also a graph showing the depths at which nitrification and denitrification are taking place
01[12] <java> and it shows that denitrification maxes out and approaches zero after only a coupe more centimeters
01[12] <java> depending on the surrounding 02 concentration, in the overlying water
01[12] <java> so
01[12] <java> back to reef - the really DSB may be overkill
01[12] <java> also, lets remember what toonen found
01[12] <java> in his expt
01[12] <java> that there wasn't much of a difference between denitrification in tanks with shallow sandbeds and those with DSBs
01[12] <java> while on it's face, and in the context of hobby lit, it seemed to not make sense
01[12] <java> in the context of this paper
01[12] <java> it does
01[12] <java> because the shallow sandbed, provided it's not TOO shallow
01[12] <java> so we're talking probably at least 1.5 inches thick
01[12] <java> maybe more if one is keeping a high-flow tank
01[12] <java> is all one needs to achieve *maxiumum* denitrification
01[12] <java> it will still happen in tanks with a DSB
01[12] <java> it's not like it can hurt (well it can if not properlay stocked/maintained)
01[12] <java> but the lower depths are somewhat extra capacity
01[12] <java> and probably not utilized
01[12] <java> another interesting bit of data in that article
01[12] <java> wass something i found surprising
01[12] <java> that the maxima of the processes of nitrification and denitrification
01[12] <java> that is, the physical location, in terms of depth
01[12] <java> where most of denitrification and nitrification occurred
01[12] <java> the respective locations were less than 0.5 mm - HALF A MILLIMETER! apart
01[12] <java> so it's not like the "gradients" we discussed
01[12] <java> were very broad
[12] <walla2butterfly> you would think barely exientant
01[12] <java> rather, they are very sharp layers in terms of large-scale measurements, like with a ruler
01[12] <java> but to a bacterium, those sharp layers are real gradients
01[12] <java> don't forget the scale of organisms we're dealilng with
[12] <walla2butterfly> right
01[12] <java> and we get back to the concept of microenvironments and biofilms
01[12] <java> really localized, small scale environments with big differences between them and the outside environment
01[12] <java> that's all i really wanted you to get out of that paper
01[12] <java> a lot of jibber jabberr and big numbers and graphs, and that was really the point
01[12] <java> so the other papers i'll similarly pass on what i thought was relevant and informative
01[12] <java> the "Biodome" papers
01[12] <java> about the microbial populations in the marine denitrification reactor at the Montreal Biodome
01[12] <java> they operate a massive denitrification reactor
01[12] <java> and looked to see what microbes were living in there
01[12] <java> now, mind you, this reactor is fed with methanol
01[12] <java> so it's a little different that a natural sccenario
01[12] <java> and will be a little more relevant when wee get into details of the "vodka method" in later weeks
01[12] <java> but still, the bacteria found are still common in some cases to normal soil/marine denitrification
01[12] <java> but notably, most all were facultative anaerobes
01[12] <java> so, why is this interesting... (hypothetical)
01[12] <java> because
01[12] <java> so much hobby literature insists that one needs a strict anaerobic environment for denitrification
01[12] <java> which, is helpful for the actual chemical reactions taking place of course
01[12] <java> but really, many insist that the presence of oxygen will KILL the denitrifying bacteria
01[12] <java> the idea goes back to the characteristics that people thought denitrifiers had to have
01[12] <java> most obligate anaerobes, that is bacteria which survive strictly under anaerobic conditions
01[12] <java> actually DO find oxygen to be toxic
01[12] <java> and many years ago, it was thought that the bacteria which accomplished denitrification were obligate anaerobes
01[12] <java> because the reactions took place under anaeerobic conditions
01[12] <java> this was Dr. Jaubert's reasoning for his plenum - he wanted to provide a stable place which NEVER saw oxygen
01[13] <java> so that the denitrifying bacteria didn't get killed by fluctuations in oxygen
01[13] <java> but, when denitrifying bacteria began to be examined more closely
01[13] <java> i know, it must seem weird that this is relatively new knowledge
01[13] <java> but that's how science works
01[13] <java> anyhow
01[13] <java> when denitrifying bacteria were more closely examined
[13] <walla2butterfly> yea look how long the world was flat
01[13] <java> lol - really - it was realized that the dominant denitrifiers were facultative anaerobes
01[13] <java> they could switch between aerobicc and anarobic respiration
01[13] <java> moreover, oxygen was NOT toxic to them
01[13] <java> in the biodome papers, almost all the denitrifiers were facultative, adn lived in a biofilm in the reactor which provided them with their own little anaerobic microenvironment
01[13] <java> no special compartments were necessary to keep O2 away
01[13] <java> and just because people like to know names
[13] <walla2butterfly> wonderful how nature works
01[13] <java> after all, on the hobby forums, we''re always hearing about Nitrobacter adn Nitrosomonas
01[13] <java> but never who does the denitrification
01[13] <java> usually it is accomplished by Pseudomonas and Paracoccus
01[13] <java> Pseudomonas is probably the most massive genus of bacteria
01[13] <java> there are dozens, if not hundreds of species
01[13] <java> so it's a very broad categorization
01[13] <java> but they are also ubiquitous and numerous in nature
01[13] <java> they're found in most water, including most tapwater
01[13] <java> (a side note, microbiological water analysis usually focuses on coliform bacteria like E. coli, but no water is actually sterile)
[13] <walla2butterfly> mmm wondering if my RO/DI takes them out
01[13] <java> yes, it would
01[13] <java> but that's okay
01[13] <java> because it's removing a lot of other stuff
01[13] <java> and Pseudomonas is already in your tank if you've got any natural material
01[13] <java> the other is Paracoccus, one of the dominant forms found in the Biodome
01[13] <java> Paracoccus is unique in that it can accomplish BOTH nitrification AND denitrification
01[13] <java> these processes are aerobic AND anaerobic, respectively
01[13] <java> alhtough it is not entirely clear exactly how that happens
01[13] <java> it does!
01[13] <java> aslo, Paracoccus can use various forms of carbon as it's carbon source
01[13] <java> so it will do well in a methanol reactor, and jsut as well without methanol, utilizing CO2
01[13] <java> it's an amazingly adaptive bacterium
01[13] <java> and it also gives rise to the notion of a reccently described phenomenon
01[13] <java> which i mentioned in the syllabus:
01[13] <java> "aerobic denitrification"
01[13] <java> that is, it has been observed that denitrification can take place in aerobic environments
01[13] <java> it has not been worked out yet how this happens
01[13] <java> and has only been observed
01[13] <java> perhaps it is the result of a highly specialized, very dense biofilm
01[13] <java> or, maybe the bacterium creates an anaerobic micro-microenvironment in a capule around itself
[13] <walla2butterfly> Like you said it ( denitrification) will happen one way or anothre
[13] <walla2butterfly> another
03[13] * olaf ([email protected]) has joined #micro08
01[13] <java> perhaps the actual metabolic reaction occurs INSIDE the bacterium, where internal compartmentaliztion creates an INTERNAL anaerobic microenvironment
[13] <walla2butterfly> survival
03[13] * olaf ([email protected]) has left #micro08
01[13] <java> yep - these guys find a way
01[13] <java> but it's not clear exactly HOW, but it has been observed
[13] <walla2butterfly> and I guess that is good for us
01[13] <java> one thing to keep in mind is that i'm not sure how efficient this aerobic denitrifiaction is compared to denitrification that occurs in large anaerobic environments like sediment layers
01[13] <java> i don't think that has been explored
[13] <walla2butterfly> probably a last resort
01[13] <java> however, it is certainly worth noting
[13] <walla2butterfly> for survival maybe
01[13] <java> yes, but it might also be the metabolic enzymes just somehow chugging along when o@ happens to be absent locally, in a molecular sense
[13] <walla2butterfly> so it works but is it the best possible way
01[13] <java> right
01[13] <java> see, everything is biochemical, they are reactions
01[13] <java> so if the enzyme for anaerobic respiration happens to get a "cloud" of material drift by it without o@
01[13] <java> o2
01[13] <java> sorry
01[13] <java> then it might process some nitrate
01[13] <java> all these enzymes reside in a aqueous envirnment
01[13] <java> so there might be molecular eddies and swirls of material around them
01[13] <java> and o2 concentration
01[13] <java> a momentary lack of o2 might allow for processing a molecule or two of nitate to nirogen
01[13] <java> then when o2 is back, the otehr enzymes functioning in aerobic respiration are working
[13] <walla2butterfly> (was wondering the diff. in energy between when they use o2 or not)
[13] <walla2butterfly> (used)
01[13] <java> in facultative anaerobes, all this stuff is there and "on"
01[13] <java> yeah, i'm not sure the answer to that is known
[13] <walla2butterfly> (was still wondering)
01[13] <java> that is, whether the bacteria itself "prefers" which path to use
[13] <walla2butterfly> (hook up a microheart mon to them)
01[13] <java> or if the metabolic enzymes jsut chug away with whatever is available
01[13] <java> or not
[13] <walla2butterfly> right
01[13] <java> so, the one last paper i haven't mentioned yet
01[13] <java> was one which bacteria which function in denitrification actually can relocate themselves to a place they find favorbale
[13] <walla2butterfly> ( I guess one way might be to see where they thrive at better)
01[13] <java> hm - yeah, but these guys are typically happy ANYWHERE lol
01[13] <java> bacteria like this is what makes NASA worry about "reverse contamination"
01[13] <java> sending out a mars probe with these guys on it might colonize the planet
[13] <walla2butterfly> ( and too many varibles in the enviroment) sorry go on with the next paper
01[13] <java> well, one thing i haven't really covered is that many bacteria are "motile", they can move about
01[13] <java> not hugely important, but in this context the idea plays a role
01[13] <java> because sometimes the idea of disrupting sandbeds comes up
01[13] <java> and really it's jsut interesting to see that regardless of how one manipulated setup
01[13] <java> depth, plenum, etc
01[13] <java> manipulates
01[13] <java> most bacteria will find their way to the location they find comfortable
01[13] <java> in terms of oxygen content
01[13] <java> dissolved nutrients, i.e. nitrites, nitrates, ammonia, etc
01[13] <java> another way to demonstrate that the n-cycle is "unbreakable"
[13] <Rob> Is it actually a movement or a die-off and growth in a specific direction?
01[13] <java> actual movement
[13] <Rob> How?
01[13] <java> some bacteria possess appendages called flagella or fimbriae
01[13] <java> flagella swirl in a circle like a propeller
01[13] <java> fimbriae twitch
[13] <Rob> Now I remember from earlier reading. THX
01[13] <java> and the bacteria turns these on and off based on sensing a particualar gradient
01[13] <java> it can "sniff" through a gradient of dissolved nutrients, towrds higher concentrations
[13] <walla2butterfly> okay
01[13] <java> they work sort of like a Roomba vacuum
01[13] <java> they just keep running in the direction that is "favorable" in terms of target solute concentration
01[13] <java> and if it goes lower, they stop and turn
01[13] <java> stop and turn
01[13] <java> "sniff" - there it is!
01[13] <java> run!
[13] <walla2butterfly> animal grazing comes to mind
01[13] <java> yeah, but they're really jerky and awkward about it
01[13] <java> not very efficient
[13] <Rob> When there's a film is it together or independent?
[13] <walla2butterfly> good ? ROb
01[13] <java> it can be within the film, or out free in water, say between grains of sand, wherever the flow isn't disruptive
01[13] <java> to the gradient
01[13] <java> and as that other paper shows, the gradient can be within a half a millimenter
01[13] <java> if you could see the path they take, it's not pretty
01[13] <java> all jerky, seemimgly random looking at a small timeframe
01[13] <java> but if you sit back, watch long term, they trend towards their target
[13] <Rob> Once they find a suitable location do they remain or try to find a better one? Nomads?
01[13] <java> they can actually stop for periods
01[13] <java> the concentration of what they're looking for turns them "on" or "off"
01[13] <java> so if it's really high, it shuts off their motors, to sit and eat a while
01[13] <java> it's very basic molecular machinery
01[13] <java> on/off, in terms of
01[13] <java> and the stimulus/switch
01[13] <java> presence/absence
01[13] <java> gradients are like grayscale, look real close and it's really the porportion of black to white
01[13] <java> so, i've finished covering what i wanted to 20 mins early, any other questions?
[13] <walla2butterfly> about water
[13] <walla2butterfly> in the forums you see where some transfer water when changing takes others say well guess it saves them on water. Is there any reason to reuse/continue to use the water
[13] <walla2butterfly> takes = tanks
[13] <walla2butterfly> on a micro level
01[13] <java> so reusing water from water changes?
[13] <walla2butterfly> no, as in moving everything to another tank as in an upgrade
01[13] <java> oh - yeah, i think it's probably wise to transfer SOME of the water when doing a tank transfer, maybe as much as you could, depending on your occupants
01[13] <java> because
01[13] <java> we're also transferring nutrients, the DOCs, DOMs along with it, at concentrations that the microrganisms have become accustomed to
01[13] <java> it's their food, at amount they are used to being dissolved in the water
01[13] <java> there are other consideration, if you have corals, why you're doing the transfer, the original quality, etc.
01[13] <java> so that all factors in
01[13] <java> but i belive in water being "alive", like live rock or live sand as well
01[13] <java> believe
[13] <walla2butterfly> I have heard that and agree
01[13] <java> yeah, your also dealing with other levels of equilibia
[13] <walla2butterfly> just didnt know if it was sufficient "live water" for it to matter
01[13] <java> it probably would do MUCH harm to the n-cycle guys
[13] <walla2butterfly> one way or another , assuming the water is good quality of course
01[13] <java> but your corals might not be too happy
01[13] <java> something like xenia which takes a lot of nutrients directly from water might prefer keeping a lot of the old water
[13] <walla2butterfly> was just wondering because is one of those thing you hear both ways
[13] <walla2butterfly> wow cant believe that this is almost over with
[13] <walla2butterfly> couple of weeks left
01[13] <java> so many things work either way, this is something that probably for 95% of transfers either approach would be fine, although i actually wouldn't think that 100% new water would be a good idea
01[13] <java> yeah, 2 weeks
01[13] <java> next week
01[13] <java> we're going to look more closely at cycling methods, aquarium setups, and curing live rock
[13] <walla2butterfly> mini cycle that wouldnt be good for LS that needs a more established tank
[13] <walla2butterfly> curing live rock, should be good
01[13] <java> i think everyone will look at these topics a little differntly now that we've learned a lot about microbiolgoy
[13] <walla2butterfly> but I think someone might have scared me off with all the unknowns on the rock
01[13] <java> the last two weeks are to tie together real reef applications in the context of what we've learned
[13] <walla2butterfly> I guess I could use the "MOM" power on my boys to get them to do the touching LOL
[13] <walla2butterfly> that will be good to tie it all together, knowledge with application
01[13] <java> lol - boys should be pretty gung ho about it too
[13] <walla2butterfly> ya that is my boys LOL
01[13] <java> handy
01[13] <java> literally
[13] <walla2butterfly> but I have to make it look like a privligae or they will charge me cash if they see any squimishness
01[13] <java> lol - any other questions? Rob?
[13] <Rob> Good information this week. Seeing things in a different light. thx
[13] <walla2butterfly> yes, too bad so few made it, so next week is back to sat.
01[13] <java> yes, back to saturday
01[13] <java> thanks for coming, sorry for any inconvenience
[13] <walla2butterfly> sorry about that thread, that was just uncalled for
01[13] <java> yeah, i was asking him a question, if he was really busy that early, not TELLING him he had time
01[13] <java> a "really?"
01[13] <java> not calling bs
[13] <walla2butterfly> and he hasnt even made it to any of them , so what was the big deal. obviously he has other prorities
01[13] <java> that's what surprised me - he doesn't come anyhow, but suddenly when it's sched. for superbowl sunday it's time to write letters of complaint?
[13] <walla2butterfly> and the same crowd that comes here, and 3 people that couldnt make sat., seemed like a good idea to change it
[13] <walla2butterfly> same=small
01[13] <java> yeah, either way i think we covered some good material
[13] <walla2butterfly> yes it was good
01[13] <java> the papers alone without some explanation are probably a little too much
[13] <walla2butterfly> thanks
01[13] <java> thank you
01[13] <java> your welcome lol
[13] <walla2butterfly> well you take what you want from anything
02[13] * Rob ([email protected]) Quit (Quit: Leaving)
[13] <walla2butterfly> probably why so many wars over the years LOL
[13] <walla2butterfly> well see you next week
01[13] <java> ok, see you next week or on the forum!
[13] <walla2butterfly> k
[13] <walla2butterfly> bye
03[13] * walla2butterfly ([email protected]) has left #micro08
Session Ident: #micro08
03[10] * Now talking in #micro08
03[10] * Topic is 'Welcome to MACO - Reef Microbiology 2008'
03[10] * Set by wade on Wed Dec 31 19:00:01
[10] <walla2butterfly> morning
03[11] * Bob ([email protected]) has joined #micro08
01[11] <java> good morning
01[11] <java> now we're getting to the good stuff
[11] <Bob> good morning
01[11] <java> and hopefully understanding it differently now
01[11] <java> did people like the reading?
[11] <Bob> yes, very good
01[11] <java> good, thanks
[11] <walla2butterfly> yes
01[11] <java> areyou guys familiar with the controversy around sandbed depths?
[11] <walla2butterfly> yes that there is controversy
01[11] <java> the "DSB vs. BB" debates" and all that?
01[11] <java> ah
[11] <Bob> also plenum & no plenum
01[11] <java> yep
[11] <walla2butterfly> found that research interesting
[11] <walla2butterfly> about the no difference with the LR and critters
01[11] <java> yeah, it was a very interesting experiment and result
01[11] <java> both the experiments with and without animals
[11] <walla2butterfly> made me really think
[11] <walla2butterfly> about all that I thought I knew
01[11] <java> but now you know certain things about microbio that explain it
01[11] <java> explains
01[11] <java> the most significant, i think
01[11] <java> is that the n-cycle is "unbreakable"
01[11] <java> and will occur no matter what you do
[11] <walla2butterfly> which only made since
[11] <walla2butterfly> nature is nature
01[11] <java> but also makes one re-assess the risk associated with the jaubert plenum
[11] <walla2butterfly> remind me
01[11] <java> is it really necessary
01[11] <java> oops
01[11] <java> go ahead
[11] <walla2butterfly> still waking up out here in the west LOL
01[11] <java> shall i get into the jaubert method a little deeper? and what i meant?
[11] <walla2butterfly> if others are for it
01[11] <java> so as we all know the jaubert method is intended to provide an area of anaerobic environment
01[11] <java> by creating a space of very slow-circulating water under the sandbed
01[11] <java> typically eggcrate, plastic grids are used
01[11] <java> on the bottom of the tank, with a layer of fine mesh over it
01[11] <java> then the substrate is layered over that, to some significant depth
01[11] <java> the idea is that once you go to a certain depth in the substrate, anything under that will be anaerobic
01[11] <java> the risk involved
01[11] <java> is that water exchange will not occur at all
01[11] <java> because don't forget
01[11] <java> even though it may be annaerobic, that doesn't mean it doesn't have ANY water circulation
01[11] <java> so if the water stops circulating, nutrients can't get in, and wastes accumulate
01[11] <java> in the case of anaerobic respiration, a common end product is hydrogen sulfide
01[11] <java> which can be toxic if concentrations become too high
03[11] * Rob ([email protected]) has joined #micro08
01[11] <java> so getting back to biofilms
01[11] <java> and that they can slow water circulaiton in a poorly turned over sandbed
01[11] <java> one can see that the mesh used over the eggcrate
01[11] <java> may become clogged with bacterial biofilms over time
01[11] <java> slow water circulation, and end up crossing the threshold of too-little circulation
01[11] <java> because knowledge of the kinetics of denitrification is actually fairly new
01[11] <java> and the fact that facultative anaerobes participate is new as well
01[11] <java> makes one reassess the necessity of a plenum
01[11] <java> because if water circ is really low, that stagnant water can't be compartmentalized forever
01[11] <java> and you don't know if it's "bad" unless it's realeased
01[11] <java> so if one had to do a tank transfer or otherwise disrupt the apparatus
01[11] <java> you might be dealing with a nuking event
01[11] <java> so that research by toonen and wee was very useful
02[11] * mchia ([email protected]) Quit (Quit: mchia)
01[11] <java> in that it demonstrated that one does not need to take special pains
01[11] <java> to facilitate denitrification
02[11] * Bob ([email protected]) Quit (Ping timeout)
01[11] <java> what was fascinating was that even the shallow beds had significant denitrification
01[11] <java> all these things are still hotly debated today on various message boards and between hobby experts
01[11] <java> people still insist that denitrification simply CANNOT occur in a home aquarium
01[11] <java> because you need some massive anaerobic space
01[11] <java> obviously this article dispels that notion, fairly solidly
[11] <Rob> If you're one of those prior miss informed people what are the recommendaitons for an existing plenum?
01[11] <java> well, i'm actually a big fan of the "nothing is flat out incorrect" school of thought
01[11] <java> i don't think that there's anything inherently "wrong" about the plenum
01[11] <java> because those tanks still can work fine in terms of n-cycle
01[11] <java> but it jsut hass to be very carefully thought out
01[11] <java> during setup
01[11] <java> for one, don't make the mesh super-duper fine
01[11] <java> two, don't make the sandbed super thick, like 6 inches
01[11] <java> maybe 3 inches makes more sense for a sb depth
01[11] <java> possibly in one area, periodically disturb the sand down to the mesh to make sure there's at least one area which is "open"
01[11] <java> to circulation
01[11] <java> so it's jsut a little riskier
01[11] <java> and i don't want to dump on the method, because for it's time, and the existing knowledge, it was good work
01[11] <java> and can obviously be made to work
01[11] <java> but i think now it's been shown to be an unnecessary amount of effort
01[11] <java> with some extra unnecessary risk involved
01[11] <java> i'm curious - that means you have one set up?
[11] <Rob> yes
01[11] <java> tell me about it a little - how long have you had it, how big the tank, sb depth, plenum size, etc.
[11] <Rob> I've had it for a year. 240 gal tank. ~ 4 in of sand with two layers of window screen mess and an egg carton plenum.
01[11] <java> eggcrate about an inch thick?
[11] <Rob> The plenum depth is about 1/2"
01[11] <java> so proportionally it's not a HUGE plenum - i've seen some in smaller tanks which are proportionally much larger
01[11] <java> you ever notice gas bubbles coming out of the sandbed?
[11] <Rob> No
01[11] <java> look for that, it a high water circulation tank it may not be very noticeable
[11] <Rob> I have a trigger & puffer that like to dig into the sand
[11] <walla2butterfly> is that a bad sign
01[11] <java> oh, that'll mask it as well
01[11] <java> no - gas bubbles are good
01[11] <java> usually they are free nitrogen \
[11] <walla2butterfly> k
01[11] <java> N2, the final product of denitrification
01[11] <java> a lot of times if you look closely at live rock
01[11] <java> you'll notice timy bubbles on the surface, heree and there
01[11] <java> that's nitrogen from denitrification
[11] <walla2butterfly> have seen that
01[11] <java> so although i can't say whether rob most deffinitely SHOULD see as much bubbling as live rock
01[11] <java> i thought he might
01[11] <java> it's good that he has things stirring the sand on a big scale
01[11] <java> biofilms are jsut that - films
01[11] <java> very easily disrupted in sand
01[11] <java> has the plenum worked in terms of dentrification for you Rob?
[11] <Rob> Yes I don't see any problems with high levels of nitrates.
01[11] <java> sounds like you did a proper setup!
[11] <Rob> I had a problem with PO4 but it seemed to be short lived.
01[11] <java> interesting
01[11] <java> sort of mirrors the conclusions in the toonen paper
01[11] <java> plus your sandbed is on the deeper sidde
01[11] <java> how did you correct the PO4?
[11] <Rob> I wanted to experiment with something different.
01[11] <java> did it go away on it's own?
[11] <Rob> I had a GHA problem which was significantly reduced by turning off my MH's and kept removing it from the tank and it dropped.
01[11] <java> oh
01[11] <java> "removing" gha, lol
01[11] <java> nightmare!
[11] <Rob> I also added mangroves and spaghetti algae.
01[11] <java> there you go
01[11] <java> rob knows what he's doing
01[11] <java> which brings us to the only real difference in tank chemistry in the toonen papers
01[11] <java> phosphates
[11] <Rob> It's chat's like this that keep me on track.
01[11] <java> cool!
01[11] <java> so i was thinking about the phosphate difference in the tank setups in that paper
01[11] <java> i think it was a... not really the right term, but an "artifact"
01[11] <java> i think what toonen was seeing was the result of a highly artificial experimental settup
01[11] <java> not really a flaw, because i'm guessing he kept the tanks dark
01[11] <java> to make sure algae and photosynthsis didn't confound the results
01[11] <java> but since photosythesis on a natural reef is part of the overall nutrient cycling
01[11] <java> removing it from this experimental setup led to an accumulation of PO4
01[11] <java> in tanks with deeper sandbeds, which probably trapped more detritus and had slower detritus breakdown
01[11] <java> my theory, at least
01[11] <java> because as rob so perfectly demonstrated
01[11] <java> without enough photosynthesis going on
01[11] <java> or in his case, a more preferable form
01[11] <java> MAcro and mangroves over hair algae
01[11] <java> the PO4 accumulates and doesn't get cycled out
01[11] <java> jsut like the nitrogen cycle
01[11] <java> in nature there are other nutrient cycles
01[11] <java> one of them being the phosphate cycle
01[11] <java> it's not really discussed much in reef topics
01[11] <java> because the idea of a "cycle" is tied in our hobby to tank startup
01[11] <java> and some people get confused when it's used in terms of an ongoing phenomenon
01[11] <java> so the PO4 cycle gets left out
01[11] <java> but suffice to say, it rears an ugly head with algae, or in the case of this experiment
01[11] <java> can confound the results a bit, because it was a measured experimental variable
01[11] <java> although not really experimentally manipulated
01[11] <java> so i thought i'd touch on that since it was an unresolved part of the conclusions
[11] <walla2butterfly> k
01[11] <java> so tami, the take-home for the phosphate topic
01[11] <java> is that photosynthsis can take care of it
[11] <walla2butterfly> lol
01[11] <java> well, i only want to make sure everyone understands
01[11] <java> and only you and rob are here
[11] <walla2butterfly> "the take home" as in a test was how I read it...
01[11] <java> haha - maybe i should! anyhow - you'd rather remove phosphates with macroalgae
01[11] <java> than lest nuisance alge come in uninvited
01[11] <java> let
01[11] <java> because naturally SOMETHING will take advantage of the PO4
01[11] <java> sooner or later
[11] <walla2butterfly> by the way
01[11] <java> yes
[11] <walla2butterfly> how is it that the macro algae dominate over the univited algeas
[11] <walla2butterfly> oops
01[11] <java> i get it - it's thought that the macroalgaes are more efficient at removing nutrients
01[11] <java> so they "beat" the nuisance algaes to suspended nutrients
[11] <walla2butterfly> thought maybe that or have a higher demand
01[11] <java> that plays a role in cerrtain macros as well
01[11] <java> which is why Chaetomorpha - spaghetti algae
01[11] <java> is so desirable
01[11] <java> it adds mass so quickly
[11] <walla2butterfly> k
[11] <Rob> My experiment is to put the macros in a fuge and leave the light on more then the main tank. Make sense?
01[11] <java> hair algae, bryopsis, etc., can't compete
01[11] <java> R - yes
01[11] <java> because as long ass it's compartmentalized and under control
01[11] <java> as, oops
[11] <walla2butterfly> how would they work out in a cycling tank
01[11] <java> then you'd want it growing as fast as possible
01[11] <java> Tami - well, i'd slowly introduce macro to a cycling tank
01[11] <java> it's a nice idea to get ahead of PO4 before it becomes a problem
01[11] <java> and to start a cycle with some
01[11] <java> but photosynthesis also has an effeect on the diurnal pH swing, the change in pH over the course of 24 hrs
[11] <walla2butterfly> just a thought that crossed my mind while I was sitting here
01[11] <java> so without active respiration from other tank inhabitants
01[11] <java> pH might get a little swingy with too much
01[11] <java> no - i like that idea
01[12] <java> good idea, actually
01[12] <java> just something that has to be felt out
01[12] <java> in order to allow a stable environment establish over the period of the cycle
[12] <walla2butterfly> what would the effect of ammonia, etc that you would have from a traditional cycle have on them
01[12] <java> it depends on what you're using
[12] <walla2butterfly> (because you know that some people will never move away from that type
01[12] <java> some macroalgae incorporate ammonia as well
01[12] <java> caulerpa takes up nitrogenous wasstes
01[12] <java> so whilw it might be "good" to get rid of the ammonia
01[12] <java> and might be useful in a "spike" event
01[12] <java> it will outcompete your denitrifying bacteria
[12] <walla2butterfly> k
01[12] <java> and your microbial denitrification capacity might not be able to mature as well without it
[12] <walla2butterfly> so would make the cycling take longer'
01[12] <java> theoretically, it might. (lol)
[12] <walla2butterfly>
01[12] <java> hard to say, because the toonen papers demonstrate something else really really imnportant
01[12] <java> really really
01[12] <java> that theory only gets you so far
01[12] <java> and you never really knwo until you do the experiment
01[12] <java> biology on this level is so weblike, with so many processes intertwining
[12] <walla2butterfly> I was thinking that just a few min ago
01[12] <java> that focusing on one and making hypothesis and accurate predictions is very difficult
[12] <walla2butterfly> almost a which came first the chicken or the egg mentality
01[12] <java> yeah - so i think your idea of exploring the role of macroalgae in initial cycling is really interesting
[12] <walla2butterfly> could be
01[12] <java> because it might be a useful tool in something like a soft-cycle
01[12] <java> to keep ammonia spike down
01[12] <java> spikes
[12] <walla2butterfly> can see that
01[12] <java> but it might affect bacterial populations.... *shrug!
[12] <walla2butterfly> that too
[12] <walla2butterfly> "oh, the pain"
01[12] <java> lol
01[12] <java> but that's what makes this hobby so interesting to me
[12] <walla2butterfly> problem solving can be fun
01[12] <java> so many variables that interact, so many things to tweak
[12] <walla2butterfly> and the "what ifs"
01[12] <java> the best part is that nature tends to balance things out in the end
01[12] <java> so a lot of time patience solves a lot
01[12] <java> not everything, but usually in terms of the n-cycle it does
[12] <walla2butterfly> yea, had a friend with a hair algae problem for 2 years
[12] <walla2butterfly> time finally took care of it when her lights burnt out and she didnt replace them, she really shouldnt have a tank
01[12] <java> ouch - phosphate is a whole 'nother animal
01[12] <java> yes, there are some people who certainly should try something else
[12] <walla2butterfly> or get a job to support your hobby
01[12] <java> particualrly when corals are involved, i mean, fish too, but corals... ouch
[12] <walla2butterfly> anyway back to the subject
01[12] <java> i hate seeing threads ont eh forums with nice wild-caught specimens RTNing or otherwise jsut getting toasted
[12] <walla2butterfly> LRWfO
01[12] <java> yes
01[12] <java> FOWLR
[12] <walla2butterfly>
still early here, my excuse and I sticking with it01[12] <java> lol
[12] <Rob> Can you elaborate on using Xenia for the N cycle?
[12] <walla2butterfly> ( I was actually in my mind thinking what she had it in and typeing
01[12] <java> wow - i wass just typing that up
01[12] <java> you were tight on time with the phosphates too
01[12] <java> right
01[12] <java> Ron Shimek did an experiment a few years ago
[12] <walla2butterfly> sorry for the tangent ROb
[12] <Rob> always good to hear about other things
01[12] <java> similar to toonens, in terms of a water column with a certain amount of DOCs
01[12] <java> and he assayed the absorption of nitrogenous wastes
01[12] <java> he found that Xenia actually removed more nitrogen from the water by weight than caulerpa
01[12] <java> give me a moment, i'll find the article and link it here
01[12] <java> http://www.reefkeeping.com/issues/2002- ... /index.php
01[12] <java> he found that Xenia is an extremely efficient exporter of nitrogenous waste in the form of ammonia.
01[12] <java> By weight, it removes ammonia and total kjeldahl nitrogen more efficiently than Caulerpa.
01[12] <java> FYI, total kjeldahl nitrogen [TKN] is the total of organic nitrogen)
01[12] <java> in that article, the relevant data is in table 5
01[12] <java> and one other thing about that article
01[12] <java> the last couple of tables show that although xenia grows only 1/4 the rate of caulerpa in terms of biomass
01[12] <java> it is much richer in organics by weeight
[12] <walla2butterfly> will have to read that
01[12] <java> and is more efficient at removing heavy metals such as copper
[12] <Rob> I did some googling and found that raising Xenia can be unpredictable. Any tips?
01[12] <java> some people claim it can get out of control like some macro
01[12] <java> but i don't know - it's still a coral, and jsut isn't as aggressively growing as macro
[12] <Rob> I heard its dependent on iodine.
01[12] <java> i think it's really really pretty, and the pulsing action is cool lol
01[12] <java> yeah, one might have to dose iodine, but only if water changes were infrequent
[12] <walla2butterfly> does the article imply any type is better then another
01[12] <java> not really, it's all preferences
[12] <walla2butterfly> k
01[12] <java> recently i've heard people throwing around the idea of using a xenia bed in their sump
01[12] <java> to replace the macroalgae
01[12] <java> figuring it does the same, plus removing heavy metals
01[12] <java> but it can be kept in the display, i would, at least
01[12] <java> because i really like xenia
01[12] <java> but since it has been reported to overgrow sections of tanks
01[12] <java> and if one had a high nutrient load
01[12] <java> so it grew faster than a low nutrient tank
01[12] <java> keeping it in the sump might not be a bad idea
01[12] <java> anyhow, check out the article if you're interested
01[12] <java> it's nice to see actual data on things like this
01[12] <java> which are usually anecdotal
01[12] <java> any other questions?
01[12] <java> i'm thinkinig 10 min break
[12] <walla2butterfly> great see you in a few
[12] <Rob> good for me
01[12] <java> k
[12] <walla2butterfly> made it
[12] <Rob> i'm here
[12] <walla2butterfly> Don't recall ever being able to run and take a quick shower during a 10 min class break
[12] <walla2butterfly> a first for sure
01[12] <java> wow that's impressive
01[12] <java> first for one of my students ass well lol
[12] <walla2butterfly>
the dripping wet hair will make me think more about the ocean01[12] <java> ok, so i wanted to talk a bit about the other papers assigned
[12] <walla2butterfly> k
01[12] <java> first, the jensen and revsbech
01[12] <java> "estimation of nitrification and denitrification...
01[12] <java> so sorry if these are a little teechnical
01[12] <java> but i like people to be able to see with their own eyes
01[12] <java> get the papers in hand
01[12] <java> ratehr than just take my word for it
[12] <walla2butterfly> trying
01[12] <java> well i'll point out what i think are the immportant items
[12] <Rob> got it
01[12] <java> one - the oxic/anoxic boundary in marine sediments is only 1-2 centimeters down
01[12] <java> mind you, this is in a natural setting
01[12] <java> they're looking at oxygen levels in nature, not a tank where flow may be hiigher
01[12] <java> i didn't expect you to deccipher the data panels
01[12] <java> but there is also a graph showing the depths at which nitrification and denitrification are taking place
01[12] <java> and it shows that denitrification maxes out and approaches zero after only a coupe more centimeters
01[12] <java> depending on the surrounding 02 concentration, in the overlying water
01[12] <java> so
01[12] <java> back to reef - the really DSB may be overkill
01[12] <java> also, lets remember what toonen found
01[12] <java> in his expt
01[12] <java> that there wasn't much of a difference between denitrification in tanks with shallow sandbeds and those with DSBs
01[12] <java> while on it's face, and in the context of hobby lit, it seemed to not make sense
01[12] <java> in the context of this paper
01[12] <java> it does
01[12] <java> because the shallow sandbed, provided it's not TOO shallow
01[12] <java> so we're talking probably at least 1.5 inches thick
01[12] <java> maybe more if one is keeping a high-flow tank
01[12] <java> is all one needs to achieve *maxiumum* denitrification
01[12] <java> it will still happen in tanks with a DSB
01[12] <java> it's not like it can hurt (well it can if not properlay stocked/maintained)
01[12] <java> but the lower depths are somewhat extra capacity
01[12] <java> and probably not utilized
01[12] <java> another interesting bit of data in that article
01[12] <java> wass something i found surprising
01[12] <java> that the maxima of the processes of nitrification and denitrification
01[12] <java> that is, the physical location, in terms of depth
01[12] <java> where most of denitrification and nitrification occurred
01[12] <java> the respective locations were less than 0.5 mm - HALF A MILLIMETER! apart
01[12] <java> so it's not like the "gradients" we discussed
01[12] <java> were very broad
[12] <walla2butterfly> you would think barely exientant
01[12] <java> rather, they are very sharp layers in terms of large-scale measurements, like with a ruler
01[12] <java> but to a bacterium, those sharp layers are real gradients
01[12] <java> don't forget the scale of organisms we're dealilng with
[12] <walla2butterfly> right
01[12] <java> and we get back to the concept of microenvironments and biofilms
01[12] <java> really localized, small scale environments with big differences between them and the outside environment
01[12] <java> that's all i really wanted you to get out of that paper
01[12] <java> a lot of jibber jabberr and big numbers and graphs, and that was really the point
01[12] <java> so the other papers i'll similarly pass on what i thought was relevant and informative
01[12] <java> the "Biodome" papers
01[12] <java> about the microbial populations in the marine denitrification reactor at the Montreal Biodome
01[12] <java> they operate a massive denitrification reactor
01[12] <java> and looked to see what microbes were living in there
01[12] <java> now, mind you, this reactor is fed with methanol
01[12] <java> so it's a little different that a natural sccenario
01[12] <java> and will be a little more relevant when wee get into details of the "vodka method" in later weeks
01[12] <java> but still, the bacteria found are still common in some cases to normal soil/marine denitrification
01[12] <java> but notably, most all were facultative anaerobes
01[12] <java> so, why is this interesting... (hypothetical)
01[12] <java> because
01[12] <java> so much hobby literature insists that one needs a strict anaerobic environment for denitrification
01[12] <java> which, is helpful for the actual chemical reactions taking place of course
01[12] <java> but really, many insist that the presence of oxygen will KILL the denitrifying bacteria
01[12] <java> the idea goes back to the characteristics that people thought denitrifiers had to have
01[12] <java> most obligate anaerobes, that is bacteria which survive strictly under anaerobic conditions
01[12] <java> actually DO find oxygen to be toxic
01[12] <java> and many years ago, it was thought that the bacteria which accomplished denitrification were obligate anaerobes
01[12] <java> because the reactions took place under anaeerobic conditions
01[12] <java> this was Dr. Jaubert's reasoning for his plenum - he wanted to provide a stable place which NEVER saw oxygen
01[13] <java> so that the denitrifying bacteria didn't get killed by fluctuations in oxygen
01[13] <java> but, when denitrifying bacteria began to be examined more closely
01[13] <java> i know, it must seem weird that this is relatively new knowledge
01[13] <java> but that's how science works
01[13] <java> anyhow
01[13] <java> when denitrifying bacteria were more closely examined
[13] <walla2butterfly> yea look how long the world was flat
01[13] <java> lol - really - it was realized that the dominant denitrifiers were facultative anaerobes
01[13] <java> they could switch between aerobicc and anarobic respiration
01[13] <java> moreover, oxygen was NOT toxic to them
01[13] <java> in the biodome papers, almost all the denitrifiers were facultative, adn lived in a biofilm in the reactor which provided them with their own little anaerobic microenvironment
01[13] <java> no special compartments were necessary to keep O2 away
01[13] <java> and just because people like to know names
[13] <walla2butterfly> wonderful how nature works
01[13] <java> after all, on the hobby forums, we''re always hearing about Nitrobacter adn Nitrosomonas
01[13] <java> but never who does the denitrification
01[13] <java> usually it is accomplished by Pseudomonas and Paracoccus
01[13] <java> Pseudomonas is probably the most massive genus of bacteria
01[13] <java> there are dozens, if not hundreds of species
01[13] <java> so it's a very broad categorization
01[13] <java> but they are also ubiquitous and numerous in nature
01[13] <java> they're found in most water, including most tapwater
01[13] <java> (a side note, microbiological water analysis usually focuses on coliform bacteria like E. coli, but no water is actually sterile)
[13] <walla2butterfly> mmm wondering if my RO/DI takes them out
01[13] <java> yes, it would
01[13] <java> but that's okay
01[13] <java> because it's removing a lot of other stuff
01[13] <java> and Pseudomonas is already in your tank if you've got any natural material
01[13] <java> the other is Paracoccus, one of the dominant forms found in the Biodome
01[13] <java> Paracoccus is unique in that it can accomplish BOTH nitrification AND denitrification
01[13] <java> these processes are aerobic AND anaerobic, respectively
01[13] <java> alhtough it is not entirely clear exactly how that happens
01[13] <java> it does!
01[13] <java> aslo, Paracoccus can use various forms of carbon as it's carbon source
01[13] <java> so it will do well in a methanol reactor, and jsut as well without methanol, utilizing CO2
01[13] <java> it's an amazingly adaptive bacterium
01[13] <java> and it also gives rise to the notion of a reccently described phenomenon
01[13] <java> which i mentioned in the syllabus:
01[13] <java> "aerobic denitrification"
01[13] <java> that is, it has been observed that denitrification can take place in aerobic environments
01[13] <java> it has not been worked out yet how this happens
01[13] <java> and has only been observed
01[13] <java> perhaps it is the result of a highly specialized, very dense biofilm
01[13] <java> or, maybe the bacterium creates an anaerobic micro-microenvironment in a capule around itself
[13] <walla2butterfly> Like you said it ( denitrification) will happen one way or anothre
[13] <walla2butterfly> another
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01[13] <java> perhaps the actual metabolic reaction occurs INSIDE the bacterium, where internal compartmentaliztion creates an INTERNAL anaerobic microenvironment
[13] <walla2butterfly> survival
03[13] * olaf ([email protected]) has left #micro08
01[13] <java> yep - these guys find a way
01[13] <java> but it's not clear exactly HOW, but it has been observed
[13] <walla2butterfly> and I guess that is good for us
01[13] <java> one thing to keep in mind is that i'm not sure how efficient this aerobic denitrifiaction is compared to denitrification that occurs in large anaerobic environments like sediment layers
01[13] <java> i don't think that has been explored
[13] <walla2butterfly> probably a last resort
01[13] <java> however, it is certainly worth noting
[13] <walla2butterfly> for survival maybe
01[13] <java> yes, but it might also be the metabolic enzymes just somehow chugging along when o@ happens to be absent locally, in a molecular sense
[13] <walla2butterfly> so it works but is it the best possible way
01[13] <java> right
01[13] <java> see, everything is biochemical, they are reactions
01[13] <java> so if the enzyme for anaerobic respiration happens to get a "cloud" of material drift by it without o@
01[13] <java> o2
01[13] <java> sorry
01[13] <java> then it might process some nitrate
01[13] <java> all these enzymes reside in a aqueous envirnment
01[13] <java> so there might be molecular eddies and swirls of material around them
01[13] <java> and o2 concentration
01[13] <java> a momentary lack of o2 might allow for processing a molecule or two of nitate to nirogen
01[13] <java> then when o2 is back, the otehr enzymes functioning in aerobic respiration are working
[13] <walla2butterfly> (was wondering the diff. in energy between when they use o2 or not)
[13] <walla2butterfly> (used)
01[13] <java> in facultative anaerobes, all this stuff is there and "on"
01[13] <java> yeah, i'm not sure the answer to that is known
[13] <walla2butterfly> (was still wondering)
01[13] <java> that is, whether the bacteria itself "prefers" which path to use
[13] <walla2butterfly> (hook up a microheart mon to them)
01[13] <java> or if the metabolic enzymes jsut chug away with whatever is available
01[13] <java> or not
[13] <walla2butterfly> right
01[13] <java> so, the one last paper i haven't mentioned yet
01[13] <java> was one which bacteria which function in denitrification actually can relocate themselves to a place they find favorbale
[13] <walla2butterfly> ( I guess one way might be to see where they thrive at better)
01[13] <java> hm - yeah, but these guys are typically happy ANYWHERE lol
01[13] <java> bacteria like this is what makes NASA worry about "reverse contamination"
01[13] <java> sending out a mars probe with these guys on it might colonize the planet
[13] <walla2butterfly> ( and too many varibles in the enviroment) sorry go on with the next paper
01[13] <java> well, one thing i haven't really covered is that many bacteria are "motile", they can move about
01[13] <java> not hugely important, but in this context the idea plays a role
01[13] <java> because sometimes the idea of disrupting sandbeds comes up
01[13] <java> and really it's jsut interesting to see that regardless of how one manipulated setup
01[13] <java> depth, plenum, etc
01[13] <java> manipulates
01[13] <java> most bacteria will find their way to the location they find comfortable
01[13] <java> in terms of oxygen content
01[13] <java> dissolved nutrients, i.e. nitrites, nitrates, ammonia, etc
01[13] <java> another way to demonstrate that the n-cycle is "unbreakable"
[13] <Rob> Is it actually a movement or a die-off and growth in a specific direction?
01[13] <java> actual movement
[13] <Rob> How?
01[13] <java> some bacteria possess appendages called flagella or fimbriae
01[13] <java> flagella swirl in a circle like a propeller
01[13] <java> fimbriae twitch
[13] <Rob> Now I remember from earlier reading. THX
01[13] <java> and the bacteria turns these on and off based on sensing a particualar gradient
01[13] <java> it can "sniff" through a gradient of dissolved nutrients, towrds higher concentrations
[13] <walla2butterfly> okay
01[13] <java> they work sort of like a Roomba vacuum
01[13] <java> they just keep running in the direction that is "favorable" in terms of target solute concentration
01[13] <java> and if it goes lower, they stop and turn
01[13] <java> stop and turn
01[13] <java> "sniff" - there it is!
01[13] <java> run!
[13] <walla2butterfly> animal grazing comes to mind
01[13] <java> yeah, but they're really jerky and awkward about it
01[13] <java> not very efficient
[13] <Rob> When there's a film is it together or independent?
[13] <walla2butterfly> good ? ROb
01[13] <java> it can be within the film, or out free in water, say between grains of sand, wherever the flow isn't disruptive
01[13] <java> to the gradient
01[13] <java> and as that other paper shows, the gradient can be within a half a millimenter
01[13] <java> if you could see the path they take, it's not pretty
01[13] <java> all jerky, seemimgly random looking at a small timeframe
01[13] <java> but if you sit back, watch long term, they trend towards their target
[13] <Rob> Once they find a suitable location do they remain or try to find a better one? Nomads?
01[13] <java> they can actually stop for periods
01[13] <java> the concentration of what they're looking for turns them "on" or "off"
01[13] <java> so if it's really high, it shuts off their motors, to sit and eat a while
01[13] <java> it's very basic molecular machinery
01[13] <java> on/off, in terms of
01[13] <java> and the stimulus/switch
01[13] <java> presence/absence
01[13] <java> gradients are like grayscale, look real close and it's really the porportion of black to white
01[13] <java> so, i've finished covering what i wanted to 20 mins early, any other questions?
[13] <walla2butterfly> about water
[13] <walla2butterfly> in the forums you see where some transfer water when changing takes others say well guess it saves them on water. Is there any reason to reuse/continue to use the water
[13] <walla2butterfly> takes = tanks
[13] <walla2butterfly> on a micro level
01[13] <java> so reusing water from water changes?
[13] <walla2butterfly> no, as in moving everything to another tank as in an upgrade
01[13] <java> oh - yeah, i think it's probably wise to transfer SOME of the water when doing a tank transfer, maybe as much as you could, depending on your occupants
01[13] <java> because
01[13] <java> we're also transferring nutrients, the DOCs, DOMs along with it, at concentrations that the microrganisms have become accustomed to
01[13] <java> it's their food, at amount they are used to being dissolved in the water
01[13] <java> there are other consideration, if you have corals, why you're doing the transfer, the original quality, etc.
01[13] <java> so that all factors in
01[13] <java> but i belive in water being "alive", like live rock or live sand as well
01[13] <java> believe
[13] <walla2butterfly> I have heard that and agree
01[13] <java> yeah, your also dealing with other levels of equilibia
[13] <walla2butterfly> just didnt know if it was sufficient "live water" for it to matter
01[13] <java> it probably would do MUCH harm to the n-cycle guys
[13] <walla2butterfly> one way or another , assuming the water is good quality of course
01[13] <java> but your corals might not be too happy
01[13] <java> something like xenia which takes a lot of nutrients directly from water might prefer keeping a lot of the old water
[13] <walla2butterfly> was just wondering because is one of those thing you hear both ways
[13] <walla2butterfly> wow cant believe that this is almost over with
[13] <walla2butterfly> couple of weeks left
01[13] <java> so many things work either way, this is something that probably for 95% of transfers either approach would be fine, although i actually wouldn't think that 100% new water would be a good idea
01[13] <java> yeah, 2 weeks
01[13] <java> next week
01[13] <java> we're going to look more closely at cycling methods, aquarium setups, and curing live rock
[13] <walla2butterfly> mini cycle that wouldnt be good for LS that needs a more established tank
[13] <walla2butterfly> curing live rock, should be good
01[13] <java> i think everyone will look at these topics a little differntly now that we've learned a lot about microbiolgoy
[13] <walla2butterfly> but I think someone might have scared me off with all the unknowns on the rock
01[13] <java> the last two weeks are to tie together real reef applications in the context of what we've learned
[13] <walla2butterfly> I guess I could use the "MOM" power on my boys to get them to do the touching LOL
[13] <walla2butterfly> that will be good to tie it all together, knowledge with application
01[13] <java> lol - boys should be pretty gung ho about it too
[13] <walla2butterfly> ya that is my boys LOL
01[13] <java> handy
01[13] <java> literally
[13] <walla2butterfly> but I have to make it look like a privligae or they will charge me cash if they see any squimishness
01[13] <java> lol - any other questions? Rob?
[13] <Rob> Good information this week. Seeing things in a different light. thx
[13] <walla2butterfly> yes, too bad so few made it, so next week is back to sat.
01[13] <java> yes, back to saturday
01[13] <java> thanks for coming, sorry for any inconvenience
[13] <walla2butterfly> sorry about that thread, that was just uncalled for
01[13] <java> yeah, i was asking him a question, if he was really busy that early, not TELLING him he had time
01[13] <java> a "really?"
01[13] <java> not calling bs
[13] <walla2butterfly> and he hasnt even made it to any of them , so what was the big deal. obviously he has other prorities
01[13] <java> that's what surprised me - he doesn't come anyhow, but suddenly when it's sched. for superbowl sunday it's time to write letters of complaint?
[13] <walla2butterfly> and the same crowd that comes here, and 3 people that couldnt make sat., seemed like a good idea to change it
[13] <walla2butterfly> same=small
01[13] <java> yeah, either way i think we covered some good material
[13] <walla2butterfly> yes it was good
01[13] <java> the papers alone without some explanation are probably a little too much
[13] <walla2butterfly> thanks
01[13] <java> thank you
01[13] <java> your welcome lol
[13] <walla2butterfly> well you take what you want from anything
02[13] * Rob ([email protected]) Quit (Quit: Leaving)
[13] <walla2butterfly> probably why so many wars over the years LOL
[13] <walla2butterfly> well see you next week
01[13] <java> ok, see you next week or on the forum!
[13] <walla2butterfly> k
[13] <walla2butterfly> bye
03[13] * walla2butterfly ([email protected]) has left #micro08
